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Chao Yang

Chao Yang
Staff Scientist
Scientific Computing
Phone: +1 510 486 6424
Fax: +1 510 486 5812
Computationa Research Division
1 Cyclotron Rd, MS-50F
Berkeley, CA 94720 US

Short Bio

Chao Yang got his Ph.D in computational mathematics from Rice Universisty in 1998. He worked at NEC Systems Lab, Inc, a subsidiary of NEC from 1998 to 1999. He was awarded the 1999 Householder fellow in scientific computing by Oak Ridge National Laboratory. He joined Lawrence Berkeley National Laboratory in 2000, and is currently a staff scientist. His research interests include:

  • developing numerical algorithms and fast implementation to accelerate scientific simulations
  • developing efficient and robust algorithms and implementations for solving inverse problems

His core expertise is in numerical linear algebra, optimization, and high performance computing. Over the last several years, he has successfully applied the latest development in these areas to solve problems in electronic structure calcuations, nuclear structure calculations, cavity design for accelerator models, single-particle analysis for cryo-electron microscopy, single molecular diffractive imaging, phase retrieval, ptychography etc.

Journal Articles

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,

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

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,

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

L. Lin, C. Yang, "Elliptic preconditioner for accelerating the self-consistent field iteration in Kohn-Sham Density Functional Theory", submitted to SIAM J. Sci. Comp., 2012,

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

L. Lin, M. Chen, C. Yang, L. He, "Accelerating Atomic Orbital-based Electronic Structure Calculation via Pole Expansion and Selected Inversion", submitted to J. Comp. Phys., 2012,

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

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,

Conference Papers

M. Jung, E. H. Wilson III, W. Choi, J. Shalf, H. M. Aktulga, C. Yang, E. Saule, U. V. Catalyurek, M. Kandemir, "Exploring the Future of Out-of-core Computing with Compute-Local Non-Volatile Memory", International Conference for High Performance Computing, Networking, Storage and Analysis 2013 (SC13), NY, USA, ACM New York, November 17, 2013, doi: 10.1145/2503210.2503261

P. Maris, H. M. Aktulga, S. Binder, A. Calci, U. V. Catalyurek, J. Langhammer, E. G. Ng, E. Saule, R. Roth, J. P. Vary, C. Yang, "No Core CI calculations for light nuclei with chiral 2- and 3-body forces", J. Phys. Conf. Ser., IOP Publishing, August 1, 2013, 454:012063, doi: 10.1088/1742-6596/454/1/012063

P. Maris, H. M. Aktulga, M. A. Caprio, U. V. Catalyurek, E. G. Ng, D. Oryspayev, H. Potter, E.
Saule, M. Sosonkina, J. P. Vary, C. Yang, Z. Zhou,
"Large-scale Ab-initio Configuration Interaction Calculations for Light Nuclei", J. Phys. Conf. Ser., IOP Publishing, December 18, 2012, 403:012019, doi: doi:10.1088/1742-6596/403/1/012019

Z. Zhou, E. Saule, H. M. Aktulga, C. Yang, E. G. Ng, P. Maris, J. P. Vary, U. V. Catalyurek, "An Out-of-core Eigensolver on SSD-equipped Clusters", 2012 IEEE International Conference on Cluster Computing (CLUSTER), Beijing, China, September 26, 2012, 248 - 256, doi: 10.1109/CLUSTER.2012.76

Z. Zhou, E. Saule, H. M. Aktulga, C. Yang, E. G. Ng, P. Maris, J. P. Vary, U. V. Catalyurek, "An Out-Of-Core Dataflow Middleware to Reduce the Cost of Large Scale Iterative Solvers", 2012 41st International Conference on Parallel Processing Workshops (ICPPW), Pittsburgh, PA, September 10, 2012, 71 - 80, doi: 10.1109/ICPPW.2012.13

H. M. Aktulga, C. Yang, P. Maris, J. P. Vary, E. G. Ng, "Topology-Aware Mappings for Large-Scale Eigenvalue Problems", Euro-Par 2012 Parallel Processing Conference, Rhode Island, Greece, August 31, 2012, LNCS 748:830-842, doi: 10.1007/978-3-642-32820-6_82

H. M. Aktulga, C. Yang, U. V. Catalyurek, P. Maris, J. P. Vary, E. G. Ng, "On Reducing I/O Overheads in Large-Scale Invariant Subspace Projections", Euro-Par 2011: Parallel Processing Workshops, Bordeaux, France, August 29, 2011, LNCS 715:305-314, doi: 10.1007/978-3-642-29737-3_35

E. G. Ng, J. Sarich, S. M.Wild, T. Munson, H. M. Aktulga, C. Yang, P. Maris, J. P. Vary, N. Schunck, M. G. Bertolli, M. Kortelainen, W. Nazarewicz, T. Papenbrock, M. V. Stoitsov, "Advancing Nuclear Physics Through TOPS Solvers and Tools", SciDAC 2011 Conference, Denver, CO, July 10, 2011, arXiv:1110.1708,

H. M. Aktulga, C. Yang, P. Maris, J. P. Vary, E. G. Ng, "Large-scale Parallel Null Space Calculation for Nuclear Configuration Interaction", 2011 International Conference on High Performance Computing and Simulation (HPCS), Istanbul, Turkey, July 8, 2011, 176 - 185, doi: 10.1109/HPCSim.2011.5999822

Book Chapters

E. Saule, H. M. Aktulga, C. Yang, E. G. Ng, U. V. Catalyurek, "An Out-of-core Task-based Middleware for Data Intensive Scientific Computing", Handbook on Data Centers, in press, (Springer: February 1, 2014)