Elber, Ron - The University of Texas at Austin

个人简介

American Physical Society Fellow, 2009 Alon Fellow, 1994 Bergman Award, 1993 Camille and Henry Dreyfus New Faculty, 1992 University of Illinois Fellow, 1991 Stein Award, 1984

研究领域

The Center for Computational Life Sciences and Biology, directed by Dr. Ron Elber, resides in the Institute for Computational Engineering and Sciences (ICES) at The University of Texas at Austin. We are located in the ACES building at 201 E. 24th Street, Austin Texas. (map) Our research is theoretical and computational. We study structure, dynamics, thermodynamics and kinetics of proteins, poly-nucleotides, and membranes and their aqueous solution. Frequently we study these bio-macromolecules in atomic details, but we also investigate these systems at multiple spatial and temporal scales. group photo We develop the theory and algorithms to study reaction paths in biomolecules, and we implement the algorithms in our program MOIL. The code was used (for example) to investigate the recovery stroke in myosin. Since the calculations are highly demanding, we also develop optimized parallel, and GPU-based software, all source codes are freely available. On the Structural Bioinformatics front we develop algorithms to predict protein structures using homolgoy modeling. We are at the front of developing machine learning algorithms to learn scoring functions. We introduced an enhanced version of SVM for that purpose. These efforts are summarized in our server LOOPP. We also model the structure of protein complexes by looking at mode of interactions of pairs of proteins using similar learning techniques. We have a server for that purpose too called DOCK-PIE

近期论文

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Michele Di Pierro and Ron Elber, “Automated Optimization of Potential Parameters”, Journal of Chemical Theory and Computation, 9,3311-3320(2013) Steven Kreuzer and Ron Elber, “Catch Bond-Like Kinetics of Helix Cracking: Network Analysis by Molecular Dynamics and Milestoning”, Journal of Chemical Physics, 139, 121902(2013) Steven Kreuzer and Ron Elber, “Coiled-Coil Response to Mechanical Force: Global Stability and Local Cracking", Biophysical Journal, 105,951-961(2013) Serdal Kirmizialtin and Ron Elber, “Molecular Machines”, Current Opinion in Structural Biology 23,206-211(2013) Shruthi Viswanath, D. V. S. Ravikant, and Ron Elber, “Improving ranking of models for protein complexes with side chain reconstruction and atomic potentials”, Proteins, Structure, Function and Bioinformatics, 81,592-606(2013). A Peter Ruymgaart and Ron Elber, “Revisiting Molecular Dynamics on a CPU/GPU system: Water Kernel and SHAKE Parallelization”, Journal of Chemical Theory and Computations, 8,4624-4636(2012). Mauro Mugnai and Ron Elber, “Thermodynamic Cycle Without Turning Off Self-Interactions: Formal Discussion and a Numerical Example”, Journal of Chemical Theory and Computations, 8,3022-3033(2012). Ron Elber, “Reaction Paths and Rates”, an entry to “Encyclopedia of Biophysics”, Editor, Roberts Gordon, Springer, New York and Heidelberg, 2012 Steven Kreuzer, Ron Elber and Tess J Moon, “Early Events in Helix Unfolding Under External Forces: A Milestoning Analysis”, J. Phys. Chem. B, 116,8662–8691(2012) Grazia Cottone, Gianluca Lattanzi, Giovanni Ciccotti and Ron Elber, “Multiphoton absorption of Myoglobin Nitric-Oxide complex: relaxation by D-NEMD of a stationary state”, J. Phys. Chem. B, 116,3397-3410(2012) Ron Elber, “Progress at last”, Structure, 19,1725(2011). Serdal Kirmizialtin, Virginia Nguyen, Kenneth A Johnson, and Ron Elber, “How Conformational Dynamics of DNA Polymerase Select Correct Substrates: Experiments and Simulations”, Structure, 20,618-627(2012) Kirmizialtin Serdal, Alexander R.J. Silalahi, Elber Ron, and Marcia O. Fenley, “The ionic atmosphere around A-RNA: Poisson-Boltzmann and Molecular Dynamics Simulation”, Biophys. J., 102,829-838(2012). Alfredo E. Cardenas, Gouri S. Jas, Krzysztof Kuczera, and Ron Elber, “Unassisted transport of N-acetly-L-tryptophanamide through DOPC membrane: Experiment and simulation”, J. Phys. Chem. B, 116,2739-2750(2012). Serdal Kirmizialtin, Suzette A. Pabit, Steve P. Meisburger, Lois Pollack and Ron Elber, “RNA and its ionic cloud: Solution scattering experiments and atomically detailed simulations”, Biophys. J., 102,819-828(2012). Alfredo E. Cardenas and Ron Elber, ”Enhancing the capacity of molecular dynamics simulations with trajectory fragments”, a chapter in “Innovation in Biomolecular Modeling and Simulation: Vol 1”, RSC Biomolecular Sciences 23. Ed. T. Schlick, Royal Society of Chemistry, London, UK, 2012. Gouri S. Jas, Wendy Hegefeld, Peter M�jek, Krzysztof Kuczera, and Ron Elber, “Experiments and comprehensive simulations of the formation of a helical turn”, J. Phys. Chem. B, 6598–6610,116(2012). A Peter Ruymgaart, Alfredo E Cardenas, and Ron Elber, “MOIL-OPT: Energy-Conserving Molecular Dynamics on a GPU/CPU system”, J. Chem. Theory and Computations, 3072-3082,7(2011). Sean Burke and Ron Elber, “Super folds, networks, and barriers”, Proteins, Structure, Function, and Bioinformatics, 80,463-470(2012) Ron Elber, A. Peter Ruymgaart, and Berk Hess, “SHAKE Parallelization”, European Journal of Physics, Special Topics, 200,211-223(2011).