Transition path sampling and forward flux sampling. Applications to biological systems

Two-state protein folding kinetics through all-atom molecular dynamics based sampling

(2009) Peter et al.   Frontiers in Bioscience-Landmark

Kinetics and reaction coordinate for the isomerization of alanine dipeptide by a forward flux sampling protocol

(2009) Camilo Velez-Vega et al.   JOURNAL OF CHEMICAL PHYSICS

Nonequilibrium umbrella sampling in spaces of many order parameters

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

Simulating the Kinetics and Thermodynamics of Transitions via Forward Flux/Umbrella Sampling

(2009) Ernesto E. Borrero et al.   JOURNAL OF PHYSICAL CHEMISTRY B

DNA looping provides stability and robustness to the bacteriophage   switch

(2009) M. J. Morelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rate Constant and Reaction Coordinate of Trp-Cage Folding in Explicit Water

(2008) Jarek Juraszek et al.   BIOPHYSICAL JOURNAL

Reaction Coordinates for the Flipping of Genetic Switches

(2008) Marco J. Morelli et al.   BIOPHYSICAL JOURNAL

Multiple state transition path sampling

(2008) Jutta Rogal et al.   JOURNAL OF CHEMICAL PHYSICS

Optimizing the sampling and staging for simulations of rare events via forward flux sampling schemes

(2008) Ernesto E. Borrero et al.   JOURNAL OF CHEMICAL PHYSICS

Rare events via multiple reaction channels sampled by path replica exchange

(2008) Peter G. Bolhuis   JOURNAL OF CHEMICAL PHYSICS

Folding of polyglutamine chains

(2008) Manan Chopra et al.   JOURNAL OF CHEMICAL PHYSICS

Improved transition path sampling methods for simulation of rare events

(2008) Manan Chopra et al.   JOURNAL OF CHEMICAL PHYSICS

The rate constant of polymer reversal inside a pore

(2008) Lei Huang et al.   JOURNAL OF CHEMICAL PHYSICS

On the assumptions underlying milestoning

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

Pathways for Conformational Change in Nitrogen Regulatory Protein C from Discrete Path Sampling

(2008) Mey Khalili 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

A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT

(2008) J. Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Atomic detail of chemical transformation at the transition state of an enzymatic reaction

(2008) S. Saen-oon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In Silico Protein Fragmentation Reveals the Importance of Critical Nuclei on Domain Reassembly

(2007) Lydia M. Contreras Martínez et al.   BIOPHYSICAL JOURNAL