Time Integrators for Molecular Dynamics

Robust and efficient configurational molecular sampling via Langevin dynamics

(2013) Benedict Leimkuhler et al.   JOURNAL OF CHEMICAL PHYSICS

Strong convergence of an explicit numerical method for SDEs with nonglobally Lipschitz continuous coefficients

(2012) Martin Hutzenthaler et al.   ANNALS OF APPLIED PROBABILITY

Diffusion limits of the random walk Metropolis algorithm in high dimensions

(2012) Jonathan C. Mattingly et al.   ANNALS OF APPLIED PROBABILITY

Biomolecular Simulation: A Computational Microscope for Molecular Biology

(2012) Ron O. Dror et al.   Annual Review of Biophysics

To milliseconds and beyond: challenges in the simulation of protein folding

(2012) Thomas J Lane et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Stochastic ordinary differential equations in applied and computational mathematics

(2011) D. J. Higham   IMA JOURNAL OF APPLIED MATHEMATICS

A patch that imparts unconditional stability to explicit integrators for Langevin-like equations

(2011) Nawaf Bou-Rabee et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Strong and weak divergence in finite time of Euler's method for stochastic differential equations with non-globally Lipschitz continuous coefficients

(2010) M. Hutzenthaler et al.   PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Long-Run Accuracy of Variational Integrators in the Stochastic Context

(2010) Nawaf Bou-Rabee et al.   SIAM JOURNAL ON NUMERICAL ANALYSIS

Optimal scalings for local Metropolis–Hastings chains on nonproduct targets in high dimensions

(2009) Alexandros Beskos et al.   ANNALS OF APPLIED PROBABILITY

A Metropolis adjusted Nosé-Hoover thermostat

(2009) Benedict Leimkuhler et al.   ESAIM-MATHEMATICAL MODELLING AND NUMERICAL ANALYSIS-MODELISATION MATHEMATIQUE ET ANALYSE NUMERIQUE

Markovian milestoning with Voronoi tessellations

(2009) Eric Vanden-Eijnden et al.   JOURNAL OF CHEMICAL PHYSICS

Exact rate calculations by trajectory parallelization and tilting

(2009) Eric Vanden-Eijnden et al.   JOURNAL OF CHEMICAL PHYSICS

A Gentle Stochastic Thermostat for Molecular Dynamics

(2009) Ben Leimkuhler et al.   JOURNAL OF STATISTICAL PHYSICS

Transition-Path Theory and Path-Finding Algorithms for the Study of Rare Events

(2008) Weinan E et al.   Annual Review of Physical Chemistry

Ten-Microsecond Molecular Dynamics Simulation of a Fast-Folding WW Domain

(2008) Peter L. Freddolino et al.   BIOPHYSICAL JOURNAL

Multiscale methods for macromolecular simulations

(2008) Paul Sherwood et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Molecular simulation as an aid to experimentalists

(2008) Wilfred F van Gunsteren et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

GSHMC: An efficient method for molecular simulation

(2008) Elena Akhmatskaya et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Calculating effective diffusivities in the limit of vanishing molecular diffusion

(2008) G.A. Pavliotis et al.   JOURNAL OF COMPUTATIONAL PHYSICS

A comparison of generalized hybrid Monte Carlo methods with and without momentum flip

(2008) Elena Akhmatskaya et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Coarse-grained models of protein folding: toy models or predictive tools?

(2007) Cecilia Clementi   CURRENT OPINION IN STRUCTURAL BIOLOGY