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Trajectory stratification of stochastic dynamics.
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Steered transition path sampling.
J Chem Phys. 2012 Jun 21;136(23):234103. doi: 10.1063/1.4724301.
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Computing transition path theory quantities with trajectory stratification.
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Estimating time-correlation functions by sampling and unbiasing dynamically activated events.
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Girsanov reweighting for path ensembles and Markov state models.
J Chem Phys. 2017 Jun 28;146(24):244112. doi: 10.1063/1.4989474.
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Sampling rare trajectories using stochastic bridges.
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Optimization for customized trajectories in cone beam computed tomography.
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Dynamical Computation of the Density of States and Bayes Factors Using Nonequilibrium Importance Sampling.
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BAD-NEUS: Rapidly converging trajectory stratification.
J Chem Phys. 2024 Aug 28;161(8). doi: 10.1063/5.0215975.
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Tertiary Plasticity Drives the Efficiency of Enterocin 7B Interactions with Lipid Membranes.
J Phys Chem B. 2024 Mar 7;128(9):2100-2113. doi: 10.1021/acs.jpcb.3c08199. Epub 2024 Feb 27.
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ScMiles2: A Script to Conduct and Analyze Milestoning Trajectories for Long Time Dynamics.
J Chem Theory Comput. 2022 Nov 8;18(11):6952-6965. doi: 10.1021/acs.jctc.2c00708. Epub 2022 Oct 3.
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Computing transition path theory quantities with trajectory stratification.
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OPTIMIZING WEIGHTED ENSEMBLE SAMPLING OF STEADY STATES.
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Long-Time-Scale Predictions from Short-Trajectory Data: A Benchmark Analysis of the Trp-Cage Miniprotein.
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Enhanced Jarzynski free energy calculations using weighted ensemble.
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ScMile: A Script to Investigate Kinetics with Short Time Molecular Dynamics Trajectories and the Milestoning Theory.
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Galerkin approximation of dynamical quantities using trajectory data.
J Chem Phys. 2019 Jun 28;150(24):244111. doi: 10.1063/1.5063730.
10
Entropic constraints on the steady-state fitness of competing self-replicators.
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本文引用的文献

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Eigenvector method for umbrella sampling enables error analysis.
J Chem Phys. 2016 Aug 28;145(8):084115. doi: 10.1063/1.4960649.
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Flow-Dependent Unfolding and Refolding of an RNA by Nonequilibrium Umbrella Sampling.
J Chem Theory Comput. 2011 Sep 13;7(9):2710-20. doi: 10.1021/ct200371n. Epub 2011 Aug 23.
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Exact milestoning.
J Chem Phys. 2015 Mar 7;142(9):094102. doi: 10.1063/1.4913399.
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All-atom empirical potential for molecular modeling and dynamics studies of proteins.
J Phys Chem B. 1998 Apr 30;102(18):3586-616. doi: 10.1021/jp973084f.
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Relation between ordering and shear thinning in colloidal suspensions.
Proc Natl Acad Sci U S A. 2013 Mar 5;110(10):3771-6. doi: 10.1073/pnas.1301055110. Epub 2013 Feb 19.
6
Steered transition path sampling.
J Chem Phys. 2012 Jun 21;136(23):234103. doi: 10.1063/1.4724301.
7
Markov state models based on milestoning.
J Chem Phys. 2011 May 28;134(20):204105. doi: 10.1063/1.3590108.
8
Escorted free energy simulations.
J Chem Phys. 2011 Feb 7;134(5):054107. doi: 10.1063/1.3544679.
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Separating forward and backward pathways in nonequilibrium umbrella sampling.
J Chem Phys. 2009 Oct 21;131(15):154104. doi: 10.1063/1.3244561.
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Enhanced sampling of nonequilibrium steady states.
Annu Rev Phys Chem. 2010;61:441-59. doi: 10.1146/annurev.physchem.012809.103433.

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