Sampling diffusive transition paths.

Title Sampling diffusive transition paths

Stochastic actions for diffusive dynamics: reweighting, sampling, and minimization.

In numerical studies of diffusive dynamics, two different action functionals are often used to specify the probability distribution of trajectories, one of which requires the evaluation of the second derivative of the potential in addition to the force. Here it is argued that both actions are equivalent prescriptions for the purposes of reweighting and sampling trajectories, whereas the most pr...

Transition paths, diffusive processes, and preequilibria of protein folding.

Fundamental relationships between the thermodynamics and kinetics of protein folding were investigated using chain models of natural proteins with diverse folding rates by extensive comparisons between the distribution of conformations in thermodynamic equilibrium and the distribution of conformations sampled along folding trajectories. Consistent with theory and single-molecule experiment, dur...

Structure-guided Protein Transition Modeling with a Probabilistic Roadmap Algorithm.

Proteins are macromolecules in perpetual motion, switching between structural states to modulate their function. A detailed characterization of the precise yet complex relationship between protein structure, dynamics, and function requires elucidating transitions between functionally-relevant states. Doing so challenges both wet and dry laboratories, as protein dynamics involves disparate tempo...

Efficient transition path sampling: Application to Lennard-Jones cluster rearrangements

We develop an efficient Monte-Carlo algorithm to sample an ensemble of stochastic transition paths between stable states. In our description, paths are represented by chains of states linked by Markovian transition probabilities. Rate constants and mechanisms characterizing the transition may be determined from the path ensemble. We have previously devised several algorithms for sampling the pa...