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pro vyhledávání: '"Copperman, Jeremy"'
This article introduces an advanced Koopman mode decomposition (KMD) technique -- coined Featurized Koopman Mode Decomposition (FKMD) -- that uses delay embedding and a learned Mahalanobis distance to enhance analysis and prediction of high dimension
Externí odkaz:
http://arxiv.org/abs/2312.09146
Publikováno v:
Journal of Chemical Physics; 8/14/2024, Vol. 161 Issue 6, p1-11, 11p
Markov state models (MSMs) have been broadly adopted for analyzing molecular dynamics trajectories, but the approximate nature of the models that results from coarse-graining into discrete states is a long-known limitation. We show theoretically that
Externí odkaz:
http://arxiv.org/abs/2105.13402
We present two algorithms by which a set of short, unbiased trajectories can be iteratively reweighted to obtain various observables. The first algorithm estimates the stationary (steady state) distribution of a system by iteratively reweighting the
Externí odkaz:
http://arxiv.org/abs/2006.09451
Autor:
Copperman, Jeremy, Zuckerman, Daniel
The weighted ensemble (WE) simulation strategy provides unbiased sampling of non-equilibrium processes, such as molecular folding or binding, but the extraction of rate constants relies on characterizing steady state behavior. Unfortunately, WE simul
Externí odkaz:
http://arxiv.org/abs/1903.04673
Autor:
Copperman, Jeremy
A novel approach is developed to describe the dynamics of proteins, the coarse-grained Langevin Equation for Protein Dynamics (LE4PD). The approach describes proteins as fundamentally semiflexible objects collapsed into the free energy well represent
Externí odkaz:
http://hdl.handle.net/1794/20447
Autor:
Copperman, Jeremy, Aristoff, David, Makarov, Dmitrii E., Simpson, Gideon, Zuckerman, Daniel M.
Probability currents are fundamental in characterizing the kinetics of non-equilibrium processes. Notably, the steady-state current $J_{ss}$ for a source-sink system can provide the exact mean-first-passage time (MFPT) for the transition from source
Externí odkaz:
http://arxiv.org/abs/1810.09964
Autor:
Copperman, Jeremy1 (AUTHOR) copperma@ohsu.edu, Gross, Sean M.1 (AUTHOR), Chang, Young Hwan1,2 (AUTHOR), Heiser, Laura M.1,2 (AUTHOR) heiserl@ohsu.edu, Zuckerman, Daniel M.1,2 (AUTHOR) zuckermd@ohsu.edu
Publikováno v:
Communications Biology. 2023, Vol. 6 Issue 1, p1-12. 12p.
Autor:
Copperman, Jeremy, Aristoff, David, Makarov, Dmitrii E., Simpson, Gideon, Zuckerman, Daniel M.
Publikováno v:
Journal of Chemical Physics; 11/7/2019, Vol. 151 Issue 17, pN.PAG-N.PAG, 12p, 1 Diagram, 4 Graphs
Akademický článek
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