Search Results - "T. McGibbon, Robert"

Variational cross-validation of slow dynamical modes in molecular kinetics by McGibbon, Robert T, Pande, Vijay S

“…Markov state models are a widely used method for approximating the eigenspectrum of the molecular dynamics propagator, yielding insight into the long-timescale…”
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MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories by McGibbon, Robert T., Beauchamp, Kyle A., Harrigan, Matthew P., Klein, Christoph, Swails, Jason M., Hernández, Carlos X., Schwantes, Christian R., Wang, Lee-Ping, Lane, Thomas J., Pande, Vijay S.

“…As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of…”
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OpenMM 7: Rapid development of high performance algorithms for molecular dynamics by Eastman, Peter, Swails, Jason, Chodera, John D, McGibbon, Robert T, Zhao, Yutong, Beauchamp, Kyle A, Wang, Lee-Ping, Simmonett, Andrew C, Harrigan, Matthew P, Stern, Chaya D, Wiewiora, Rafal P, Brooks, Bernard R, Pande, Vijay S

“…OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility. It allows users to easily add new features, including forces with novel…”
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MSMBuilder: Statistical Models for Biomolecular Dynamics by Harrigan, Matthew P., Sultan, Mohammad M., Hernández, Carlos X., Husic, Brooke E., Eastman, Peter, Schwantes, Christian R., Beauchamp, Kyle A., McGibbon, Robert T., Pande, Vijay S.

“…MSMBuilder is a software package for building statistical models of high-dimensional time-series data. It is designed with a particular focus on the analysis…”
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Automated Discovery and Refinement of Reactive Molecular Dynamics Pathways by Wang, Lee-Ping, McGibbon, Robert T, Pande, Vijay S, Martinez, Todd J

“…We describe a flexible and broadly applicable energy refinement method, “nebterpolation,” for identifying and characterizing the reaction events in a molecular…”
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Optimized parameter selection reveals trends in Markov state models for protein folding by Husic, Brooke E, McGibbon, Robert T, Sultan, Mohammad M, Pande, Vijay S

“…As molecular dynamics simulations access increasingly longer time scales, complementary advances in the analysis of biomolecular time-series data are…”
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Electrocatalytic Carbon Dioxide Activation: The Rate-Determining Step of Pyridinium-Catalyzed CO2 Reduction by Morris, Amanda J., McGibbon, Robert T., Bocarsly, Andrew B.

“…The reactivity of reduced pyridinium with CO2 was investigated as a function of catalyst concentration, temperature, and pressure at platinum electrodes…”
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Efficient maximum likelihood parameterization of continuous-time Markov processes by McGibbon, Robert T, Pande, Vijay S

“…Continuous-time Markov processes over finite state-spaces are widely used to model dynamical processes in many fields of natural and social science. Here, we…”
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Quantum chemical benchmark databases of gold-standard dimer interaction energies by Donchev, Alexander G., Taube, Andrew G., Decolvenaere, Elizabeth, Hargus, Cory, McGibbon, Robert T., Law, Ka-Hei, Gregersen, Brent A., Li, Je-Luen, Palmo, Kim, Siva, Karthik, Bergdorf, Michael, Klepeis, John L., Shaw, David E.

“…Advances in computational chemistry create an ongoing need for larger and higher-quality datasets that characterize noncovalent molecular interactions. We…”
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Statistical Model Selection for Markov Models of Biomolecular Dynamics by McGibbon, Robert T, Schwantes, Christian R, Pande, Vijay S

“…Markov state models provide a powerful framework for the analysis of biomolecular conformation dynamics in terms of their metastable states and transition…”
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Identification of simple reaction coordinates from complex dynamics by McGibbon, Robert T, Husic, Brooke E, Pande, Vijay S

“…Reaction coordinates are widely used throughout chemical physics to model and understand complex chemical transformations. We introduce a definition of the…”
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Learning Kinetic Distance Metrics for Markov State Models of Protein Conformational Dynamics by McGibbon, Robert T, Pande, Vijay S

“…Statistical modeling of long timescale dynamics with Markov state models (MSMs) has been shown to be an effective strategy for building quantitative and…”
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SciPy 1.0: fundamental algorithms for scientific computing in Python by Virtanen, Pauli, Gommers, Ralf, Oliphant, Travis E., Haberland, Matt, Reddy, Tyler, Cournapeau, David, Burovski, Evgeni, Peterson, Pearu, Weckesser, Warren, Bright, Jonathan, van der Walt, Stéfan J., Brett, Matthew, Wilson, Joshua, Millman, K. Jarrod, Mayorov, Nikolay, Nelson, Andrew R. J., Jones, Eric, Kern, Robert, Larson, Eric, Carey, C J, Polat, İlhan, Feng, Yu, Moore, Eric W., VanderPlas, Jake, Laxalde, Denis, Perktold, Josef, Cimrman, Robert, Henriksen, Ian, Quintero, E. A., Harris, Charles R., Archibald, Anne M., Ribeiro, Antônio H., Pedregosa, Fabian, van Mulbregt, Paul

“…SciPy is an open-source scientific computing library for the Python programming language. Since its initial release in 2001, SciPy has become a de facto…”
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Accelerating the Molecular Dynamics Sampling of Mutants: A Hierarchical Bayesian Markov State Model Strategy by McGibbon, Robert T., Pande, Vijay S.

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Electrocatalytic Carbon Dioxide Activation: The Rate‐Determining Step of Pyridinium‐Catalyzed CO 2 Reduction by Morris, Amanda J., McGibbon, Robert T., Bocarsly, Andrew B.

“…Abstract The reactivity of reduced pyridinium with CO 2 was investigated as a function of catalyst concentration, temperature, and pressure at platinum…”
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Statistical Models of Protein Conformational Dynamics by McGibbon, Robert T

“…Understanding the conformational dynamics of biological macromolecules at atomic resolution remains a grand challenge at the intersection of biology,…”
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Osprey: Hyperparameter Optimization for Machine Learning by T. McGibbon, Robert, X. Hernández, Carlos, P. Harrigan, Matthew, Kearnes, Steven, M. Sultan, Mohammad, Jastrzebski, Stanislaw, E. Husic, Brooke, S. Pande, Vijay

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Efficient hyperparameter optimization by way of PAC-Bayes bound minimization by Cherian, John J, Taube, Andrew G, McGibbon, Robert T, Angelikopoulos, Panagiotis, Blanc, Guy, Snarski, Michael, Richman, Daniel D, Klepeis, John L, Shaw, David E

“…Identifying optimal values for a high-dimensional set of hyperparameters is a problem that has received growing attention given its importance to large-scale…”
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Efficient maximum likelihood parameterization of continuous-time Markov processes by McGibbon, Robert T, Pande, Vijay S

“…Continuous-time Markov processes over finite state-spaces are widely used to model dynamical processes in many fields of natural and social science. Here, we…”
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Identification of simple reaction coordinates from complex dynamics by McGibbon, Robert T, Husic, Brooke E, Pande, Vijay S

“…Reaction coordinates are widely used throughout chemical physics to model and understand complex chemical transformations. We introduce a definition of the…”
Get full text