Reaction coordinates, one-dimensional Smoluchowski equations, and a test for dynamical self-consistency

Steady-state nucleation rate and flux of composite nucleus at saddle point

(2012) Masao Iwamatsu   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

Transition path sampling of protein conformational changes

(2011) Jarek Juraszek et al.   CHEMICAL PHYSICS

Coarse-graining entropy, forces, and structures

(2011) Joseph F. Rudzinski et al.   JOURNAL OF CHEMICAL PHYSICS

Polymer reversal rate calculated via locally scaled diffusion map

(2011) Wenwei Zheng et al.   JOURNAL OF CHEMICAL PHYSICS

Determination of reaction coordinates via locally scaled diffusion map

(2011) Mary A. Rohrdanz et al.   JOURNAL OF CHEMICAL PHYSICS

Numerical Construction of thepfold(Committor) Reaction Coordinate for a Markov Process

(2011) Sergei V. Krivov   JOURNAL OF PHYSICAL CHEMISTRY B

Comment on “Toward Identification of the Reaction Coordinate Directly from the Transition State Ensemble Using the Kernel PCA Method”

(2011) Baron Peters   JOURNAL OF PHYSICAL CHEMISTRY B

Toward Identification of the Reaction Coordinate Directly from the Transition State Ensemble Using the Kernel PCA Method

(2011) Dimitri Antoniou et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Computer Simulations of Homogeneous Nucleation of Benzene from the Melt

(2011) Manas Shah et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Optimizing Nucleus Size Metrics for Liquid–Solid Nucleation from Transition Paths of Near-Nanosecond Duration

(2011) Gregg T. Beckham et al.   Journal of Physical Chemistry Letters

Splitting Probabilities as a Test of Reaction Coordinate Choice in Single-Molecule Experiments

(2011) John D. Chodera et al.   PHYSICAL REVIEW LETTERS

Dynamics of protein folding: Probing the kinetic network of folding–unfolding transitions with experiment and theory

(2010) Ginka S. Buchner et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

p(TP|q) peak maximization: Necessary but not sufficient for reaction coordinate accuracy

(2010) Baron Peters   CHEMICAL PHYSICS LETTERS

Nonlinear reaction coordinate analysis in the reweighted path ensemble

(2010) Wolfgang Lechner et al.   JOURNAL OF CHEMICAL PHYSICS

Molecular Mechanism of Acid-Catalyzed Hydrolysis of Peptide Bonds Using a Model Compound

(2010) Bin Pan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Recent advances in transition path sampling: accurate reaction coordinates, likelihood maximisation and diffusive barrier-crossing dynamics

(2010) Baron Peters   MOLECULAR SIMULATION

Identification of the protein folding transition state from molecular dynamics trajectories

(2009) S. Muff et al.   JOURNAL OF CHEMICAL PHYSICS

Estimating diffusivity along a reaction coordinate in the high friction limit: Insights on pulse times in laser-induced nucleation

(2009) Brandon C. Knott et al.   JOURNAL OF CHEMICAL PHYSICS

Density-dependent analysis of nonequilibrium paths improves free energy estimates

(2009) David D. L. Minh   JOURNAL OF CHEMICAL PHYSICS

Reactive flux and folding pathways in network models of coarse-grained protein dynamics

(2009) Alexander Berezhkovskii et al.   JOURNAL OF CHEMICAL PHYSICS

Competing nucleation pathways in a mixture of oppositely charged colloids: Out-of-equilibrium nucleation revisited

(2009) Baron Peters   JOURNAL OF CHEMICAL PHYSICS

Nucleation in a Potts lattice gas model of crystallization from solution

(2009) Nathan Duff et al.   JOURNAL OF CHEMICAL PHYSICS

Artificial reaction coordinate “tunneling” in free-energy calculations: The catalytic reaction of RNase H

(2009) Edina Rosta et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Detecting intrinsic slow variables in stochastic dynamical systems by anisotropic diffusion maps

(2009) A. Singer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coordinate-dependent diffusion in protein folding

(2009) R. B. Best et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Microsecond Simulations of Spontaneous Methane Hydrate Nucleation and Growth

(2009) M. R. Walsh et al.   SCIENCE

The Protein Folding Problem

(2008) Ken A. Dill et al.   Annual Review of Biophysics

Transition-Path Theory and Path-Finding Algorithms for the Study of Rare Events

(2008) Weinan E et al.   Annual Review of Physical Chemistry

Nucleation in the presence of slow microscopic dynamics

(2008) Richard P. Sear   JOURNAL OF CHEMICAL PHYSICS

The relative entropy is fundamental to multiscale and inverse thermodynamic problems

(2008) M. Scott Shell   JOURNAL OF CHEMICAL PHYSICS

One-Dimensional Barrier-Preserving Free-Energy Projections of a β-sheet Miniprotein: New Insights into the Folding Process

(2008) Sergei V. Krivov et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Kinetic Reconstruction of the Free-Energy Landscape

(2008) Jan Wedekind et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Finding Transition Pathways Using the String Method with Swarms of Trajectories

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

Homogeneous Bubble Nucleation Driven by Local Hot Spots: A Molecular Dynamics Study†

(2008) Zun-Jing Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Diffusive reaction dynamics on invariant free energy profiles

(2008) S. V. Krivov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA