Markov state models (MSMs) are a powerful framework for analyzing dynamical systems,
such as molecular dynamics (MD) simulations, that have gained widespread use over the …

Drug action is inherently multiscale: it connects molecular interactions to emergent
properties at cellular and larger scales. Simulation techniques at each of these different …

Conformational changes (ie, dynamic transitions between pairs of conformational states)
play important roles in many chemical and biological processes. Constructing the Markov …

A critical step of β-amyloid fibril formation is fibril elongation in which amyloid-β monomers
undergo structural transitions to fibrillar structures upon their binding to fibril tips. The atomic …

Replica-exchange molecular dynamics (REMD) and their variants have been widely used in
simulations of the biomolecular structure and dynamics. Replica exchange with solute …

Finite Markov chains, memoryless random walks on complex networks, appear commonly
as models for stochastic dynamics in condensed matter physics, biophysics, ecology …

Understanding the mechanisms by which proteins fold from disordered amino-acid chains to
spatially ordered structures remains an area of active inquiry. Molecular simulations can …

Understanding how kinetics in the unfolded state affects protein folding is a fundamentally
important yet less well-understood issue. Here we employ three different models to analyze …

Replica exchange molecular dynamics is a multicanonical simulation technique commonly
used to enhance the sampling of solvated biomolecules on rugged free energy landscapes …

The Binding energy distribution analysis method (BEDAM) is employed to compute the
standard binding free energies of a series of ligands to a FK506 binding protein (FKBP12) …