Markov State Models for Rare Events in Molecular Dynamics

A structure-preserving numerical discretization of reversible diffusions

(2013) Carsten Hartmann et al.   Communications in Mathematical Sciences

Approximating selected non-dominant timescales by Markov state models

(2013) Marco Sarich et al.   Communications in Mathematical Sciences

Characterization of Rare Events in Molecular Dynamics

(2013) Carsten Hartmann et al.   Entropy

Quantifying the rebinding effect in multivalent chemical ligand-receptor systems

(2012) Marcus Weber et al.   JOURNAL OF CHEMICAL PHYSICS

Optimal control of molecular dynamics using Markov state models

(2012) Christof Schütte et al.   MATHEMATICAL PROGRAMMING

Markov state models based on milestoning

(2011) Christof Schütte et al.   JOURNAL OF CHEMICAL PHYSICS

Markov models of molecular kinetics: Generation and validation

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

Probing molecular kinetics with Markov models: metastable states, transition pathways and spectroscopic observables

(2011) Jan-Hendrik Prinz et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Taming the complexity of protein folding

(2010) Gregory R Bowman et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

On the Approximation Quality of Markov State Models

(2010) Marco Sarich et al.   MULTISCALE MODELING & SIMULATION

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

(2009) Gregory R. Bowman et al.   METHODS

Transition Path Theory for Markov Jump Processes

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

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

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

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

Coarse Master Equations for Peptide Folding Dynamics†

(2008) Nicolae-Viorel Buchete et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Macroscopic Dynamics of Complex Metastable Systems: Theory, Algorithms, and Application to B-DNA

(2008) Illia Horenko et al.   SIAM JOURNAL ON APPLIED DYNAMICAL SYSTEMS