Simulating rare events using a weighted ensemble-based string method

Erratum: “Separating forward and backward pathways in nonequilibrium umbrella sampling” [J. Chem. Phys. 131, 154104 (2009)]

(2012) Alex Dickson et al.   JOURNAL OF CHEMICAL PHYSICS

Erratum: “Nonequilibrium umbrella sampling in spaces of many order parameters” [J. Chem. Phys. 130, 074104 (2009)]

(2012) Alex Dickson et al.   JOURNAL OF CHEMICAL PHYSICS

Characterization of a Dynamic String Method for the Construction of Transition Pathways in Molecular Reactions

(2012) Margaret E. Johnson et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Unrestrained Computation of Free Energy along a Path

(2012) Bradley M. Dickson et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Simulations of the Alternating Access Mechanism of the Sodium Symporter Mhp1

(2011) Joshua L. Adelman et al.   BIOPHYSICAL JOURNAL

A Conformational Transition in the Myosin VI Converter Contributes to the Variable Step Size

(2011) V. Ovchinnikov et al.   BIOPHYSICAL JOURNAL

Markov models of molecular kinetics: Generation and validation

(2011) Jan-Hendrik Prinz et al.   JOURNAL OF CHEMICAL PHYSICS

Efficient Explicit-Solvent Molecular Dynamics Simulations of Molecular Association Kinetics: Methane/Methane, Na+/Cl−, Methane/Benzene, and K+/18-Crown-6 Ether

(2011) Matthew C. Zwier et al.   Journal of Chemical Theory and Computation

Flow-Dependent Unfolding and Refolding of an RNA by Nonequilibrium Umbrella Sampling

(2011) Alex Dickson et al.   Journal of Chemical Theory and Computation

The Mechanical Properties of PCNA: Implications for the Loading and Function of a DNA Sliding Clamp

(2010) Joshua L. Adelman et al.   BIOPHYSICAL JOURNAL

Reaching biological timescales with all-atom molecular dynamics simulations

(2010) Matthew C Zwier et al.   CURRENT OPINION IN PHARMACOLOGY

The reweighted path ensemble

(2010) Jutta Rogal et al.   JOURNAL OF CHEMICAL PHYSICS

Steady-state simulations using weighted ensemble path sampling

(2010) Divesh Bhatt et al.   JOURNAL OF CHEMICAL PHYSICS

The “weighted ensemble” path sampling method is statistically exact for a broad class of stochastic processes and binning procedures

(2010) Bin W. Zhang et al.   JOURNAL OF CHEMICAL PHYSICS

Heterogeneous Path Ensembles for Conformational Transitions in Semiatomistic Models of Adenylate Kinase

(2010) Divesh Bhatt et al.   Journal of Chemical Theory and Computation

Pore opening and closing of a pentameric ligand-gated ion channel

(2010) F. Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nonequilibrium umbrella sampling in spaces of many order parameters

(2009) Alex Dickson et al.   JOURNAL OF CHEMICAL PHYSICS

Revisiting the finite temperature string method for the calculation of reaction tubes and free energies

(2009) Eric Vanden-Eijnden et al.   JOURNAL OF CHEMICAL PHYSICS

Exact rate calculations by trajectory parallelization and tilting

(2009) Eric Vanden-Eijnden et al.   JOURNAL OF CHEMICAL PHYSICS

Separating forward and backward pathways in nonequilibrium umbrella sampling

(2009) Alex Dickson et al.   JOURNAL OF CHEMICAL PHYSICS

Free Energy and Kinetics of Conformational Transitions from Voronoi Tessellated Milestoning with Restraining Potentials

(2009) Luca Maragliano et al.   Journal of Chemical Theory and Computation

Segmented Transition Pathway of the Signaling Protein Nitrogen Regulatory Protein C

(2009) Ming Lei et al.   JOURNAL OF MOLECULAR BIOLOGY

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations

(2009) Frank Noé et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Self-guided Langevin dynamics study of regulatory interactions in NtrC

(2009) Ana Damjanović et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Systematic Multiscale Parameterization of Heterogeneous Elastic Network Models of Proteins

(2008) Edward Lyman et al.   BIOPHYSICAL JOURNAL

Building Markov state models along pathways to determine free energies and rates of transitions

(2008) Albert C. Pan et al.   JOURNAL OF CHEMICAL PHYSICS

Statistically optimal analysis of samples from multiple equilibrium states

(2008) Michael R. Shirts et al.   JOURNAL OF CHEMICAL PHYSICS

Finding Transition Pathways Using the String Method with Swarms of Trajectories

(2008) Albert C. Pan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Close Correspondence between the Motions from Principal Component Analysis of Multiple HIV-1 Protease Structures and Elastic Network Modes

(2008) Lei Yang et al.   STRUCTURE