about
Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and DynamicsEquilibrium sampling in biomolecular simulationsComputation of steady-state probability distributions in stochastic models of cellular networksPath Similarity Analysis: A Method for Quantifying Macromolecular PathwaysUnbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of TrajectoriesSimulations of the alternating access mechanism of the sodium symporter Mhp1.A practical perspective on the implementation of hyperdynamics for accelerated simulation.Coupled folding and binding with 2D Window-Exchange Umbrella Sampling.Perspective: Computer simulations of long time dynamicsSimulating rare events using a weighted ensemble-based string method.Relation between ordering and shear thinning in colloidal suspensionsPath-sampling strategies for simulating rare events in biomolecular systems.The "weighted ensemble" path sampling method is statistically exact for a broad class of stochastic processes and binning procedures.Estimating first-passage time distributions from weighted ensemble simulations and non-Markovian analyses.WExplore: hierarchical exploration of high-dimensional spaces using the weighted ensemble algorithm.Markovian and Non-Markovian Modeling of Membrane Dynamics with Milestoning.Milestoning without a Reaction CoordinateSimultaneous Computation of Dynamical and Equilibrium Information Using a Weighted Ensemble of Trajectories.Efficient stochastic simulation of chemical kinetics networks using a weighted ensemble of trajectories.Steady-state simulations using weighted ensemble path sampling.An adaptive weighted ensemble procedure for efficient computation of free energies and first passage rates.Exact milestoning.A MATHEMATICAL FRAMEWORK FOR EXACT MILESTONING.Heterogeneous path ensembles for conformational transitions in semi-atomistic models of adenylate kinase.Milestoning with coarse memory.Adaptive single replica multiple state transition interface sampling.Peptide kinetics from picoseconds to microseconds using boxed molecular dynamics: power law rate coefficients in cyclisation reactions.Transition path sampling for discrete master equations with absorbing states.Automatic, optimized interface placement in forward flux sampling simulations.Weighted-ensemble Brownian dynamics simulation: sampling of rare events in nonequilibrium systems.Rare-event sampling for driven inertial systems via the nonequilibrium distribution function.Automated placement of interfaces in conformational kinetics calculations using machine learning.Computation of transit times using the milestoning method with applications to polymer translocation.A new paradigm for atomically detailed simulations of kinetics in biophysical systems.Adaptive free energy sampling in multidimensional collective variable space using boxed molecular dynamics.A global reaction route mapping-based kinetic Monte Carlo algorithm.Using multiscale preconditioning to accelerate the convergence of iterative molecular calculations.Steady-state simulation of metastable stochastic chemical systems.Steered transition path sampling.Simultaneous estimation of free energies and rates using forward flux sampling and mean first passage times.
P2860
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P2860
description
2007 nî lūn-bûn
@nan
2007年の論文
@ja
2007年学术文章
@wuu
2007年学术文章
@zh
2007年学术文章
@zh-cn
2007年学术文章
@zh-hans
2007年学术文章
@zh-my
2007年学术文章
@zh-sg
2007年學術文章
@yue
2007年學術文章
@zh-hant
name
Umbrella sampling for nonequilibrium processes.
@en
Umbrella sampling for nonequilibrium processes.
@nl
type
label
Umbrella sampling for nonequilibrium processes.
@en
Umbrella sampling for nonequilibrium processes.
@nl
prefLabel
Umbrella sampling for nonequilibrium processes.
@en
Umbrella sampling for nonequilibrium processes.
@nl
P2860
P356
P1476
Umbrella sampling for nonequilibrium processes.
@en
P2093
Aaron R Dinner
Prabhakar Bhimalapuram
P2860
P304
P356
10.1063/1.2784118
P407
P577
2007-10-01T00:00:00Z