Barsegov, Valeri - University of Massachusetts-Lowell

个人简介

Postdoctoral (2003-2006): Institute for Physical Science and Technology, University of Maryland (with Prof. Devarajan Thirumalai) Postdoctoral (2001-2003): Department of Chemistry, University of Rochester (with Prof. Shaul Mukamel) Ph.D. (1994-2000): Department of Chemistry & Biochemistry (with Prof. Peter Rossky) and Department of Physics (with Prof. Ilya Prigogine), University of Texas at Austin B.S., 1994, Department of Chemistry, Moscow State University, Moscow, Russia

研究领域

Our research objectives are to advance both conceptual and microscopic understanding of biomolecular interactions, including protein-protein, protein-DNA, and ligand-receptor interactions, using theoretical approaches and computer simulations, and to understand the role of these interactions in diverse biological processes from formation and dissociation of biomolecular complexes and aggregates to mechano-chemical signal transduction in cell-adhesion systems, to functions of long protein fibers, to membrane fusion, and to viral infectivity of cells. To achieve these goals, we develop and use new theoretical approaches, including theoretical models and statistical data analyses, and advanced computational methodology (numerical algorithms and tools) for molecular simulations of biochemical and biological systems on graphics processors, or Graphics Processing Units (GPUs), and on combined CPU-GPU platforms. Contemporary GPUs allow us to speedup simulations 10-250-fold, depending on the system size, as compared with heavily tuned implementations of the simulation algorithms on a CPU. We use the GPU-based acceleration to energize computational exploration of large-size biological systems, and to attain the experimentally relevant timescale. Current state of the art experiments on single molecules, which include, e.g., FRET, and AFM and laser-tweezer-based dynamic force spectroscopy among many others, enable researchers to go beyound the ensemble averaged picture and to analyze the entire distributions of the relevant biomolecular characteristics. We strive to describe the biomolecular processes and biological systems under the experimentally and physiologically relevant conditions. We collaborate with experimental groups, wherever possible, to relate the simulation output with the experimental results, and to provide meaningful interpretation of the experimental data.

近期论文

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O. Kononova, Y. Kholodov, K. E. Theisen, K. A. Marx, R. I. Dima, F. I. Ataullakhanov, E. L. Grishchuk and V. Barsegov, "Tubulin bond energies and microtubule biomechanics determined from nanoindentation in silico", J. Am. Chem. Soc., 136, 17036-17045 (2014) [PDF] R. Kumar, R. V. Kukreja, L. Li, A. Zhmurov, O. Kononova, S. Cai, S. A. Ahmed, V. Barsegov, and B. R. Singh, "Botulinum neurotoxin: unique folding of enzyme domain of the most-poisonous poison", J. Biomol. Struct. Dyn., 32, 804-815 (2014) [PDF] R. I. Litvinov, S. V. Yarovoi, L. Rauova, V. Barsegov, B. S. Sachais, A. H. Rux, J. L. Hinds, G. M. Arepally, D. B. Cines and J. W. Weisel, "Distinct specificity and single-molecule kinetics characterize the interaction of pathogenic and non-pathogenic antibodies against platelet factor 4-heparin complexes with platelet factor 4", J. Biol. Chem., 288, 33060-33070 (2013) [PDF] O. Kononova, J. Snijder, M. Brasch, J. Cornelissen, R. I. Dima, K. A Marx, G. J. L. Wuite, W. H. Roos and V. Barsegov, "Structural transitions and energy landscape for cowpea chlorotic mottle virus capsid mechanics from nanomanipulation in vitro and in silico", Biophys. J., 105, 1893-1903 (2013) [PDF] O. Kononova, L. Jones and V. Barsegov, "Order statistics inference for describing topological coupling and mechanical symmetry breaking in multidomain proteins", J. Chem. Phys., 139, 121913 (2013) [PDF] O. Kononova, R. I. Litvinov, A. Zhmurov, A. Alekseenko, C.-H. Cheng, S. Agarwal, K. A. Marx, J. W. Weisel and V. Barsegov, "Molecular mechanisms, thermodynamics, and dissociation kinetics of knob-hole interactions in fibrin", J. Biol. Chem., 288, 22681-22692 (2013) [PDF] R. A. Toubar, A. Zhmurov, V. Barsegov, and K. A. Marx, "Comparative simulation studies of native and single-site mutant human beta-defensin-1 peptides", J. Biomol. Struct. Dyn., 31, 174-194 (2013) [PDF] A. Zhmurov, O. Kononova, R. I. Litvinov, R. I. Dima, V. Barsegov and J. W. Weisel, "Mechanical transition from α-helical coiled coils to β-sheets in fibrin(ogen)", J. Am. Chem. Soc., 134, 20396-20402 (2012) [PDF] K. E. Theisen, A. Zhmurov, M. E. Newberry, V. Barsegov and R. I. Dima, "Multiscale modeling of the nanomechanics of microtubule protofilaments", J. Phys. Chem., 116, 8545-8555 (2012) [PDF] A. Zhmurov, A. E. X. Brown, R. I. Litvinov, R. I. Dima, J. W. Weisel, and V. Barsegov, "Mechanism of fibrin(ogen) forced unfolding", Structure, 19, 1615-1624 (2011) [PDF] L. Duan, A. Zhmurov, V. Barsegov and R. I. Dima, "Exploring the Mechanical Stability of the C2 Domains in Human Synaptotagmin 1", J. Phys. Chem B, 115, 10133-10146 (2011) [PDF] R. Litvinov, V. Barsegov, A. Schissler, A. Fisher, J. Bennett, J. Weisel, H. Shuman, "Dissociation of biomolecular αIIβ3-fibrinogen complex under a constant tensile force", Biophys J., 100, 165-173 (2011) [PDF] A. Zhmurov, K. Rybnikov, Y. Kholodov, and V. Barsegov, "Generation of random numbers on graphics processors: Forced indentation in silico of the bacteriophage HK97", J. Phys. Chem. B, 115, 5278-5288 (2011) [PDF] A. Zhmurov, R. I. Dima, Y. Kholodov, and V. Barsegov, "SOP-GPU: Accelerating biomolecular simulations in the centisecond timescale using graphics processors", Proteins, 78, 2984-2999 (2010) [PDF] A. Zhmurov, R. I. Dima, and V. Barsegov, "Order Statistics theory of unfolding of multimeric proteins, "Biophys. J., 99, 1959-1268 (2010) [PDF] E Bura, A. Zhmurov, and V. Barsegov, "Nonparametric density estimation and optimal bandwidth selection for protein unfolding and unbinding data, "J. Chem. Phys., 130, 015102 (2009) [PDF] V. Barsegov, G. Morrison, and D. Thirumalai, "Role of internal chain dynamics on the rupture kinetics of adhesive contacts, "Phys. Rev. Lett., 100, 248102 (2008) [PDF] E. Bura, D. K. Klimov and V. Barsegov , "Analyzing forced unfolding of protein tandems by ordered variates: 2. Dependent unfolding times", Biophys. J., 94, 2516-2528 (2008) [PDF]. E. P. Raman, T. Takeda, V. Barsegov and D. K. Klimov , "Mechanical unbinding of Aβ peptides from amyloid fibrils", J. Mol. Biol., 373, 785-800 (2007) [PDF]. E. Bura, D. K. Klimov and V. Barsegov, "Analyzing forced unfolding of protein tandems by ordered variates: 1. Independent unfolding times", Biophys. J., 93, 1100-1115 (2007) [PDF].