# Publications

## Journal Article

### 2017

### Jose Oñorbe, Joseph F. Hennawi, Zarija Lukić, and Michael Walther, "Constraining Reionization with the z ~ 5-6 Lyman-alpha Forest Power Spectrum: the Outlook after Planck", The Astrophysical Journal, 2017,

### Frederick B. Davies, Joseph F. Hennawi, Anna-Christina Eilers, and Zarija Lukić, "A New Method to Measure the Post-Reionization Ionizing Background from the Joint Distribution of Lyman-alpha and Lyman-beta Forest Transmission", The Astrophysical Journal, 2017,

### Nishant Nangia, Hans Johansen, Neelesh A. Patankar, Amneet Pal Singh Bhalla, "A moving control volume approach to computing hydrodynamic forces and torques on immersed bodies", Journal of Computational Physics, June 29, 2017, doi: 10.1016/j.jcp.2017.06.047

### Dharshi Devendran, Daniel T. Graves, Hans Johansen,Terry Ligocki, "A Fourth Order Cartesian Grid Embedded Boundary Method for Poisson's Equation", Communications in Applied Mathematics and Computational Science, edited by Silvio Levy, May 12, 2017, 12:51-79, doi: DOI 10.2140/camcos.2017.12.51

- Download File: poisson-eb-4th-order.pdf (pdf: 1.1 MB)

### Anna-Christina Eilers, Frederick B. Davies, Joseph F. Hennawi, J. Xavier Prochaska, Zarija Lukić, and Chiara Mazzucchelli, "Implications of z ~ 6 Quasar Proximity Zones for the Epoch of Reionization and Quasar Lifetimes", The Astrophsyical Journal, 2017, 840:24,

### Bei Wang, Stephane Ethier, William Tang, Khaled Ibrahim, Kamesh Madduri, Samuel Williams, Leonid Oliker, "Modern Gyrokinetic Particle-in-cell Simulation of Fusion Plasmas on Top Supercomputers", (to appear) International Journal of High-Performance Computing Applications (IJHPCA), May 2017,

### Alberto Rorai, Joseph F. Hennawi, Jose Oñorbe, Martin White, J. Xavier Prochaska, Girish Kulkarni, Michael Walther, Zarija Lukić, and Khee-Gan Lee, "Measurement of the small-scale structure of the intergalactic medium using close quasar pairs", Science, 2017, 356:418,

### Sergi Molins, David Trebotich, Gregory H. Miller, Carl I. Steefel, "Mineralogical and transport controls on the evolution of porous media texture using direct numerical simulation", Water Resources Research, April 7, 2017, doi: 10.1002/2016WR020323

### Protonu Basu, Samuel Williams, Brian Van Straalen, Leonid Oliker, Phillip Colella, Mary Hall, "Compiler-Based Code Generation and Autotuning for Geometric Multigrid on GPU-Accelerated Supercomputers", Parallel Computing (PARCO), April 2017, doi: 10.1016/j.parco.2017.04.002

### Jose Oñorbe, Joseph F. Hennawi, and Zarija Lukić, "Self-consistent Modeling of Reionization in Cosmological Hydrodynamical Simulations", The Astrophysical Journal, 2017, 837:106,

### Leon J. Osterweil, Matt Bishop, Heather M. Conboy, Huong Phan, Borislava I. Simidchieva, George S. Avrunin, Lori A. Clarke, Sean Peisert, "A Comprehensive Framework for Using Iterative Analysis to Improve Human-Intensive Process Security: An Election Example", ACM Transactions on Privacy and Security (TOPS), 2017, 20(2), doi: https://doi.org/10.1145/3041041

### Alex Krolewski, Khee-Gan Lee, Zarija Lukić, and Martin White, "Measuring Alignments between Galaxies and the Cosmic Web at z ~ 2-3 Using IGM Tomography", The Astrophysical Journal, 2017, 837:31,

### Khaled Z. Ibrahim, Evgeny Epifanovsky, Samuel Williams, Anna I. Krylov, "Cross-scale efficient tensor contractions for coupled cluster computations through multiple programming model backends", Journal of Parallel and Distributed Computing (JPDC), February 2017, doi: 10.1016/j.jpdc.2017.02.010

### Ma, S., T. Zhou, D. A. Stone, D. Polson, A. Dai, P. A. Stott, H. von Storch, Y. Qian, C. Burke, P. Wu, L. Zou, and A. Ciavarella, "Detectable anthropogenic shift toward heavy precipitation over eastern China", Journal of Climate, 2017, 30:1381-1396, doi: 10.1175/JCLI-D-16-0311.1

### Timmermans, B., D. Stone, M. Wehner, and H. Krishnan, "Impact of tropical cyclones on modeled wind-wave climate", Geophysical Research Letters, 2017, 44:1393-1401, doi: 10.1002/2016GL071681

### Mitchell, D., K. AchutaRao, M. Allen, I. Bethke, U. Beyerle, A. Ciavarella, P. M. Forster, J. Fuglestvedt, N. Gillett, K. Haustein, W. Ingram, T. Iverson, V. Kharin, N. Klingaman, N. Massey, E. Fischer, C.-F. Schleussner, J. Scinocca, O. Seland, H. Shiogama, E. Shuckburgh, S. Sparrow, D. Stone, P. Uhe, D. Wallom, M. Wehner, and R. Zaaboul, "Half a degree additional warming, prognosis and projected impacts (HAPPI): background and experimental design", Geoscientific Model Development, 2017, 10:571-583, doi: 10.5194/gmd-10-571-2017

### Sean Peisert, "Challenges and Opportunities for Security in High-Performance Computing Environments", Communications of the ACM (CACM), 2017,

### E. Vecharynski and C. Yang, "Preconditioned iterative methods for eigenvalue counts", Lecture Notes in Computational Science, January 1, 2017,

### Angélil, O., D. Stone, M. Wehner, C. J. Paciorek, H. Krishnan, W. Collins, "An independent assessment of anthropogenic attribution statements for recent extreme temperature and rainfall events", Journal of Climate, 2017, 30:5-16, doi: 10.1175/JCLI-D-16-0077.1

### 2016

### M. Jacquelin, L. Lin and C. Yang, "A Distributed Memory Parallel Algorithm for Selected Inversion: the non-symmetric case", PMAA, December 30, 2016,

### M. Wehner, D. Stone, H. Krishnan, K. AchutaRao, F. Castillo, "The deadly combination of heat and humidity in India and Pakistan in summer 201", Bulletin of the American Meteorological Society, 2016, 97:S81-S86, doi: 10.1175/BAMS-D-16-0145.2

### K. A. Lawal, A. A. Abatan, O. Ang\'elil, E. Olaniyan, V. H. Olusoji, P. G. Oguntunde, B. Lamptey, B. J. Abiodun, H. Shiogama, M. F. Wehner, D. A. Stone, "The late onset of the 2015 wet season in Nigeria", Bulletin of the American Meteorological Society, 2016, 97:S63-S69, doi: 10.1175/BAMS-D-16-0131.2

### E. Vecharynski, A. Knyazev, "Preconditioned steepest descent-like methods for symmetric indefinite systems", Linear Algebra and its Applications, Vol. 511, pp. 274–295, 2016,

We construct preconditioned steepest descent (PSD)-like methods for iterative solution of symmetric indefinite linear systems using symmetric and positive definite (SPD) preconditioners. Our construction is based on a locally optimal residual minimization over two-dimensional subspaces, mathematically equivalent in exact arithmetic to preconditioned MINRES (PMINRES) restarted after every two steps. A convergence bound is derived. If certain information on the spectrum of the preconditioned system is available, we present a simpler PSD-like algorithm that performs only one-dimensional residual minimization. Search direction randomization for accelerating this algorithm is discussed. Our primary goal is to bridge the theoretical gap between the optimal (PMINRES) and PSD-like methods for solving symmetric indefinite systems. We also demonstrate situations where the suggested PSD-like schemes can be preferable to the optimal PMINRES iteration.

### R. Atta-Fynn, E.J. Bylaska, W.A. de Jong, "Strengthening of the Coordination Shell by Counter Ions in Aqueous Th4+ Solutions", J. Phys. Chem. A, December 1, 2016, 120:10216–1022, doi: 10.1021/acs.jpca.6b09878

### S.V. Venkatakrishnan, Jeffrey Donatelli, Dinesh Kumar, Abhinav Sarje, Sunil K. Sinha, Xiaoye S. Li, Alexander Hexemer, "A Multi-slice Simulation Algorithm for Grazing-Incidence Small-Angle X-ray Scattering", Journal of Applied Crystallography, December 2016, 49-6, doi: 10.1107/S1600576716013273

Grazing-incidence small-angle X-ray scattering (GISAXS) is an important technique in the characterization of samples at the nanometre scale. A key aspect of GISAXS data analysis is the accurate simulation of samples to match the measurement. The distorted-wave Born approximation (DWBA) is a widely used model for the simulation of GISAXS patterns. For certain classes of sample such as nanostructures embedded in thin films, where the electric field intensity variation is significant relative to the size of the structures, a multi-slice DWBA theory is more accurate than the conventional DWBA method. However, simulating complex structures in the multi-slice setting is challenging and the algorithms typically used are designed on a case-by-case basis depending on the structure to be simulated. In this paper, an accurate algorithm for GISAXS simulations based on the multi-slice DWBA theory is presented. In particular, fundamental properties of the Fourier transform have been utilized to develop an algorithm that accurately computes the average refractive index profile as a function of depth and the Fourier transform of the portion of the sample within a given slice, which are key quantities required for the multi-slice DWBA simulation. The results from this method are compared with the traditionally used approximations, demonstrating that the proposed algorithm can produce more accurate results. Furthermore, this algorithm is general with respect to the sample structure, and does not require any sample-specific approximations to perform the simulations.

### Utkarsh Ayachit, Andrew Bauer, Earl P. N. Duque, Greg Eisenhauer, Nicola Ferrier, Junmin Gu, Kenneth E. Jansen, Burlen Loring, Zarija Lukić, Suresh Menon, Dmitriy Morozov, Patrick O'Leary, Reetesh Ranjan, Michel Rasquin, Christopher P. Stone, Venkat Vishwanath, Gunther H. Weber, Brad Whitlock, Matthew Wolf, K. John Wu, E. Wes Bethel, "Performance analysis, design considerations, and applications of extreme-scale in situ infrastructures", Supercomputing, 2016, 79,

### Jared O. Ferguson, Christiane Jablonowski, Hans Johansen, Peter McCorquodale, Phillip Colella, Paul A. Ullrich, "Analyzing the adaptive mesh refinement (AMR) characteristics of a high-order 2D cubed-sphere shallow-water model", Mon. Wea. Rev., November 9, 2016, 144:4641–4666, doi: 10.1175/MWR-D-16-0197.1

### Ariful Azad, Grey Ballard, Aydin Buluc, James Demmel, Laura Grigori, Oded Schwartz, Sivan Toledo, Samuel Williams, "Exploiting multiple levels of parallelism in sparse matrix-matrix multiplication", SIAM Journal on Scientific Computing, 38(6), C624–C651, November 2016, doi: 10.1137/15M104253X

- Download File: SISC-SpGEMM.pdf (pdf: 1.5 MB)

### Nicholas Chaimov, Khaled Z. Ibrahim, Samuel Williams, Costin Iancu, "Reaching Bandwidth Saturation Using Transparent Injection Parallelization", International Journal of High Performance Computing Applications (IJHPCA), November 2016, doi: 10.1177/1094342016672720

### Hasan Metin Aktulga, Md. Afibuzzaman, Samuel Williams, Aydın Buluc, Meiyue Shao, Chao Yang, Esmond G. Ng, Pieter Maris, James P. Vary, "A High Performance Block Eigensolver for Nuclear Configuration Interaction Calculations", IEEE Transactions on Parallel and Distributed Systems (TPDS), November 2016, doi: 10.1109/TPDS.2016.2630699

- Download File: ieeetpds-mfdn-lobpcg-rev.pdf (pdf: 889 KB)

### Gillett, N. P., H. Shiogama, B. Funke, G. Hegerl, R. Knutti, K. Matthes, B. D. Santer, D. Stone, C. Tebaldi, "The Detection and Attribution Model Intercomparison Project (DAMIP v1.0) contribution to CMIP6", Geoscientific Model Development, 2016, 9:3685-3697, doi: 10.5194/gmd-9-3685-2016

### A. S. Banerjee, L. Lin, W. Hu, C. Yang and J. E. Pask, "Chebyshev polynomial filtered subspace iteration in the discontinuous Galerkin method for large-scale electronic structure calculations", Journal of Chemical Physics, October 1, 2016,

### Pieter Ghysels, Xiaoye S. Li, François-Henry Rouet, Samuel Williams, Artem Napov, "An Efficient Multicore Implementation of a Novel HSS-Structured Multifrontal Solver Using Randomized Sampling", SIAM J. Sci. Comput. 38-5, pp. S358-S384, October 2016, doi: 10.1137/15M1010117

### C. Huggel, I. Wallimann-Helmer, D. Stone, W. Cramer, "Reconciling justice and attribution research to advance climate policy", Nature Climate Change, 2016, 6:901-908, doi: 10.1038/NCLIMATE3104

### S.L. Cornford, D.F.Martin, V. Lee, A.J. Payne, E.G. Ng, "Adaptive mesh refinement versus subgrid friction interpolation in simulations of Antarctic ice dynamics", Annals of Glaciology, September 2016, 57 (73), doi: 10.1017/aog.2016.13

### W. Yoo, A. Sim, "Time-series Forecast Modeling on High-Bandwidth Wide Area Network Measurements", Journal of Grid Computing, 2016, 14:3:463–476, doi: 10.1007/s10723-016-9368-9

### Lingfei Wu, Kesheng Wu, Alex Sim, Michael Churchill, Jong Choi, Andreas Stathopoulos, Choong-Seock Chang, Scott Klasky, "Towards Real-Time Detection and Tracking of Spatio-Temporal Features: Blob-Filaments in Fusion Plasma", IEEE Transactions on Big Data (TBD), 2016, 2:3:262-275, doi: 10.1109/TBDATA.2016.2599929

### Mahdi Jamei, Emma Stewart, Sean Peisert, Anna Scaglione, Chuck McParland, Ciaran Roberts, Alex McEachern, "Micro Synchrophasor-Based Intrusion Detection in Automated Distribution Systems: Towards Critical Infrastructure Security", IEEE Internet Computing, September 2016, 20(5):18-27, doi: 10.1109/MIC.2016.102

### Ariful Azad, Bartek Rajwa, Alex Pothen, "Immunophenotype Discovery, Hierarchical Organization, and Template-based Classification of Flow Cytometry Samples", Frontiers in Oncology, August 31, 2016,

- Download File: frontier-immunophenotypes.pdf (pdf: 15 MB)

### David H. Bailey, Jonathan M. Borwein, "Computation and experimental evaluation of Mordell-Tornheim-Witten sum derivatives", Experimental Mathematics, August 29, 2016,

### David H. Bailey, Jonathan M. Borwein, Jason Kimberley, Watson Ladd, "Computer discovery and analysis of large Poisson polynomials", Experimental Mathematics, August 27, 2016, doi: http://dx.doi.org/10.1080/10586458.2016.1180565

### Brian Friesen, Ann Almgren, Zarija Lukić, Gunther Weber, Dmitriy Morozov, Vincent Beckner, Marcus Day, "In situ and in-transit analysis of cosmological simulations", Computational Astrophysics and Cosmology, 2016, 3:4,

### David H. Bailey, Jonathan M. Borwein, Richard Brent, Mohsen Reisi Ardali, "Reproducibility in computational science: a case study: Randomness of the digits of Pi", Experimental mathematics, August 24, 2016, doi: http://dx.doi.org/10.1080/10586458.2016.1163755

### R. Li, Y. Xi, E. Vecharynski, C. Yang, and Y. Saad, "A Thick-Restart Lanczos algorithm with polynomial filtering for Hermitian eigenvalue problems", SIAM Journal on Scientific Computing, Vol. 38, Issue 4, pp. A2512–A2534, 2016, doi: 10.1137/15M1054493

Polynomial filtering can provide a highly effective means of computing all eigenvalues of a real symmetric (or complex Hermitian) matrix that are located in a given interval, anywhere in the spectrum. This paper describes a technique for tackling this problem by combining a Thick-Restart version of the Lanczos algorithm with deflation ('locking') and a new type of polynomial filters obtained from a least-squares technique. The resulting algorithm can be utilized in a 'spectrum-slicing' approach whereby a very large number of eigenvalues and associated eigenvectors of the matrix are computed by extracting eigenpairs located in different sub-intervals independently from one another.

### H. Shiogama, Y. Imada, M. Mori, R. Mizuta, D. Stone, K. Yoshida, O. Arakawa, M. Ikeda, C. Takahashi, M. Arai, M. Ishii, M. Watanabe, and M. Kimoto, "Attributing historical changes in probabilities of record-breaking daily temperature and precipitation extreme events", Scientific Online Letters on the Atmosphere, 2016, 12:225-231, doi: 10.2151/sola.2016-045

### Daniele Sorini, José Oñorbe, Zarija Lukić, Joseph Hennawi, "Modeling the Lyman-alpha Forest in Collisionless Simulations", The Astrophysical Journal, 2016, 827:97,

### Zhangpeng Guo, Nicolas Zweibaum, Meiyue Shao, Lakshana R. Huddar, Per F. Peterson, and Suizheng Qiu, "Development of the FHR advanced natural circulation analysis code and application to FHR safety analysis", Progress in Nuclear Energy, 2016, 91:56–67, doi: 10.1016/j.pnucene.20

### Xylar S. Asay-Davis, Stephen L. Cornford, Gaël Durand, Benjamin K. Galton-Fenzi, Rupert M. Gladstone, G. Hilmar Gudmundsson, Tore Hattermann, David M. Holland, Denise Holland, Paul R. Holland, Daniel F. Martin, Pierre Mathiot, Frank Pattyn, Hélène Seroussi, "Experimental design for three interrelated marine ice sheet and ocean model intercomparison projects: MISMIP v. 3 (MISMIP +), ISOMIP v. 2 (ISOMIP +) and MISOMIP v. 1 (MISOMIP1)", Geoscientific Model Development, July 2016, 9(7), doi: doi:10.5194/gmd-9-2471-2016

### David H. Bailey, Jonathan M. Borwein, Marcos Lopez de Prado,, "Backtest overfitting in financial markets", Journal of Portfolio Management, July 19, 2016,

### Sugeerth Murugesan, Kristofer Bouchard, Jesse A. Brown, Bernd Hamann, William W. Seeley, Andrew Trujillo, Gunther H. Weber, "Brain Modulyzer: Interactive Visual Analysis of Functional Brain Connectivity", IEEE Transactions on Computational Biology and Bioinformatics, 2016, LBNL 1005732, doi: 10.1109/TCBB.2016.2564970

### Fabien Bruneval, Tonatiuh Rangel, Samia M. Hamed, Meiyue Shao, Chao Yang, Jeffrey B. Neaton, "MOLGW 1: many-body perturbation theory software for atoms, molecules, and clusters", Computer Physics Communications, 2016, 208:149–161, doi: 10.1016/j.cpc.2016.06.019

### Ariful Azad, Bartek Rajwa, Alex Pothen, "flowVS: Channel-Specic Variance Stabilization in Flow Cytometry", BMC Bioinformatics, June 2016,

### Weiqun Zhang, Ann Almgren, Marcus Day, Tan Nguyen, John Shalf, Didem Unat, "BoxLib with Tiling: An AMR Software Framework", SIAM Journal on Scientific Computing, 2016,

### Robert Saye, James Sethian, "Multiscale modelling of evolving foams", Journal of Computational Physics, June 15, 2016, doi: 10.1016/j.jcp.2016.02.077

### Ariful Azad, Aydın Buluç, "A matrix-algebraic formulation of distributed-memory maximal cardinality matching algorithms in bipartite graphs", Parallel Computing, June 2016,

### Meiyue Shao, Lin Lin, Chao Yang, Fang Liu, Felipe H. da Jornada, Jack Deslippe and Steven G. Louie, "Low rank approximation in G0W0 calculations", Science China Mathematics, June 4, 2016, 59:1593–1612, doi: 10.1007/s11425-016-0296-x

### Dmitriy Morozov and Zarija Lukić, "Master of Puppets: Cooperative Multitasking for In Situ Processing", HPDC, 2016, 285,

### Mark R. Krumholz, Andrew T. Myers, Richard I. Klein, Christopher F. McKee,, "What Physics Determines the Peak of the IMF? Insights from the Structure of Cores in Radiation-Magnetohydrodynamic Simulations", accepted by MNRAS, May 19, 2016,

### Ariful Azad, Aydın Buluç, Alex Pothen, "Computing Maximum Cardinality Matchings in Parallel on Bipartite Graphs via Tree-Grafting", IEEE Transactions on Parallel and Distributed Systems (TPDS), May 2016,

- Download File: matchingGraft-TPDS.pdf (pdf: 1.4 MB)

### Sean Peisert, William K. Barnett, Eli Dart, James Cuff, Robert L. Grossman, Edward Balas, Ari Berman, Anurag Shankar, Brian Tierney, "The Medical Science DMZ", Journal of the American Medical Informatics Association (JAMIA), May 2, 2016, 23(6):1199-1201, doi: 10.1093/jamia/ocw032

### Nils E. R. Zimmermann, Maciej Haranczyk, "History and Utility of Zeolite Framework-Type Discovery from a Data-Science Perspective", Crystal Growth & Design, May 2, 2016,

Mature applications such as fluid catalytic cracking and hydrocracking rely critically on early zeolite structures. With a data-driven approach, we find that the discovery of exceptional zeolite framework types around the new millennium was spurred by exciting new utilization routes. The promising processes have yet not been successfully implemented (“valley of death” effect), mainly because of the lack of thermal stability of the crystals. This foreshadows limited deployability of recent zeolite discoveries that were achieved by novel crystal synthesis routes.

Watch a movie illustrating our seeded simulation strategy here.

### Hansen, G., and D. Stone, "Assessing the observed impact of anthropogenic climate change", Nature Climate Change, 2016, 6:532-537, doi: 10.1038/nclimate2896

### M. Jacquelin, L. Lin, W. Jia, Y. Zhao and C. Yang, "A Left-looking selected inversion algorithm and task parallelism on shared memory systems", April 9, 2016,

### J. R. Jones, F.-H. Rouet, K. V. Lawler, E. Vecharynski, K. Z. Ibrahim, S. Williams, B. Abeln, C. Yang, C. W. McCurdy, D. J. Haxton, X. S. Li, T. N. Rescigno, "An efficient basis set representation for calculating electrons in molecules", Journal of Molecular Physics, 2016, doi: 10.1080/00268976.2016.1176262

The method of McCurdy, Baertschy, and Rescigno, J. Phys. B, 37, R137 (2004) is generalized to obtain a straightforward, surprisingly accurate, and scalable numerical representation for calculating the electronic wave functions of molecules. It uses a basis set of product sinc functions arrayed on a Cartesian grid, and yields 1 kcal/mol precision for valence transition energies with a grid resolution of approximately 0.1 bohr. The Coulomb matrix elements are replaced with matrix elements obtained from the kinetic energy operator. A resolution-of-the-identity approximation renders the primitive one- and two-electron matrix elements diagonal; in other words, the Coulomb operator is local with respect to the grid indices. The calculation of contracted two-electron matrix elements among orbitals requires only O(N log(N)) multiplication operations, not O(N^4), where N is the number of basis functions; N = n^3 on cubic grids. The representation not only is numerically expedient, but also produces energies and properties superior to those calculated variationally. Absolute energies, absorption cross sections, transition energies, and ionization potentials are reported for one- (He^+, H_2^+ ), two- (H_2, He), ten- (CH_4) and 56-electron (C_8H_8) systems.

### David H. Bailey, Jonathan M. Borwein, Marcos Lopez de Prado, "Backtest overfitting in financial markets", Automated Trader, March 16, 2016, to appea,

### Z. Wen, C. Yang, X. Liu and Y. Zhang, "A Penalty-based Trace Minimization Method for Large-scale Eigenspace Computation", J. Sci. Comp., March 1, 2016, 66:1175-1203, doi: 10.1007/s10915-015-0061-0

### J. Mueller, "MISO: Mixed-Integer Surrogate Optimization Framework", Optimization and Engineering, March 2016, 17:177-203,

### E. Vecharynski, C. Yang, and F. Xue, "Generalized preconditioned locally harmonic residual method for non-Hermitian eigenproblems", SIAM Journal on Scientific Computing, Vol. 38, No. 1, pp. A500–A527, 2016, doi: 10.1137/15M1027413

We introduce the Generalized Preconditioned Locally Harmonic Residual (GPLHR) method for solving standard and generalized non-Hermitian eigenproblems. The method is particularly useful for computing a subset of eigenvalues, and their eigen- or Schur vectors, closest to a given shift. The proposed method is based on block iterations and can take advantage of a preconditioner if it is available. It does not need to perform exact shift-and-invert transformation. Standard and generalized eigenproblems are handled in a unified framework. Our numerical experiments demonstrate that GPLHR is generally more robust and efficient than existing methods, especially if the available memory is limited.

### D.M.L. Brown, H.M. Cho, W.A. de Jong, "Bridging experiment and theory: a template for unifying NMR data and electronic structure calculations", J. Cheminfo., February 9, 2016, 8:8, doi: 10.1186/s13321-016-0120-z

### Wei Hu, Lin Lin, Chao Yang, Jun Dai and Jinlong Yang, "Edge-Modied Phosphorene Nano ake Heterojunctions as Highly Ecient Solar Cells", Nano Lett, February 5, 2016, 16:1675–1682, doi: 10.1021/acs.nanolett.5b04593

### P. Li, X. Liu, M. Chen, P. Lin, X. Ren, L. Lin, C. Yang, L. He, "Large-scale ab initio simulations based on systematically improvable atomic basis", Computational Materials Science, February 1, 2016, 112:503–517, doi: doi:10.1016/j.commatsci.2015.07.004

### R.M. Cox, P.B. Armentrout, W.A. de Jong, "Reactions of Th+ + H2, D2, and HD Studied by Guided Ion Beam Tandem Mass Spectrometry and Quantum Chemical Calculations", J. Phys. Chem. B – Bruce Garrett Festschrift, February 1, 2016, 120:1601, doi: 10.1021/acs.jpcb.5b08008

### L. Lin, Y. Saad and C. Yang, "Approximating spectral densities of large matrices", SIAM Review, February 1, 2016, 58:34–65, doi: 10.1137/130934283

### Andrew Myers, Phillip Colella, Brian Van Straalen, "A 4th-Order Particle-in-Cell Method with Phase-Space Remapping for the Vlasov-Poisson Equation", submitted to SISC, February 1, 2016,

### J. Brabec, C. Yang, E. Epifanovsky, A.I. Krylov, and E. Ng, "Reduced-cost sparsity-exploiting algorithm for solving coupled-cluster equations", Journal of Computational Chemistry, January 24, 2016, 37:1059–1067, doi: 10.1002/jcc.24293

### Shiogama, H., , D. Stone, S. Emori, K. Takahashi, S. Mori, A. Maeda, Y. Ishizaki, and M. R. Allen, "Predicting future uncertainty constraints on global warming projections", Scientific Reports, 2016, doi: 10.1038/srep18903

- Download File: 2016-Shiogamaetal-SREP-pressrelease.pdf (pdf: 283 KB)

### E. Vecharynski, "A generalization of Saad's bound on harmonic Ritz vectors of Hermitian matrices", Linear Algebra and its Applications, Vol. 494, pp. 219-235, 2016, doi: 10.1016/j.laa.2016.01.013

We prove a Saad's type bound for harmonic Ritz vectors of a Hermitian matrix. The new bound reveals a dependence of the harmonic Rayleigh-Ritz procedure on the condition number of a shifted problem operator. Several practical implications are discussed. In particular, the bound motivates incorporation of preconditioning into the harmonic Rayleigh-Ritz scheme.

### Andrew Myers, Phillip Colella, Brian Van Straalen, "The Convergence of Particle-in-Cell Schemes for Cosmological Dark Matter Simulations", The Astrophysical Journal, Volume 816, Issue 2, article id. 56, 2016,

### Meiyue Shao, Felipe H. da Jornada, Chao Yang, Jack Deslippe, Steven G. Louie, "Structure preserving parallel algorithms for solving the Bethe–Salpeter eigenvalue problem", Linear Algebra and its Applications, 2016, 488:148–167, doi: 10.1016/j.laa.2015.09.036

### David H. Bailey, Jonathan M. Borwein, "Computation and structure of character polylogarithms with applications to character Mordell-Tornheim-Witten sums", Mathematics of Computation, January 1, 2016, 85:295-324,

### Deborah A Agarwal, Boris Faybishenko, Vicky L, Harinarayan Krishnan, Carina Lansing Gary Kushner, Ellen Porter, Alexandru Romosan Arie Shoshani, Haruko Wainwright, Arthur, Kesheng Wu, "A Science Data Gateway for Environmental Management", Concurrency and Computation: Practice and Experience, 2016, 28:1994--2004, doi: 10.1002/cpe.3697

### Salman Habib, Adrian Pope, Hal Finkel, Nicholas Frontiere, Katrin Heitmann, David Daniel, Patricia Fasel, Vitali Morozov, George Zagaris, Tom Peterka, Venkatram Vishwanath, Zarija Lukić, Saba Sehrish, Wei-keng Liao, "HACC: Simulating sky surveys on state-of-the-art supercomputing architectures", New Astronomy, 2016, 42:49,

### 2015

### M. Day, S. Tachibana, J. Bell, M. Lijewski, V. Beckner and R. Cheng, "A Combined Computational and Experimental Characterization of Lean Premixed Turbulent Low Swirl Laboratory Flames. II. Hydrogen Flames", Combustion and Flame, 2015,

### Stephen M. Guzik, Xinfeng Gao, Landon D. Owen, Peter McCorquodale, Phillip Colella, "A freestream-preserving fourth-order finite-volume method in mapped coordinates with adaptive-mesh refinement", Computers & Fluids, December 21, 2015, 123:202–217, doi: 10.1016/j.compfluid.2015.10.001

### D. B. Szyld, E. Vecharynski, and F. Xue, "Preconditioned eigensolvers for large-scale nonlinear Hermitian eigenproblems with variational characterizations. II. Interior eigenvalues.", SIAM Journal on Scientific Computing, Vol. 37, Issue 6, pp. A2969-A2997, 2015,

We consider the solution of large-scale nonlinear algebraic Hermitian eigenproblems of the form $T(\lambda)v=0$ that admit a variational characterization of eigenvalues. These problems arise in a variety of applications and are generalizations of linear Hermitian eigenproblems $Av\!=\!\lambda Bv$. In this paper, we propose a Preconditioned Locally Minimal Residual (PLMR) method for efficiently computing interior eigenvalues of problems of this type. We discuss the development of search subspaces, preconditioning, and eigenpair extraction procedure based on the refined Rayleigh-Ritz projection. Extension to the block methods is presented, and a moving-window style soft deflation is described. Numerical experiments demonstrate that PLMR methods provide a rapid and robust convergence towards interior eigenvalues. The approach is also shown to be efficient and reliable for computing a large number of extreme eigenvalues, dramatically outperforming standard preconditioned conjugate gradient methods.

### George Michelogiannakis, Xiaoye S. Li, David H. Bailey, John Shalf, "Extending Summation Precision for Network Reduction Operations", Springer International Journal of Parallel Programming, December 2015, 43:6:1218-1243, doi: 10.1007/s10766-014-0326-5

### David H. Bailey and Marcos Lopez de Prado, "Stop-outs under serial correlation and the 'triple penance' rule", Journal of Risk, November 23, 2015, 18(2):61-93,

### Soyoung Jeon, Prabhat, Suren Byna, Junmin Gu, William Collins, and Michael Wehner,, "Characterization of extreme precipitation within atmospheric river events over California", Advances in Statistical Climatology, Meteorology and Oceanography (ASCMO), November 21, 2015, 1:45-57, doi: 10.5194/ascmo-1-45-2015

### Stone, D. A., and G. Hansen, "Rapid systematic assessment of the detection and attribution of regional anthropogenic climate change", 2015, doi: 10.1007/s00382-015-2909-2

### M. A. Patwary, S. Byna, N. Satish, N. Sundaram, Z. Lukić, V. Roytershteyn, M. Anderson, Y. Yao, Prabhat, P. Dubey, "BD–CATS: Big Data Clustering at Trillion Particles Scale", Supercomputing, 2015, 6,

### Grey Ballard, James Demmel, Laura Grigori, Mathias Jacquelin, Nicholas Knight, Hong Diep Nguyen, "Reconstructing Householder vectors from Tall-Skinny QR", Journal of Parallel and Distributed Computing, November 1, 2015, 85:3-31, doi: 10.1016/j.jpdc.2015.06.003

### Andrew Myers, Christopher McKee, Pak Shing Li, "The CH+ abundance in turbulent, diffuse molecular clouds", Monthly Notices of the Royal Astronomical Society, Volume 453, Issue 3, p.2747-2758, November 1, 2015,

### David H. Bailey, Jonathan M. Borwein, "Crandall's computation of the incomplete gamma function and the Hurwitz zeta function with applications to Dirichlet L-series", Applied Mathematics and Computation, November 1, 2015, 268C:462-477,

### E. Vecharynski, A. Knyazev, "Preconditioned Locally Harmonic Residual Method for computing interior eigenpairs of certain classes of Hermitian matrices", SIAM Journal on Scientific Computing, Vol. 37, Issue 5, pp. S3–S29, 2015,

We propose a Preconditioned Locally Harmonic Residual (PLHR) method for computing several interior eigenpairs of a generalized Hermitian eigenvalue problem, without traditional spectral transformations, matrix factorizations, or inversions. PLHR is based on a short-term recurrence, easily extended to a block form, computing eigenpairs simultaneously. PLHR can take advantage of Hermitian positive definite preconditioning, e.g., based on an approximate inverse of an absolute value of a shifted matrix, introduced in [SISC, 35 (2013), pp. A696–A718]. Our numerical experiments demonstrate that PLHR is efficient and robust for certain classes of large-scale interior eigenvalue problems, involving Laplacian and Hamiltonian operators, especially if memory requirements are tight.

### M. van Setten; F. Carouso; S. Sharifzadeh; X. Ren; M. Scheffler; F. Liu; J. Lischner; L. Lin; J. Deslippe; S. Louie; C. Yang; F. Weigend; J. Neaton; F. Evers; P. Rinke, "GW 100: Benchmarking G0W0 for molecular systems", Journal of Chemical Theory and Computation, October 22, 2015,

### J. Mueller, R. Paudel, J. Woodbury, Y. Wang, C. Shoemaker, N. Mahowald, "CH4 Parameter Estimation in CLM4.5bgc Using Surrogate Global Optimization", Geoscientific Model Development, October 2015, 8:3285-3310,

### Tobias Titze, Alexander Lauerer, Lars Heinke, Christian Chmelik, Nils E. R. Zimmermann, Frerich J. Keil, Douglas M. Ruthven, Jörg Kärger, "Transport in Nanoporous Materials Including MOFs: The Applicability of Fick’s Laws", Angew. Chem. Int. Ed., 2015, doi: 10.1002/anie.201506954

Diffusion in nanoporous host–guest systems is often considered to be too complicated to comply with such “simple” relationships as Fick’s first and second law of diffusion. However, it is shown herein that the microscopic techniques of diffusion measurement, notably the pulsed field gradient (PFG) technique of NMR spectroscopy and microimaging by interference microscopy (IFM) and IR microscopy (IRM), provide direct experimental evidence of the applicability of Fick’s laws to such systems. This remains true in many situations, even when the detailed mechanism is complex. The limitations of the diffusion model are also discussed with reference to the extensive literature on this subject.

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### Jiri Brabec, Lin Lin, Meiyue Shao, Niranjan Govind, Chao Yang, Yousef Saad, Esmond G. Ng, "Fast Algorithms for Estimating the Absorption Spectrum within Linear Response Time-dependent Density Functional Theory", Journal of Chemical Theory and Computation, 2015, 11:5197–5208, doi: 10.1021/acs.jctc.5b00887

### Robert Granat, Bo Kågström, Daniel Kressner, Meiyue Shao, "Algorithm 953: Parallel library software for the multishift QR algorithm with aggressive early deflation", ACM Transactions on Mathematical Software, 2015, 41:29:1--29:2, doi: 10.1145/2699471

### Nils E. R. Zimmermann, Bart Vorselaars, David Quigley, Baron Peters, "Nucleation of NaCl from Aqueous Solution: Critical Sizes, Ion-Attachment Kinetics, and Rates", J. Am. Chem. Soc., 2015, doi: 10.1021/jacs.5b08098

Nucleation and crystal growth are important in material synthesis, climate modeling, biomineralization, and pharmaceutical formulation. Despite tremendous efforts, the mechanisms and kinetics of nucleation remain elusive to both theory and experiment. Here we investigate sodium chloride (NaCl) nucleation from supersaturated brines using seeded atomistic simulations, polymorph-specific order parameters, and elements of classical nucleation theory. We find that NaCl nucleates via the common rock salt structure. Ion desolvation—not diffusion—is identified as the limiting resistance to attachment. Two different analyses give approximately consistent attachment kinetics: diffusion along the nucleus size coordinate and reaction-diffusion analysis of approach-to-coexistence simulation data from Aragones et al. (*J. Chem. Phys.* **2012**, *136*, 244508). Our simulations were performed at realistic supersaturations to enable the first direct comparison to experimental nucleation rates for this system. The computed and measured rates converge to a common upper limit at extremely high supersaturation. However, our rate predictions are between 15 and 30 orders of magnitude too fast. We comment on possible origins of the large discrepancy.

Watch a movie illustrating our seeded simulation strategy here.

### S. L. Cornford, D. F. Martin, A. J. Payne, E. G. Ng, A. M. Le Brocq, R. M. Gladstone, T. L. Edwards, S. R. Shannon, C. Agosta, M. R. van den Broeke, H. H. Hellmer, G. Krinner, S. R. M. Ligtenberg, R. Timmermann, D. G. Vaughan, "Century-scale simulations of the response of the West Antarctic Ice Sheet to a warming climate", The Cryosphere, August 18, 2015, doi: 10.5194/tc-9-1579-2015, 2015

### Nathan Hanford, Vishal Ahuja, Mehmet Balman, Matthew. Farrens, Dipak Ghosal, Eric Pouyoul, Brian Tierney, "Improving Network Performance on Multicore Systems: Impact of Core Affinities on High Throughput Flows", The International Journal of eScience, Elsevier, 2015, doi: doi:10.1016/j.future.2015.09.012

Network throughput is scaling-up to higher data rates while end-system processors are scaling-out to multiple cores. In order to optimize high speed data transfer into multicore end-systems, techniques such as network adaptor offloads and performance tuning have received a great deal of attention. Furthermore, several methods of multi-threading the network receive process have been proposed. However, thus far attention has been focused on how to set the tuning parameters and which offloads to select for higher performance, and little has been done to understand why the various parameter settings do (or do not) work. In this paper, we build on previous research to track down the sources of the end-system bottleneck for high-speed TCP flows. We define protocol processing efficiency to be the amount of system resources (such as CPU and cache) used per unit of achieved throughput (in Gbps). The amount of various system resources consumed are measured using low-level system event counters. In a multicore end-system, affinitization, or core binding, is the decision regarding how the various tasks of network receive process including interrupt, network, and application processing are assigned to the different processor cores. We conclude that affinitization has a significant impact on protocol processing efficiency, and that the performance bottleneck of the network receive process changes significantly with different affinitization.

### Brian Tierney, Mehmet Balman, Cees de Laat, "Special section on high-performance networking for distributed data-intensive science", Future Generation Computer Systems, The International Journal of eScience, Elsevier, 2015, doi: doi:10.1016/j.future.2015.10.006

### Mahantesh Halappanavar, Alex Pothen, Ariful Azad, Fredrik Manne, Johannes Langguth, Arif Khan, "Codesign Lessons Learned from Implementing Graph Matching on Multithreaded Architectures", IEEE Computer, August 2015,

### Aydin Buluc, John Gilbert, Leonid Oliker, "Special Issue: Graph Analysis for Scientific Discovery", Parallel Computing Journal Special Issue Editors, August 1, 2015,

### Štěpán Timr, Jiří Brabec, Alexey Bondar, Tomáš Ryba, Miloš Železný, Josef Lazar, Pavel Jungwirth, "Non-Linear Optical Properties of Fluorescent Dyes Allow for Accurate Determination of Their Molecular Orientations in Phospholipid Membranes", The Journal of Physical Chemistry, July 6, 2015,

Several methods based on single- and two-photon fluorescence detected linear dichroism have recently been used to determine the orientational distributions of fluorescent dyes in lipid membranes. However, these determinations relied on simplified descriptions of non-linear anisotropic properties of the dye molecules, using a transition dipole moment-like vector instead of an absorptivity tensor. To investigate the validity of the vector approximation, we have now carried out a combination of computer simulations and polarization microscopy experiments on two representative fluorescent dyes (DiI and F2N12S) embedded in aqueous phosphatidylcholine bilayers. Our results indicate that a simplified vector-like treatment of the two-photon transition tensor is applicable for molecular geometries sampled in the membrane at ambient conditions. Furthermore, our results allow evaluation of several distinct polarization microscopy techniques. In combination, our results point to a robust and accurate experimental and computational treatment of orientational distributions of DiI, F2N12S and related dyes (including Cy3, Cy5, and others), with implications to monitoring physiologically relevant processes in cellular membranes in a novel way.

### M. Ulbrich, Z. Wen, C. Yang, D. Klockner, Z. Lu, "A proximal gradient method for ensemble density functional theory", SIAM J. Sci. Comp., June 20, 2015, 37:A1975--A20, doi: 10.1137/14098973X

### Huggel, C., D. Stone, H. Eicken, and G. Hansen, "Potential and limitations of the attribution of climate change impacts for informing loss and damage discussions and policies", Climatic Change, 2015, 133:453-467, doi: 10.1007/s10584-015-1441-z

### P. McCorquodale, P.A. Ullrich, H. Johansen, P. Colella, "An adaptive multiblock high-order finite-volume method for solving the shallow-water equations on the sphere", Comm. App. Math. and Comp. Sci., 2015, 10:121-162, doi: 10.2140/camcos.2015.10.121

### Mathias Jacquelin, Lin Lin, Chao Yang, "A Distributed Memory Parallel Algorithm for Selected Inversion : the Symmetric Case", To appear in ACM Transactions on Mathematical Software (TOMS), May 28, 2015,

### David H. Bailey, Jonathan M. Borwein, "High-precision arithmetic in mathematical physics", Mathematics, May 12, 2015, 3:337-367,

### Wehner, M., Prabhat, K. A. Reed, D. Stone, W. D. Collins, and J. Bacmeister, "Resolution dependence of future tropical cyclone projections of CAM5.1 in the US CLIVAR Hurricane Working Group idealized configurations", Journal of Climate, 2015, 28:3905-3925, doi: 10.1175/JCLI-D-14-00311.1

### K. Hu, J. Choi, A. Sim, J. Jiang, "Best Predictive Generalized Linear Mixed Model with Predictive Lasso for High-Speed Network Data Analysis", International Journal of Statistics and Probability, 2015,

### Didem Unat, Cy Chan, Weiqun Zhang, Samuel Williams, John Bachan, John Bell, John Shalf, "ExaSAT: An Exascale Co-Design Tool for Performance Modeling", International Journal of High Performance Computing Applications (IJHPCA), May 2015, doi: 10.1177/1094342014568690

- Download File: International-Journal-of-High-Performance-Computing-Applications-2015-Unat-209-32.pdf (pdf: 4.3 MB)

### P. McCorquodale, M.R. Dorr, J.A.F. Hittinger, P. Colella, "High-order finite-volume methods for hyperbolic conservation laws on mapped multiblock grids", J. Comput. Phys., May 1, 2015, 288:181-195, doi: 10.1016/j.jcp.2015.01.006

### Robert Saye, "High-Order Quadrature Methods for Implicitly Defined Surfaces and Volumes in Hyperrectangles", SIAM Journal on Scientific Computing, April 23, 2015, doi: 10.1137/140966290

### Y. Gong, W.A. de Jong, J.K. Gibson, "Gas Phase Uranyl Activation: Formation of a Uranium Nitrosyl Complex from Uranyl Azide", Journal of the American Chemical Society, April 23, 2015, 137:5911, doi: 10.1021/jacs.5b02420

### Nicholas Chaimov, Khaled Ibrahim, Samuel Williams, Costin Iancu, "Exploiting Communication Concurrency on High Performance Computing Systems", IJHPCA, April 17, 2015,

- Download File: thorserv2.pdf (pdf: 1.7 MB)

### D. Devendran, D. T. Graves, H. Johansen, "A higher-order finite-volume discretization method for Poisson's equation in cut cell geometries", submitted to SIAM Journal on Scientific Computing (preprint on arxiv), 2015,

### Fang Liu, Lin Lin , Derek Vigil-Fowlerd , Johannes Lischnerd, Alexander F. Kemper, , Sahar Sharifzadehe, Felipe H. da Jornadad, Jack Deslippef, Chao Yangc, Jeffrey B. Neaton, Steven G. Louied,, "Numerical integration for ab initio many-electron self energy calculations within the GW approximation", Journal of Computational Physics, April 1, 2015,

### Elaheh Pourabbas, Arie Shoshani, "The Composite Data Model: A Unified Approach for Combining and Querying Multiple Data Models", IEEE Trans. Knowl. Data Eng, 2015, 27(5):1424-1437,

### Peter Schwartz, Julie Percelay, Terry J. Ligocki, Hans Johansen, Daniel T. Graves, Dharshi Devendran, Phillip Colella, Eli Ateljevich, "High-accuracy embedded boundary grid generation using the divergence theorem", Communications in Applied Mathematics and Computational Science 10-1 (2015), 83--96. DOI 10.2140/camcos.2015.10.83, March 31, 2015,

### Subrata Banik , Lalitha Ravichandran , Jiri Brabec , Ivan Hubac , Karol Kowalski , Jiri Pittner, "Iterative universal state selective correction for the Brillouin-Wigner multireference coupled-cluster theory", J. Chem. Phys., March 21, 2015, 142:114106,

### R.M. Cox, P.B. Armentrout, W.A. de Jong, "Activation of CH4 by Th+ as Studied by Guided Ion Beam Mass Spectrometry and Quantum Chemistry", Inorganic Chemistry, March 13, 2015, 54:3584, doi: 10.1021/acs.inorgchem.5b00137

### E. Vecharynski, C. Yang, J. E. Pask, "A projected preconditioned conjugate gradient algorithm for computing many extreme eigenpairs of a Hermitian matrix", Journal of Computational Physics, Vol. 290, pp. 73–89, 2015,

We present an iterative algorithm for computing an invariant subspace associated with the algebraically smallest eigenvalues of a large sparse or structured Hermitian matrix *A*. We are interested in the case in which the dimension of the invariant subspace is large (e.g., over several hundreds or thousands) even though it may still be small relative to the dimension of *A*. These problems arise from, for example, density functional theory (DFT) based electronic structure calculations for complex materials. The key feature of our algorithm is that it performs fewer Rayleigh–Ritz calculations compared to existing algorithms such as the locally optimal block preconditioned conjugate gradient or the Davidson algorithm. It is a block algorithm, and hence can take advantage of efficient BLAS3 operations and be implemented with multiple levels of concurrency. We discuss a number of practical issues that must be addressed in order to implement the algorithm efficiently on a high performance computer.

### Hansen, G., D. Stone, M. Auffhammer, C. Huggel, W. Cramer, "Linking local impacts to changes in climate: a guide to attribution", Regional Environmental Change, 2015, doi: 10.1007/s10113-015-0760-y

### Wei Hu, Lin Lin and Chao Yang, "Edge reconstruction in armchair phosphorene nanoribbons revealed by discontinuous Galerkin density functional theory", Phys. Chem. Chem. Phys., 2015, Advance Article, February 11, 2015, doi: 10.1039/C5CP00333D

With the help of our recently developed massively parallel DGDFT (Discontinuous Galerkin Density Functional Theory) methodology, we perform large-scale Kohn–Sham density functional theory calculations on phosphorene nanoribbons with armchair edges (ACPNRs) containing a few thousands to ten thousand atoms. The use of DGDFT allows us to systematically achieve a conventional plane wave basis set type of accuracy, but with a much smaller number (about 15) of adaptive local basis (ALB) functions per atom for this system. The relatively small number of degrees of freedom required to represent the Kohn–Sham Hamiltonian, together with the use of the pole expansion the selected inversion (PEXSI) technique that circumvents the need to diagonalize the Hamiltonian, results in a highly efficient and scalable computational scheme for analyzing the electronic structures of ACPNRs as well as their dynamics. The total wall clock time for calculating the electronic structures of large-scale ACPNRs containing 1080–10 800 atoms is only 10–25 s per self-consistent field (SCF) iteration, with accuracy fully comparable to that obtained from conventional planewave DFT calculations. For the ACPNR system, we observe that the DGDFT methodology can scale to 5000–50 000 processors. We use DGDFT based ab initio molecular dynamics (AIMD) calculations to study the thermodynamic stability of ACPNRs. Our calculations reveal that a 2 × 1 edge reconstruction appears in ACPNRs at room temperature.

### Sang-Yun Oh, Bala Rajaratnam, Joong-Ho Won, "On the Solution Path of Regularized Covariance Estimators", (submitted), 2015,

### Zarija Lukić, Casey Stark, Peter Nugent, Martin White, Avery Meiksin, Ann Almgren, "The Lyman α forest in optically thin hydrodynamical simulations", Monthly Notices of the Royal Astronomical Society, 2015, 446:3697,

### Lawal, K., D. Stone, T. Aina, C. Rye, B. Abiodun, "Trends in the potential spread of seasonal climate simulations over South Africa", International Journal of Climatology, 2015, doi: 10.1002/joc.4234

### Thorsten Kurth, Andrew Pochinsky, Abhinav Sarje, Sergey Syritsyn, Andre Walker-Loud, "High-Performance I/O: HDF5 for Lattice QCD", arXiv:1501.06992, January 2015,

Practitioners of lattice QCD/QFT have been some of the primary pioneer users of the state-of-the-art high-performance-computing systems, and contribute towards the stress tests of such new machines as soon as they become available. As with all aspects of high-performance-computing, I/O is becoming an increasingly specialized component of these systems. In order to take advantage of the latest available high-performance I/O infrastructure, to ensure reliability and backwards compatibility of data files, and to help unify the data structures used in lattice codes, we have incorporated parallel HDF5 I/O into the SciDAC supported USQCD software stack. Here we present the design and implementation of this I/O framework. Our HDF5 implementation outperforms optimized QIO at the 10-20% level and leaves room for further improvement by utilizing appropriate dataset chunking.

### David Trebotich, Daniel T. Graves, "An Adaptive Finite Volume Method for the Incompressible Navier-Stokes Equations in Complex Geometries", Communications in Applied Mathematics and Computational Science, January 15, 2015, 10-1:43-82, doi: 10.2140/camcos.2015.10.43

- Download File: camcos-v10-n1-p03-s3.pdf (pdf: 9.1 MB)

### J. Chapman, M. Mascher, A. Buluç, K. Barry, E. Georganas, A. Session, V. Strnadova, J. Jenkins, S. Sehgal, L. Oliker, J Schmutz, K. Yelick, U. Scholz, R. Waugh, J. Poland, G. Muehlbauer, N. Stein, D. Rokhsar, "A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome", Genome biology, 2015,

### Max Duarte, Ann Almgren, John Bell, "A Low Mach Number Model for Moist Atmospheric Flows", Journal of Atmospheric Sciences, to appear, 2015,

### Y.-C. Pan, M. Sullivan, K. Maguire, A. Gal-Yam, I. M., D. A. Howell, P. E. Nugent, P. A. Mazzali, "Type Ia supernova spectral features in the context of their host galaxy properties", Monthly Notices of the Royal Astronomical Society, 2015, 446:354-368, doi: 10.1093/mnras/stu2121

### A. Amato, M. Day, R. K. Cheng, J. Bell, T. Lieuwen, "Topology and Burning Rates of Turbulent, Lean, H2-Air Flames", submitted for publication, 2015,

### Max Duarte, Matthew Emmett, "High order schemes based on operator splitting and deferred corrections for stiff time-dependent PDEs", submitted for publication, 2015,

### J.C. Dolence, A. Burrows, and W. Zhang,, "Two-Dimensional Core-Collapse Supernova Models with Multi-Dimensional Transport", submitted for publication, 2015,

### P.A.R. Ade, N. Aghanim, C. Armitage-Caplan, M. Arnaud, M. Ashdown, F. Atrio-Barandela, J. Aumont, H. Aussel, C. Baccigalupi, A.J. Banday, R.B. Barreiro, R. Barrena, M. Bartelmann, J.G. Bartlett, E. Battaner, K. Benabed, A. Benoît, A. Benoit-Lévy, J.-P. Bernard, M. Bersanelli, P. Bielewicz, I. Bikmaev, J. Bobin, J.J. Bock, H. Böhringer, A. Bonaldi, J.R. Bond, J. Borrill, F.R. Bouchet, M. Bridges, M. Bucher, R. Burenin, C. Burigana, R.C. Butler, J.-F. Cardoso, P. Carvalho, A. Catalano, A. Challinor, A. Chamballu, R.-R. Chary, X. Chen, H.C. Chiang, L.-Y. Chiang, G. Chon, P.R. Christensen, E. Churazov, S. Church, D.L. Clements, S. Colombi, L.P.L. Colombo, B. Comis, F. Couchot, A. Coulais, B.P. Crill, A. Curto, F. Cuttaia, A. Da Silva, H. Dahle, L. Danese, R.D. Davies, R.J. Davis, P. De Bernardis, A. De Rosa, G. De Zotti, J. Delabrouille, J.-M. Delouis, J. Démoclès, F.-X. Désert, C. Dickinson, J.M. Diego, K. Dolag, H. Dole, S. Donzelli, O. Doré, M. Douspis, X. Dupac, G. Efstathiou, T.A. Enßlin, H.K. Eriksen, F. Feroz, A. Ferragamo, F. Finelli, I. Flores-Cacho, O. Forni, M. Frailis, E. Franceschi, S. Fromenteau, S. Galeotta, K. Ganga, R.T. Génova-Santos, M. Giard, G. Giardino, M. Gilfanov, Y. Giraud-Héraud, J. González-Nuevo, K.M. Górski, K.J.B. Grainge, S. Gratton, A. Gregorio, N.E. Groeneboom, A. Gruppuso, F.K. Hansen, D. Hanson, D. Harrison, A. Hempel, S. Henrot-Versillé, C. Hernández-Monteagudo, D. Herranz, S.R. Hildebrandt, E. Hivon, M. Hobson, W.A. Holmes, A. Hornstrup, W. Hovest, K.M. Huffenberger, G. Hurier, N. Hurley-Walker, A.H. Jaffe, T.R. Jaffe, W.C. Jones, M. Juvela, E. Keihänen, R. Keskitalo, I. Khamitov, T.S. Kisner, R. Kneissl, J. Knoche, L. Knox, M. Kunz, H. Kurki-Suonio, G. Lagache, A. Lähteenmäki, J.-M. Lamarre, A. Lasenby, R.J. Laureijs, C.R. Lawrence, J.P. Leahy, R. Leonardi, J. León-Tavares, J. Lesgourgues, C. Li, A. Liddle, M. Liguori, P.B. Lilje, M. Linden-Vørnle, M. López-Caniego, P.M. Lubin, J.F. Macías-Pérez, C.J. Mactavish, B. Maffei, D. Maino, N. Mandolesi, M. Maris, D.J. Marshall, P.G. Martin, E. Martínez-González, S. Masi, M. Massardi, S. Matarrese, F. Matthai, P. Mazzotta, S. Mei, P.R. Meinhold, A. Melchiorri, J.-B. Melin, L. Mendes, A. Mennella, M. Migliaccio, K. Mikkelsen, S. Mitra, M.-A. Miville-Deschênes, A. Moneti, L. Montier, G. Morgante, D. Mortlock, D. Munshi, J.A. Murphy, P. Naselsky, A. Nastasi, F. Nati, P. Natoli, N.P.H. Nesvadba, C.B. Netterfield, H.U. Nørgaard-Nielsen, F. Noviello, D. Novikov, I. Novikov, I.J. O Dwyer, M. Olamaie, S. Osborne, C.A. Oxborrow, F. Paci, L. Pagano, F. Pajot, D. Paoletti, F. Pasian, G. Patanchon, T.J. Pearson, O. Perdereau, L. Perotto, Y.C. Perrott, F. Perrotta, F. Piacentini, M. Piat, E. Pierpaoli, D. Pietrobon, S. Plaszczynski, E. Pointecouteau, G. Polenta, N. Ponthieu, L. Popa, T. Poutanen, G.W. Pratt, G. Prézeau, S. Prunet, J.-L. Puget, J.P. Rachen, W.T. Reach, R. Rebolo, M. Reinecke, M. Remazeilles, C. Renault, S. Ricciardi, T. Riller, I. Ristorcelli, G. Rocha, C. Rosset, G. Roudier, M. Rowan-Robinson, J.A. Rubiño-Martín, C. Rumsey, B. Rusholme, M. Sandri, D. Santos, R.D.E. Saunders, G. Savini, M.P. Schammel, D. Scott, M.D. Seiffert, E.P.S. Shellard, T.W. Shimwell, L.D. Spencer, J.-L. Starck, V. Stolyarov, R. Stompor, A. Streblyanska, R. Sudiwala, R. Sunyaev, F. Sureau, D. Sutton, A.-S. Suur-Uski, J.-F. Sygnet, J.A. Tauber, D. Tavagnacco, L. Terenzi, L. Toffolatti, M. Tomasi, D. Tramonte, M. Tristram, M. Tucci, J. Tuovinen, M. Türler, G. Umana, L. Valenziano, J. Valiviita, B. Van Tent, L. Vibert, P. Vielva, F. Villa, N. Vittorio, L.A. Wade, B.D. Wandelt, M. White, S.D.M. White, D. Yvon, A. Zacchei, A. Zonca, "Planck 2013 results. XXXII. the updated Planck catalogue of Sunyaev-Zeldovich sources", Astronomy and Astrophysics, 2015, 581, doi: 10.1051/0004-6361/201525787

### Jarrod R McClean, Alan Aspuru-Guzik, "Clock quantum Monte Carlo technique: An imaginary-time method for real-time quantum dynamics", Physical Review A, 2015, 91:012311,

### P.A.R. Ade, N. Aghanim, M. Arnaud, M. Ashdown, J. Aumont, C. Baccigalupi, A.J. Banday, R.B. Barreiro, E. Battaner, K. Benabed, A. Benoit-Lévy, J.-P. Bernard, M. Bersanelli, P. Bielewicz, J.R. Bond, J. Borrill, F.R. Bouchet, C. Burigana, R.C. Butler, E. Calabrese, A. Chamballu, H.C. Chiang, P.R. Christensen, D.L. Clements, L.P.L. Colombo, F. Couchot, A. Curto, F. Cuttaia, L. Danese, R.D. Davies, R.J. Davis, P. De Bernardis, A. De Rosa, G. De Zotti, J. Delabrouille, J.M. Diego, H. Dole, O. Doré, X. Dupac, T.A. Enßlin, H.K. Eriksen, O. Fabre, F. Finelli, O. Forni, M. Frailis, E. Franceschi, S. Galeotta, S. Galli, K. Ganga, M. Giard, J. González-Nuevo, K.M. Górski, A. Gregorio, A. Gruppuso, F.K. Hansen, D. Hanson, D.L. Harrison, S. Henrot-Versillé, C. Hernández-Monteagudo, D. Herranz, S.R. Hildebrandt, E. Hivon, M. Hobson, W.A. Holmes, A. Hornstrup, W. Hovest, K.M. Huffenberger, A.H. Jaffe, W.C. Jones, E. Keihänen, R. Keskitalo, R. Kneissl, J. Knoche, M. Kunz, H. Kurki-Suonio, J.-M. Lamarre, A. Lasenby, C.R. Lawrence, R. Leonardi, J. Lesgourgues, M. Liguori, P.B. Lilje, M. Linden-Vørnle, M. López-Caniego, P.M. Lubin, J.F. Macías-Pérez, N. Mandolesi, M. Maris, P.G. Martin, E. Martínez-González, S. Masi, S. Matarrese, P. Mazzotta, P.R. Meinhold, A. Melchiorri, L. Mendes, E. Menegoni, A. Mennella, M. Migliaccio, M.-A. Miville-Deschênes, A. Moneti, L. Montier, G. Morgante, A. Moss, D. Munshi, J.A. Murphy, P. Naselsky, F. Nati, P. Natoli, H.U. Nørgaard-Nielsen, F. Noviello, D. Novikov, I. Novikov, C.A. Oxborrow, L. Pagano, F. Pajot, D. Paoletti, F. Pasian, G. Patanchon, O. Perdereau, L. Perotto, F. Perrotta, F. Piacentini, M. Piat, E. Pierpaoli, D. Pietrobon, S. Plaszczynski, E. Pointecouteau, G. Polenta, N. Ponthieu, L. Popa, G.W. Pratt, S. Prunet, J.P. Rachen, R. Rebolo, M. Reinecke, M. Remazeilles, C. Renault, S. Ricciardi, I. Ristorcelli, G. Rocha, G. Roudier, B. Rusholme, M. Sandri, G. Savini, D. Scott, L.D. Spencer, V. Stolyarov, R. Sudiwala, D. Sutton, A.-S. Suur-Uski, J.-F. Sygnet, J.A. Tauber, D. Tavagnacco, L. Terenzi, L. Toffolatti, M. Tomasi, M. Tristram, M. Tucci, J.-P. Uzan, L. Valenziano, J. Valiviita, B. Van Tent, P. Vielva, F. Villa, L.A. Wade, D. Yvon, A. Zacchei, A. Zonca, "Planck intermediate results: XXIV. Constraints on variations in fundamental constants", Astronomy and Astrophysics, 2015, 580, doi: 10.1051/0004-6361/201424496

### Ryan Babbush, Jarrod McClean, Dave Wecker, Alan Aspuru-Guzik, Nathan Wiebe, "Chemical basis of Trotter-Suzuki errors in quantum chemistry simulation", Physical Review A, 2015, 91:022311,

### A. Donev, A. Nonaka, A. K. Bhattacharjee, A. L. Garcia, J. B. Bell, "Low Mach Number Fluctuating Hydrodynamics of Multispecies Liquid Mixtures", submitted for publication, 2015,

### J. Borrill, R. Keskitalo, T. Kisner, "Big bang, big data, big iron: Fifteen years of cosmic microwave background data analysis at NERSC", Computing in Science and Engineering, 2015, 17:22-29, doi: 10.1109/MCSE.2015.1

### Andrew Tranter, Sarah Sofia, Jake Seeley, Michael Kaicher, Jarrod McClean, Ryan Babbush, Peter V Coveney, Florian Mintert, Frank Wilhelm, Peter J Love, "The Bravyi--Kitaev transformation: Properties and applications", International Journal of Quantum Chemistry, 2015, 115:1431--1441,

### M. Zingale, C. M. Malone, A. Nonaka, A. S. Almgren, and J. B. Bell, "Comparisons of Two- and Three-Dimensional Convection in Type I X-ray Bursts", submitted for publication, 2015,

### P.A.R. Ade, M.I.R. Alves, G. Aniano, C. Armitage-Caplan, M. Arnaud, F. Atrio-Barandela, J. Aumont, C. Baccigalupi, A.J. Banday, R.B. Barreiro, E. Battaner, K. Benabed, A. Benoit-Lévy, J.-P. Bernard, M. Bersanelli, P. Bielewicz, J.J. Bock, J.R. Bond, J. Borrill, F.R. Bouchet, F. Boulanger, C. Burigana, J.-F. Cardoso, A. Catalano, A. Chamballu, H.C. Chiang, L.P.L. Colombo, C. Combet, F. Couchot, A. Coulais, B.P. Crill, A. Curto, F. Cuttaia, L. Danese, R.D. Davies, R.J. Davis, P. De Bernardis, G. De Zotti, J. Delabrouille, F.-X. Désert, C. Dickinson, J.M. Diego, S. Donzelli, O. Doré, M. Douspis, J. Dunkley, X. Dupac, T.A. Enßlin, H.K. Eriksen, E. Falgarone, F. Finelli, O. Forni, M. Frailis, A.A. Fraisse, E. Franceschi, S. Galeotta, K. Ganga, T. Ghosh, M. Giard, J. González-Nuevo, K.M. Górski, A. Gregorio, A. Gruppuso, V. Guillet, F.K. Hansen, D.L. Harrison, G. Helou, C. Hernández-Monteagudo, S.R. Hildebrandt, E. Hivon, M. Hobson, W.A. Holmes, A. Hornstrup, A.H. Jaffe, T.R. Jaffe, W.C. Jones, E. Keihänen, R. Keskitalo, T.S. Kisner, R. Kneissl, J. Knoche, M. Kunz, H. Kurki-Suonio, G. Lagache, J.-M. Lamarre, A. Lasenby, C.R. Lawrence, J.P. Leahy, R. Leonardi, F. Levrier, M. Liguori, P.B. Lilje, M. Linden-Vørnle, M. López-Caniego, P.M. Lubin, J.F. Macías-Pérez, B. Maffei, A.M. Magalhães, D. Maino, N. Mandolesi, M. Maris, D.J. Marshall, P.G. Martin, E. Martínez-González, S. Masi, S. Matarrese, P. Mazzotta, A. Melchiorri, L. Mendes, A. Mennella, M. Migliaccio, M.-A. Miville-Deschênes, A. Moneti, L. Montier, G. Morgante, D. Mortlock, D. Munshi, J.A. Murphy, P. Naselsky, F. Nati, P. Natoli, C.B. Netterfield, F. Noviello, D. Novikov, I. Novikov, N. Oppermann, C.A. Oxborrow, L. Pagano, F. Pajot, D. Paoletti, F. Pasian, O. Perdereau, L. Perotto, F. Perrotta, F. Piacentini, D. Pietrobon, S. Plaszczynski, E. Pointecouteau, G. Polenta, L. Popa, G.W. Pratt, J.P. Rachen, W.T. Reach, M. Reinecke, M. Remazeilles, C. Renault, S. Ricciardi, T. Riller, I. Ristorcelli, G. Rocha, C. Rosset, G. Roudier, J.A. Rubiño-Martín, B. Rusholme, E. Salerno, M. Sandri, G. Savini, D. Scott, L.D. Spencer, V. Stolyarov, R. Stompor, R. Sudiwala, D. Sutton, A.-S. Suur-Uski, J.-F. Sygnet, J.A. Tauber, L. Terenzi, L. Toffolatti, M. Tomasi, M. Tristram, M. Tucci, L. Valenziano, J. Valiviita, B. Van Tent, P. Vielva, F. Villa, B.D. Wandelt, A. Zacchei, A. Zonca, "Planck intermediate results. XXII. Frequency dependence of thermal emission from Galactic dust in intensity and polarization", Astronomy and Astrophysics, 2015, 576, doi: 10.1051/0004-6361/201424088

### Jarrod R. McClean, Jonathan Romero, Ryan Babbush, Alan Aspuru-Guzik, "The theory of variational hybrid quantum-classical algorithms", arXiv:1509.04279 [quant-ph], 2015,

### David H. Bailey, David Borwein, Jonathan M. Borwein, "On Eulerian log-gamma integrals and Tornheim-Witten zeta functions", Ramanujan Journal, January 1, 2015, 36:43-68,

### D. Zuev, E. Vecharynski, C. Yang, N. Orms, and A.I. Krylov, "New algorithms for iterative matrix-free eigensolvers in quantum chemistry", Journal of Computational Chemistry, Vol. 36, Issue 5, pp. 273–284, 2015,

New algorithms for iterative diagonalization procedures that solve for a small set of eigen-states of a large matrix are described. The performance of the algorithms is illustrated by calculations of low and high-lying ionized and electronically excited states using equation-of-motion coupled-cluster methods with single and double substitutions (EOM-IP-CCSD and EOM-EE-CCSD). We present two algorithms suitable for calculating excited states that are close to a specified energy shift (interior eigenvalues). One solver is based on the Davidson algorithm, a diagonalization procedure commonly used in quantum-chemical calculations. The second is a recently developed solver, called the “Generalized Preconditioned Locally Harmonic Residual (GPLHR) method.” We also present a modification of the Davidson procedure that allows one to solve for a specific transition. The details of the algorithms, their computational scaling, and memory requirements are described. The new algorithms are implemented within the EOM-CC suite of methods in the Q-Chem electronic structure program.

### A. Nonaka, Y. Sun, J. B. Bell, and A. Donev, "Low Mach Number Fluctuating Hydrodynamics of Binary Liquid Mixtures", submitted for publication, 2015,

### P.A.R. Ade, N. Aghanim, D. Alina, M.I.R. Alves, C. Armitage-Caplan, M. Arnaud, D. Arzoumanian, M. Ashdown, F. Atrio-Barandela, J. Aumont, C. Baccigalupi, A.J. Banday, R.B. Barreiro, E. Battaner, K. Benabed, A. Benoit-Lévy, J.-P. Bernard, M. Bersanelli, P. Bielewicz, J.J. Bock, J.R. Bond, J. Borrill, F.R. Bouchet, F. Boulanger, A. Bracco, C. Burigana, R.C. Butler, J.-F. Cardoso, A. Catalano, A. Chamballu, R.-R. Chary, H.C. Chiang, P.R. Christensen, S. Colombi, L.P.L. Colombo, C. Combet, F. Couchot, A. Coulais, B.P. Crill, A. Curto, F. Cuttaia, L. Danese, R.D. Davies, R.J. Davis, P. De Bernardis, E.M. De Gouveia Dal Pino, A. De Rosa, G. De Zotti, J. Delabrouille, F.-X. Désert, C. Dickinson, J.M. Diego, S. Donzelli, O. Doré, M. Douspis, J. Dunkley, X. Dupac, G. Efstathiou, T.A. Enßlin, H.K. Eriksen, E. Falgarone, K. Ferrière, F. Finelli, O. Forni, M. Frailis, A.A. Fraisse, E. Franceschi, S. Galeotta, K. Ganga, T. Ghosh, M. Giard, Y. Giraud-Héraud, J. González-Nuevo, K.M. Górski, A. Gregorio, A. Gruppuso, V. Guillet, F.K. Hansen, D.L. Harrison, G. Helou, C. Hernández-Monteagudo, S.R. Hildebrandt, E. Hivon, M. Hobson, W.A. Holmes, A. Hornstrup, K.M. Huffenberger, A.H. Jaffe, T.R. Jaffe, W.C. Jones, M. Juvela, E. Keihänen, R. Keskitalo, T.S. Kisner, R. Kneissl, J. Knoche, M. Kunz, H. Kurki-Suonio, G. Lagache, A. Lähteenmäki, J.-M. Lamarre, A. Lasenby, C.R. Lawrence, J.P. Leahy, R. Leonardi, F. Levrier, M. Liguori, P.B. Lilje, M. Linden-Vørnle, M. López-Caniego, P.M. Lubin, J.F. Macías-Pérez, B. Maffei, A.M. Magalhães, D. Maino, N. Mandolesi, M. Maris, D.J. Marshall, P.G. Martin, E. Martínez-González, S. Masi, S. Matarrese, P. Mazzotta, A. Melchiorri, L. Mendes, A. Mennella, M. Migliaccio, M.-A. Miville-Deschênes, A. Moneti, L. Montier, G. Morgante, D. Mortlock, D. Munshi, J.A. Murphy, P. Naselsky, F. Nati, P. Natoli, C.B. Netterfield, F. Noviello, D. Novikov, I. Novikov, C.A. Oxborrow, L. Pagano, F. Pajot, R. Paladini, D. Paoletti, F. Pasian, T.J. Pearson, O. Perdereau, L. Perotto, F. Perrotta, F. Piacentini, M. Piat, D. Pietrobon, S. Plaszczynski, F. Poidevin, E. Pointecouteau, G. Polenta, L. Popa, G.W. Pratt, S. Prunet, J.-L. Puget, J.P. Rachen, W.T. Reach, R. Rebolo, M. Reinecke, M. Remazeilles, C. Renault, S. Ricciardi, T. Riller, I. Ristorcelli, G. Rocha, C. Rosset, G. Roudier, J.A. Rubiño-Martín, B. Rusholme, M. Sandri, G. Savini, D. Scott, L.D. Spencer, V. Stolyarov, R. Stompor, R. Sudiwala, D. Sutton, A.-S. Suur-Uski, J.-F. Sygnet, J.A. Tauber, L. Terenzi, L. Toffolatti, M. Tomasi, M. Tristram, M. Tucci, G. Umana, L. Valenziano, J. Valiviita, B. Van Tent, P. Vielva, F. Villa, L.A. Wade, B.D. Wandelt, A. Zacchei, A. Zonca, "Planck intermediate results. XIX. An overview of the polarized thermal emission from Galactic dust", Astronomy and Astrophysics, 2015, 576, doi: 10.1051/0004-6361/201424082

### P.A.R. Ade, N. Aghanim, D. Alina, M.I.R. Alves, G. Aniano, C. Armitage-Caplan, M. Arnaud, D. Arzoumanian, M. Ashdown, F. Atrio-Barandela, J. Aumont, C. Baccigalupi, A.J. Banday, R.B. Barreiro, E. Battaner, K. Benabed, A. Benoit-Lévy, J.-P. Bernard, M. Bersanelli, P. Bielewicz, J.R. Bond, J. Borrill, F.R. Bouchet, F. Boulanger, A. Bracco, C. Burigana, J.-F. Cardoso, A. Catalano, A. Chamballu, H.C. Chiang, P.R. Christensen, S. Colombi, L.P.L. Colombo, C. Combet, F. Couchot, A. Coulais, B.P. Crill, A. Curto, F. Cuttaia, L. Danese, R.D. Davies, R.J. Davis, P. De Bernardis, A. De Rosa, G. De Zotti, J. Delabrouille, C. Dickinson, J.M. Diego, S. Donzelli, O. Doré, M. Douspis, X. Dupac, G. Efstathiou, T.A. Enßlin, H.K. Eriksen, E. Falgarone, L. Fanciullo, K. Ferrière, F. Finelli, O. Forni, M. Frailis, A.A. Fraisse, E. Franceschi, S. Galeotta, K. Ganga, T. Ghosh, M. Giard, Y. Giraud-Héraud, J. González-Nuevo, K.M. Górski, A. Gregorio, A. Gruppuso, V. Guillet, F.K. Hansen, D.L. Harrison, G. Helou, C. Hernández-Monteagudo, S.R. Hildebrandt, E. Hivon, M. Hobson, W.A. Holmes, A. Hornstrup, K.M. Huffenberger, A.H. Jaffe, T.R. Jaffe, W.C. Jones, M. Juvela, E. Keihänen, R. Keskitalo, T.S. Kisner, R. Kneissl, J. Knoche, M. Kunz, H. Kurki-Suonio, G. Lagache, J.-M. Lamarre, A. Lasenby, C.R. Lawrence, R. Leonardi, F. Levrier, M. Liguori, P.B. Lilje, M. Linden-Vørnle, M. López-Caniego, P.M. Lubin, J.F. Macías-Pérez, D. Maino, N. Mandolesi, M. Maris, D.J. Marshall, P.G. Martin, E. Martínez-González, S. Masi, S. Matarrese, P. Mazzotta, A. Melchiorri, L. Mendes, A. Mennella, M. Migliaccio, M.-A. Miville-Deschênes, A. Moneti, L. Montier, G. Morgante, D. Mortlock, D. Munshi, J.A. Murphy, P. Naselsky, F. Nati, P. Natoli, C.B. Netterfield, F. Noviello, D. Novikov, I. Novikov, C.A. Oxborrow, L. Pagano, F. Pajot, D. Paoletti, F. Pasian, V.-M. Pelkonen, O. Perdereau, L. Perotto, F. Perrotta, F. Piacentini, M. Piat, D. Pietrobon, S. Plaszczynski, E. Pointecouteau, G. Polenta, L. Popa, G.W. Pratt, S. Prunet, J.-L. Puget, J.P. Rachen, M. Reinecke, M. Remazeilles, C. Renault, S. Ricciardi, T. Riller, I. Ristorcelli, G. Rocha, C. Rosset, G. Roudier, B. Rusholme, M. Sandri, D. Scott, J.D. Soler, L.D. Spencer, V. Stolyarov, R. Stompor, R. Sudiwala, D. Sutton, A.-S. Suur-Uski, J.-F. Sygnet, J.A. Tauber, L. Terenzi, L. Toffolatti, M. Tomasi, M. Tristram, M. Tucci, G. Umana, L. Valenziano, J. Valiviita, B. Van Tent, P. Vielva, F. Villa, L.A. Wade, B.D. Wandelt, A. Zonca, "Planck intermediate results. XX. Comparison of polarized thermal emission from Galactic dust with simulations of MHD turbulence", Astronomy and Astrophysics, 2015, 576, doi: 10.1051/0004-6361/201424086

### A. Amato, M. Day, R. K. Cheng, J. Bell, T. Lieuwen, "Leading Edge Statistics of Turbulent, Lean, H2-Air Flames", submitted for publication, 2015,

### P.A.R. Ade, N. Aghanim, D. Alina, G. Aniano, C. Armitage-Caplan, M. Arnaud, M. Ashdown, F. Atrio-Barandela, J. Aumont, C. Baccigalupi, A.J. Banday, R.B. Barreiro, E. Battaner, C. Beichman, K. Benabed, A. Benoit-Lévy, J.-P. Bernard, M. Bersanelli, P. Bielewicz, J.J. Bock, J.R. Bond, J. Borrill, F.R. Bouchet, F. Boulanger, C. Burigana, J.-F. Cardoso, A. Catalano, A. Chamballu, R.-R. Chary, H.C. Chiang, P.R. Christensen, S. Colombi, L.P.L. Colombo, C. Combet, F. Couchot, A. Coulais, B.P. Crill, A. Curto, F. Cuttaia, L. Danese, R.D. Davies, R.J. Davis, P. De Bernardis, A. De Rosa, G. De Zotti, J. Delabrouille, F.-X. Désert, C. Dickinson, J.M. Diego, S. Donzelli, O. Doré, M. Douspis, J. Dunkley, X. Dupac, G. Efstathiou, T.A. Enßlin, H.K. Eriksen, E. Falgarone, L. Fanciullo, F. Finelli, O. Forni, M. Frailis, A.A. Fraisse, E. Franceschi, S. Galeotta, K. Ganga, T. Ghosh, M. Giard, Y. Giraud-Héraud, J. González-Nuevo, K.M. Górski, A. Gregorio, A. Gruppuso, V. Guillet, F.K. Hansen, D.L. Harrison, G. Helou, C. Hernández-Monteagudo, S.R. Hildebrandt, E. Hivon, M. Hobson, W.A. Holmes, A. Hornstrup, K.M. Huffenberger, A.H. Jaffe, T.R. Jaffe, W.C. Jones, M. Juvela, E. Keihänen, R. Keskitalo, T.S. Kisner, R. Kneissl, J. Knoche, M. Kunz, H. Kurki-Suonio, G. Lagache, A. Lähteenmäki, J.-M. Lamarre, A. Lasenby, C.R. Lawrence, R. Leonardi, F. Levrier, M. Liguori, P.B. Lilje, M. Linden-Vørnle, M. López-Caniego, P.M. Lubin, J.F. Macías-Pérez, B. Maffei, A.M. Magalhães, D. Maino, N. Mandolesi, M. Maris, D.J. Marshall, P.G. Martin, E. Martínez-González, S. Masi, S. Matarrese, P. Mazzotta, A. Melchiorri, L. Mendes, A. Mennella, M. Migliaccio, M.-A. Miville-Deschênes, A. Moneti, L. Montier, G. Morgante, D. Mortlock, D. Munshi, J.A. Murphy, P. Naselsky, F. Nati, P. Natoli, C.B. Netterfield, F. Noviello, D. Novikov, I. Novikov, C.A. Oxborrow, L. Pagano, F. Pajot, R. Paladini, D. Paoletti, F. Pasian, O. Perdereau, L. Perotto, F. Perrotta, F. Piacentini, M. Piat, D. Pietrobon, S. Plaszczynski, F. Poidevin, E. Pointecouteau, G. Polenta, L. Popa, G.W. Pratt, S. Prunet, J.-L. Puget, J.P. Rachen, W.T. Reach, R. Rebolo, M. Reinecke, M. Remazeilles, C. Renault, S. Ricciardi, T. Riller, I. Ristorcelli, G. Rocha, C. Rosset, G. Roudier, B. Rusholme, M. Sandri, G. Savini, D. Scott, L.D. Spencer, V. Stolyarov, R. Stompor, R. Sudiwala, D. Sutton, A.-S. Suur-Uski, J.-F. Sygnet, J.A. Tauber, L. Terenzi, L. Toffolatti, M. Tomasi, M. Tristram, M. Tucci, G. Umana, L. Valenziano, J. Valiviita, B. Van Tent, P. Vielva, F. Villa, L.A. Wade, B.D. Wandelt, A. Zonca, "Planck intermediate results. XXI. Comparison of polarized thermal emission from Galactic dust at 353 GHz with interstellar polarization in the visible", Astronomy and Astrophysics, 2015, 576, doi: 10.1051/0004-6361/201424087

### A Chien, P Balaji, P Beckman, N Dun, A Fang, H Fujita, K Iskra, Z Rubenstein, Z Zheng, R Schreiber, others, "Versioned Distributed Arrays for Resilience in Scientific Applications: Global View Resilience", Journal of Computational Science, 2015,

### K.N. Abazajian, K. Arnold, J. Austermann, B.A. Benson, C. Bischoff, J. Bock, J.R. Bond, J. Borrill, E. Calabrese, J.E. Carlstrom, C.S. Carvalho, C.L. Chang, H.C. Chiang, S. Church, A. Cooray, T.M. Crawford, K.S. Dawson, S. Das, M.J. Devlin, M. Dobbs, S. Dodelson, O. Doré, J. Dunkley, J. Errard, A. Fraisse, J. Gallicchio, N.W. Halverson, S. Hanany, S.R. Hildebrandt, A. Hincks, R. Hlozek, G. Holder, W.L. Holzapfel, K. Honscheid, W. Hu, J. Hubmayr, K. Irwin, W.C. Jones, M. Kamionkowski, B. Keating, R. Keisler, L. Knox, E. Komatsu, J. Kovac, C.-L. Kuo, C. Lawrence, A.T. Lee, E. Leitch, E. Linder, P. Lubin, J. McMahon, A. Miller, L. Newburgh, M.D. Niemack, H. Nguyen, H.T. Nguyen, L. Page, C. Pryke, C.L. Reichardt, J.E. Ruhl, N. Sehgal, U. Seljak, J. Sievers, E. Silverstein, A. Slosar, K.M. Smith, D. Spergel, S.T. Staggs, A. Stark, R. Stompor, A.G. Vieregg, G. Wang, S. Watson, E.J. Wollack, W.L.K. Wu, K.W. Yoon, O. Zahn, "Neutrino physics from the cosmic microwave background and large scale structure", Astroparticle Physics, 2015, 63:66-80, doi: 10.1016/j.astropartphys.2014.05.014

### Patrick R. Amestoy, Iain S. Duff, Jean-Yves L'Excellent, François-Henry Rouet, "Parallel computation of entries of A-1", Siam Journal on Scientific Computing, 2015. To appear., 2015,

### R. E. Firth, M. Sullivan, A. Gal-Yam, D. A. Howell, K., P. Nugent, A. L. Piro, C. Baltay, U., E. Hadjiyksta, R. McKinnon, E. Ofek, D. Rabinowitz, E. S. Walker, "The rising light curves of Type Ia supernovae", Monthly Notices of the Royal Astronomical Society, 2015, 446:3895-3910, doi: 10.1093/mnras/stu2314

### K.N. Abazajian, K. Arnold, J. Austermann, B.A. Benson, C. Bischoff, J. Bock, J.R. Bond, J. Borrill, I. Buder, D.L. Burke, E. Calabrese, J.E. Carlstrom, C.S. Carvalho, C.L. Chang, H.C. Chiang, S. Church, A. Cooray, T.M. Crawford, B.P. Crill, K.S. Dawson, S. Das, M.J. Devlin, M. Dobbs, S. Dodelson, O. Doré, J. Dunkley, J.L. Feng, A. Fraisse, J. Gallicchio, S.B. Giddings, D. Green, N.W. Halverson, S. Hanany, D. Hanson, S.R. Hildebrandt, A. Hincks, R. Hlozek, G. Holder, W.L. Holzapfel, K. Honscheid, G. Horowitz, W. Hu, J. Hubmayr, K. Irwin, M. Jackson, W.C. Jones, R. Kallosh, M. Kamionkowski, B. Keating, R. Keisler, W. Kinney, L. Knox, E. Komatsu, J. Kovac, C.-L. Kuo, A. Kusaka, C. Lawrence, A.T. Lee, E. Leitch, A. Linde, E. Linder, P. Lubin, J. Maldacena, E. Martinec, J. McMahon, A. Miller, V. Mukhanov, L. Newburgh, M.D. Niemack, H. Nguyen, H.T. Nguyen, L. Page, C. Pryke, C.L. Reichardt, J.E. Ruhl, N. Sehgal, U. Seljak, L. Senatore, J. Sievers, E. Silverstein, A. Slosar, K.M. Smith, D. Spergel, S.T. Staggs, A. Stark, R. Stompor, A.G. Vieregg, G. Wang, S. Watson, E.J. Wollack, W.L.K. Wu, K.W. Yoon, O. Zahn, M. Zaldarriaga, "Inflation physics from the cosmic microwave background and large scale structure", Astroparticle Physics, 2015, 63:55-65, doi: 10.1016/j.astropartphys.2014.05.013

### M. Minion, R. Speck, M. Bolten, M. Emmett, and D. Ruprecht, "Interweaving PFASST and parallel multigrid", submitted for publication, 2015,

### C. Saunders, G. Aldering, P. Antilogus, C. Aragon, S., C. Baltay, S. Bongard, C. Buton, A., F. Cellier-Holzem, M. Childress, N., Y. Copin, H. K. Fakhouri, U. Feindt, E., J. Guy, M. Kerschhaggl, A. G. Kim, M., J. Nordin, P. Nugent, K. Paech, R., E. Pecontal, R. Pereira, S. Perlmutter, D., M. Rigault, D. Rubin, K. Runge, R., G. Smadja, C. Tao, R. C. Thomas, B. A., C. Wu, (. Nearby Supernova Factory, "Type Ia Supernova Distance Modulus Bias and Dispersion from K-correction Errors: A Direct Measurement Using Light Curve Fits to Observed Spectral Time Series", Astrophysical Journal, 2015, 800:57, doi: 10.1088/0004-637X/800/1/57

### R. Speck, D. Ruprecht, M. Emmett, M. Minion, and R. Krause, "Inexact spectral deferred corrections using single-cycle multigrid", submitted for publication, 2015,

### R. Speck, D. Ruprecht, M. Emmett, M. Bolten, and R. Krause, "A space-time parallel solver for the three-dimensional heat equation", submitted for publication, 2015,

### A. G. Kim, N. Padmanabhan, G. Aldering, S. W. Allen, C., R. N. Cahn, C. B. D Andrea, N. Dalal, K. S., K. D. Denney, D. J. Eisenstein, D. A., W. L. Freedman, S. Ho, D. E. Holz, D., S. M. Kent, R. Kessler, S. Kuhlmann, E. V., P. Martini, P. E. Nugent, S. Perlmutter, B. M., A. G. Riess, D. Rubin, M. Sako, N. V., N. Suzuki, R. C. Thomas, W. M. Wood-Vasey, S. E. Woosley, "Distance probes of dark energy", Astroparticle Physics, 2015, 63:2-22, doi: 10.1016/j.astropartphys.2014.05.007

### 2014

### Siegfried Cools, Pieter Ghysels, Wim van Aarle, Wim Vanroose, "A multi-level preconditioned Krylov method for the efficient solution of algebraic tomographic reconstruction problems", To appear in Journal of Computational and Applied Mathematics, December 28, 2014,

### François-Henry Rouet, Xiaoye S. Li, Pieter Ghysels, Artem Napov, "A distributed-memory package for dense Hierarchically Semi-Separable matrix computations using randomization", Submitted to ACM Transactions on Mathematical Software, December 2014,

### Sang-Yun Oh, Onkar Dalal, Kshitij Khare, Bala Rajaratnam, "Optimization Methods for Sparse Pseudo-Likelihood Graphical Model Selection", Neural Information Processing Systems, 2014,

### Wei Hu, Lin Lin, Chao Yang and Jinlong Yang, "Electronic structure and aromaticity of large-scale hexagonal graphene nanoflakes", J. Chem. Phys. 141, 214704 (2014), December 2, 2014, 141:214704, doi: 10.1063/1.4902806

- Download File: JCPGNFs.pdf (pdf: 3.7 MB)

With the help of the recently developed SIESTA-PEXSI method [L. Lin, A. García, G. Huhs, and C. Yang, J. Phys.: Condens. Matter26, 305503 (2014)], we perform Kohn-Sham density functional theory calculations to study the stability and electronic structure of hydrogen passivated hexagonal graphene nanoflakes (GNFs) with up to 11 700 atoms. We find the electronic properties of GNFs, including their cohesive energy, edge formation energy, highest occupied molecular orbital-lowest unoccupied molecular orbital energy gap, edge states, and aromaticity, depend sensitively on the type of edges (armchair graphene nanoflakes (ACGNFs) and zigzag graphene nanoflakes (ZZGNFs)), size and the number of electrons. We observe that, due to the edge-induced strain effect in ACGNFs, large-scale ACGNFs’ edge formation energydecreases as their size increases. This trend does not hold for ZZGNFs due to the presence of many edge states in ZZGNFs. We find that the energy gaps E g of GNFs all decay with respect to 1/L, where L is the size of the GNF, in a linear fashion. But as their size increases, ZZGNFs exhibit more localized edge states. We believe the presence of these states makes their gap decrease more rapidly. In particular, when L is larger than 6.40 nm, we find that ZZGNFs exhibit metallic characteristics. Furthermore, we find that the aromatic structures of GNFs appear to depend only on whether the system has 4N or 4N + 2 electrons, where N is an integer.

### David Trebotich, Mark F. Adams, Sergi Molins, Carl I. Steefel, Chaopeng Shen, "High-Resolution Simulation of Pore-Scale Reactive Transport Processes Associated with Carbon Sequestration", Computing in Science and Engineering, December 2014, 16:22-31, doi: 10.1109/MCSE.2014.77

- Download File: CISE-16-06-Trebotichappeared.pdf (pdf: 2.7 MB)

### Chuck McParland, Sean Peisert, Anna Scaglione, "Monitoring Security of Networked Control Systems: It's the Physics", IEEE Security and Privacy, November 2014, 12(6):32-39, doi: 10.1109/MSP.2014.122

### David H. Bailey, Jonathan M. Borwein, "Computation and theory of extended Mordell-Tornheim-Witten sums II", Journal of Approximation Theory, October 30, 2014,

### J.A. Sobota, S.-L. Yang, D. Leuenberger, A.F. Kemper, J.G. Analytis, I.R. Fisher, P.S. Kirchmann, T.P. Devereaux, Z.-X. Shen, "Distinguishing Bulk and Surface Electron-Phonon Coupling in a Photoexcited Topological Insulator", Phys. Rev. Lett. 113, 157401 (2014), October 10, 2014,

### David H. Bailey and Marcos Lopez de Prado, "The deflated Sharpe ratio: Correcting for selection bias, backtest overfitting and non-normality", Journal of Portfolio Management, October 1, 2014, 40:94-107,

### David H. Bailey and Jonathan M. Borwein, "Opportunities and challenges in experimental mathematics", SIAM News, October 1, 2014, to appea,

### Funk, C., A. Hoell, D. Stone, "Examining the contribution of the observed global warming trend to the California droughts of 2012/2013 and 2013/2014", Bulletin of the American Meterological Society, 2014, 95:S11-S15,

### Kshitij Khare, Sang-Yun Oh, Bala Rajaratnam, "A convex pseudo-likelihood framework for high dimensional partial correlation estimation with convergence guarantees", Journal of the Royal Statistical Society: Series B (Statistical Methodology), 2014,

### Wen Shen, A.F. Kemper, T.P. Devereaux, J.K. Freericks, "Exact solution for high harmonic generation and the response to an AC driving field for a charge density wave insulator", Phys. Rev. B 90, 115113 (2014), September 5, 2014,

### Adam Lugowski, Shoaib Kamil, Aydın Buluç, Samuel Williams, Erika Duriakova, Leonid Oliker, Armando Fox, John R. Gilbert,, "Parallel processing of filtered queries in attributed semantic graphs", Journal of Parallel and Distributed Computing (JPDC), September 2014, doi: 10.1016/j.jpdc.2014.08.010

### Wenqi Xia, Wei Hu, Zhenyu Li and Jinlong Yang, "A first-principles study of gas adsorption on germanene", Phys. Chem. Chem. Phys., 2014,16, 22495-22498, August 29, 2014, doi: 10.1039/C4CP03292F

- Download File: PCCPGasGermanene.pdf (pdf: 2 MB)

The adsorption of common gas molecules (N2, CO, CO2, H2O, NH3, NO, NO2, and O2) on germanene is studied with density functional theory. The results show that N2, CO, CO2, and H2O are physisorbed on germanene via van der Waals interactions, while NH3, NO, NO2, and O2 are chemisorbed on germanene via strong covalent (Ge–N or Ge–O) bonds. The chemisorption of gas molecules on germanene opens a band gap at the Dirac point of germanene. NO2 chemisorption on germanene shows strong hole doping in germanene. O2 is easily dissociated on germanene at room temperature. Different adsorption behaviors of common gas molecules on germanene provide a feasible way to exploit chemically modified germanene.

### G.V. Vogman, P. Colella, U. Shumlak, "Dory-Guest-Harris instability as a benchmark for continuum kinetic Vlasov-Poisson simulations of magnetized plasmas", Journal of Computational Physics, 2014, 277:101 - 120, doi: 10.1016/j.jcp.2014.08.014

### A.F. Kemper, M.A. Sentef, B. Moritz, J.K. Freericks, T.P. Devereaux, "Effect of dynamical spectral weight distribution on effective interactions in time- resolved spectroscopy", Phys. Rev. B 90, 075126 (2014), August 1, 2014,

### Schizophrenia Working Group of the Psychiatric Genomics Consortium, "Biological insights from 108 schizophrenia-associated genetic loci", July 24, 2014, 511:421-427, doi: doi:10.1038/nature13595

### Folland, C., D. Stone, C. Frederiksen, D. Karoly, and J. Kinter, "The International CLIVAR Climate of the 20th Century Plus (C20C+) Project: Report of the Sixth Workshop", CLIVAR Exchanges, 2014, 19:57-59,

- Download File: FollandCStoneDetalii2014.pdf (pdf: 424 KB)

### Bin Dong, Xiuqiao Li, Limin Xiao, Li Ruan, "Towards minimizing disk I/O contention: A partitioned file assignment approach", Future Generation Computer Systems, Volume 37, July 2014, Pages 178-190, 2014,

### Mark Adams, Jed Brown, Matt Knepley, Ravi Samtaney, "Segmental Refinement: A Multigrid Technique for Data Locality", Submitted to SISC, June 30, 2014,

### Sergi Molins, David Trebotich, Li Yang, Jonathan B. Ajo-Franklin, Terry J. Ligocki, Chaopeng Shen and Carl Steefel, "Pore-Scale Controls on Calcite Dissolution Rates from Flow-through Laboratory and Numerical Experiments", Environmental Science and Technology, May 27, 2014, 48:7453-7460, doi: 10.1021/es5013438

- Download File: MolinsETALappearedonline2014-06-09.pdf (pdf: 2.4 MB)

### Robert Saye, "High-order methods for computing distances to implicitly defined surfaces", Communications in Applied Mathematics and Computational Science, May 17, 2014, doi: 10.2140/camcos.2014.9.107

### O. Angélil, D. A. Stone, P. Pall, "Attributing the probability of South African weather extremes to anthropogenic greenhouse gas emissions: spatial characteristics", Geophysical Research Letters, 2014, 41:3238-3243, doi: 10.1002/2014GL059760

### Peter G. Neumann, Sean Peisert, Marvin Schaefer, "The IEEE Symposium on Security and Privacy, in Retrospect", IEEE Security and Privacy, May 2014, 12(3):15-17, doi: 10.1109/MSP.2014.59

### M. Emmett, W. Zhang, and J.B. Bell, "High-Order Algorithms for Compressible Reacting Flow with Complex Chemistry", Combustion Theory and Modelling, May 2014, 361-387,

### David H. Bailey, Jonathan M. Borwein, Marcos Lopez de Prado, Qiji Jim Zhu, "Pseudo-mathematics and financial charlatanism: The effects of backtest over fitting on out-of-sample performance", Notices of the American Mathematical Society, May 1, 2014, 458-471,

Recent computational advances allow investment managers to search for profitable investment strategies. In many instances, that search involves a pseudo-mathematical argument, which is spuriously validated through a simulation of its historical performance (also called backtest).

We prove that high performance is easily achievable after backtesting a relatively small number of alternative strategy configurations, a practice we denote “backtest overfitting”. The higher the number of configurations tried, the greater is the probability that the backtest is overfit. Because financial analysts rarely report the number of configurations tried for a given backtest, investors cannot evaluate the degree of overfitting in most investment proposals.

The implication is that investors can be easily misled into allocating capital to strategies that appear to be mathematically sound and empirically supported by an outstanding backtest. This practice is particularly pernicious, because due to the nature of financial time series, backtest overfitting has a detrimental effect on the future strategy’s performance.

### Khaled Z. Ibrahim, Steven Hofmeyr, Costin Iancu, "The Case for Partitioning Virtual Machines on Manycore Architectures", IEEE TPDS, April 17, 2014,

- Download File: TPDSsubmit.pdf (pdf: 5.6 MB)

### Andrew Myers, Richard Klein, Mark Krumholz, Christopher McKee, "Star cluster formation in turbulent, magnetized dense clumps with radiative and outflow feedback", Monthly Notices of the Royal Astronomical Society, Volume 439, Issue 4, p.3420-3438, April 1, 2014,

### E. Vecharynski and Y. Saad, "Fast updating algorithms for latent semantic indexing", SIAM Journal on Matrix Analysis and Applications, Vol. 35, Issue 3, pp. 1105–1131, 2014,

This paper discusses a few algorithms for updating the approximate singular value decomposition (SVD) in the context of information retrieval by latent semantic indexing (LSI) methods. A unifying framework is considered which is based on Rayleigh–Ritz projection methods. First, a Rayleigh–Ritz approach for the SVD is discussed and it is then used to interpret the Zha and Simon algorithms [SIAM J. Sci. Comput., 21 (1999), pp. 782–791]. This viewpoint leads to a few alternatives whose goal is to reduce computational cost and storage requirement by projection techniques that utilize subspaces of much smaller dimension. Numerical experiments show that the proposed algorithms yield accuracies comparable to those obtained from standard ones at a much lower computational cost.

### O. Angélil, D. A. Stone, M. Tadross, F. Tummon, M. Wehner, R. Knutti, "Attribution of extreme weather to anthropogenic greenhouse gas emissions: sensitivity to spatial and temporal scales", Geophysical Research Letters, 2014, 41:2150-2155, doi: 10.1002/2014GL059234

### Sisi Duan, Sean Peisert, and Karl Levitt, "hBFT: Speculative Byzantine Fault Tolerance With Minimum Cost", IEEE Transactions on Dependable and Secure Computing (TDSC), March 19, 2014, 12(1):58-70, doi: 10.1109/TDSC.2014.2312331

### Richard L. Martin, Cory M. Simon, Berend Smit, Maciej Haranczyk, "In-silico design of porous polymer networks: high-throughput screening for methane storage materials", Journal of the American Chemical Society, March 10, 2014,

Porous polymer networks (PPNs) are a class of advanced porous materials that combine the advantages of cheap and stable polymers with the high surface areas and tunable chemistry of metal-organic frameworks. They are of particular interest for gas separation or storage applications, for instance as methane adsorbents for a vehicular natural gas tank or other portable applications.

### D. Oryspayev, P. Maris, J. P. Vary, M. Sosonkina, H. M. Aktulga, "A Memory-efficient Scalable Symmetric Sparse Matrix Vector Multiplication Algorithm for Distributed Memory Architectures", Concurrency and Computation: Practice and Experience, in preparation, March 8, 2014,

### S. B. Kylasa, H. M. Aktulga, A. Y. Grama, "PG-PuReMD: A Parallel-GPU Reactive Molecular Dynamics Package", Computer Physics Communications, in preparation, March 7, 2014,

### Richard L. Martin, Maciej Haranczyk, "Construction and Characterization of Structure Models of Crystalline Porous Polymers", Crystal Growth & Design, March 6, 2014,

Metal-organic frameworks (MOFs) and covalent organic frameworks (COFs) are examples of advanced porous polymeric materials that have emerged in recent years. Their crystalline structure and modular synthesis offer unmatched versatility in their design. By exchanging chemical building blocks, one can both explore the unlimited space of possible structural chemistry within an isoreticular (same crystal topology) series, as well as achieve a wide range of alternative topologies.

### S. B. Kylasa, H. M. Aktulga, A. Y. Grama, "PuReMD-GPU: A Reactive Molecular Dynamics Simulation Package for GPUs", Journal of Computational Physics, under revision, March 5, 2014,

### David H. Bailey, Jonathan M. Borwein, "Pi day is upon us again, and we still do not know if pi is normal", American Mathematical Monthly, March 1, 2014, 191-206,

### Upakarasamy Lourderaj, Rui Sun, Swapnil C. Kohale, George L. Barnes, Wibe A. de Jong, Theresa L. Windus, William L. Hase, "The VENUS/NWChem software package. Tight coupling between chemical dynamics simulations and electronic structure theory", Computer Physics Communications, 2014, 185:1074-1080, doi: 10.1016/j.cpc.2013.11.011

### Niranjan Govind, Wibe A. de Jong, "Simulating Cl K-edge X-ray absorption spectroscopy in MCl6 (2-) (M U, Np, Pu) complexes and UOCl5 (-) using time-dependent density functional theory", Theoretical Chemistry Accounts, 2014, 133, doi: 10.1007/s00214-014-1463-z

### P. Wolski, D. Stone, M. Tadross, M. Wehner, B. Hewitson, "Attribution of floods in the Okavango basin, Southern Africa", Journal of Hydrology, 2014, 511:350-358,

### Lev Sarkisov, Richard L. Martin, Maciej Haranczyk, Berend Smit, "On the Flexibility of Metal-Organic Frameworks", Journal of the American Chemical Society, January 24, 2014,

Occasional, large amplitude flexibility in metal-organic frameworks (MOFs) is one of the most intriguing recent discoveries in chemistry and material science. Yet, there is at present no theoretical framework that permits the identification of flexible structures in the rapidly expanding universe of MOFs. Here, we propose a simple method to predict whether a MOF is flexible, based on treating it as a system of rigid elements, connected by hinges. This proposition is correct in application to MOFs based on rigid carboxylate linkers.

### Wei Hu, Nan Xia, Xiaojun Wu, Zhenyu Li and Jinlong Yang, "Silicene as a highly sensitive molecule sensor for NH3, NO and NO2", Phys. Chem. Chem. Phys., 2014,16, 6957-6962, January 23, 2014, doi: 10.1039/C3CP55250K

- Download File: PCCPNH3Silicene.pdf (pdf: 1.6 MB)

On the basis of first-principles calculations, we demonstrate the potential application of silicene as a highly sensitive molecule sensor for NH3, NO, and NO2 molecules. NH3, NO and NO2 molecules chemically adsorb on silicene via strong chemical bonds. With distinct charge transfer from silicene to molecules, silicene and chemisorbed molecules form charge-transfer complexes. The adsorption energy and charge transfer in NO2-adsorbed silicene are larger than those of NH3- and NO-adsorbed silicones. Depending on the adsorbate types and concentrations, the silicene-based charge-transfer complexes exhibit versatile electronic properties with tunable band gap opening at the Dirac point of silicene. The calculated charge carrier concentrations of NO2-chemisorbed silicene are 3 orders of magnitude larger than intrinsic charge carrier concentration of graphene at room temperature. The results present a great potential of silicene for application as a highly sensitive molecule sensor.

### J.A. Sobota, S.-L. Yang, D. Leuenberger, A.F. Kemper, J.G. Analytis, I.R. Fisher, P.S. Kirchmann, T.P. Devereaux, Z.-X. Shen, "Ultrafast electron dynamics in the topological insulator Bi2Se3 studied by time-resolved photoemission spectroscopy", Journal of Electron Spectroscopy and Related Phenomena, January 22, 2014,

We characterize the topological insulator Bi_{2}Se_{3} using time- and angle-resolved photoemission spectroscopy. By employing two-photon photoemission, a complete picture of the unoccupied electronic structure from the Fermi level up to the vacuum level is obtained. We demonstrate that the unoccupied states host a second Dirac surface state which can be resonantly excited by 1.5 eV photons. We then study the ultrafast relaxation processes following optical excitation. We find that they culminate in a persistent non-equilibrium population of the first Dirac surface state, which is maintained by a meta-stable population of the bulk conduction band. Finally, we perform a temperature-dependent study of the electron–phonon scattering processes in the conduction band, and find the unexpected result that their rates decrease with increasing sample temperature. We develop a model of phonon emission and absorption from a population of electrons, and show that this counter-intuitive trend is the natural consequence of fundamental electron–phonon scattering processes. This analysis serves as an important reminder that the decay rates extracted by time-resolved photoemission are not in general equal to single electron scattering rates, but include contributions from filling and emptying processes from a continuum of states.

### M.A. Sentef, M. Claassen, A.F. Kemper, B. Moritz, T. Oka, J.K. Freericks, T.P. Devereaux, "Theory of pump-probe photoemission in graphene and the generation of light-induced Haldane multilayers", arXiv pre-print, January 20, 2014,

The combination of time-reversal and inversion symmetry protects massless Dirac fermions in graphene and on the surface of topological insulators. In a milestone paper, Haldane envisioned that breaking either or both of these symmetries would open a gap at the Dirac points, allowing one to tune between a trivial insulator and a Chern insulator. While equilibrium band gap engineering has become a major theme since the first synthesis of monolayer graphene, it was only recently proposed that circularly polarized laser light could turn trivial equilibrium bands into topological nonequilibrium bands. Here we observe ultrafast band gap openings and paradoxical gap closings at a critical field strength. Importantly, the gap openings are accompanied by nontrivial changes of the band topology, realizing a photo-induced Haldane multilayer system. We show that pump-probe photoemission spectroscopy can track these transitions in real time via energy gaps exceeding 100 meV. The analogy with Haldane multilayers is revealed by nontrivial pseudospin textures, going from a monolayer p-wave to a bilayer d-wave symmetry at the critical field strength. We thus predict a nonequilibrium realization of a tunable Haldane multilayer model with a Berry curvature that can be tipped optically by small changes in external fields on femtosecond time scales. Since we are focused on the physics of chiral Dirac fermions, these results apply equally to all systems possessing Dirac points, such as surface states of topological insulators.

### J. Kaye, L. Lin and C. Yang, "A posteriori error estimator for adaptive local basis functions to solve Kohn-Sham density functional theory", Comm. Math. Sci., January 5, 2014, 13:1741--1740, doi: http://dx.doi.org/10.4310/CMS.2015.v13.n7.a5

### Marek Pederzoli, Lukáš Sobek, Jiří Brabec, Karol Kowalski, Lukasz Cwiklik, Jiří Pittner, "Fluorescence of PRODAN in water: A computational QM/MM MD study", Chemical Physics Letters, 2014, 597:57-62, doi: 10.1016/j.cplett.2014.02.031

### A. Donev, A. Nonaka, Y. Sun, T. Fai, A. Garcia and J. Bell, "Low Mach Number Fluctuating Hydrodynamics of Diffusively Mixing Fluids", Comm. App. Math. and Comp. Sci., 2014, 9(1),

### C. M. Malone, M. Zingale, A. Nonaka, A. S. Almgren, and J. B. Bell, "Multidimensional Modeling of Type I X-ray Bursts. II. Two-Dimensional Convection in a Mixed H/He Accretor", Astrophysical Journal, 2014, 788:115,

### S. Tang, L. Bildsten, W. M. Wolf, K. L. Li, A. K. H., Y. Cao, S. B. Cenko, A. De Cia, M. M., S. R. Kulkarni, R. R. Laher, F., P. E. Nugent, D. A. Perley, T. A. Prince, J. Surace, "An Accreting White Dwarf near the Chandrasekhar Limit in the Andromeda Galaxy", Astrophysical Journal, 2014, 786:61, doi: 10.1088/0004-637X/786/1/61

### Max Duarte, Ann S Almgren, Kaushik Balakrishnan, John B. Bell, David M. Romps, "A Numerical Study of Methods for Moist Atmospheric Flows: Compressible Equations", Monthly Weather Review, 2014, 142:4269-4283,

### W. Schmidt, A.S. Almgren, H. Braun, J.F. Engels, J.C. Niemeyer, R.R. Mekuria, A.J. Aspden, J.B. Bell, "Cosmological Fluid Mechanics with Adaptively Refined Large Eddy Simulations", Monthly Notices of the Royal Astronomical Society, 2014, 440:3051-3077,

### E. O. Ofek, I. Arcavi, D. Tal, M. Sullivan, A., S. R. Kulkarni, P. E. Nugent, S., D. Bersier, Y. Cao, S. B. Cenko, A. Cia, A. V. Filippenko, C. Fransson, M. M., R. Laher, J. Surace, R. Quimby, O. Yaron, "Interaction-powered Supernovae: Rise-time versus Peak-luminosity Correlation and the Shock-breakout Velocity", Astrophysical Journal, 2014, 788:154, doi: 10.1088/0004-637X/788/2/154

### J Langguth, A Azad, M Halappanavar, F Manne, "On parallel push–relabel based algorithms for bipartite maximum matching", Parallel Computing, January 2014,

### Anuj Chaudhri, John Bell, Alejandro Garcia, Aleksandar Donev, "Modeling Multi-Phase Flow using Fluctuating Hydrodynamics", Phys. Rev. E, 2014, 90(3):033014,

### K. Balakrishnan, A. Garcia, A. Donev, and J. Bell, "Fluctuating hydrodynamics of multispecies nonreactive mixtures", Physical Review E,, 2014, 89(1),

### A. Gal-Yam, I. Arcavi, E. O. Ofek, S. Ben-Ami, S. B., M. M. Kasliwal, Y. Cao, O. Yaron, D., J. M. Silverman, A. Horesh, A. De Cia, F., J. Sollerman, D. Perley, P. M. Vreeswijk, S. R., P. E. Nugent, A. V. Filippenko, J. C. Wheeler, "A Wolf-Rayet-like progenitor of SN 2013cu from spectral observations of a stellar wind", Nature, 2014, 509:471-474, doi: 10.1038/nature13304

### W. Schmidt, J. Schulz, L. Iapichino, A.S. Almgren,, "Influence of adaptive mesh refinement and the hydro solver on shear-induced mass stripping in a minor merger scenario,", Astronomy and Computing, 2014,

### C. M. Malone, A. Nonaka, S. E. Woosley, A. S. Almgren, J. B. Bell, S. Dong, and M. Zingale, "The Deflagration Stage of Chandrasekhar Mass Models for Type Ia Supernovae: I. Early Evolution", Astrophysical Journal, 2014, 782:11,

### E. S. Walker, P. A. Mazzali, E. Pian, K. Hurley, I., S. B. Cenko, A. Gal-Yam, A. Horesh, M., D. Poznanski, J. M. Silverman, M., J. S. Bloom, A. V. Filippenko, S. R., P. E. Nugent, E. Ofek, S. Barthelmy, W., J. Goldsten, S. Golenetskii, M. Ohno, M. S. Tashiro, K. Yamaoka, X. L.-. Zhang, "Optical follow-up observations of PTF10qts, a luminous broad-lined Type Ic supernova found by the Palomar Transient Factory", Monthly Notices of the Royal Astronomical Society, 2014, 442:2768-2779, doi: 10.1093/mnras/stu1017

### Ke-Jung Chen, Alexander Heger, Stan Woosley, Ann Almgren, and Daniel Whalen, "Pair Instability Supernovae of Very Massive Population III Stars", Astrophysical Journal, January 2014, 792:44,

### R. Amanullah, A. Goobar, J. Johansson, D. P. K. Banerjee, V., V. Joshi, N. M. Ashok, Y. Cao, M. M., S. R. Kulkarni, P. E. Nugent, T. Petrushevska, V. Stanishev, "The Peculiar Extinction Law of SN 2014J Measured with the Hubble Space Telescope", Astrophysical Journal, 2014, 788:L21, doi: 10.1088/2041-8205/788/2/L21

### Antonio Valles, Weiqun Zhang, "Optimizing For Reacting Navier-Stokes Equations", High Performance Parallelism Pearls: Multicore And Many-Core Programming Approaches, edited by James Reinder, Jim Jeffers, 2014,

### Ke-Jung Chen, Alexander Heger, S.E. Woosley, Ann S. Almgren, and Daniel J. Whalen, "Two-Dimensional Simulations of Pulsational Pair-Instability Supernova", Astrophysical Journal, 2014, 792:28,

### M-H Yung, J Casanova, Antonio Mezzacapo, J McClean, L Lamata, A Aspuru-Guzik, E Solano, "From transistor to trapped-ion computers for quantum chemistry", Scientific reports, 2014, 4,

### A.J. Aspden, M. S. Day, and J. B. Bell, "Turbulence-Chemistry Interaction in Lean Premixed Hydrogen Combustion", Proc. Comb. Inst., 2014,

### Ke-Jung Chen, Alexander Heger, S.E. Woosley, Ann Almgren, and Daniel J. Whalen, and Jarrett L. Johnson, "The General Relativitistic Instability Supernova of a Supermassive Population III Star", Astrophysical Journal, 2014, 790:162,

### M. Nicholl, S. J. Smartt, A. Jerkstrand, C. Inserra, J. P., C. Baltay, S. Benetti, T.-W. Chen, N., U. Feindt, M. Fraser, A. Gal-Yam, E., D. A. Howell, R. Kotak, A. Lawrence, G., S. Margheim, S. Mattila, M. McCrum, R., A. Mead, P. Nugent, D. Rabinowitz, A., K. W. Smith, J. Sollerman, M. Sullivan, F., S. Valenti, E. S. Walker, D. R. Young, "Superluminous supernovae from PESSTO", Monthly Notices of the Royal Astronomical Society, 2014, 444:2096-2113, doi: 10.1093/mnras/stu1579

### Alberto Peruzzo, Jarrod McClean, Peter Shadbolt, Man-Hong Yung, Xiao-Qi Zhou, Peter J Love, Alan Aspuru-Guzik, Jeremy L O’Brien, "A variational eigenvalue solver on a photonic quantum processor", Nature communications, 2014, 5,

### E. Vecharynski, Y. Saad, and M. Sosonkina, "Graph partitioning using matrix values for preconditioning symmetric positive definite systems", SIAM Journal on Scientific Computing Vol. 36, Issue 1, pp. A63-A87, 2014,

Prior to the parallel solution of a large linear system, it is required to perform a partitioning of its equations/unknowns. Standard partitioning algorithms are designed using the considerations of the efficiency of the parallel matrix-vector multiplication, and typically disregard the information on the coefficients of the matrix. This information, however, may have a significant impact on the quality of the preconditioning procedure used within the chosen iterative scheme. In the present paper, we suggest a spectral partitioning algorithm, which takes into account the information on the matrix coefficients and constructs partitions with respect to the objective of enhancing the quality of the nonoverlapping additive Schwarz (block Jacobi) preconditioning for symmetric positive definite linear systems. For a set of test problems with large variations in magnitudes of matrix coefficients, our numerical experiments demonstrate a noticeable improvement in the convergence of the resulting solution scheme when using the new partitioning approach.

### Anshu Dubey, Ann Almgren, John Bell, Martin Berzins, Steve Brandt, Greg Bryan, Phillip Colella, Daniel Graves, Michael Lijewski, Frank L\ offler, others, "A survey of high level frameworks in block-structured adaptive mesh refinement packages", Journal of Parallel and Distributed Computing, 2014, 74:3217--3227, doi: 10.1016/j.jpdc.2014.07.001

### M. Cai, A. Nonaka, B. E. Griffith, J. B. Bell, and A. Donev, "Efficient Variable-Coefficient Finite-Volume Stokes Solvers", Commun. Comput. Phys., 2014, 16:1263-1297,

### Meiyue Shao, "On the finite section method for computing exponentials of doubly-infinite skew-Hermitian matrices", Linear Algebra and its Applications, 2014, 451:65--92, doi: 10.1016/j.laa.2014.03.021

### K. Maguire, M. Sullivan, Y.-C. Pan, A. Gal-Yam, I. M., D. A. Howell, P. E. Nugent, P. Mazzali, N., K. I. Clubb, A. V. Filippenko, M. M., M. T. Kandrashoff, D. Poznanski, C. M., J. M. Silverman, E. Walker, D. Xu, "Exploring the spectral diversity of low-redshift Type Ia supernovae using the Palomar Transient Factory", Monthly Notices of the Royal Astronomical Society, 2014, 444:3258-3274, doi: 10.1093/mnras/stu1607

### Jarrod R McClean, Ryan Babbush, Peter J Love, Alan Aspuru-Guzik, "Exploiting locality in quantum computation for quantum chemistry", The Journal of Physical Chemistry Letters, 2014, 5:4368--4380,

### J. González-Domínguez, O. Marques, M. J. Martín and J. Touriño, "A 2D Algorithm with Asymmetric Workload for the UPC Conjugate Gradient Method", The Journal of Supercomputing, 2014, 70:816-829,

### Daniel Kressner, Marija Miloloža Pandur, Meiyue Shao, "An indefinite variant of LOBPCG for definite matrix pencils", Numerical Algorithms, 2014, 66:681--703, doi: 10.1007/s11075-013-9754-3

### Jarrod R McClean, Alan Aspuru-Guzik, "Compact wavefunctions from compressed imaginary time evolution", arXiv preprint arXiv:1409.7358, 2014,

### A. Fujii, O. Marques, "Axis Communication Method for Algebraic Multigrid Solver", IEICE Transactions on Information and Systems, 2014, E97-D:2955-2958,

### R. Speck, D. Ruprecht, M. Emmett, M. Minion, M. Bolten, and R. Krause, "A multi-level spectral deferred correction method", BIT Numerical Mathematics, 2014,

### Meiyue Shao, Weiguo Gao, Jungong Xue, "Aggressively truncated Taylor series method for accurate computation of exponentials of essentially nonnegative matrices", SIAM Journal on Matrix Analysis and Applications, 2014, 35:317--338, doi: 10.1137/120894294

### Joonsuk Huh, Gian Giacomo Guerreschi, Borja Peropadre, Jarrod R McClean, Al\ an Aspuru-Guzik, "Boson Sampling for Molecular Vibronic Spectra", arXiv preprint arXiv:1412.8427, 2014,

### David H. Bailey, Jonathan M. Borwein, Alexander D. Kaiser, "Automated simplification of large symbolic expressions", Journal of Symbolic Computation, January 1, 2014, 60:120-136,

### Stephane Descombes, Max Duarte, Thierry Dumont, Frederique Laurent, Violaine Louvet, Marc Massot, "Analysis of operator splitting in the non-asymptotic regime for nonlinear reaction-diffusion equations. Application to the dynamics of premixed flames", SIAM J. Num. Anal., 2014, 52:1311-1334,

### P. A. Mazzali, M. Sullivan, S. Hachinger, R. S., P. E. Nugent, D. A. Howell, A. Gal-Yam, K., J. Cooke, R. Thomas, K. Nomoto, E. S. Walker, "Hubble Space Telescope spectra of the Type Ia supernova SN 2011fe: a tail of low-density, high-velocity material with Z < Z⊙", Monthly Notices of the RAS, 2014, 439:1959-1979, doi: 10.1093/mnras/stu077

### R. A. Scalzo, M. Childress, B. Tucker, F. Yuan, B., P. J. Brown, C. Contreras, N. Morrell, E., C. Burns, M. M. Phillips, A. Campillay, C., K. Krisciunas, M. Stritzinger, M. L., J. Parrent, S. Valenti, C. Lidman, B., N. Scott, M. Fraser, A. Gal-Yam, C., K. Maguire, S. J. Smartt, J. Sollerman, M., F. Taddia, O. Yaron, D. R. Young, S., C. Baltay, N. Ellman, U. Feindt, E., R. McKinnon, P. E. Nugent, D. Rabinowitz, E. S. Walker, "Early ultraviolet emission in the Type Ia supernova LSQ12gdj: No evidence for ongoing shock interaction", Monthly Notices of the Royal Astronomical Society, 2014, 445:30-48, doi: 10.1093/mnras/stu1723

### A. Corsi, E. O. Ofek, A. Gal-Yam, D. A. Frail, S. R., D. B. Fox, M. M. Kasliwal, M., A. Horesh, J. Carpenter, K. Maguire, I., S. B. Cenko, Y. Cao, K. Mooley, Y.-C., B. Sesar, A. Sternberg, D. Xu, D., P. James, J. S. Bloom, P. E. Nugent, "A Multi-wavelength Investigation of the Radio-loud Supernova PTF11qcj and its Circumstellar Environment", Astrophysical Journal, 2014, 782:42, doi: 10.1088/0004-637X/782/1/42

### P. M. Vreeswijk, S. Savaglio, A. Gal-Yam, A. Cia, R. M. Quimby, M. Sullivan, S. B. Cenko, D. A., A. V. Filippenko, K. I. Clubb, F., J. Sollerman, G. Leloudas, I. Arcavi, A., M. M. Kasliwal, Y. Cao, O. Yaron, D., E. O. Ofek, J. Capone, A. S. Kutyrev, V., P. E. Nugent, R. Laher, J. Surace, S. R. Kulkarni, "The Hydrogen-poor Superluminous Supernova iPTF 13ajg and its Host Galaxy in Absorption and Emission", Astrophysical Journal, 2014, 797:24, doi: 10.1088/0004-637X/797/1/24

### A. G. Kim, G. Aldering, P. Antilogus, C. Aragon, S., C. Baltay, S. Bongard, C. Buton, A., F. Cellier-Holzem, M. Childress, N., Y. Copin, H. K. Fakhouri, U. Feindt, M., E. Gangler, P. Greskovic, J. Guy, M., S. Lombardo, J. Nordin, P. Nugent, R., E. Pecontal, R. Pereira, S. Perlmutter, D., M. Rigault, K. Runge, C. Saunders, R., G. Smadja, C. Tao, R. C. Thomas, B. A. Weaver, "Type Ia Supernova Hubble Residuals and Host-galaxy Properties", Astrophysical Journal, 2014, 784:51, doi: 10.1088/0004-637X/784/1/51

### Jung Heon Song, Kesheng Wu, Horst D Simon, "Parameter Analysis of the VPIN (Volume synchronized of Informed Trading) Metric", Quantitative Financial Risk Management: Theory and, 2014,

### H. Braun, W. Schmidt, J.C. Niemeyer, and A.S. Almgren, "Large-eddy simulations of isolated disk galaxies with thermal and turbulent feedback", Monthly Notices of the Royal Astronomical Society, January 2014, 442:3407-3426,

### 2013

### Michael Sentef, Alexander F. Kemper, Brian Moritz, James K. Freericks, Zhi-Xun Shen, and Thomas P. Devereaux, "Examining Electron-Boson Coupling Using Time-Resolved Spectroscopy", Phys. Rev. X 3, 041033 (2013), December 26, 2013,

Nonequilibrium pump-probe time-domain spectroscopies can become an important tool to disentangle degrees of freedom whose coupling leads to broad structures in the frequency domain. Here, using the time-resolved solution of a model photoexcited electron-phonon system, we show that the relaxational dynamics are directly governed by the equilibrium self-energy so that the phonon frequency sets a window for “slow” versus “fast” recovery. The overall temporal structure of this relaxation spectroscopy allows for a reliable and quantitative extraction of the electron-phonon coupling strength without requiring an effective temperature model or making strong assumptions about the underlying bare electronic band dispersion.

### Daniel T. Graves, Phillip Colella, David Modiano, Jeffrey Johnson, Bjorn Sjogreen, Xinfeng Gao, "A Cartesian Grid Embedded Boundary Method for the Compressible Navier Stokes Equations", Communications in Applied Mathematics and Computational Science, December 23, 2013,

- Download File: gravesetal.pdf (pdf: 964 KB)

In this paper, we present an unsplit method for the time-dependent

compressible Navier-Stokes equations in two and three dimensions.

We use a a conservative, second-order Godunov algorithm.

We use a Cartesian grid, embedded boundary method to resolve complex

boundaries. We solve for viscous and conductive terms with a

second-order semi-implicit algorithm. We demonstrate second-order

accuracy in solutions of smooth problems in smooth geometries and

demonstrate robust behavior for strongly discontinuous initial

conditions in complex geometries.

### H. M. Aktulga, L. Lin, C. Haine, E. G. Ng, C. Yang, "Parallel Eigenvalue Calculation based on Multiple Shift-invert Lanczos and Contour Integral based Spectral Projection Method", Parallel Computing, December 6, 2013, in press,

### Cory M. Simon, Jihan Kim, Li-Chiang Lin, Richard L. Martin, Maciej Haranczyk, Berend Smit, "Optimizing nanoporous materials for gas storage", Physical Chemistry Chemical Physics, December 4, 2013,

Natural gas, mostly methane, is an attractive replacement of petroleum fuels for automotive vehicles because of its economic and environmental advantages. The technological obstacle to using methane as a vehicular fuel is its comparatively low volumetric energy density, necessitating densification strategies to yield reasonable driving ranges from a reasonably sized tank.

### Samuel O. Odoh, Eric J. Bylaska, Wibe A. de Jong, "Coordination and Hydrolysis of Plutonium Ions in Aqueous Solution Using Car-Parrinello Molecular Dynamics Free Energy Simulations", Journal of Physical Chemistry A, 2013, 117:12256-1226, doi: 10.1021/jp4096248

### N. Plonka, A. F. Kemper, S. Graser, A. P. Kampf, T. P. Devereaux, "Tunneling spectroscopy for probing orbital anisotropy in iron pnictides", Phys. Rev. B 88, 174518 (2013), November 27, 2013,

Using realistic multiorbital tight-binding Hamiltonians and the T-matrix formalism, we explore the effects of a nonmagnetic impurity on the local density of states in Fe-based compounds. We show that scanning tunneling spectroscopy (STS) has very specific anisotropic signatures that track the evolution of orbital splitting (OS) and antiferromagnetic gaps. Both anisotropies exhibit two patterns that split in energy with decreasing temperature, but for OS these two patterns map onto each other under 90∘ rotation. STS experiments that observe these signatures should expose the underlying magnetic and orbital order as a function of temperature across various phase transitions.

### C. Steefel, S. Molins, D. Trebotich, "Pore scale processes associated with subsurface CO2 injection and sequestration”, Reviews in Mineralogy and Geochemistry", Reviews in Mineralogy and Geochemistry, November 1, 2013,

- Download File: SteefelMolinsTrebotich2013.pdf (pdf: 5.9 MB)

### Slim T. Chourou, Abhinav Sarje, Xiaoye Li, Elaine Chan and Alexander Hexemer, "HipGISAXS: a high-performance computing code for simulating grazing-incidence X-ray scattering data", Journal of Applied Crystallography, 2013, 46:1781-1795, doi: 10.1107/ S0021889813025843

We have implemented a flexible Grazing Incidence Small-Angle Scattering (GISAXS) simulation code in the framework of the Distorted Wave Born Approximation (DWBA) that effectively utilizes the parallel processing power provided by graphics processors and multicore processors. This constitutes a handy tool for experimentalists facing a massive flux of data, allowing them to accurately simulate the GISAXS process and analyze the produced data. The software computes the diffraction image for any given superposition of custom shapes or morphologies in a user-defined region of the reciprocal space for all possible grazing incidence angles and sample orientations. This flexibility then allows to easily tackle a wide range of possible sample structures such as nanoparticles on top of or embedded in a substrate or a multilayered structure. In cases where the sample displays regions of significant refractive index contrast, an algorithm has been implemented to perform a slicing of the sample and compute the averaged refractive index profile to be used as the reference geometry of the unperturbed system. Preliminary tests show good agreement with experimental data for a variety of commonly encountered nanostrutures.

### Salman Habib, Vitali Morozov, Nicholas Frontiere, Hal Finkel, Adrian Pope, Katrin Heitmann, Kalyan Kumaran, Venkat Vishwanath, Tom Peterka, Joe Insley, David Daniel, Patricia Fasel, Zarija Lukić, "HACC: Extreme Scaling and Performance Across Diverse Architectures", Supercomputing, 2013, 6,

### L. Oliker and R. Vuduc, "Introduction for Special Issue on Autotuning", International Journal of High Performance Computing Applications (IJHPCA), 2013,

### Maciej Haranczyk, Li-Chiang Lin, Kyuho Lee, Richard L. Martin, Jeffrey B. Neaton, Berend Smit, "Methane storage capabilities of diamond analogues", Physical Chemistry Chemical Physics, October 31, 2013,

Methane can be an alternative fuel for vehicular usage provided that new porous materials are developed for its efficient adsorption-based storage. Herein, we search for materials for this application within the family of diamond analogues. We used density functional theory to investigate structures in which tetrahedral C atoms of diamond are separated by-CC-or-BN-groups, as well as ones involving substitution of tetrahedral C atoms with Si and Ge atoms.

### Wei Hu, Zhenyu Li and Jinlong Yang, "Structural, electronic, and optical properties of hybrid silicene and graphene nanocomposite", J. Chem. Phys. 139, 154704 (2013), October 16, 2013, doi: 10.1063/1.4824887

- Download File: JCPSiliceneGraphene.pdf (pdf: 924 KB)

Structural, electronic, and optical properties of hybrid silicene and graphene (S/G) nanocomposite are examined with density functional theory calculations. It turns out that weak van der Waals interactions dominate between silicene and graphene with their intrinsic electronic properties preserved. Interestingly, interlayer interactions in hybrid S/G nanocomposite induce tunable p-type and n-type doping of silicene and graphene, respectively, showing their doping carrier concentrations can be modulated by their interfacial spacing.

### A. Buluç, K. Madduri, "Graph partitioning for scalable distributed graph computations", AMS Contemporary Mathematics, Graph Partitioning and Graph Clustering (Proc. 10th DIMACS Implementation Challenge), 2013,

- Download File: DIMACSprocfinal.pdf (pdf: 2.1 MB)

### Samuel O. Odoh, Niranjan Govind, Georg Schreckenbach, Wibe A. de Jong, "Cation-Cation Interactions in [(UO2)(2)(OH)(n)](4-n) Complexes", Inorganic Chemistry, 2013, 52:11269-1127, doi: 10.1021/ic4015338

### Robert Saye, "An algorithm to mesh interconnected surfaces via the Voronoi interface", Engineering with Computers, October 6, 2013, doi: 10.1007/s00366-013-0335-9

### Alexander Knebe, Frazer R. Pearce, Hanni Lux, Yago Ascasibar, Peter Behroozi, Javier Casado, Christine Corbett Moran, Juerg Diemand, Klaus Dolag, Rosa Dominguez-Tenreiro, Pascal Elahi, Bridget Falck, Stefan Gottlöber, Jiaxin Han, Anatoly Klypin, Zarija Lukić, Michal Maciejewski, Cameron K. McBride, Manuel E. Merchán, Stuart I. Muldrew, Mark Neyrinck, Julian Onions, Susana Planelles, Doug Potter, Vicent Quilis, Yann Rasera, Paul M. Ricker, Fabrice Roy, Andrés N. Ruiz, Mario A. Sgró, Volker Springel, Joachim Stadel, Paul M. Sutter, Dylan Tweed, Marcel Zemp, "Structure finding in cosmological simulations: the state of affairs", Monthly Notices of the Royal Astronomical Society, 2013, 435:1618,

### Wei Hu, Zhenyu Li and Jinlong Yang, "Surface and size effects on the charge state of NV center in nanodiamonds", Computational and Theoretical Chemistry, 2013, 1021, 49-53, October 1, 2013, doi: 10.1016/j.comptc.2013.06.015

- Download File: NVNanodiamondsCTC.pdf (pdf: 1.1 MB)

Electronic structures and stability of nitrogen–vacancy (NV) centers doped in nanodiamonds (NDs) have been investigated with large-scale density functional theory (DFT) calculations. Spin polarized defect states are not affected by the particle sizes and surface decorations, while the band gap is sensitive to these effects. Induced by the spherical surface electric dipole layer, surface functionalization has a long-ranged impact on the stability of charged NV centers doped in NDs. NV− center doped in DNs is more favorable for n-type fluorinated diamond, while NV0 is preferred for p-type hydrogenated NDs. Therefore, surface decoration provides a useful way for defect state engineering.

### J. A. Sobota, S.-L. Yang, A. F. Kemper, J. J. Lee, F. T. Schmitt, W. Li, R. G. Moore, J. G. Analytis, I. R. Fisher, P. S. Kirchmann, T. P. Devereaux, and Z.-X. Shen, "Direct Optical Coupling to an Unoccupied Dirac Surface State in the Topological Insulator Bi2Se3", Phys. Rev. Lett. 111, 136802 (2013), September 24, 2013,

We characterize the occupied and unoccupied electronic structure of the topological insulator Bi_{2}Se_{3} by one-photon and two-photon angle-resolved photoemission spectroscopy and slab band structure calculations. We reveal a second, unoccupied Dirac surface state with similar electronic structure and physical origin to the well-known topological surface state. This state is energetically located 1.5 eV above the conduction band, which permits it to be directly excited by the output of a Ti:sapphire laser. This discovery demonstrates the feasibility of direct ultrafast optical coupling to a topologically protected, spin-textured surface state.

### Y. F. Kung, W.-S. Lee, C.-C. Chen, A. F. Kemper, A. P. Sorini, B. Moritz, and T. P. Devereaux, "Time-dependent charge-order and spin-order recovery in striped systems", Phys. Rev. B 88, 125114 (2013), September 24, 2013,

Using time-dependent Ginzburg-Landau theory, we study the role of amplitude and phase fluctuations in the recovery of charge-stripe and spin-stripe phases in response to a pump pulse that melts the orders. For parameters relevant to the case where charge order precedes spin order thermodynamically, amplitude recovery governs the initial time scales, while phase recovery controls behavior at longer times. In addition to these intrinsic effects, there is a longer spin reorientation time scale related to the scattering geometry that dominates the recovery of the spin phase. Coupling between the charge and spin orders locks the amplitude and similarly the phase recovery, reducing the number of distinct time scales. Our results well reproduce the major experimental features of pump-probe x-ray diffraction measurements on the striped nickelate La_{1.75}Sr_{0.25}NiO_{4}. They highlight the main idea of this work, which is the use of time-dependent Ginzburg-Landau theory to study systems with multiple coexisting order parameters.

### Richard L Martin, Mahdi Niknam Shahrak, Joseph A Swisher, Cory M Simon, Julian P Sculley, Hong-Cai Zhou, Berend Smit, Maciej Haranczyk, "Modeling Methane Adsorption in Interpenetrating Porous Polymer Networks", The Journal of Physical Chemistry C, September 19, 2013,

Porous polymer networks (PPNs) are a class of porous materials of particular interest in a variety of energy-related applications because of their stability, high surface areas, and gas uptake capacities. Computationally derived structures for five recently synthesized PPN frameworks, PPN-2,-3,-4,-5, and-6, were generated for various topologies, optimized using semiempirical electronic structure methods, and evaluated using classical grand-canonical Monte Carlo simulations.

### Richard L. Martin, Maciej Haranczyk, "Insights into Multi-Objective Design of Metal–Organic Frameworks", Crystal Growth & Design, September 18, 2013,

Metal-organic framework (MOF) crystal topologies which permit the highest internal surface areas are identified by means of multiobjective optimization and abstract structure models. We demonstrate that MOF design efforts can be focused within five underlying nets to engineer distinct, Pareto-optimal compromises between high gravimetric and high volumetric surface area materials.

### H. M. Aktulga, C. Yang, E. G. Ng, P. Maris, J. P. Vary, "Improving the Scalability of a Symmetric Iterative Eigensolver for Multi-core Platforms", Concurrency and Computation: Practice & Experience, September 12, 2013, online, doi: 10.1002/cpe.3129

### Marielle Pinheiro, Richard L. Martin, Chris H. Rycroft, Maciej Haranczyk, "High accuracy geometric analysis of crystalline porous materials", CrystEngComm, September 5, 2013,

A number of algorithms to analyze crystalline porous materials and their porosity employ the Voronoi tessellation, whereby the space in the material is divided into irregular polyhedral cells that can be analyzed to determine the pore topology and structure. However, the Voronoi tessellation is only appropriate when atoms all have equal radii, and the natural generalization to structures with unequal radii leads to cells with curved boundaries, which are computationally expensive to compute.

### David H. Bailey, Jonathan M. Borwein, Richard E. Crandall, Michael G. Rose, "Expectations on fractal sets", Applied Mathematics and Computation, September 1, 2013, 220:695-721,

### B. Moritz, A. F. Kemper, M. Sentef, T. P. Devereaux, J. K. Freericks, "Electron-Mediated Relaxation Following Ultrafast Pumping of Strongly Correlated Materials: Model Evidence of a Correlation-Tuned Crossover between Thermal and Nonthermal States", Phys. Rev. Lett. 111, 077401 (2013), 2013,

We examine electron-electron mediated relaxation following ultrafast electric field pump excitation of the fermionic degrees of freedom in the Falicov-Kimball model for correlated electrons. The results reveal a dichotomy in the temporal evolution of the system as one tunes through the Mott metal-to-insulator transition: in the metallic regime relaxation can be characterized by evolution toward a steady state well described by Fermi-Dirac statistics with an increased effective temperature; however, in the insulating regime this quasithermal paradigm breaks down with relaxation toward a nonthermal state with a complicated electronic distribution as a function of momentum. We characterize the behavior by studying changes in the energy, photoemission response, and electronic distribution as functions of time. This relaxation may be observable qualitatively on short enough time scales that the electrons behave like an isolated system not in contact with additional degrees of freedom which would act as a thermal bath, especially when using strong driving fields and studying materials whose physics may manifest the effects of correlations.

### Shen Wang, Xiaoye S. Li, François-Henry Rouet, Jianlin Xia, Maarten V. de Hoop, "A parallel geometric multifrontal solver using hierarchically semiseparable structure", Submitted to ACM Transaction on Mathematical Software, 2013,

### C. L. Morris, Jeffrey Bacon, Konstantin Borozdin, Haruo Miyadera, John Perry, Evan Rose, Scott Watson, Tim White, Derek Aberle, J. Andrew Green, George G. McDuff, Zarija Lukić, Edward C. Milner, "A new method for imaging nuclear threats using cosmic ray muons", AIP Advances, 2013, 3:082128,

### Marielle Pinheiro, Richard L. Martin, Chris H. Rycroft, Andrew Jones, Enrique Iglesia, Maciej Haranczyk, "Characterization and comparison of pore landscapes in crystalline porous materials", Journal of Molecular Graphics and Modelling, July 31, 2013,

Crystalline porous materials have many applications, including catalysis and separations. Identifying suitable materials for a given application can be achieved by screening material databases. Such a screening requires automated high-throughput analysis tools that characterize and represent pore landscapes with descriptors, which can be compared using similarity measures in order to select, group and classify materials. Here, we discuss algorithms for the calculation of two types of pore landscape descriptors.

### Pawel Tecmer, Niranjan Govind, Karol Kowalski, Wibe A de Jong, Lucas Visscher, "Reliable modeling of the electronic spectra of realistic uranium complexes.", The Journal of Chemical Physics, 2013, 139:034301, doi: 10.1063/1.4812360

### Khaled Z Ibrahim, Kamesh Madduri, Samuel Williams, Bei Wang, Stephane Ethier, Leonid Oliker, "Analysis and optimization of gyrokinetic toroidal simulations on homogenous and heterogenous platforms", International Journal of High Performance Computing Applications (IJHPCA), July 2013, doi: 10.1177/1094342013492446

### Wei Hu, Xiaojun Wu, Zhenyu Li and Jinlong Yang, "Helium separation via porous silicene based ultimate membrane", Nanoscale, 2013, 5, 9062-9066, July 11, 2013, doi: 10.1039/C3NR02326E

- Download File: NanoscaleHeSilicene.pdf (pdf: 489 KB)

Helium purification has become more important for increasing demands in scientific and industrial applications. In this work, we demonstrated that the porous silicene can be used as an effective ultimate membrane for helium purification on the basis of first-principles calculations. Prinstine silicene monolayer is impermeable to helium gas with a high penetration energy barrier (1.66 eV). However, porous silicene with either Stone–Wales (SW) or divacancy (555[thin space (1/6-em)]777 or 585) defect presents a surmountable barrier for helium (0.33 to 0.78 eV) but formidable for Ne, Ar, and other gas molecules. In particular, the porous silicene with divacancy defects shows high selectivity for He/Ne and He/Ar, superior to graphene, polyphenylene, and traditional membranes.

### Raymond Atta-Fynn, Eric J. Bylaska, Wibe A. de Jong, "Importance of Counteranions on the Hydration Structure of the Curium Ion", Journal of Physical Chemistry Letters, 2013, 4:2166-2170, doi: 10.1021/jz400887a

### Laurent Bouchet, Patrick Amestoy, Alfredo Buttari, François-Henry Rouet, Maxime Chauvin, "INTEGRAL/SPI data segmentation to retrieve sources intensity variations.", Astronomy & Astrophysics, July 1, 2013, 555:A52, doi: 10.1051/0004-6361/201219605

### David H. Bailey, Jonathan M. Borwein, Victoria Stodden, "Set the default to 'open'", Notices of the American Mathematical Society, July 1, 2013, Jun/Jul:679,

### A.F. Kemper, M. Sentef, B. Moritz, C.C. Kao, Z.X. Shen, J.K. Freericks, T.P. Devereaux, "Mapping of the unoccupied states and relevant bosonic modes via the time dependent momentum distribution", Phys. Rev. B 87, 235139 (2013), June 28, 2013,

The unoccupied states of complex materials are difficult to measure, yet they play a key role in determining their properties. We propose a technique that can measure the unoccupied states, called time-resolved Compton scattering, which measures the time-dependent momentum distribution (TDMD). Using a nonequilibrium Keldysh formalism, we study the TDMD for electrons coupled to a lattice in a pump-probe setup. We find a direct relation between temporal oscillations in the TDMD and the dispersion of the underlying unoccupied states, suggesting that both can be measured by time-resolved Compton scattering. We demonstrate the experimental feasibility by applying the method to a model of MgB_{2} with realistic material parameters.

### P. Ghysels, W. Vanroose, "Hiding global synchronization latency in the preconditioned Conjugate Gradient algorithm", Parallel Computing, June 24, 2013, doi: 10.1016/j.parco.2013.06.001

### Donald F. Johnson, Kiran Bhaskaran-Nair, Eric J. Bylaska, Wibe A. de Jong, "Thermodynamics of Tetravalent Thorium and Uranium Complexes from First-Principles Calculations", Journal of Physical Chemistry A, 2013, 117:4988-4995, doi: 10.1021/jp404656y

### Victoria Stodden, Jonathan M. Borwein, David H. Bailey, "'Setting the default to reproducible' in computational science research", SIAM News, June 1, 2013, 46:4-6,

### Y. S. Lee, S. J. Moon, Scott C. Riggs, M. C. Shapiro, I. R. Fisher, Bradford W. Fulfer, Julia Y. Chan, A. F. Kemper, and D. N. Basov, "Infrared study of the electronic structure of the metallic pyrochlore iridate Bi2Ir2O7", Phys. Rev. B 87, 195143 (2013), May 30, 2013,

We investigated the electronic properties of a single crystal of metallic pyrochlore iridate Bi_{2}Ir_{2}O_{7} by means of infrared spectroscopy. Our optical conductivity data show the splitting of t_{2g}bands into J_{eff} ones due to strong spin-orbit coupling. We observed a sizable midinfrared absorption near 0.2 eV which can be attributed to the optical transition within the J_{eff,1/2} bands. More interestingly, we found an abrupt suppression of optical conductivity in the very far-infrared region. Our results suggest that the electronic structure of Bi_{2}Ir_{2}O_{7} is governed by the strong spin-orbit coupling and correlation effects, which are a prerequisite for theoretically proposed nontrivial topological phases in pyrochlore iridates.

### Wibe A. de Jong, Andrew M. Walker, Marcus D. Hanwell, "From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language", Journal of Cheminformatics, 2013, 5, doi: 10.1186/1758-2946-5-25

### Richard L. Martin, Maciej Haranczyk, "Optimization-Based Design of Metal-Organic Framework Materials", Journal of Chemical Theory and Computation, May 16, 2013,

Metal–organic frameworks (MOFs) are a class of porous materials constructed from metal or metal oxide building blocks connected by organic linkers. MOFs are highly tunable structures that can in theory be custom designed to meet the specific pore geometry and chemistry required for a given application such as methane storage or carbon capture. However, due to the sheer number of potential materials, identification of optimal MOF structures is a significant challenge.

### Robert Saye, James Sethian, "Multiscale Modeling of Membrane Rearrangement, Drainage, and Rupture in Evolving Foams", Science, May 10, 2013, doi: 10.1126/science.1230623

### Haruo Miyadera, Konstantin N. Borozdin, Steve J. Greene, Zarija Lukić, Koji Masuda, Edward C. Milner, Christopher L. Morris, John O. Perry, "Imaging Fukushima Daiichi reactors with muons", AIP Advances, 2013, 3:052133,

### Hank Childs, Berk Geveci, William J. Schroeder, Jeremy S. Meredith, Kenneth Moreland, Christopher Sewell, Torsten Kuhlen, E.Wes Bethel, "Research Challenges for Visualization Software", IEEE Computer, May 1, 2013, 46:34-43, LBNL 6239E,

### Emmanuel Agullo, Patrick R. Amestoy, Alfredo Buttari, Abdou Guermouche, Jean-Yves L'Excellent, François-Henry Rouet, "Robust memory-aware mappings for parallel multifrontal factorizations", Submitted to SISC, 2013,

### John Perry, Mara Azzouz, Jeffrey Bacon, Konstantin Borozdin, Elliott Chen, Joseph Fabritius II, Edward Milner, Haruo Miyadera, Christopher Morris, Jonathan Roybal, Zhehui Wang, Bob Busch, Ken Carpenter, Adam A. Hecht, Koji Masuda, Candace Spore, Nathan Toleman, Derek Aberle and Zarija Lukić, "Imaging a nuclear reactor using cosmic ray muons", Journal of Applied Physics, 2013, 113:184909,

### Richard L. Martin, Li-Chiang Lin, Kuldeep Jariwala, Berend Smit, Maciej Haranczyk, "Mail-Order Metal–Organic Frameworks (MOFs): Designing Isoreticular MOF-5 Analogues Comprising Commercially Available Organic Molecules", The Journal of Physical Chemistry C, April 17, 2013,

Metal–organic frameworks (MOFs), a class of porous materials, are of particular interest in gas storage and separation applications due largely to their high internal surface areas and tunable structures. MOF-5 is perhaps the archetypal MOF; in particular, many isoreticular analogues of MOF-5 have been synthesized, comprising alternative dicarboxylic acid ligands. In this contribution we introduce a new set of hypothesized MOF-5 analogues, constructed from commercially available organic molecules.

### David H. Bailey, Marcos M. Lopez de Prado and Eva del Pozo, "The strategy approval decision: A Sharpe ratio indifference curve approach", Algorithmic Finance, April 2, 2013, 2:99-109,

### Nils E. R. Zimmermann, Timm J. Zabel, Frerich J. Keil, "Transport into Nanosheets: Diffusion Equations Put to Test", J. Phys. Chem. C, 2013, 117:7384-7390, doi: 10.1021/jp400152q

Ultrathin porous materials, such as zeolite nanosheets, are prominent candidates for performing catalysis, drug supply, and separation processes in a highly efficient manner due to exceptionally short transport paths. Predictive design of such processes requires the application of diffusion equations that were derived for macroscopic, homogeneous surroundings to nanoscale, nanostructured host systems. Therefore, we tested different analytical solutions of Fick’s diffusion equations for their applicability to methane transport into two different zeolite nanosheets (AFI, LTA) under instationary conditions. Transient molecular dynamics simulations provided hereby concentration profiles and uptake curves to which the different solutions were fitted. Two central conclusions were deduced by comparing the fitted transport coefficients. First, the transport can be described correctly only if concentration profiles are used and the transport through the solid–gas interface is explicitly accounted for by the surface permeability. Second and most importantly, we have unraveled a size limitation to applying the diffusion equations to nanoscale objects. This is because transport-diffusion coefficients, *D*_{T}, and surface permeabilities, α, of methane in AFI become dependent on nanosheet thickness. Deviations can amount to factors of 2.9 and 1.4 for *D*_{T} and α, respectively, when, in the worst case, results from the thinnest AFI nanosheet are compared with data from the thickest sheet. We present a molecular explanation of the size limitation that is based on memory effects of entering molecules and therefore only observable for smooth pores such as AFI and carbon nanotubes. Hence, our work provides important tools to accurately predict and intuitively understand transport of guest molecules into porous host structures, a fact that will become the more valuable the more tiny nanotechnological objects get.

Watch a movie illustrating the transient molecular dynamics approach, which was critical for this study, here.

### Andrew Myers, Christopher McKee, Andrew Cunningham, Richard Klein, Mark Krumholz, "The Fragmentation of Magnetized, Massive Star-forming Cores with Radiative Feedback", The Astrophysical Journal, Volume 766, Issue 2, article id. 97, April 1, 2013,

### M. Montanari, E. Chan, K. Larson, W. Yoo, R. H. Campbell, "Distributed security policy conformance", Computers & Security, March 31, 2013,

### Wei Hu, Zhenyu Li and Jinlong Yang, "Electronic and optical properties of graphene and graphitic ZnO nanocomposite structures", J. Chem. Phys. 138, 124706 (2013), March 28, 2013, doi: 10.1063/1.4796602

- Download File: JCPGraphenegZnO.pdf (pdf: 967 KB)

Electronic and optical properties of graphene and graphitic ZnO (G/g-ZnO) nanocomposites have been investigated with density functional theory. Graphene interacts overall weakly with g-ZnO monolayer via van der Waals interaction. There is no charge transfer between the graphene and g-ZnO monolayer, while a charge redistribution does happen within the graphene layer itself, forming well-defined electron-hole puddles. When Al or Li is doped in the g-ZnO monolayer, substantial electron (n-type) and hole (p-type) doping can be induced in graphene, leading to well-separated electron-hole pairs at their interfaces. Improved optical properties in graphene/g-ZnO nanocomposite systems are also observed, with potential photocatalytic and photovoltaic applications.

### Jochen Mikosch, Jiaxu Zhang, Sebastian Trippel, Christoph Eichhorn, Rico Otto, Rui Sun, Wibe A de Jong, Matthias Weidemuller, William L Hase, Roland Wester, "Indirect dynamics in a highly exoergic substitution reaction.", Journal of the American Chemical Society, 2013, 135:4250-9, doi: 10.1021/ja308042v

### Francisco J. Aragon Artacho, David H. Bailey, Jonathan M. Borwein, Peter B. Borwein, "Walking on real numbers", Mathematical Intelligencer, March 15, 2013, 35:42-60,

### Anubhav Jain, Ivano E. Castelli, Geoffroy Hautier, David H. Bailey, Karsten W. Jacobsen, "Performance of genetic algorithms in search for water splitting perovskites", Journal of Materials Science, March 14, 2013,

### N. Aghaeepour, G. Finak, D. Dougall, A. Hadj-Khodabakhshi, P. Mah, G. Obermoser, J. Spidlen, I. Taylor, S. A Wuensch, J. Bramson, C. Eaves, A. P. Weng, E. Fortuno III, K. Ho, T. Kollmann, W. Rogers, S. Rosa, B. Dalal, A. Azad, A. Pothen, A. Brandes, H. Bretschneider, R. Bruggner, R. Finck, R. Jia, N. Zimmerman, M. Linderman, D. Dill, G. Nolan, C. Chan, F. Khettabi, K. Neill, M. Chikina, A. Gupta, P. Shooshtari, H. Zare, P. Jager, M. Jiang, J. Keilwagen, J. M. Maisog, P. Majek, J. Vilcek, T. Manninen, H. Huttunen, P. Ruusuvuori, M. Nykter, G. J. McLachlan, K. Wang, I. Naim, G. Sharma, R. Nikolic, S. Pyne, Y. Qian, P. Qiu, J. Quinn, A. Roth, R. Norel, G. Stolovitzky, P. Meyer, J. Saez-Rodriguez, M. Bhattacharjee, M. Biehl, P. Bucher, K. Bunte, B. .Camillo, S. Dimitrieva, J. Grau, I. Grosse, S. Posch, N. Guex, J. Keilwagen, M. Kursa, B. Liu, M. Maienschein-Cline, T. Manninen, G. J. McLachlan, P. Seifert, M. Strickert, J. Vilar, H. Hoos, T. Mosmann, R. Brinkman, R. Gottardo, and R. Scheuermann, "Critical Assessment of Automated Flow Cytometry Analysis Techniques", Nature Methods, 2013,

### E. Vecharynski and A. Knyazev, "Absolute value preconditioning for symmetric indefinite linear systems", SIAM Journal on Scientific Computing Vol. 35, Issue 2, pp. A696-A718, 2013,

We introduce a novel strategy for constructing symmetric positive definite (SPD) preconditioners for linear systems with symmetric indefinite matrices. The strategy, called absolute value preconditioning, is motivated by the observation that the preconditioned minimal residual method with the inverse of the absolute value of the matrix as a preconditioner converges to the exact solution of the system in at most two steps. Neither the exact absolute value of the matrix nor its exact inverse are computationally feasible to construct in general. However, we provide a practical example of an SPD preconditioner that is based on the suggested approach. In this example we consider a model problem with a shifted discrete negative Laplacian and suggest a geometric multigrid (MG) preconditioner, where the inverse of the matrix absolute value appears only on the coarse grid, while operations on finer grids are based on the Laplacian. Our numerical tests demonstrate practical effectiveness of the new MG preconditioner, which leads to a robust iterative scheme with minimalist memory requirements.

### A. S. Almgren, J. B. Bell, M.J. Lijewski, Z. Lukić, E. Van Andel, "Nyx: A Massively Parallel AMR Code for Computational Cosmology", The Astrophysical Journal, 2013, 765:39,

### Patrick Oesterling, Christian Heine, Gunther H. Weber, Gerik Scheuermann, "Visualizing global structure of nD point clouds as topological 1D height to enable supervised local data analysis", IEEE Transactions on Visualization and Computer Graphics, 2013, 19:514-526, LBNL 5694E,

### Han Suk Kim, Didem Unat, Scott Baden, Jurgen Schulze, "A new approach to interactive viewpoint selection for volume data sets", Information Visualization, February 25, 2013,

### Wei Hu, Xiaojun Wu, Zhenyu Li and Jinlong Yang, "Porous silicene as a hydrogen purification membrane", Phys. Chem. Chem. Phys., 2013, 15, 5753-5757, February 22, 2013, doi: 10.1039/C3CP00066D

- Download File: PCCPH2Silicene.pdf (pdf: 1.8 MB)

We investigated theoretically the hydrogen permeability and selectivity of a porous silicene membrane via first-principles calculations. The subnanometer pores of the silicene membrane are designed as divacancy defects with octagonal and pentagonal rings (585-divacancy). The porous silicene exhibits high selectivity comparable with graphene-based membranes for hydrogen over various gas molecules (N2, CO, CO2, CH4, and H2O). The divacancy defects in silicene are chemically inert to the considered gas molecules. Our results suggest that the porous silicene membrane is expected to find great potential in gas separation and filtering applications.

### Abhinav Sarje, Srinivas Aluru, "All-pairs computations on many-core graphics processors", Parallel Computing, 2013, 39-2:79-93, doi: 10.1016/j.parco.2013.01.002

Developing high-performance applications on emerging multi- and many-core architectures requires efficient mapping techniques and architecture-specific tuning methodologies to realize performance closer to their peak compute capability and memory bandwidth. In this paper, we develop architecture-aware methods to accelerate all-pairs computations on many-core graphics processors. Pairwise computations occur frequently in numerous application areas in scientific computing. While they appear easy to parallelize due to the independence of computing each pairwise interaction from all others, development of techniques to address multi-layered memory hierarchies, mapping within the restrictions imposed by the small and low-latency on-chip memories, striking the right balanced between concurrency, reuse and memory traffic etc., are crucial to obtain high-performance. We present a hierarchical decomposition scheme for GPUs based on decomposition of the output matrix and input data. We demonstrate that a careful tuning of the involved set of decomposition parameters is essential to achieve high efficiency on the GPUs. We also compare the performance of our strategies with an implementation on the STI Cell processor as well as multi-core CPU parallelizations using OpenMP and Intel Threading Building Blocks.

### Richard L. Martin, Maciej Haranczyk, "Exploring frontiers of high surface area metal-organic frameworks", Chemical Science, February 6, 2013, 4:1781-1785,

### David H. Bailey, Jonathan M. Borwein, Richard E. Crandall, John Zucker, "Lattice sums arising from the Poisson equation", Journal of Physics A: Mathematical and Theoretical, February 5, 2013, to appea,

### Laurent Bouchet, Patrick Amestoy, Alfredo Buttari, François-Henry Rouet, Maxime Chauvin, "Simultaneous analysis of large INTEGRAL/SPI datasets: optimizing the computation of the solution and its variance using sparse matrix algorithms", Astronomy and Computing, February 1, 2013, 1:59--69, doi: 10.1016/j.ascom.2013.03.002

### Sean Whalen, Sean Peisert, Matt Bishop, "Multiclass Classification of Distributed Memory Parallel Computations", Pattern Recognition Letters (PRL), February 2013, 34(3):322-329, doi: 10.1016/j.patrec.2012.10.007

### Wei Hu, Zhenyu Li and Jinlong Yang, "Diamond as an inert substrate of graphene", J. Chem. Phys. 138, 054701 (2013), February 1, 2013, doi: 10.1063/1.4789420

- Download File: JCPGrapheneDiamond.pdf (pdf: 912 KB)

Interaction between graphene and semiconducting diamond substrate has been examined with large-scale density functional theory calculations. Clean and hydrogenated diamond (100) and (111) surfaces have been studied. It turns out that weak van der Waals interactions dominate for graphene on all these surfaces. High carrier mobility of graphene is almost not affected, except for a negligible energy gap opening at the Dirac point. No charge transfer between graphene and diamond (100) surfaces is detected, while different charge-transfer complexes are formed between graphene and diamond (111) surfaces, inducing either p-type or n-type doping on graphene. Therefore, diamond can be used as an excellent substrate of graphene, which almost keeps its electronic structures at the same time providing the flexibility of charge doping.

### Kumari Gaurav Rana, Takeaki Yajima, Subir Parui, Alexander F. Kemper, Thomas P.Devereaux, Yasuyuki Hikita, Harold Y. Hwang, Tamalika Banerjee, "Hot electron transport in a strongly correlated transition-metal oxide", Nature Scientific Reports, Volume 3, id. 1274 (2013)., February 2013,

Oxide heterointerfaces are ideal for investigating strong correlation effects to electron transport, relevant for oxide-electronics. Using hot-electrons, we probe electron transport perpendicular to the La_{0.7}Sr_{0.3}MnO_{3} (LSMO)- Nb-doped SrTiO_{3} (Nb:STO) interface and find the characteristic hot-electron attenuation length in LSMO to be 1.48 +/- 0.10 unit cells (u.c.) at -1.9 V, increasing to 2.02 +/- 0.16 u.c. at -1.3 V at room temperature. Theoretical analysis of this energy dispersion reveals the dominance of electron-electron and polaron scattering. Direct visualization of the local electron transport shows different transmission at the terraces and at the step-edges.

### M. Dandouna, N. Emad and L.A. Drummond, "A Proposed Programming Model for Writing Sustainable Numerical Libraries for Extreme Scale Computing", Conc. and Compt., January 16, 2013,

The promise of computer systems with very large orders of processing elements cannot be realized without an effective solution that targets the programming model with a suitable programming environ- ment. Nowadays, it is necessary to identify and rapidly make available robust software technologies to enable high-end computer applications to run efficiently on these emerging systems, and to enable the development of more complex and capable simulation codes for scientific and engineering applica- tions. We review some of numerical libraries that have achieved modularity, scalability and extensibility thanks to their use of object-oriented programming approaches. However, only a few of these libraries have managed to effectively implement sequential and parallel code reusability.

Here, we discuss what is currently missing from existing library implementations and propose a pro- gramming model based on a modular and multi-level parallelism approach that has a strict separation between computational operations, data management and communication. We illustrate how this model makes it possible to design more scalable libraries by exploiting better their functionalities and even enable the formulation of hybrid numerical scheme to be run efficiently on multi-level parallel systems with a large number of heterogeneous processing units without confining the parallelism to the program- ming model of the communication library. We use the multiple explicitly restarted Arnoldi method as our test case and our implementations require full reuse of serial/parallel kernels in their implementation. Our experiments include comparisons with state-of-the-art numerical libraries on high-end computing systems.

### Wei Hu, Zhenyu Li, Jinlong Yang and Jianguo Hou, "Nondecaying long range effect of surface decoration on the charge state of NV center in diamond", J. Chem. Phys. 138, 034702 (2013), January 15, 2013, doi: 10.1063/1.4775364

- Download File: JCPNVDiamondSurface.pdf (pdf: 911 KB)

### P. Ghysels, T. J. Ashby, K. Meerbergen, W. Vanroose, "Hiding Global Communication Latency in the GMRES Algorithm on Massively Parallel Machines", SIAM Journal on Scientific Computing, January 8, 2013, 35:1, doi: 10.1137/12086563X

### Haitao Ma, Stan Woosley, Chris Malone, Ann Almgren, and J.B. Bell, "Carbon Deflagration in Type Ia Supernovae: I. Centrally Ignited Models", Astrophysical Journal, 2013, 771:58,

### U. Feindt, M. Kerschhaggl, M. Kowalski, G. Aldering, P., C. Aragon, S. Bailey, C. Baltay, S., C. Buton, A. Canto, F. Cellier-Holzem, M., N. Chotard, Y. Copin, H. K. Fakhouri, E., J. Guy, A. Kim, P. Nugent, J., K. Paech, R. Pain, E. Pecontal, R., S. Perlmutter, D. Rabinowitz, M., K. Runge, C. Saunders, R. Scalzo, G., C. Tao, R. C. Thomas, B. A. Weaver, C. Wu, "Measuring cosmic bulk flows with Type Ia supernovae from the Nearby Supernova Factory", Astronomy & Astrophysics, 2013, 560:A90, doi: 10.1051/0004-6361/201321880

### C. Gilet, A.S. Almgren, J.B. Bell, A. Nonaka, S.E. Woosley and M. Zingale, "Low-Mach Number Modeling of Core Convection in Massive Stars", Astrophysical Journal, 2013, 773:137,

### Jack Dongarra, Mathieu Faverge, Thomas Herault, Mathias Jacquelin, Julien Langou, Yves Robert, "Hierarchical QR factorization algorithms for multi-core clusters", Parallel Computing, 2013, 39:212--232,

### M. Rigault, Y. Copin, G. Aldering, P. Antilogus, C., S. Bailey, C. Baltay, S. Bongard, C., A. Canto, F. Cellier-Holzem, M. Childress, N., H. K. Fakhouri, U. Feindt, M. Fleury, E., P. Greskovic, J. Guy, A. G. Kim, M., S. Lombardo, J. Nordin, P. Nugent, R., E. Pecontal, R. Pereira, S. Perlmutter, D., K. Runge, C. Saunders, R. Scalzo, G., C. Tao, R. C. Thomas, B. A. Weaver, "Evidence of environmental dependencies of Type Ia supernovae from the Nearby Supernova Factory indicated by local H$\alpha$", Astronomy and Astrophysics, 2013, 560:A66, doi: 10.1051/0004-6361/201322104

### E. O. Ofek, D. Fox, S. B. Cenko, M. Sullivan, O., D. A. Frail, A. Horesh, A. Corsi, R. M., N. Gehrels, S. R. Kulkarni, A., P. E. Nugent, O. Yaron, A. V. Filippenko, M. M., L. Bildsten, J. S. Bloom, D., I. Arcavi, R. R. Laher, D. Levitan, B. Sesar, J. Surace, "X-Ray Emission from Supernovae in Dense Circumstellar Matter Environments: A Search for Collisionless Shocks", Astrophysical Journal, 2013, 763:42, doi: 10.1088/0004-637X/763/1/42

The optical light curve of some supernovae (SNe) may be powered by the

outward diffusion of the energy deposited by the explosion shock (the

so-called shock breakout) in optically thick (

### K. Chen, A. Heger, S. Woosley, A. Almgren, and W. Zhang, "The Most Powerful Stellar Explosion", Bulletin of the American Physical Society, 2013, 58(4),

### W. Zheng, J. M. Silverman, A. V. Filippenko, D., P. E. Nugent, M. Graham, X. Wang, S., F. Ciabattari, P. L. Kelly, O. D. Fox, I., K. I. Clubb, S. B. Cenko, D. Balam, D. A., E. Hsiao, W. Li, G. H. Marion, D., J. Vinko, J. C. Wheeler, J. Zhang, "The Very Young Type Ia Supernova 2013dy: Discovery, and Strong Carbon Absorption in Early-time Spectra", Astrophysical Journal, 2013, 778:L15, doi: 10.1088/2041-8205/778/1/L15

### C. Buton, Y. Copin, G. Aldering, P. Antilogus, C., S. Bailey, C. Baltay, S. Bongard, A., F. Cellier-Holzem, M. Childress, N., H. K. Fakhouri, E. Gangler, J. Guy, E. Y., M. Kerschhaggl, M. Kowalski, S., P. Nugent, K. Paech, R. Pain, E., R. Pereira, S. Perlmutter, D., M. Rigault, K. Runge, R. Scalzo, G., C. Tao, R. C. Thomas, B. A. Weaver, C. Wu, Nearby SuperNova Factory, "Atmospheric extinction properties above Mauna Kea from the Nearby SuperNova Factory spectro-photometric data set", Astronomy & Astrophysics, 2013, 549:A8, doi: 10.1051/0004-6361/201219834

### C. Huggel, D. Stone, M. Auffhammer, G. Hansen, "Loss and damage attribution", Nature Climate Change, 2013, 3:694--696,

### Ke-Jung Chen, Alexander Heger, and Ann S. Almgren, "Numerical Approaches for Multidimensional Simulations of Stellar Explosions", Astronomy and Computing, January 2013, 3-4:70-78,

### L. P. Singer, S. B. Cenko, M. M. Kasliwal, D. A., E. O. Ofek, D. A. Brown, P. E. Nugent, S. R., A. Corsi, D. A. Frail, E. Bellm, J., I. Arcavi, T. Barlow, J. S. Bloom, Y., N. Gehrels, A. Horesh, F. J. Masci, J., A. Rau, J. A. Surace, O. Yaron, "Discovery and Redshift of an Optical Afterglow in 71 deg$^2$: iPTF13bxl and GRB 130702A", Astrophysical Journal, 2013, 776:L34, doi: 10.1088/2041-8205/776/2/L34

### D. Stone, M. Auffhammer, M. Carey, G. Hansen, C. Huggel, W. Cramer, D. Lobell, U. Molau, A. Solow, L. Tibig, G. Yohe, "The challenge to detect and attribute effects of climate change on human and natural systems", Clim. Change, 2013, 121:381--395, doi: 10.1007/s10584-013-0873-6

- Download File: StoneDAuffhammerMetalii2013.pdf (pdf: 476 KB)
- Download File: StoneDAuffhammerMetalii2013.supp.pdf (pdf: 51 KB)

### Y. Cao, M. M. Kasliwal, I. Arcavi, A. Horesh, P., S. Valenti, S. B. Cenko, S. R. Kulkarni, A., E. Gorbikov, E. O. Ofek, D. Sand, O., M. Graham, J. M. Silverman, J. C. Wheeler, G. H., E. S. Walker, P. Mazzali, D. A. Howell, K. L., A. K. H. Kong, J. S. Bloom, P. E. Nugent, J., F. Masci, J. Carpenter, N. Degenaar, C. R. Gelino, "Discovery, Progenitor and Early Evolution of a Stripped Envelope Supernova iPTF13bvn", Astrophysical Journal, 2013, 775:L7, doi: 10.1088/2041-8205/775/1/L7

### S. Taubenberger, M. Kromer, S. Hachinger, P. A., S. Benetti, P. E. Nugent, R. A. Scalzo, R., V. Stanishev, J. Spyromilio, F. Bufano, S. A. Sim, B. Leibundgut, W. Hillebrandt, "Super-Chandrasekhar Type Ia Supernovae at nebular epochs", Monthly Notices of the Royal Astronomical Society, 2013, 432:3117-3130, doi: 10.1093/mnras/stt668

### Michael F. Wehner, "Very extreme seasonal precipitation in the NARCCAP ensemble: model performance and projections", Climate Dynamics, January 2013, 40:59-80, doi: 10.1007/s00382-012-1393-1

Seasonal extreme daily precipitation is analyzed in the ensemble of NARCAPP regional climate models. Significant variation in these models’ abilities to reproduce observed precipitation extremes over the contiguous United States is found. Model performance metrics are introduced to characterize overall biases, seasonality, spatial extent and the shape of the precipitation distribution. Comparison of the models to gridded observations that include an elevation correction is found to be better than to gridded observations without this correction. A complicated model weighting scheme based on model performance in simulating observations is found to cause significant improvements in ensemble mean skill only if some of the models are poorly performing outliers. The effect of lateral boundary conditions are explored by comparing the integrations driven by reanalysis to those driven by global climate models. Projected mid-century future changes in seasonal precipitation means and extremes are presented and discussions of the sources of uncertainty and the mechanisms causing these changes are presented.

### D. J. Frame, D. A. Stone, "Assessment of the first consensus prediction on climate change", Nature Climate Change, 2013, 3:357--359,

### Hubertus J. J. van Dam, Abhinav Vishnu, Wibe A. de Jong, "A Case for Soft Error Detection and Correction in Computational Chemistry", Journal of Chemical Theory and Computation, 2013, 9:3995-4005, doi: 10.1021/ct400489c

### J. M. Silverman, P. E. Nugent, A. Gal-Yam, M., D. A. Howell, A. V. Filippenko, Y.-C. Pan, S. B. Cenko, I. M. Hook, "Late-time Spectral Observations of the Strongly Interacting Type Ia Supernova PTF11kx", Astrophysical Journal, 2013, 772:125, doi: 10.1088/0004-637X/772/2/125

### George Michelogiannakis, William J. Dally, "Elastic Buffer Flow Control for On-Chip Networks", Transactions on Computers, 2013,

- Download File: TC2012.pdf (pdf: 547 KB)

Networks-on-chip (NoCs) were developed to meet the communication requirements of large-scale systems. The majority of current NoCs spend considerable area and power for router buffers. In our past work, we have developed elastic buffer (EB) flow control which adds simple control logic in the channels to use pipeline flip-flops (FFs) as EBs with two storage locations. This way, channels act as distributed FIFOs and input buffers are no longer required. Removing buffers and virtual channels (VCs) significantly simplifies router design. Compared to VC networks, EB networks provide an up to 45% shorter cycle time, 16% more throughput per unit power or 22% more throughput per unit area. EB networks provide traffic classes using duplicate physical subnetworks. However, this approach negates the cost gains or becomes infeasible for a large number of traffic classes. Therefore, in this paper we propose a hybrid EB-VC router which provides an arbitrary number of traffic classes by using an input buffer to drain flits facing severe contention or deadlock. Thus, hybrid routers operate as EB routers in the common case, and as VC routers when necessary. For this reason, the hybrid EB-VC scheme offers 21% more throughput per unit power than VC networks and 12% than EB networks.

### X. Rodó, M. Pascual, F. J. Doblas-Reyes, A. Gershunov, D. A. Stone, F. Giorgi, P. J. Hudson, J. Kinter, M.-À. Rodríguez-Arias, N. Ch. Stenseth, D. Alonso, J. García-Serrano, A. P. Dobson, "Climate change and infectious diseases: Can we meet the needs for better prediction?", Clim. Change, 2013, 118:625--640,

### A Dubey, B Van Straalen, "Experiences from software engineering of large scale AMR multiphysics code frameworks", arXiv preprint arXiv:1309.1781, January 1, 2013, doi: http://dx.doi.org/10.5334/jors.am

### J. M. Silverman, P. E. Nugent, A. Gal-Yam, M., D. A. Howell, A. V. Filippenko, I., S. Ben-Ami, J. S. Bloom, S. B. Cenko, Y., R. Chornock, K. I. Clubb, A. L. Coil, R. J., M. L. Graham, C. V. Griffith, A., M. M. Kasliwal, S. R. Kulkarni, D. C., W. Li, T. Matheson, A. A. Miller, M., E. O. Ofek, Y.-C. Pan, D. A. Perley, D., R. M. Quimby, T. N. Steele, A. Sternberg, D. Xu, O. Yaron, "Type Ia Supernovae Strongly Interacting with Their Circumstellar Medium", Astrophysical Journals, 2013, 207:3, doi: 10.1088/0067-0049/207/1/3

### S. B. Cenko, S. R. Kulkarni, A. Horesh, A. Corsi, D. B., J. Carpenter, D. A. Frail, P. E. Nugent, D. A., D. Gruber, A. Gal-Yam, P. J. Groot, G., E. O. Ofek, A. Rau, C. L. MacLeod, A. A., J. S. Bloom, A. V. Filippenko, M. M., N. M. Law, A. N. Morgan, D. Polishook, D., R. M. Quimby, B. Sesar, K. J. Shen, J. M. Silverman, A. Sternberg, "Discovery of a Cosmological, Relativistic Outburst via its Rapidly Fading Optical Emission", Astrophysical Journal, 2013, 769:130, doi: 10.1088/0004-637X/769/2/130

### R. Pereira, R. C. Thomas, G. Aldering, P. Antilogus, C., S. Benitez-Herrera, S. Bongard, C., A. Canto, F. Cellier-Holzem, J. Chen, M., N. Chotard, Y. Copin, H. K. Fakhouri, M., D. Fouchez, E. Gangler, J. Guy, W., E. Y. Hsiao, M. Kerschhaggl, M., M. Kromer, J. Nordin, P. Nugent, K., R. Pain, E. P\ econtal, S. Perlmutter, D., M. Rigault, K. Runge, C. Saunders, G., C. Tao, S. Taubenberger, A. Tilquin, C. Wu, "Spectrophotometric time series of SN 2011fe from the Nearby Supernova Factory", Astronomy & Astrophysics, 2013, 554:A27, doi: 10.1051/0004-6361/201221008

### L. Lin, M. Chen, C. Yang, L. He, "Accelerating Atomic Orbital-based Electronic Structure Calculation via Pole Expansion and Selected Inversion", J Phsy: Condens Matter, 2013,

### Jan Rajczak, Pardeep Pall, Christoph Schär, "Projections of extreme precipitation events in regional climate simulations for Europe and the Alpine Region", Journal of Geophysical Research: Atmospheres, 2013,

### D. Levitan, T. Kupfer, P. J. Groot, S. R. Kulkarni, T. A., G. V. Simonian, I. Arcavi, J. S. Bloom, R., P. E. Nugent, E. O. Ofek, B. Sesar, J. Surace, "Five new outbursting AM CVn systems discovered by the Palomar Transient Factory", Monthly Notices of the Royal Astronomical Society, 2013, 430:996-1007, doi: 10.1093/mnras/sts672

### L. Lin, C. Yang, "Elliptic preconditioner for accelerating the self-consistent field iteration in Kohn-Sham Density Functional Theory", SIAM J. Sci. Comp., 2013,

### Per-Olof Persson, "A sparse and high-order accurate line-based discontinuous Galerkin method for unstructured meshes", Journal of Computational Physics, 2013, 233:414--429, doi: 10.1016/j.jcp.2012.09.008

### D. A. Stone, C. J. Paciorek, Prabhat, P. Pall, M. F. Wehner, "Inferring the anthropogenic contribution to local temperature extremes", Proceedings of the National Academy of Sciences, 2013, 110:E1543, doi: 10.1073/pnas.1221461110

### S. Tang, Y. Cao, L. Bildsten, P. Nugent, E., S. R. Kulkarni, R. Laher, D. Levitan, F., E. O. Ofek, T. A. Prince, B. Sesar, J. Surace, "R Coronae Borealis Stars in M31 from the Palomar Transient Factory", Astrophysical Journal, 2013, 767:L23, doi: 10.1088/2041-8205/767/2/L23

### E. Y. Hsiao, G. H. Marion, M. M. Phillips, C. R., C. Winge, N. Morrell, C. Contreras, W. L., M. Kromer, E. E. E. Gall, C. L., P. H\ oflich, M. Im, Y. Jeon, R. P., P. E. Nugent, S. E. Persson, G., M. Roth, V. Stanishev, M. Stritzinger, N. B. Suntzeff, "The Earliest Near-infrared Time-series Spectroscopy of a Type Ia Supernova", Astrophysical Journal, 2013, 766:72, doi: 10.1088/0004-637X/766/2/72

### Kesheng Wu, Wes Bethel, Ming Gu, David, Oliver R\ ubel, "A Big Data Approach to Analyzing Market Volatility", Algorithmic Finance, 2013, 2:241--267, LBNL LBNL-6382E, doi: 10.3233/AF-13030

Understanding the microstructure of the financial market requires the processing of a vast amount of data related to individual trades, and sometimes even multiple levels of quotes. Analyzing such a large volume of data requires tremendous computing power that is not easily available to financial academics and regulators. Fortunately, public funded High Performance Computing (HPC) power is widely available at the National Laboratories in the US. In this paper we demonstrate that the HPC resource and the techniques for data-intensive sciences can be used to greatly accelerate the computation of an early warning indicator called Volume-synchronized Probability of Informed trading (VPIN). The test data used in this study contains five and a half year's worth of trading data for about 100 most liquid futures contracts, includes about 3 billion trades, and takes 140GB as text files. By using (1) a more efficient file format for storing the trading records, (2) more effective data structures and algorithms, and (3) parallelizing the computations, we are able to explore 16,000 different ways of computing VPIN in less than 20 hours on a 32-core IBM DataPlex machine. Our test demonstrates that a modest computer is sufficient to monitor a vast number of trading activities in real-time -- an ability that could be valuable to regulators.

Our test results also confirm that VPIN is a strong predictor of liquidity-induced volatility. With appropriate parameter choices, the false positive rates are about 7% averaged over all the futures contracts in the test data set. More specifically, when VPIN values rise above a threshold (CDF > 0.99), the volatility in the subsequent time windows is higher than the average in 93% of the cases.

### E. O. Ofek, M. Sullivan, S. B. Cenko, M. M. Kasliwal, A., S. R. Kulkarni, I. Arcavi, L. Bildsten, J. S., A. Horesh, D. A. Howell, A. V. Filippenko, R., D. Murray, E. Nakar, P. E. Nugent, J. M., N. J. Shaviv, J. Surace, O. Yaron, "An outburst from a massive star 40days before a supernova explosion", Nature, 2013, 494:65-67, doi: 10.1038/nature11877

### Jarrod R McClean, John A Parkhill, Alan Aspuru-Guzik, "Feynman’s clock, a new variational principle, and parallel-in-time quantum dynamics", Proceedings of the National Academy of Sciences, 2013, 110:E3901--E39,

### R. L. Barone, P. Nugent, "Erratum: Near-infrared observations of type Ia supernovae: The known standard candle for cosmology", Monthly Notices of the Royal Astronomical Society, 2013, L90, doi: 10.1093/mnrasl/slt038

### S.L. Cornford, D.F. Martin, D.T. Graves, D.F. Ranken, A.M. Le Brocq, R.M. Gladstone, A.J. Payne, E.G. Ng, W.H. Lipscomb, "Adaptive mesh, finite volume modeling of marine ice sheets", Journal of Computational Physics, 232(1):529-549, 2013,

- Download File: cornfordmartinJCP2012.pdf (pdf: 1 MB)

### Weiqun Zhang, L. Howell, A. Almgren, A. Burrows, J. Dolence, and J. Bell., "CASTRO: A New Compressible Astrophysical Solver. III. Multigroup Radiation Hydrodynamics", Astrophysical Journal Supplement Series, 2013, 204:7,

### A. Horesh, C. Stockdale, D. B. Fox, D. A. Frail, J., S. R. Kulkarni, E. O. Ofek, A., M. M. Kasliwal, I. Arcavi, R. Quimby, S. B., P. E. Nugent, J. S. Bloom, N. M. Law, D., E. Gorbikov, D. Polishook, O. Yaron, S., K. W. Weiler, F. Bauer, S. D. Van Dyk, S., N. Panagia, D. Pooley, N. Kassim, "An early and comprehensive millimetre and centimetre wave and X-ray study of SN 2011dh: a non-equipartition blast wave expanding into a massive stellar wind", Monthly Notices of the Royal Astronomical Society, 2013, 436:1258-1267, doi: 10.1093/mnras/stt1645

### A.S. Almgren, A.J. Aspden, J. B. Bell, and M. L. Minion, "On the Use of Higher-Order Projection Methods for Incompressible Turbulent Flow", SIAM J. Sci. Comput., 2013, 35(1):B35-B42,

### M. Zingale, A. Nonaka, A. S. Almgren, J. B. Bell, C. Malone, and R. Orvedahl, "Low Mach Number Modeling of Convection in Helium Shells on Sub-Chandrasekhar White Dwarfs. I. Methodology", Astrophysical Journal, 2013, 764:97,

### J. M. Silverman, J. Vinko, M. M. Kasliwal, O. D., Y. Cao, J. Johansson, D. A. Perley, D., J. C. Wheeler, R. Amanullah, I. Arcavi, J. S., A. Gal-Yam, A. Goobar, S. R. Kulkarni, R., W. H. Lee, G. H. Marion, P. E. Nugent, I. Shivvers, "SN 2000cx and SN 2013bh: extremely rare, nearly twin Type Ia supernovae", Monthly Notices of the Royal Astronomical Society, 2013, 436:1225-1237, doi: 10.1093/mnras/stt1647

### 2012

### Mitesh Meswani, Laura Carrington, Didem Unat, Allan Snavely, Scott Baden, Stephen Poole, "Modeling and predicting performance of high performance computing applications on hardware accelerators", International Journal of High Performance Computing Applications, December 28, 2012,

### H.-M. Eiter, M. Lavagnini, R. Hackl, E.A. Nowadnick, A.F. Kemper, T.P. Devereaux, J.-H. Chu, J.G. Analytis, I.R. Fisher, L. Degiorgi, "Alternative route to charge density wave formation in multiband systems", Proceedings of the National Academy of Sciences, 2012, doi: 10.1073/pnas.1214745110

Charge and spin density waves, periodic modulations of the electron, and magnetization densities, respectively, are among the most abundant and nontrivial low-temperature ordered phases in condensed matter. The ordering direction is widely believed to result from the Fermi surface topology. However, several recent studies indicate that this common view needs to be supplemented. Here, we show how an enhanced electron–lattice interaction can contribute to or even determine the selection of the ordering vector in the model charge density wave system ErTe3. Our joint experimental and theoretical study allows us to establish a relation between the selection rules of the electronic light scattering spectra and the enhanced electron–phonon coupling in the vicinity of band degeneracy points. This alternative proposal for charge density wave formation may be of general relevance for driving phase transitions into other broken-symmetry ground states, particularly in multiband systems, such as the iron-based superconductors.

### Planck Collaboration, "Planck Intermediate Results. X. Physics of the hot gas in the Coma cluster", ArXiv e-prints, December 10, 2012,

### Daniel Rios, George Schoendorff, Michael J. Van Stipdonk, Mark S. Gordon, Theresa L. Windus, John K. Gibson, Wibe A. de Jong, "Roles of Acetone and Diacetone Alcohol in Coordination and Dissociation Reactions of Uranyl Complexes", Inorganic Chemistry, 2012, 51:12768-1277, doi: 10.1021/ic3015964

### David H. Bailey and Jonathan M. Borwein, "Compressed lattice sums arising from the Poisson equation: Dedicated to Professor Hari Sirvastava", Boundary Value Problems, special issue, Proceedings of the International Congress in Honour of Professor Hari M. Srivastava, December 2, 2012, to appea,

### Donald Wuebbles, Gerald Meehl, Katharine Hayhoe, Thomas R. Karl, Kenneth Kunkel, Benjamin Santer, Michael Wehner, Brian Colle, Erich M. Fischer, Rong Fu, Alex Goodman, Emily Janssen, Huikyo Lee, Wenhong Li, Lindsey N. Long, Seth Olsen, Anji Seth, Justin Sheffield, Liqiang Sun, "CMIP5 Climate Model Analyses: Climate Extremes in the United States", Bulletin of the American Meteorological Society (submitted), 2012,

### David H. Bailey, Jonathan M. Borwein, Christian S. Calude, Michael J. Dinneen, Monica Dumitrescu, Alex Yee, "An empirical approach to the normality of pi", Experimental Mathematics, 2012, 21:375-384,

### H. Hu, C. Yang, K. Zhao, "Absorption correction A* for cylindrical and spherical crystals with extended range and high accuracy calculated by Thorkildsen & Larsen analytical method", in press Acta Crystallographica, A, 2012,

### C. L. Morris, Konstantin Borozdin, Jeffrey Bacon, Elliott Chen, Zarija Lukić, Edward Milner, Haruo Miyadera, John Perry, Dave Schwellenbach, Derek Aberle, Wendi Dreesen, J. Andrew Green, George G. McDuff, Kanetada Nagamine, Michael Sossong, Candace Spore, Nathan Toleman, "Obtaining material identification with cosmic ray radiography", AIP Advances, 2012, 2:042128,

### Seung-Ki Min, Xuebin Zhang, Francis Zwiers, Hideo Shiogama, Yu-Shiang Tung, and Michael Wehner, "Multi-Model Detection and Attribution of Extreme Temperature Changes", Journal of Climate (submitted), 2012,

### C. Mendl, L. Lin, "Towards the Kantorovich dual solution for strictly correlated electrons in atoms and molecules", submitted to Phys. Rev. B, 2012,

### Pak Shing Li, Andrew Myers, Christopher McKee, "Ambipolar Diffusion Heating in Turbulent Systems", The Astrophysical Journal, Volume 760, Issue 1, article id. 33, November 1, 2012,

### Zaiwen Wen, Chao Yang, Xin Liu, Stefano Marchesini, "Alternating direction methods for classical and ptychographic phase retrieval", Inverse Problems, November 2012, 28, doi: 10.1088/0266-5611/28/11/115010

### E. Wes Bethel and Mark Howison, "Multi-core and Many-core Shared-memory Parallel Raycasting Volume Rendering Optimization and Tuning", International Journal of High Performance Computing Applications, 2012, LBNL 5362E,

### Salman Habib, Vitali Morozov, Hal Finkel, Adrian Pope, Katrin Heitmann, Kalyan Kumaran, Tom Peterka, Joe Insley, David Daniel, Patricia Fasel, Nicholas Frontiere, Zarija Lukić, "The universe at extreme scale: multi-petaflop sky simulation on the BG/Q", Supercomputing, 2012, 4,

### L. Lin, S. Shao, W.E, "Efficient iterative method for solving the Dirac-Kohn-Sham density functional theory", submitted to J. Comput. Phys., 2012,

### Konstantin Borozdin, Steven Greene, Zarija Lukić, Edward Milner, Haruo Miyadera, Christopher Morris, John Perry, "Cosmic Ray Radiography of the Damaged Cores of the Fukushima Reactors", Physical Review Letters, 2012, 109:152501,

### Bin Dong, Xiuqiao Li, Qimeng Wu, Limin Xiao, Li Ruan, "A dynamic and adaptive load balancing strategy for parallel file system with large-scale I/O servers", Journal of Parallel and Distributed Computing (JPDC), Volume 72, Issue 10, October 2012, Pages 1254-1268, 2012,

### K. Madduri, J. Su, S. Williams, L. Oliker, S. Ethier, K. Yelick, "Optimization of Parallel Particle-to-Grid Interpolation on Leading Multicore Platforms", Transactions on Parallel and Distributed Systems (TPDS), October 1, 2012, doi: 10.1109/TPDS.2012.28

### Tamay M. Ozgokmen, Andrew C. Poje, Paul F. Fischer, Hank Childs, Harinarayan Krishnan, Christoph Garth, Angelique C. Haza, Edward Ryan, "On multi-scale dispersion under the influence of surface mixed layer instabilities", Ocean Modelling, October 2012, 56:16-30,

### David H. Bailey, Jonathan M. Borwein, "Ancient Indian square roots: An exercise in forensic paleo-mathematics", American Mathematical Monthly, October 2012, 119:646-657,

### Jun Zhou, Didem Unat, Dong Ju Choi, Clark C. Guest, Yifeng Cui, "Hands-on Performance Tuning of 3D Finite Difference Earthquake Simulation on GPU Fermi Chipset", Procedia CS, 2012, Vol 9:976-985,

### B. Kallemov, G. H. Miller, S. Mitran and D. Trebotich, "Calculation of Viscoelastic Bead-Rod Flow Mediated by a Homogenized Kinetic Scale with Holonomic Constraints", Molecular Simulation, 2012, doi: 10.1080/08927022.2011.654206

- Download File: molsim2012.pdf (pdf: 204 KB)

### Matt Bishop, Sean Peisert, "Security and Elections", IEEE Security & Privacy, September 2012, 10(5):64-67, doi: 10.1109/MSP.2012.127

### Douglas F Levinson, Jianxin Shi, Kai Wang, Sang Oh, Brien Riley, Ann E Pulver, Dieter B Wildenauer, Claudine Laurent, Bryan J Mowry, Pablo V Gejman, Michael J Owen, Kenneth S Kendler, Gerald Nestadt, Sibylle G Schwab, Jacques Mallet, Deborah Nertney, Alan R Sanders, Nigel M Williams, Brandon Wormley, Virginia K Lasseter, Margot Albus, Stephanie Godard-Bauché, Madeline Alexander, Jubao Duan, Michael C O’Donovan, Dermot Walsh, Anthony O’Neill, George N Papadimitriou, Dimitris Dikeos, Wolfgang Maier, Bernard Lerer, Dominique Campion, David Cohen, Maurice Jay, Ayman Fanous, Peter Eichhammer, Jeremy M Silverman, Nadine Norton, Nancy Zhang, Hakon Hakonarson, Cynthia Gao, Ami Citri, Mark Hansen, Stephan Ripke, Frank Dudbridge, Peter A Holmans, "Genome-wide association study of multiplex schizophrenia pedigrees", The American Journal of Psychiatry, September 1, 2012, doi: doi:10.1176/appi.ajp.2012.11091423

### Nils E. R. Zimmermann, Berend Smit, Frerich J. Keil, "Predicting Local Transport Coefficients at Solid-Gas Interfaces", J. Phys. Chem. C, 2012, 116:18878-1888, doi: 10.1021/jp3059855

The regular nanoporous structure make zeolite membranes attractive candidates for separating molecules on the basis of differences in transport rates (diffusion). Since improvements in synthesis have led to membranes as thin as several hundred nanometers by now, the slow transport in the boundary layer separating bulk gas and core of the nanoporous membrane is becoming increasingly important. Therefore, we investigate the predictability of the coefficient quantifying this local process, the surface permeability α, by means of a two-scale simulation approach. Methane tracer-release from the one-dimensional nanopores of an AFI-type zeolite is employed. Besides a pitfall in determining α on the basis of tracer exchange, we, importantly, present an accurate prediction of the surface permeability using readily available information from molecular simulations. Moreover, we show that the prediction is strongly influenced by the degree of detail with which the boundary region is modeled. It turns out that not accounting for the fact that molecules aiming to escape the host structure must indeed overcome two boundary regions yields too large a permeability by a factor of 1.7–3.3, depending on the temperature. Finally, our results have far-reaching implications for the design of future membrane applications.

Watch a movie illustrating the conditions of self- or tracer-diffusion here.

### Richard L. Martin, Thomas F. Willems, Li-Chiang Lin, Jihan Kim, Joseph A. Swisher, Berend Smit & Maciej Haranczyk, "Similarity-Driven Discovery of Zeolite Materials for Adsorption-Based Separations", ChemPhysChem, August 22, 2012, 13:3595-3597,

Crystalline porous materials can be exploited in many applications. Discovery of materials with optimum adsorption properties typically involves expensive brute-force characterization of large sets of materials. An alternative approach based on similarity searching that enables discovery of materials with optimum adsorption for CO_{2} and other molecules at a fraction of the cost of brute-force characterization is demonstrated.

This work was featured on the front cover of the journal, available here: http://onlinelibrary.wiley.com/doi/10.1002/cphc.201290074/abstract

### David H. Bailey, Jonathan M. Borwein and Richard E. Crandall, "Computation and theory of extended Mordell-Tornheim-Witten sums", Mathematics of Computation, July 31, 2012, to appea,

### Rui Sun, Kyoyeon Park, Wibe A. de Jong, Hans Lischka, Theresa L. Windus, William L. Hase, "Direct dynamics simulation of dioxetane formation and decomposition via the singlet center dot O-O-CH2-CH2 center dot biradical: Non-RRKM dynamics", Journal of Chemical Physics, 2012, 137, doi: 10.1063/1.4736843

### David H. Bailey and Jonathan M. Borwein, "Nonnormality of Stoneham constants", Ramanujan Journal, July 24, 2012, 29:409-422,

### Jihan Kim, Li-Chiang Lin, Richard L. Martin, Joseph A. Swisher, Maciej Haranczyk & Berend Smit, "Large-Scale Computational Screening of Zeolites for Ethane/Ethene Separation", Langmuir, July 11, 2012, 28:11914–1191,

Large-scale computational screening of thirty thousand zeolite structures was conducted to find optimal structures for separation of ethane/ethene mixtures. Efficient grand canonical Monte Carlo (GCMC) simulations were performed with graphics processing units (GPUs) to obtain pure component adsorption isotherms for both ethane and ethene. We have utilized the ideal adsorbed solution theory (IAST) to obtain the mixture isotherms, which were used to evaluate the performance of each zeolite structure based on its working capacity and selectivity. In our analysis, we have determined that specific arrangements of zeolite framework atoms create sites for the preferential adsorption of ethane over ethene. The majority of optimum separation materials can be identified by utilizing this knowledge and screening structures for the presence of this feature will enable the efficient selection of promising candidate materials for ethane/ethene separation prior to performing molecular simulations.

### Kelly P. Gaither, Hank Childs, Karl Schulz, Cyrus Harrison, Bill Barth, Diego Donzis, P.K. Yeung, "Using Visualization and Data Analysis to Understand Critical Structures in Massive Time Varying Turbulent Flow Simulations", IEEE Computer Graphics and Applications, July 2012, 32:34-45, LBNL 5911E,

### G. H. Miller and D. Trebotich, "An Embedded Boundary Method for the Navier-Stokes Equations on a Time-Dependent Domain", Communications in Applied Mathematics and Computational Science, 7(1):1-31, 2012,

- Download File: camcos-v7-n1-p01-p.pdf (pdf: 1.2 MB)

### Patrick R. Amestoy, Iain S. Duff, Jean-Yves L Excellent, Yves Robert, François-Henry Rouet, Bora Uçar, "On computing inverse entries of a sparse matrix in an out-of-core environment", SIAM Journal on Scientific Computing, July 2012, 34:1975--1999, doi: 10.1137/100799411

### J. K. Freericks, A. Y. Liu, A. F. Kemper, T. P. Devereaux, "Pulsed high harmonic generation of light due to pumped Bloch oscillations in noninteracting metals", Physica Scripta, 2012, T151:014062, doi: 10.1088/0031-8949/2012/T151/014062

We derive a simple theory for high-order harmonic generation due to pumping a noninteracting metal with a large amplitude oscillating electric field. The model assumes that the radiated light field arises from the acceleration of electrons due to the time-varying current generated by the pump, and also assumes that the system has a constant density of photoexcited carriers, hence it ignores the dipole excitation between bands (which would create carriers in semiconductors). We examine the circumstances under which odd harmonic frequencies would be expected to dominate the spectrum of radiated light, and we also apply the model to real materials like ZnO, for which high-order harmonic generation has already been demonstrated in experiments.

### Santer, B.D., J. Painter, C. Mears, C. Doutriaux, P. Caldwell, J.M. Arblaster, P. Cameron-Smith, N.P. Gillett, P.J. Gleckler, J.R. Lanzante, J. Perlwitz, S. Solomon, P.A. Stott, K.E. Taylor, L. Terray, P.W. Thorne, M.F. Wehner, F.J. Wentz, T.M.L. Wigley, L. Wilcox and C.-Z. Zou, "Identifying Human Influences on Atmospheric Temperature: Are Results Robust to Uncertainties?", Proceedings of the National Academy of Sciences, June 22, 2012,

### S Hofmeyr, J Colmenares, J Kubiatowicz, C Iancu, "Juggle: Addressing Extrinsic Load Imbalances in SPMD Applications on Multicore Computer", Cluster Computing, 2012,

### L. Lin, L. Ying, "Element orbitals for Kohn-Sham density functional theory", Phys. Rev. B, 2012, 85:235144,

### A. Buluç, J. Gilbert, "Parallel sparse matrix-matrix multiplication and indexing: Implementation and experiments", SIAM Journal on Scientific Computing (SISC), 2012,

- Download File: spgemmsisc12.pdf (pdf: 1.2 MB)

### J. Nordhaus, T.D. Brandt, A. Burrows, A. Almgren, "The Hydrodynamic Origin of Neutron Star Kicks", Monthly Notices of the Royal Astronomical Society, 2012, 423:2,

### Jessica B. Voytek, Bradley Voytek, "Automated cognome construction and semi-automated hypothesis generation", Journal of Neuroscience Methods, June 2012, 208:92–100,

### Li-Chiang Lin, Adam H. Berger, Richard L. Martin, Jihan Kim, Joseph A. Swisher, Kuldeep Jariwala, Chris H. Rycroft, Abhoyjit S. Bhown, Michael W. Deem, Maciej Haranczyk & Berend Smit, "In Silico Screening of Carbon Capture Materials", Nature Materials, May 27, 2012, 11:633–641,

One of the main bottlenecks to deploying large-scale carbon dioxide capture and storage (CCS) in power plants is the energy required to separate the CO_{2} from flue gas. For example, near-term CCS technology applied to coal-fired power plants is projected to reduce the net output of the plant by some 30% and to increase the cost of electricity by 60–80%. Developing capture materials and processes that reduce the parasitic energy imposed by CCS is therefore an important area of research. We have developed a computational approach to rank adsorbents for their performance in CCS. Using this analysis, we have screened hundreds of thousands of zeolite and zeolitic imidazolate framework structures and identified many different structures that have the potential to reduce the parasitic energy of CCS by 30–40% compared with near-term technologies.

### Yili Zheng, Qiu Wang, Peter C. Doerschuk, "Three-dimensional reconstruction of the statistics of heterogeneous objects from a collection of one projection image of each object", J. Opt. Soc. Am. A, 2012, 29:959-970,

### W.S. Lee, Y.D. Chuang, R.G. Moore, Y. Zhu, L. Patthey, M. Trigo, D.H. Lu, P.S. Kirchmann, O. Krupin, M. Yi, M. Langner, N. Huse, J.S. Robinson, Y. Chen, S.Y. Zhou, G. Coslovich, B. Huber, D.A. Reis, R.A. Kaindl, R.W. Schoenlein, D. Doering, P. Denes, W.F. Schlotter, J.J. Turner, S.L. Johnson, M. Först, T. Sasagawa, Y.F. Kung, A.P. Sorini, A.F. Kemper, B. Moritz, T.P. Devereaux, D.-H. Lee, Z.X. Shen & Z. Hussain, "Phase fluctuations and the absence of topological defects in a photo-excited charge-ordered nickelate", Nature Communications 3, Article number: 838, May 15, 2012,

The dynamics of an order parameter's amplitude and phase determines the collective behaviour of novel states emerging in complex materials. Time- and momentum-resolved pump-probe spectroscopy, by virtue of measuring material properties at atomic and electronic time scales out of equilibrium, can decouple entangled degrees of freedom by visualizing their corresponding dynamics in the time domain. Here we combine time-resolved femotosecond optical and resonant X-ray diffraction measurements on charge ordered La1.75Sr0.25NiO4 to reveal unforeseen photoinduced phase fluctuations of the charge order parameter. Such fluctuations preserve long-range order without creating topological defects, distinct from thermal phase fluctuations near the critical temperature in equilibrium. Importantly, relaxation of the phase fluctuations is found to be an order of magnitude slower than that of the order parameter's amplitude fluctuations, and thus limits charge order recovery. This new aspect of phase fluctuations provides a more holistic view of the phase's importance in ordering phenomena of quantum matter.

### Didem Unat, Jun Zhou, Yifeng Cui, Scott B. Baden, Xing Cai, "Accelerating a 3D Finite Difference Earthquake Simulation with a C-to-CUDA Translator", Computing in Science and Engineering, May 2012, Vol 14:48-59,

### Sean Whalen, Sophie Engle, Sean Peisert, Matt Bishop, "Network-Theoretic Classification of Parallel Computation Patterns", International Journal of High Performance Computing Applications (IJHPCA), May 2012, 26(2):159-169, doi: 10.1177/1094342012436618

### Ariful Azad, Saumyadipta Pyne, Alex Pothen, "Matching phosphorylation response patterns of antigen-receptor-stimulated T cells via flow cytometry", BMC Bioinformatics, 2012,

### Fuyu Li, Daniele Rosa, William D. Collins, and Michael F. Wehner, "“Super-parameterization”: A better way to simulate regional extreme precipitation?", Journal of Advances in Modeling Earth Systems, April 4, 2012, 4, doi: 10.1029/2011MS000106

Extreme precipitation is generally underestimated by current climate models relative to observations of present-day rainfall distributions. Possible causes of this systematic error include the convective parameterization in these models that have been designed to reproduce measurements of climatological mean precipitation. One possible approach to improve the interaction of subgrid-scale physical processes and large-scale climate is to replace the conventional convective parameterizations with a high-resolution cloud-system resolving model. A “super-parameterized” Community Atmosphere Model (SP-CAM) utilizing this approach is used in this study to investigate the distribution of extreme precipitation in the United States. Results show that SP-CAM better simulates the distributions of both light and intense precipitation compared to the standard version of CAM based upon conventional parameterizations. The improvements are mostly seen in regions dominated by convective precipitation, suggesting that super-parameterization provides a better representation of subgrid convective processes.

### H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, "Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques", Parallel Computing, 38 (4-5), 245-259, April 2, 2012, doi: 10.1016/j.parco.2011.08.005

### S. Molins, D. Trebotich, C. I. Steefel and C. Shen, "An Investigation of the Effect of Pore Scale Flow on Average Geochemical Reaction Rates Using Direct Numerical Simulation", Water Resour. Res., 48(3) W03527, DOI:10.1029/2011WR011404, 2012,

- Download File: wrcr13375.pdf (pdf: 1.4 MB)

### Erjun Kan, Wei Hu, Chuanyun Xiao, Ruifeng Lu, Kaiming Deng, Jinlong Yang and Haibin Su, "Half-Metallicity in Organic Single Porous Sheets", J. Am. Chem. Soc., 2012, 134 (13), 5718–5721, March 22, 2012, doi: 10.1021/ja210822c

- Download File: JACS.pdf (pdf: 512 KB)

The unprecedented applications of two-dimensional (2D) atomic sheets in spintronics are formidably hindered by the lack of ordered spin structures. Here we present first-principles calculations demonstrating that the recently synthesized dimethylmethylene-bridged triphenylamine (DTPA) porous sheet is a ferromagnetic half-metal and that the size of the band gap in the semiconducting channel is roughly 1 eV, which makes the DTPA sheet an ideal candidate for a spin-selective conductor. In addition, the robust half-metallicity of the 2D DTPA sheet under external strain increases the possibility of applications in nanoelectric devices. In view of the most recent experimental progress on controlled synthesis, organic porous sheets pave a practical way to achieve new spintronics.

### Jihan Kim, Richard L. Martin, Oliver Rübel, Maciej Haranczyk & Berend Smit, "High-throughput Characterization of Porous Materials Using Graphics Processing Units", Journal of Chemical Theory and Computation, March 16, 2012, 8:1684–1693, LBNL 5409E, doi: 10.1021/ct200787v

We have developed a high-throughput graphics processing unit (GPU) code that can characterize a large database of crystalline porous materials. In our algorithm, the GPU is utilized to accelerate energy grid calculations, where the grid values represent interactions (i.e., Lennard-Jones + Coulomb potentials) between gas molecules (i.e., CH_{4} and CO_{2}) and materials’ framework atoms. Using a parallel flood fill central processing unit (CPU) algorithm, inaccessible regions inside the framework structures are identified and blocked, based on their energy profiles. Finally, we compute the Henry coefficients and heats of adsorption through statistical Widom insertion Monte Carlo moves in the domain restricted to the accessible space. The code offers significant speedup over a single core CPU code and allows us to characterize a set of porous materials at least an order of magnitude larger than those considered in earlier studies. For structures selected from such a prescreening algorithm, full adsorption isotherms can be calculated by conducting multiple Grand Canonical Monte Carlo (GCMC) simulations concurrently within the GPU.

### L. Lin, J. Lu, L. Ying and W. E, "Optimized local basis set for Kohn-Sham density functional theory", J. Comput. Phys., 2012, 231:4515,

### Xiaodan Gu, Zuwei Liu, Ilja Gunkel, Slim Chourou, Sung Woo Hong, Deirdre Olynick, Thomas P. Russell, "High Aspect Ratio Sub-15nm Silicon Trenches From Block Copolymer Templates", Advanced Materials, 2012, 24:5688,

High-aspect-ratio sub-15-nm silicon trenches are fabricated directly from plasma etching of a block copolymer mask. A novel method that combines a block copolymer reconstruction process and reactive ion etching is used to make the polymer mask. Silicon trenches are characterized by various methods and used as a master for subsequent imprinting of different materials. Silicon nanoholes are generated from a block copolymer with cylindrical microdomains oriented normal to the surface.

### Raymond Atta-Fynn, Donald F. Johnson, Eric J. Bylaska, Eugene S. Ilton, Gregory K. Schenter, Wibe A. de Jong, "Structure and Hydrolysis of the U(IV), U(V), and U(VI) Aqua Ions from Ab Initio Molecular Simulations", Inorganic chemistry, 2012, 51:3016-24,

### Richard L. Martin, Prabhat, David D. Donofrio, James A. Sethian & Maciej Haranczyk, "Accelerating Analysis of void spaces in porous materials on multicore and GPU platforms", International Journal of High Performance Computing Applications, February 5, 2012, 26:347-357,

Developing computational tools that enable discovery of new materials for energy-related applications is a challenge. Crystalline porous materials are a promising class of materials that can be used for oil refinement, hydrogen or methane storage as well as carbon dioxide capture. Selecting optimal materials for these important applications requires analysis and screening of millions of potential candidates. Recently, we proposed an automatic approach based on the Fast Marching Method (FMM) for performing analysis of void space inside materials, a critical step preceding expensive molecular dynamics simulations. This breakthrough enables unsupervised, high-throughput characterization of large material databases. The algorithm has three steps: (1) calculation of the cost-grid which represents the structure and encodes the occupiable positions within the void space; (2) using FMM to segment out patches of the void space in the grid of (1), and find how they are connected to form either periodic channels or inaccessible pockets; and (3) generating blocking spheres that encapsulate the discovered inaccessible pockets and are used in proceeding molecular simulations. In this work, we expand upon our original approach through (A) replacement of the FMM-based approach with a more computationally efficient flood fill algorithm; and (B) parallelization of all steps in the algorithm, including a GPU implementation of the most computationally expensive step, the cost-grid generation. We report the acceleration achievable in each step and in the complete application, and discuss the implications for high-throughput material screening.

### P. Ghysels, P. Kłosiewicz, W. Vanroose, "Improving the arithmetic intensity of multigrid with the help of polynomial smoothers", Numerical Linear Algebra with Applications, February 1, 2012, 19:2, doi: 10.1002/nla.1808

### D. Y. Parkinson, C. Yang, C. Knoechel, C. A. Larabell, M. Le Gros, "Automatic alignment and reconstruction of images for soft X-ray tomography", J Struct Biol, February 2012, 177:259--266, doi: 10.1016/j.jsb.2011.11.027

### Nils E. R. Zimmermann, Sayee P. Balaji, Frerich J. Keil, "Surface Barriers of Hydrocarbon Transport Triggered by Ideal Zeolite Structures", J. Phys. Chem. C, 2012, 116:3677-3683, doi: 10.1021/jp2112389

Shedding light on the nature of surface barriers of nanoporous materials, molecular simulations (Monte Carlo, Reactive Flux) have been employed to investigate the tracer-exchange characteristics of hydrocarbons in defect-free single-crystal zeolite membranes. The concept of a critical membrane thickness as a quantitative measure of surface barriers is shown to be appropriate and advantageous. Nanopore smoothness, framework density, and thermodynamic state of the fluid phase have been identified as the most important influencing variables of surface barriers. Despite the ideal character of the adsorbent, our simulation results clearly support current experimental findings on MOF Zn(tbip) where a larger number of crystal defects caused exceptionally strong surface barriers. Most significantly, our study predicts that the ideal crystal structure without any such defects will already be a critical aspect of experimental analysis and process design in many cases of the upcoming class of extremely thin and highly oriented nanoporous membranes.

Watch here a movie that highlights how n-hexane molecules are adsorbed in a zeolite slab.

### H. M. Aktulga, S. A. Pandit, A. C. T. van Duin, A. Y. Grama, "Reactive Molecular Dynamics: Numerical Methods and Algorithmic Tehniques", SIAM J. Sci. Comput., 34(1), C1–C23, January 31, 2012, doi: 10.1137/100808599

### P.S. Li, D.F. Martin, R.I. Klein, and C.F. McKee, "A Stable, Accurate Methodology for High Mach Number, Strong Magnetic Field MHD Turbulence with Adaptive Mesh Refinement: Resolution and Refinement Studies", The Astrophysical Journal Supplement Series, 2012,

- Download File: LiMartinKleinMcKee.pdf (pdf: 1.5 MB)

### Planck Collaboration, "Planck Intermediate Results. IX. Detection of the Galactic haze with Planck", ArXiv e-prints, January 2012,

### L. Lin, J. Lu, L. Ying and W. E, "Adaptive local basis set for Kohn-Sham density functional theory in a discontinuous Galerkin framework I: Total energy calculation", J. Comput. Phys., 2012, 231:2140,

### Planck Collaboration, "Planck intermediate results. VIII. Filaments between interacting clusters", ArXiv e-prints, January 2012,

### D. Flammini, A. Pietropaolo, R. Senesi, C. Andreani, F. McBride, A. Hodgson, M. Adams, L. Lin, and R. Car,, "Spherical momentum distribution of the protons in hexagonal ice from modeling of inelastic neutron scattering data", J. Chem. Phys., 2012, 136:024504,

### Planck Collaboration, "Planck intermediate results. VII. Statistical properties of infrared and radio extragalactic sources from the Planck Early Release Compact Source Catalogue at frequencies between 100 and 857 GHz", ArXiv e-prints, January 2012,

### Planck Collaboration, "Planck intermediate results. VI: The dynamical structure of PLCKG214.6+37.0, a Planck discovered triple system of galaxy clusters", ArXiv e-prints, January 2012,

### Planck Collaboration, "Planck Intermediate Results. V. Pressure profiles of galaxy clusters from the Sunyaev-Zeldovich effect", ArXiv e-prints, January 2012,

### Planck Collaboration, "Planck Intermediate Results. IV. The XMM-Newton validation programme for new Planck clusters", ArXiv e-prints, January 2012,

### Planck Collaboration, "Planck intermediate results. III. The relation between galaxy cluster mass and Sunyaev-Zeldovich signal", ArXiv e-prints, January 2012,

### V. V. Kharin, F. W. Zwiers, X. Zhang, M. Wehner, "Changes in temperature and precipitation extremes in the CMIP5 ensemble", Climatic Change, 2012,

### Planck & AMI Collaborations, "Planck Intermediate Results II: Comparison of Sunyaev-Zeldovich measurements from Planck and from the Arcminute Microkelvin Imager for 11 galaxy clusters", ArXiv e-prints, January 2012,

### G. S. H. Pau, J. B. Bell, A. S. Almgren, K. M. Fagnan and M. J. Lijewski, "An Adaptive Mesh Refinement Algorithm for Compressible Two-Phase Flow In Porous Media", Computational Geosciences, 2012, 16:577-592,

### T.C. Peterson, R. Heim, R. Hirsch, D. Kaiser, H. Brooks, N.S. Diffenbaugh, R. Dole, J. Giovannettone, K. Guiguis, T.R. Karl, R.W. Katz, K. Kunkel, D. Lettenmaier, G. J. McCabe, C.J. Paciorek, K.Ryberg, S.Schubert, V.B.S. Silva, B. Stewart, A.V. Vecchia, G. Villarini, R.S. Vose, J. Walsh, M.Wehner, D. Wolock, K. Wolter, C.A. Woodhouse and D. Wuebbles, "Monitoring and Understanding Changes in Heatwaves, Coldwaves, Floods and Droughts in the United States: State of Knowledge", Bulletin of the American Meteorological Society (accepted), 2012,

### Y. Cao, M. M. Kasliwal, J. D. Neill, S. R. Kulkarni, Y.-Q., S. Ben-Ami, J. S. Bloom, S. B. Cenko, N. M., P. E. Nugent, E. O. Ofek, D. Poznanski, R. M. Quimby, "Classical Novae in Andromeda: Light Curves from the Palomar Transient Factory and GALEX", Astrophysical Journal, 2012, 752:133, doi: 10.1088/0004-637X/752/2/133

### Maria Garzon, L. J. Gray, James A. Sethian, "Droplet and bubble pinch-off computations using level sets", Journal of Computational and Applied Mathematics, 2012, 236:3034--3041, doi: 10.1016/j.cam.2011.03.032

### M. Day, S. Tachibana, J. Bell, M. Lijewski, V. Beckner and R. Cheng, "A Combined Computational and Experimental Characterization of Lean Premixed Turbulent Low Swirl Laboratory Flames. I. Methane Flames", Combustion and Flame, 159(1) 275-290, 2012,

- Download File: LMCCH4LSBpaperSUBMIT382011.pdf (pdf: 5.9 MB)

### K. Balakrishnan, A. L. Kuhl, J. B. Bell and V. E. Beckner, "An Empirical Model for the Ignition of Explosively Dispersed Aluminum Particle Clouds", Shock Waves, 2012, 22:591,

### Planck Collaboration, "Planck Intermediate Results. I. Further validation of new Planck clusters with XMM-Newton", ArXiv e-prints, January 2012, 543:A102, doi: 10.1051/0004-6361/201118731

### D. Polishook, E. O. Ofek, A. Waszczak, S. R. Kulkarni, A., O. Aharonson, R. Laher, J. Surace, C., J. Bloom, N. Brosch, D. Prialnik, C., S. B. Cenko, M. Kasliwal, N. Law, D., P. Nugent, D. Poznanski, R. Quimby, "Asteroid rotation periods from the Palomar Transient Factory survey", Monthly Notices of the Royal Astronomical Society, 2012, 421:2094-2108, doi: 10.1111/j.1365-2966.2012.20462.x

### Sanjay Govindjee, Per-Olof Persson, "A time-domain Discontinuous Galerkin method for mechanical resonator quality factor computations", Journal of Computational Physics, 2012, 231:6380--6392, doi: 10.1016/j.jcp.2012.05.034

### Kiran Bhaskaran-Nair, Jiri Brabec, Edoardo Apra, Hubertus J. J. van Dam, Jiri Pittner, Karol Kowalski, "Implementation of the multireference Brillouin-Wigner and Mukherjee s coupled cluster methods with non-iterative triple excitations utilizing reference-level parallelism", Journal of Chemical Physics, 2012, 137, doi: 10.1063/1.4747698

### A. Napov and Y. Notay, "An Algebraic Multigrid Method with Guaranteed Convergence Rate", SIAM J. Sci. Comput., vol.43, pp. A1079-A1109, 2012,

- Download File: SISC12-amg.pdf (pdf: 2.4 MB)

### David H. Bailey and Jonathan M. Borwein, "Hand-to-hand combat with thousand-digit integrals", Journal of Computational Science, 2012, 3:77-86,

### Fuyu Li, William D. Collins, Michael F. Wehner, Ruby L. Leung, "Hurricanes in an Aquaplanet World: Implications of the Impacts of External Forcing and Model Horizontal Resolution", Journal of Advances in Modeling Earth Systems, 2012,

### X. Wang, L. Wang, A. V. Filippenko, E. Baron, M., D. Jack, T. Zhang, G. Aldering, P., W. D. Arnett, D. Baade, B. J. Barris, S., P. Bouchet, A. S. Burrows, R. Canal, E., R. G. Carlberg, E. di Carlo, P. J., A. P. S. Crotts, J. I. Danziger, M. Valle, M. Fink, R. J. Foley, C. Fransson, A., P. M. Garnavich, C. L. Gerardy, G., M. Hamuy, W. Hillebrandt, P. H\ oflich, S. T., D. E. Holz, J. P. Hughes, D. J. Jeffery, S. W., D. Kasen, A. M. Khokhlov, R. P. Kirshner, R. A., C. Kozma, K. Krisciunas, B. C. Lee, B., E. J. Lentz, D. C. Leonard, W. H. G., W. Li, M. Livio, P. Lundqvist, D., T. Matheson, P. A. Mazzali, P. Meikle, G., P. A. Milne, S. W. Mochnacki, K., P. E. Nugent, E. S. Oran, N. Panagia, S., M. M. Phillips, P. Pinto, D. Poznanski, C. J., M. Reinecke, A. G. Riess, P., R. A. Scalzo, E. M. Schlegel, B. P., J. Siegrist, A. M. Soderberg, J., G. Sonneborn, A. Spadafora, J., R. A. Sramek, S. G. Starrfield, L. G., N. B. Suntzeff, R. C. Thomas, J. L., A. Tornambe, J. W. Truran, M. Turatto, M., S. D. Van Dyk, K. W. Weiler, J. C. Wheeler, M. Wood-Vasey, S. E. Woosley, H. Yamaoka, "Evidence for Type Ia Supernova Diversity from Ultraviolet Observations with the Hubble Space Telescope", Astrophysical Journal, 2012, 749:126, doi: 10.1088/0004-637X/749/2/126

### M. Morzfeld, A. J. Chorin, "Implicit particle filtering for models with partial noise, and an application to geomagnetic data assimilation", Nonlinear Processes in Geophysics, 2012, 19:365--382, doi: 10.5194/npg-19-365-2012

### Jiri Brabec, Kiran Bhaskaran-Nair, Niranjan Govind, Jiri Pittner, Karol Kowalski, "Communication: Application of state-specific multireference coupled cluster methods to core-level excitations", Journal of Chemical Physics, 2012, 137, doi: 10.1063/1.4764355

### John C. H. Chiang, C. Y. Chang and M.F. Wehner, "Long-term trends of the Atlantic Interhemispheric SST Gradient in the CMIP5 Historical Simulations", J. Climate, 2012,

### S. B. Cenko, J. S. Bloom, S. R. Kulkarni, L. E., A. A. Miller, N. R. Butler, R. M., A. Gal-Yam, E. O. Ofek, E. Quataert, L., D. Poznanski, D. A. Perley, A. N. Morgan, A. V., D. A. Frail, I. Arcavi, S., A. Cucchiara, C. D. Fassnacht, Y., I. M. Hook, D. A. Howell, D. J. Lagattuta, N. M., M. M. Kasliwal, P. E. Nugent, J. M. Silverman, M. Sullivan, S. P. Tendulkar, O. Yaron, "PTF10iya: a short-lived, luminous flare from the nuclear region of a star-forming galaxy", Monthly Notices of the Royal Astronomical Society, 2012, 420:2684-2699, doi: 10.1111/j.1365-2966.2011.20240.x

### Jiri Brabec, Kiran Bhaskaran-Nair, Karol Kowalski, Jiri Pittner, Hubertus J. J. van Dam, "Towards large-scale calculations with State-Specific Multireference Coupled Cluster methods: Studies on dodecane, naphthynes, and polycarbenes", Chemical Physics Letters, 2012, 542:128-133, doi: 10.1016/j.cplett.2012.05.064

### David H. Bailey, Marcos M. Lopez de Prado, "The Sharpe ratio efficient frontier", Journal of Risk, January 1, 2012, 15:3-44,

### R. L. Barone-Nugent, "Near-infrared observations of Type Ia supernovae: the best known candle for cosmology", Monthly Notices of the Royal Astronomical Society, 2012, 1007, doi: 10.1111/j.1365-2966.2012.21412.x

### A. Corsi, E. O. Ofek, A. Gal-Yam, D. A. Frail, D., P. A. Mazzali, S. R. Kulkarni, M. M., I. Arcavi, S. Ben-Ami, S. B. Cenko, A. V., D. B. Fox, A. Horesh, J. L. Howell, I. K. W., E. Nakar, I. Rabinak, R. Sari, J. M., D. Xu, J. S. Bloom, N. M. Law, P. E. Nugent, R. M. Quimby, "Evidence for a Compact Wolf-Rayet Progenitor for the Type Ic Supernova PTF 10vgv", Astrophysical Journal, 2012, 747:L5, doi: 10.1088/2041-8205/747/1/L5

### P.-O. Persson, D.J. Willis, J. Peraire, "Numerical simulation of flapping wings using a panel method and a high-order Navier–Stokes solver", International Journal for Numerical Methods in Engineering, 2012, 89:1296--1316, doi: 10.1002/nme.3288

### Jiri Brabec, Jiri Pittner, Hubertus J. J. van Dam, Edoardo Apra, Karol Kowalski, "Parallel Implementation of Multireference Coupled-Cluster Theories Based on the Reference-Level Parallelism", Journal of Chemical Theory and Computation, 2012, 8:487-497, doi: 10.1021/ct200809m

### Mark Howison, E. Wes Bethel, Hank Childs, "Hybrid Parallelism for Volume Rendering on Large, Multi- and Many-core Systems", IEEE Transactions on Visualization and Computer Graphics, January 2012, 18:17-29, LBNL 4370E,

### U. Shumlak, J. Chadney, R.P. Golingo, D.J. Den Hartog, M.C. Hughes, S.D. Knecht, W. Lowrie, V.S. Lukin, B.A. Nelson, R.J. Oberto, J.L. Rohrbach, M.P. Ross, G.V. Vogman, "The Sheared-Flow Stabilized Z-Pinch", Fusion Science and Technology, 61 (1t), 119, 2012,

### E. O. Ofek, R. Laher, J. Surace, D. Levitan, B., A. Horesh, N. Law, J. C. van Eyken, S. R., T. A. Prince, P. Nugent, M. Sullivan, O., A. Pickles, M. Ag\ ueros, I. Arcavi, L., J. Bloom, S. B. Cenko, A. Gal-Yam, C., G. Helou, M. M. Kasliwal, D. Poznanski, R. Quimby, "The Palomar Transient Factory photometric catalog 1.0", Publications of the Astronomical Society of the Pacific, 2012, 124:854-860, doi: 10.1086/666978

### A. Horesh, S. R. Kulkarni, D. B. Fox, J. Carpenter, M. M., E. O. Ofek, R. Quimby, A. Gal-Yam, S. B., A. G. de Bruyn, A. Kamble, R. A. M. J. Wijers, A. J. der Horst, C. Kouveliotou, P. Podsiadlowski, M., K. Maguire, D. A. Howell, P. E. Nugent, N., N. M. Law, D. Poznanski, M. Shara, "Early Radio and X-Ray Observations of the Youngest nearby Type Ia Supernova PTF 11kly (SN 2011fe)", Astrophysical Journal, 2012, 746:21, doi: 10.1088/0004-637X/746/1/21

### Chris H. Rycroft, Frédéric Gibou, "Simulations of a stretching bar using a plasticity model from the shear transformation zone theory", Journal of Computational Physics, 2012, 231:2155--2179, doi: 10.1016/j.jcp.2011.10.009

### Jiri Brabec, Hubertus J. J. van Dam, Jiri Pittner, Karol Kowalski, "Universal state-selective corrections to multi-reference coupled-cluster theories with single and double excitations", Journal of Chemical Physics, 2012, 136, doi: 10.1063/1.3692969

### David H. Bailey, Roberto Barrio, Jonathan M. Borwein, "High precision computation: Mathematical physics and dynamics", Applied Mathematics and Computation, 2012, 218:10106-1012,

### N. Smith, S. B. Cenko, N. Butler, J. S. Bloom, M. M., A. Horesh, S. R. Kulkarni, N. M., P. E. Nugent, E. O. Ofek, D. Poznanski, R. M., B. Sesar, S. Ben-Ami, I. Arcavi, A., D. Polishook, D. Xu, O. Yaron, D. A. Frail, M. Sullivan, "SN 2010jp (PTF10aaxi): a jet in a Type II supernova", Monthly Notices of the Royal Astronomical Society, 2012, 420:1135-1144, doi: 10.1111/j.1365-2966.2011.20104.x

### E. O. Ofek, R. Laher, N. Law, J. Surace, D., B. Sesar, A. Horesh, D. Poznanski, J. C. Eyken, S. R. Kulkarni, P. Nugent, J., R. Walters, M. Sullivan, M. Ag\ ueros, L., J. Bloom, S. B. Cenko, A. Gal-Yam, C., G. Helou, M. M. Kasliwal, R. Quimby, "The Palomar Transient Factory Photometric Calibration", Publications of the Astronomical Society of the Pacific, 2012, 124:62-73, doi: 10.1086/664065

### Alexandre J. Chorin, Xuemin Tu, "An iterative implementation of the implicit nonlinear filter", ESAIM: Mathematical Modelling and Numerical Analysis, 2012, 46:535--543,

Implicit sampling is a sampling scheme for particle filters, designed to move particles one-by-one so that they remain in high-probability domains. We present a new derivation of implicit sampling, as well as a new iteration method for solving the resulting algebraic equations.

### R. I. Saye, J. A. Sethian, "Analysis and applications of the Voronoi Implicit Interface Method", Journal of Computational Physics, 2012, 231:6051 - 608, doi: 10.1016/j.jcp.2012.04.004

### D. J. Rowlands, D. J. Frame, D. Ackerley, T. Aina, B. B. B. Booth, C. Christensen, M. Collins, N. Faull, C. E. Forest, B. S. Grandey, E. E. Gryspeerdt, E. J. Highwood, W. J. Ingram, S. Knight, A. Lopez, N. Massey, N. Meinshausen, C. Piani, S. M. Rosier, B. M. Sanderson, L. A. Smith, D. A. Stone, M. Thurston, K. Yamazaki, Y. H. Yamazaki, M. R. Allen, "Broad range of 2050 warming from an observationally constrained large climate model ensemble", Nature Geoscience, 2012, 5:256--260,

### David H. Bailey, Jonathan M. Borwein, "Exploration, Experimentation and Computation", International Advances in Mathematics, 2012, 31:1-14,

### T.C. Peterson, R. Heim, R. Hirsch, D. Kaiser, H. Brooks, N.S. Diffenbaugh, R. Dole, J. Giovannettone, K. Guiguis, T.R. Karl, R.W. Katz, K. Kunkel, D. Lettenmaier, G. J. McCabe, C.J. Paciorek, K.Ryberg, S.Schubert, V.B.S. Silva, B. Stewart, A.V. Vecchia, G. Villarini, R.S. Vose, J. Walsh, M.Wehner, D. Wolock, K. Wolter, C.A. Woodhouse and D. Wuebbles, "Monitoring and Understanding Trends in Extreme Storms: State of Knowledge", Bulletin of the American Meteorological Society, 2012, doi: 10.1175/BAMS-D-11-00262.1

The state of knowledge regarding trends and an understanding of their causes is presented for a specific subset of extreme weather and climate types. For severe convective storms (tornadoes, hail storms, and severe thunderstorms), differences in time and space of practices of collecting reports of events make the use of the reporting database to detect trends extremely difficult. Overall, changes in the frequency of environments favorable for severe thunderstorms have not been statistically significant. For extreme precipitation, there is strong evidence for a nationally-averaged upward trend in the frequency and intensity of events. The causes of the observed trends have not been determined with certainty, although there is evidence that increasing atmospheric water vapor may be one factor. For hurricanes and typhoons, robust detection of trends in Atlantic and western North Pacific tropical cyclone (TC) activity is significantly constrained by data heterogeneity and deficient quantification of internal variability. Attribution of past TC changes is further challenged by a lack of consensus on the physical linkages between climate forcing and TC activity. As a result, attribution of trends to anthropogenic forcing remains controversial. For severe snowstorms and ice storms, the number of severe regional snowstorms that occurred since 1960 was more than twice that of the preceding 60 years. There are no significant multi-decadal trends in the areal percentage of the contiguous U.S. impacted by extreme seasonal snowfall amounts since 1900. There is no distinguishable trend in the frequency of ice storms for the U.S. as a whole since 1950.

### J. S. Bloom, D. Kasen, K. J. Shen, P. E. Nugent, N. R., M. L. Graham, D. A. Howell, U., S. Holmes, C. A. Haswell, V. Burwitz, J. Rodriguez, M. Sullivan, "A Compact Degenerate Primary-star Progenitor of SN 2011fe", Astrophysical Journal, 2012, 744:L17, doi: 10.1088/2041-8205/744/2/L17

### Trevor Potter, "Effective Dynamics for N-Solitons of the Gross–Pitaevskii Equation", Journal of Nonlinear Science, 2012, 22:351-370, doi: 10.1007/s00332-011-9120-3

### Robert I. Saye, James A. Sethian, "The Voronoi Implicit Interface Method and Computational Challenges in Multiphase Physics", Milan Journal of Mathematics, 2012, 80:369--379, doi: 10.1007/s00032-012-0187-6

### H. Shiogama, D. A. Stone, T. Nagashima, T. Nozawa, S. Emori, "On the linear additivity of climate forcing-response relationships at global and continental scales", International Journal of Climatology, 2012, 33:2542--2550,

### Ilia Lebedev, Christopher Fletcher, Shaoyi Cheng, James Martin, Austin Doupnik, Daniel Burke, Mingjie Lin, John Wawrzynek, "Exploring Many-Core Design Templates for FPGAs and ASICs", International Journal of Reconfigurable Computing, 2012, 2012, doi: 10.1155/2012/439141

### R. Speck, D. Ruprecht, R. Krause, M. Emmett, M. Minion, M. Winkel, P. Gibbon, "A massively space-time parallel N-body solver", Proceedings of the International Conference on High Performance Computing, SC'12, 2012, 92:1-11,

### Matthew R. Siebert, Adelia J. A. Aquino, Wibe A. de Jong, Giovanni Granucci, William L. Hase, "Potential energy surface for C2H4I2+center dot dissociation including spin-orbit effects", Molecular Physics, 2012, 110:2599-2609, doi: 10.1080/00268976.2012.725137

### A. Nonaka, J. B. Bell, M. S. Day, C. Gilet, A. S. Almgren, and M. L. Minion, "A Deferred Correction Coupling Strategy for Low Mach Number Flow with Complex Chemistry", Combustion Theory and Modelling, 2012, 16(6):1053-1088,

- Download File: LMCSDC.pdf (pdf: 601 KB)

### David H. Bailey and Marcos M. Lopez de Prado, "Balanced baskets: A new approach to trading and hedging risks", Journal of Investment Strategies, January 1, 2012, 14,

### S. Ben-Ami, A. Gal-Yam, A. V. Filippenko, P. A., M. Modjaz, O. Yaron, I. Arcavi, S. B., A. Horesh, D. A. Howell, M. L. Graham, J. C., M. Im, Y. Jeon, S. R. Kulkarni, D. C., D. Perley, E. Pian, D. J. Sand, M., J. C. Becker, D. Bersier, J. S. Bloom, M., P. J. Brown, K. I. Clubb, B. Dilday, R. C., A. L. Fortinsky, D. B. Fox, L. A. Gonzalez, A., M. M. Kasliwal, W. Li, M. A. Malkan, I., T. Matheson, N. A. Moskovitz, P. S., P. E. Nugent, E. O. Ofek, R. M., J. W. Richards, N. R. Ross, K. J., J. M. Silverman, N. Smith, A. Vanderburg, E. S. Walker, "Discovery and Early Multi-wavelength Measurements of the Energetic Type Ic Supernova PTF12gzk: A Massive-star Explosion in a Dwarf Host Galaxy", Astrophysical Journal, 2012, 760:L33, doi: 10.1088/2041-8205/760/2/L33

### Matthias Morzfeld, Xuemin Tu, Ethan Atkins, Alexandre J. Chorin, "A random map implementation of implicit filters", Journal of Computational Physics, 2012, 231:2049--2066, doi: 10.1016/j.jcp.2011.11.022

### R. Speck, D. Ruprecht, R. Krause, M. Emmett, M. Minion, M. Winkel, and P. Gibbon, "Integrating an N-body problem with SDC and PFASST", Proceedings of the 21st International Conference on Domain Decomposition Methods, DD21, 2012,

### A. Nonaka, A. J. Aspden, M. Zingale, A. S. Almgren, J. B. Bell, and S. E. Woosley, "High-Resolution Simulations of Convection Preceding Ignition in Type Ia Supernovae Using Adaptive Mesh Refinement", Astrophysical Journal, 745, 73, 2012,

- Download File: wdTurb.pdf (pdf: 4.6 MB)

### J. S. Bloom, J. W. Richards, P. E. Nugent, R. M., M. M. Kasliwal, D. L. Starr, D., E. O. Ofek, S. B. Cenko, N. R. Butler, S. R. Kulkarni, A. Gal-Yam, N. Law, "Automating Discovery and Classification of Transients and Variable Stars in the Synoptic Survey Era", Publications of the Astronomical Society of the Pacific, 2012, 124:1175-1196, doi: 10.1086/668468

### Maxime Theillard, Chris H. Rycroft, Frédéric Gibou, "A Multigrid Method on Non-Graded Adaptive Octree and Quadtree Cartesian Grids", Journal of Scientific Computing, 2012, 1--15, doi: 10.1007/s10915-012-9619-2

### M Emmett, M Minion, "Efficient implementation of a multi-level parallel in time algorithm", Proceedings of the 21st International Conference on Domain Decomposition Methods, DD21, 2012,

### K. Maguire, M. Sullivan, R. S. Ellis, P. E. Nugent, D. A., A. Gal-Yam, J. Cooke, P. Mazzali, Y.-C., B. Dilday, R. C. Thomas, I. Arcavi, S., D. Bersier, F. B. Bianco, B. J. Fulton, I., A. Horesh, E. Hsiao, P. A. James, P., E. S. Walker, O. Yaron, M. M., R. R. Laher, N. M. Law, E. O. Ofek, D. Poznanski, J. Surace, "Hubble Space Telescope studies of low-redshift Type Ia supernovae: evolution with redshift and ultraviolet spectral trends", Monthly Notices of the Royal Astronomical Society, 2012, 426:2359-2379, doi: 10.1111/j.1365-2966.2012.21909.x

### J. B. Bell, M. S. Day and M. J. Lijewski, "Simulation of Nitrogen Emissions in a Premixed Hydrogen Flame Stabilized on a Low Swirl Burner", Proceedings of the Combustion Institute, 2012,

- Download File: H2LSBemissions.pdf (pdf: 8.3 MB)

### Samuel Gerber, Oliver Rübel, Peer-Timo Bremer, Valerio Pascucci and Ross T. Whitaker, "Morse-Smale Regression", Journal of Computational and Graphical Statistics, January 2012, doi: 10.1080/10618600.2012.657132

- Download File: MSR.pdf (pdf: 292 KB)

### R. L. Barone-Nugent, C. Lidman, J. S. B. Wyithe, J., D. A. Howell, I. M. Hook, M. Sullivan, P. E., I. Arcavi, S. B. Cenko, J. Cooke, A., E. Y. Hsiao, M. M. Kasliwal, K. Maguire, E. Ofek, D. Poznanski, D. Xu, "Near-infrared observations of Type Ia supernovae: the best known standard candle for cosmology", Monthly Notices of the Royal Astronomical Society, 2012, 425:1007-1012, doi: 10.1111/j.1365-2966.2012.21412.x

### Thomas F. Willems, Chris H. Rycroft, Michaeel Kazi, Juan C. Meza, Maciej Haranczyk, "Algorithms and tools for high-throughput geometry-based analysis of crystalline porous materials", Microporous and Mesoporous Materials, 2012, 149:134--141, doi: 10.1016/j.micromeso.2011.08.020

### G. F. Lofstead, Q. Liu, J. Logan, Y. Tian, Abbasi, N. Podhorszki, J. Y. Choi, S., R. Tchoua, R. A. Oldfield, others, "Hello ADIOS: The Challenges and Lessons of Leadership Class I/O Frameworks", 2012,

### F. Balboa, J. Bell, R. Delgado-Buscalioni, A. Donev, T. Fai, B. Griffith, C. Peskin, "Staggered Schemes for Fluctuating Hydodynamics", Multiscale Modeling and Simulation, 2012, 10(4):1360-1408,

- Download File: FluctHydroStaggered.pdf (pdf: 1.5 MB)

### Daniela M. Ushizima, Dmitriy Morozov, Gunther H. Weber, Andrea G.C. Bianchi, James A. Sethian, E. Wes Bethel, "Augmented Topological Descriptors of Pore Networks for Material Science", IEEE Transactions on Visualization and Computer Graphics (Proc. IEEE Vis 2012), 2012, 18:2041-2050, LBNL 5964E,

- Download File: LBNL-5964E.pdf (pdf: 5.4 MB)

### J. C. van Eyken, D. R. Ciardi, K. von Braun, S. R., P. Plavchan, C. F. Bender, T. M. Brown, J. R., B. J. Fulton, A. W. Howard, S. B. Howell, S., G. W. Marcy, A. Shporer, P. Szkody, R. L., C. A. Beichman, A. F. Boden, D. M., D. W. Hoard, S. V. Ram\ \irez, L. M., J. R. Stauffer, J. S. Bloom, S. B., M. M. Kasliwal, S. R. Kulkarni, N. M., P. E. Nugent, E. O. Ofek, D. Poznanski, R. M., R. Walters, C. J. Grillmair, R., D. B. Levitan, B. Sesar, J. A. Surace, "The PTF Orion Project: A Possible Planet Transiting a T-Tauri Star", Astrophysical Journal, 2012, 755:42, doi: 10.1088/0004-637X/755/1/42

### M. Williams, E. Shlizerman, J. Wilkening, J. Kutz, "The Low Dimensionality of Time-Periodic Standing Waves in Water of Finite and Infinite Depth", SIAM Journal on Applied Dynamical Systems, 2012, 11:1033--1061, doi: 10.1137/11084621X

### Sven Kotlarski, T Bosshard, D Luthi, P Pall, C Schär, "Elevation gradients of European climate change in the regional climate model COSMO-CLM", Climatic change, 2012, 112:189--215,

### R. Tiron, A.S. Almgren, R. Camassa, "Shear Instability of Internal Solitary Waves in Euler Fluids with Thin Pycnoclines", Journal of Fluid Mechanics, 2012, 710:324-361,

### E. W. Bethel and D. Leinweber and O. Rubel and K. Wu, "Federal Market Information Technology in the Post Flash Crash Era: Roles of Supercomputing", The Journal of Trading, 2012, 7:9-24, LBNL 5263E, doi: 10.3905/jot.2012.7.2.009

### Russell S. Vose, Scott Applequist, Mark A. Bourassa, Sara C. Pryor, Rebecca J. Barthelmie, Brian Blanton, Peter D. Bromirski, Harold E. Brooks, Arthur T. DeGaetano, Randall M. Dole, David R. Easterling, Robert E. Jensen, Thomas R. Karl, Katherine Klink, Richard W. Katz, Michael C. Kruk, Kenneth E. Kunkel, Michael C. MacCracken, Thomas C. Peterson, Bridget R. Thomas, Xiaolan L. Wang, John E. Walsh, Michael F. Wehner, Donald J. Wuebbles, and Robert S. Young, "Monitoring and Understanding Changes in Extremes: Extratropical Storms, Winds, and Waves", Bulletin of the American Meteorological Society (submitted), 2012,

### J. P. Bernstein, R. Kessler, S. Kuhlmann, R., E. Kovacs, G. Aldering, I. Crane, C. B., D. A. Finley, J. A. Frieman, T., M. J. Jarvis, A. G. Kim, J. Marriner, P., R. C. Nichol, P. Nugent, D. Parkinson, R. R. R., M. Sako, H. Spinka, M. Sullivan, "Supernova Simulations and Strategies for the Dark Energy Survey", Astrophysical Journal, 2012, 753:152, doi: 10.1088/0004-637X/753/2/152

### M. J. Cantero, F. A. Grünbaum, L. Moral, L. Veláquez, "One-Dimensional Quantum Walks with One Defect", Reviews in Mathematical Physics, 2012, 24:1250002, doi: 10.1142/S0129055X1250002X

### J. T. Parrent, D. A. Howell, B. Friesen, R. C. Thomas, R. A., D. Milisavljevic, F. B. Bianco, B., P. Nugent, E. Baron, I. Arcavi, S., D. Bersier, L. Bildsten, J. Bloom, Y., S. B. Cenko, A. V. Filippenko, A. Gal-Yam, M. M., N. Konidaris, S. R. Kulkarni, N. M., D. Levitan, K. Maguire, P. A. Mazzali, E. O., Y. Pan, D. Polishook, D. Poznanski, R. M., J. M. Silverman, A. Sternberg, M., E. S. Walker, D. Xu, C. Buton, R. Pereira, "Analysis of the Early-time Optical Spectra of SN 2011fe in M101", Astrophysical Journal, 2012, 752:L26, doi: 10.1088/2041-8205/752/2/L26

### M. Garzon, L. J. Gray, J. A. Sethian, "Axisymmetric boundary integral formulation for a two-fluid system", International Journal for Numerical Methods in Fluids, 2012, 69:1124--1134, doi: 10.1002/fld.2633

### 2011

### Planck Collaboration, "Planck Early Results. XXVI. Detection with Planck and Confirmation by XMM-Newton of PLCK G266.6-27.3, an Exceptionally X-Ray Luminous and Massive Galaxy Cluster at z~1", Astronomy and Astrophysics, December 2011, 536:A26, doi: 10.1051/0004-6361/201117430

### Planck Collaboration, "Planck Early Results. XIX. All-Sky Temperature and Dust Optical Depth from Planck and IRAS. Constraints on the Dark Gas in our Galaxy", Astronomy and Astrophysics, December 2011, 536:A19, doi: 10.1051/0004-6361/201116479

### B. Wang, G.H. Miller, and P. Colella, "A Particle-in-Cell Method with Adaptive Phase-Space Remapping for Kinetic Plasmas", SIAM J. Sci. Comput, 2011,

### Filipe R.N.C. Maia, Chao Yang, Stefano Marchesini, "Compressive auto-indexing in femtosecond nanocrystallography", Ultramicroscopy, 2011, 111:807--811, LBNL 4598E,

### Gary S. Groenewold, Michael J. van Stipdonk, Jos Oomens, Wibe A. de Jong, Michael E. McIlwain, "The gas-phase bis-uranyl nitrate complex [(UO2)(2)(NO3)(5)](-): Infrared spectrum and structure", International Journal of Mass Spectrometry, 2011, 308:175-180, doi: 10.1016/j.ijms.2011.06.002

### Ujjaini Alam, Zarija Lukić, Suman Bhattacharya, "Galaxy Clusters as a Probe of Early Dark Energy", The Astrophysical Journal, 2011, 727:87,

### George Schoendorff, Wibe A. de Jong, Michael J. Van Stipdonk, John K. Gibson, Daniel Rios, Mark S. Gordon, Theresa L. Windus, "On the Formation of Hypercoordinated Uranyl Complexes (vol 50, pg 8490, 2011)", Inorganic Chemistry, 2011, 50:11846-1184, doi: 10.1021/ic202173r

### Richard L. Martin, Berend Smit & Maciej Haranczyk, "Addressing Challenges of Identifying Geometrically Diverse Sets of Crystalline Porous Materials", Journal of Chemical Information and Modeling, November 18, 2011, 52:308–318,

Crystalline porous materials have a variety of uses, such as for catalysis and separations. Identifying suitable materials for a given application can, in principle, be done by screening material databases. Such a screening requires automated high-throughput analysis tools that calculate topological and geometrical parameters describing pores. These descriptors can be used to compare, select, group, and classify materials. Here, we present a descriptor that captures shape and geometry characteristics of pores. Together with proposed similarity measures, it can be used to perform diversity selection on a set of porous materials. Our representations are histogram encodings of the probe-accessible fragment of the Voronoi network representing the void space of a material. We discuss and demonstrate the application of our approach on the International Zeolite Association (IZA) database of zeolite frameworks and the Deem database of hypothetical zeolites, as well as zeolitic imidazolate frameworks constructed from IZA zeolite structures. The diverse structures retrieved by our method are complementary to those expected by emphasizing diversity in existing one-dimensional descriptors, e.g., surface area, and similar to those obtainable by a (subjective) manual selection based on materials’ visual representations. Our technique allows for reduction of large sets of structures and thus enables the material researcher to focus efforts on maximally dissimilar structures.

### Q. Zhang, "High-Order, Multidimensional, and Conservative Coarse-Fine Interpolation for Adaptive Mesh Refinement", Comput. Methods Appl. Mech. Engrg., 200(45-46):3159-3168 (2011), 2011,

- Download File: interpolation.pdf (pdf: 647 KB)

### H. J. J. van Dam, W. A. de Jong, E. Bylaska, N. Govind, K. Kowalski, T. P. Straatsma, M. Valiev, "NWChem: scalable parallel computational chemistry", Wiley Interdisciplinary Reviews-Computational Molecular Science, 2011, 1:888-894, doi: 10.1002/wcms.62

### David Camp, Christoph Garth, Hank Childs, Dave Pugmire, Kenneth I. Joy, "Streamline Integration Using MPI-Hybrid Parallelism on a Large Multicore Architecture", IEEE Transactions on Visualization and Computer Graphics, November 2011, 17:1702-1713, LBNL 4563E, doi: http://doi.ieeecomputersociety.org/10.1109/TVCG.2010.259

- Download File: LBNL-4563E.pdf (pdf: 3.5 MB)

### B.D. Santer, Carl Mears , Charles Doutriaux , Peter Gleckler , Tom Wigley , Nathan Gillett , Detelina Ivanova , Thomas Karl , John Lanzante , Gerald Meehl , Peter Stott , Karl Taylor , Peter Thorne , Michael Wehner, and Frank Wentz, "Separating signal and noise in atmospheric temperature changes: The importance of timescale", Journal of Geophysical Research-Atmospheres, November 2011, 116, D22, doi: 10.1029/2011JD016263

### David H. Bailey, Jonathan M. Borwein, "Exploratory experimentation and computation", Notices of the American Mathematical Society, November 2011, 58:1410-1419,

### Monika Srebro, Niranjan Govind, Wibe A. de Jong, Jochen Autschbach, "Optical Rotation Calculated with Time-Dependent Density Functional Theory: The OR45 Benchmark", Journal of Physical Chemistry A, 2011, 115:10930-1094, doi: 10.1021/jp2055409

### L. Lin, C. Yang, J. Lu, L. Ying, W. E, "A fast parallel algorithm for selected inversion of structured sparse matrices with application to 2D electronic structure calculations", SIAM J. Sci. Comput., 2011, 33:1329,

### G.V. Vogman, U. Shumlak, "Deconvolution of Stark Broadened Spectra for Multi-point Density Measurements in a Flow Z-Pinch", Review of Scientific Instruments, 82 (10) 103504, October 2011, doi: 10.1063/1.3647975

### George Schoendorff, Wibe A. de Jong, Michael J. Van Stipdonk, John K. Gibson, Daniel Rios, Mark S. Gordon, Theresa L. Windus, "On the Formation of Hypercoordinated Uranyl Complexes", Inorganic Chemistry, 2011, 50:8490-8493, doi: 10.1021/ic201080z

### L. Lin, C. Yang, J. Meza, J. Lu, L. Ying, W. E, "SelInv -- An algorithm for selected inversion of a sparse symmetric matrix", ACM Trans. Math. Software, 2011, 37:40,

### L. Lin, J.A. Morrone and R. Car, "Correlated tunneling in hydrogen bonds", J. Stat. Phys., 2011, 145:365,

### Michael Philpott, Prabhat and Yoshiyuki Kawazoe, "Magnetism and Bonding in Graphene Nanodots with H modified Interior, Edge and Apex", J. Chem Physics, August 2011,

### T. Kosar, M. Balman, E. Yildirim, S. Kulasekaran, B. Ross, "Stork Data Scheduler: Mitigating the Data Bottleneck in e-Science", Philosophical Transactions of the Royal Society A, Vol.369 (2011), pp. 3254-3267, July 18, 2011, doi: 10.1098/rsta.2011.0148

In this paper, we present the Stork data scheduler as a solution for mitigating the data bottleneck in e-Science and data-intensive scientific discovery. Stork focuses on planning, scheduling, monitoring and management of data placement tasks and application-level end-to-end optimization of networked inputs/outputs for petascale distributed e-Science applications. Unlike existing approaches, Stork treats data resources and the tasks related to data access and movement as first-class entities just like computational resources and compute tasks, and not simply the side-effect of computation. Stork provides unique features such as aggregation of data transfer jobs considering their source and destination addresses, and an application-level throughput estimation and optimization service. We describe how these two features are implemented in Stork and their effects on end-to-end data transfer performance.

### David H. Bailey, Jonathan M. Borwein, Andrew Mattingly, Glenn Wightwick, "The computation of previously inaccessible digits of Pi^2 and Catalan's constant", Notices of the American Mathematical Society, July 5, 2011, 60:844-854,

### J. Gu, D. Katramatos, X. Liu, V. Natarajan, A. Shoshani, A. Sim, D. Yu, S. Bradley, S. McKee, "StorNet: Integrated Dynamic Storage and Network Resource Provisioning and Management for Automated Data Transfers", Journal of Physics: Conf. Ser., 2011, 331, doi: 10.1088/1742- 6596/331/1/012002

### George Michelogiannakis, Nan Jiang, Daniel U. Becker, William J. Dally, "Packet Chaining: Efficient Single-Cycle Allocation for On-Chip Networks", Computer Architecture Letters, July 1, 2011,

- Download File: chainingcal11.pdf (pdf: 119 KB)

This paper introduces packet chaining, a simple and effective method to increase allocator matching efficiency and hence network performance, particularly suited to networks with short packets and short cycle times. Packet chaining operates by chaining packets destined to the same output together, to reuse the switch connection of a departing packet. This allows an allocator to build up an efficient matching over a number of cycles, like incremental allocation, but not limited by packet length. For a 64-node 2D mesh at maximum injection rate and with single-flit packets, packet chaining increases network throughput by 15% compared to a conventional single-iteration separable iSLIP allocator, outperforms a wavefront allocator, and gives comparable throughput with an augmenting paths allocator. Packet chaining achieves this performance with a cycle time comparable to a single-iteration separable allocator. Packet chaining also reduces average network latency by 22.5%. Finally, packet chaining increases IPC up to 46% (16% average) for application benchmarks because short packets are critical in a typical cache-coherent CMP. These are considerable improvements given the maturity of network-on-chip routers and allocators.

### G. Garzoglio, J. Bester, K. Chadwick, D. Dykstra, D. Groep, J. Gu, T. Hesselroth, O. Koeroo, T. Levshina, S. Martin, M. Salle, N. Sharma, A. Sim, S. Timm, A. Verstegen, "Adoption of a SAML-XACML Profile for Authorization Interoperability across Grid Middleware in OSG and EGEE", Journal of Physics: Conf. Ser., 2011, 331, doi: 10.1088/1742-6596/331/6/062011

### Andrew Myers, Mark Krumholz, Richard Klein, Christopher McKee, "Metallicity and the Universality of the Initial Mass Function", The Astrophysical Journal, Volume 735, Issue 1, article id. 49, 2011,

### Nils E. R. Zimmermann, Maciej Haranczyk, Manju Sharma, Bei Liu, Berend Smit, Frerich J. Keil, "Adsorption and diffusion in zeolites: The pitfall of isotypic crystal structures", Mol. Simul., 2011, 37:986-989, doi: 10.1080/08927022.2011.562502

The influence of isotypic crystal structures on adsorption and diffusion of methane in all-silica LTA, SAS and ITE zeolites is studied. Results obtained with the experimental structures are compared with structure predictions and approximations that are commonly employed. The results indicate that diffusion coefficients are much more affected than Henry coefficients. In fact, orders of magnitude deviations in the diffusivity can be observed and a systematic parameter study finally gives rise to the correlation between structure sensitivity and diffusion-window size.

### F. Miniati and D.F. Martin, "Constrained-transport Magnetohydrodynamics with Adaptive Mesh Refinement in CHARM", The Astrophysical Journal Supplement Series, 195(1):5, 2011,

### L Yang, R Taylor, WA de Jong, WL Hase, "A Model DMMP/TiO2 (110) Intermolecular Potential Energy Function Developed from ab Initio Calculations", Journal of Physical Chemistry C, 2011, 115:12403-1241, doi: 10.1021/jp1112137

### George Michelogiannakis, Daniel U. Becker, William J. Dally, "Evaluating Elastic Buffer and Wormhole Flow Control", Transactions on Computers, 2011,

- Download File: ebwormholetc.pdf (pdf: 911 KB)

With the emergence of on-chip networks, router buffer power has become a primary concern. Elastic buffer (EB) flow control utilizes existing pipeline flip-flops in the channels to implement distributed FIFOs, eliminating the need for input buffers at the routers. EB routers have been shown to be more efficient than virtual channel routers, as they do not require input buffers or complex logic for managing virtual channels and tracking credits. Wormhole routers are more comparable in terms of complexity because they also lack virtual channels. This paper compares EB and wormhole routers and explores novel hybrid designs to more closely examine the effect of design simplicity and input buffer cost. Our results show that EB routers have up to 25 percent smaller cycle time compared to wormhole and hybrid routers. Moreover, EB flow control requires 10 percent less energy to transfer a single bit through a router and offers three percent more throughput per unit energy as well as 62 percent more throughput per unit area. The main contributor to these results is the cost and delay overhead of the input buffer.

### A. Buluç, J. Gilbert, "The Combinatorial BLAS: Design, implementation, and applications", International Journal of High-Perormance Computing Applications (IJHPCA), 2011,

- Download File: combblas-r2.pdf (pdf: 288 KB)

### Beketayev, K., Weber, G.H., Haranczyk, M., Bremer, P.-T., Hlawitschka, M., and Hamann, B., "Topology-based Visualization of Transformation Pathways in Complex Chemical Systems", Computer Graphics Forum (Special Issue, Proc. Eurographics / IEEE Symposium on Visualization), June 2011, 663-672, LBNL 5242E,

- Download File: LBNL-5242E.pdf (pdf: 5.2 MB)

### L. Lin, J.A. Morrone, R. Car, M. Parrinello, "Momentum distribution, vibrational dynamics and the potential of the mean force in ice", Phys. Rev. B (Rapid Communication), 2011, 83:220302,

### Suman Bhattacharya, Katrin Heitmann, Martin White, Zarija Lukić, Christian Wagner, and Salman Habib, "Mass Function Predictions Beyond ΛCDM", The Astrophysical Journal, 2011, 732:122,

### R Atta-Fynn, EJ Bylaska, GK Schenter, WA de Jong, "Hydration Shell Structure and Dynamics of Curium(III) in Aqueous Solution: First Principles and Empirical Studies", Journal of Physical Chemistry a, 2011, 115:4665-4677, doi: 10.1021/jp201043f

### L. Lin, J. Lu and L. Ying, "Fast construction of hierarchical matrix representation from matrix-vector multiplication", J. Comput. Phys., 2011, 230:4071,

### Douglas F Levinson, Jubao Duan, Sang Oh, Kai Wang, Alan R Sanders, Jianxin Shi, Nancy Zhang, Bryan J Mowry, Ann Olincy, Farooq Amin, C Robert Cloninger, Jeremy M Silverman, Nancy G Buccola, William F Byerley, Donald W Black, Kenneth S Kendler, Robert Freedman, Frank Dudbridge, Itsik Pe'er, Hakon Hakonarson, Sarah E Bergen, Ayman H Fanous, Peter A Holmans, Pablo V Gejman, "Copy number variants in schizophrenia: confirmation of five previous findings and new evidence for 3q29 microdeletions and VIPR2 duplications", The American Journal of Psychiatry, March 1, 2011, doi: doi:10.1176/appi.ajp.2010.10060876

### C. M. Malone, A. Nonaka, A. S. Almgren, J. B. Bell, and M. Zingale, "Multidimensional Modeling of Type I X-ray Bursts. I. Two-Dimensional Convection Prior to the Outburst of a pure 4He Accretor", Astrophysical Journal, 728, 118, February 2011,

- Download File: xrb.pdf (pdf: 6.6 MB)

### VA Glezakou, WA deJong, "Cluster-Models for Uranyl(VI) Adsorption on alpha-Alumina", Journal of Physical Chemistry A, 2011, 115:1257-1263, doi: 10.1021/jp1092509

### David H. Bailey, Jonathan M. Borwein, "High-precision numerical integration: Progress and challenges", Journal of Symbolic Computation, 2011, 46:741-754,

### P. Colella, M.R. Dorr, J.A.F. Hittinger, and D.F. Martin, "High-Order Finite-Volume Methods in Mapped Coordinates", Journal of Computational Physics, 230(8):2952-2976 (2011), 2011,

- Download File: HOFiniteVolume2010.pdf (pdf: 1.1 MB)

### P.A.R. Ade, N. Aghanim, M. Arnaud, M. Ashdown, J. Aumont, C. Baccigalupi, A. Balbi, A.J. Banday, R.B. Barreiro, J.G. Bartlett, E. Battaner, K. Benabed, A. Benoît, J.-P. Bernard, M. Bersanelli, R. Bhatia, J.J. Bock, A. Bonaldi, J.R. Bond, J. Borrill, F.R. Bouchet, M. Bucher, C. Burigana, P. Cabella, J.-F. Cardoso, A. Catalano, L. Cayón, A. Challinor, A. Chamballu, R.-R. Chary, L.-Y. Chiang, P.R. Christensen, D.L. Clements, S. Colombi, F. Couchot, A. Coulais, B.P. Crill, F. Cuttaia, L. Danese, R.D. Davies, R.J. Davis, P. De Bernardis, G. De Gasperis, A. De Rosa, G. De Zotti, J. Delabrouille, J.-M. Delouis, F.-X. Désert, C. Dickinson, H. Dole, S. Donzelli, O. Doré, U. Dörl, M. Douspis, X. Dupac, G. Efstathiou, T.A. Enßlin, F. Finelli, O. Forni, M. Frailis, E. Franceschi, S. Galeotta, K. Ganga, M. Giard, G. Giardino, Y. Giraud-Héraud, J. González-Nuevo, K.M. Górski, S. Gratton, A. Gregorio, A. Gruppuso, F.K. Hansen, D. Harrison, G. Helou, S. Henrot-Versillé, D. Herranz, S.R. Hildebrandt, E. Hivon, M. Hobson, W.A. Holmes, W. Hovest, R.J. Hoyland, K.M. Huffenberger, A.H. Jaffe, W.C. Jones, M. Juvela, E. Keihänen, R. Keskitalo, T.S. Kisner, R. Kneissl, L. Knox, H. Kurki-Suonio, G. Lagache, A. Lähteenmäki, J.-M. Lamarre, A. Lasenby, R.J. Laureijs, C.R. Lawrence, S. Leach, R. Leonardi, M. Linden-Vørnle, M. López-Caniego, P.M. Lubin, J.F. MacÍas-Pérez, C.J. MacTavish, S. Madden, B. Maffei, D. Maino, N. Mandolesi, R. Mann, M. Maris, E. Martínez-González, S. Masi, S. Matarrese, F. Matthai, P. Mazzotta, A. Melchiorri, L. Mendes, A. Mennella, M.-A. Miville-Deschênes, A. Moneti, L. Montier, G. Morgante, D. Mortlock, D. Munshi, A. Murphy, P. Naselsky, P. Natoli, C.B. Netterfield, H.U. Nørgaard-Nielsen, F. Noviello, D. Novikov, I. Novikov, S. Osborne, F. Pajot, B. Partridge, F. Pasian, G. Patanchon, M. Peel, O. Perdereau, L. Perotto, F. Perrotta, F. Piacentini, M. Piat, S. Plaszczynski, E. Pointecouteau, G. Polenta, N. Ponthieu, T. Poutanen, G. Prézeau, S. Prunet, J.-L. Puget, W.T. Reach, R. Rebolo, M. Reinecke, C. Renault, S. Ricciardi, T. Riller, I. Ristorcelli, G. Rocha, C. Rosset, M. Rowan-Robinson, J.A. Rubiño-Martín, B. Rusholme, M. Sandri, G. Savini, D. Scott, M.D. Seiffert, P. Shellard, G.F. Smoot, J.-L. Starck, F. Stivoli, V. Stolyarov, R. Sudiwala, J.-F. Sygnet, J.A. Tauber, L. Terenzi, L. Toffolatti, M. Tomasi, J.-P. Torre, M. Tristram, J. Tuovinen, M. Türler, G. Umana, L. Valenziano, J. Varis, P. Vielva, F. Villa, N. Vittorio, L.A. Wade, B.D. Wandelt, D. Yvon, A. Zacchei, A. Zonca, "Planck early results. XVI. The Planck view of nearby galaxies", Astronomy and Astrophysics, January 2011, 536:A16, doi: 10.1051/0004-6361/201116454

### C. M. Cantalupo, J. D. Borrill, A. H. Jaffe, T. S. Kisner, R. Stompor, "MADmap: Fast Parallel Maximum Likelihood CMB Map Making Code", Astrophysics Source Code Library, January 2011, 10018,

### J. Cooke, R. S. Ellis, M. Sullivan, P. Nugent, D. A., A. Gal-Yam, C. Lidman, J. S. Bloom, S. B., M. M. Kasliwal, S. R. Kulkarni, N. M. Law, E. O. Ofek, R. M. Quimby, "Hubble Space Telescope Studies of Nearby Type Ia Supernovae: The Mean Maximum Light Ultraviolet Spectrum and its Dispersion", Astrophysical Journal, 2011, 727:L35, doi: 10.1088/2041-8205/727/2/L35

### Robert I. Saye, James A. Sethian, "The Voronoi Implicit Interface Method for computing multiphase physics", Proceedings of the National Academy of Sciences, 2011, 108:19498--195, doi: 10.1073/pnas.1111557108

We introduce a numerical framework, the Voronoi Implicit Interface Method for tracking multiple interacting and evolving regions (phases) whose motion is determined by complex physics (fluids, mechanics, elasticity, etc.), intricate jump conditions, internal constraints, and boundary conditions. The method works in two and three dimensions, handles tens of thousands of interfaces and separate phases, and easily and automatically handles multiple junctions, triple points, and quadruple points in two dimensions, as well as triple lines, etc., in higher dimensions. Topological changes occur naturally, with no surgery required. The method is first-order accurate at junction points/lines, and of arbitrarily high-order accuracy away from such degeneracies. The method uses a single function to describe all phases simultaneously, represented on a fixed Eulerian mesh. We test the method’s accuracy through convergence tests, and demonstrate its applications to geometric flows, accurate prediction of von Neumann’s law for multiphase curvature flow, and robustness under complex fluid flow with surface tension and large shearing forces.

### Alexander Knebe, Steffen R. Knollmann, Stuart I. Muldrew, Frazer R. Pearce, Miguel Angel Aragon-Calvo, Yago Ascasibar, Peter S. Behroozi, Daniel Ceverino, Stephane Colombi, Juerg Diemand, Klaus Dolag, Bridget L. Falck, Patricia Fasel, Jeff Gardner, Stefan Gottlöber, Chung-Hsing Hsu, Francesca Iannuzzi, Anatoly Klypin, Zarija Lukić, Michal Maciejewski, Cameron McBride, Mark C. Neyrinck, Susana Planelles, Doug Potter, Vicent Quilis, Yann Rasera, Justin I. Read, Paul M. Ricker, Fabrice Roy, Volker Springel, Joachim Stadel, Greg Stinson, P. M. Sutter, Victor Turchaninov, Dylan Tweed, Gustavo Yepes, Marcel Zemp, "Haloes gone MAD: The Halo-Finder Comparison Project", Monthly Notices of the Royal Astronomical Society, 2011, 415:2293,

### A. Napov and Y. Notay, "Smoothing Factor, Order of Prolongation and Actual Multigrid Convergence", Numerische Mathematik , vol.118, pp. 457-483, 2011,

- Download File: NumerMath11-smoothing-factor.pdf (pdf: 315 KB)

### J. Aatrokoski, P.A.R. Ade, N. Aghanim, H.D. Aller, M.F. Aller, E. Angelakis, M. Arnaud, M. Ashdown, J. Aumont, C. Baccigalupi, A. Balbi, A.J. Banday, R.B. Barreiro, J.G. Bartlett, E. Battaner, K. Benabed, A. Benoît, A. Berdyugin, J.-P. Bernard, M. Bersanelli, R. Bhatia, A. Bonaldi, L. Bonavera, J.R. Bond, J. Borrill, F.R. Bouchet, M. Bucher, C. Burigana, D.N. Burrows, P. Cabella, M. Capalbi, B. Cappellini, J.-F. Cardoso, A. Catalano, E. Cavazzuti, L. Cayón, A. Challinor, A. Chamballu, R.-R. Chary, L.-Y. Chiang, P.R. Christensen, D.L. Clements, S. Colafrancesco, S. Colombi, F. Couchot, A. Coulais, S. Cutini, F. Cuttaia, L. Danese, R.D. Davies, R.J. Davis, P. De Bernardis, G. De Gasperis, A. De Rosa, G. De Zotti, J. Delabrouille, J.-M. Delouis, C. Dickinson, H. Dole, S. Donzelli, O. Doré, U. Dörl, M. Douspis, X. Dupac, G. Efstathiou, T.A. Enßlin, F. Finelli, O. Forni, M. Frailis, E. Franceschi, L. Fuhrmann, S. Galeotta, K. Ganga, F. Gargano, D. Gasparrini, N. Gehrels, M. Giard, G. Giardino, N. Giglietto, P. Giommi, F. Giordano, Y. Giraud-Héraud, J. González-Nuevo, K.M. Górski, S. Gratton, A. Gregorio, A. Gruppuso, D. Harrison, S. Henrot-Versillé, D. Herranz, S.R. Hildebrandt, E. Hivon, M. Hobson, W.A. Holmes, W. Hovest, R.J. Hoyland, K.M. Huffenberger, A.H. Jaffe, M. Juvela, E. Keihänen, R. Keskitalo, O. King, T.S. Kisner, R. Kneissl, L. Knox, T.P. Krichbaum, H. Kurki-Suonio, G. Lagache, A. Lähteenmäki, J.-M. Lamarre, A. Lasenby, R.J. Laureijs, N. Lavonen, C.R. Lawrence, S. Leach, R. Leonardi, J. León-Tavares, M. Linden-Vørnle, E. Lindfors, M. López-Caniego, P.M. Lubin, J.F. MacÍas-Pérez, B. Maffei, D. Maino, N. Mandolesi, R. Mann, M. Maris, E. Martínez-González, S. Masi, M. Massardi, S. Matarrese, F. Matthai, W. Max-Moerbeck, M.N. Mazziotta, P. Mazzotta, A. Melchiorri, L. Mendes, A. Mennella, P.F. Michelson, M. Mingaliev, S. Mitra, M.-A. Miville-Deschênes, A. Moneti, C. Monte, L. Montier, G. Morgante, D. Mortlock, D. Munshi, A. Murphy, P. Naselsky, P. Natoli, I. Nestoras, C.B. Netterfield, E. Nieppola, K. Nilsson, H.U. Nørgaard-Nielsen, F. Noviello, D. Novikov, I. Novikov, I.J. O Dwyer, S. Osborne, F. Pajot, B. Partridge, F. Pasian, G. Patanchon, V. Pavlidou, T.J. Pearson, O. Perdereau, L. Perotto, M. Perri, F. Perrotta, F. Piacentini, M. Piat, S. Plaszczynski, P. Platania, E. Pointecouteau, G. Polenta, N. Ponthieu, T. Poutanen, G. Prézeau, P. Procopio, S. Prunet, J.-L. Puget, J.P. Rachen, S. Rainò, W.T. Reach, A. Readhead, R. Rebolo, R. Reeves, M. Reinecke, R. Reinthal, C. Renault, S. Ricciardi, J. Richards, T. Riller, D. Riquelme, I. Ristorcelli, G. Rocha, C. Rosset, M. Rowan-Robinson, J.A. Rubiño-Martín, B. Rusholme, J. Saarinen, M. Sandri, P. Savolainen, D. Scott, M.D. Seiffert, A. Sievers, A. Sillanpää, G.F. Smoot, Y. Sotnikova, J.-L. Starck, M. Stevenson, F. Stivoli, V. Stolyarov, R. Sudiwala, J.-F. Sygnet, L. Takalo, J. Tammi, J.A. Tauber, L. Terenzi, D.J. Thompson, L. Toffolatti, M. Tomasi, M. Tornikoski, J.-P. Torre, G. Tosti, A. Tramacere, M. Tristram, J. Tuovinen, M. Türler, M. Turunen, G. Umana, H. Ungerechts, L. Valenziano, E. Valtaoja, J. Varis, F. Verrecchia, P. Vielva, F. Villa, N. Vittorio, B.D. Wandelt, J. Wu, D. Yvon, A. Zacchei, J.A. Zensus, X. Zhou, A. Zonca, "Planck early results. XV. Spectral energy distributions and radio continuum spectra of northern extragalactic radio sources", Astronomy and Astrophysics, January 2011, 536:A15, doi: 10.1051/0004-6361/201116466

### B. Keating, S. Moyerman, D. Boettger, J. Edwards, G., F. Matsuda, N. Miller, H. Paar, G., I. Schanning, M. Shimon, N. Stebor, K., D. Flanigan, W. Holzapfel, J. Howard, Z., A. Lee, M. Lungu, M. Myers, H., R. O Brient, E. Quealy, C. Reichardt, P., C. Shimmin, B. Steinbach, A. Suzuki, O., J. Borrill, C. Cantalupo, E. Kisner, E., M. Sholl, H. Spieler, A. Anthony, N., J. Errard, G. Fabbian, M. Le Jeune, R., A. Jaffe, D. O Dea, Y. Chinone, M., M. Hazumi, T. Matsumura, H. Morii, A., T. Tomaru, P. Hyland, M. Dobbs, P. Ade, W. Grainger, C. Tucker, "Ultra High Energy Cosmology with POLARBEAR", ArXiv e-prints, January 2011,

### Lavanya Ramakrishnan, Dennis Gannon, Jeffrey Chase, Daniel Nurmi, Rich Wolski, "Deadline-Sensitive Workflow Orchestration Without Explicit Resource Control", Journal of Parallel and Distributed Computing, 2011,

### R. L. C. Starling, K. Wiersema, A. J. Levan, T., D. Bersier, P. Goldoni, S. R. Oates, A., S. Campana, J. Sollerman, N. R. Tanvir, D., J. P. U. Fynbo, S. Covino, P. D Avanzo, P. T., K. L. Page, J. P. Osborne, S. D., S. Barthelmy, D. N. Burrows, Z., P. A. Curran, M. de Pasquale, V. D Elia, P. A., H. Flores, A. S. Fruchter, P. Garnavich, N., J. Gorosabel, J. Hjorth, S. T. Holland, A. J. der Horst, C. P. Hurkett, P. Jakobsson, A. P., C. Kouveliotou, N. P. M. Kuin, L., P. A. Mazzali, P. E. Nugent, E. Pian, M., C. C. Th\ one, S. E. Woosley, "Discovery of the nearby long, soft GRB 100316D with an associated supernova", Monthly Notices of the Royal Astronomical Society, 2011, 411:2792-2803, doi: 10.1111/j.1365-2966.2010.17879.x

### Benjamin Stamm, "A posteriori estimates for the Bubble Stabilized Discontinuous Galerkin Method", J. Comput. Appl. Math., 2011, 235:4309--4324, doi: 10.1016/j.cam.2011.03.017

### HJJ van Dam, A Vishnu, WA de Jong, "Designing a Scalable Fault Tolerance Model for High Performance Computational Chemistry: A Case Study with Coupled Cluster Perturbative Triples", Journal of Chemical Theory and Computation, 2011, 7:66-75, doi: 10.1021/ct100439u

### A. Napov and Y. Notay, "Algebraic Analysis of Aggregation-Based Multigrid", Numer. Lin. Alg. Appl., vol.18, pp. 539-564, 2011,

- Download File: NLAA10-analysis-of-aggregation-mg.pdf (pdf: 347 KB)

*the short version of the paper, winner of the Student Paper competition of 11th Copper Mountain Conference on Iterative Methods*

### P.A.R. Ade, N. Aghanim, E. Angelakis, M. Arnaud, M. Ashdown, J. Aumont, C. Baccigalupi, A. Balbi, A.J. Banday, R.B. Barreiro, J.G. Bartlett, E. Battaner, K. Benabed, A. Benoît, J.-P. Bernard, M. Bersanelli, R. Bhatia, A. Bonaldi, L. Bonavera, J.R. Bond, J. Borrill, F.R. Bouchet, M. Bucher, C. Burigana, P. Cabella, B. Cappellini, J.-F. Cardoso, A. Catalano, L. Cayón, A. Challinor, A. Chamballu, R.-R. Chary, X. Chen, L.-Y. Chiang, P.R. Christensen, D.L. Clements, S. Colombi, F. Couchot, A. Coulais, B.P. Crill, F. Cuttaia, L. Danese, R.D. Davies, R.J. Davis, P. De Bernardis, G. De Gasperis, A. De Rosa, G. De Zotti, J. Delabrouille, J.-M. Delouis, F.-X. Désert, C. Dickinson, S. Donzelli, O. Doré, U. Dörl, M. Douspis, X. Dupac, G. Efstathiou, T.A. Enßlin, F. Finelli, O. Forni, M. Frailis, E. Franceschi, L. Fuhrmann, S. Galeotta, K. Ganga, M. Giard, G. Giardino, Y. Giraud-Héraud, J. González-Nuevo, K.M. Górski, S. Gratton, A. Gregorio, A. Gruppuso, D. Harrison, S. Henrot-Versillé, D. Herranz, S.R. Hildebrandt, E. Hivon, M. Hobson, W.A. Holmes, W. Hovest, R.J. Hoyland, K.M. Huffenberger, M. Huynh, A.H. Jaffe, M. Juvela, E. Keihänen, R. Keskitalo, T.S. Kisner, R. Kneissl, L. Knox, T.P. Krichbaum, H. Kurki-Suonio, G. Lagache, A. Lähteenmäki, J.-M. Lamarre, A. Lasenby, R.J. Laureijs, N. Lavonen, C.R. Lawrence, S. Leach, J.P. Leahy, R. Leonardi, J. León-Tavares, M. Linden-Vørnle, M. López-Caniego, P.M. Lubin, J.F. MacÍas-Pérez, B. Maffei, D. Maino, N. Mandolesi, R. Mann, M. Maris, F. Marleau, E. Martínez-González, S. Masi, M. Massardi, S. Matarrese, F. Matthai, P. Mazzotta, P.R. Meinhold, A. Melchiorri, L. Mendes, A. Mennella, M. Mingaliev, M.-A. Miville-Deschênes, A. Moneti, L. Montier, G. Morgante, D. Mortlock, D. Munshi, A. Murphy, P. Naselsky, P. Natoli, I. Nestoras, C.B. Netterfield, E. Nieppola, H.U. Nørgaard-Nielsen, F. Noviello, D. Novikov, I. Novikov, S. Osborne, F. Pajot, R. Paladini, B. Partridge, F. Pasian, G. Patanchon, T.J. Pearson, O. Perdereau, L. Perotto, F. Perrotta, F. Piacentini, M. Piat, E. Pierpaoli, S. Plaszczynski, P. Platania, E. Pointecouteau, G. Polenta, N. Ponthieu, T. Poutanen, G. Prézeau, P. Procopio, S. Prunet, J.-L. Puget, J.P. Rachen, W.T. Reach, R. Rebolo, M. Reinecke, C. Renault, S. Ricciardi, T. Riller, D. Riquelme, I. Ristorcelli, G. Rocha, C. Rosset, M. Rowan-Robinson, J.A. Rubiño-Martín, B. Rusholme, A. Sajina, M. Sandri, P. Savolainen, D. Scott, M.D. Seiffert, A. Sievers, G.F. Smoot, Y. Sotnikova, J.-L. Starck, F. Stivoli, V. Stolyarov, R. Sudiwala, J.-F. Sygnet, J. Tammi, J.A. Tauber, L. Terenzi, L. Toffolatti, M. Tomasi, M. Tornikoski, J.-P. Torre, M. Tristram, J. Tuovinen, M. Türler, M. Turunen, G. Umana, H. Ungerechts, L. Valenziano, J. Varis, P. Vielva, F. Villa, N. Vittorio, L.A. Wade, B.D. Wandelt, A. Wilkinson, D. Yvon, A. Zacchei, J.A. Zensus, A. Zonca, "Planck early results. XIV. ERCSC validation and extreme radio sources", Astronomy and Astrophysics, January 2011, 536:A14, doi: 10.1051/0004-6361/201116475

### T. Kosar, I. Akturk, M. Balman, X. Wang, "PetaShare: A Reliable, Efficient, and Transparent Distributed Storage Management System", Journal Scientific Programming archive Volume 19 Issue 1, January 2011 Pages 27-43, 2011,

Modern collaborative science has placed increasing burden on data management infrastructure to handle the increasingly large data archives generated. Beside functionality, reliability and availability are also key factors in delivering a data management system that can efficiently and effectively meet the challenges posed and compounded by the unbounded increase in the size of data generated by scientific applications. We have developed a reliable and efficient distributed data storage system, PetaShare, which spans multiple institutions across the state of Louisiana. At the back-end, PetaShare provides a unified name space and efficient data movement across geographically distributed storage sites. At the front-end, it provides light-weight clients the enable easy, transparent and scalable access. In PetaShare, we have designed and implemented an asynchronously replicated multi-master metadata system for enhanced reliability and availability, and an advanced buffering system for improved data transfer performance. In this paper, we present the details of our design and implementation, show performance results, and describe our experience in developing a reliable and efficient distributed data management system for data-intensive science.

### Jihan Kim, Alice Koniges, Richard L. Martin, Maciej Haranczyk, Joseph A. Swisher & Berend Smit, "GPU Computational Screening of Carbon Capture Materials", Scientific Discovery through Advanced Computing 2011, 2011,

### Keith R. Jackson, Krishna Muriki, Lavanya Ramakrishnan, Karl J. Runge, Rollin C. Thomas, "Performance and cost analysis of the Supernova factory on the Amazon AWS cloud", Sci. Program., 2011, 19:107--119,

### A. Uranga, P.-O. Persson, M. Drela, J. Peraire, "Implicit Large Eddy Simulation of transition to turbulence at low Reynolds numbers using a Discontinuous Galerkin method", International Journal for Numerical Methods in Engineering, 2011, 87:232--261, doi: 10.1002/nme.3036

### I. K. W. Kleiser, D. Poznanski, D. Kasen, T. R., R. Chornock, A. V. Filippenko, P., M. Ganeshalingam, R. P. Kirshner, W., T. Matheson, P. E. Nugent, J. M. Silverman, "Peculiar Type II supernovae from blue supergiants", Monthly Notices of the Royal Astronomical Society, 2011, 415:372-382, doi: 10.1111/j.1365-2966.2011.18708.x

### W. Zhang, L. Howell, A. Almgren, A. Burrows, and J. Bell, "CASTRO: A New Compressible Astrophysical Solver. II. Gray Radiation Hydrodynamics", Astrophysical Journal Supplement Series, 2011, 196:20,

- Download File: castro2.pdf (pdf: 1 MB)

### P.A.R. Ade, N. Aghanim, F. Argüeso, M. Arnaud, M. Ashdown, J. Aumont, C. Baccigalupi, A. Balbi, A.J. Banday, R.B. Barreiro, J.G. Bartlett, E. Battaner, K. Benabed, J.-P. Bernard, M. Bersanelli, R. Bhatia, A. Bonaldi, L. Bonavera, J.R. Bond, J. Borrill, F.R. Bouchet, M. Bucher, C. Burigana, P. Cabella, B. Cappellini, J.-F. Cardoso, A. Catalano, L. Cayón, A. Challinor, A. Chamballu, R.-R. Chary, X. Chen, L.-Y. Chiang, P.R. Christensen, D.L. Clements, S. Colafrancesco, S. Colombi, F. Couchot, B.P. Crill, F. Cuttaia, L. Danese, R.D. Davies, R.J. Davis, P. De Bernardis, G. De Gasperis, A. De Rosa, G. De Zotti, J. Delabrouille, J.-M. Delouis, F.-X. Désert, C. Dickinson, H. Dole, S. Donzelli, O. Doré, U. Dörl, M. Douspis, X. Dupac, G. Efstathiou, T.A. Enßlin, H.K. Eriksen, F. Finelli, O. Forni, M. Frailis, E. Franceschi, S. Galeotta, K. Ganga, M. Giard, G. Giardino, Y. Giraud-Héraud, J. González-Nuevo, K.M. Górski, S. Gratton, A. Gregorio, A. Gruppuso, F.K. Hansen, D. Harrison, S. Henrot-Versillé, D. Herranz, S.R. Hildebrandt, E. Hivon, M. Hobson, W.A. Holmes, W. Hovest, R.J. Hoyland, K.M. Huffenberger, A.H. Jaffe, M. Juvela, E. Keihänen, R. Keskitalo, T.S. Kisner, R. Kneissl, L. Knox, H. Kurki-Suonio, G. Lagache, A. Lähteenmäki, A. Lasenby, R.J. Laureijs, C.R. Lawrence, S. Leach, J.P. Leahy, R. Leonardi, P.B. Lilje, M. Linden-Vørnle, M. López-Caniego, P.M. Lubin, J.F. MacÍas-Pérez, B. Maffei, M. Magliocchetti, D. Maino, N. Mandolesi, R. Mann, M. Maris, E. Martínez-González, S. Masi, M. Massardi, S. Matarrese, F. Matthai, P. Mazzotta, P.R. Meinhold, A. Melchiorri, L. Mendes, A. Mennella, M.-A. Miville-Deschênes, A. Moneti, L. Montier, G. Morgante, D. Mortlock, D. Munshi, A. Murphy, P. Naselsky, P. Natoli, C.B. Netterfield, H.U. Nørgaard-Nielsen, F. Noviello, D. Novikov, I. Novikov, I.J. O Dwyer, S. Osborne, F. Pajot, R. Paladini, B. Partridge, F. Pasian, G. Patanchon, T.J. Pearson, O. Perdereau, L. Perotto, F. Perrotta, F. Piacentini, M. Piat, E. Pierpaoli, S. Plaszczynski, P. Platania, E. Pointecouteau, G. Polenta, N. Ponthieu, T. Poutanen, G. Prézeau, S. Prunet, J.-L. Puget, J.P. Rachen, R. Rebolo, M. Reinecke, S. Ricciardi, T. Riller, I. Ristorcelli, G. Rocha, C. Rosset, M. Rowan-Robinson, J.A. Rubiño-Martín, B. Rusholme, A. Sajina, M. Sandri, D. Scott, M.D. Seiffert, S. Serjeant, P. Shellard, G.F. Smoot, J.-L. Starck, F. Stivoli, V. Stolyarov, R. Stompor, R. Sudiwala, J.-F. Sygnet, J.A. Tauber, L. Terenzi, L. Toffolatti, M. Tomasi, J.-P. Torre, M. Tristram, J. Tuovinen, M. Türler, G. Umana, L. Valenziano, J. Varis, P. Vielva, F. Villa, N. Vittorio, L.A. Wade, B.D. Wandelt, A. Wilkinson, D. Yvon, A. Zacchei, A. Zonca, "Planck early results. XIII. Statistical properties of extragalactic radio sources in the Planck Early Release Compact Source Catalogue", Astronomy and Astrophysics, January 2011, 536:A13, doi: 10.1051/0004-6361/201116471

### F. Alberto Grünbaum, Mizan Rahman, "A System of Multivariable Krawtchouk Polynomials and a Probabilistic Application", Symmetry, Integrability and Geometry: Methods and Applications (SIGMA), 2011, 7, doi: 10.3842/SIGMA.2011.119

### M. M. Kasliwal, S. R. Kulkarni, I. Arcavi, R. M., E. O. Ofek, P. Nugent, J. Jacobsen, A., Y. Green, O. Yaron, D. B. Fox, J. L., S. B. Cenko, I. Kleiser, J. S. Bloom, A., W. Li, A. V. Filippenko, D. Starr, D., N. M. Law, G. Helou, D. A. Frail, J. D., K. Forster, D. C. Martin, S. P. Tendulkar, N., J. Kennea, M. Sullivan, L. Bildsten, R., G. Rahmer, D. Hale, R. Smith, J., V. Velur, R. Walters, J. Henning, K. Bui, D. McKenna, C. Blake, "PTF 10fqs: A Luminous Red Nova in the Spiral Galaxy Messier 99", Astrophysical Journal, 2011, 730:134, doi: 10.1088/0004-637X/730/2/134

### A. Donev, A. de la Fuente, J. B. Bell, and A. L. Garcia, "Enhancement of Diffusive Transport by Nonequilibrium Thermal Fluctuations", JSTAT, Vol. 2011, P06014, 2011,

- Download File: DiffusionRenormalization.pdf (pdf: 2.5 MB)

### A. J. Aspden, M. S. Day, and J. B. Bell, "Characterization of Low Lewis Number Flames", Proc. Combust. Inst., 2011, 33:1463-1471,

### N. Aghanim, M. Arnaud, M. Ashdown, J. Aumont, C. Baccigalupi, A. Balbi, A.J. Banday, R.B. Barreiro, M. Bartelmann, J.G. Bartlett, E. Battaner, K. Benabed, A. Benoît, J.-P. Bernard, M. Bersanelli, R. Bhatia, J.J. Bock, A. Bonaldi, J.R. Bond, J. Borrill, F.R. Bouchet, M.L. Brown, M. Bucher, C. Burigana, P. Cabella, J.-F. Cardoso, A. Catalano, L. Cayón, A. Challinor, A. Chamballu, L.-Y. Chiang, C. Chiang, G. Chon, P.R. Christensen, E. Churazov, D.L. Clements, S. Colafrancesco, S. Colombi, F. Couchot, A. Coulais, B.P. Crill, F. Cuttaia, A. Da Silva, H. Dahle, L. Danese, R.J. Davis, P. De Bernardis, G. De Gasperis, A. De Rosa, G. De Zotti, J. Delabrouille, J.-M. Delouis, F.-X. Désert, J.M. Diego, K. Dolag, S. Donzelli, O. Doré, U. Dörl, M. Douspis, X. Dupac, G. Efstathiou, T.A. Enßlin, F. Finelli, I. Flores-Cacho, O. Forni, M. Frailis, E. Franceschi, S. Fromenteau, S. Galeotta, K. Ganga, R.T. Génova-Santos, M. Giard, G. Giardino, Y. Giraud-Héraud, J. González-Nuevo, K.M. Górski, S. Gratton, A. Gregorio, A. Gruppuso, D. Harrison, S. Henrot-Versillé, C. Hernández-Monteagudo, D. Herranz, S.R. Hildebrandt, E. Hivon, M. Hobson, W.A. Holmes, W. Hovest, R.J. Hoyland, K.M. Huffenberger, A.H. Jaffe, W.C. Jones, M. Juvela, E. Keihänen, R. Keskitalo, T.S. Kisner, R. Kneissl, L. Knox, H. Kurki-Suonio, G. Lagache, J.-M. Lamarre, A. Lasenby, R.J. Laureijs, C.R. Lawrence, S. Leach, R. Leonardi, M. Linden-Vørnle, M. López-Caniego, P.M. Lubin, J.F. MacÍas-Pérez, C.J. MacTavish, B. Maffei, D. Maino, N. Mandolesi, R. Mann, M. Maris, F. Marleau, E. Martínez-González, S. Masi, S. Matarrese, F. Matthai, P. Mazzotta, S. Mei, A. Melchiorri, J.-B. Melin, L. Mendes, A. Mennella, S. Mitra, M.-A. Miville-Deschênes, A. Moneti, L. Montier, G. Morgante, D. Mortlock, D. Munshi, A. Murphy, P. Naselsky, P. Natoli, C.B. Netterfield, H.U. Nørgaard-Nielsen, F. Noviello, D. Novikov, I. Novikov, I.J. O Dwyer, S. Osborne, F. Pajot, F. Pasian, G. Patanchon, O. Perdereau, L. Perotto, F. Perrotta, F. Piacentini, M. Piat, E. Pierpaoli, R. Piffaretti, S. Plaszczynski, E. Pointecouteau, G. Polenta, N. Ponthieu, T. Poutanen, G.W. Pratt, G. Prézeau, S. Prunet, J.-L. Puget, R. Rebolo, M. Reinecke, C. Renault, S. Ricciardi, T. Riller, I. Ristorcelli, G. Rocha, C. Rosset, J.A. Rubiño-Martín, B. Rusholme, M. Sandri, G. Savini, B.M. Schaefer, D. Scott, M.D. Seiffert, P. Shellard, G.F. Smoot, J.-L. Starck, F. Stivoli, V. Stolyarov, R. Sudiwala, R. Sunyaev, J.-F. Sygnet, J.A. Tauber, L. Terenzi, L. Toffolatti, M. Tomasi, J.-P. Torre, M. Tristram, J. Tuovinen, L. Valenziano, L. Vibert, P. Vielva, F. Villa, N. Vittorio, B.D. Wandelt, S.D.M. White, M. White, D. Yvon, A. Zacchei, A. Zonca, "Planck early results. XII. Cluster Sunyaev-Zeldovich optical scaling relations", Astronomy and Astrophysics, January 2011, 536:A12, doi: 10.1051/0004-6361/201116489

### Rajesh Nishtala, Yili Zheng, Paul Hargrove, Katherine A. Yelick, "Tuning collective communication for Partitioned Global Address Space programming models", Parallel Computing, 2011, 37(9):576-591,

### F.A. Grünbaum, I. Pacharoni, J. Tirao, "Two stochastic models of a random walk in the U(n)-spherical duals of U(n + 1)", Annali di Matematica Pura ed Applicata, 2011, 1-27, doi: 10.1007/s10231-011-0232-z

### Jon Wilkening, Jia Yu, "A local construction of the Smith normal form of a matrix polynomial", J. Symb. Comput., 2011, 46:1--22, doi: 10.1016/j.jsc.2010.06.025

### A. Donev, A. de la Fuente, J. B. Bell, and A. L. Garcia, "Diffusive Transport by Thermal Velocity Fluctuations", Phys. Rev. Lett., Vol. 106, No. 20, page 204501, 2011,

- Download File: RenormalizationPRL.pdf (pdf: 325 KB)

### A. J. Aspden, M. S. Day, and J. B. Bell, "Lewis Number Effects in Distributed Flames", Proc. Combust. Inst., 2011, 33:1473-1480,

### P.A.R. Ade, N. Aghanim, M. Arnaud, M. Ashdown, J. Aumont, C. Baccigalupi, A. Balbi, A.J. Banday, R.B. Barreiro, M. Bartelmann, J.G. Bartlett, E. Battaner, K. Benabed, A. Benoît, J.-P. Bernard, M. Bersanelli, R. Bhatia, J.J. Bock, A. Bonaldi, J.R. Bond, J. Borrill, F.R. Bouchet, H. Bourdin, M.L. Brown, M. Bucher, C. Burigana, P. Cabella, J.-F. Cardoso, A. Catalano, L. Cayón, A. Challinor, A. Chamballu, L.-Y. Chiang, C. Chiang, G. Chon, P.R. Christensen, E. Churazov, D.L. Clements, S. Colafrancesco, S. Colombi, F. Couchot, A. Coulais, B.P. Crill, F. Cuttaia, A. Da Silva, H. Dahle, L. Danese, P. De Bernardis, G. De Gasperis, A. De Rosa, G. De Zotti, J. Delabrouille, J.-M. Delouis, F.-X. Désert, J.M. Diego, K. Dolag, S. Donzelli, O. Doré, U. Dörl, M. Douspis, X. Dupac, G. Efstathiou, T.A. Enßlin, F. Finelli, I. Flores-Cacho, O. Forni, M. Frailis, E. Franceschi, S. Fromenteau, S. Galeotta, K. Ganga, R.T. Génova-Santos, M. Giard, G. Giardino, Y. Giraud-Héraud, J. González-Nuevo, K.M. Górski, S. Gratton, A. Gregorio, A. Gruppuso, D. Harrison, S. Henrot-Versillé, C. Hernández-Monteagudo, D. Herranz, S.R. Hildebrandt, E. Hivon, M. Hobson, W.A. Holmes, W. Hovest, R.J. Hoyland, K.M. Huffenberger, A.H. Jaffe, W.C. Jones, M. Juvela, E. Keihänen, R. Keskitalo, T.S. Kisner, R. Kneissl, L. Knox, H. Kurki-Suonio, G. Lagache, J.-M. Lamarre, J. Lanoux, A. Lasenby, R.J. Laureijs, C.R. Lawrence, S. Leach, R. Leonardi, A. Liddle, P.B. Lilje, M. Linden-Vørnle, M. López-Caniego, P.M. Lubin, J.F. MacÍas-Pérez, C.J. MacTavish, B. Maffei, D. Maino, N. Mandolesi, R. Mann, M. Maris, F. Marleau, E. Martínez-González, S. Masi, S. Matarrese, F. Matthai, P. Mazzotta, A. Melchiorri, J.-B. Melin, L. Mendes, A. Mennella, S. Mitra, M.-A. Miville-Deschênes, A. Moneti, L. Montier, G. Morgante, D. Mortlock, D. Munshi, A. Murphy, P. Naselsky, P. Natoli, C.B. Netterfield, H.U. Nørgaard-Nielsen, F. Noviello, D. Novikov, I. Novikov, S. Osborne, F. Pajot, F. Pasian, G. Patanchon, O. Perdereau, L. Perotto, F. Perrotta, F. Piacentini, M. Piat, E. Pierpaoli, R. Piffaretti, S. Plaszczynski, E. Pointecouteau, G. Polenta, N. Ponthieu, T. Poutanen, G.W. Pratt, G. Prézeau, S. Prunet, J.-L. Puget, J.P. Rachen, R. Rebolo, M. Reinecke, C. Renault, S. Ricciardi, T. Riller, I. Ristorcelli, G. Rocha, C. Rosset, J.A. Rubiño-Martín, B. Rusholme, M. Sandri, D. Santos, G. Savini, B.M. Schaefer, D. Scott, M.D. Seiffert, P. Shellard, G.F. Smoot, J.-L. Starck, F. Stivoli, V. Stolyarov, R. Sudiwala, R. Sunyaev, J.-F. Sygnet, J.A. Tauber, L. Terenzi, L. Toffolatti, M. Tomasi, J.-P. Torre, M. Tristram, J. Tuovinen, L. Valenziano, L. Vibert, P. Vielva, F. Villa, N. Vittorio, L.A. Wade, B.D. Wandelt, S.D.M. White, M. White, D. Yvon, A. Zacchei, A. Zonca, "Planck early results. XI. Calibration of the local galaxy cluster Sunyaev-Zeldovich scaling relations", Astronomy and Astrophysics, January 2011, 536:A11, doi: 10.1051/0004-6361/201116458

### F. Alberto Grünbaum, Manuel D. de la Iglesia, Andrei Martínez-Finkelshtein, "Properties of Matrix Orthogonal Polynomials via their Riemann-Hilbert Characterization", Symmetry, Integrability and Geometry: Methods and Applications (SIGMA), 2011, 7, doi: 10.3842/SIGMA.2011.098

### M.O. Williams, J. Wilkening, E. Shlizerman, J. N. Kutz, "Continuation of periodic solutions in the waveguide array mode-locked laser", Physica D: Nonlinear Phenomena, 2011, 240:1791--1804, doi: 10.1016/j.physd.2011.06.018

We apply the adjoint continuation method to construct highly accurate, periodic solutions that are observed to play a critical role in the multi-pulsing transition of mode-locked laser cavities. The method allows for the construction of solution branches and the identification of their bifurcation structure. Supplementing the adjoint continuation method with a computation of the Floquet multipliers allows for explicit determination of the stability of each branch. This method reveals that, when gain is increased, the multi-pulsing transition starts with a Hopf bifurcation, followed by a period-doubling bifurcation, and a saddle-node bifurcation for limit cycles. Finally, the system exhibits chaotic dynamics and transitions to the double-pulse solutions. Although this method is applied specifically to the waveguide array mode-locking model, the multi-pulsing transition is conjectured to be ubiquitous and these results agree with experimental and computational results from other models.

### A. J. Aspden, J. B. Bell, S. Dong, and S. E. Woosley, "Burning Thermals in Type Ia Supernovae", Astrophysical Journal, 738, 94-107, 2011,

- Download File: abdw.pdf (pdf: 3.7 MB)

### N. Aghanim, M. Arnaud, M. Ashdown, J. Aumont, C. Baccigalupi, A. Balbi, A.J. Banday, R.B. Barreiro, M. Bartelmann, J.G. Bartlett, E. Battaner, K. Benabed, A. Benoît, J.-P. Bernard, M. Bersanelli, R. Bhatia, J.J. Bock, A. Bonaldi, J.R. Bond, J. Borrill, F.R. Bouchet, M.L. Brown, M. Bucher, C. Burigana, P. Cabella, J.-F. Cardoso, A. Catalano, L. Cayón, A. Challinor, A. Chamballu, R.-R. Chary, L.-Y. Chiang, C. Chiang, G. Chon, P.R. Christensen, E. Churazov, D.L. Clements, S. Colafrancesco, S. Colombi, F. Couchot, A. Coulais, B.P. Crill, F. Cuttaia, A. Da Silva, H. Dahle, L. Danese, P. De Bernardis, G. De Gasperis, A. De Rosa, G. De Zotti, J. Delabrouille, J.-M. Delouis, F.-X. Désert, J.M. Diego, K. Dolag, S. Donzelli, O. Doré, U. Dörl, M. Douspis, X. Dupac, G. Efstathiou, T.A. Enßlin, F. Finelli, I. Flores-Cacho, O. Forni, M. Frailis, E. Franceschi, S. Fromenteau, S. Galeotta, K. Ganga, R.T. Génova-Santos, M. Giard, G. Giardino, Y. Giraud-Héraud, J. González-Nuevo, K.M. Górski, S. Gratton, A. Gregorio, A. Gruppuso, D. Harrison, S. Henrot-Versillé, C. Hernández-Monteagudo, D. Herranz, S.R. Hildebrandt, E. Hivon, M. Hobson, W.A. Holmes, W. Hovest, R.J. Hoyland, K.M. Huffenberger, A.H. Jaffe, W.C. Jones, M. Juvela, E. Keihänen, R. Keskitalo, T.S. Kisner, R. Kneissl, L. Knox, H. Kurki-Suonio, G. Lagache, J.-M. Lamarre, A. Lasenby, R.J. Laureijs, C.R. Lawrence, S. Leach, R. Leonardi, M. Linden-Vørnle, M. López-Caniego, P.M. Lubin, J.F. MacÍas-Pérez, C.J. MacTavish, B. Maffei, D. Maino, N. Mandolesi, R. Mann, M. Maris, F. Marleau, E. Martínez-González, S. Masi, S. Matarrese, F. Matthai, P. Mazzotta, A. Melchiorri, J.-B. Melin, L. Mendes, A. Mennella, S. Mitra, M.-A. Miville-Deschênes, A. Moneti, L. Montier, G. Morgante, D. Mortlock, D. Munshi, A. Murphy, P. Naselsky, P. Natoli, C.B. Netterfield, H.U. Nørgaard-Nielsen, F. Noviello, D. Novikov, I. Novikov, S. Osborne, F. Pajot, F. Pasian, G. Patanchon, O. Perdereau, L. Perotto, F. Perrotta, F. Piacentini, M. Piat, E. Pierpaoli, R. Piffaretti, S. Plaszczynski, E. Pointecouteau, G. Polenta, N. Ponthieu, T. Poutanen, G.W. Pratt, G. Prézeau, S. Prunet, J.-L. Puget, R. Rebolo, M. Reinecke, C. Renault, S. Ricciardi, T. Riller, I. Ristorcelli, G. Rocha, C. Rosset, J.A. Rubiño-Martín, B. Rusholme, M. Sandri, D. Santos, B.M. Schaefer, D. Scott, M.D. Seiffert, G.F. Smoot, J.-L. Starck, F. Stivoli, V. Stolyarov, R. Sunyaev, J.-F. Sygnet, J.A. Tauber, L. Terenzi, L. Toffolatti, M. Tomasi, M. Tristram, J. Tuovinen, L. Valenziano, L. Vibert, P. Vielva, F. Villa, N. Vittorio, B.D. Wandelt, S.D.M. White, M. White, D. Yvon, A. Zacchei, A. Zonca, "Planck early results. X. Statistical analysis of Sunyaev-Zeldovich scaling relations for X-ray galaxy clusters", Astronomy and Astrophysics, January 2011, 536:A10, doi: 10.1051/0004-6361/201116457

### P. E. Nugent, M. Sullivan, S. B. Cenko, R. C. Thomas, D., D. A. Howell, D. Bersier, J. S. Bloom, S. R., M. T. Kandrashoff, A. V. Filippenko, J. M., G. W. Marcy, A. W. Howard, H. T., K. Maguire, N. Suzuki, J. E. Tarlton, Y.-C., L. Bildsten, B. J. Fulton, J. T. Parrent, D., P. Podsiadlowski, F. B. Bianco, B. Dilday, M. L., J. Lyman, P. James, M. M. Kasliwal, N. M., R. M. Quimby, I. M. Hook, E. S. Walker, P., E. Pian, E. O. Ofek, A. Gal-Yam, D. Poznanski, "Supernova SN 2011fe from an exploding carbon-oxygen white dwarf star", Nature, 2011, 480:344-347, doi: 10.1038/nature10644

### Jon Wilkening, "Breakdown of Self-Similarity at the Crests of Large-Amplitude Standing Water Waves", Phys. Rev. Lett., 2011, 107:184501, doi: 10.1103/PhysRevLett.107.184501

### Jiri Brabec, Sriram Krishnamoorthy, Hubertus J. J. van Dam, Karol Kowalski, Jiri Pittner, "Massively parallel implementation of the multireference Brillouin-Wigner CCSD method", Chemical Physics Letters, 2011, 514:347-351, doi: 10.1016/j.cplett.2011.08.016

### Tudor David, Mathias Jacquelin, Loris Marchal, "Scheduling streaming applications on a complex multicore platform", Concurrency and Computation: Practice and Experience, 2011, n/a--n/a, doi: 10.1002/cpe.1874

### R. C. Thomas, P. E. Nugent, J. C. Meza, "SYNAPPS: Data-Driven Analysis for Supernova Spectroscopy", Publications of the Astronomical Society of the Pacific, 2011, 123:237-248, doi: 10.1086/658673

### M. Wehner, L. Oliker, J. Shalf, D. Donofrio, L. Drummond, et al., "Hardware/Software Co-design of Global Cloud System Resolving Models", Journal of Advances in Modeling Earth Systems (JAMES), 2011, 3, M1000:22, doi: 10.1029/2011MS000073

- Download File: james11-climate.pdf (pdf: 1.7 MB)

### M. Zingale, A. Nonaka, A. S. Almgren, J. B. Bell, C. M. Malone, and S. E. Woosley, "The Convective Phase Preceding Type Ia Supernovae", Astrophysical Journal, 740, 8, 2011,

- Download File: wdconvect.pdf (pdf: 2.8 MB)

### A. Abergel, P.A.R. Ade, N. Aghanim, M. Arnaud, M. Ashdown, J. Aumont, C. Baccigalupi, A. Balbi, A.J. Banday, R.B. Barreiro, J.G. Bartlett, E. Battaner, K. Benabed, A. Benoît, J.-P. Bernard, M. Bersanelli, R. Bhatia, J.J. Bock, A. Bonaldi, J.R. Bond, J. Borrill, F.R. Bouchet, F. Boulanger, M. Bucher, C. Burigana, P. Cabella, J.-F. Cardoso, A. Catalano, L. Cayón, A. Challinor, A. Chamballu, L.-Y. Chiang, C. Chiang, P.R. Christensen, D.L. Clements, S. Colombi, F. Couchot, A. Coulais, B.P. Crill, F. Cuttaia, L. Danese, R.D. Davies, R.J. Davis, P. De Bernardis, G. De Gasperis, A. De Rosa, G. De Zotti, J. Delabrouille, J.-M. Delouis, F.-X. Désert, C. Dickinson, K. Dobashi, S. Donzelli, O. Doré, U. Dörl, M. Douspis, X. Dupac, G. Efstathiou, T.A. Enßlin, H.K. Eriksen, F. Finelli, O. Forni, M. Frailis, E. Franceschi, S. Galeotta, K. Ganga, M. Giard, G. Giardino, Y. Giraud-Héraud, J. González-Nuevo, K.M. Górski, S. Gratton, A. Gregorio, A. Gruppuso, V. Guillet, F.K. Hansen, D. Harrison, S. Henrot-Versillé, D. Herranz, S.R. Hildebrandt, E. Hivon, M. Hobson, W.A. Holmes, W. Hovest, R.J. Hoyland, K.M. Huffenberger, A.H. Jaffe, A. Jones, W.C. Jones, M. Juvela, E. Keihänen, R. Keskitalo, T.S. Kisner, R. Kneissl, L. Knox, H. Kurki-Suonio, G. Lagache, J.-M. Lamarre, A. Lasenby, R.J. Laureijs, C.R. Lawrence, S. Leach, R. Leonardi, C. Leroy, M. Linden-Vørnle, M. López-Caniego, P.M. Lubin, J.F. MacÍas-Pérez, C.J. MacTavish, B. Maffei, N. Mandolesi, R. Mann, M. Maris, D.J. Marshall, P. Martin, E. Martínez-González, S. Masi, S. Matarrese, F. Matthai, P. Mazzotta, P. McGehee, P.R. Meinhold, A. Melchiorri, L. Mendes, A. Mennella, S. Mitra, M.-A. Miville-Deschênes, A. Moneti, L. Montier, G. Morgante, D. Mortlock, D. Munshi, A. Murphy, P. Naselsky, P. Natoli, C.B. Netterfield, H.U. Nørgaard-Nielsen, F. Noviello, D. Novikov, I. Novikov, S. Osborne, F. Pajot, R. Paladini, F. Pasian, G. Patanchon, O. Perdereau, L. Perotto, F. Perrotta, F. Piacentini, M. Piat, S. Plaszczynski, E. Pointecouteau, G. Polenta, N. Ponthieu, T. Poutanen, G. Prézeau, S. Prunet, J.-L. Puget, W.T. Reach, R. Rebolo, M. Reinecke, C. Renault, S. Ricciardi, T. Riller, I. Ristorcelli, G. Rocha, C. Rosset, J.A. Rubiño-Martín, B. Rusholme, M. Sandri, D. Santos, G. Savini, D. Scott, M.D. Seiffert, P. Shellard, G.F. Smoot, J.-L. Starck, F. Stivoli, V. Stolyarov, R. Sudiwala, J.-F. Sygnet, J.A. Tauber, L. Terenzi, L. Toffolatti, M. Tomasi, J.-P. Torre, M. Tristram, J. Tuovinen, G. Umana, L. Valenziano, L. Verstraete, P. Vielva, F. Villa, N. Vittorio, L.A. Wade, B.D. Wandelt, D. Yvon, A. Zacchei, A. Zonca, "Planck early results. XXV. Thermal dust in nearby molecular clouds", Astronomy and Astrophysics, January 2011, 536:A25, doi: 10.1051/0004-6361/201116483

### N. Aghanim, M. Arnaud, M. Ashdown, J. Aumont, C. Baccigalupi, A. Balbi, A.J. Banday, R.B. Barreiro, M. Bartelmann, J.G. Bartlett, E. Battaner, K. Benabed, A. Benoît, J.-P. Bernard, M. Bersanelli, R. Bhatia, J.J. Bock, A. Bonaldi, J.R. Bond, J. Borrill, F.R. Bouchet, M.L. Brown, M. Bucher, C. Burigana, P. Cabella, C.M. Cantalupo, J.-F. Cardoso, P. Carvalho, A. Catalano, L. Cayón, A. Challinor, A. Chamballu, L.-Y. Chiang, G. Chon, P.R. Christensen, E. Churazov, D.L. Clements, S. Colafrancesco, S. Colombi, F. Couchot, A. Coulais, B.P. Crill, F. Cuttaia, A. Da Silva, H. Dahle, L. Danese, P. De Bernardis, G. De Gasperis, A. De Rosa, G. De Zotti, J. Delabrouille, J.-M. Delouis, F.-X. Désert, J.M. Diego, K. Dolag, S. Donzelli, O. Doré, U. Dörl, M. Douspis, X. Dupac, G. Efstathiou, T.A. Enßlin, F. Finelli, I. Flores-Cacho, O. Forni, M. Frailis, E. Franceschi, S. Fromenteau, S. Galeotta, K. Ganga, R.T. Génova-Santos, M. Giard, G. Giardino, Y. Giraud-Héraud, J. González-Nuevo, R. González-Riestra, K.M. Górski, S. Gratton, A. Gregorio, A. Gruppuso, D. Harrison, P. Heinämäki, S. Henrot-Versillé, C. Hernández-Monteagudo, D. Herranz, S.R. Hildebrandt, E. Hivon, M. Hobson, W.A. Holmes, W. Hovest, R.J. Hoyland, K.M. Huffenberger, G. Hurier, A.H. Jaffe, M. Juvela, E. Keihänen, R. Keskitalo, T.S. Kisner, R. Kneissl, L. Knox, H. Kurki-Suonio, G. Lagache, J.-M. Lamarre, A. Lasenby, R.J. Laureijs, C.R. Lawrence, M. Le Jeune, S. Leach, R. Leonardi, A. Liddle, M. Linden-Vørnle, M. López-Caniego, P.M. Lubin, J.F. MacÍas-Pérez, B. Maffei, D. Maino, N. Mandolesi, R. Mann, M. Maris, F. Marleau, E. Martínez-González, S. Masi, S. Matarrese, F. Matthai, P. Mazzotta, A. Melchiorri, J.-B. Melin, L. Mendes, A. Mennella, S. Mitra, M.-A. Miville-Deschênes, A. Moneti, L. Montier, G. Morgante, D. Mortlock, D. Munshi, A. Murphy, P. Naselsky, P. Natoli, C.B. Netterfield, H.U. Nørgaard-Nielsen, F. Noviello, D. Novikov, I. Novikov, S. Osborne, F. Pajot, F. Pasian, G. Patanchon, O. Perdereau, L. Perotto, F. Perrotta, F. Piacentini, M. Piat, E. Pierpaoli, R. Piffaretti, S. Plaszczynski, E. Pointecouteau, G. Polenta, N. Ponthieu, T. Poutanen, G.W. Pratt, G. Prézeau, S. Prunet, J.-L. Puget, R. Rebolo, M. Reinecke, C. Renault, S. Ricciardi, T. Riller, I. Ristorcelli, G. Rocha, C. Rosset, J.A. Rubiño-Martín, B. Rusholme, E. Saar, M. Sandri, D. Santos, B.M. Schaefer, D. Scott, M.D. Seiffert, G.F. Smoot, J.-L. Starck, F. Stivoli, V. Stolyarov, R. Sunyaev, J.-F. Sygnet, J.A. Tauber, L. Terenzi, L. Toffolatti, M. Tomasi, J.-P. Torre, M. Tristram, J. Tuovinen, L. Valenziano, L. Vibert, P. Vielva, F. Villa, N. Vittorio, B.D. Wandelt, S.D.M. White, D. Yvon, A. Zacchei, A. Zonca, "Planck early results. IX. XMM-Newton follow-up for validation of Planck cluster candidates", Astronomy and Astrophysics, January 2011, 536:A9, doi: 10.1051/0004-6361/201116460

### Maciej Haranczyk, Richard L. Martin, Prabhat, James A. Sethian & E. Wes Bethel, "Computational Approaches for the High-Throughput Analysis of Porous materials for Energy related applications", Scientific Discovery through Advanced Computing 2011, 2011,

### Abhinav Sarje, Srinivas Aluru, "Accelerating Pairwise Computations on Cell Processors", Transactions on Parallel and Distributed Systems (TPDS), January 2011, 22-1:69-77, doi: 10.1109/TPDS.2010.65

Direct computation of all pairwise distances or interactions is a fundamental problem that arises in many application areas including particle or atomistic simulations, fluid dynamics, computational electromagnetics, materials science, genomics and systems biology, and clustering and data mining. In this paper, we present methods for performing such pairwise computations efficiently in parallel on Cell processors. This problem is particularly challenging on the Cell processor due to the small sized Local Stores of the Synergistic Processing Elements, the main computational cores of the processor. We present techniques for different variants of this problem including those with large number of entities or when the dimensionality of the information per entity is large. We demonstrate our methods in the context of multiple applications drawn from fluid dynamics, materials science and systems biology, and present detailed experimental results. Our software library is an open source and can be readily used by application scientists to accelerate pairwise computations using Cell accelerators.

### K. Maguire, M. Sullivan, R. C. Thomas, P. Nugent, D. A., A. Gal-Yam, I. Arcavi, S. Ben-Ami, S., J. Botyanszki, C. Buton, J. Cooke, R. S., I. M. Hook, M. M. Kasliwal, Y.-C. Pan, R., P. Podsiadlowski, A. Sternberg, N., D. Xu, O. Yaron, J. S. Bloom, S. B., S. R. Kulkarni, N. Law, E. O. Ofek, D. Poznanski, R. M. Quimby, "PTF10ops - a subluminous, normal-width light curve Type Ia supernova in the middle of nowhere", Monthly Notices of the Royal Astronomical Society, 2011, 418:747-758, doi: 10.1111/j.1365-2966.2011.19526.x

### Daniel T. Kawano, Matthias Morzfeld, Fai Ma, "The decoupling of defective linear dynamical systems in free motion", Journal of Sound and Vibration, 2011, 330:5165--5183, doi: 10.1016/j.jsv.2011.05.013

### J. D. Neill, M. Sullivan, A. Gal-Yam, R. Quimby, E., T. K. Wyder, D. A. Howell, P. Nugent, M., D. C. Martin, R. Overzier, T. A. Barlow, K., P. G. Friedman, P. Morrissey, S. G. Neff, D., L. Bianchi, J. Donas, T. M. Heckman, Y.-W., B. F. Madore, B. Milliard, R. M. Rich, A. S. Szalay, "The Extreme Hosts of Extreme Supernovae", Astrophysical Journal, 2011, 727:15, doi: 10.1088/0004-637X/727/1/15

### A. Nonaka, S. May, A. S. Almgren, and J. B. Bell, "A Three-Dimensional, Unsplit Godunov Method for Scalar Conservation Laws", SIAM J. Sci. Comput., vol. 33, no. 4, 2011,

- Download File: BDS3d.pdf (pdf: 1 MB)

### A. Abergel, P.A.R. Ade, N. Aghanim, M. Arnaud, M. Ashdown, J. Aumont, C. Baccigalupi, A. Balbi, A.J. Banday, R.B. Barreiro, J.G. Bartlett, E. Battaner, K. Benabed, A. Benoît, J.-P. Bernard, M. Bersanelli, R. Bhatia, K. Blagrave, J.J. Bock, A. Bonaldi, J.R. Bond, J. Borrill, F.R. Bouchet, F. Boulanger, M. Bucher, C. Burigana, P. Cabella, C.M. Cantalupo, J.-F. Cardoso, A. Catalano, L. Cayón, A. Challinor, A. Chamballu, L.-Y. Chiang, C. Chiang, P.R. Christensen, D.L. Clements, S. Colombi, F. Couchot, A. Coulais, B.P. Crill, F. Cuttaia, L. Danese, R.D. Davies, R.J. Davis, P. De Bernardis, G. De Gasperis, A. De Rosa, G. De Zotti, J. Delabrouille, J.-M. Delouis, F.-X. Désert, C. Dickinson, S. Donzelli, O. Doré, U. Dörl, M. Douspis, X. Dupac, G. Efstathiou, T.A. Enßlin, H.K. Eriksen, F. Finelli, O. Forni, M. Frailis, E. Franceschi, S. Galeotta, K. Ganga, M. Giard, G. Giardino, Y. Giraud-Héraud, J. González-Nuevo, K.M. Górski, S. Gratton, A. Gregorio, A. Gruppuso, F.K. Hansen, D. Harrison, G. Helou, S. Henrot-Versillé, D. Herranz, S.R. Hildebrandt, E. Hivon, M. Hobson, W.A. Holmes, W. Hovest, R.J. Hoyland, K.M. Huffenberger, A.H. Jaffe, G. Joncas, A. Jones, W.C. Jones, M. Juvela, E. Keihänen, R. Keskitalo, T.S. Kisner, R. Kneissl, L. Knox, H. Kurki-Suonio, G. Lagache, J.-M. Lamarre, A. Lasenby, R.J. Laureijs, C.R. Lawrence, S. Leach, R. Leonardi, C. Leroy, M. Linden-Vørnle, F.J. Lockman, M. López-Caniego, P.M. Lubin, J.F. MacÍas-Pérez, C.J. MacTavish, B. Maffei, D. Maino, N. Mandolesi, R. Mann, M. Maris, D.J. Marshall, P. Martin, E. Martínez-González, S. Masi, S. Matarrese, F. Matthai, P. Mazzotta, P. McGehee, P.R. Meinhold, A. Melchiorri, L. Mendes, A. Mennella, M.-A. Miville-Deschênes, A. Moneti, L. Montier, G. Morgante, D. Mortlock, D. Munshi, A. Murphy, P. Naselsky, F. Nati, P. Natoli, C.B. Netterfield, H.U. Nørgaard-Nielsen, F. Noviello, D. Novikov, I. Novikov, I.J. O Dwyer, S. Osborne, F. Pajot, R. Paladini, F. Pasian, G. Patanchon, O. Perdereau, L. Perotto, F. Perrotta, F. Piacentini, M. Piat, D. Pinheiro Gonçalves, S. Plaszczynski, E. Pointecouteau, G. Polenta, N. Ponthieu, T. Poutanen, G. Prézeau, S. Prunet, J.-L. Puget, J.P. Rachen, W.T. Reach, M. Reinecke, C. Renault, S. Ricciardi, T. Riller, I. Ristorcelli, G. Rocha, C. Rosset, M. Rowan-Robinson, J.A. Rubiño-Martín, B. Rusholme, M. Sandri, D. Santos, G. Savini, D. Scott, M.D. Seiffert, P. Shellard, G.F. Smoot, J.-L. Starck, F. Stivoli, V. Stolyarov, R. Stompor, R. Sudiwala, J.-F. Sygnet, J.A. Tauber, L. Terenzi, L. Toffolatti, M. Tomasi, J.-P. Torre, M. Tristram, J. Tuovinen, G. Umana, L. Valenziano, P. Vielva, F. Villa, N. Vittorio, L.A. Wade, B.D. Wandelt, A. Wilkinson, D. Yvon, A. Zacchei, A. Zonca, "Planck early results. XXIV. Dust in the diffuse interstellar medium and the Galactic halo", Astronomy and Astrophysics, January 2011, 536:A24, doi: 10.1051/0004-6361/201116485

### P.A.R. Ade, N. Aghanim, M. Arnaud, M. Ashdown, J. Aumont, C. Baccigalupi, A. Balbi, A.J. Banday, R.B. Barreiro, M. Bartelmann, J.G. Bartlett, E. Battaner, R. Battye, K. Benabed, A. Benoît, J.-P. Bernard, M. Bersanelli, R. Bhatia, J.J. Bock, A. Bonaldi, J.R. Bond, J. Borrill, F.R. Bouchet, M.L. Brown, M. Bucher, C. Burigana, P. Cabella, C.M. Cantalupo, J.-F. Cardoso, P. Carvalho, A. Catalano, L. Cayón, A. Challinor, A. Chamballu, R.-R. Chary, L.-Y. Chiang, C. Chiang, G. Chon, P.R. Christensen, E. Churazov, D.L. Clements, S. Colafrancesco, S. Colombi, F. Couchot, A. Coulais, B.P. Crill, F. Cuttaia, A. Da Silva, H. Dahle, L. Danese, R.J. Davis, P. De Bernardis, G. De Gasperis, A. De Rosa, G. De Zotti, J. Delabrouille, J.-M. Delouis, F.-X. Désert, C. Dickinson, J.M. Diego, K. Dolag, H. Dole, S. Donzelli, O. Doré, U. Dörl, M. Douspis, X. Dupac, G. Efstathiou, P. Eisenhardt, T.A. Enßlin, F. Feroz, F. Finelli, I. Flores-Cacho, O. Forni, P. Fosalba, M. Frailis, E. Franceschi, S. Fromenteau, S. Galeotta, K. Ganga, R.T. Génova-Santos, M. Giard, G. Giardino, Y. Giraud-Héraud, J. González-Nuevo, R. González-Riestra, K.M. Górski, K.J.B. Grainge, S. Gratton, A. Gregorio, A. Gruppuso, D. Harrison, P. Heinämäki, S. Henrot-Versillé, C. Hernández-Monteagudo, D. Herranz, S.R. Hildebrandt, E. Hivon, M. Hobson, W.A. Holmes, W. Hovest, R.J. Hoyland, K.M. Huffenberger, G. Hurier, N. Hurley-Walker, A.H. Jaffe, W.C. Jones, M. Juvela, E. Keihänen, R. Keskitalo, T.S. Kisner, R. Kneissl, L. Knox, H. Kurki-Suonio, G. Lagache, J.-M. Lamarre, A. Lasenby, R.J. Laureijs, C.R. Lawrence, M. Le Jeune, S. Leach, R. Leonardi, C. Li, A. Liddle, P.B. Lilje, M. Linden-Vørnle, M. López-Caniego, P.M. Lubin, J.F. MacÍas-Pérez, C.J. MacTavish, B. Maffei, D. Maino, N. Mandolesi, R. Mann, M. Maris, F. Marleau, E. Martínez-González, S. Masi, S. Matarrese, F. Matthai, P. Mazzotta, S. Mei, P.R. Meinhold, A. Melchiorri, J.-B. Melin, L. Mendes, A. Mennella, S. Mitra, M.-A. Miville-Deschênes, A. Moneti, L. Montier, G. Morgante, D. Mortlock, D. Munshi, A. Murphy, P. Naselsky, F. Nati, P. Natoli, C.B. Netterfield, H.U. Nørgaard-Nielsen, F. Noviello, D. Novikov, I. Novikov, M. Olamaie, S. Osborne, F. Pajot, F. Pasian, G. Patanchon, T.J. Pearson, O. Perdereau, L. Perotto, F. Perrotta, F. Piacentini, M. Piat, E. Pierpaoli, R. Piffaretti, S. Plaszczynski, E. Pointecouteau, G. Polenta, N. Ponthieu, T. Poutanen, G.W. Pratt, G. Prézeau, S. Prunet, J.-L. Puget, J.P. Rachen, W.T. Reach, R. Rebolo, M. Reinecke, C. Renault, S. Ricciardi, T. Riller, I. Ristorcelli, G. Rocha, C. Rosset, J.A. Rubiño-Martín, B. Rusholme, E. Saar, M. Sandri, D. Santos, R.D.E. Saunders, G. Savini, B.M. Schaefer, D. Scott, M.D. Seiffert, P. Shellard, G.F. Smoot, A. Stanford, J.-L. Starck, F. Stivoli, V. Stolyarov, R. Stompor, R. Sudiwala, R. Sunyaev, D. Sutton, J.-F. Sygnet, N. Taburet, J.A. Tauber, L. Terenzi, L. Toffolatti, M. Tomasi, J.-P. Torre, M. Tristram, J. Tuovinen, L. Valenziano, L. Vibert, P. Vielva, F. Villa, N. Vittorio, L.A. Wade, B.D. Wandelt, J. Weller, S.D.M. White, M. White, D. Yvon, A. Zacchei, A. Zonca, "Planck early results. VIII. The all-sky early Sunyaev-Zeldovich cluster sample", Astronomy and Astrophysics, January 2011, 536:A8, doi: 10.1051/0004-6361/201116459

### I. Arcavi, A. Gal-Yam, O. Yaron, A. Sternberg, I., E. Waxman, M. M. Kasliwal, R. M. Quimby, E. O., A. Horesh, S. R. Kulkarni, A. V. Filippenko, J. M., S. B. Cenko, W. Li, J. S. Bloom, M., P. E. Nugent, D. Poznanski, E. Gorbikov, B. J., D. A. Howell, D. Bersier, A. Riou, S., T. Griga, J. G. Cohen, S., D. Polishook, D. Xu, S. Ben-Ami, I., E. S. Walker, K. Maguire, Y.-C. Pan, T., P. A. Mazzali, E. Pian, D. B. Fox, N., N. Law, P. James, J. M. Marchant, R. J., C. J. Mottram, R. M. Barnsley, M. T. Kandrashoff, K. I. Clubb, "SN 2011dh: Discovery of a Type IIb Supernova from a Compact Progenitor in the Nearby Galaxy M51", Astrophysical Journal, 2011, 742:L18, doi: 10.1088/2041-8205/742/2/L18

### K. Krisciunas, W. Li, T. Matheson, D. A. Howell, M., G. Aldering, P. L. Berlind, M., P. Challis, R. Chornock, A. Conley, A. V., M. Ganeshalingam, L. Germany, S., S. D. Gooding, E. Hsiao, D., R. P. Kirshner, G. H. Howie Marion, C., P. E. Nugent, M. Phelps, M. M. Phillips, Y., R. Quimby, K. Rines, J. M. Silverman, N. B. Suntzeff, R. C. Thomas, L. Wang, "The Most Slowly Declining Type Ia Supernova 2001ay", Astronomical Journal, 2011, 142:74, doi: 10.1088/0004-6256/142/3/74

### S. May, A. Nonaka, A. S. Almgren, and J. B. Bell, "An Unsplit, Higher-Order Godunov Method Using Quadratic Reconstruction for Advection in Two Dimensions", Comm. App. Math. and Comp. Sci., vol. 6, no. 1, 2011,

### P.A.R. Ade, N. Aghanim, M. Arnaud, M. Ashdown, J. Aumont, C. Baccigalupi, A. Balbi, A.J. Banday, R.B. Barreiro, J.G. Bartlett, E. Battaner, K. Benabed, A. Benoît, J.-P. Bernard, M. Bersanelli, R. Bhatia, J.J. Bock, A. Bonaldi, J.R. Bond, J. Borrill, F.R. Bouchet, F. Boulanger, M. Bucher, C. Burigana, P. Cabella, C.M. Cantalupo, J.-F. Cardoso, A. Catalano, L. Cayón, A. Challinor, A. Chamballu, R.-R. Chary, L.-Y. Chiang, P.R. Christensen, D.L. Clements, S. Colombi, F. Couchot, A. Coulais, B.P. Crill, F. Cuttaia, L. Danese, R.D. Davies, R.J. Davis, P. De Bernardis, G. De Gasperis, A. De Rosa, G. De Zotti, J. Delabrouille, J.-M. Delouis, F.-X. Désert, C. Dickinson, K. Dobashi, S. Donzelli, O. Doré, U. Dörl, M. Douspis, X. Dupac, G. Efstathiou, T.A. Enßlin, E. Falgarone, F. Finelli, O. Forni, M. Frailis, E. Franceschi, S. Galeotta, K. Ganga, M. Giard, G. Giardino, Y. Giraud-Héraud, J. González-Nuevo, K.M. Górski, S. Gratton, A. Gregorio, A. Gruppuso, F.K. Hansen, D. Harrison, G. Helou, S. Henrot-Versillé, D. Herranz, S.R. Hildebrandt, E. Hivon, M. Hobson, W.A. Holmes, W. Hovest, R.J. Hoyland, K.M. Huffenberger, A.H. Jaffe, G. Joncas, W.C. Jones, M. Juvela, E. Keihänen, R. Keskitalo, T.S. Kisner, R. Kneissl, L. Knox, H. Kurki-Suonio, G. Lagache, J.-M. Lamarre, A. Lasenby, R.J. Laureijs, C.R. Lawrence, S. Leach, R. Leonardi, C. Leroy, M. Linden-Vørnle, M. López-Caniego, P.M. Lubin, J.F. MacÍas-Pérez, C.J. MacTavish, B. Maffei, N. Mandolesi, R. Mann, M. Maris, D.J. Marshall, P. Martin, E. Martínez-González, G. Marton, S. Masi, S. Matarrese, F. Matthai, P. Mazzotta, P. McGehee, A. Melchiorri, L. Mendes, A. Mennella, S. Mitra, M.-A. Miville-Deschênes, A. Moneti, L. Montier, G. Morgante, D. Mortlock, D. Munshi, A. Murphy, P. Naselsky, F. Nati, P. Natoli, C.B. Netterfield, H.U. Nørgaard-Nielsen, F. Noviello, D. Novikov, I. Novikov, S. Osborne, F. Pajot, R. Paladini, F. Pasian, G. Patanchon, T.J. Pearson, V.-M. Pelkonen, O. Perdereau, L. Perotto, F. Perrotta, F. Piacentini, M. Piat, S. Plaszczynski, E. Pointecouteau, G. Polenta, N. Ponthieu, T. Poutanen, G. Prézeau, S. Prunet, J.-L. Puget, W.T. Reach, R. Rebolo, M. Reinecke, C. Renault, S. Ricciardi, T. Riller, I. Ristorcelli, G. Rocha, C. Rosset, M. Rowan-Robinson, J.A. Rubiño-Martín, B. Rusholme, M. Sandri, D. Santos, G. Savini, D. Scott, M.D. Seiffert, G.F. Smoot, J.-L. Starck, F. Stivoli, V. Stolyarov, R. Sudiwala, J.-F. Sygnet, J.A. Tauber, L. Terenzi, L. Toffolatti, M. Tomasi, J.-P. Torre, V. Toth, M. Tristram, J. Tuovinen, G. Umana, L. Valenziano, P. Vielva, F. Villa, N. Vittorio, L.A. Wade, B.D. Wandelt, N. Ysard, D. Yvon, A. Zacchei, S. Zahorecz, A. Zonca, "Planck early results. XXIII. The first all-sky survey of Galactic cold clumps", Astronomy and Astrophysics, January 2011, 536:A23, doi: 10.1051/0004-6361/201116472

### P.A.R. Ade, N. Aghanim, M. Arnaud, M. Ashdown, J. Aumont, C. Baccigalupi, A. Balbi, A.J. Banday, R.B. Barreiro, J.G. Bartlett, E. Battaner, K. Benabed, A. Benoît, J.-P. Bernard, M. Bersanelli, R. Bhatia, A. Bonaldi, L. Bonavera, J.R. Bond, J. Borrill, F.R. Bouchet, M. Bucher, C. Burigana, R.C. Butler, P. Cabella, C.M. Cantalupo, B. Cappellini, J.-F. Cardoso, P. Carvalho, A. Catalano, L. Cayón, A. Challinor, A. Chamballu, R.-R. Chary, X. Chen, L.-Y. Chiang, C. Chiang, P.R. Christensen, D.L. Clements, S. Colombi, F. Couchot, A. Coulais, B.P. Crill, F. Cuttaia, L. Danese, R.J. Davis, P. De Bernardis, A. De Rosa, G. De Zotti, J. Delabrouille, J.-M. Delouis, F.-X. Désert, C. Dickinson, J.M. Diego, K. Dolag, H. Dole, S. Donzelli, O. Doré, U. Dörl, M. Douspis, X. Dupac, G. Efstathiou, T.A. Enßlin, H.K. Eriksen, F. Finelli, O. Forni, P. Fosalba, M. Frailis, E. Franceschi, S. Galeotta, K. Ganga, M. Giard, Y. Giraud-Héraud, J. González-Nuevo, K.M. Górski, S. Gratton, A. Gregorio, A. Gruppuso, J. Haissinski, F.K. Hansen, D. Harrison, G. Helou, S. Henrot-Versillé, C. Hernández-Monteagudo, D. Herranz, S.R. Hildebrandt, E. Hivon, M. Hobson, W.A. Holmes, A. Hornstrup, W. Hovest, R.J. Hoyland, K.M. Huffenberger, M. Huynh, A.H. Jaffe, W.C. Jones, M. Juvela, E. Keihänen, R. Keskitalo, T.S. Kisner, R. Kneissl, L. Knox, H. Kurki-Suonio, G. Lagache, A. Lähteenmäki, J.-M. Lamarre, A. Lasenby, R.J. Laureijs, C.R. Lawrence, S. Leach, J.P. Leahy, R. Leonardi, J. León-Tavares, C. Leroy, P.B. Lilje, M. Linden-Vørnle, M. López-Caniego, P.M. Lubin, J.F. MacÍas-Pérez, C.J. MacTavish, B. Maffei, G. Maggio, D. Maino, N. Mandolesi, R. Mann, M. Maris, F. Marleau, D.J. Marshall, E. Martínez-González, S. Masi, M. Massardi, S. Matarrese, F. Matthai, P. Mazzotta, P. McGehee, P.R. Meinhold, A. Melchiorri, J.-B. Melin, L. Mendes, A. Mennella, S. Mitra, M.-A. Miville-Deschênes, A. Moneti, L. Montier, G. Morgante, D. Mortlock, D. Munshi, A. Murphy, P. Naselsky, P. Natoli, C.B. Netterfield, H.U. Nørgaard-Nielsen, F. Noviello, D. Novikov, I. Novikov, I.J. O Dwyer, S. Osborne, F. Pajot, R. Paladini, B. Partridge, F. Pasian, G. Patanchon, T.J. Pearson, O. Perdereau, L. Perotto, F. Perrotta, F. Piacentini, M. Piat, R. Piffaretti, S. Plaszczynski, P. Platania, E. Pointecouteau, G. Polenta, N. Ponthieu, T. Poutanen, G.W. Pratt, G. Prézeau, S. Prunet, J.-L. Puget, J.P. Rachen, W.T. Reach, R. Rebolo, M. Reinecke, C. Renault, S. Ricciardi, T. Riller, I. Ristorcelli, G. Rocha, C. Rosset, M. Rowan-Robinson, J.A. Rubiño-Martín, B. Rusholme, A. Sajina, M. Sandri, D. Santos, G. Savini, B.M. Schaefer, D. Scott, M.D. Seiffert, P. Shellard, G.F. Smoot, J.-L. Starck, F. Stivoli, V. Stolyarov, R. Sudiwala, R. Sunyaev, J.-F. Sygnet, J.A. Tauber, D. Tavagnacco, L. Terenzi, L. Toffolatti, M. Tomasi, J.-P. Torre, M. Tristram, J. Tuovinen, M. Türler, G. Umana, L. Valenziano, J. Valiviita, J. Varis, P. Vielva, F. Villa, N. Vittorio, L.A. Wade, B.D. Wandelt, S.D.M. White, A. Wilkinson, D. Yvon, A. Zacchei, A. Zonca, "Planck early results. VII. The Early Release Compact Source Catalogue", Astronomy and Astrophysics, January 2011, 536:A7, doi: 10.1051/0004-6361/201116474

### Z. Cano, D. Bersier, C. Guidorzi, S. Kobayashi, A. J., N. R. Tanvir, K. Wiersema, P. D Avanzo, A. S., P. Garnavich, A. Gomboc, J. Gorosabel, D., D. Kopa\v c, R. Margutti, P. A. Mazzali, A., C. G. Mundell, P. E. Nugent, E., R. J. Smith, I. Steele, R. A. M. J. Wijers, S. E. Woosley, "XRF 100316D/SN 2010bh and the Nature of Gamma-Ray Burst Supernovae", Astrophysical Journal, 2011, 740:41, doi: 10.1088/0004-637X/740/1/41

### J. C. van Eyken, D. R. Ciardi, L. M. Rebull, J. R., R. L. Akeson, C. A. Beichman, A. F., K. von Braun, D. M. Gelino, D. W. Hoard, S. B., S. R. Kane, P. Plavchan, S. V. Ramirez, J. S., S. B. Cenko, M. M. Kasliwal, S. R., N. M. Law, P. E. Nugent, E. O. Ofek, D., R. M. Quimby, C. J. Grillmair, R., D. Levitan, S. Mattingly, J. A. Surace, "The Palomar Transient Factory Orion Project: Eclipsing Binaries and Young Stellar Objects", Astronomical Journal, 2011, 142:60, doi: 10.1088/0004-6256/142/2/60

### A. J. Aspden, M. S. Day, and J. B. Bell, "Turbulence-Flame Interactions in Lean Premixed Hydrogen: Transition to the Distributed Burning Regime", Journal of Fluid Mechanics, 680, 287-320, doi:10.1017/jfm.2011.164, 2011,

- Download File: adbjfm10.pdf (pdf: 3.5 MB)

### Emmanouela Rantsiou, Adam Burrows, Jason Nordhaus, Ann Almgren, "Induced Rotation in Three-Dimensional Simulations of Core-Collapse Supernovae: Implications for Pulsar Spins", Astrophysical Journal, 732, 57, 2011,

### P.A.R. Ade, N. Aghanim, M. Arnaud, M. Ashdown, J. Aumont, C. Baccigalupi, A. Balbi, A.J. Banday, R.B. Barreiro, J.G. Bartlett, E. Battaner, K. Benabed, A. Benoît, J.-P. Bernard, M. Bersanelli, R. Bhatia, J.J. Bock, A. Bonaldi, J.R. Bond, J. Borrill, F.R. Bouchet, F. Boulanger, M. Bucher, C. Burigana, P. Cabella, C.M. Cantalupo, J.-F. Cardoso, A. Catalano, L. Cayón, A. Challinor, A. Chamballu, L.-Y. Chiang, P.R. Christensen, D.L. Clements, S. Colombi, F. Couchot, A. Coulais, B.P. Crill, F. Cuttaia, L. Danese, R.D. Davies, P. De Bernardis, G. De Gasperis, A. De Rosa, G. De Zotti, J. Delabrouille, J.-M. Delouis, F.-X. Désert, C. Dickinson, Y. Doi, S. Donzelli, O. Doré, U. Dörl, M. Douspis, X. Dupac, G. Efstathiou, T.A. Enßlin, E. Falgarone, F. Finelli, O. Forni, M. Frailis, E. Franceschi, S. Galeotta, K. Ganga, M. Giard, G. Giardino, Y. Giraud-Héraud, J. González-Nuevo, K.M. Górski, S. Gratton, A. Gregorio, A. Gruppuso, F.K. Hansen, D. Harrison, G. Helou, S. Henrot-Versillé, D. Herranz, S.R. Hildebrandt, E. Hivon, M. Hobson, W.A. Holmes, W. Hovest, R.J. Hoyland, K.M. Huffenberger, N. Ikeda, A.H. Jaffe, W.C. Jones, M. Juvela, E. Keihänen, R. Keskitalo, T.S. Kisner, Y. Kitamura, R. Kneissl, L. Knox, H. Kurki-Suonio, G. Lagache, J.-M. Lamarre, A. Lasenby, R.J. Laureijs, C.R. Lawrence, S. Leach, R. Leonardi, C. Leroy, M. Linden-Vørnle, M. López-Caniego, P.M. Lubin, J.F. MacÍas-Pérez, C.J. MacTavish, B. Maffei, J. Malinen, N. Mandolesi, R. Mann, M. Maris, D.J. Marshall, P. Martin, E. Martínez-González, S. Masi, S. Matarrese, F. Matthai, P. Mazzotta, P. McGehee, A. Melchiorri, L. Mendes, A. Mennella, C. Meny, S. Mitra, M.-A. Miville-Deschênes, A. Moneti, L. Montier, G. Morgante, D. Mortlock, D. Munshi, A. Murphy, P. Naselsky, F. Nati, P. Natoli, C.B. Netterfield, H.U. Nørgaard-Nielsen, F. Noviello, D. Novikov, I. Novikov, S. Osborne, L. Pagani, F. Pajot, R. Paladini, F. Pasian, G. Patanchon, V.-M. Pelkonen, O. Perdereau, L. Perotto, F. Perrotta, F. Piacentini, M. Piat, S. Plaszczynski, E. Pointecouteau, G. Polenta, N. Ponthieu, T. Poutanen, G. Prézeau, S. Prunet, J.-L. Puget, W.T. Reach, R. Rebolo, M. Reinecke, C. Renault, S. Ricciardi, T. Riller, I. Ristorcelli, G. Rocha, C. Rosset, M. Rowan-Robinson, J.A. Rubiño-Martín, B. Rusholme, M. Sandri, D. Santos, G. Savini, D. Scott, M.D. Seiffert, G.F. Smoot, J.-L. Starck, F. Stivoli, V. Stolyarov, R. Sudiwala, J.-F. Sygnet, J.A. Tauber, L. Terenzi, L. Toffolatti, M. Tomasi, J.-P. Torre, V. Toth, M. Tristram, J. Tuovinen, G. Umana, L. Valenziano, P. Vielva, F. Villa, N. Vittorio, L.A. Wade, B.D. Wandelt, N. Ysard, D. Yvon, A. Zacchei, A. Zonca, "Planck early results. XXII. The submillimetre properties of a sample of Galactic cold clumps", Astronomy and Astrophysics, January 2011, 536:A22, doi: 10.1051/0004-6361/201116481

### P.A.R. Ade, N. Aghanim, R. Ansari, M. Arnaud, M. Ashdown, J. Aumont, A.J. Banday, M. Bartelmann, J.G. Bartlett, E. Battaner, K. Benabed, A. Benoît, J.-P. Bernard, M. Bersanelli, J.J. Bock, J.R. Bond, J. Borrill, F.R. Bouchet, F. Boulanger, T. Bradshaw, M. Bucher, J.-F. Cardoso, G. Castex, A. Catalano, A. Challinor, A. Chamballu, R.-R. Chary, X. Chen, C. Chiang, S. Church, D.L. Clements, J.-M. Colley, S. Colombi, F. Couchot, A. Coulais, C. Cressiot, B.P. Crill, M. Crook, P. De Bernardis, J. Delabrouille, J.-M. Delouis, F.-X. Désert, K. Dolag, H. Dole, O. Doré, M. Douspis, J. Dunkley, G. Efstathiou, C. Filliard, O. Forni, P. Fosalba, K. Ganga, M. Giard, D. Girard, Y. Giraud-Héraud, R. Gispert, K.M. Górski, S. Gratton, M. Griffin, G. Guyot, J. Haissinski, D. Harrison, G. Helou, S. Henrot-Versillé, C. Hernández-Monteagudo, S.R. Hildebrandt, R. Hills, E. Hivon, M. Hobson, W.A. Holmes, K.M. Huffenberger, A.H. Jaffe, W.C. Jones, J. Kaplan, R. Kneissl, L. Knox, M. Kunz, G. Lagache, J.-M. Lamarre, A.E. Lange, A. Lasenby, A. Lavabre, C.R. Lawrence, M. Le Jeune, C. Leroy, J. Lesgourgues, J.F. MacÍas-Pérez, C.J. MacTavish, B. Maffei, N. Mandolesi, R. Mann, F. Marleau, D.J. Marshall, S. Masi, T. Matsumura, I. McAuley, P. McGehee, J.-B. Melin, C. Mercier, S. Mitra, M.-A. Miville-Deschênes, A. Moneti, L. Montier, D. Mortlock, A. Murphy, F. Nati, C.B. Netterfield, H.U. Nørgaard-Nielsen, C. North, F. Noviello, D. Novikov, S. Osborne, F. Pajot, G. Patanchon, T. Peacocke, T.J. Pearson, O. Perdereau, L. Perotto, F. Piacentini, M. Piat, S. Plaszczynski, E. Pointecouteau, N. Ponthieu, G. Prézeau, S. Prunet, J.-L. Puget, W.T. Reach, M. Remazeilles, C. Renault, A. Riazuelo, I. Ristorcelli, G. Rocha, C. Rosset, G. Roudier, M. Rowan-Robinson, B. Rusholme, R. Saha, D. Santos, G. Savini, B.M. Schaefer, P. Shellard, L. Spencer, J.-L. Starck, V. Stolyarov, R. Stompor, R. Sudiwala, R. Sunyaev, D. Sutton, J.-F. Sygnet, J.A. Tauber, C. Thum, J.-P. Torre, F. Touze, M. Tristram, F. Van Leeuwen, L. Vibert, D. Vibert, L.A. Wade, B.D. Wandelt, S.D.M. White, H. Wiesemeyer, A. Woodcraft, V. Yurchenko, D. Yvon, A. Zacchei, "Planck early results. VI. The High Frequency Instrument data processing", Astronomy and Astrophysics, January 2011, 536:A6, doi: 10.1051/0004-6361/201116462

### Bremer, P.-T., Weber, G.H., Tierny, J., Pascucci, V., Day, M.S., and Bell, J.B., "Interactive Exploration and Analysis of Large Scale Turbulent Combustion Using Topology-based Data Segmentatio", IEEE Transactions on Visualization and Computer Graphics, 2011, 17(9):1307-1324, LBNL 5921E, doi: 10.1109/TVCG.2010.253

### D. Levitan, B. J. Fulton, P. J. Groot, S. R. Kulkarni, E. O., T. A. Prince, A. Shporer, J. S. Bloom, S. B., M. M. Kasliwal, N. M. Law, P. E. Nugent, D., R. M. Quimby, A. Horesh, B. Sesar, A. Sternberg, "PTF1 J071912.13+485834.0: An Outbursting AM CVn System Discovered by a Synoptic Survey", Astrophysical Journal, 2011, 739:68, doi: 10.1088/0004-637X/739/2/68

### Matthias Morzfeld, Fai Ma, "The decoupling of damped linear systems in configuration and state spaces", Journal of Sound and Vibration, 2011, 330:155--161, doi: 10.1016/j.jsv.2010.09.005

### Z. Cano, D. Bersier, C. Guidorzi, R. Margutti, K. M., S. Kobayashi, A. Melandri, K., A. Pozanenko, A. J. van der Horst, G. G., A. Fernandez-Soto, A. J. Castro-Tirado, A. D. U., M. Im, A. P. Kamble, D. Sahu, J., G. Anupama, J. L. Bibby, M. J., N. Clay, P. A. Curran, T. A. Fatkhullin, A. S., P. Garnavich, A. Gomboc, J. Gorosabel, J. F., U. Gurugubelli, J. Haislip, K., A. Huxor, M. Ibrahimov, Y. Jeon, Y.-B., K. Ivarsen, D. Kasen, E. Klunko, C., A. Lacluyze, A. J. Levan, V., P. A. Mazzali, A. S. Moskvitin, C., C. G. Mundell, P. E. Nugent, M. Nysewander, P. T., W.-K. Park, V. Peris, E. Pian, D., J. E. Rhoads, E. Rol, V. Rumyantsev, V., D. Shakhovskoy, E. Small, R. J. Smith, V. V., R. L. C. Starling, I. Steele, R. G., N. R. Tanvir, Y. Tsapras, Y. Urata, O., A. Volnova, A. Volvach, R. A. M. J. Wijers, S. E. Woosley, D. R. Young, "A tale of two GRB-SNe at a common redshift of z=0.54", Monthly Notices of the Royal Astronomical Society, 2011, 413:669-685, doi: 10.1111/j.1365-2966.2010.18164.x

### M. Sullivan, M. M. Kasliwal, P. E. Nugent, D. A., R. C. Thomas, E. O. Ofek, I. Arcavi, S., J. Cooke, A. Gal-Yam, I. M. Hook, P., P. Podsiadlowski, R. Quimby, L. Bildsten, J. S., S. B. Cenko, S. R. Kulkarni, N. Law, D. Poznanski, "The Subluminous and Peculiar Type Ia Supernova PTF 09dav", Astrophysical Journal, 2011, 732:118, doi: 10.1088/0004-637X/732/2/118

### "Emerging Programming Paradigms for Large-Scale Scientific Computing", Guest editors, Parallel Computing special issue,'Emerging Programming Paradigms for Large-Scale Scientific Computing", 2011,

- Download File: parco11-guestintro.pdf (pdf: 82 KB)

### J. Bell and M. Day, "Adaptive Methods for Simulation of Turbulent Combustion", Turbulent Combustion Modeling, Advances, New Trends and Perspectives Series: Fluid Mechanics and Its Applications", Echekki and Epaminondas (Eds.), Springer, Vol. 95, 2011,

### A. Abergel, P.A.R. Ade, N. Aghanim, M. Arnaud, M. Ashdown, J. Aumont, C. Baccigalupi, A. Balbi, A.J. Banday, R.B. Barreiro, J.G. Bartlett, E. Battaner, K. Benabed, A. Benoît, J.-P. Bernard, M. Bersanelli, R. Bhatia, J.J. Bock, A. Bonaldi, J.R. Bond, J. Borrill, F.R. Bouchet, F. Boulanger, M. Bucher, C. Burigana, P. Cabella, J.-F. Cardoso, A. Catalano, L. Cayón, A. Challinor, A. Chamballu, L.-Y. Chiang, C. Chiang, P.R. Christensen, S. Colombi, F. Couchot, A. Coulais, B.P. Crill, F. Cuttaia, T.M. Dame, L. Danese, R.D. Davies, R.J. Davis, P. De Bernardis, G. De Gasperis, A. De Rosa, G. De Zotti, J. Delabrouille, J.-M. Delouis, F.-X. Désert, C. Dickinson, S. Donzelli, O. Doré, U. Dörl, M. Douspis, X. Dupac, G. Efstathiou, T.A. Enßlin, F. Finelli, O. Forni, M. Frailis, E. Franceschi, S. Galeotta, K. Ganga, M. Giard, G. Giardino, Y. Giraud-Héraud, J. González-Nuevo, K.M. Górski, S. Gratton, A. Gregorio, I.A. Grenier, A. Gruppuso, F.K. Hansen, D. Harrison, S. Henrot-Versillé, D. Herranz, S.R. Hildebrandt, E. Hivon, M. Hobson, W.A. Holmes, W. Hovest, R.J. Hoyland, K.M. Huffenberger, T.R. Jaffe, A.H. Jaffe, W.C. Jones, M. Juvela, E. Keihänen, R. Keskitalo, T.S. Kisner, R. Kneissl, L. Knox, H. Kurki-Suonio, G. Lagache, A. Lähteenmäki, J.-M. Lamarre, A. Lasenby, R.J. Laureijs, C.R. Lawrence, S. Leach, R. Leonardi, C. Leroy, P.B. Lilje, M. Linden-Vørnle, M. López-Caniego, P.M. Lubin, J.F. MacÍas-Pérez, C.J. MacTavish, B. Maffei, N. Mandolesi, R. Mann, M. Maris, D.J. Marshall, E. Martínez-González, S. Masi, S. Matarrese, F. Matthai, P. Mazzotta, P. McGehee, P.R. Meinhold, A. Melchiorri, L. Mendes, A. Mennella, M.-A. Miville-Deschênes, A. Moneti, L. Montier, G. Morgante, D. Mortlock, D. Munshi, A. Murphy, P. Naselsky, P. Natoli, C.B. Netterfield, H.U. Nørgaard-Nielsen, F. Noviello, D. Novikov, I. Novikov, S. Osborne, F. Pajot, R. Paladini, F. Pasian, G. Patanchon, O. Perdereau, L. Perotto, F. Perrotta, F. Piacentini, M. Piat, S. Plaszczynski, E. Pointecouteau, G. Polenta, N. Ponthieu, T. Poutanen, G. Prézeau, S. Prunet, J.-L. Puget, J.P. Rachen, W.T. Reach, R. Rebolo, W. Reich, C. Renault, S. Ricciardi, T. Riller, I. Ristorcelli, G. Rocha, C. Rosset, J.A. Rubiño-Martín, B. Rusholme, M. Sandri, D. Santos, G. Savini, D. Scott, M.D. Seiffert, P. Shellard, G.F. Smoot, J.-L. Starck, F. Stivoli, V. Stolyarov, R. Stompor, R. Sudiwala, J.-F. Sygnet, J.A. Tauber, L. Terenzi, L. Toffolatti, M. Tomasi, J.-P. Torre, M. Tristram, J. Tuovinen, G. Umana, L. Valenziano, J. Varis, P. Vielva, F. Villa, N. Vittorio, L.A. Wade, B.D. Wandelt, A. Wilkinson, N. Ysard, D. Yvon, A. Zacchei, A. Zonca, "Planck early results. XXI. Properties of the interstellar medium in the Galactic plane", Astronomy and Astrophysics, January 2011, 536:A21, doi: 10.1051/0004-6361/201116455

### A. Zacchei, D. Maino, C. Baccigalupi, M. Bersanelli, A. Bonaldi, L. Bonavera, C. Burigana, R.C. Butler, F. Cuttaia, G. De Zotti, J. Dick, M. Frailis, S. Galeotta, J. González-Nuevo, K.M. Górski, A. Gregorio, E. Keihänen, R. Keskitalo, J. Knoche, H. Kurki-Suonio, C.R. Lawrence, S. Leach, J.P. Leahy, M. López-Caniego, N. Mandolesi, M. Maris, F. Matthai, P.R. Meinhold, A. Mennella, G. Morgante, N. Morisset, P. Natoli, F. Pasian, F. Perrotta, G. Polenta, T. Poutanen, M. Reinecke, S. Ricciardi, R. Rohlfs, M. Sandri, A.-S. Suur-Uski, J.A. Tauber, D. Tavagnacco, L. Terenzi, M. Tomasi, J. Valiviita, F. Villa, A. Zonca, A.J. Banday, R.B. Barreiro, J.G. Bartlett, N. Bartolo, L. Bedini, K. Bennett, P. Binko, J. Borrill, F.R. Bouchet, M. Bremer, P. Cabella, B. Cappellini, X. Chen, L. Colombo, M. Cruz, A. Curto, L. Danese, R.D. Davies, R.J. Davis, G. De Gasperis, A. De Rosa, G. De Troia, C. Dickinson, J.M. Diego, S. Donzelli, U. Dörl, G. Efstathiou, T.A. Enßlin, H.K. Eriksen, M.C. Falvella, F. Finelli, E. Franceschi, T.C. Gaier, F. Gasparo, R.T. Génova-Santos, G. Giardino, F. Gómez, A. Gruppuso, F.K. Hansen, R. Hell, D. Herranz, W. Hovest, M. Huynh, J. Jewell, M. Juvela, T.S. Kisner, L. Knox, A. Lähteenmäki, J.-M. Lamarre, R. Leonardi, J. León-Tavares, P.B. Lilje, P.M. Lubin, G. Maggio, D. Marinucci, E. Martínez-González, M. Massardi, S. Matarrese, M.T. Meharga, A. Melchiorri, M. Migliaccio, S. Mitra, A. Moss, H.U. Nørgaard-Nielsen, L. Pagano, R. Paladini, D. Paoletti, B. Partridge, D. Pearson, V. Pettorino, D. Pietrobon, G. Prézeau, P. Procopio, J.-L. Puget, C. Quercellini, J.P. Rachen, R. Rebolo, G. Robbers, G. Rocha, J.A. Rubiño-Martín, E. Salerno, M. Savelainen, D. Scott, M.D. Seiffert, J.I. Silk, G.F. Smoot, J. Sternberg, F. Stivoli, R. Stompor, G. Tofani, L. Toffolatti, J. Tuovinen, M. Türler, G. Umana, P. Vielva, N. Vittorio, C. Vuerli, L.A. Wade, R. Watson, S.D.M. White, A. Wilkinson, "Planck early results. V. The Low Frequency Instrument data processing", Astronomy and Astrophysics, January 2011, 536:A5, doi: 10.1051/0004-6361/201116484

### Luke J. Gosink, Christoph Garth, John C. Anderson, E. Wes Bethel, and Kenneth I. Joy, "An Application of Multivariate Statistical Analysis for Query-Driven Visualization", IEEE Transactions on Visualization and Computer Graphics, 2011, 11:264-275, LBNL 3536E, doi: 10.1109/TVCG.2010.80

- Download File: LBNL-3536E.pdf (pdf: 13 MB)

### Michael Wehner, David R. Easterling, Jay H. Lawrimore, Richard R. Heim Jr., Russell S. Vose, and Benjamin Santer, "Projections of Future Drought in the Continental United States and Mexico", Journal of Hydrometerology, 2011, 12:1359–1377, doi: 10.1175/2011JHM1351.1

Using the Palmer drought severity index, the ability of 19 state-of-the-art climate models to reproduce observed statistics of drought over North America is examined. It is found that correction of substantial biases in the models’ surface air temperature and precipitation fields is necessary. However, even after a bias correction, there are significant differences in the models’ ability to reproduce observations. Using metrics based on the ability to reproduce observed temporal and spatial patterns of drought, the relationship between model performance in simulating present-day drought characteristics and their differences in projections of future drought changes is investigated. It is found that all models project increases in future drought frequency and severity. However, using the metrics presented here to increase confidence in the multimodel projection is complicated by a correlation between models’ drought metric skill and climate sensitivity. The effect of this sampling error can be removed by changing how the projection is presented, from a projection based on a specific time interval to a projection based on a specified temperature change. This modified class of projections has reduced intermodel uncertainty and could be suitable for a wide range of climate change impacts projections.

### A. Gal-Yam, M. M. Kasliwal, I. Arcavi, Y. Green, O., S. Ben-Ami, D. Xu, A. Sternberg, R. M., S. R. Kulkarni, E. O. Ofek, R., P. E. Nugent, D. Poznanski, J. S. Bloom, S. B., A. V. Filippenko, W. Li, J. M. Silverman, E. S., M. Sullivan, K. Maguire, D. A. Howell, P. A., D. A. Frail, D. Bersier, P. A. James, C. W., F. Yuan, N. Law, D. B. Fox, N. Gehrels, "Real-time Detection and Rapid Multiwavelength Follow-up Observations of a Highly Subluminous Type II-P Supernova from the Palomar Transient Factory Survey", Astrophysical Journal, 2011, 736:159, doi: 10.1088/0004-637X/736/2/159

### M. Garzon, L. J. Gray, J. A. Sethian, "Simulation of the droplet-to-bubble transition in a two-fluid system", Phys. Rev. E, 2011, 83:046318, doi: 10.1103/PhysRevE.83.046318

### E. Vecharynski and J. Langou, "Any admissible cycle-convergence behavior is possible for restarted GMRES at its initial cycles", Numerical Linear Algebra with Applications Vol. 18, Issue 3, pp. 499-511, 2011,

We show that any admissible cycle-convergence behavior is possible for restarted GMRES at a number of initial cycles, moreover the spectrum of the coefficient matrix alone does not determine this cycle-convergence. The latter can be viewed as an extension of the result of Greenbaum, Pták and Strakosˇ (SIAM Journal on Matrix Analysis and Applications 1996; 17(3):465–469) to the case of restarted GMRES.

### Kamesh Madduri, Eun-Jin Im, Khaled Z. Ibrahim, Samuel Williams, Stephane Ethier, Leonid Oliker, "Gyrokinetic Particle-in-cell Optimization on Emerging Multi- and Manycore Platforms", Parallel Computing (PARCO), January 2011, 37:501 - 520, doi: 10.1016/j.parco.2011.02.001

- Download File: parco11-gtc.pdf (pdf: 2 MB)

### A. J. Aspden, J. B. Bell, and S. E. Woosley, "Turbulent Oxygen Flames in Type Ia Supernovae", Astrophysical Journal, 730, 144-151, 2011,

- Download File: abwII.pdf (pdf: 2.6 MB)

### P.A.R. Ade, N. Aghanim, M. Arnaud, M. Ashdown, J. Aumont, C. Baccigalupi, A. Balbi, A.J. Banday, R.B. Barreiro, J.G. Bartlett, E. Battaner, K. Benabed, A. Benoît, J.-P. Bernard, M. Bersanelli, R. Bhatia, J.J. Bock, A. Bonaldi, J.R. Bond, J. Borrill, F.R. Bouchet, F. Boulanger, M. Bucher, C. Burigana, P. Cabella, B. Cappellini, J.-F. Cardoso, S. Casassus, A. Catalano, L. Cayón, A. Challinor, A. Chamballu, R.-R. Chary, X. Chen, L.-Y. Chiang, C. Chiang, P.R. Christensen, D.L. Clements, S. Colombi, F. Couchot, A. Coulais, B.P. Crill, F. Cuttaia, L. Danese, R.D. Davies, R.J. Davis, P. De Bernardis, G. De Gasperis, A. De Rosa, G. De Zotti, J. Delabrouille, J.-M. Delouis, C. Dickinson, S. Donzelli, O. Doré, U. Dörl, M. Douspis, X. Dupac, G. Efstathiou, T.A. Enßlin, H.K. Eriksen, F. Finelli, O. Forni, M. Frailis, E. Franceschi, S. Galeotta, K. Ganga, R.T. Génova-Santos, M. Giard, G. Giardino, Y. Giraud-Héraud, J. González-Nuevo, K.M. Górski, S. Gratton, A. Gregorio, A. Gruppuso, F.K. Hansen, D. Harrison, G. Helou, S. Henrot-Versillé, D. Herranz, S.R. Hildebrandt, E. Hivon, M. Hobson, W.A. Holmes, W. Hovest, R.J. Hoyland, K.M. Huffenberger, T.R. Jaffe, A.H. Jaffe, W.C. Jones, M. Juvela, E. Keihänen, R. Keskitalo, T.S. Kisner, R. Kneissl, L. Knox, H. Kurki-Suonio, G. Lagache, A. Lähteenmäki, J.-M. Lamarre, A. Lasenby, R.J. Laureijs, C.R. Lawrence, S. Leach, R. Leonardi, P.B. Lilje, M. Linden-Vørnle, M. López-Caniego, P.M. Lubin, J.F. MacÍas-Pérez, C.J. MacTavish, B. Maffei, D. Maino, N. Mandolesi, R. Mann, M. Maris, D.J. Marshall, E. Martínez-González, S. Masi, S. Matarrese, F. Matthai, P. Mazzotta, P. McGehee, P.R. Meinhold, A. Melchiorri, L. Mendes, A. Mennella, S. Mitra, M.-A. Miville-Deschênes, A. Moneti, L. Montier, G. Morgante, D. Mortlock, D. Munshi, A. Murphy, P. Naselsky, P. Natoli, C.B. Netterfield, H.U. Nørgaard-Nielsen, F. Noviello, D. Novikov, I. Novikov, I.J. O Dwyer, S. Osborne, F. Pajot, R. Paladini, B. Partridge, F. Pasian, G. Patanchon, T.J. Pearson, M. Peel, O. Perdereau, L. Perotto, F. Perrotta, F. Piacentini, M. Piat, S. Plaszczynski, P. Platania, E. Pointecouteau, G. Polenta, N. Ponthieu, T. Poutanen, G. Prézeau, P. Procopio, S. Prunet, J.-L. Puget, W.T. Reach, R. Rebolo, W. Reich, M. Reinecke, C. Renault, S. Ricciardi, T. Riller, I. Ristorcelli, G. Rocha, C. Rosset, M. Rowan-Robinson, J.A. Rubiño-Martín, B. Rusholme, M. Sandri, D. Santos, G. Savini, D. Scott, M.D. Seiffert, P. Shellard, G.F. Smoot, J.-L. Starck, F. Stivoli, V. Stolyarov, R. Stompor, R. Sudiwala, J.-F. Sygnet, J.A. Tauber, L. Terenzi, L. Toffolatti, M. Tomasi, J.-P. Torre, M. Tristram, J. Tuovinen, G. Umana, L. Valenziano, J. Varis, L. Verstraete, P. Vielva, F. Villa, N. Vittorio, L.A. Wade, B.D. Wandelt, R. Watson, A. Wilkinson, N. Ysard, D. Yvon, A. Zacchei, A. Zonca, "Planck early results. XX. New light on anomalous microwave emission from spinning dust grains", Astronomy and Astrophysics, January 2011, 536:A20, doi: 10.1051/0004-6361/201116470

### P.A.R. Ade, N. Aghanim, R. Ansari, M. Arnaud, M. Ashdown, J. Aumont, A.J. Banday, M. Bartelmann, J.G. Bartlett, E. Battaner, K. Benabed, A. Benoît, J.-P. Bernard, M. Bersanelli, R. Bhatia, J.J. Bock, J.R. Bond, J. Borrill, F.R. Bouchet, F. Boulanger, T. Bradshaw, E. Bréelle, M. Bucher, P. Camus, J.-F. Cardoso, A. Catalano, A. Challinor, A. Chamballu, J. Charra, M. Charra, R.-R. Chary, C. Chiang, S. Church, D.L. Clements, S. Colombi, F. Couchot, A. Coulais, C. Cressiot, B.P. Crill, M. Crook, P. De Bernardis, J. Delabrouille, J.-M. Delouis, F.-X. Désert, K. Dolag, H. Dole, O. Doré, M. Douspis, G. Efstathiou, P. Eng, C. Filliard, O. Forni, P. Fosalba, J.-J. Fourmond, K. Ganga, M. Giard, D. Girard, Y. Giraud-Héraud, R. Gispert, K.M. Górski, S. Gratton, M. Griffin, G. Guyot, J. Haissinski, D. Harrison, G. Helou, S. Henrot-Versillé, C. Hernández-Monteagudo, S.R. Hildebrandt, R. Hills, E. Hivon, M. Hobson, W.A. Holmes, K.M. Huffenberger, A.H. Jaffe, W.C. Jones, J. Kaplan, R. Kneissl, L. Knox, G. Lagache, J.-M. Lamarre, P. Lami, A.E. Lange, A. Lasenby, A. Lavabre, C.R. Lawrence, B. Leriche, C. Leroy, Y. Longval, J.F. MacÍas-Pérez, T. MacIaszek, C.J. MacTavish, B. Maffei, N. Mandolesi, R. Mann, B. Mansoux, S. Masi, T. Matsumura, P. McGehee, J.-B. Melin, C. Mercier, M.-A. Miville-Deschênes, A. Moneti, L. Montier, D. Mortlock, A. Murphy, F. Nati, C.B. Netterfield, H.U. Nørgaard-Nielsen, C. North, F. Noviello, D. Novikov, S. Osborne, C. Paine, F. Pajot, G. Patanchon, T. Peacocke, T.J. Pearson, O. Perdereau, L. Perotto, F. Piacentini, M. Piat, S. Plaszczynski, E. Pointecouteau, R. Pons, N. Ponthieu, G. Prézeau, S. Prunet, J.-L. Puget, W.T. Reach, C. Renault, I. Ristorcelli, G. Rocha, C. Rosset, G. Roudier, M. Rowan-Robinson, B. Rusholme, D. Santos, G. Savini, B.M. Schaefer, P. Shellard, L. Spencer, J.-L. Starck, P. Stassi, V. Stolyarov, R. Stompor, R. Sudiwala, R. Sunyaev, J.-F. Sygnet, J.A. Tauber, C. Thum, J.-P. Torre, F. Touze, M. Tristram, F. Van Leeuwen, L. Vibert, D. Vibert, L.A. Wade, B.D. Wandelt, S.D.M. White, H. Wiesemeyer, A. Woodcraft, V. Yurchenko, D. Yvon, A. Zacchei, "Planck early results. IV. First assessment of the High Frequency Instrument in-flight performance", Astronomy and Astrophysics, January 2011, 536:A4, doi: 10.1051/0004-6361/201116487

### Fuyu Li, William Collins, Michael Wehner, David Williamson, Jerry Olson, "Response of precipitation extremes to idealized global warming in an aqua-planet climate model: towards a robust projection across different horizontal resolutions", Tellus, January 1, 2011, 63, No.:876-883, doi: 10.1111/j.1600-0870.2011.00543.x

Current climate models produce quite heterogeneous projections for the responses of precipitation extremes to future climate change. To help understand the range of projections from multimodel ensembles, a series of idealized ‘aquaplanet’ Atmospheric General Circulation Model (AGCM) runs have been performed with the Community Atmosphere Model CAM3. These runs have been analysed to identify the effects of horizontal resolution on precipitation extreme projections under two simple global warming scenarios. We adopt the aquaplanet framework for our simulations to remove any sensitivity to the spatial resolution of external inputs and to focus on the roles of model physics and dynamics. Results show that a uniform increase of sea surface temperature (SST) and an increase of low-to-high latitude SST gradient both lead to increase of precipitation and precipitation extremes for most latitudes. The perturbed SSTs generally have stronger impacts on precipitation extremes than on mean precipitation. Horizontal model resolution strongly affects the global warming signals in the extreme precipitation in tropical and subtropical regions but not in high latitude regions. This study illustrates that the effects of horizontal resolution have to be taken into account to develop more robust projections of precipitation extremes.

### A. J. Levan, N. R. Tanvir, S. B. Cenko, D. A. Perley, K., J. S. Bloom, A. S. Fruchter, A. d. U., P. T. O Brien, N. Butler, A. J. der Horst, G. Leloudas, A. N. Morgan, K., G. C. Bower, J. Farihi, R. L. Tunnicliffe, M., J. M. Silverman, J. Hjorth, C. Th\ one, A., J. M. C. Cer\ on, A. J. Castro-Tirado, J. A., M. Bremer, J. P. Brodie, T. Carroll, M. C., P. A. Curran, R. M. Cutri, J. Ehle, D., J. Fynbo, J. Gorosabel, J. Graham, D. I., S. Guziy, P. Jakobsson, A. Kamble, T., M. M. Kasliwal, C. Kouveliotou, D. Kocevski, N. M., P. E. Nugent, E. O. Ofek, D. Poznanski, R. M., E. Rol, A. J. Romanowsky, R. S\ anchez-Ram\ \irez, S., N. Singh, L. van Spaandonk, R. L. C. Starling, R. G., J. C. Tello, O. Vaduvescu, P. J. Wheatley, R. A. M. J. Wijers, J. M. Winters, D. Xu, "An Extremely Luminous Panchromatic Outburst from the Nucleus of a Distant Galaxy", Science, 2011, 333:199-, doi: 10.1126/science.1207143

### M. Morzfeld, F. Ma, B. Parlett, "The Transformation of Second-Order Linear Systems into Independent Equations", SIAM Journal on Applied Mathematics, 2011, 71:1026-1043, doi: 10.1137/100818637

### P. Pall, T. Aina, D. A. Stone, P. A. Stott, T. Nozawa, A. G. J. Hilberts, D. Lohmann, M. R. Allen, "Anthropogenic greenhouse gas contribution to flood risk in England and Wales in Autumn 2000", Nature, 2011, 470:382--385,

### Xiaoye S. Li, Meiyue Shao, "A supernodal approach to incomplete LU factorization with partial pivoting", ACM Transactions on Mathematical Software, 2011, 37:43:1--43:2, doi: 10.1145/1916461.1916467

### B. Kallemov, G. H. Miller, S. Mitran and D. Trebotich, "Multiscale Rheology: New Results for the Kinetic Scale", NSTI-Nanotech 2011, Vol. 2, pp. 575-578 (2011), 2011,

- Download File: Nanotech2011.pdf (pdf: 203 KB)

### Ke-Jung Chen, Alexander Heger, and Ann Almgren, "Multi-Dimensional Simulations of Pair-Instability Supernovae", Computer Physics Communications, 182:1, 254-256, January 2011,

### A. Mennella, R.C. Butler, A. Curto, F. Cuttaia, R.J. Davis, J. Dick, M. Frailis, S. Galeotta, A. Gregorio, H. Kurki-Suonio, C.R. Lawrence, S. Leach, J.P. Leahy, S. Lowe, D. Maino, N. Mandolesi, M. Maris, E. Martínez-González, P.R. Meinhold, G. Morgante, D. Pearson, F. Perrotta, G. Polenta, T. Poutanen, M. Sandri, M.D. Seiffert, A.-S. Suur-Uski, D. Tavagnacco, L. Terenzi, M. Tomasi, J. Valiviita, F. Villa, R. Watson, A. Wilkinson, A. Zacchei, A. Zonca, B. Aja, E. Artal, C. Baccigalupi, A.J. Banday, R.B. Barreiro, J.G. Bartlett, N. Bartolo, P. Battaglia, K. Bennett, A. Bonaldi, L. Bonavera, J. Borrill, F.R. Bouchet, C. Burigana, P. Cabella, B. Cappellini, X. Chen, L. Colombo, M. Cruz, L. Danese, O. D Arcangelo, R.D. Davies, G. De Gasperis, A. De Rosa, G. De Zotti, C. Dickinson, J.M. Diego, S. Donzelli, G. Efstathiou, T.A. Enßlin, H.K. Eriksen, M.C. Falvella, F. Finelli, S. Foley, C. Franceschet, E. Franceschi, T.C. Gaier, R.T. Génova-Santos, D. George, F. Gómez, J. González-Nuevo, K.M. Górski, A. Gruppuso, F.K. Hansen, D. Herranz, J.M. Herreros, R.J. Hoyland, N. Hughes, J. Jewell, P. Jukkala, M. Juvela, P. Kangaslahti, E. Keihänen, R. Keskitalo, V.-H. Kilpia, T.S. Kisner, J. Knoche, L. Knox, M. Laaninen, A. Lähteenmäki, J.-M. Lamarre, R. Leonardi, J. León-Tavares, P. Leutenegger, P.B. Lilje, M. López-Caniego, P.M. Lubin, M. Malaspina, D. Marinucci, M. Massardi, S. Matarrese, F. Matthai, A. Melchiorri, L. Mendes, M. Miccolis, M. Migliaccio, S. Mitra, A. Moss, P. Natoli, R. Nesti, H.U. Nørgaard-Nielsen, L. Pagano, R. Paladini, D. Paoletti, B. Partridge, F. Pasian, V. Pettorino, D. Pietrobon, M. Pospieszalski, G. Prézeau, M. Prina, P. Procopio, J.-L. Puget, C. Quercellini, J.P. Rachen, R. Rebolo, M. Reinecke, S. Ricciardi, G. Robbers, G. Rocha, N. Roddis, J.A. Rubi No-Martín, M. Savelainen, D. Scott, R. Silvestri, A. Simonetto, P. Sjoman, G.F. Smoot, C. Sozzi, L. Stringhetti, J.A. Tauber, G. Tofani, L. Toffolatti, J. Tuovinen, M. Türler, G. Umana, L. Valenziano, J. Varis, P. Vielva, N. Vittorio, L.A. Wade, C. Watson, S.D.M. White, F. Winder, "Planck early results. III. First assessment of the Low Frequency Instrument in-flight performance", Astronomy and Astrophysics, January 2011, 536:A3, doi: 10.1051/0004-6361/201116480

### E. Wes Bethel, John van Rosendale, Dale Southard, Kelly Gaither, Hank Childs, Eric Brugger, Sean Ahern, "Visualization at Supercomputing Centers: The Tale of Little Big Iron and the Three Skinny Guys", IEEE Computer Graphics and Applications, January 2011, 31:90-95, LBNL 4180E,

- Download File: skinnyGuys.pdf (pdf: 428 KB)

### Fuyu Li, William Collins, Michael Wehner, David Williamson, Jerry Olson, and Christopher Algieri, "Impact of horizontal resolution on simulation of precipitation extremes in an aqua-planet version of Community Atmospheric Model (CAM3)", Tellus, 2011, 63, No. :884-823, doi: 10.1111/j.1600-0870.2011.00544.x

One key question regarding current climate models is whether the projection of climate extremes converges to a realistic representation as the spatial and temporal resolutions of the model are increased. Ideally the model extreme statistics should approach a fixed distribution once the resolutions are commensurate with the characteristic length and time scales of the processes governing the formation of the extreme phenomena of interest. In this study, a series of AGCM runs with idealized ‘aquaplanet-steady-state’ boundary conditions have been performed with the Community Atmosphere Model CAM3 to investigate the effect of horizontal resolution on climate extreme simulations. The use of the aquaplanet framework highlights the roles of model physics and dynamics and removes any apparent convergence in extreme statistics due to better resolution of surface boundary conditions and other external inputs. Assessed at a same large spatial scale, the results show that the horizontal resolution and time step have strong effects on the simulations of precipitation extremes. The horizontal resolution has a much stronger impact on precipitation extremes than on mean precipitation. Updrafts are strongly correlated with extreme precipitation at tropics at all the resolutions, while positive low-tropospheric temperature anomalies are associated with extreme precipitation at mid-latitudes.

### M. Childress, G. Aldering, C. Aragon, P. Antilogus, S., C. Baltay, S. Bongard, C. Buton, A., N. Chotard, Y. Copin, H. K. Fakhouri, E., M. Kerschhaggl, M. Kowalski, E. Y. Hsiao, S., P. Nugent, K. Paech, R. Pain, E., R. Pereira, S. Perlmutter, D. Rabinowitz, K., R. Scalzo, R. C. Thomas, G. Smadja, C. Tao, B. A. Weaver, C. Wu, "Keck Observations of the Young Metal-poor Host Galaxy of the Super-Chandrasekhar-mass Type Ia Supernova SN 2007if", Astrophysical Journal, 2011, 733:3, doi: 10.1088/0004-637X/733/1/3

### R. C. Thomas, G. Aldering, P. Antilogus, C. Aragon, S., C. Baltay, S. Bongard, C. Buton, A., M. Childress, N. Chotard, Y. Copin, H. K., E. Gangler, E. Y. Hsiao, M. Kerschhaggl, M., S. Loken, P. Nugent, K. Paech, R., E. Pecontal, R. Pereira, S. Perlmutter, D., M. Rigault, D. Rubin, K. Runge, R., G. Smadja, C. Tao, B. A. Weaver, C., P. J. Brown, P. A. Milne, Nearby Supernova Factory, "Type Ia Supernova Carbon Footprints", Astrophysical Journal, 2011, 743:27, doi: 10.1088/0004-637X/743/1/27

### B. Kallemov, G. H. Miller and D. Trebotich, "A Higher-Order Accurate Fluid-Particle Algorithm for Polymer Flows", Molecular Simulation, 37(8):738-745 (2011), 2011,

- Download File: MolSimPaper2011.pdf (pdf: 175 KB)

### M. S. Day, J. B. Bell, X. Gao and P. Glarborg, "Numerical Simulation of Nitrogen Oxide Formation in Lean Premixed Turbulent Flames", Proc. Combust. Inst. 33 p. 1591-1599, 2011,

### P.A.R. Ade, N. Aghanim, M. Arnaud, M. Ashdown, J. Aumont, C. Baccigalupi, A. Balbi, A.J. Banday, R.B. Barreiro, J.G. Bartlett, E. Battaner, K. Benabed, A. Benoît, J.-P. Bernard, M. Bersanelli, R. Bhatia, K. Blagrave, J.J. Bock, A. Bonaldi, L. Bonavera, J.R. Bond, J. Borrill, F.R. Bouchet, M. Bucher, C. Burigana, P. Cabella, J.-F. Cardoso, A. Catalano, L. Cayón, A. Challinor, A. Chamballu, L.-Y. Chiang, C. Chiang, P.R. Christensen, D.L. Clements, S. Colombi, F. Couchot, A. Coulais, B.P. Crill, F. Cuttaia, L. Danese, R.D. Davies, R.J. Davis, P. De Bernardis, G. De Gasperis, A. De Rosa, G. De Zotti, J. Delabrouille, J.-M. Delouis, F.-X. Désert, H. Dole, S. Donzelli, O. Doré, U. Dörl, M. Douspis, X. Dupac, G. Efstathiou, T.A. Enßlin, H.K. Eriksen, F. Finelli, O. Forni, P. Fosalba, M. Frailis, E. Franceschi, S. Galeotta, K. Ganga, M. Giard, G. Giardino, Y. Giraud-Héraud, J. González-Nuevo, K.M. Górski, J. Grain, S. Gratton, A. Gregorio, A. Gruppuso, F.K. Hansen, D. Harrison, G. Helou, S. Henrot-Versillé, D. Herranz, S.R. Hildebrandt, E. Hivon, M. Hobson, W.A. Holmes, W. Hovest, R.J. Hoyland, K.M. Huffenberger, A.H. Jaffe, W.C. Jones, M. Juvela, E. Keihänen, R. Keskitalo, T.S. Kisner, R. Kneissl, L. Knox, H. Kurki-Suonio, G. Lagache, J.-M. Lamarre, A. Lasenby, R.J. Laureijs, C.R. Lawrence, S. Leach, R. Leonardi, C. Leroy, P.B. Lilje, M. Linden-Vørnle, F.J. Lockman, M. López-Caniego, P.M. Lubin, J.F. MacÍas-Pérez, C.J. MacTavish, B. Maffei, D. Maino, N. Mandolesi, R. Mann, M. Maris, P. Martin, E. Martínez-González, S. Masi, S. Matarrese, F. Matthai, P. Mazzotta, A. Melchiorri, L. Mendes, A. Mennella, S. Mitra, M.-A. Miville-Deschênes, A. Moneti, L. Montier, G. Morgante, D. Mortlock, D. Munshi, A. Murphy, P. Naselsky, P. Natoli, C.B. Netterfield, H.U. Nørgaard-Nielsen, D. Novikov, I. Novikov, I.J. O Dwyer, S. Oliver, S. Osborne, F. Pajot, F. Pasian, G. Patanchon, O. Perdereau, L. Perotto, F. Perrotta, F. Piacentini, M. Piat, D. Pinheiro Gonçalves, S. Plaszczynski, E. Pointecouteau, G. Polenta, N. Ponthieu, T. Poutanen, G. Prézeau, S. Prunet, J.-L. Puget, J.P. Rachen, W.T. Reach, M. Reinecke, M. Remazeilles, C. Renault, S. Ricciardi, T. Riller, I. Ristorcelli, G. Rocha, C. Rosset, M. Rowan-Robinson, J.A. Rubiño-Martín, B. Rusholme, M. Sandri, D. Santos, G. Savini, D. Scott, M.D. Seiffert, P. Shellard, G.F. Smoot, J.-L. Starck, F. Stivoli, V. Stolyarov, R. Stompor, R. Sudiwala, R. Sunyaev, J.-F. Sygnet, J.A. Tauber, L. Terenzi, L. Toffolatti, M. Tomasi, J.-P. Torre, M. Tristram, J. Tuovinen, G. Umana, L. Valenziano, P. Vielva, F. Villa, N. Vittorio, L.A. Wade, B.D. Wandelt, M. White, D. Yvon, A. Zacchei, A. Zonca, "Planck early results. XVIII. The power spectrum of cosmic infrared background anisotropies", Astronomy and Astrophysics, January 2011, 536:A18, doi: 10.1051/0004-6361/201116461

### P.A.R. Ade, N. Aghanim, M. Arnaud, M. Ashdown, J. Aumont, C. Baccigalupi, M. Baker, A. Balbi, A.J. Banday, R.B. Barreiro, E. Battaner, K. Benabed, A. Benoît, J.-P. Bernard, M. Bersanelli, P. Bhandari, R. Bhatia, J.J. Bock, A. Bonaldi, J.R. Bond, J. Borders, J. Borrill, F.R. Bouchet, B. Bowman, T. Bradshaw, E. Bréelle, M. Bucher, C. Burigana, R.C. Butler, P. Cabella, P. Camus, C.M. Cantalupo, B. Cappellini, J.-F. Cardoso, A. Catalano, L. Cayón, A. Challinor, A. Chamballu, J.P. Chambelland, J. Charra, M. Charra, L.-Y. Chiang, C. Chiang, P.R. Christensen, D.L. Clements, B. Collaudin, S. Colombi, F. Couchot, A. Coulais, B.P. Crill, M. Crook, F. Cuttaia, C. Damasio, L. Danese, R.D. Davies, R.J. Davis, P. De Bernardis, G. De Gasperis, A. De Rosa, J. Delabrouille, J.-M. Delouis, F.-X. Désert, K. Dolag, S. Donzelli, O. Doré, U. Dörl, M. Douspis, X. Dupac, G. Efstathiou, T.A. Enßlin, H.K. Eriksen, C. Filliard, F. Finelli, S. Foley, O. Forni, P. Fosalba, J.-J. Fourmond, M. Frailis, E. Franceschi, S. Galeotta, K. Ganga, E. Gavila, M. Giard, G. Giardino, Y. Giraud-Héraud, J. González-Nuevo, K.M. Górski, S. Gratton, A. Gregorio, A. Gruppuso, G. Guyot, D. Harrison, G. Helou, S. Henrot-Versillé, C. Hernández-Monteagudo, D. Herranz, S.R. Hildebrandt, E. Hivon, M. Hobson, W.A. Holmes, A. Hornstrup, W. Hovest, R.J. Hoyland, K.M. Huffenberger, U. Israelsson, A.H. Jaffe, W.C. Jones, M. Juvela, E. Keihänen, R. Keskitalo, T.S. Kisner, R. Kneissl, L. Knox, H. Kurki-Suonio, G. Lagache, J.-M. Lamarre, P. Lami, A. Lasenby, R.J. Laureijs, A. Lavabre, C.R. Lawrence, S. Leach, R. Lee, R. Leonardi, C. Leroy, P.B. Lilje, M. López-Caniego, P.M. Lubin, J.F. MacÍas-Pérez, T. MacIaszek, C.J. MacTavish, B. Maffei, D. Maino, N. Mandolesi, R. Mann, M. Maris, E. Martínez-González, S. Masi, S. Matarrese, F. Matthai, P. Mazzotta, P. McGehee, P.R. Meinhold, A. Melchiorri, F. Melot, L. Mendes, A. Mennella, M.-A. Miville-Deschênes, A. Moneti, L. Montier, J. Mora, G. Morgante, N. Morisset, D. Mortlock, D. Munshi, A. Murphy, P. Naselsky, A. Nash, P. Natoli, C.B. Netterfield, D. Novikov, I. Novikov, I.J. O Dwyer, S. Osborne, F. Pajot, F. Pasian, G. Patanchon, D. Pearson, O. Perdereau, L. Perotto, F. Perrotta, F. Piacentini, M. Piat, S. Plaszczynski, P. Platania, E. Pointecouteau, G. Polenta, N. Ponthieu, T. Poutanen, G. Prézeau, M. Prina, S. Prunet, J.-L. Puget, J.P. Rachen, R. Rebolo, M. Reinecke, C. Renault, S. Ricciardi, T. Riller, I. Ristorcelli, G. Rocha, C. Rosset, J.A. Rubiño-Martín, B. Rusholme, M. Sandri, D. Santos, G. Savini, B.M. Schaefer, D. Scott, M.D. Seiffert, P. Shellard, G.F. Smoot, J.-L. Starck, P. Stassi, F. Stivoli, V. Stolyarov, R. Stompor, R. Sudiwala, J.-F. Sygnet, J.A. Tauber, L. Terenzi, L. Toffolatti, M. Tomasi, J.-P. Torre, M. Tristram, J. Tuovinen, L. Valenziano, L. Vibert, P. Vielva, F. Villa, N. Vittorio, L.A. Wade, B.D. Wandelt, C. Watson, S.D.M. White, A. Wilkinson, P. Wilson, D. Yvon, A. Zacchei, B. Zhang, A. Zonca, "Planck early results. II. The thermal performance of Planck", Astronomy and Astrophysics, January 2011, 536:A2, doi: 10.1051/0004-6361/201116486

### Chang, C.-Y., J. C. H. Chiang, M. F. Wehner, A. R. Friedman, R. Ruedy, "Sulfate Aerosol Control of Tropical Atlantic Climate over the Twentieth Century", Journal of Climate, 2011, 24:2540–2555, doi: 10.1175/2010JCLI4065.1

The tropical Atlantic interhemispheric gradient in sea surface temperature significantly influences the rainfall climate of the tropical Atlantic sector, including droughts over West Africa and Northeast Brazil. This gradient exhibits a secular trend from the beginning of the twentieth century until the 1980s, with stronger warming in the south relative to the north. This trend behavior is on top of a multidecadal variation associated with the Atlantic multidecadal oscillation. A similar long-term forced trend is found in a multimodel ensemble of forced twentieth-century climate simulations. Through examining the distribution of the trend slopes in the multimodel twentieth-century and preindustrial models, the authors conclude that the observed trend in the gradient is unlikely to arise purely from natural variations; this study suggests that at least half the observed trend is a forced response to twentieth-century climate forcings. Further analysis using twentieth-century single-forcing runs indicates that sulfate aerosol forcing is the predominant cause of the multimodel trend. The authors conclude that anthropogenic sulfate aerosol emissions, originating predominantly from the Northern Hemisphere, may have significantly altered the tropical Atlantic rainfall climate over the twentieth century.

### N. Chotard, E. Gangler, G. Aldering, P. Antilogus, C., S. Bailey, C. Baltay, S. Bongard, C., A. Canto, M. Childress, Y. Copin, H. K., E. Y. Hsiao, M. Kerschhaggl, M., S. Loken, P. Nugent, K. Paech, R., E. Pecontal, R. Pereira, S. Perlmutter, D., K. Runge, R. Scalzo, G. Smadja, C., R. C. Thomas, B. A. Weaver, C. Wu, Nearby Supernova Factory, "The reddening law of type Ia supernovae: separating intrinsic variability from dust using equivalent widths", Astronomy & Astrophysics, 2011, 529:L4, doi: 10.1051/0004-6361/201116723

### Kesheng Wu, Rishi R Sinha, Chad Jones, Ethier, Scott Klasky, Kwan-Liu Ma, Shoshani, Marianne Winslett, "Finding regions of interest on toroidal meshes", Computational Science \& Discovery, 2011, 4:015003, doi: 10.1088/1749-4699/4/1/015003

### A. L. Kay, S. M. Crooks, P. Pall, D. A. Stone, "Attribution of Autumn/Winter 2000 flood risk in England to anthropogenic climate change: a catchment-based study", J. Hydrol., 2011, 406:97--112, doi: 10.1016/j.jhydrol.2011.06.006

### R. M. Quimby, S. R. Kulkarni, M. M. Kasliwal, A., I. Arcavi, M. Sullivan, P. Nugent, R., D. A. Howell, E. Nakar, L. Bildsten, C., N. M. Law, R. Dekany, G. Rahmer, D., R. Smith, E. O. Ofek, J. Zolkower, V., R. Walters, J. Henning, K. Bui, D., D. Poznanski, S. B. Cenko, D. Levitan, "Hydrogen-poor superluminous stellar explosions", Nature, 2011, 474:487-489, doi: 10.1038/nature10095

### Dmitry Yu Zubarev, Xiaoqing You, Jarrod McClean, William A Lester Jr, Michael Frenklach, "Patterns of local aromaticity in graphene oxyradicals", Journal of Materials Chemistry, 2011, 21:3404--3409,

### P. McCorquodale and P. Colella, "A High-Order Finite-Volume Method for Conservation Laws on Locally Refined Grids", Communications in Applied Mathematics and Computational Science, Vol. 6 (2011), No. 1, 1-25, 2011,

### M. S. Day, X. Gao, and J. B. Bell, "Properties of Lean Turbulent Methane-Air Flames with Significant Hydrogen Addition", Proc. Combust. Inst. 33 p. 1601-1608, 2011,

### P.A.R. Ade, N. Aghanim, M. Arnaud, M. Ashdown, J. Aumont, C. Baccigalupi, A. Balbi, A.J. Banday, R.B. Barreiro, J.G. Bartlett, E. Battaner, K. Benabed, A. Benoît, J.-P. Bernard, M. Bersanelli, R. Bhatia, J.J. Bock, A. Bonaldi, J.R. Bond, J. Borrill, C. Bot, F.R. Bouchet, F. Boulanger, M. Bucher, C. Burigana, P. Cabella, J.-F. Cardoso, A. Catalano, L. Cayón, A. Challinor, A. Chamballu, L.-Y. Chiang, C. Chiang, P.R. Christensen, D.L. Clements, S. Colombi, F. Couchot, A. Coulais, B.P. Crill, F. Cuttaia, L. Danese, R.D. Davies, R.J. Davis, P. De Bernardis, G. De Gasperis, A. De Rosa, G. De Zotti, J. Delabrouille, J.-M. Delouis, F.-X. Désert, C. Dickinson, K. Dobashi, S. Donzelli, O. Doré, U. Dörl, M. Douspis, X. Dupac, G. Efstathiou, T.A. Enßlin, F. Finelli, O. Forni, M. Frailis, E. Franceschi, Y. Fukui, S. Galeotta, K. Ganga, M. Giard, G. Giardino, Y. Giraud-Héraud, J. González-Nuevo, K.M. Górski, S. Gratton, A. Gregorio, A. Gruppuso, D. Harrison, G. Helou, S. Henrot-Versillé, D. Herranz, S.R. Hildebrandt, E. Hivon, M. Hobson, W.A. Holmes, W. Hovest, R.J. Hoyland, K.M. Huffenberger, A.H. Jaffe, W.C. Jones, M. Juvela, A. Kawamura, E. Keihänen, R. Keskitalo, T.S. Kisner, R. Kneissl, L. Knox, H. Kurki-Suonio, G. Lagache, A. Lähteenmäki, J.-M. Lamarre, A. Lasenby, R.J. Laureijs, C.R. Lawrence, S. Leach, R. Leonardi, C. Leroy, M. Linden-Vørnle, M. López-Caniego, P.M. Lubin, J.F. MacÍas-Pérez, C.J. MacTavish, S. Madden, B. Maffei, N. Mandolesi, R. Mann, M. Maris, E. Martínez-González, S. Masi, S. Matarrese, F. Matthai, P. Mazzotta, P.R. Meinhold, A. Melchiorri, L. Mendes, A. Mennella, M.-A. Miville-Deschênes, A. Moneti, L. Montier, G. Morgante, D. Mortlock, D. Munshi, A. Murphy, P. Naselsky, F. Nati, P. Natoli, C.B. Netterfield, H.U. Nørgaard-Nielsen, F. Noviello, D. Novikov, I. Novikov, T. Onishi, S. Osborne, F. Pajot, R. Paladini, D. Paradis, F. Pasian, G. Patanchon, O. Perdereau, L. Perotto, F. Perrotta, F. Piacentini, M. Piat, S. Plaszczynski, E. Pointecouteau, G. Polenta, N. Ponthieu, T. Poutanen, G. Prézeau, S. Prunet, J.-L. Puget, W.T. Reach, R. Rebolo, M. Reinecke, C. Renault, S. Ricciardi, T. Riller, I. Ristorcelli, G. Rocha, C. Rosset, M. Rowan-Robinson, J.A. Rubiño-Martín, B. Rusholme, M. Sandri, G. Savini, D. Scott, M.D. Seiffert, G.F. Smoot, J.-L. Starck, F. Stivoli, V. Stolyarov, R. Sudiwala, J.-F. Sygnet, J.A. Tauber, L. Terenzi, L. Toffolatti, M. Tomasi, J.-P. Torre, M. Tristram, J. Tuovinen, G. Umana, L. Valenziano, J. Varis, P. Vielva, F. Villa, N. Vittorio, L.A. Wade, B.D. Wandelt, A. Wilkinson, N. Ysard, D. Yvon, A. Zacchei, A. Zonca, "Planck early results. XVII. Origin of the submillimetre excess dust emission in the Magellanic Clouds", Astronomy and Astrophysics, January 2011, 536:A17, doi: 10.1051/0004-6361/201116473

### P.A.R. Ade, N. Aghanim, M. Arnaud, M. Ashdown, J. Aumont, C. Baccigalupi, M. Baker, A. Balbi, A.J. Banday, R.B. Barreiro, J.G. Bartlett, E. Battaner, K. Benabed, K. Bennett, A. Benoît, J.-P. Bernard, M. Bersanelli, R. Bhatia, J.J. Bock, A. Bonaldi, J.R. Bond, J. Borrill, F.R. Bouchet, T. Bradshaw, M. Bremer, M. Bucher, C. Burigana, R.C. Butler, P. Cabella, C.M. Cantalupo, B. Cappellini, J.-F. Cardoso, R. Carr, M. Casale, A. Catalano, L. Cayón, A. Challinor, A. Chamballu, J. Charra, R.-R. Chary, L.-Y. Chiang, C. Chiang, P.R. Christensen, D.L. Clements, S. Colombi, F. Couchot, A. Coulais, B.P. Crill, G. Crone, M. Crook, F. Cuttaia, L. Danese, O. D Arcangelo, R.D. Davies, R.J. Davis, P. De Bernardis, J. De Bruin, G. De Gasperis, A. De Rosa, G. De Zotti, J. Delabrouille, J.-M. Delouis, F.-X. Désert, J. Dick, C. Dickinson, K. Dolag, H. Dole, S. Donzelli, O. Doré, U. Dörl, M. Douspis, X. Dupac, G. Efstathiou, T.A. Enßlin, H.K. Eriksen, F. Finelli, S. Foley, O. Forni, P. Fosalba, M. Frailis, E. Franceschi, M. Freschi, T.C. Gaier, S. Galeotta, J. Gallegos, B. Gandolfo, K. Ganga, M. Giard, G. Giardino, G. Gienger, Y. Giraud-Héraud, J. González, J. González-Nuevo, K.M. Górski, S. Gratton, A. Gregorio, A. Gruppuso, G. Guyot, J. Haissinski, F.K. Hansen, D. Harrison, G. Helou, S. Henrot-Versillé, C. Hernández-Monteagudo, D. Herranz, S.R. Hildebrandt, E. Hivon, M. Hobson, W.A. Holmes, A. Hornstrup, W. Hovest, R.J. Hoyland, K.M. Huffenberger, A.H. Jaffe, T. Jagemann, W.C. Jones, J.J. Juillet, M. Juvela, P. Kangaslahti, E. Keihänen, R. Keskitalo, T.S. Kisner, R. Kneissl, L. Knox, M. Krassenburg, H. Kurki-Suonio, G. Lagache, A. Lähteenmäki, J.-M. Lamarre, A.E. Lange, A. Lasenby, R.J. Laureijs, C.R. Lawrence, S. Leach, J.P. Leahy, R. Leonardi, C. Leroy, P.B. Lilje, M. Linden-Vørnle, M. López-Caniego, S. Lowe, P.M. Lubin, J.F. MacÍas-Pérez, T. MacIaszek, C.J. MacTavish, B. Maffei, D. Maino, N. Mandolesi, R. Mann, M. Maris, E. Martínez-González, S. Masi, M. Massardi, S. Matarrese, F. Matthai, P. Mazzotta, A. McDonald, P. McGehee, P.R. Meinhold, A. Melchiorri, J.-B. Melin, L. Mendes, A. Mennella, C. Mevi, R. Miniscalco, S. Mitra, M.-A. Miville-Deschênes, A. Moneti, L. Montier, G. Morgante, N. Morisset, D. Mortlock, D. Munshi, A. Murphy, P. Naselsky, P. Natoli, C.B. Netterfield, H.U. Nørgaard-Nielsen, F. Noviello, D. Novikov, I. Novikov, I.J. O Dwyer, I. Ortiz, S. Osborne, P. Osuna, C.A. Oxborrow, F. Pajot, R. Paladini, B. Partridge, F. Pasian, T. Passvogel, G. Patanchon, D. Pearson, T.J. Pearson, O. Perdereau, L. Perotto, F. Perrotta, F. Piacentini, M. Piat, E. Pierpaoli, S. Plaszczynski, P. Platania, E. Pointecouteau, G. Polenta, N. Ponthieu, L. Popa, T. Poutanen, G. Prézeau, S. Prunet, J.-L. Puget, J.P. Rachen, W.T. Reach, R. Rebolo, M. Reinecke, J.-M. Reix, C. Renault, S. Ricciardi, T. Riller, I. Ristorcelli, G. Rocha, C. Rosset, M. Rowan-Robinson, J.A. Rubiño-Martín, B. Rusholme, E. Salerno, M. Sandri, D. Santos, G. Savini, B.M. Schaefer, D. Scott, M.D. Seiffert, P. Shellard, A. Simonetto, G.F. Smoot, C. Sozzi, J.-L. Starck, J. Sternberg, F. Stivoli, V. Stolyarov, R. Stompor, L. Stringhetti, R. Sudiwala, R. Sunyaev, J.-F. Sygnet, D. Tapiador, J.A. Tauber, D. Tavagnacco, D. Taylor, L. Terenzi, D. Texier, L. Toffolatti, M. Tomasi, J.-P. Torre, M. Tristram, J. Tuovinen, M. Türler, M. Tuttlebee, G. Umana, L. Valenziano, J. Valiviita, J. Varis, L. Vibert, P. Vielva, F. Villa, N. Vittorio, L.A. Wade, B.D. Wandelt, C. Watson, S.D.M. White, M. White, A. Wilkinson, D. Yvon, A. Zacchei, A. Zonca, "Planck early results. I. The Planck mission", Astronomy and Astrophysics, January 2011, 536:A1, doi: 10.1051/0004-6361/201116464

### A. A. Miller, L. A. Hillenbrand, K. R. Covey, D., J. M. Silverman, I. K. W. Kleiser, B., P. S. Muirhead, S. B. Cenko, J. S., M. M. Kasliwal, A. V. Filippenko, N. M., E. O. Ofek, R. G. Dekany, G. Rahmer, D., R. Smith, R. M. Quimby, P. Nugent, J., J. Zolkower, V. Velur, R. Walters, J., K. Bui, D. McKenna, S. R. Kulkarni, C. R. Klein, M. Kandrashoff, A. Morton, "Evidence for an FU Orionis-like Outburst from a Classical T Tauri Star", Astrophysical Journal, 2011, 730:80, doi: 10.1088/0004-637X/730/2/80

### 2010

### Jaroslaw Zola, Maneesha Aluru, Abhinav Sarje, Srinivas Aluru, "Parallel Information-Theory-Based Construction of Genome-Wide Gene Regulatory Networks", Transactions on Parallel and Distributed Systems, December 2010, 21-12:1721-1733, doi: http://doi.ieeecomputersociety.org/10.1109/TPDS.2010.59

### Yili Zheng, "Optimizing UPC Programs for Multi-core Systems", Journal of Scientific Programming, 2010, 18(3-4):183-191,

### GS Groenewold, MJ van Stipdonk, J Oomens, WA de Jong, GL Gresham, ME McIlwain, "Vibrational spectra of discrete UO22+ halide complexes in the gas phase", International Journal of Mass Spectrometry, 2010, 297:67-75, doi: 10.1016/j.ijms.2010.06.013

### C. C. Joggerst, A. Almgren, and S. E. Woosley, "Three-Dimensional Simulations of Rayleigh-Taylor Mixing in Core Collapse Supernovae with CASTRO", Astrophysical Journal, 723, 353, October 2010,

### P. Ghysels, G. Samaey, P. Van Liedekerke, E. Tijskens, H. Ramon, D. Roose, "Multiscale Modeling of Viscoelastic Plant Tissue", International Journal for Multiscale Computational Engineering, 2010, 8:4, doi: 10.1615/IntJMultCompEng.v8.i4.30

### P. Ghysels, G. Samaey, P. Van Liedekerke, E. Tijskens, H. Ramon, D. Roose, "Coarse Implicit Time Integration of a Cellular Scale Particle Model for Plant Tissue Deformation", International Journal for Multiscale Computational Engineering, 2010, 8, doi: 10.1615/IntJMultCompEng.v8.i4.50

### J. Nordhaus, A. Burrows, A. Almgren, and J. Bell, "Dimension as a Key to the Neutrino Mechanism of Core-Collapse Supernova Explosions", Astrophysical Journal, 720, 694, September 2010,

### C. Rycroft, D. M. Ushizima, R. Saye, C. M. Ghajar, J. A. Sethian, "Building a physical cell simulation and comparing with confocal microscopy", Bay Area Physical Sciences - Oncology Center (NCI) Meeting 2010, UCSF Medical Sciences, September 2010,

### H Cho, WA de Jong, AP Sattelberger, F Poineau, KR Czerwinski, "Comprehensive Solid-State NMR Characterization of Electronic Structure in Ditechnetium Heptoxide", Journal of the American Chemical Society, 2010, 132:13138-1314, doi: 10.1021/ja105687j

### Hongzhang Shan, Filip Blagojevic, Seung-Jai Min, Paul Hargrove, Haoqiang Jin, Karl Fuerlinger, Alice Koniges, Nicholas J. Wright, "A Programming Model Performance Study Using the NAS Parallel Benchmarks", Scientific Programming -Exploring Languages for Expressing Medium to Massive On-Chip Parallelism, August 1, 2010, vol.18,

### G Schoendorff, WA de Jong, MS Gordon, TL Windus, "Gas Phase Computational Studies on the Competition between Nitrite and Water Ligands in Uranyl Complexes", Journal of Physical Chemistry A, 2010, 114:8902-8912, doi: 10.1021/jp103227x

### Adrian Pope, Salman Habib, Zarija Lukić, David Daniel, Patricia Fasel, Nehal Desai, Katrin Heitmann, "The Accelerated Universe", Computing in Science and Engineering, 2010, 12:17,

### David H. Bailey, Jonathan M. Borwein, Richard E. Crandall, "Advances in the theory of box integrals", Mathematics of Computation, July 2010, 79:1839-1966,

### WA de Jong, E Bylaska, N Govind, CL Janssen, K Kowalski, T Muller, IMB Nielsen, HJJ van Dam, V Veryazov, R Lindh, "Utilizing high performance computing for chemistry: parallel computational chemistry", Physical Chemistry Chemical Physics, 2010, 12:6896-6920, doi: 10.1039/c002859b

### P. Van Liedekerke, E. Tijskens, H. Ramon, P. Ghysels, G. Samaey, D. Roose, "Particle-based model to simulate the micromechanics of biological cells", Physical Review E, June 3, 2010, 81:6, doi: 10.1103/PhysRevE.81.061906

### D. Agarwal, M. Humphrey,N., Beekwilder, K. Jackson, M. Goode, and C. van Ingen, "A Data Centered Collaboration Portal to Support Global Carbon-Flux Analysis", Concurrency and Computation: Practice and Experience - Successes in Furthering Scientific Discovery, June 2010, LBNL 1827E,

### J. Meredith and H. Childs, "Visualization and Analysis-Oriented Reconstruction of Material Interfaces", Computer Graphics Forum (Proceedings of Eurographics/IEEE-VGTC Symposium on Visualization 2010 (EuroVis 2010)), June 2010, 1241-1250, LBNL 4567E,

- Download File: EuroVis2010MIR.pdf (pdf: 2.2 MB)

### A. Buluç, J. R. Gilbert, C. Budak, "Solving path problems on the GPU", Parallel Computing, 36(5-6):241 - 253., 2010, doi: http://dx.doi.org/10.1016/j.parco.2009.12.002

- Download File: parcoapsp.pdf (pdf: 160 KB)

### A. Nonaka, A.S. Almgren, J. B. Bell, M. J. Lijewski, C. M. Malone, and M. Zingale, "MAESTRO: An Adaptive Low Mach Number Hydrodynamics Algorithm for Stellar Flows", Astrophysical Journal Supplement Series, 188, 358-383, June 2010,

- Download File: multilevel.pdf (pdf: 3.8 MB)

### A. S. Almgren, V.E. Beckner, J.B. Bell, M.S. Day, L.H. Howell, C.C. Joggerst, M.J. Lijewski, A. Nonaka, M. Singer, M. Zingale, "CASTRO: A New Compressible Astrophysical Solver. I. Hydrodynamics and Self-Gravity", Astrophysical Journal, 715, 1221-1238, June 2010,

- Download File: castropaper.pdf (pdf: 1.6 MB)

### P. Van Liedekerke, P. Ghysels, E. Tijskens, G. Samaey, B. Smeedts, D. Roose, H. Ramon, "A particle-based model to simulate the micromechanics of single-plant parenchyma cells and aggregates", Physical Biology, May 26, 2010, 7:2, doi: 10.1088/1478-3975/7/2/026006

### L. Lin, J.A. Morrone, R. Car and M. Parrinello, "Displaced path integral formulation for the momentum distribution of quantum particles", Phys. Rev. Lett., 2010, 105:110602,

### J. C. Fogarty, H. M. Aktulga, A. van Duin, A. Y. Grama, S. A. Pandit, "A Reactive Simulation of the Silica-Water Interface", J. Chem. Phys. 132, 174704, May 4, 2010, doi: 10.1063/1.3407433

### A.Uselton, K.Antypas, D.M.Ushizima, J.Sukharev, "File System Monitoring as a Window Into User I/O Requirements", CUG-2010, May 2010,

- Download File: CUG2010.pdf (pdf: 593 KB)

### Martin Isenburg, Peter Lindstrom, and Hank Childs, "Parallel and Streaming Generation of Ghost Data for Structured Grids", IEEE Computer Graphics and Applications, May 2010, 30:32-44, doi: 10.1109/MCG.2010.26

### M. Veneziani, P. A. R. Ade, J. J. Bock, A. Boscaleri, B. P., P. de Bernardis, G. De Gasperis, A. Oliveira-Costa, G. De Troia, G. Di Stefano, K. M., W. C. Jones, T. S. Kisner, A. E. Lange, C. J., S. Masi, P. D. Mauskopf, T. E., P. Natoli, C. B. Netterfield, E., F. Piacentini, D. Pietrobon, G. Polenta, S. Ricciardi, G. Romeo, J. E. Ruhl, "Properties of Galactic Cirrus Clouds Observed by BOOMERANG", Astrophysical Journal, April 2010, 713:959-969, doi: 10.1088/0004-637X/713/2/959

### Daniel Sanchez, George Michelogiannakis, Christos Kozyrakis, "An Analysis of Interconnection Networks for Large Scale Chip Multiprocessors", Transactions on Architecture and Code Optimization, 2010,

- Download File: a4-sanchez.pdf (pdf: 1 MB)

With the number of cores of chip multiprocessors (CMPs) rapidly growing as technology scales down, connecting the different components of a CMP in a scalable and efficient way becomes increasingly challenging. In this article, we explore the architectural-level implications of interconnection network design for CMPs with up to 128 fine-grain multithreaded cores. We evaluate and compare different network topologies using accurate simulation of the full chip, including the memory hierarchy and interconnect, and using a diverse set of scientific and engineering workloads.

We find that the interconnect has a large impact on performance, as it is responsible for 60% to 75% of the miss latency. Latency, and not bandwidth, is the primary performance constraint, since, even with many threads per core and workloads with high miss rates, networks with enough bandwidth can be efficiently implemented for the system scales we consider. From the topologies we study, the flattened butterfly consistently outperforms the mesh and fat tree on all workloads, leading to performance advantages of up to 22%. We also show that considering interconnect and memory hierarchy together when designing large-scale CMPs is crucial, and neglecting either of the two can lead to incorrect conclusions. Finally, the effect of the interconnect on overall performance becomes more important as the number of cores increases, making interconnection choices especially critical when scaling up.

### Martin White, Adrian Pope, Jordan Carlson, Katrin Heitmann, Salman Habib, Patricia Fasel, David Daniel, and Zarija Lukić, "Particle Mesh Simulations of the Lyα Forest and the Signature of Baryon Acoustic Oscillations in the Intergalactic Medium", The Astrophysical Journal, 2010, 713:383,

### O. Rübel, G. H. Weber, M-Y Huang, E. W. Bethel, M. D. Biggin, C. C. Fowlkes, C. Luengo Hendriks, S. V. E. Keränen, M. Eisen, D. Knowles, J. Malik, H. Hagen and B. Hamann, "Integrating Data Clustering and Visualization for the Analysis of 3D Gene Expression Data", IEEE Transactions on Computational Biology and Bioinformatics, March 2010, 7:64-79, LBNL 382E,

- Download File: LBNL-382E-TCBB.pdf (pdf: 11 MB)

### D. M. Ushizima and J. Cuadros, "Ocular fundus for retinopathy characterization", Bay Area Vision Meeting, February 5, 2010,

### A. J. Aspden, J. B. Bell, and S. E. Woosley, "Distributed Flames in Type Ia Supernovae", Astrophysical Journal, 710, 1654-1663, February 2010,

- Download File: abw.pdf (pdf: 727 KB)

### GS Groenewold, WA de Jong, J Oomens, MJ Van Stipdonk, "Variable Denticity in Carboxylate Binding to the Uranyl Coordination Complexes", Journal of the American Society For Mass Spectrometry, 2010, 21:719-727, doi: 10.1016/j.jasms.2010.01.021

### Schwartz, P., and Colella P., "A Second-Order Accurate Method for Solving the Signed Distance Function Equation", Communications in Applied Mathematics and Computational Science, Vol. 5 (2010), No. 1, 81-97, 2010,

- Download File: sdfMain.pdf (pdf: 396 KB)

### J. B. Bell, A. L. Garcia, S. A. Williams, "Computational Fluctuating Fluid Dynamics", ESAIM: Mathematical Modelling and Numerical Analysis, 2010, 44:1085-1105,

- Download File: BinaryMixPaper.pdf (pdf: 665 KB)

### P. Natoli, G. De Troia, C. Hikage, E. Komatsu, M. Migliaccio, P.A.R. Ade, J.J. Bock, J.R. Bond, J. Borrill, A. Boscaleri, C.R. Contaldi, B.P. Crill, P. De Bernardis, G. De Gasperis, A. De Oliveira-Costa, G. Di Stefano, E. Hivon, T.S. Kisner, W.C. Jones, A.E. Lange, S. Masi, P.D. Mauskopf, C.J. MacTavish, A. Melchiorri, T.E. Montroy, C.B. Netterfield, E. Pascale, F. Piacentini, G. Polenta, S. Ricciardi, G. Romeo, J.E. Ruhl, M. Tegmark, M. Veneziani, N. Vittorio, "BOOMERanG constraints on primordial non-Gaussianity from analytical Minkowski functionals", Monthly Notices of the Royal Astronomical Society, January 2010, 408:1658-1665, doi: 10.1111/j.1365-2966.2010.17228.x

### Mehmet Balman, Tevfik Kosar, "Error Detection and Error Classification: Failure Awareness in Data Transfer Scheduling,", International Journal of Autonomic Computing 2010 - Vol. 1, No.4 pp. 425 - 446, DOI: 10.1504/IJAC.2010.037516, 2010, doi: http://dx.doi.org/10.1504/IJAC.2010.037516

Data transfer in distributed environment is prone to frequent failures resulting from back-end system level problems, like connectivity failure which is technically untraceable by users. Error messages are not logged efficiently, and sometimes are not relevant/useful from users' point-of-view. Our study explores the possibility of efficient error detection and reporting system for such environments. Prior knowledge about the environment and awareness of the actual reason behind a failure would enable higher level planners to make better and accurate decisions. It is necessary to have well defined error detection and error reporting methods to increase the usability and serviceability of existing data transfer protocols and data management systems. We investigate the applicability of early error detection and error classification techniques and propose an error reporting framework and a failure-aware data transfer life cycle to improve arrangement of data transfer operations and to enhance decision making of data transfer schedulers.

### David M. Ambrose, Jon Wilkening, "Computation of Time-Periodic Solutions of the Benjamin–Ono Equation", Journal of Nonlinear Science, 2010, 20:277--308, doi: 10.1007/s00332-009-9058-x

### F. Alberto Grünbaum, Mizan Rahman, "On a Family of 2-Variable Orthogonal Krawtchouk Polynomials", Symmetry, Integrability and Geometry: Methods and Applications (SIGMA), 2010, 6, doi: 10.3842/SIGMA.2010.090

### Ichitaro Yamazaki, Zhaojun Bai, Horst D. Simon Lin-Wang Wang, Kesheng Wu, "Adaptive Projection Subspace Dimension for the Lanczos Method", ACM Transactions on Mathematical Software, 2010, 37, doi: 10.1145/1824801.1824805

### Prateek Sharma, Phillip Colella, and Daniel F. Martin, "Numerical Implementation of Streaming Down the Gradient: Application to Fluid Modeling of Cosmic Rays", SIAM Journal on Scientific Computing , Vol 32(6), 3564-3583, 2010,

- Download File: crstrsiamPS.pdf (pdf: 1.1 MB)

### N. Mandolesi, M. Bersanelli, R.C. Butler, E. Artal, C. Baccigalupi, A. Balbi, A.J. Banday, R.B. Barreiro, M. Bartelmann, K. Bennett, P. Bhandari, A. Bonaldi, J. Borrill, M. Bremer, C. Burigana, R.C. Bowman, P. Cabella, C. Cantalupo, B. Cappellini, T. Courvoisier, G. Crone, F. Cuttaia, L. Danese, O. D Arcangelo, R.D. Davies, R.J. Davis, L. De Angelis, G. De Gasperis, A. De Rosa, G. De Troia, G. De Zotti, J. Dick, C. Dickinson, J.M. Diego, S. Donzelli, U. Dörl, X. Dupac, T.A. Enßlin, H.K. Eriksen, M.C. Falvella, F. Finelli, M. Frailis, E. Franceschi, T. Gaier, S. Galeotta, F. Gasparo, G. Giardino, F. Gomez, J. Gonzalez-Nuevo, K.M. Górski, A. Gregorio, A. Gruppuso, F. Hansen, R. Hell, D. Herranz, J.M. Herreros, S. Hildebrandt, W. Hovest, R. Hoyland, K. Huffenberger, M. Janssen, T. Jaffe, E. Keihänen, R. Keskitalo, T. Kisner, H. Kurki-Suonio, A. Lähteenmäki, C.R. Lawrence, S.M. Leach, J.P. Leahy, R. Leonardi, S. Levin, P.B. Lilje, M. López-Caniego, S.R. Lowe, P.M. Lubin, D. Maino, M. Malaspina, M. Maris, J. Marti-Canales, E. Martinez-Gonzalez, M. Massardi, S. Matarrese, F. Matthai, P. Meinhold, A. Melchiorri, L. Mendes, A. Mennella, G. Morgante, G. Morigi, N. Morisset, A. Moss, A. Nash, P. Natoli, R. Nesti, C. Paine, B. Partridge, F. Pasian, T. Passvogel, D. Pearson, L. Pérez-Cuevas, F. Perrotta, G. Polenta, L.A. Popa, T. Poutanen, G. Prezeau, M. Prina, J.P. Rachen, R. Rebolo, M. Reinecke, S. Ricciardi, T. Riller, G. Rocha, N. Roddis, R. Rohlfs, J.A. Rubiño-Martin, E. Salerno, M. Sandri, D. Scott, M. Seiffert, J. Silk, A. Simonetto, G.F. Smoot, C. Sozzi, J. Sternberg, F. Stivoli, L. Stringhetti, J. Tauber, L. Terenzi, M. Tomasi, J. Tuovinen, M. Türler, L. Valenziano, J. Varis, P. Vielva, F. Villa, N. Vittorio, L. Wade, M. White, S. White, A. Wilkinson, A. Zacchei, A. Zonca, "Planck pre-launch status: The Planck-LFI programme", Astronomy and Astrophysics, January 2010, 520:A3, doi: 10.1051/0004-6361/200912837

### Michael F. Wehner, G. Bala, Phillip Duffy, Arthur A. Mirin, and Raquel Romano, "Towards Direct Simulation of Future Tropical Cyclone Statistics in a High-Resolution Global Atmospheric Model", Advances in Meteorology, 2010, 2010:Article ID, doi: 10.1155/2010/915303

### V. Carey, D. Estep, A. Johansson, M. Larson, S. Tavener, "Blockwise Adaptivity for Time Dependent Problems Based on Coarse Scale Adjoint Solutions", SIAM Journal on Scientific Computing, 2010, 32:2121-2145, doi: 10.1137/090753826

### L. C. Lee, S. J. S. Morris, J. Wilkening, "Stress concentrations, diffusionally accommodated grain boundary sliding and the viscoelasticity of polycrystals", Proceedings of the Royal Society A: Mathematical, Physical and Engineering Science, 2010, doi: 10.1098/rspa.2010.0447

Using analytical and numerical methods, we analyse the Raj–Ashby bicrystal model of diffusionally accommodated grain-boundary sliding for finite interface slopes. Two perfectly elastic layers of finite thickness are separated by a given fixed spatially periodic interface. Dissipation occurs by time-periodic shearing of the viscous interfacial region, and by time-periodic grain-boundary diffusion. Although two time scales govern these processes, of particular interest is the characteristic time tD for grain-boundary diffusion to occur over distances of order of the grain size. For seismic frequencies ωtD≫1, we find that the spectrum of mechanical loss Q−1 is controlled by the local stress field near corners. For a simple piecewise linear interface having identical corners, this localization leads to a simple asymptotic form for the loss spectrum: for ωtD≫1, Q−1∼const.ω−α. The positive exponent α is determined by the structure of the stress field near the corners, but depends both on the angle subtended by the corner and on the orientation of the interface; the value of α for a sawtooth interface having 120° angles differs from that for a truncated sawtooth interface whose corners subtend the same 120° angle. When corners on an interface are not all identical, the behaviour is even more complex. Our analysis suggests that the loss spectrum of a finely grained solid results from volume averaging of the dissipation occurring in the neighbourhood of a randomly oriented three-dimensional network of grain boundaries and edges.

### G. S. H. Pau, J. B. Bell, K. Pruess, A. S. Almgren, M. J. Lijewski, K. Zhang, "High Resolution Simulation and Characterization of Density-Driven Flow in CO2 Storage in Saline Aquifers", Advances in Water Resources, 33(4):443-455, 2010,

- Download File: paperco2awrv2.pdf (pdf: 20 MB)

### Wehner, M.F., "Sources of uncertainty in the extreme value statistics of climate data", Extremes, 2010, 13:205-217, doi: 10.1007/s10687-010-0105-7

- Download File: 10.1007s10687-010-0105-7.pdf (pdf: 650 KB)

We investigate three sources of uncertainty in the calculation of extreme

value statistics for observed and modeled climate data. Inter-model differences in

formulation, unforced internal variability and choice of statistical model all contribute

to uncertainty. Using fits to the GEV distribution to obtain 20 year return

values, we quantify these uncertainties for the annual maximum daily mean surface

air temperatures of pre-industrial control runs from 15 climate models in the CMIP3

dataset.

### S. Koz\lowski, C. S. Kochanek, D. Stern, J. L., K. Z. Stanek, T. A. Thompson, R. J., A. J. Drake, D. M. Szczygie\l, P. R., P. Nugent, M. L. N. Ashby, E., M. J. I. Brown, A. Dey, R. Griffith, F., B. T. Jannuzi, S. Larson, K. Madsen, B., G. Pojma\ nski, J. Skowron, W. T. Vestrand, J. A. Wren, "SDWFS-MT-1: A Self-obscured Luminous Supernova at z \ 0.2", Astrophysical Journal, 2010, 722:1624-1632, doi: 10.1088/0004-637X/722/2/1624

### Alexandre J. Chorin, Xuemin Tu, "Interpolation and iteration for nonlinear filters", ESAIM: Mathematical Modelling and Numerical Analysis. Submitted, 2010, arXiv:0910,

We present a general form of the iteration and interpolation process used in implicit particle filters. Implicit filters are based on a pseudo-Gaussian representation of posterior densities, and are designed to focus the particle paths so as to reduce the number of particles needed in nonlinear data assimilation. Examples are given.

### A. Napov and Y. Notay, "When Does Two-Grid Optimality Carry Over to the V-Cycle?", Numer. Lin. Alg. Appl., vol.17, pp. 273-290, 2010,

- Download File: 2010NLAA2.pdf (pdf: 153 KB)

### A. Donev, J. B. Bell, A. L. Garcia, and B. J. Alder, "A Hybrid Particle-Continuum Method for Hydrodynamics of Complex Fluids", SIAM J. Multiscale Modeling and Simulation, 8(3):871-911, 2010,

- Download File: HybridLLNS.pdf (pdf: 1.7 MB)

### Wehner, M.F. ,R. Smith, P. Duffy, G. Bala, "The effect of horizontal resolution on simulation of very extreme US precipitation events in a global atmosphere model.", Climate Dynamics, 2010, 32:241-247, doi: 10.1007/s00382-009-0656-y

- Download File: 10.1007s00382-009-0656-y.pdf (pdf: 389 KB)

We investigate the ability of a global atmospheric general circulation model (AGCM) to reproduce observed 20 year return values of the annual maximum daily precipitation totals over the continental United States as a function of horizontal resolution. We find that at the high resolutions enabled by contemporary supercomputers, the AGCM can produce values of comparable magnitude to high quality observations. However, at the resolutions typical of the coupled general circulation models used in the Fourth Assessment Report of the Intergovernmental Panel on Climate Change, the precipitation return values are severely underestimated.

### S. Darbha, B. D. Metzger, E. Quataert, D. Kasen, P. Nugent, R. Thomas, "Nickel-rich outflows produced by the accretion-induced collapse of white dwarfs: light curves and spectra", Monthly Notices of the Royal Astronomical Society, 2010, 409:846-854, doi: 10.1111/j.1365-2966.2010.17353.x

### Alexandre J. Chorin, Xuemin Tu, Matthias Morzfeld, "Implicit Particle Filters for Data Assimilation", Comm. Appl. Math. Comp. Sc., 2010, 5:221--240,

### A. Napov and Y. Notay, "Comparison of Bounds for V-Cycle Multigrid", Appl. Numer. Math., vol.60, pp.176-192, 2010,

- Download File: 2010APNUM.pdf (pdf: 262 KB)

### R. Keskitalo, M.A.J. Ashdown, P. Cabella, T. Kisner, T. Poutanen, R. Stompor, J.G. Bartlett, J. Borrill, C. Cantalupo, G. De Gasperis, A. De Rosa, G. De Troia, H.K. Eriksen, F. Finelli, K.M. Górski, A. Gruppuso, E. Hivon, A. Jaffe, E. Keihänen, H. Kurki-Suonio, C.R. Lawrence, P. Natoli, F. Paci, G. Polenta, G. Rocha, "Residual noise covariance for Planck low-resolution data analysis", Astronomy and Astrophysics, January 2010, 522:A94, doi: 10.1051/0004-6361/200912606

### J.P. Leahy, M. Bersanelli, O. D Arcangelo, K. Ganga, S.M. Leach, A. Moss, E. Keihänen, R. Keskitalo, H. Kurki-Suonio, T. Poutanen, M. Sandri, D. Scott, J. Tauber, L. Valenziano, F. Villa, A. Wilkinson, A. Zonca, C. Baccigalupi, J. Borrill, R.C. Butler, F. Cuttaia, R.J. Davis, M. Frailis, E. Francheschi, S. Galeotta, A. Gregorio, R. Leonardi, N. Mandolesi, M. Maris, P. Meinhold, L. Mendes, A. Mennella, G. Morgante, G. Prezeau, G. Rocha, L. Stringhetti, L. Terenzi, M. Tomasi, "Planck pre-launch status: Expected LFI polarisation capability", Astronomy and Astrophysics, January 2010, 520:A8, doi: 10.1051/0004-6361/200912855

### M. M. Kasliwal, S. R. Kulkarni, A. Gal-Yam, O., R. M. Quimby, E. O. Ofek, P. Nugent, D., J. Jacobsen, A. Sternberg, I. Arcavi, D. A., M. Sullivan, D. J. Rich, P. F. Burke, J., D. Milisavljevic, R. Fesen, L., K. Shen, S. B. Cenko, J. S. Bloom, E., N. M. Law, N. Gehrels, S. Immler, R., G. Rahmer, D. Hale, R. Smith, J., V. Velur, R. Walters, J. Henning, K. Bui, D. McKenna, "Rapidly Decaying Supernova 2010X: A Candidate .Ia Explosion", Astrophysical Journal, 2010, 723:L98-L102, doi: 10.1088/2041-8205/723/1/L98

### Maciej Haranczyk, James A. Sethian, "Automatic Structure Analysis in High-Throughput Characterization of Porous Materials", Journal of Chemical Theory and Computation, 2010, 6:3472-3480, doi: 10.1021/ct100433z

### H Cho, WA de Jong, CZ Soderquist, "Probing the oxygen environment in UO22+ by solid-state O-17 nuclear magnetic resonance spectroscopy and relativistic density functional calculations", Journal of Chemical Physics, 2010, 132, doi: 10.1063/1.3308499

### E. Pourabbas, A. Shoshani, "Improving Estimation Accuracy of Aggregate Queries on Data Cubes", Data & Knowledge Engineering 69 (2010), January 1, 2010, 69:50-72,

### J.A. Tauber, N. Mandolesi, J.-L. Puget, T. Banos, M. Bersanelli, F.R. Bouchet, R.C. Butler, J. Charra, G. Crone, J. Dodsworth, G. Efstathiou, R. Gispert, G. Guyot, A. Gregorio, J.J. Juillet, J.-M. Lamarre, R.J. Laureijs, C.R. Lawrence, H.U. Nørgaard-Nielsen, T. Passvogel, J.M. Reix, D. Texier, L. Vibert, A. Zacchei, P.A.R. Ade, N. Aghanim, B. Aja, E. Alippi, L. Aloy, P. Armand, M. Arnaud, A. Arondel, A. Arreola-Villanueva, E. Artal, E. Artina, A. Arts, M. Ashdown, J. Aumont, M. Azzaro, A. Bacchetta, C. Baccigalupi, M. Baker, M. Balasini, A. Balbi, A.J. Banday, G. Barbier, R.B. Barreiro, M. Bartelmann, P. Battaglia, E. Battaner, K. Benabed, J.-L. Beney, R. Beneyton, K. Bennett, A. Benoit, J.-P. Bernard, P. Bhandari, R. Bhatia, M. Biggi, R. Biggins, G. Billig, Y. Blanc, H. Blavot, J.J. Bock, A. Bonaldi, R. Bond, J. Bonis, J. Borders, J. Borrill, L. Boschini, F. Boulanger, J. Bouvier, M. Bouzit, R. Bowman, E. Bréelle, T. Bradshaw, M. Braghin, M. Bremer, D. Brienza, D. Broszkiewicz, C. Burigana, M. Burkhalter, P. Cabella, T. Cafferty, M. Cairola, S. Caminade, P. Camus, C.M. Cantalupo, B. Cappellini, J.-F. Cardoso, R. Carr, A. Catalano, L. Cayón, M. Cesa, M. Chaigneau, A. Challinor, A. Chamballu, J.P. Chambelland, M. Charra, L.-Y. Chiang, G. Chlewicki, P.R. Christensen, S. Church, E. Ciancietta, M. Cibrario, R. Cizeron, D. Clements, B. Collaudin, J.-M. Colley, S. Colombi, A. Colombo, F. Colombo, O. Corre, F. Couchot, B. Cougrand, A. Coulais, P. Couzin, B. Crane, B. Crill, M. Crook, D. Crumb, F. Cuttaia, U. Dörl, P. Da Silva, R. Daddato, C. Damasio, L. Danese, G. D Aquino, O. D Arcangelo, K. Dassas, R.D. Davies, W. Davies, R.J. Davis, P. De Bernardis, D. De Chambure, G. De Gasperis, M.L. De La Fuente, P. De Paco, A. De Rosa, G. De Troia, G. De Zotti, M. Dehamme, J. Delabrouille, J.-M. Delouis, F.-X. Désert, G. Di Girolamo, C. Dickinson, E. Doelling, K. Dolag, I. Domken, M. Douspis, D. Doyle, S. Du, D. Dubruel, C. Dufour, C. Dumesnil, X. Dupac, P. Duret, C. Eder, A. Elfving, T.A. Enßlin, P. Eng, K. English, H.K. Eriksen, P. Estaria, M.C. Falvella, F. Ferrari, F. Finelli, A. Fishman, S. Fogliani, S. Foley, A. Fonseca, G. Forma, O. Forni, P. Fosalba, J.-J. Fourmond, M. Frailis, C. Franceschet, E. Franceschi, S. François, M. Frerking, M.F. Gómez-Reñasco, K.M. Górski, T.C. Gaier, S. Galeotta, K. Ganga, J. García Lázaro, A. Garnica, M. Gaspard, E. Gavila, M. Giard, G. Giardino, G. Gienger, Y. Giraud-Heraud, J.-M. Glorian, M. Griffin, A. Gruppuso, L. Guglielmi, D. Guichon, B. Guillaume, P. Guillouet, J. Haissinski, F.K. Hansen, J. Hardy, D. Harrison, A. Hazell, M. Hechler, V. Heckenauer, D. Heinzer, R. Hell, S. Henrot-Versillé, C. Hernández-Monteagudo, D. Herranz, J.M. Herreros, V. Hervier, A. Heske, A. Heurtel, S.R. Hildebrandt, R. Hills, E. Hivon, M. Hobson, D. Hollert, W. Holmes, A. Hornstrup, W. Hovest, R.J. Hoyland, G. Huey, K.M. Huffenberger, N. Hughes, U. Israelsson, B. Jackson, A. Jaffe, T.R. Jaffe, T. Jagemann, N.C. Jessen, J. Jewell, W. Jones, M. Juvela, J. Kaplan, P. Karlman, F. Keck, E. Keihänen, M. King, T.S. Kisner, P. Kletzkine, R. Kneissl, J. Knoche, L. Knox, T. Koch, M. Krassenburg, H. Kurki-Suonio, A. Lähteenmäki, G. Lagache, E. Lagorio, P. Lami, J. Lande, A. Lange, F. Langlet, R. Lapini, M. Lapolla, A. Lasenby, M. Le Jeune, J.P. Leahy, M. Lefebvre, F. Legrand, G. Le Meur, R. Leonardi, B. Leriche, C. Leroy, P. Leutenegger, S.M. Levin, P.B. Lilje, C. Lindensmith, M. Linden-Vørnle, A. Loc, Y. Longval, P.M. Lubin, T. Luchik, I. Luthold, J.F. MacIas-Perez, T. MacIaszek, C. MacTavish, S. Madden, B. Maffei, C. Magneville, D. Maino, A. Mambretti, B. Mansoux, D. Marchioro, M. Maris, F. Marliani, J.-C. Marrucho, J. Martí-Canales, E. Martínez-González, A. Martín-Polegre, P. Martin, C. Marty, W. Marty, S. Masi, M. Massardi, S. Matarrese, F. Matthai, P. Mazzotta, A. McDonald, P. McGrath, A. Mediavilla, P.R. Meinhold, J.-B. Mélin, F. Melot, L. Mendes, A. Mennella, C. Mervier, L. Meslier, M. Miccolis, M.-A. Miville-Deschenes, A. Moneti, D. Montet, L. Montier, J. Mora, G. Morgante, G. Morigi, G. Morinaud, N. Morisset, D. Mortlock, S. Mottet, J. Mulder, D. Munshi, A. Murphy, P. Murphy, P. Musi, J. Narbonne, P. Naselsky, A. Nash, F. Nati, P. Natoli, B. Netterfield, J. Newell, M. Nexon, C. Nicolas, P.H. Nielsen, N. Ninane, F. Noviello, D. Novikov, I. Novikov, I.J. O Dwyer, P. Oldeman, P. Olivier, L. Ouchet, C.A. Oxborrow, L. Pérez-Cuevas, L. Pagan, C. Paine, F. Pajot, R. Paladini, F. Pancher, J. Panh, G. Parks, P. Parnaudeau, B. Partridge, B. Parvin, J.P. Pascual, F. Pasian, D.P. Pearson, T. Pearson, M. Pecora, O. Perdereau, L. Perotto, F. Perrotta, F. Piacentini, M. Piat, E. Pierpaoli, O. Piersanti, E. Plaige, S. Plaszczynski, P. Platania, E. Pointecouteau, G. Polenta, N. Ponthieu, L. Popa, G. Poulleau, T. Poutanen, G. Prézeau, L. Pradell, M. Prina, S. Prunet, J.P. Rachen, D. Rambaud, F. Rame, I. Rasmussen, J. Rautakoski, W.T. Reach, R. Rebolo, M. Reinecke, J. Reiter, C. Renault, S. Ricciardi, P. Rideau, T. Riller, I. Ristorcelli, J.B. Riti, G. Rocha, Y. Roche, R. Pons, R. Rohlfs, D. Romero, S. Roose, C. Rosset, S. Rouberol, M. Rowan-Robinson, J.A. Rubiño-Martín, P. Rusconi, B. Rusholme, M. Salama, E. Salerno, M. Sandri, D. Santos, J.L. Sanz, L. Sauter, F. Sauvage, G. Savini, M. Schmelzel, A. Schnorhk, W. Schwarz, D. Scott, M.D. Seiffert, P. Shellard, C. Shih, M. Sias, J.I. Silk, R. Silvestri, R. Sippel, G.F. Smoot, J.-L. Starck, P. Stassi, J. Sternberg, F. Stivoli, V. Stolyarov, R. Stompor, L. Stringhetti, D. Strommen, T. Stute, R. Sudiwala, R. Sugimura, R. Sunyaev, J.-F. Sygnet, M. Türler, E. Taddei, J. Tallon, C. Tamiatto, M. Taurigna, D. Taylor, L. Terenzi, S. Thuerey, J. Tillis, G. Tofani, L. Toffolatti, E. Tommasi, M. Tomasi, E. Tonazzini, J.-P. Torre, S. Tosti, F. Touze, M. Tristram, J. Tuovinen, M. Tuttlebee, G. Umana, L. Valenziano, D. Vallée, M. Van Der Vlis, F. Van Leeuwen, J.-C. Vanel, B. Van-Tent, J. Varis, E. Vassallo, C. Vescovi, F. Vezzu, D. Vibert, P. Vielva, J. Vierra, F. Villa, N. Vittorio, C. Vuerli, L.A. Wade, A.R. Walker, B.D. Wandelt, C. Watson, D. Werner, M. White, S.D.M. White, A. Wilkinson, P. Wilson, A. Woodcraft, B. Yoffo, M. Yun, V. Yurchenko, D. Yvon, B. Zhang, O. Zimmermann, A. Zonca, D. Zorita, "Planck pre-launch status: The Planck mission", Astronomy and Astrophysics, January 2010, 520:A1, doi: 10.1051/0004-6361/200912983

### D. Poznanski, P. E. Nugent, A. V. Filippenko, "Type II-P Supernovae as Standard Candles: The SDSS-II Sample Revisited", Astrophysical Journal, 2010, 721:956-959, doi: 10.1088/0004-637X/721/2/956

### C. C. Joggerst, A. Almgren, J. Bell, Alexander Heger, Daniel Whalen, and S. E. Woosley, "Primordial Core-Collapse Supernovae and the Chemical Abundances of Metal-Poor Stars", Astrophysical Journal, 709, 11-26, January 2010,

### I. Arcavi, A. Gal-Yam, M. M. Kasliwal, R. M. Quimby, E. O., S. R. Kulkarni, P. E. Nugent, S. B., J. S. Bloom, M. Sullivan, D. A. Howell, D., A. V. Filippenko, N. Law, I. Hook, J., S. Blake, J. Cooke, R. Dekany, G., D. Hale, R. Smith, J. Zolkower, V., R. Walters, J. Henning, K. Bui, D. McKenna, J. Jacobsen, "Core-collapse Supernovae from the Palomar Transient Factory: Indications for a Different Population in Dwarf Galaxies", Astrophysical Journal, 2010, 721:777-784, doi: 10.1088/0004-637X/721/1/777

### Gladeston C. Leite, Daniela M. Ushizima, Fátima N. S. Medeiros, Gilson G. De Lima, "Wavelet Analysis for Wind Fields Estimation", Sensors, 2010, 10:5994--6016, doi: 10.3390/s100605994

### N. Vasudeo, T. Echekki, M. Day, and J. Bell, "The Regime Diagram for Premixed Flame Kernel-Vortex Interactions - Revisited", Phys. Fluids (22) 043602, 2010,

### B. D. Metzger, G. Mart\ \inez-Pinedo, S. Darbha, E., A. Arcones, D. Kasen, R. Thomas, P. Nugent, I. V. Panov, N. T. Zinner, "Electromagnetic counterparts of compact object mergers powered by the radioactive decay of r-process nuclei", Monthly Notices of the Royal Astronomical Society, 2010, 406:2650-2662, doi: 10.1111/j.1365-2966.2010.16864.x

### A. Donev, E. Vanden-Eijnden, A. Garcia, and J. Bell, "On the Accuracy of Explicit Finite-Volume Schemes for Fluctuating Hydrodynamics", Communications in Applied Mathematics and Computational Science, 5(2):149-197, 2010,

- Download File: LLNSSk.pdf (pdf: 937 KB)

### R. Amanullah, C. Lidman, D. Rubin, G. Aldering, P., K. Barbary, M. S. Burns, A. Conley, K. S., S. E. Deustua, M. Doi, S. Fabbro, L., H. K. Fakhouri, G. Folatelli, A. S., H. Furusawa, G. Garavini, G., A. Goobar, D. E. Groom, I. Hook, D. A., N. Kashikawa, A. G. Kim, R. A. Knop, M., E. Linder, J. Meyers, T. Morokuma, S., J. Nordin, P. E. Nugent, L. \ Ostman, R., N. Panagia, S. Perlmutter, J. Raux, P., A. L. Spadafora, M. Strovink, N., L. Wang, W. M. Wood-Vasey, N. Yasuda, T. Supernova Cosmology Project, "Spectra and Hubble Space Telescope Light Curves of Six Type Ia Supernovae at 0.511 \lt z \lt 1.12 and the Union2 Compilation", Astrophysical Journal, 2010, 716:712-738, doi: 10.1088/0004-637X/716/1/712

### Fai Ma, Matthias Morzfeld, Ali Imam, "The decoupling of damped linear systems in free or forced vibration", Journal of Sound and Vibration, 2010, 329:3182--3202, doi: 10.1016/j.jsv.2010.02.017

### Q. Zhang, H. Johansen and P. Colella, "A Fourth-Order Accurate Finite-Volume Method with Structured Adaptive Mesh Refinement for Solving the Advection-Diffusion Equation", SIAM Journal on Scientific Computing, Vol. 34, No. 2. (2012), B179, doi:10.1137/110820105, 2010,

- Download File: O4AdvDiff.pdf (pdf: 599 KB)

### A. Cooray, S. Eales, S. Chapman, D. L. Clements, O., D. Farrah, M. J. Jarvis, M. Kaplinghat, M. Negrello, A. Melchiorri, et al., "The Herschel-SPIRE Legacy Survey (HSLS): the scientific goals of a shallow and wide submillimeter imaging survey with SPIRE", ArXiv e-prints, January 2010,

### Hank Childs, David Pugmire, Sean Ahern, Brad Whitlock, Mark Howison, Prabhat, Gunther Weber, E. Wes Bethel, "Extreme Scaling of Production Visualization Software on Diverse Architectures", IEEE Computer Graphics and Applications, January 2010, 30:22--31, LBNL 3403E,

### A. A. Miller, J. M. Silverman, N. R. Butler, J. S., R. Chornock, A. V. Filippenko, M., C. R. Klein, W. Li, P. E. Nugent, N. Smith, T. N. Steele, "SN 2008iy: an unusual Type IIn Supernova with an enduring 400-d rise time", Monthly Notices of the Royal Astronomical Society, 2010, 404:305-317, doi: 10.1111/j.1365-2966.2010.16280.x

### Vinh-Tan Nguyen, Jaime Peraire, Boo Cheong Khoo, Per-Olof Persson, "A discontinuous Galerkin front tracking method for two-phase flows with surface tension", Computers & Fluids, 2010, 39:1--14, doi: 10.1016/j.compfluid.2009.06.007

### M Valiev, EJ Bylaska, N Govind, K Kowalski, TP Straatsma, HJJ Van Dam, D Wang, J Nieplocha, E Apra, TL Windus, W de Jong, "NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations", Computer Physics Communications, 2010, 181:1477-1489, doi: 10.1016/j.cpc.2010.04.018

### Q. Zhang and P. L.-F. Liu, "Handling Solid-Fluid Interfaces for Viscous Flows: Explicit Jump Approximation vs. Ghost Cell Approaches", Journal of Computational Physics, 229(11):4225-4246, 2010,

- Download File: EJA.pdf (pdf: 373 KB)

### C.M. Cantalupo, J.D. Borrill, A.H. Jaffe, T.S. Kisner, R. Stompor, "MADmap: A massively parallel maximum likelihood cosmic microwave background map-maker", Astrophysical Journal, Supplement Series, January 2010, 187:212-227, doi: 10.1088/0067-0049/187/1/212

### R. A. Scalzo, G. Aldering, P. Antilogus, C. Aragon, S., C. Baltay, S. Bongard, C. Buton, M., N. Chotard, Y. Copin, H. K. Fakhouri, A., E. Gangler, S. Hoyer, M. Kasliwal, S., P. Nugent, R. Pain, E. P\ econtal, R., S. Perlmutter, D. Rabinowitz, A., G. Rigaudier, K. Runge, G. Smadja, C. Tao, R. C. Thomas, B. Weaver, C. Wu, "Nearby Supernova Factory Observations of SN 2007if: First Total Mass Measurement of a Super-Chandrasekhar-Mass Progenitor", Astrophysical Journal, 2010, 713:1073-1094, doi: 10.1088/0004-637X/713/2/1073

### R.K. Crockett, P. Colella, and D.T. Graves, "A Cartesian Grid Embedded Boundary Method for Solving the Poisson and Heat Equations with Discontinuous Coefficients in Three Dimensions", Journal of Computational Physics , 230(7):2451-2469, 2010,

- Download File: YJCPH3372.pdf (pdf: 1008 KB)

### N. Smith, A. Miller, W. Li, A. V. Filippenko, J. M., A. W. Howard, P. Nugent, G. W., J. S. Bloom, A. M. Ghez, J. Lu, S. Yelda, R. A. Bernstein, J. E. Colucci, "Discovery of Precursor Luminous Blue Variable Outbursts in Two Recent Optical Transients: The Fitfully Variable Missing Links UGC 2773-OT and SN 2009ip", Astronomical Journal, 2010, 139:1451-1467, doi: 10.1088/0004-6256/139/4/1451

### P. A. Stott, N. P. Gillett, G. C. Hegerl, D. J. Karoly, D. A. Stone, X. Zhang, F. Zwiers, "Detection and attribution of climate change: a regional perspective", Wiley Interdisciplinary Reviews: Climate Change, 2010, 1:192--211,

### S.T. Bailey, G. Aldering, P. Antilogus, C. Aragon, C. Baltay, S. Bongard, C. Buton, M. Childress, N. Chotard, Y. Copin, H. Fakhouri, E. Gangler, S. Loken, P. Nugent, R.Pain, E. Pecontal, R. Pereira, S. Perlmutter, D. Rabinowitz, G. Rigaudier, K. Tunge, R. Scalzo, G. Smadja, C. Tao, R.C. Thomas, and C. Wu, "Using Spectra to Make Cosmology's Best Standard Candles Even Better", Bulletin of the American Astronomical Society, 2010, 42:313,

### E. Vecharynski, J. Langou, "The cycle-convergence of restarted GMRES for normal matrices is sublinear", SIAM Journal on Scientific Computing Vol. 32, Issue 1, pp. 186-196, 2010,

We prove that the cycle-convergence of the restarted GMRES applied to a system of linear equations with a normal coefficient matrix is sublinear.

### J. Wang, D. Domin, B. Austin, D.Y. Zubarev, J. McClean, M. Frenklach, T. Cui, and W. A. Lester, Jr., "A Diffusion Monte Carlo Study of the O-H Bond Dissociation of Phenol", J. Phys. Chem. A, 2010, 114:9832,

### E. A. Carvalho, D. M. Ushizima, F. N. S. Medeiros, C. I. O. Martins, R. C. P. Marques, I. N. S. Oliveira, "SAR imagery segmentation by statistical region growing and hierarchical merging", Digital Signal Processing, 2010, 20:1365-1378, doi: 10.1016/j.dsp.2009.10.014

### P.-T. Bremer, G.H. Weber, V. Pascucci, M.S. Day and John B. Bell, "Analyzing and Tracking Burning Structures in Lean Premixed Hydrogen Flames", IEEE Transactions on Visualization and Computer Graphics, 2010, 16:248-260, LBNL 2276E, doi: 10.1109/TVCG.2009.69

- Download File: LBNL-2276E.pdf (pdf: 8.5 MB)

### Chris H. Rycroft, Yee Lok Wong, Martin Z. Bazant, "Fast spot-based multiscale simulations of granular drainage", Powder Technology, 2010, 200:1-11, doi: 10.1016/j.powtec.2010.01.009

### Meiyue Shao, Weiguo Gao, Yunxin Zhang, "Robust projection method for Fredholm integral equation of the second kind", International Journal of Computer Mathematics, 2010, 87:3455--3466, doi: 10.1080/00207160903089921

### Scott Callaghan, Ewa Deelman, Dan Gunter, Gideon Juve, Philip Maechling, Christopher Brooks, Karan Vahi, Kevin Milner, Robert Graves, Edward Field, David Okaya, Thomas Jordan, "Scaling up Workflow-based Applications", Journal of Computer and System Sciences, 2010, 76:428--446,

### Michael Westdickenberg, Jon Wilkening, "Variational particle schemes for the porous medium equation and for the system of isentropic Euler equations", ESAIM: Mathematical Modelling and Numerical Analysis, 2010, 44:133--166, doi: 10.1051/m2an/2009043

### D. Poznanski, R. Chornock, P. E. Nugent, J. S. Bloom, A. V., M. Ganeshalingam, D. C. Leonard, W. Li, R. C. Thomas, "An Unusually Fast-Evolving Supernova", Science, 2010, 327:58-, doi: 10.1126/science.1181709

### Caroline Gatti-Bono, Phillip Colella and David Trebotich, "A Second-Order Accurate Conservative Front-Tracking Method in One Dimension", SIAM J. Sci. Comput., 31(6):4795-4813, 2010,

- Download File: BonoSISC.pdf (pdf: 414 KB)

### Shoaib Kamil, Oliker, Pinar, John Shalf, "Communication Requirements and Interconnect Optimization for High-End Scientific Applications", IEEE Transactions on Parallel and Distributed Systems, Volume (TPDS), January 1, 2010, 21:188-202,

- Download File: tpds09-hfast.pdf (pdf: 8.3 MB)

### The Polarbear Collaboration, J. Errard, P. A. R. Ade, A., K. Arnold, F. Aubin, D. Boettger, J., C. Cantalupo, M. A. Dobbs, D. Flanigan, A., N. Halverson, M. Hazumi, W. L. Holzapfel, J., P. Hyland, A. Jaffe, B. Keating, T., Z. Kermish, A. T. Lee, E. Linder, M., T. Matsumura, N. Miller, X. Meng, M., H. Nishino, R. O Brient, D. O Dea, C., I. Schanning, A. Shimizu, C. Shimmin, M., H. Spieler, B. Steinbach, R. Stompor, A., T. Tomaru, H. T. Tran, C. Tucker, E. Quealy, P. L. Richards, O. Zahn, "The new generation CMB B-mode polarization experiment: POLARBEAR", ArXiv e-prints, January 2010,

### David M. Ambrose, Jon Wilkening, "Computation of symmetric, time-periodic solutions of the vortex sheet with surface tension", Proceedings of the National Academy of Sciences, 2010, doi: 10.1073/pnas.0910830107

A numerical method is introduced for the computation of time-periodic vortex sheets with surface tension separating two immiscible, irrotational, two-dimensional ideal fluids of equal density. The approach is based on minimizing a nonlinear functional of the initial conditions and supposed period that is positive unless the solution is periodic, in which case it is zero. An adjoint-based optimal control technique is used to efficiently compute the gradient of this functional. Special care is required to handle singular integrals in the adjoint formulation. Starting with a solution of the linearized problem about the flat rest state, a family of smooth, symmetric breathers is found that, at quarter-period time intervals, alternately pass through a flat state of maximal kinetic energy, and a rest state in which all the energy is stored as potential energy in the interface. In some cases, the interface overturns before returning to the initial, flat configuration. It is found that the bifurcation diagram describing these solutions contains several disjoint curves separated by near-bifurcation events.

### S. B. Cenko, N. R. Butler, E. O. Ofek, D. A. Perley, A. N., D. A. Frail, J. Gorosabel, J. S. Bloom, A. J., J. Cepa, P. Chandra, A. Ugarte Postigo, A. V. Filippenko, C. R. Klein, S. R., A. A. Miller, P. E. Nugent, D. L. Starr, "Unveiling the Origin of Grb 090709A: Lack of Periodicity in a Reddened Cosmological Long-Duration Gamma-Ray Burst", Astronomical Journal, 2010, 140:224-234, doi: 10.1088/0004-6256/140/1/224

### 2009

### Nils E. R. Zimmermann, Berend Smit, Frerich J. Keil, "On the Effects of the External Surface on the Equilibrium Transport in Zeolite Crystals", J. Phys. Chem. C, 2009, 114:300-310, doi: 10.1021/jp904267a

With the aid of molecular simulation techniques (molecular dynamics, grand-canonical Monte Carlo, and reactive flux correlation function RFCF), the influence of the external surface on the equilibrium permeation of methane and ethane into and out of an AFI-type zeolite crystal has been studied. In particular, “extended dynamically corrected transition state theory”, which has been proven to describe the transport of tracers in periodic crystals correctly, has been applied to surface problems. The results suggest that the molecules follow paths that are close to the pore wall in the interior and also at the crystal surface. Moreover, the recrossing rate at the surface turns out to be non-negligible, yet, in contrast to the intracrystalline recrossing rate, remains almost constant over loading which gives indication to diffusive barrier crossing at the crystal surface. As a consequence of very different adsorption and desorption barriers, the corresponding permeabilities are shown to be not equal for one and the same condition (*T* and *p*). The critical crystal length, beyond which surface effects can be certainly neglected, is computed on basis of flux densities. Entrance/exit effects, in the present cases, are practically important solely for ethane at low pressures. The influence of the type of external surface on the surface flux is, hereby, rather small, because the transport at the surface is controlled by the slow supply from the gas phase. This has been evidenced by a simplified thermodynamic model that has been derived within this work and which is based on rapidly assessable simulation data. Finally, we propose a procedure for estimating the importance of different factors that have an impact on surface effects.

### O. Rübel, C.G.R. Geddes, E. Cormier-Michel, K. Wu, Prabhat, G.H. Weber, D.M. Ushizima, P. Messmer, H. Hagen, B. Hamann, and E.W. Bethel, "Automatic Beam Path Analysis of laser Wakefield Particle Acceleration Data", IOP Computational Science & Discovery, November 2009, 2, LBNL 2734E,

- Download File: LBNL-2734E.pdf (pdf: 15 MB)

### U. Shumlak, J. M. Blakely, B.J. Chan, R.P. Golingo, S.D. Knecht, B.A. Nelson, R.J. Oberto, M.R. Sybouts, G.V. Vogman, D.J. Den Hartog, "Stabilization in the ZaP flow Z-Pinch", Journal of Fusion Energy, 28 (2), pg 208--211, November 2009,

### Abhinav Sarje, Srinivas Aluru, "Parallel Genomic Alignments on the Cell Broadband Engine", Transactions on Parallel and Distributed Systems (TPDS), November 2009, 20-11:1600-1610, doi: http://doi.ieeecomputersociety.org/10.1109/TPDS.2008.254

### AS LIPTON, RW HECK, WA DE JONG, AR GAO, XJ WU, A ROEHRICH, GS HARBISON, PD ELLIS, "Low Temperature Cu-65 NMR Spectroscopy of the Cu+ Site in Azurin", JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2009, 131:13992-1399, doi: 10.1021/ja901308v

### David H. Bailey, Jonathan M. Borwein, "PSLQ: An algorithm to discover integer relations", Computeralgebra Rundbrief, October 2009, 45:8-11,

### M. Wehner, L. Oliker., and J. Shalf, "Low Power Supercomputers", IEEE Spectrum, October 2009,

High-performance computing for such things as climate modeling is not going to advance at anything like the pace it has during the last two decades unless we apply fundamentally new ideas. Here we describe one possible approach. Rather than constructing supercomputers from the kinds of microprocessors found in fast desktop computers or servers, we propose adopting designs and design principles drawn, oddly enough, from the portable-electronics marketplace.

### L. A. Drummond, Vicente Galiano, Violeta Migallon, Jose Penades, "Interfaces for Parallel Numerical Linear Algebra Libraries in High-Level Languages", Advances in Engineering Software, 2009, 40:8,

### L. Lin, J. Lu, L. Ying, W. E, "Pole-based approximation of the Fermi-Dirac function", Chin. Ann. Math., 2009, 30B:729,

### S. Zhou, D. Duffy, T. Clune, M. Suarez, S. Williams, M. Halem, "The Impact of IBM Cell Technology on the Programming Paradigm in the Context of Computer Systems for Climate and Weather Models", Concurrency and Computation:Practice and Experience (CCPE), August 2009, doi: 10.1002/cpe.1482

### Y. Park, H. M. Aktulga, A. Y. Grama, A. Strachan, "Strain relaxation in Si/Ge/Si nanoscale bars from molecular dynamics simulations", J. Appl. Phys. 106, 034304 (2009), August 6, 2009, doi: 10.1063/1.3168424

### James Albrecht, Cy Chan, and Alan Edelman, "Sturm Sequences and Random Eigenvalue Distributions", Foundations of Computational Mathematics, August 2009,

- Download File: Sturm.pdf (pdf: 581 KB)

### G SCHOENDORFF, TL WINDUS, WA DE JONG, "Density Functional Studies on the Complexation and Spectroscopy of Uranyl Ligated with Acetonitrile and Acetone Derivatives", JOURNAL OF PHYSICAL CHEMISTRY A, 2009, 113:12525-1253, doi: 10.1021/jp9038623

### Salman Habib, Adrian Pope, Zarija Lukić, David Daniel, Patricia Fasel, Nehal Desai, Katrin Heitmann, Chung-Hsing Hsu, Lee Ankeny, Graham Mark, "Hybrid petacomputing meets cosmology: The Roadrunner Universe project", Journal of Physics, 2009, 180:012019,

### U. Shumlak, C.S. Adams, J.M. Blakely, B.J. Chan, R.P. Golingo, S.D. Knecht, B.A. Nelson, R.J. Oberto, M.R. Sybouts, G.V. Vogman, "Equilibrium, Flow Shear and Stability Measurements in the Z-pinch", Nuclear Fusion, 49 (7), 075039, July 2009,

### D. N. Williams, R. Ananthakrishnan, D. E. Bernholdt, S. Bharathi, D. Brown, M. Chen, A. L. Chervenak, L. Cinquini, R. Drach, I. T. Foster, P. Fox, D. Fraser, J. Garcia, S. Hankin, P. Jones, D. E. Middleton, J. Schwidder, R. Schweitzer, R. Schuler, A. Shoshani, F. Siebenlist, A. Sim, W. G. Strand, M. Su, N. Wilhelmi, "The Earth System Grid: Enabling Access to Multimodel Climate Simulation Data", American Meteorological Society, 2009, 90(2):195-205,

### S.E. Woosley, A.S. Almgren, A.J. Aspden, J.B. Bell, D. Kasen, A.R. Kerstein, H. Ma, A. Nonaka and M. Zingale, "Type Ia Supernovae: Advances in Large Scale Simulation", SciDAC 2009, J. of Physics: Conference Series, 180, July 2009,

### C. M. Cantalupo, J. D. Borrill, A. H. Jaffe, T. S. Kisner, R. Stompor, "MADmap: A Massively Parallel Maximum-Likelihood Cosmic Microwave Background Map-Maker", ArXiv e-prints (submitted to Astrophysical Journal Supplement), June 2009,

### L. Lin, J. Lu, L. Ying, R. Car, W. E, "Fast algorithm for extracting the diagonal of the inverse matrix with application to the electronic structure analysis of metallic systems", Commun. Math. Sci., 2009, 7:755,

### F AUBRIET, JJ GAUMET, WA DE JONG, GS GROENEWOLD, AK GIANOTTO, ME MCILWAIN, MJ VAN STIPDONK, CM LEAVITT, "Cerium Oxyhydroxide Clusters: Formation, Structure, and Reactivity", JOURNAL OF PHYSICAL CHEMISTRY A, 2009, 113:6239-6252, doi: 10.1021/jp9015432

### J. Jensen, R. Downing, D. Ross, A. Sim, "Practical Grid Storage Interoperation", Journal of Grid Computing, 2009, 7:3, doi: 10.1007/s10723-009-9127-2

### M. Riedel, E. Laure, Th. Soddemann, L. Field, J. P. Navarro, J. Casey, M. Litmaath, J. Ph. Baud, B. Koblitz, C. Catlett, D. Skow, C. Zheng, P. M. Papadopoulos, M. Katz, N. Sharma, O. Smirnova, B. Kónya, P. Arzberger, F. Würthwein, A. S. Rana, T. Martin, M. Wan, V. Welch, T. Rimovsky, S. Newhouse, A. Vanni, Y. Tanaka, Y. Tanimura, T. Ikegami, D. Abramson, C. Enticott, G. Jenkins, R. Pordes, N. Sharma, S. Timm, N. Sharma, G. Moont, M. Aggarwal, D. Colling, O. van der Aa, A. Sim, V. Natarajan, A. Shoshani, J. Gu, S. Chen, G. Galang, R. Zappi, L. Magnoni, V. Ciaschini, M. Pace, V. Venturi, M. Marzolla, P. Andreetto, B. Cowles, S. Wang, Y. Saeki, H. Sato, S. Matsuoka, P. Uthayopas, S. Sriprayoonsakul, O. Koeroo, M. Viljoen, L. Pearlman, S. Pickles, David Wallom, G. Moloney, J. Lauret, J. Marsteller, P. Sheldon, S. Pathak, S. De Witt, J. Mencák, J. Jensen, M. Hodges, D. Ross, S. Phatanapherom, G. Netzer, A. R. Gregersen, M. Jones, S. Chen, P. Kacsuk, A. Streit, D. Mallmann, F. Wolf, T. Lippert, Th. Delaitre, E. Huedo, N. Geddes, "Interoperation of world-wide production e-Science infrastructures", Concurrency and Computation: Practice and Experience, 2009, 21(8):961-990,

### J.A. Morrone, L. Lin, R. Car, "Tunneling and delocalization effects in hydrogen bonded systems: A study in position and momentum space", J. Chem. Phys., 2009, 130:204511,

### S. Williams, A. Waterman, D. Patterson, "Roofline: an insightful visual performance model for multicore architectures", Communications of the ACM (CACM), April 2009, doi: 10.1145/1498765.1498785

### Easterling, D. R., and M. F. Wehner, "Is the climate warming or cooling?", Geophys. Res. Lett., April 2009, 36, L087, doi: 10.1029/2009GL037810

- Download File: grl25859.pdf (pdf: 246 KB)

Numerous websites, blogs and articles in the media have claimed that the climate is no longer warming, and is now cooling. Here we show that periods of no trend or even cooling of the globally averaged surface air temperature are found in the last 34 years of the observed record, and in climate model simulations of the 20^{th} and 21^{st} century forced with increasing greenhouse gases. We show that the climate over the 21^{st} century can and likely will produce periods of a decade or two where the globally averaged surface air temperature shows no trend or even slight cooling in the presence of longer-term warming.

### M. Veneziani, A. Amblard, A. Cooray, F. Piacentini, D., P. Serra, P. A. R. Ade, J. J. Bock, J. R., J. Borrill, A. Boscaleri, P. Cabella, C. R., B. P. Crill, P. de Bernardis, G. Gasperis, A. de Oliveira-Costa, G. De Troia, G. Stefano, K. M. Ganga, E. Hivon, W. C. Jones, T. S., A. E. Lange, C. J. MacTavish, S., P. D. Mauskopf, A. Melchiorri, T. E. Montroy, P., C. B. Netterfield, E. Pascale, G., S. Ricciardi, G. Romeo, J. E. Ruhl, P. Santini, M. Tegmark, N. Vittorio, "Sub-Degree Sunyaev-Zel dovich Signal from Multi-Frequency BOOMERanG observations", ArXiv e-prints (submitted to Astrophysical Journal Letters), April 2009,

### S. E. Dillard, V. Natarjan, G. H. Weber, V. Pascucci and B. Hamann, "Topology-guided Tessellation of Quadratic Elements", International Journal of Computational Geometry & Applications (IJCGA), April 2009, 19:195-211, LBNL 63771,

- Download File: LBNL-63771.pdf (pdf: 635 KB)

### P. Ghysels, G. Samaey, B. Tijskens, P Van Liedekerke, H Ramon, D Roose, "Multi-scale simulation of plant tissue deformation using a model for individual cell mechanics", Physical Biology, March 25, 2009, 6:1, doi: 10.1088/1478-3975/6/1/016009

### CM LEAVITT, VS BRYANTSEV, WA DE JONG, MS DIALLO, WA GODDARD, GS GROENEWOLD, MJ VAN STIPDONK, "Addition of H2O and O-2 to Acetone and Dimethylsulfoxide Ligated Uranyl(V) Dioxocations", JOURNAL OF PHYSICAL CHEMISTRY A, 2009, 113:2350-2358, doi: 10.1021/jp807651c

### David H. Bailey, "Can an evolutionary process generate English text?", Biological Theory, March 1, 2009, 4:125-131,

### Zarija Lukić, Darren Reed, Salman Habib, Katrin Heitmann, "The Structure of Halos: Implications for Group and Cluster Cosmology", The Astrophysical Journal, 2009, 692:217,

### P NICHOLS, N GOVIND, EJ BYLASKA, WA DE JONG, "Gaussian Basis Set and Planewave Relativistic Spin-Orbit Methods in NWChem", JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2009, 5:491-499, doi: 10.1021/ct8002892

### L. Lin, J. Lu, R. Car, W. E, "Multipole representation of the Fermi operator with application to the electronic structure analysis of metallic systems", Phys. Rev. B, 2009, 79:115133,

### S. Kamil, L. Oliker, A. Pinar, J. Shalf, "Communication Requirements and Interconnect Optimization for High-End Scientific Applications", IEEE Transactions on Parallel and Distributed Systems (TPDS), 2009,

- Download File: TPDS09-comm.pdf (pdf: 8.3 MB)

### S. Kamil, L. Oliker, A. Pinar, J. Shalf, "Communication Requirements and Interconnect Optimization for High-End Scientific Applications\", IEEE Transactions on Parallel and Distributed Systems (TPDS), 2009,

### D. Poznanski, N. Butler, A. V. Filippenko, M., W. Li, J. S. Bloom, R. Chornock, R. J., P. E. Nugent, J. M. Silverman, S. B., E. L. Gates, D. C. Leonard, A. A. Miller, M., F. J. D. Serduke, N. Smith, B. J. Swift, D. S. Wong, "Improved Standardization of Type II-P Supernovae: Application to an Expanded Sample", Astrophysical Journal, 2009, 694:1067-1079, doi: 10.1088/0004-637X/694/2/1067

### M. Garzon, L. J. Gray, J. A. Sethian, "Numerical simulation of non-viscous liquid pinch-off using a coupled level set-boundary integral method", Journal of Computational Physics, 2009, 228:6079--6106, doi: 10.1016/j.jcp.2009.04.048

### JX ZHANG, U LOURDERAJ, SV ADDEPALLI, WA DE JONG, WL HASE, "Quantum Chemical Calculations of the Cl- + CH3I -> CH3Cl + I- Potential Energy Surface", JOURNAL OF PHYSICAL CHEMISTRY A, 2009, 113:1976-1984, doi: 10.1021/jp808146c

### D. Rubin, E. V. Linder, M. Kowalski, G. Aldering, R., K. Barbary, N. V. Connolly, K. S., L. Faccioli, V. Fadeyev, G. Goldhaber, A., I. Hook, C. Lidman, J. Meyers, S., P. E. Nugent, R. Pain, S. Perlmutter, P., A. L. Spadafora, M. Strovink, N. Suzuki, H. Swift, "Looking Beyond Lambda with the Union Supernova Compilation", Astrophysical Journal, 2009, 695:391-403, doi: 10.1088/0004-637X/695/1/391

### John Shalf and Jason Hick (Arie Shoshani and Doron Rotem), "Storage Technology Fundamentals", Scientific Data Management: Challenges, Technology, and Deployment, Volume . Chapman & Hall/CRC, 2009,

- Download File: iobook08.pdf (pdf: 1.2 MB)

### M. Sullivan, R. S. Ellis, D. A. Howell, A. Riess, P. E. Nugent, A. Gal-Yam, "The Mean Type Ia Supernova Spectrum Over the Past Nine Gigayears", Astrophysical Journal, 2009, 693:L76-L80, doi: 10.1088/0004-637X/693/2/L76

### M. Haranczyk, J. A. Sethian, "Navigating molecular worms inside chemical labyrinths", Proceedings of the National Academy of Sciences, 2009, 106:21472-2147, doi: 10.1073/pnas.0910016106

Predicting whether a molecule can traverse chemical labyrinths of channels, tunnels, and buried cavities usually requires performing computationally intensive molecular dynamics simulations. Often one wants to screen molecules to identify ones that can pass through a given chemical labyrinth or screen chemical labyrinths to identify those that allow a given molecule to pass. Because it is impractical to test each molecule/labyrinth pair using computationally expensive methods, faster, approximate methods are used to prune possibilities, “triaging” the ability of a proposed molecule to pass through the given chemical labyrinth. Most pruning methods estimate chemical accessibility solely on geometry, treating atoms or groups of atoms as hard spheres with appropriate radii. Here, we explore geometric configurations for a moving “molecular worm,” which replaces spherical probes and is assembled from solid blocks connected by flexible links. The key is to extend the fast marching method, which is an ordered upwind one-pass Dijkstra-like method to compute optimal paths by efficiently solving an associated Eikonal equation for the cost function. First, we build a suitable cost function associated with each possible configuration, and second, we construct an algorithm that works in ensuing high-dimensional configuration space: at least seven dimensions are required to account for translational, rotational, and internal degrees of freedom. We demonstrate the algorithm to study shortest paths, compute accessible volume, and derive information on topology of the accessible part of a chemical labyrinth. As a model example, we consider an alkane molecule in a porous material, which is relevant to designing catalysts for oil processing.

### Kaushik Datta, Kamil, Williams, Oliker, Shalf, Katherine A. Yelick, "Optimization and Performance Modeling of Stencil Computations on Modern Microprocessors", SIAM Review, 2009, 51:129-159, doi: 10.1137/070693199

- Download File: sirev09-stencil.pdf (pdf: 2.8 MB)

### J. Borrill, L. Oliker, J. Shalf, H. Shan, A. Uselton, "HPC global file system performance analysis using a scientific-application derived benchmark", Parallel Computing, 2009, 35:358-373, doi: 10.1016/j.parco.2009.02.002

- Download File: parco09-MADbench.pdf (pdf: 4.4 MB)

### K. Barbary, K. S. Dawson, K. Tokita, G. Aldering, R., N. V. Connolly, M. Doi, L. Faccioli, V., A. S. Fruchter, G. Goldhaber, A., A. Gude, X. Huang, Y. Ihara, K., M. Kowalski, C. Lidman, J. Meyers, T., P. Nugent, S. Perlmutter, D. Rubin, D., A. L. Spadafora, N. Suzuki, H. K. Swift, N. Takanashi, R. C. Thomas, N. Yasuda, "Discovery of an Unusual Optical Transient with the Hubble Space Telescope", Astrophysical Journal, 2009, 690:1358-1362, doi: 10.1088/0004-637X/690/2/1358

### R. Biswas, J. Vetter, L. Oliker, "Revolutionary Technologies for Acceleration of Emerging Petascale Applications", Guest Editors, Parallel Computing Journal, 2009,

- Download File: parco09-abstract.pdf (pdf: 49 KB)

### A. S. Almgren, J. B. Bell, A. Nonaka, M. Zingale, "A New Low Mach Number Approach in Astrophysics", Computing in Science and Engineering, vol. 11, no. 2, pp. 24-33, March/April, 2009,

### Lavanya Ramakrishnan, Daniel A. Reed, "Predictable Quality of Service Atop Degradable Distributed Systems", Journal of Cluster Computing, 2009,

### M. Day, J. Bell, P.-T. Bremer, V. Pascucci, V. Beckner, M. Lijewski, "Turbulence Effects on Cellular Burning Structures in Lean Premixed Hydrogen Flames", Combustion and Flame156 1035-1045, 2009,

### Regis C. P. Marques, Fatima N. S. Medeiros, Daniela M. Ushizima, "Target Dectection on SAR Images Using Level Set Methods", IEEE Transactions on Systems, Man and Cybernetics, 2009, 39:214-222, LBNL 958E, doi: 10.1109/TSMCC.2008.2006685

### P.O. Persson, J. Bonet, J. Peraire, "Discontinuous Galerkin solution of the Navier--Stokes equations on deformable domains", Computer Methods in Applied Mechanics and Engineering, 2009, 198:1585--1595,

### Samuel Williams, Carter, Oliker, Shalf, Katherine A. Yelick, "Optimization of a lattice Boltzmann computation on state-of-the-art multicore platforms", Journal of Parallel Distributed Computing (JPDC), 2009, 69:762-777, doi: 10.1016/j.jpdc.2009.04.002

- Download File: jpdc09-lbmhd.pdf (pdf: 1.1 MB)

### D.E.A. van Odyck, J.B. Bell, F. Monmont, N. Nikiforakis, "The Mathematical Structure of Multiphase Thermal Models of Flow in Porous Media", Proc. Royal Soc. A, 465:523,549, 2009,

- Download File: porthermform.pdf (pdf: 386 KB)

### David H. Bailey, Jonathan M. Borwein, Richard E. Crandall, "Resolution of the Quinn-Rand-Strogatz constant of nonlinear physics", Experimental Mathematics, 2009, 18:107-116,

### A. Gal-Yam, P. Mazzali, E. O. Ofek, P. E. Nugent, S. R., M. M. Kasliwal, R. M. Quimby, A. V., S. B. Cenko, R. Chornock, R., D. Kasen, M. Sullivan, E. C. Beshore, A. J., R. C. Thomas, J. S. Bloom, D. Poznanski, A. A., R. J. Foley, J. M. Silverman, I. Arcavi, R. S. Ellis, J. Deng, "Supernova 2007bi as a pair-instability explosion", Nature, 2009, 462:624-627, doi: 10.1038/nature08579

### M.A.J. Ashdown, C. Baccigalupi, J.G. Bartlett, J. Borrill, C. Cantalupo, G. De Gasperis, G. De Troia, K.M. Górski, E. Hivon, K. Huffenberger, E. Keihänen, R. Keskitalo, T. Kisner, H. Kurki-Suonio, C.R. Lawrence, P. Natoli, T. Poutanen, G. Prézeau, M. Reinecke, G. Rocha, M. Sandri, R. Stompor, F. Villa, B. Wandelt, "Making maps from Planck LFI 30 GHz data with asymmetric beams and cooler noise", Astronomy and Astrophysics, January 2009, 493:753-783, doi: 10.1051/0004-6361:200810381

### B.D. Santer, K.E. Taylor, P.J. Gleckler, C. Bonﬁls, T.P. Barnett, D.W. Pierce, T.M.L. Wigley, C. Mears, F.J. Wentz, W. Brueggemann, N.P. Gillett, S.A. Klein, S. Solomon, P.A. Stott, and M.F. Wehner, "Incorporating Model Quality Information in Climate Change Detection and Attribution Studies.", Proceeding of the National Academy of Sciences, 2009,

In a recent multimodel detection and attribution (D&A) study using the pooled results from 22 different climate models, the simulated “fingerprint” pattern of anthropogenically caused changes in water vapor was identifiable with high statistical confidence in satellite data. Each model received equal weight in the D&A analysis, despite large differences in the skill with which they simulate key aspects of observed climate. Here, we examine whether water vapor D&A results are sensitive to model quality. The “top 10” and “bottom 10” models are selected with three different sets of skill measures and two different ranking approaches. The entire D&A analysis is then repeated with each of these different sets of more or less skillful models. Our performance metrics include the ability to simulate the mean state, the annual cycle, and the variability associated with El Niño. We find that estimates of an anthropogenic water vapor fingerprint are insensitive to current model uncertainties, and are governed by basic physical processes that are well-represented in climate models. Because the fingerprint is both robust to current model uncertainties and dissimilar to the dominant noise patterns, our ability to identify an anthropogenic influence on observed multidecadal changes in water vapor is not affected by “screening” based on model quality.

### Khaled Z. Ibrahim, F. Bodin, "Efficient SIMDization and Data Management of the Lattice QCD Computation on the Cell Broadband Engine", Journal of Scientific computing, 2009, 17:153--172,

### Lifeng He, Yuyan Chao, Kenji Suzuki, Kesheng, "Fast Connected-Component Labeling", Pattern Recognition, 2009, 42:1977--1987, doi: 10.1016/j.patcog.2008.10.013

### David Donofrio, Oliker, Shalf, F. Wehner, Rowen, Krueger, Kamil, Marghoob Mohiyuddin, "Energy-Efficient Computing for Extreme-Scale Science", IEEE Computer, January 2009, 42:62-71, doi: 10.1109/MC.2009.35

### B. Kallemov, G. H. Miller and D. Trebotich, "A Duhamel Approach for the Langevin Equations with Holonomic Constraints", Molecular Simulation, 35(6):440-447, 2009,

- Download File: MolSim.pdf (pdf: 186 KB)

### Kesheng Wu, Ekow Otoo, Kenji Suzuki, "Optimizing two-pass connected-component labeling", Pattern Analysis \& Applications, 2009, 12:117--135,

### M. Migliaccio, P. Natoli, G. De Troia, C. Hikage, E. Komatsu, P.A.R. Ade, J.J. Bock, J.R. Bond, J. Borrill, A. Boscaleri, C.R. Contaldi, B.P. Crill, P. de Bernardis, G. de Gasperis, A. de Oliveira-Costa, G. Di Stefano, E. Hivon, T.S. Kisner, W.C. Jones, A.E. Lange, S. Masi, P.D. Mauskopf, C.J. MacTavish, A. Melchiorri, T.E. Montroy, C.B. Netterfield, E. Pascale, F. Piacentini, G. Polenta, S. Ricciardi, G. Romeo, J.E. Ruhl, M. Tegmark, M. Veneziani, N. Vittorio, "Probing primordial non Gaussianity in the BOOMERanG CMB maps: an analysis based on analytical Minkowski functionals", Nuclear Physics B - Proceedings Supplements, January 2009, 194:278-286, doi: 10.1016/j.nuclphysbps.2009.07.092

### David M. Ambrose, Jon Wilkening, "Global paths of time-periodic solutions of the Benjamin-Ono equation connecting pairs of traveling waves", Communications in Applied Mathematics and Computational Science, 2009, 4:177-215, doi: 10.2140/camcos.2009.4.177

### Chris H. Rycroft, "VORO++: A three-dimensional Voronoi cell library in C++", Chaos: An Interdisciplinary Journal of Nonlinear Science, 2009, 19:041111, LBNL 1432E, doi: 10.1063/1.3215722

Voro++ is a free software library for the computation of three dimensional Voronoi cells. It is primarily designed for applications in physics and materials science, where the Voronoi tessellation can be a useful tool in the analysis of densely-packed particle systems, such as granular materials or glasses. The software comprises of several C++ classes that can be modified and incorporated into other programs. A command-line utility is also provided that can use most features of the code. Voro++ makes use of a direct cell-by-cell construction, which is particularly suited to handling special boundary conditions and walls. It employs algorithms which are tolerant for numerical precision errors, and it has been successfully employed on very large particle systems.

### A. Nonaka, D. Trebotich, G. H. Miller, D. T. Graves, and P. Colella, "A Higher-Order Upwind Method for Viscoelastic Flow", Comm. App. Math. and Comp. Sci., 4(1):57-83, 2009,

- Download File: nonakaetal.pdf (pdf: 709 KB)

### M. Veneziani, A. Amblard, A. Cooray, F. Piacentini, D. Pietrobon, P. Serra, P.A.R. Ade, J.J. Bock, J.R. Bond, J. Borrill, A. Boscaleri, P. Cabella, C.R. Contaldi, B.P. Crill, P. De Bernardis, G. De Gasperis, A. De Oliveira-Costa, G. De Troia, G. Di Stefano, K.M. Ganga, E. Hivon, W.C. Jones, T.S. Kisner, A.E. Lange, C.J. MacTavish, S. Masi, P.D. Mauskopf, A. Melchiorri, T.E. Montroy, P. Natoli, C.B. Netterfield, E. Pascale, G. Polenta, S. Ricciardi, G. Romeo, J.E. Ruhl, P. Santini, M. Tegmark, N. Vittorio, "Subdegree sunyaev-zel dovich signal from multifrequency boomerang observations", Astrophysical Journal, January 2009, 702:L61-L65, doi: 10.1088/0004-637X/702/1/L61

### N. M. Law, S. R. Kulkarni, R. G. Dekany, E. O. Ofek, R. M., P. E. Nugent, J. Surace, C. C. Grillmair, J. S., M. M. Kasliwal, L. Bildsten, T., S. B. Cenko, D. Ciardi, E. Croner, S. G., J. van Eyken, A. V. Filippenko, D. B., A. Gal-Yam, D. Hale, N. Hamam, G., J. Henning, D. A. Howell, J. Jacobsen, R., S. Mattingly, D. McKenna, A. Pickles, D., G. Rahmer, A. Rau, W. Rosing, M., R. Smith, D. Starr, M. Sullivan, V. Velur, R. Walters, J. Zolkower, "The Palomar Transient Factory: System Overview, Performance, and First Results", Publications of the Astronomical Society of the Pacific, 2009, 121:1395-1408, doi: 10.1086/648598

### M. K. Cameron, S. B. Fomel, J. A. Sethian, "Analysis and algorithms for a regularized cauchy problem arising from a non-linear elliptic PDE for seismic velocity estimation", J. Comput. Phys., 2009, 228:7388--7411, doi: 10.1016/j.jcp.2009.06.036

### Chris H. Rycroft, Ken Kamrin, Martin Z. Bazant, "Assessing continuum postulates in simulations of granular flow", Journal of the Mechanics and Physics of Solids, 2009, 57:828--839, doi: 10.1016/j.jmps.2009.01.009

### J. Aguirre, A. Amblard, A. Ashoorioon, C. Baccigalupi, A., J. Bartlett, N. Bartolo, D. Benford, M., J. Bock, D. Bond, J. Borrill, F., M. Bridges, E. Bunn, E. Calabrese, C., A. Caramete, C. Carbone, S. Chatterjee, S., D. Chuss, C. Contaldi, A. Cooray, S., F. De Bernardis, P. De Bernardis, G. Zotti, J. Delabrouille, F. -Xavier Dsert, M., C. Dickinson, S. Dicker, M. Dobbs, S., O. Dore, J. Dotson, J. Dunkley, M. C., D. Fixsen, P. Fosalba, J. Fowler, E., W. Gear, S. Golwala, K. Gorski, A., J. Gundersen, M. Halpern, S. Hanany, M., C. Hernandez-Monteagudo, M. Hertzberg, G., C. Hirata, E. Hivon, W. Holmes, W., W. Hu, J. Hubmayr, K. Huffenberger, K., M. Jackson, A. Jaffe, B. Johnson, W., M. Kaplinghat, B. Keating, R. Keskitalo, J., W. Kinney, T. Kisner, L. Knox, A., E. Komatsu, A. Kosowsky, J. Kovac, L., H. Kurki-Suonio, S. Landau, C. Lawrence, S., A. Lee, E. Leitch, R. Leonardi, J., A. Liddle, E. Lim, M. Limon, M., P. Lubin, A. Magalhaes, D. Maino, T., V. Martin, S. Matarrese, J. Mather, H., T. Matsumura, P. Meerburg, A. Melchiorri, S., A. Miller, M. Milligan, K. Moodley, M., H. Nguyen, I. O Dwyer, A. Orlando, L., L. Page, B. Partridge, T. Pearson, H., F. Piacentini, L. Piccirillo, E. Pierpaoli, D., G. Pisano, L. Pogosian, D. Pogosyan, N., L. Popa, C. Pryke, C. Raeth, S., C. Reichardt, S. Ricciardi, P. Richards, G., L. Rudnick, J. Ruhl, B. Rusholme, C., D. Scott, C. Sealfon, N. Sehgal, M., L. Senatore, P. Serra, S. Shandera, M., P. Shirron, J. Sievers, K. Sigurdson, J., R. Silverberg, E. Silverstein, S. Staggs, A., F. Stivoli, R. Stompor, N. Sugiyama, D., A. Tartari, M. Tegmark, P. Timbie, M., G. Tucker, J. Urrestilla, J. Vaillancourt, M., L. Verde, J. Vieira, S. Watson, B., G. Wilson, E. Wollack, M. Wyman, A., G.-H. Yannick, O. Zahn, M. Zaldarriaga, M. Zemcov, J. Zwart, "Observing the Evolution of the Universe", ArXiv e-prints, January 2009,

### A. Rau, S. R. Kulkarni, N. M. Law, J. S. Bloom, D., G. S. Djorgovski, D. B. Fox, A. Gal-Yam, C. C., M. M. Kasliwal, P. E. Nugent, E. O., R. M. Quimby, W. T. Reach, M. Shara, L., S. B. Cenko, A. J. Drake, A. V. Filippenko, D. J., G. Helou, D. A. Howell, D. Poznanski, M. Sullivan, "Exploring the Optical Transient Sky with the Palomar Transient Factory", Publications of the Astronomical Society of the Pacific, 2009, 121:1334-1351, doi: 10.1086/605911

### Alexandre J. Chorin, Xuemin Tu, "Implicit sampling for particle filters", Proceedings of the National Academy of Sciences, 2009, 106:17249-1725, doi: 10.1073/pnas.0909196106

We present a particle-based nonlinear filtering scheme, related to recent work on chainless Monte Carlo, designed to focus particle paths sharply so that fewer particles are required. The main features of the scheme are a representation of each new probability density function by means of a set of functions of Gaussian variables (a distinct function for each particle and step) and a resampling based on normalization factors and Jacobians. The construction is demonstrated on a standard, ill-conditioned test problem.

### Chris H. Rycroft, Ashish V. Orpe, Arshad Kudrolli, "Physical test of a particle simulation model in a sheared granular system", Phys. Rev. E, 2009, 80:031305, LBNL 1430E, doi: 10.1103/PhysRevE.80.031305

### Bronis R de Supinski, Sadaf Alam, David H Bailey, Laura, Chris Daley, Anshu Dubey, Todd Gamblin, Dan, Paul D Hovland, Heike Jagode, Karen Karavanic, Marin, John Mellor-Crummey, Shirley Moore, Boyana, Leonid Oliker, Catherine Olschanowsky, Philip C, Martin Schulz, Sameer Shende, Allan Snavely, Wyatt, Mustafa Tikir, Jeff Vetter, Pat Worley, Nicholas Wright, "Modeling the Office of Science ten year facilities plan: The PERI Architecture Tiger Team", Journal of Physics: Conference Series, 2009, 180:012039, doi: 10.1088/1742-6596/180/1/012039

- Download File: arch-tiger-team.pdf (pdf: 605 KB)

### G. H. Weber, O. Rübel, M.-Y. Huang, A. H. DePace, C. C. Fowlkes, S. V. E. Keränen, C. L. Luengo Hendriks, H. Hagen, D. W. Knowles, J. Malik, M. D. Biggin and B. Hamann, "Visual exploration of three-dimensional gene expression using physical views and linked abstract views", IEEE Transactions on Computational Biology and Bioinformatics, 2009, 6:296-309, LBNL 63776, doi: 10.1109/TCBB.2007.70249

- Download File: LBNL-63776.pdf (pdf: 11 MB)

### J. D. Simon, A. Gal-Yam, O. Gnat, R. M. Quimby, M., J. M. Silverman, S. Blondin, W., A. V. Filippenko, J. C. Wheeler, R. P. Kirshner, F., P. Nugent, R. J. Foley, S. S. Vogt, R. P., K. M. G. Peek, E. Rosolowsky, G. J. Herczeg, D. N. Sauer, P. A. Mazzali, "Variable Sodium Absorption in a Low-extinction Type Ia Supernova", Astrophysical Journal, 2009, 702:1157-1170, doi: 10.1088/0004-637X/702/2/1157

### J. Wilkening, "Practical error estimates for Reynolds' lubrication approximation and its higher order corrections", SIAM Journal on Mathematical Analysis, 2009, 41:588--630,

### M. Zingale, A. S. Almgren, J. B. Bell, A. Nonaka, and S. E. Woosley, "Low Mach Number Modeling of Type Ia Supernovae. IV. White Dwarf Convection", Astrophysical Journal, 704, 196-210, 2009,

- Download File: LowMach4.pdf (pdf: 1.9 MB)

### S. Nobili, V. Fadeyev, G. Aldering, R. Amanullah, K., M. S. Burns, K. S. Dawson, S. E. Deustua, L., A. S. Fruchter, G. Goldhaber, A., I. Hook, D. A. Howell, A. G. Kim, R. A., C. Lidman, J. Meyers, P. E. Nugent, R., N. Panagia, S. Perlmutter, D. Rubin, A. L., M. Strovink, N. Suzuki, Supernova Cosmology Project, "Constraining Dust and Color Variations of High-z SNe Using NICMOS on the Hubble Space Telescope", Astrophysical Journal, 2009, 700:1415-1427, doi: 10.1088/0004-637X/700/2/1415

### L. A. Drummond, Vicente Galiano, Violeta Migallon andJose Penades, "PyACTS: A Python Based Interface to ACTS Tools and Parallel Scientific Applications", International Journal of Parallel Programming, 2009, 37(1):58-77,

### D. A. Stone, M. R. Allen, P. A. Stott, P. Pall, S.-K. Min, T. Nozawa, S. Yukimoto, "The detection and attribution of human influence on climate", Annu. Rev. Env. Resour., 2009, 34:1--16,

### Dmitry Yu Zubarev, Neil Robertson, Dominik Domin, Jarrod McClean, Jinhua Wang, William A Lester Jr, Russell Whitesides, Xiaoqing You, Michael Frenklach, "Local Electronic Structure and Stability of Pentacene Oxyradicals", The Journal of Physical Chemistry C, 2009, 114:5429--5437,

### 2008

### GS GROENEWOLD, J OOMENS, WA DE JONG, GL GRESHAM, ME MCILWAIN, MJ VAN STIPDONK, "Vibrational spectroscopy of anionic nitrate complexes of UO22+ and Eu3+ isolated in the gas phase", PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2008, 10:1192-1202, doi: 10.1039/b715337f

### A. J. Aspden, J. B. Bell, M. S. Day, S. E. Woosley, M. Zingale, "Turbulence-Flame Interactions in Type Ia Supernovae", Astrophysical Journal, 689, pp.1173-1185, December 20, 2008,

- Download File: 74937.web.pdf (pdf: 4.5 MB)
- Download File: abdwzrev.pdf (pdf: 3.1 MB)

### K KOWALSKI, JR HAMMOND, WA DE JONG, AJ SADLEJ, "Coupled cluster calculations for static and dynamic polarizabilities of C-60", JOURNAL OF CHEMICAL PHYSICS, 2008, 129, doi: 10.1063/1.3028541

### Baron Peters, Nils E. R. Zimmermann, Gregg T. Beckham, Jefferson W. Tester, Bernhardt L. Trout, "Path Sampling Calculation of Methane Diffusivity in Natural Gas Hydrates from a Water-Vacancy Assisted Mechanism", J. Am. Chem. Soc., 2008, 130:17342-1735, doi: 10.1021/ja802014m

Increased interest in natural gas hydrate formation and decomposition, coupled with experimental difficulties in diffusion measurements, makes estimating transport properties in hydrates an important technological challenge. This research uses an equilibrium path sampling method for free energy calculations [Radhakrishnan, R.; Schlick, T. *J. Chem. Phys.* **2004**, *121*, 2436] with reactive flux and kinetic Monte Carlo simulations to estimate the methane diffusivity within a structure I gas hydrate crystal. The calculations support a water-vacancy assisted diffusion mechanism where methane hops from an occupied “donor” cage to an adjacent “acceptor” cage. For pathways between cages that are separated by five-membered water rings, the free energy landscape has a high barrier with a shallow well at the top. For pathways between cages that are separated by six-membered water rings, the free energy calculations show a lower barrier with no stable intermediate. Reactive flux simulations confirm that many reactive trajectories become trapped in the shallow intermediate at the top of the barrier leading to a small transmission coefficient for these paths. Stable intermediate configurations are identified as doubly occupied off-pathway cages and methane occupying the position of a water vacancy. Rate constants are computed and used to simulate self-diffusion with a kinetic Monte Carlo algorithm. Self-diffusion rates were much slower than the Einstein estimate because of lattice connectivity and methane’s preference for large cages over small cages. Specifically, the fastest pathways for methane hopping are arranged in parallel (nonintersecting) channels, so methane must hop via a slow pathway to escape the channel. From a computational perspective, this paper demonstrates that equilibrium path sampling can compute free energies for a broader class of coordinates than umbrella sampling with molecular dynamics. From a technological perspective, this paper provides one estimate for an important transport property that has been difficult to measure. In a hydrate I crystal at 250 K with nearly all cages occupied by methane, we estimate *D* ≈ 7 × 10^{−15}*X* m^{2}/s where *X* is the fraction of unoccupied cages.

### Katrin Heitmann, Zarija Lukić, Patricia Fasel, Salman Habib, Michael S Warren, Martin White, James Ahrens, Lee Ankeny, Ryan Armstrong, Brian O'Shea, Paul M Ricker, Volker Springel, Joachim Stadel, Hy Trac, "The cosmic code comparison project", Computational Science & Discovery, 2008, 1:015003,

### C. Voemel, S. Tomov, O. Marques, A. Canning, L.-W. Wang, J. Dongarra, "State-of-the-art Eigensolvers for Electronic Structure Calculations of Large Scale Nano-systems", Journal of Computational Physics, 2008, 227:7113-7124,

### J.M. Rabaey, D. Burke, K. Lutz, J. Wawrzynek, "Workloads of the Future", IEEE Design Test of Computers, July 8, 2008, 25:358-365, doi: 10.1109/MDT.2008.118

Along with changing technologies and design techniques, target applications span a wide range: from large-scale computing to personal services and perceptual interfaces. The authors of this article characterize these workloads of the future and argue for a new set of benchmarks to guide the exploration and optimization of future systems.

### VS BRYANTSEV, WA DE JONG, KC COSSEL, MS DIALLO, WA GODDARD, GS GROENEWOLD, W CHIEN, MJ VAN STIPDONK, "Two-electron three-centered bond in side-on (eta(2)) uranyl(V) superoxo complexes", JOURNAL OF PHYSICAL CHEMISTRY A, 2008, 112:5777-5780, doi: 10.1021/jp804202q

### O. Marques, J. Demmel, C. Voemel, B. Parlett, "A Testing Infrastructure for Symmetric Tridiagonal Eigensolvers", ACM TOMS, 2008, 35,

### D. Bailey, J. Chame, C. Chen, J. Dongarra, M. Hall, J. Hollingsworth, P. Hovland, S. Moore, K. Seymour, J. Shin, A. Tiwari, S. Williams, H. You, "PERI Auto-tuning", SciDAC PI Meeting, Journal of Physics: Conference Series, 125 012001, 2008,

- Download File: jpconf8125012038.pdf (pdf: 1.2 MB)

### S. Williams, K. Datta, J. Carter, L. Oliker, J. Shalf, K. Yelick, D. Bailey, "PERI: Auto-tuning Memory Intensive Kernels for Multicore", SciDAC PI Meeting, Journal of Physics: Conference Series, 125 012038, July 2008, doi: 10.1088/1742-6596/125/1/012038

- Download File: jpconf8125012089.pdf (pdf: 874 KB)

### P. Jakl, J. Lauret, A. Hanushevsky, A. Shoshani, A. Sim, J. Gu, "Grid data access on widely distributed worker nodes using scalla and SRM", Journal of Physics: Conf. Ser., 2008, 119, doi: 10.1088/1742-6596/119/7/072019

### JR HAMMOND, WA DE JONG, K KOWALSKI, "Coupled-cluster dynamic polarizabilities including triple excitations", JOURNAL OF CHEMICAL PHYSICS, 2008, 128, doi: 10.1063/1.2929840

### GS GROENEWOLD, MJ VAN STIPDONK, WA DE JONG, J OOMENS, GL GRESHAM, ME MCLLWAIN, D GAO, B SIBOULET, L VISSCHER, M KULLMAN, N POLFER, "Infrared spectroscopy of dioxouranium(V) complexes with solvent molecules: Effect of reduction", CHEMPHYSCHEM, 2008, 9:1278-1285, doi: 10.1002/cphc.200800034

### B. Paul, S. Ahern, E. W. Bethel, E. Brugger, R. Cook, J. Daniel, K. Lewis, J. Owen, and D. Southard, "Chromium Renderserver: Scalable and Open Remote Rendering Infrastructure", IEEE Transactions on Visualization and Computer Graphics, May 2008, 14:627-639, LBNL 63693,

- Download File: LBNL-63693-CRRS.pdf (pdf: 2.7 MB)

### David H. Bailey, Jonathan M. Borwein, "Computer-assisted discovery and proof", Tapas in Experimental Mathematics, edited by Tewodros Amdeberhan, Victor H. Moll, May 2008, 21-52,

### C S Chang, S Klasky, J Cummings, R. Samtaney, A Shoshani, L Sugiyama, D Keyes, S Ku, G Park, S Parker, N Podhorszki, H. Strauss, H Abbasi, M Adams, R Barreto, G Bateman, K Bennett, Y Chen, E D’Azevedo, C Docan, S Ethier, E Feibush, L Greengard, T Hahm, F Hinton, C Jin, A. Khan, A Kritz, P Krsti, T Lao, W Lee, Z Lin, J Lofstead, P Mouallem, M Nagappan, A Pankin, M Parashar, M Pindzola, C Reinhold, D Schultz, K Schwan, D. Silver, A Sim, D Stotler, M Vouk, M Wolf, H Weitzner, P Worley, Y Xiao, E Yoon, D Zorin, "Toward a first- principles integrated simulation of tokamak edge plasmas", Journal of Physics: Conf. Ser., 2008, 125, doi: 10.1088/1742-6596/125/1/012042

### R Ananthakrishnan, D E Bernholdt, S Bharathi, D Brown, M Chen, A L Chervenak, L Cinquini, R Drach, I T Foster, P Fox, D Fraser, K Halliday, S Hankin, P Jones, C Kesselman, D E Middleton, J Schwidder, R Schweitzer, R Schuler, A Shoshani, F Siebenlist, A Sim, W G Strand, N Wilhelmi, M Su, D N Williams, "Building a global federation system for climate change research: the earth system grid center for enabling technologies (ESG-CET)", Journal of Physics: Conf. Ser., 2008, 78, doi: 10.1088/1742-6596/78/1/012050

### C. C. Fowlkes, C. L. Luengo Hendriks, S. V. E. Keränen, G. H. Weber, O. Rübel, M.-Y. Huang, S. Chatoor, A. H. DePace, L. Simirenko, C. Henriquez, A. Beaton, R. Weiszmann, S. Celniker, B. Hamann, D. W. Knowles, M. D. Biggin, M. B. Eisen, J. Malik, "A Quantitative Spatio-temporal Atlas of Gene Expression in the Drosophila Blastoderm", Cell, April 18, 2008, 133:364-374,

### AS LIPTON, RW HECK, GR STAEHELI, M VALIEV, WA DE JONG, PD ELLIS, "A QM/MM approach to interpreting Zn-67 solid-state NMR data in zinc proteins", JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2008, 130:6224-6230, doi: 10.1021/ja711240t

### Sean Peisert, Matt Bishop, Keith Marzullo, "Computer Forensics In Forensis", ACM Operating Systems Review (OSR), April 2008, 42:112-122, doi: 10.1109/TDSC.2007.1003

### M. Wehner, L. Oliker, J. Shalf, "Performance Characterization of the World's Most Powerful Supercomputers", Internation Journal of High Performance Computing Applications (IJHPCA), April 2008,

- Download File: IJHPCA08Abstract.pdf (pdf: 64 KB)

### Patrick Nichols, Eric J. Bylaska, Gregory K. Schenter, Wibe de Jong, "Equatorial and apical solvent shells of the UO(2)(2+) ion", Journal of Chemical Physics, 2008, 128, doi: 10.1063/1.2884861

### VE JACKSON, R CRACIUN, DA DIXON, KA PETERSON, WA DE JONG, "Prediction of vibrational frequencies of UO22+ at the CCSD(T) level", JOURNAL OF PHYSICAL CHEMISTRY A, 2008, 112:4095-4099, doi: 10.1021/jp710334b

### J. Chen, I. Yoon and E. W. Bethel, "Interactive, Internet Delivery of Visualization via Structured, Prerendered Multiresolution Imagery.", IEEE Transactions on Visualization and Computer Graphics, March 2008, 14:302-312, LBNL 62252,

- Download File: LBNL-62252-chen-tvcg.pdf (pdf: 2.1 MB)

### S. Bailey, C. Aragon, R. Romano, R. C. Thomas, B. A. Weaver and D. Wong, "Object classification at the Nearby Supernova Factory", Astronomische Nachrichten, March 2008, 329:292, LBNL 696E, doi: 10.1002/asna.200710932

### B. M. Sanderson, R. Knutti, T. Aina, C. Christensen, N. Faull, D. J. Frame, W. J. Ingram, C. Piani, D. A. Stainforth, D. A. Stone, M. R. Allen, "Constraints on model response to greenhouse gas forcing and the role of subgrid-scale processes", J. Climate, 2008, 21:2384--2400,

### David H. Bailey, Jonathan M. Borwein, David Broadhurst, M. L. Glasser, "Elliptic integral evaluations of Bessel moments", Journal of Physics A: Mathematical and General, 2008, 41:205203,

### Leonid Oliker, Canning, Carter, Shalf, St\ ephane Ethier, "Scientific Application Performance On Leading Scalar and Vector Supercomputering Platforms", Internation Journal of High Performance Computing Applications (IJHPCA), 2008, 22:5-20, doi: 10.1177/1094342006085020

### B. M. Sanderson, C. Piani, W. J. Ingram, D. A. Stone, M. R. Allen, "Towards constraining climate sensitivity by linear analysis of feedback patterns in thousands of perturbed-physics GCM simulations", Clim. Dyn., 2008, 30:175--190,

### LGM DE MACEDO, WA DE JONG, "Fully relativistic calculations on the potential energy surfaces of the lowest 23 states of molecular chlorine", JOURNAL OF CHEMICAL PHYSICS, 2008, 128, doi: 10.1063/1.2827457

### David H. Bailey, "Review of An Introduction to Parallel and Vector Scientific Computing", Scientific Programming, January 1, 2008, 16:97-98,

### J. Demmel, O. Marques, C. Voemel, B. Parlett, "Performance and Accuracy of LAPACK's Symmetric Tridiagonal Eigensolvers", SIAM Journal on Scientific Computing, 2008, 30:1508–1526,

### George Vahala, Min Soe, Brian Keating, Jeffrey Yepez, Linda Vahala, Jonathan Carter, Sean Ziegeler, "MHD Turbulence Studies Using Lattice Boltzmann Algorithms", Commun. Comput. Phys., 2008, 4:624-646,

### GS GROENEWOLD, AK GIANOTTO, ME MCILWAIN, MJ VAN STIPDONK, M KULLMAN, DT MOORE, N POLFER, J OOMENS, I INFANTE, L VISSCHER, B SIBOULET, WA DE JONG, "Infrared spectroscopy of discrete uranyl anion complexes", JOURNAL OF PHYSICAL CHEMISTRY A, 2008, 112:508-521, doi: 10.1021/jp077309q

### S. A. Williams, J. B. Bell, and A. L. Garcia, "Algorithm Refinement for Fluctuating Hydrodynamics", Multiscale Model. Simul. 6, 1256-1280, 2008,

- Download File: FluctHybrid.pdf (pdf: 356 KB)

### M. Kowalski, D. Rubin, G. Aldering, R. J. Agostinho, A., R. Amanullah, C. Balland, K. Barbary, G., P. J. Challis, A. Conley, N. V. Connolly, R., K. S. Dawson, S. E. Deustua, R., S. Fabbro, V. Fadeyev, X. Fan, B., G. Folatelli, B. L. Frye, G. Garavini, E. L., L. Germany, G. Goldhaber, B. Goldman, A., D. E. Groom, J. Haissinski, D. Hardin, I., S. Kent, A. G. Kim, R. A. Knop, C., E. V. Linder, J. Mendez, J. Meyers, G. J., M. Moniez, A. M. Mour\ ao, H., S. Nobili, P. E. Nugent, R. Pain, O., S. Perlmutter, M. M. Phillips, V., R. Quimby, N. Regnault, J. Rich, E. P., P. Ruiz-Lapuente, F. D. Santos, B. E., R. A. Schommer, R. C. Smith, A. M., A. L. Spadafora, L.-G. Strolger, M., N. B. Suntzeff, N. Suzuki, R. C. Thomas, N. A., L. Wang, W. M. Wood-Vasey, J. L. Yun, Supernova Cosmology Project, "Improved Cosmological Constraints from New, Old, and Combined Supernova Data Sets", Astrophysical Journal, 2008, 686:749-778, doi: 10.1086/589937

### A. J. Aspden, N. Nikiforakis, S. B. Dalziel, and J.B.Bell, "Analysis of Implicit LES Methods", Communications in Applied Mathematics and Computational Science, 3, pp.103-126, 2008,

- Download File: andbCamcos.pdf (pdf: 675 KB)

### R. S. Ellis, M. Sullivan, P. E. Nugent, D. A. Howell, A., P. Astier, D. Balam, C. Balland, S., R. G. Carlberg, A. Conley, D. Fouchez, J., D. Hardin, I. Hook, R. Pain, K. Perrett, C. J. Pritchet, N. Regnault, "Verifying the Cosmological Utility of Type Ia Supernovae: Implications of a Dispersion in the Ultraviolet Spectra", Astrophysical Journal, 2008, 674:51-69, doi: 10.1086/524981

### C.I.O. Martins, R.M.S. Veras, G.L.B. Ramalho, F.N.S. Medeiros, D. M. Ushizima, "Automatic Microaneurysm Detection and Characterization Through Digital Color Fundus Images", Brazilian Artificial Intelligence Community Conference, Tenth Brazilian Symposium on Neural Networks, Proceedings of IEEE SBRN'2008, 2008,

### Samuel Williams, Oliker, W. Vuduc, Shalf, A. Yelick, James Demmel, "Optimization of sparse matrix-vector multiplication on emerging multicore platforms", Parallel Computing, 2008, 35:38, doi: 10.1016/j.parco.2008.12.006

- Download File: parco08-spmv.pdf (pdf: 1.5 MB)

### D. Trebotich, G. H. Miller and M. D. Bybee, "A Penalty Method to Model Particle Interactions in DNA-laden Flows", J. Nanosci. Nanotechnol., 8(7):3749-3756, 2008,

- Download File: JNNpreprint.pdf (pdf: 269 KB)

### Luke J. Gosink, John C. Anderson, E. Wes Bethel, Kenneth I. Joy, "Query-Driven Visualization of Time-Varying Adaptive Mesh Refinement Data", IEEE Transactions on Visualization and Computer Graphics, 2008, 14:1715-1722, LBNL 803E,

- Download File: LBNL-803E.pdf (pdf: 4.3 MB)

### D. A. Stone, "Predicted climate changes for the years to come and implications for disease impact studies", Revue scientifique et technique -- Office international des epizooties, 2008, 27:319--330,

- Download File: StoneDA2008.pdf (pdf: 407 KB)

### Michael F. Wehner, L. Oliker, John Shalf, "Towards Ultra-High Resolution Models of Climate and Weather", Internation Journal of High Performance Computing Applications (IJHPCA), January 2008, 22:149-165,

- Download File: IJHPCA08-climate.pdf (pdf: 580 KB)

### S. Ethier, W. M. Tang, R. Walkup, L. Oliker, "Large-Scale Gyrokenetic particle simulation of Microturbulence in Magnetically Confined Fusion Plasmas", IBM Journal of Research and Development, 2008,

- Download File: IBMJRD08-fusion.pdf (pdf: 365 KB)

### N. P. Gillett, D. A. Stone, P. A. Stott, T. Nozawa, A. Yu. Karpechko, G. C. Hegerl, M. F. Wehner, P. D. Jones, "Attribution of polar warming to human influence", Nat. Geosci., 2008, 1:750--754,,

### Colella, P. and Sekora, M. D., "A Limiter for PPM that Preserves Accuracy at Smooth Extrema", Submitted to Journal of Computational Physics, 2008,

- Download File: ColellaSekora.pdf (pdf: 111 KB)

### Khaled Z. Ibrahim, F. Bodin, Olivier Pene, "Fine-grained Parallelization of Lattice QCD Kernel Routine on GPUs", Journal of Parallel and Distributed Computing, 2008, 68:1350-1359,

### C. J. Raxworthy, R. G. Pearson, N. Rabibisoa, A. M. Rakotondrazafy, J.-B. Ramanamanjato, A. P. Wu Raselimanana, R. A. Nussbaum, D. A. Stone, "Extinction vulnerability of tropical montane endemism from warming and upslope displacement: a preliminary appraisal for the highest massif in Madagascar", Global Change Biology, 2008, 14:1703--1720,

### Martin, D.F., Colella, P., and Graves, D.T., "A Cell-Centered Adaptive Projection Method for the Incompressible Navier-Stokes Equations in Three Dimensions", Journal of Computational Physics Vol 227 (2008) pp. 1863-1886., 2008, LBNL 62025,

- Download File: martinColellaGraves2008.pdf (pdf: 3.1 MB)

### Cecilia Aragon, Stephen Bailey, Sarah Poon, Karl Runge, and Rollin Thomas, "Sunfall: A Collaborative Visual Analytics System for Astrophysics", J. Phys.: Conf. Ser. 125 012091 (Proceedings of SciDAC 2008), 2008, LBNL 657E,

- Download File: jpconf8125012091.pdf (pdf: 3.3 MB)

### D. T. Graves, D Trebotich, G. H. Miller, P. Colella, "An Efficient Solver for the Equations of Resistive MHD with Spatially-Varying Resistivity", Journal of Computational Physics Vol 227 (2008) pp.4797-4804., 2008,

- Download File: gravesTrebMillerColella2008.pdf (pdf: 155 KB)

### J. S. Bloom, D. L. Starr, N. R. Butler, P. Nugent, M. Rischard, D. Eads, D. Poznanski, "Towards a real-time transient classification engine", Astronomische Nachrichten, 2008, 329:284, doi: 10.1002/asna.200710957

### Shantenu Jha, Hartmut Kaiser, Andre Merzky, John Shalf, "SAGA - The Simple API for Grid Applications - Motivation, Design, and Implementation", Encyclopedia of Grid Technologies and Applications, Volume 1. Information Science Reference (www.info-sci-ref.com), 2008,

- Download File: egc2007.pdf (pdf: 227 KB)

### Miniati, F. and Colella, P., "A Modified higher-Order Godunov's Scheme for Stiff Source Conservative Hydrodynamics", Journal of Computational Physics Vol. 224 (2007), pp. 519-538., 2008, LBNL 59902,

- Download File: JCPMiniatiColellaJun2007.pdf (pdf: 585 KB)

### L. Pilipchuk, E. Vecharynski, Yu. H. Pesheva, "Solution of Large Linear Systems with Embedded Network Structure for a Non-Homogeneous Network Flow Programming Problem", Mathematica Balkanica Vol. 22, Fasc. 3-4, p. 235-254, 2008,

In the paper the linear underdetermined system of a special type is considered. Systems of this type appear in non-homogeneous network flow programming problems in the form of systems of constraints and can be characterized as systems with a large sparse submatrix representing the embedded network structure. A direct method for finding solutions of the system is developed. The algorithm is based on the theoretic-graph specificities for the structure of the support and properties of the basis of a solution space of a homogeneous system. One of the key steps is decomposition of the system. A simple example is regarded at the end of the paper.

### A. S. Almgren, J. B. Bell, A. Nonaka, and M. Zingale, "Low Mach Number Modeling of Type Ia Supernovae. III. Reactions", Astrophysical Journal, 684, 449-470, 2008, LBNL 58673,

- Download File: LowMach3.pdf (pdf: 1.2 MB)

### 2007

### H. M. Aktulga, I. Kontoyiannis, L. Lyznik, L. Szpankowski, W. Szpankowski, A. Y. Grama, "Identifying Statistical Dependence in Genomic Sequences via Mutual Information", EURASIP Journal on Bioinformatics and Systems Biology, 2007:1474, December 5, 2007, doi: 10.1155/2007/14741

### Zarija Lukić, Katrin Heitmann, Salman Habib, Sergei Bashinsky, Paul M. Ricker, "The Halo Mass Function: High-Redshift Evolution and Universality", The Astrophysical Journal, 2007, 671:1160,

### David H. Bailey, Robert Lucas, Paul Hovland, Boyana Norris, Kathy Yelick, Dan Gunter, Bronis de Supinski, Dan Quinlan, Pat Worley, Jeff Vetter, Phil Roth, John Mellor-Crummey, Allan Snavely, Jeff Hollingsworth, Dan Reed, Rob Fowler, Ying Zhang, Mary Hall, Jacque Chame, Jack Dongarra, Shirley Moore, "Performance engineering: Understanding and improving the performance of large-scale codes", CT Watch Quarterly, November 2007, 3:18-23,

### JR HAMMOND, K KOWALSKI, WA DEJONG, "Dynamic polarizabilities of polyaromatic hydrocarbons using coupled-cluster linear response theory", JOURNAL OF CHEMICAL PHYSICS, 2007, 127:-, doi: 10.1063/1.2772853

### Nils E. R. Zimmermann, Sven Jakobtorweihen, Edith Beerdsen, Berend Smit, Frerich J. Keil, "In-Depth Study of the Influence of Host-Framework Flexibility on the Diffusion of Small Gas Molecules in One-Dimensional Zeolitic Pore Systems", J. Phys. Chem. C, 2007, 111:17370-1738, doi: 10.1021/jp0746446

Molecular-dynamics simulations are performed to understand the role of host−framework flexibility on the diffusion of methane molecules in the one-dimensional pores of AFI-, LTL-, and MTW-type zeolites. In particular, the impact of the choice of the host model is studied. Dynamically corrected Transition State Theory is used to provide insights into the diffusion mechanism on a molecular level. Free-energy barriers and dynamical correction factors can change significantly by introducing lattice flexibility. In order to understand the phenomenon of free-energy barriers reduction, we investigate the motion of the window atoms. The influence that host−framework flexibility exerts on gas diffusion in zeolites is, generally, a complex function of material, host model, and loading such that transferability of conclusions from one zeolite to the other is not guaranteed.

### K KOWALSKI, JR HAMMOND, WA DE JONG, "Linear response coupled cluster singles and doubles approach with modified spectral resolution of the similarity transformed Hamiltonian", JOURNAL OF CHEMICAL PHYSICS, 2007, 127:-, doi: 10.1063/1.2795708

### W. C. Jones, T. E. Montroy, B. P. Crill, C. R. Contaldi, T. S., A. E. Lange, C. J. MacTavish, C. B. Netterfield, J. E. Ruhl, "Instrumental and Analytic Methods for Bolometric Polarimetry", Astronomy and Astrophysics, August 2007, 470:771-785,

### Sean Peisert, Matt Bishop, "I'm a Scientist, Not a Philosopher!", IEEE Security and Privacy, July 2007, 5(4):48-51, doi: 10.1109/MSP.2007.84

### Katherine A. Yelick, Dan Bonachea, Wei-Yu Chen, Phillip Colella, Kaushik Datta, Jason Duell, Susan L. Graham, Paul Hargrove, Paul N. Hilfinger, Parry Husbands, Costin Iancu, Amir Kamil, Rajesh Nishtala, Jimmy Su, Michael L. Welcome, Tong Wen, "Productivity and performance using partitioned global address space languages", Parallel Symbolic Computation (PASCO), 2007,

### JR HAMMOND, M VALIEV, WA DEJONG, et al., "Calculations of molecular properties in hybrid coupled-cluster and molecular mechanics approach", JOURNAL OF PHYSICAL CHEMISTRY A, 2007, 111:5492-5498, doi: 10.1021/jp070553x

### F. Donno, L. Abadie, P. Badino, J. Baud, E. Corso, M. Crawford, S. De Witt, A. Forti, P. Fuhrmann, G. Grosdidier, J. Gu , J. Jensen, S. Lemaitre, M. Litmaath, D. Litvinsev, G. Lo Presti, L. Magnoni, T. Mkrtchan, A. Moibenko, V. Natarajan, G. Oleynik, T. Perelmutov, D. Petravick, A. Shoshani, A. Sim, M. Sponza, R. Zappi, "Storage Resource Manager version 2.2: design, implementation, and testing experience", Journal of Physics: Conf. Ser., 2007, 119, doi: 10.1088/1742-6596/119/6/062028

### Sean Peisert, Matt Bishop, Sidney Karin, Keith Marzullo,, "Analysis of Computer Intrusions Using Sequences of Function Calls", IEEE Transactions on Dependable and Secure Computing (TDSC), April 2007, 4(2):137-150, doi: 10.1109/TDSC.2007.1003

### Elaheh Pourabbas, Arie Shoshani, "Efficient Estimation of Joint Queries from Multiple OLAP Databases", ACM Transactions on Database Systems (TODS), March 1, 2007, Volume 3,

### M. Allen, P. Pall, D. Stone, P. Stott, D. Frame, S.-K. Min, T. Nozawa, S. Yukimoto, "Scientific challenges in the attribution of harm to human influence on climate", U. Pa. L. Rev., 2007, 155:1353--1400,

### G. H. Miller and D. Trebotich, "Toward a Mesoscale Model for the Dynamics of Polymer Solutions", J. Comput. Theoret. Nanosci. 4(4):797-801, 2007,

- Download File: JCTNpreprint.pdf (pdf: 271 KB)

### P Pall, MR Allen, DA Stone, "Testing the Clausius–Clapeyron constraint on changes in extreme precipitation under CO₂ warming", Climate Dynamics, 2007, 28:351--363,

### Samuel Williams, Shalf, Oliker, Kamil, Husbands, Katherine A. Yelick, "Scientific Computing Kernels on the Cell Processor", International Journal of Parallel Programming, January 2007, 35:263-298, doi: 10.1007/s10766-007-0034-5

- Download File: ijpp07-cell.pdf (pdf: 1000 KB)

### D. Trebotich, G. H. Miller and M. D. Bybee, "A Hard Constraint Algorithm to Model Particle Interactions in DNA-laden Flows", Nanoscale and Microscale Thermophysical Engineering 11(1):121-128, 2007,

- Download File: NMTE.pdf (pdf: 132 KB)

### D. Trebotich, "Toward a Solution to the High Weissenberg Number Problem", Proc. Appl. Math. Mech. 7(1):2100073-2100074, 2007,

- Download File: HWNPPAMM2007.pdf (pdf: 160 KB)

### G. De Troia, P.A.R. Ade, J.J. Bock, J.R. Bond, J. Borrill, A. Boscaleri, P. Cabella, C.R. Contaldi, B.P. Crill, P. De Bernardis, G. De Gasperis, A. De Oliveira-Costa, G. Di Stefano, P.G. Ferreira, E. Hivon, A.H. Jaffe, T.S. Kisner, M. Kunz, W.C. Jones, A.E. Lange, M. Liguori, S. Masi, S. Matarrese, P.D. Mauskopf, C.J. MacTavish, A. Melchiorri, T.E. Montroy, P. Natoli, C.B. Netterfield, E. Pascale, F. Piacentini, D. Pogosyan, G. Polenta, S. Prunet, S. Ricciardi, G. Romeo, J.E. Ruhl, P. Santini, M. Tegmark, M. Veneziani, N. Vittorio, "Searching for non-gaussian signals in the BOOMERANG 2003 CMB maps", Astrophysical Journal, January 2007, 670:L73-L76, doi: 10.1086/524402

### D. Trebotich, "Simulation of Biological Flow and Transport in Complex Geometries using Embedded Boundary / Volume-of-Fluid Methods", Journal of Physics: Conference Series 78 (2007) 012076, 2007,

- Download File: SciDAC2007.pdf (pdf: 453 KB)

### J.H.P. Wu, J. Zuntz, M.E. Abroe, P.A.R. Ade, J. Bock, J. Borrill, J. Collins, S. Hanany, A.H. Jaffe, B.R. Johnson, T. Jones, A.T. Lee, T. Matsumura, B. Rabii, T. Renbarger, P.L. Richards, G.F. Smoot, R. Stompor, H.T. Tran, C.D. Winant, "Maxipol: Data analysis and results", Astrophysical Journal, January 2007, 665:55-66, doi: 10.1086/518112

### B.R. Johnson, J. Collins, M.E. Abroe, P.A.R. Ade, J. Bock, J. Borrill, A. Boscaleri, P. De Bernardis, S. Hanany, A.H. Jaffe, T. Jones, A.T. Lee, L. Levinson, T. Matsumura, B. Rabii, T. Renbarger, P.L. Richards, G.F. Smoot, R. Stompor, H.T. Tran, C.D. Winant, J.H.P. Wu, J. Zuntz, "Maxipol: Cosmic microwave background polarimetry using a rotating half-wave plate", Astrophysical Journal, January 2007, 665:42-54, doi: 10.1086/518105

### G. Garavini, G. Folatelli, S. Nobili, G. Aldering, R., P. Antilogus, P. Astier, G. Blanc, T., M. S. Burns, A. Conley, S. E. Deustua, M., S. Fabbro, V. Fadeyev, R. Gibbons, G., A. Goobar, D. E. Groom, I. Hook, D. A., N. Kashikawa, A. G. Kim, M. Kowalski, N., B. C. Lee, C. Lidman, J. Mendez, T., K. Motohara, P. E. Nugent, R. Pain, S., R. Quimby, J. Raux, N. Regnault, P., G. Sainton, K. Schahmaneche, E., A. L. Spadafora, V. Stanishev, R. C. Thomas, N. A., L. Wang, W. M. Wood-Vasey, N. Yasuda, "Quantitative comparison between type Ia supernova spectra at low and high redshifts: a case study", Astronomy & Astrophysics, 2007, 470:411-424, doi: 10.1051/0004-6361:20065400

### M.A.J. Ashdown, C. Baccigalupi, A. Balbi, J.G. Bartlett, J. Borrill, C. Cantalupo, G. De Gasperis, K.M. Górski, V. Heikkilä, E. Hivon, E. Keihänen, H. Kurki-Suonio, C.R. Lawrence, P. Natoli, T. Poutanen, S. Prunet, M. Reinecke, R. Stompor, B. Wandelt, "Making maps from Planck LFI 30 GHz data", Astronomy and Astrophysics, January 2007, 471:361-380, doi: 10.1051/0004-6361:20077312

### D. Kasen, S. Woosley, P. Nugent, F. R\ opke, "The light curves and spectra of supernova explosions: multi-dimensional time-dependent Monte Carlo radiative transfer calculations", Journal of Physics Conference Series, 2007, 78:012037, doi: 10.1088/1742-6596/78/1/012037

### G. De Troia, P.A.R. Ade, J.J. Bock, J.R. Bond, J. Borrill, A. Boscaleri, P. Cabella, C.R. Contaldi, B.P. Crill, P. de Bernardis, G. de Gasperis, A. de Oliveira-Costa, G. Di Stefano, P.G. Ferreira, E. Hivon, A. Jaffe, T. Kisner, M. Kunz, W.C. Jones, A.E. Lange, S. Masi, P.D. Mauskopf, C. MacTavish, A. Melchiorri, T. Montroy, P. Natoli, C.B. Netterfield, E. Pascale, F. Piacentini, D. Pogosyan, G. Polenta, S. Prunet, S. Ricciardi, G. Romeo, J.E. Ruhl, P. Santini, M. Tegmark, M. Veneziani, N. Vittorio, "Searching for non-Gaussian signals in the BOOMERanG 2003 CMB map: Preliminary results", New Astronomy Reviews, January 2007, 51:250-255, doi: 10.1016/j.newar.2006.11.064

### R. C. Thomas, G. Aldering, P. Antilogus, C. Aragon, S., C. Baltay, E. Baron, A. Bauer, C., S. Bongard, Y. Copin, E. Gangler, S., R. Kessler, S. Loken, P. Nugent, R., J. Parrent, E. P\ econtal, R. Pereira, S., D. Rabinowitz, G. Rigaudier, K., R. Scalzo, G. Smadja, L. Wang, B. A. Weaver, Nearby Supernova Factory, "Nearby Supernova Factory Observations of SN 2006D: On Sporadic Carbon Signatures in Early Type Ia Supernova Spectra", Astrophysical Journal, 2007, 654:L53-L56, doi: 10.1086/510780

### John B. Bell, Alejandro L. Garcia and Sarah A. Williams, "Numerical Methods for the Stochastic Landau-Lifshitz Navier-Stokes Equations", Phys. Rev. E 76, 016708, 2007,

- Download File: FluctHydroPaper.pdf (pdf: 472 KB)

### M.A.J. Ashdown, C. Baccigalupi, A. Balbi, J.G. Bartlett, J. Borrill, C. Cantalupo, G. De Gasperis, K.M. Górski, E. Hivon, E. Keihänen, H. Kurki-Suonio, C.R. Lawrence, P. Natoli, T. Poutanen, S. Prunet, M. Reinecke, R. Stompor, B. Wandelt, "Making sky maps from Planck data", Astronomy and Astrophysics, January 2007, 467:761-775, doi: 10.1051/0004-6361:20065829

### David H. Bailey, David Borwein, Jonathan M. Borwein, Richard Crandall, "Hypergeometric forms for Ising-class integrals", Experimental Mathematics, 2007, 16:257-276,

### F. Piacentini, P.A.R. Ade, J.J. Bock, J.R. Bond, J. Borrill, A. Boscaleri, P. Cabella, C.R. Contaldi, B.P. Crill, P. de Bernardis, G. De Gasperis, A. de Oliveira-Costa, G. De Troia, G. Di Stefano, E. Hivon, A.H. Jaffe, T.S. Kisner, W.C. Jones, A.E. Lange, C. Marini-Bettolo, S. Masi, P.D. Mauskopf, C.J. MacTavish, A. Melchiorri, T.E. Montroy, F. Nati, L. Nati, P. Natoli, C.B. Netterfield, E. Pascale, D. Pogosyan, G. Polenta, S. Prunet, S. Ricciardi, G. Romeo, J.E. Ruhl, P. Santini, M. Tegmark, M. Veneziani, N. Vittorio, "CMB polarization with Boomerang 2003", New Astronomy Reviews, January 2007, 51:244-249, doi: 10.1016/j.newar.2006.11.058

### S. Masi, P.A.R. Ade, J.J. Bock, J.R. Bond, J. Borrill, A. Boscaleri, P. Cabella, C.R. Contaldi, B.P. Crill, P. de Bernardis, G. De Gasperis, A. De Oliveira-Costa, G. De Troia, G. Di Stefano, P. Ehlers, E. Hivon, V. Hristov, A. Iacoangeli, A.H. Jaffe, W.C. Jones, T.S. Kisner, A.E. Lange, C.J. MacTavish, C. Marini Bettolo, P. Mason, P.D. Mauskopf, T.E. Montroy, F. Nati, L. Nati, P. Natoli, C.B. Netterfield, E. Pascale, F. Piacentini, D. Pogosyan, G. Polenta, S. Prunet, S. Ricciardi, G. Romeo, J.E. Ruhl, P. Santini, M. Tegmark, E. Torbet, M. Veneziani, N. Vittorio, "The millimeter sky as seen with BOOMERanG", New Astronomy Reviews, January 2007, 51:236-243, doi: 10.1016/j.newar.2006.11.063

### David H. Bailey, Jonathan M. Borwein, Richard E. Crandall, "Box integrals", Journal of Computational and Applied Mathematics, 2007, 206:196-208,

### Khaled Z. Ibrahim, Smail Niar, "Power-aware Bus Coscheduling for Periodic Realtime Applications Running on Multiprocessor SoC", Transactions on High-Performance Embedded Architectures and Compilers, 2007, 4:170--192,

### D. A. Stone, M. R. Allen, F. Selten, M. Kliphuis, P. A. Stott, "The detection and attribution of climate change using an ensemble of opportunity", J. Climate, 2007, 20:504--516,

- Download File: StoneDAAllenMRetalii2007.pdf (pdf: 1.3 MB)

### John Shalf, "The New Landscape of Parallel Computer Architecture", Journal of Physics: Conference Series, Volume . IOP Electronics Journals, 2007,

- Download File: ShalfSciDAC2007JPCSfinal.pdf (pdf: 4.3 MB)

### D. A. Stone, M. R. Allen, P. A. Stott, "A multi-model update on the detection and attribution of global surface warming", J. Climate, 2007, 20:517--530,

- Download File: StoneDAAllenMRStottPA2007.pdf (pdf: 1.6 MB)

### Miniati, F. and Colella, P., "Block Structured Adaptive Mesh and Time Refinement for Hybrid, Hyperbolic + N-body Systems", Journal of Computational Physics Vol. 227 (2007), pp. 400-430., 2007,

- Download File: JCPMiniatiColellaNov2007.pdf (pdf: 1.1 MB)

### McCorquodale, P., Colella, P., Balls, G.T., and Baden, S.B., "A Local Corrections Algorithm for Solving Poisson's Equation in Three Dimensions", Communications in Applied Mathematics and Computational Science Vol. 2, No. 1 (2007), pp. 57-81., 2007,

### E. Y. Hsiao, A. Conley, D. A. Howell, M. Sullivan, C. J., R. G. Carlberg, P. E. Nugent, M. M. Phillips, "K-Corrections and Spectral Templates of Type Ia Supernovae", Astrophysical Journal, 2007, 663:1187-1200, doi: 10.1086/518232

### 2006

### K KOWALSKI, WA DE JONG, "Noniterative inclusion of the triply and quadruply excited clusters: The locally renormalized perspective", JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 2006, 768:45-52, doi: 10.1016/j.theochem.2006.04.049

### T. E. Montroy, P. A. R. Ade, J. J. Bock, J. R. Bond, J., A. Boscaleri, P. Cabella, C. R. Contaldi, B. P., P. de Bernardis, G. De Gasperis, A. Oliveira-Costa, G. De Troia, G. di Stefano, E., A. H. Jaffe, T. S. Kisner, W. C. Jones, A. E., S. Masi, P. D. Mauskopf, C. J. MacTavish, A., P. Natoli, C. B. Netterfield, E., F. Piacentini, D. Pogosyan, G. Polenta, S., S. Ricciardi, G. Romeo, J. E. Ruhl, P., M. Tegmark, M. Veneziani, N. Vittorio, "A Measurement of the CMB $<$EE$>$ Spectrum from the 2003 Flight of BOOMERANG", Astrophysical Journal, August 2006, 647:813-822,

### T. E. Montroy, P. A. R. Ade, J. J. Bock, J. R. Bond, J., A. Boscaleri, P. Cabella, C. R. Contaldi, B. P., P. de Bernardis, G. De Gasperis, A. Oliveira-Costa, G. De Troia, G. di Stefano, E., A. H. Jaffe, T. S. Kisner, W. C. Jones, A. E., S. Masi, P. D. Mauskopf, C. J. MacTavish, A., P. Natoli, C. B. Netterfield, E., F. Piacentini, D. Pogosyan, G. Polenta, S., S. Ricciardi, G. Romeo, J. E. Ruhl, P., M. Tegmark, M. Veneziani, N. Vittorio, "A Measurement of the CMB \ltEE\gt Spectrum from the 2003 Flight of BOOMERANG", Astrophysical Journal, August 2006, 647:813-822, doi: 10.1086/505560

### Katherine Yelick, Paul Hilfinger, Susan Graham, Dan Bonachea, Jimmy Su, Amir Kamil, Kaushik Datta, Phillip Colella, and Tong Wen, "Parallel Languages and Compilers: Perspective from the Titanium Experience", The International Journal Of High Performance Computing Applications, June 16, 2006, 21,

We describe the rationale behind the design of key features of Titanium—an explicitly parallel dialect of JavaTM for high-performance scientific programming—and our experiences in building applications with the language. Specifically, we address Titanium’s Partitioned Global Address Space model, SPMD parallelism support, multi-dimensional arrays and array-index calculus, memory management, immutable classes (class-like types that are value types rather than reference types), operator overloading, and generic programming. We provide an overview of the Titanium compiler implementation, covering various parallel analyses and optimizations, Titanium runtime technology and the GASNet network communication layer. We summarize results and lessons learned from implementing the NAS parallel benchmarks, elliptic and hyperbolic solvers using Adaptive Mesh Refinement, and several applications of the Immersed Boundary method.

### Katrin Heitmann, Zarija Lukić, Salman Habib, and Paul M. Ricker, "Capturing Halos at High Redshifts", The Astrophysical Journal, 2006, 642:85,

### Gatti-Bono, C., Colella, P., "An Anelastic Allspeed Projection Method for Gravitationally Stratified Flows", J. Comput. Phys. Vol. 216 (2006), pp. 589-615, 2006, LBNL 57158,

- Download File: B114.pdf (pdf: 632 KB)

### Colella, P., Graves, D.T., Keen, B.J., Modiano, D., "A Cartesian Grid Embedded Boundary Method for Hyperbolic Conservation Laws", Journal of Computational Physics. Vol. 211 (2006), pp. 347-366., 2006, LBNL 56420,

- Download File: A162.pdf (pdf: 354 KB)

### Schwartz, P., Barad, M., Colella, P., Ligocki, T.J., "A Cartesian Grid Embedded Boundary Method for the Heat Equation and Poisson's Equation in Three Dimensions", Journal of Computational Physics. Vol. 211 (2006), pp. 531-550., 2006, LBNL 56607,

- Download File: A161.pdf (pdf: 364 KB)

### Kesheng Wu, Ekow Otoo, Arie Shoshani, "Optimizing bitmap indices with efficient compression", ACM Transactions on Database Systems, 2006, 31:1--38, doi: 10.1145/1132863.1132864

### J. Bell, M. Day, A. Almgren, M. Lijewski, C. Rendleman, R. Cheng, I. Shepherd, "Simulation of Lean Premixed Turbulent Combustion", SciDAC 2006, J. of Physics: Conference Series, (William Tang, Ed.), 46, 1-15, 2006, 2006, LBNL 63091,

- Download File: bellscidac2006.pdf (pdf: 943 KB)

### O. Marques, C. Voemel, J. Riedy, "Benefits of IEEE-754 Features in Modern Symmetric Tridiagonal Eigensolvers", SIAM J. Sci. Comput., 2006, 28:1613-1633,

### M. Day and J. Bell, "Simulation of Premixed Turbulent Flames", SciDAC 2006, J. of Physics: Conference Series, (William Tang, Ed.), 46, 43-47, 2006, LBNL 63090,

- Download File: scidac2006-comb.pdf (pdf: 1.9 MB)

### O. Marques, B. Parlett, C. Voemel, "Computations of Eigenpair Subsets with the MRRR Algorithm", Numer. Linear Algebra Appl., 2006, 13:643–653,

### M. Zingale, A.S. Almgren, J.B. Bell, M.S. Day, C.A. Rendleman, and S.E. Woosley, "New Approaches for Modeling Type Ia Supernovae", SciDAC 2006, J. of Physics: Conference Series, (William Tang, Ed.), 46, 385-392, 2006, LBNL 63087,

### A. S. Almgren, J. B. Bell, C. A. Rendleman, and M. Zingale, "Low Mach Number Modeling of Type Ia Supernovae. II. Energy Evolution", Astrophysical Journal, 649, 927-938, 2006, LBNL 58673,

- Download File: LowMachSNIapaperII.pdf (pdf: 1.3 MB)

### Kurt Stockinger, Kesheng Wu, Rene Brun, Canal, "Bitmap indices for fast end-user physics analysis in", Nuclear Instruments and Methods in Physics Research A: Accelerators, Spectrometers, Detectors and Equipment, 2006, 559:99--102,

### A. S. Almgren, J. B. Bell, C. A. Rendleman, and M. Zingale, "Low Mach Number Modeling of Type Ia Supernovae. I. Hydrodynamics", Astrophysical Journal, 637, 922-936.(revised), 2006, LBNL 58673,

- Download File: LowMachSNIa.pdf (pdf: 849 KB)

### David H. Bailey, "Review of Accuracy and Reliability in Scientific Computing", Scientific Programming, January 1, 2006, 14:41-42,

### Jiri Brabec, Jiri Pittner, "The singlet-triplet gap in trimethylenmethane and the ring-opening of methylenecyclopropane: A multireference Brillouin-Wigner coupled cluster study", Journal of Physical Chemistry a, 2006, 110:11765-1176, doi: 10.1021/jp057546y

### D. Kasen, R. C. Thomas, P. Nugent, "Time-dependent Monte Carlo Radiative Transfer Calculations for Three-dimensional Supernova Spectra, Light Curves, and Polarization", Astrophysical Journal, 2006, 651:366-380, doi: 10.1086/506190

### D. J. Frame, D. A. Stone, P. A. Stott, M. R. Allen, "Alternatives to stabilization scenarios", Geophys. Res. Lett., 2006, 33, doi: 10.1029/2006GL025801

### J.B. Bell, J. Foo, and A.L. Garcia, "Algorithm Refinement for the Stochastic Burgers' Equation", J. Comp. Phys., 223, pp. 603-708, 2006,

- Download File: HybridBurg.pdf (pdf: 472 KB)

### G. Aldering, P. Antilogus, S. Bailey, C. Baltay, A., N. Blanc, S. Bongard, Y. Copin, E., S. Gilles, R. Kessler, D. Kocevski, B. C., S. Loken, P. Nugent, R. Pain, E., R. Pereira, S. Perlmutter, D., G. Rigaudier, R. Scalzo, G. Smadja, R. C., L. Wang, B. A. Weaver, Nearby Supernova Factory, "Nearby Supernova Factory Observations of SN 2005gj: Another Type Ia Supernova in a Massive Circumstellar Envelope", Astrophysical Journal, 2006, 650:510-527, doi: 10.1086/507020

### L. Oliker, J. Carter, M. Wehner, A. Canning, S. Ethier, A. Mirin, G. Bala, D. Parks, P. Worley, S. Kitawaki, Y. Tsuda, "Scientific Application Performance on Leading Scalar and Vector Supercomputing Platforms", International Journal of High Performance Computing Applications (IJHPCA), 2006,

- Download File: IJHPCA06-eval.pdf (pdf: 7.2 MB)

### S. Masi, P.A.R. Ade, J.J. Bock, J.R. Bond, J. Borrill, A. Boscaleri, P. Cabella, C.R. Contaldi, B.P. Crill, P. De Bernardis, G. De Gasperis, A. De Oliveira-Costa, G. De Troia, G. Di Stefano, P. Ehlers, E. Hivon, V. Hristov, A. Iacoangeli, A.H. Jaffe, W.C. Jones, T.S. Kisner, A.E. Lange, C.J. MacTavish, C.M. Bettolo, P. Mason, P.D. Mauskopf, T.E. Montroy, F. Nati, L. Nati, P. Natoli, C.B. Netterfield, E. Pascale, F. Piacentini, D. Pogosyan, G. Polenta, S. Prunet, S. Ricciardi, G. Romeo, J.E. Ruhl, P. Santini, M. Tegmark, E. Torbet, M. Veneziani, N. Vittorio, "Instrument, method, brightness, and polarization maps from the 2003 flight of BOOMERanG", Astronomy and Astrophysics, January 2006, 458:687-716, doi: 10.1051/0004-6361:20053891

### David H. Bailey, Jonathan M. Borwein, Richard E. Crandall, "Integrals of the Ising class", Journal of Physics A: Mathematical and General, 2006, 39:12271-1230,

### D. A. Howell, M. Sullivan, P. E. Nugent, R. S. Ellis, A. J., D. Le Borgne, R. G. Carlberg, J., D. Balam, S. Basa, D. Fouchez, I. M., E. Y. Hsiao, J. D. Neill, R. Pain, K. M. Perrett, C. J. Pritchet, "The type Ia supernova SNLS-03D3bb from a super-Chandrasekhar-mass white dwarf star", Nature, 2006, 443:308-311, doi: 10.1038/nature05103

### Tom Goodale, Shantenu Jha, Hartmut Kaiser, Thilo Kielmann, Pascal Kleijer, Gregor von Laszewski, Craig Lee, Andre Merzky, Hrabri Rajic, Hrabri, John Shalf, "SAGA: A Simple API for Grid Applications -- High-Level Application Programming on the Grid", Computational Methods in Science and Technology, Volume 12(1). Poznan, 2006, LBNL 59066,

- Download File: SAGAJournal.pdf (pdf: 1 MB)

### F. Piacentini, P.A.R. Ade, J.J. Bock, J.R. Bond, J. Borrill, A. Boscaleri, P. Cabella, C.R. Contaldi, B.P. Grill, P. De Bernardis, G. De Gasperis, A. De Oliveira-Costa, G. De Troia, G. Di Stefano, E. Hivon, A.H. Jaffe, T.S. Kisner, W.C. Jones, A.E. Lange, S. Masi, P.D. Mauskopf, C.J. MacTavish, A. Melchiorri, T.E. Montroy, P. Natoli, C.B. Netterfield, E. Pascale, D. Pogosyan, G. Polenta, S. Prunet, S. Ricciardi, G. Romeo, J.E. Ruhl, P. Santini, M. Tegmark, M. Veneziani, N. Vittorio, "A measurement of the polarization-temperature angular cross-power spectrum of the cosmic microwave background from the 2003 flight of Boomerang", Astrophysical Journal, January 2006, 647:833-839, doi: 10.1086/505557

### W.C. Jones, P.A.R. Ade, J.J. Bock, J.R. Bond, J. Borrill, A. Boscaleri, P. Cabella, C.R. Contaldi, B.P. Crill, P. de Bernardis, G. De Gasperis, A. de Oliveira-Costa, G. De Troia, G. Di Stefano, E. Hivon, A.H. Jaffe, T.S. Kisner, A.E. Lange, C.J. MacTavish, S. Masi, P.D. Mauskopf, A. Melchiorri, T.E. Montroy, P. Natoli, C.B. Netterfield, E. Pascale, F. Piacentini, D. Pogosyan, G. Polenta, S. Prunet, S. Ricciardi, G. Romeo, J.E. Ruhl, P. Santini, M. Tegmark, M. Veneziani, N. Vittorio, "Observations of the temperature and polarization anisotropies with Boomerang 2003", New Astronomy Reviews, January 2006, 50:945-950, doi: 10.1016/j.newar.2006.09.014

### A. S. Fruchter, A. J. Levan, L. Strolger, P. M., S. E. Thorsett, D. Bersier, I., J. M. Castro Cer\ on, A. J. Castro-Tirado, C., T. Dahlen, H. C. Ferguson, J. P. U. Fynbo, P. M., R. A. Gibbons, J. Gorosabel, T. R., J. Hjorth, S. T. Holland, C. Kouveliotou, Z., M. Livio, M. R. Metzger, P. E. Nugent, L., E. Pian, J. E. Rhoads, A. G. Riess, K. C., A. Smette, N. R. Tanvir, R. A. M. J. Wijers, S. E. Woosley, "Long $\gamma$-ray bursts and core-collapse supernovae have different environments", Nature, 2006, 441:463-468, doi: 10.1038/nature04787

### P. Nugent, M. Sullivan, R. Ellis, A. Gal-Yam, D. C., D. A. Howell, P. Astier, R. G. Carlberg, A., S. Fabbro, D. Fouchez, J. D. Neill, R., K. Perrett, C. J. Pritchet, N. Regnault, "Toward a Cosmological Hubble Diagram for Type II-P Supernovae", Astrophysical Journal, 2006, 645:841-850, doi: 10.1086/504413

### C.J. Mactavish, P.A.R. Ade, J.J. Bock, J.R. Bond, J. Borrill, A. Boscaleri, P. Cabella, C.R. Contaldi, B.P. Crill, P. De Bernardis, G. De Gasperis, A. De Oliveira-Costa, G. De Troia, G. Di Stefano, E. Hivon, A.H. Jaffe, W.C. Jones, T.S. Kisner, A.E. Lange, A.M. Lewis, S. Masi, P.D. Mauskopf, A. Melchiorri, T.E. Montroy, P. Natoli, C.B. Netterfield, E. Pascale, F. Piacentini, D. Pogosyan, G. Polenta, S. Prunet, S. Ricciardi, G. Romeo, J.E. Ruhl, P. Santini, M. Tegmark, M. Veneziani, N. Vittorio, "Cosmological parameters from the 2003 flight of Boomerang", Astrophysical Journal, January 2006, 647:799-812, doi: 10.1086/505558

### M. Sullivan, D. A. Howell, K. Perrett, P. E. Nugent, P., E. Aubourg, D. Balam, S. Basa, R. G., A. Conley, S. Fabbro, D. Fouchez, J., I. Hook, H. Lafoux, J. D. Neill, R., N. Palanque-Delabrouille, C. J. Pritchet, N., J. Rich, R. Taillet, G. Aldering, S., J. Bronder, M. Filiol, R. A. Knop, S. Perlmutter, C. Tao, "Photometric Selection of High-Redshift Type Ia Supernova Candidates", Astronomical Journal, 2006, 131:960-972, doi: 10.1086/499302

### W.C. Jones, P.A.R. Ade, J.J. Bock, J.R. Bond, J. Borrill, A. Boscaleri, P. Cabella, C.R. Contaldi, B.P. Crill, P. De Bernardis, G. De Gasperis, A. De Oliveira-Costa, G. De Troia, G. Di Stefano, E. Hivon, A.H. Jaffe, T.S. Kisner, A.E. Lange, C.J. MacTavish, S. Masi, P.D. Mauskopf, A. Melchiorri, T.E. Montroy, P. Natoli, C.B. Netterfield, E. Pascale, F. Piacentini, D. Pogosyan, G. Polenta, S. Prunet, S. Ricciardi, G. Romeo, J.E. Ruhl, P. Santini, M. Tegmark, M. Veneziani, N. Vittorio, "A measurement of the angular power spectrum of the CMB temperature anisotropy from the 2003 flight of Boomerang", Astrophysical Journal, January 2006, 647:823-832, doi: 10.1086/505559

### B. Rabii, C.D. Winant, J.S. Collins, A.T. Lee, P.L. Richards, M.E. Abroe, S. Hanany, B.R. Johnson, P. Ade, A. Balbi, J.J. Bock, J. Borrill, R. Stompor, A. Boscaleri, E. Pascale, P. De Bernardis, P.G. Ferreira, V.V. Hristov, A.E. Lange, A.H. Jaffe, C.B. Netterfield, G.F. Smoot, J.H.P. Wu, "MAXIMA: A balloon-borne cosmic microwave background anisotropy experiment", Review of Scientific Instruments, January 2006, 77:071101, doi: 10.1063/1.2219723

### D. Trebotich, "Modeling Complex Biological Flows in Multi-Scale Systems Using the APDEC Framework", Journal of Physics: Conference Series 46 (2006) 316-321., 2006,

- Download File: SciDAC2006.pdf (pdf: 786 KB)

### T. Poutanen, G. De Gasperis, E. Hivon, H. Kurki-Suonio, A. Balbi, J. Borrill, C. Cantalupo, O. Doré, E. Keihänen, C.R. Lawrence, D. Maino, P. Natoli, S. Prunet, R. Stompor, R. Teyssier, "Comparison of map-making algorithms for CMB experiments", Astronomy and Astrophysics, 2006, 449:1311-1322, doi: 10.1051/0004-6361:20052845

### 2005

### WA DE JONG, E APRA, TL WINDUS, et al., "Complexation of the carbonate, nitrate, and acetate anions with the uranyl dication: Density functional studies with relativistic effective core potentials", JOURNAL OF PHYSICAL CHEMISTRY A, 2005, 109:11568-1157, doi: 10.1021/jp0541462

### S. Hofmeyr, "The information security technology arms race", Crosstalk: The Journal of Defense Software Engineering, October 1, 2005,

### L POLLACK, TL WINDUS, WA DE JONG, et al., "Thermodynamic properties of the C-5, C-6, and C-8 n-alkanes from ab initio electronic structure theory", JOURNAL OF PHYSICAL CHEMISTRY A, 2005, 109:6934-6938, doi: 10.1021/jp044564r

### Sean Peisert, "Forensics for System Administrators", ;login:, August 2005, 30(4):34-42,

### DA DIXON, WA DE JONG, KA PETERSON, et al., "Heats of formation of xenon fluorides and the fluxionality of XeF6 from high level electronic structure calculations", JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2005, 127:8627-8634, doi: 10.1021/ja0423116

### LS CHEN, WA DE JONG, J YE, "Characterization of the molecular iodine electronic wave functions and potential energy curves through hyperfine interactions in the B0(u)(+)((IIu)-I-3) state", JOURNAL OF THE OPTICAL SOCIETY OF AMERICA B-OPTICAL PHYSICS, 2005, 22:951-961, doi: 10.1364/JOSAB.22.000951

### D. Bernholdt, S. Bharathi, D. Brown, K. Chanchio, M. Chen, A. Chervenak, L. Cinquini, B. Zrach, I. Foster, P. Fox, J. Garcia, C. Kesselman, R. Markel, D. Middleton, V. Nefedova, L. Pouchard, A. Shoshani, A. Sim, G. Strand, D. Williams, "The Earth System Grid: Supporting the Next Generation of Climate Modeling Research", IEEE, 2005, 93(3):485-495,

### DA DIXON, WA DE JONG, KA PETERSON, et al., "Methyl cation affinities of rare gases and nitrogen and the heat of formation of diazomethane", JOURNAL OF PHYSICAL CHEMISTRY A, 2005, 109:4073-4080, doi: 10.1021/jp044561e

### GS FANOURGAKIS, E APRA, WA DE JONG, SS Xantheas, "High-level ab initio calculations for the four low-lying families of minima of(H2O)(20). II. Spectroscopic signatures of the dodecahedron, fused cubes, face-sharing pentagonal prisms, and edge-sharing pentagonal prisms hydrogen bonding networks", JOURNAL OF CHEMICAL PHYSICS, 2005, 122:-, doi: 10.1063/1.1864892

### S. Hofmeyr, "Host intrusion detection: part of the operating system or on top of the operating system", Computers & Security, February 1, 2005,

### H. Simon, W. Kramer, W. Saphir, J. Shalf, D. Bailey, L. Oliker, et al, "Science Driven System Architecture: A New Process for Leadsership Class Computing", Journal of the Earth Simulator, 2005,

- Download File: JES2-Simon.pdf (pdf: 110 KB)

### G. Polenta, P.A.R. Ade, A. Balbi, J.J. Bock, J.R. Bond, J. Borrill, A. Boscaleri, P. Cabella, C.R. Contaldi, B.P. Crill, P. De Bernardis, G. De Gasperis, A. De Oliveira-Costa, G. De Troia, G. Di Stefano, K. Ganga, E. Hivon, V.V. Hristov, A. Iacoangeli, A.H. Jaffe, T.S. Kisner, W.C. Jones, A.E. Lange, C. MacTavish, C.M. Bettolo, S. Masi, P.D. Mauskopf, A. Melchiorri, T. Montroy, F. Nati, P. Natoli, C.B. Netterfield, E. Pascale, F. Piacentini, D. Pogosyan, S. Prunet, S. Ricciardi, G. Romeo, J.E. Ruhl, E. Torbet, M. Tegmark, N. Vittorio, "BOOMERanG results", Advances in Space Research, 2005, 36:1064-1069, doi: 10.1016/j.asr.2005.06.080

### R. J. Foley, A. V. Filippenko, D. C. Leonard, A. G. Riess, P. Nugent, S. Perlmutter, "A Definitive Measurement of Time Dilation in the Spectral Evolution of the Moderate-Redshift Type Ia Supernova 1997ex", Astrophysical Journal, 2005, 626:L11-L14, doi: 10.1086/431241

### L. Oliker, A. Canning, J. Carter, J. Shalf, H. Simon, S. Ethier, D. Parks, S. Kitawaki, Y. Tsuda, T. Sato, "Performance of Ultra-Scale Applications on Leading Vector and Scalar HPC Platforms", Journal of the Earth Simulator, January 2005, 3,

- Download File: JES3-Oliker.pdf (pdf: 101 KB)

### John Shalf, John Bell, Andrew Canning, Lin-Wang Wang, Juan Meza, Rob Ryne, Ji Qiang, Kathy Yelick, "Berkeley Petascale Applications", 2005,

- Download File: BerkeleyPetascaleApps.doc (doc: 45 KB)

### Schwartz, P., Adalsteinsson, D., Colella, P., Arkin, A.P., Onsum, M., "A Tightly Coupled Particle-Fluid Model for DNA-laden Flows in Complex Microscale Geometries", Proc. Nat. Acad. Sci. Vol. 102 (2005), pp. 11151-11156, 2005,

- Download File: SchwartzETALPNAS.pdf (pdf: 357 KB)

### Leonid Oliker, Canning, Carter, Shalf, Skinner, Ethier, Biswas, Jahed Djomehri, Rob F. Van der Wijngaart, "Performance evaluation of the SX-6 vector architecture for scientific computations", Concurrency - Practice and Experience, January 2005, 17:69-93, doi: 10.1002/cpe.884

- Download File: CCPE05-sx6.pdf (pdf: 1 MB)

### Martin, D.F., Colella, P., Anghel, M., Alexander, F., "Adaptive Mesh Refinement for Multiscale Nonequilibrium Physics", Computing in Science and Engineering Vol.7 N.3 (2005), pp. 24-31, 2005,

- Download File: A159.pdf (pdf: 324 KB)

### Barad, M., Colella, P., "A Fourth-Order Accurate Local Refinement Method for Poisson's Equation", J. Comput. Phys. Vol.209 (2005), pp. 1-18, 2005,

- Download File: A158.pdf (pdf: 533 KB)

### Kelvin K. Droegemeier, Dennis Gannon, Daniel Reed, Beth Plale, Jay Alameda, Tom Baltzer, Keith Brewster, Richard Clark, Ben Domenico, Sara Graves, Everette Joseph, Donald Murray, Rahul Ramachandran, Mohan Ramamurthy, Lavanya Ramakrishnan, John A. Rushing, Daniel Weber, Robert Wilhelmson, Anne Wilson, Ming Xue, Sepideh Yalda, "Service-Oriented Environments for Dynamically Interacting with Mesoscale Weather", Computing in Science and Engg., 2005, 7:12--29, doi: http://dx.doi.org/10.1109/MCSE.2005.124

### Trebotich, D., Colella, P., Miller, G.H., "A Stable and Convergent Scheme for Viscoelastic Flow in Contraction Channels", J. Comput. Phys. Vol.205 (2005), pp. 315-342, 2005,

- Download File: A157.pdf (pdf: 827 KB)

### Crockett, R.K., Colella, P., Fisher, R., Klein, R.I., McKee, C.F., "An Unsplit, Cell-Centered Godunov Method for Ideal MHD", J. Comput. Phys. Vol.203 (2005), pp. 422-448, 2005,

- Download File: A156.pdf (pdf: 558 KB)

### Trebotich, D., Miller, G.H., Colella, P., Graves, D.T., Martin, D.F., Schwartz, P.O., "A Tightly Coupled Particle-Fluid Model for DNA-Laden Flows in Complex Microscale Geometries", Computational Fluid and Solid Mechanics 2005, pp. 1018-1022, Elsevier (K. J. Bathe editor), 2005,

- Download File: MIT3.pdf (pdf: 431 KB)

### D. A. Stone, J. C. Fyfe, "The effect of ocean mixing parametrisation on the enhanced CO2 response of the Southern Hemisphere mid latitude jet", Geophys. Res. Lett, 2005, 32, doi: 10.1029/2004GL022007

- Download File: StoneDAFyfeJC2005.pdf (pdf: 140 KB)

### J.B. Bell, M.S. Day, I.G. Shepherd, M. Johnson, R.K. Cheng, J.F. Grcar, V.E. Beckner, M.J. Lijewski, "Numerical Simulation of a Labratory-Scale Turbulent V-flame", Journal, Proc. Natl. Acad. Sci. USA, 102(29), 10006-10011, 2005, LBNL 54198,

- Download File: LBNL-54198-Journal.pdf (pdf: 2.8 MB)

### D. A. Stone, M. R. Allen, "The end-to-end attribution problem: From emissions to impacts", Clim. Change, 2005, 71:303--318,

- Download File: StoneDAAllenMR2005a.pdf (pdf: 1 MB)

### M. Zingale, S.e. Woosley, C.A. Rendleman, M.S. Day, and J.B. Bell, "Three-Dimensional Numerical Simulations of Rayleigh-Taylor Unstable Flames in Type Ia Supernovae", Astrophysical Journal, 632, 1021-1034, 2005, LBNL 56966,

- Download File: SNRayleighTaylor3D.pdf (pdf: 978 KB)

### D. A. Stone, M. R. Allen, "Attribution of global surface warming without dynamical models", Geophys. Res. Lett., 2005, 32:L18711, 10, doi: 10.1029/2005GL023682

- Download File: StoneDAAllenMR2005.pdf (pdf: 123 KB)

### I. M. Hook, D. A. Howell, G. Aldering, R. Amanullah, M. S., A. Conley, S. E. Deustua, R. Ellis, S., V. Fadeyev, G. Folatelli, G. Garavini, R., G. Goldhaber, A. Goobar, D. E. Groom, A. G., R. A. Knop, M. Kowalski, C. Lidman, S., P. E. Nugent, R. Pain, C. R. Pennypacker, S., P. Ruiz-Lapuente, G. Sainton, B. E., E. Smith, A. L. Spadafora, V., R. C. Thomas, N. A. Walton, L., W. M. Wood-Vasey, Supernova Cosmology Project, "Spectra of High-Redshift Type Ia Supernovae and a Comparison with Their Low-Redshift Counterparts", Astronomical Journal, 2005, 130:2788-2803, doi: 10.1086/497635

### F. H. Lambert, N. P. Gillett, D. A. Stone, C. Huntingford, "Attribution of changes in observed land precipitation with nine coupled models", Geophys. Res. Lett., 2005, 32:L18704, 10, doi: 10.1029/2005GL023654

### A. Aspuru-Guzik, R. Salomon-Ferrer, B. Austin, R. Perusquia-Flores, M.A. Griffin, R. A. Oliva, D. Skinner, D. Domin, and W. A. Lester, Jr., "Zori 1.0: A Parallel Quantum Monte Carlo Electronic Structure Package", Software News and Updates, 2005, 26:856,

### A. Levan, P. Nugent, A. Fruchter, I. Burud, D., J. Rhoads, A. Castro-Tirado, J. Gorosabel, J. M. Cer\ on, S. E. Thorsett, C. Kouveliotou, S., J. Fynbo, P. Garnavich, S. Holland, J., P. M\oller, E. Pian, N. Tanvir, M. Ulanov, R. Wijers, S. Woosley, "GRB 020410: A Gamma-Ray Burst Afterglow Discovered by Its Supernova Light", Astrophysical Journal, 2005, 624:880-888, doi: 10.1086/428657

### L.A. Drummond and O. A. Marques, "An Overview of the Advanced CompuTational Software (ACTS) Collection", ACM TOMS, 2005, 31:282-301,

### S. Nobili, R. Amanullah, G. Garavini, A. Goobar, C., V. Stanishev, G. Aldering, P. Antilogus, P., M. S. Burns, A. Conley, S. E. Deustua, R., S. Fabbro, V. Fadeyev, G. Folatelli, R., G. Goldhaber, D. E. Groom, I. Hook, D. A., A. G. Kim, R. A. Knop, P. E. Nugent, R., S. Perlmutter, R. Quimby, J. Raux, N., P. Ruiz-Lapuente, G. Sainton, K., E. Smith, A. L. Spadafora, R. C., L. Wang, Supernova Cosmology Project, "Restframe I-band Hubble diagram for type Ia supernovae up to redshift z \tilde 0.5", Astronomy and Astrophysics, 2005, 437:789-804, doi: 10.1051/0004-6361:20042463

### C. Lidman, D. A. Howell, G. Folatelli, G. Garavini, S., G. Aldering, R. Amanullah, P. Antilogus, P., G. Blanc, M. S. Burns, A. Conley, S. E., M. Doi, R. Ellis, S. Fabbro, V., R. Gibbons, G. Goldhaber, A. Goobar, D. E., I. Hook, N. Kashikawa, A. G. Kim, R. A., B. C. Lee, J. Mendez, T. Morokuma, K., P. E. Nugent, R. Pain, S. Perlmutter, V., R. Quimby, J. Raux, N. Regnault, P., G. Sainton, B. E. Schaefer, K., E. Smith, A. L. Spadafora, V., N. A. Walton, L. Wang, W. M. Wood-Vasey, N. Yasuda, Supernova Cosmology Project, "Spectroscopic confirmation of high-redshift supernovae with the ESO VLT.", Astronomy & Astrophysics, 2005, 430:843-851, doi: 10.1051/0004-6361:20041504

### B Bode, R Bradshaw, E DeBenedictus, N Desai, J Duell, G A Geist, P Hargrove, D Jackson, S Jackson, J Laros, C Lowe, E Lusk, W McLendon, J Mugler, T Naughton, J P Navarro, R Oldfield, N Pundit, S L Scott, M Showerman, C Steffen, K Walker, "Scalable system software: a component-based approach", Journal of Physics: Conference Series, January 2005, 16:546-550, doi: 10.1088/1742-6596/16/1/075

### J. Gorosabel, J. P. U. Fynbo, A. Fruchter, A., J. Hjorth, P. Nugent, A. J. Castro-Tirado, J. M. Cer\ on, J. Rhoads, D. Bersier, I. Burud, "A possible bright blue supernova in the afterglow of GRB 020305", Astronomy & Astrophysics, 2005, 437:411-418, doi: 10.1051/0004-6361:20052783

## Conference Paper

### 2017

### Yang You, Aydin Buluc, James Demmel, "Scaling deep learning on GPU and Knights Landing clusters", Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC'17), 2017,

### Sean Peisert, Matt Bishop, Ed Talbot,, "A Model of Owner Controlled, Full-Provenance, Non-Persistent, High-Availability Information Sharing", Proceedings of the 2017 New Security Paradigms Workshop (NSPW), Islamorada, FL, October 2017,

### Jonathan Ganz, Sean Peisert, "ASLR: How Robust is the Randomness", Proceedings of the IEEE Secure Development Conference (SecDev), Cambridge, MA, IEEE Computer Society, September 24, 2017,

### Marquita Ellis, Evangelos Georganas, Rob Egan, Steven Hofmeyr, Aydin Buluc, Brandon Cook, Leonid Oliker, Katherine Yelick, "Performance characterization of de novo genome assembly on leading parallel systems", Europar - International European Conference on Parallel and Distributed Computing, 2017,

### Muhammad Nufail Farooqi, Didem Unat, Tan Nguyen, Weiqun Zhang, Ann Almgren and John Shalf, "Nonintrusive AMR Asynchrony for Communication Optimization", EURO-PAR 2017, August 30, 2017,

### Jinoh Kim, Alex Sim, "A New Approach to Online, Multivariate Network Traffic Analysis", 2nd Workshop on Network Security Analytics and Automation (NSAA), in conjunction with the 26th International Conference on Computer Communications and Networks (ICCCN 2017), 2017,

### Mahdi Jamei, Anna Scaglione, Ciaran Roberts, Alex McEachern, Emma Stewart, Sean Peisert, Chuck McParland, "Online Thevenin Parameter Tracking Using Synchrophasor Data", Proceedings of the 2017 IEEE Power Engineering Society (PES) General Meeting (GM), Chicago, IL, IEEE, July 2017,

### Dongeun Lee, Alex Sim, Jaesik Choi, Kesheng Wu, "Improving Statistical Similarity Based Data Reduction for Non-Stationary Data", 29th International Conference on Scientific and Statistical Database Management (SSDBM2017), 2017, doi: 10.1145/3085504.3085583

### Bin Dong, Kesheng Wu, Surendra Byna, Jialin Liu, Weijie Zhao, Florin Rusu, "ArrayUDF: User-Defined Scientific Data Analysis on Arrays", The ACM International Symposium on High-Performance Parallel and Distributed Computing (HPDC) 2017 (Acceptance rate:19%), June 26, 2017,

- Download File: hpdc02.pdf (pdf: 921 KB)

### Alberto Gonzalez, Jason Leigh, Sean Peisert, Brian Tierney, Andrew Lee, Jennifer M. Schopf, "Monitoring Big Data Transfers Over International Research Network Connections", Proceedings of IEEE BigData Congress 2017, Honolulu, Hawaii, June 2017,

### Hongzhang Shan, Samuel Williams, Calvin Johnson, Kenneth McElvain, "A Locality-based Threading Algorithm for the Configuration-Interaction Method", Parallel and Distributed Scientific and Engineering Computing (PDSEC), June 2017,

- Download File: pdsec17-bigstick.pdf (pdf: 715 KB)

### Bryce Adelstein Lelbach, Hans Johansen, Samuel Williams, "Solving Large Quantities of Small Matrix Problems on Cache-Coherent Many-Core SIMD Architectures", Parallel and Distributed Scientific and Engineering Computing (PDSEC), June 2017,

### Brandon Cook, Thorsten Kurth, Brian Austin, Samuel Williams, Jack Deslippe, "Performance Variability on Xeon Phi", Intel Xeon Phi Users Group (IXPUG), June 2017,

### Thorsten Kurth, William Arndt, Taylor Barnes, Brandon Cook, Jack Deslippe, Doug Doerfler, Brian Friesen, Yun (Helen) He, Tuomas Koskela, Mathieu Lobet, Tareq Malas, Leonid Oliker, Andrey Ovsyannikov, Samuel Williams, Woo-Sun Yang, and Zhengji Zhao, "Analyzing Performance on Selected NESAP Applications on the Cori HPC System", Intel Xeon Phi Users Group (IXPUG), June 2017,

### Ariful Azad, Aydin Buluc, "Towards a GraphBLAS Library in Chapel", IPDPS Workshops, Orlando, FL, May 2017,

- Download File: GraphBLAS-Chapel.pdf (pdf: 368 KB)

### Aydin Buluc, Tim Mattson, Scott McMillan, Jose Moreira, Carl Yang, "Design of the GraphBLAS API for C", IEEE Workshop on Graph Algorithm Building Blocks, IPDPSW, 2017,

- Download File: GABB17.pdf (pdf: 359 KB)