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- University of California, BerkeleyUS33 papers
- Lawrence Berkeley National LaboratoryUS11 papers
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- Biologie Computationnelle, Quantitative et SynthétiqueFR3 papers
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5 papers · 1 filter
Using nonequilibrium fluctuation theorems to understand and correct errors in equilibrium and nonequilibrium discrete Langevin dynamics simulations
David A. Sivak, John D. Chodera, Gavin E. Crooks
Common algorithms for computationally simulating Langevin dynamics must discretize the stochastic differential equations of motion. These resulting finite time step integrators nec…
RNA structure characterization from chemical mapping experiments
Sharon Aviran, Julius B. Lucks, Lior Pachter
Despite great interest in solving RNA secondary structures due to their impact on function, it remains an open problem to determine structure from sequence. Among experimental appr…
Replica exchange and expanded ensemble simulations as Gibbs sampling: Simple improvements for enhanced mixing
John D. Chodera, Michael R. Shirts
The widespread popularity of replica exchange and expanded ensemble algorithms for simulating complex molecular systems in chemistry and biophysics has generated much interest in e…
Nonequilibrium candidate Monte Carlo: A new tool for efficient equilibrium simulation
Jerome P. Nilmeier, Gavin E. Crooks, David D. L. Minh +1
Metropolis Monte Carlo simulation is a powerful tool for studying the equilibrium properties of matter. In complex condensed-phase systems, however, it is difficult to design Monte…
Splitting probabilities as a test of reaction coordinate choice in single-molecule experiments
John D. Chodera, Vijay S. Pande
To explain the observed dynamics in equilibrium single-molecule measurements of biomolecules, the experimental observable is often chosen as a putative reaction coordinate along wh…