Calculating Iso-Committor Surfaces as Optimal Reaction Coordinates with Milestoning

Nonparametric variational optimization of reaction coordinates

(2015) Polina V. Banushkina et al.   JOURNAL OF CHEMICAL PHYSICS

Exact milestoning

(2015) Juan M. Bello-Rivas et al.   JOURNAL OF CHEMICAL PHYSICS

Flows in Complex Networks: Theory, Algorithms, and Application to Lennard–Jones Cluster Rearrangement

(2014) Maria Cameron et al.   JOURNAL OF STATISTICAL PHYSICS

Analyzing milestoning networks for molecular kinetics: Definitions, algorithms, and examples

(2013) Shruthi Viswanath et al.   JOURNAL OF CHEMICAL PHYSICS

MOIL-opt: Energy-Conserving Molecular Dynamics on a GPU/CPU System

(2011) A. Peter Ruymgaart et al.   Journal of Chemical Theory and Computation

Revisiting and Computing Reaction Coordinates with Directional Milestoning

(2011) Serdal Kirmizialtin et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Nonlinear reaction coordinate analysis in the reweighted path ensemble

(2010) Wolfgang Lechner 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

Milestoning without a Reaction Coordinate

(2010) Peter Májek et al.   Journal of Chemical Theory and Computation

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

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

Markovian milestoning with Voronoi tessellations

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

Forward flux sampling for rare event simulations

(2009) Rosalind J Allen et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Transition Path Theory for Markov Jump Processes

(2009) Philipp Metzner et al.   MULTISCALE MODELING & SIMULATION

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

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

On the assumptions underlying milestoning

(2008) Eric Vanden-Eijnden et al.   JOURNAL OF CHEMICAL PHYSICS