Simulation methods

Trajectory reweighting for non-equilibrium steady states

P. B. Warren and R. J. Allen

Molecular Physics 116, 3103-3113 (2018)

Malliavin Weight Sampling: a Practical Guide

P. B. Warren and R. J. Allen 

Entropy 16, 221-232 (2014).

Automatic, optimal interface placement in forward flux sampling simulations

K. Kratzer, A. Arnold and R. J. Allen 

J. Chem. Phys. 138, 164112 (2013).

Malliavin weight sampling for computing sensitivity coefficients in Brownian dynamics simulations

P. B. Warren and R. J. Allen 

Phys. Rev. Lett. 109, 250601 (2012).

Steady-state parameter sensitivity in stochastic modeling via trajectory reweighting

P. B. Warren and R. J. Allen, 

J. Chem. Phys. 136, 104106 (2012).

Non-stationary forward flux sampling

N. Becker, R. J. Allen and P. R. ten Wolde, 

J. Chem. Phys. 136, 174118 (2012).

Forward Flux Sampling for rare event simulations

R. J. Allen, C. Valeriani and P. R. ten Wolde, Topical Review, 

Journal of Physics Condensed Matter 21, 463102 (2009).

Computing stationary distributions in equilibrium and non-equilibrium systems with Forward Flux Sampling

C. Valeriani, R. J. Allen, M. J. Morelli, D. Frenkel and P. R. ten Wolde, 

J. Chem. Phys. 127, 114109 (2007).

reprinted in 

Virtual Journal of Biological Physics Research

Forward flux sampling-type schemes for simulating rare events: Efficiency analysis

R. J. Allen, D. Frenkel and P. R. ten Wolde, 

J. Chem. Phys. 124, 194111 (2006).

Simulating rare events in equilibrium or nonequilibrium stochastic simulations

R. J. Allen, D. Frenkel and P. R. ten Wolde, 

J. Chem. Phys. 124, 024102 (2006).

reprinted in 

Virtual Journal of Biological Physics Research

Sampling rare switching events in biochemical networks

R. J. Allen, P. B. Warren and P. R. ten Wolde, 

Phys. Rev. Lett. 94, 018104 (2005).

reprinted in 

Virtual Journal of Biological Physics Research