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).
- 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
01/11/2022
A warm welcome to our new group assistant Mr Moritz Wiegand!
30/10/2022
Congratulations to Nia Verdon who has submitted her PhD thesis!
15/10/2022
We are advertising an experimental postdoc position on biophysics of microbial aggregation in the context of the human gut microbiome. Please publicise it! Deadline is 22nd November.
01/10/2022
Check out our student Patrick Sinclair's paper in Physical Review Letters presenting a model for stochastic initiation of bacterial biofilms - and a commentary on it in Nature Reviews Physics.
30/09/2022
Congratulations to Patrick Sinclair who has successfully defended his PhD thesis!