We present a new mathematical framework for unifying various two-state rate theories presented in the physical chemistry literature over many decades, and provide a quantitative way to measure reaction coordinate quality.
We describe how reweighing techniques can provide optimal estimates of temperature-dependent dynamical properties from simulations conducted at multiple temperatures.
A review of current best practices for the generation and validation of Markov state models for describing the stochastic dynamics of biomolecular systems.
We present a new framework for comparing essential features of the dynamics between experiment and simulation to identify the kinetics processes contributing to individual relaxation timescales in perturbation-response or correlation spectroscopy experiments.
Molecular simulations of the PCNA clamp responsible for DNA polymerase processivity show a surprisingly small energetic penalty for the deformation required for clamp loading.
A review of the utility of the proposed zipping and assembly mechanism for the concomitant formation of secondary and tertiary structure in protein folding for predicting folding pathways and native structures.
Proposing one of the first automated algorithms for discovering kinetically metastable states of biomolecules from molecular simulations, this paper shows how many biomolecules can possess numerous distinct long-lived conformational states even though the the equilibrium populations of these states may too small for standard structural biology techniques to detect.
We show how the long-time dynamics of biomolecular systems can be recapitulated from statistics collected from short molecular simulations sampling transitions between kinetically metastable states.