Uncertainty in a Markov state model with missing states and rates: Application to a room temperature kinetic model obtained using high temperature molecular dynamics

Perspective: Insight into reaction coordinates and dynamics from the potential energy landscape

(2015) D. J. Wales   JOURNAL OF CHEMICAL PHYSICS

Molecular dynamics saddle search adaptive kinetic Monte Carlo

(2014) Samuel T. Chill et al.   JOURNAL OF CHEMICAL PHYSICS

Accelerating rare events while overcoming the low-barrier problem using a temperature program

(2014) Srikanth Divi et al.   JOURNAL OF CHEMICAL PHYSICS

Perspective: Markov models for long-timescale biomolecular dynamics

(2014) C. R. Schwantes et al.   JOURNAL OF CHEMICAL PHYSICS

Seeking kinetic pathways relevant to the structural evolution of metal nanoparticles

(2014) Paramita Haldar et al.   MODELLING AND SIMULATION IN MATERIALS SCIENCE AND ENGINEERING

Accuracy of a Markov state model generated by searching for basin escape pathways

(2013) Vijesh J. Bhute et al.   JOURNAL OF CHEMICAL PHYSICS

Building a kinetic Monte Carlo model with a chosen accuracy

(2013) Vijesh J. Bhute et al.   JOURNAL OF CHEMICAL PHYSICS

From Metadynamics to Dynamics

(2013) Pratyush Tiwary et al.   PHYSICAL REVIEW LETTERS

Improved coarse-graining of Markov state models via explicit consideration of statistical uncertainty

(2012) Gregory R. Bowman   JOURNAL OF CHEMICAL PHYSICS

EMMA: A Software Package for Markov Model Building and Analysis

(2012) Martin Senne et al.   Journal of Chemical Theory and Computation

Multiple state transition interface sampling of alanine dipeptide in explicit solvent

(2011) Wei-Na Du et al.   JOURNAL OF CHEMICAL PHYSICS

Markov models of molecular kinetics: Generation and validation

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

MSMBuilder2: Modeling Conformational Dynamics on the Picosecond to Millisecond Scale

(2011) Kyle A. Beauchamp et al.   Journal of Chemical Theory and Computation

Water-Mediated Conformations of the Alanine Dipeptide as Revealed by Distributed Umbrella Sampling Simulations, Quantum Mechanics Based Calculations, and Experimental Data

(2011) Víctor Cruz et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Equilibrium Distribution from Distributed Computing (Simulations of Protein Folding)

(2011) Riccardo Scalco et al.   JOURNAL OF PHYSICAL CHEMISTRY B

What Is the Time Scale for α-Helix Nucleation?

(2011) David De Sancho et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Probability distributions of molecular observables computed from Markov models. II. Uncertainties in observables and their time-evolution

(2010) John D. Chodera et al.   JOURNAL OF CHEMICAL PHYSICS

Accurate acceleration of kinetic Monte Carlo simulations through the modification of rate constants

(2010) Abhijit Chatterjee et al.   JOURNAL OF CHEMICAL PHYSICS

Everything you wanted to know about Markov State Models but were afraid to ask

(2010) Vijay S. Pande et al.   METHODS

Challenges in protein-folding simulations

(2010) Peter L. Freddolino et al.   Nature Physics

A self-learning algorithm for biased molecular dynamics

(2010) Gareth A. Tribello et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

ETNA: Equilibrium Transitions Network and Arrhenius Equation for Extracting Folding Kinetics from REMD Simulations

(2009) S. Muff et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Bayesian Single-Exponential Kinetics in Single-Molecule Experiments and Simulations

(2009) Daniel L. Ensign et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Using generalized ensemble simulations and Markov state models to identify conformational states

(2009) Gregory R. Bowman et al.   METHODS

Estimating the sampling error: Distribution of transition matrices and functions of transition matrices for given trajectory data

(2009) Philipp Metzner et al.   PHYSICAL REVIEW E

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

Free energy surfaces from an extended harmonic superposition approach and kinetics for alanine dipeptide

(2008) Birgit Strodel et al.   CHEMICAL PHYSICS LETTERS

Molecular simulations of protein dynamics: new windows on mechanisms in biology

(2008) Guy G Dodson et al.   EMBO REPORTS

Peptide folding kinetics from replica exchange molecular dynamics

(2008) Nicolae-Viorel Buchete et al.   PHYSICAL REVIEW E