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Jiri Brabec

20130e
Jiri Brabec
Postdoctoral Fellow
Computational Research Division
Phone: +1 510-486-5541
Lawrence Berkeley National Laboratory
1 Cyclotron Rd, MS-50F-1650
Berkeley, CA 94720 US

Journal Articles

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

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

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.

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,

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

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

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

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

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

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

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

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

Book Chapters

Karol Kowalski, Kiran Bhaskaran-Nair, Jiří Brabec, Jiří Pittner, "Coupled Cluster Theories for Strongly Correlated Molecular Systems", Springer Series in Solid-State Sciences, (Springer Berlin Heidelberg: 2013) Pages: 237-271 doi: 10.1007/978-3-642-35106-8_9

Reports

E. Vecharynski, J. Brabec, M. Shao, N. Govind, C. Yang, "Efficient Block Preconditioned Eigensolvers for Linear Response Time-dependent Density Functional Theory", submitted to JCC, 2015,

We present two efficient iterative algorithms for solving the linear response eigenvalue problem arising fromthe time dependent density functional theory. Although the matrix to be diagonalized is nonsymmetric, it has a special structure that can be exploited to save both memory and floating point operations. In particular, the nonsymmetric eigenvalue problem can be transformed into a product eigenvalue problem that is self-adjoint with respect to a K-inner product. This product eigenvalue problem can be solved efficiently by a modified Davidson algorithm and a modified locally optimal block preconditioned conjugate gradient (LOBPCG) algorithm that make use of the K-inner product. The solution of the product eigenvalue problem yields one component of the eigenvector associated with the original eigenvalue problem. However, the other component of the eigenvector can be easily recovered in a postprocessing procedure. Therefore, the algorithms we present here are more efficient than existing algorithms that try to approximate both components of the eigenvectors simultaneously.The efficiency of the new algorithms is demonstrated by numerical examples.