Publications

Microbial population dynamics, ecosystems and evolution

Interplay between mutational pathway and spatial drug distribution controls time to evolution of drug resistance
P. Greulich*, B. Waclaw* and R. J. Allen (submitted; *=equal contribution)

Noise-driven oscillations in microbial population dynamics
B. S. Khatri, A. Free and R. J. Allen (submitted)

Selection history affects the predictability of microbial ecosystem development
E. Pagaling, F. Strathdee, B. Spears, M. E. Cates, R. J. Allen* and A. Free* (submitted; *=equal contribution)

A dynamical phase transition in a model for evolution with migration
B. Waclaw, R. J. Allen and M. R. Evans Phys. Rev. Lett. 105, 268101 (2010)

Switching and growth for microbial populations in catastrophic responsive environments
P. Visco, R. J. Allen, S. Majumdar and M. R. Evans, Biophys. J. 98, 1099-1108 (2010)

Genetic switches

Effects of macromolecular crowding on genetic switches
M. J. Morelli, R. J. Allen and P. R. ten Wolde, Biophys. J. 101, 2882-2891 (2011)

DNA looping provides stability and robustness to the bacteriophage lambda switch
M. J. Morelli, P. R. ten Wolde and R. J. Allen, Proc. Natl. Acad. Sci. U. S. A. 106, 8101-8106 (2009)

Statistical physics of a model binary genetic switch with linear feedback
P. Visco, R. J. Allen and M. R. Evans, Phys. Rev. E 79, 031923 (2009)
reprinted in Virtual Journal of Biological Physics Research

Exact solution of a model DNA-inversion genetic switch with orientational control
P. Visco, R. J. Allen and M. R. Evans Phys. Rev. Lett. 101, 118104 (2008)
reprinted in Virtual Journal of Biological Physics Research

Reaction co-ordinates for the flipping of genetic switches
M. J. Morelli, S. Tanase-Nicola, R. J. Allen and P. R. ten Wolde Biophys. J. 94, 3413 (2008)

Eliminating fast reactions in stochastic simulations of biochemical networks: a bistable genetic switch
M. J. Morelli, R. J. Allen, S. Tanase-Nicola and P. R. ten Wolde J. Chem. Phys. 128, 045105 (2008).
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

Hydrostatic pressure

Computing the local pressure in molecular dynamics simulations
T. W. Lion and R. J. Allen (submitted).

A multi-purpose modular system for high-resolution microscopy at high hydrostatic pressure
H. Vass, S. L. Black, E. M. Herzig, F. B. Ward, P. S. Clegg and R. J. Allen Review of Scientific Instruments 81, 053710 (2010).

Simulation methods

Steady-state parameter sensitivity in stochastic modeling via trajectory reweighting
P. B. Warren and R. J. Allen, Journal of Chemical Physics 136, 104106 (2012).

Non-stationary forward flux sampling
N. Becker, R. J. Allen and P. R. ten Wolde, Journal of Chemical Physics 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

Soft matter and statistical physics

A mixed population of competing TASEPs with a shared reservoir of particles
P. Greulich^, L. Ciandrini^, R. J. Allen* and M. C. Romano* Phys. Rev. E 85, 011142 (2012) (* and ^=equal contribution)

Non-equilibrium dynamics of an active colloidal "chucker"
C. Valeriani, R. J. Allen* and D. Marenduzzo* J. Chem. Phys. 132, 204904 (2010) (*=equal contribution).

Nucleation in a sheared two-dimensional Ising model: effects of external field (Conference Proceeding)
R. J. Allen, C. Valeriani and S. Tanase-Nicola, Progress of Theoretical Physics Supplement 175, 144 (2008).

Homogeneous nucleation under shear in a two-dimensional Ising model: cluster growth, coalescence and breakup
R. J. Allen, C. Valeriani, S. Tanase-Nicola, P. R. ten Wolde and D. Frenkel J. Chem. Phys. 129, 134704 (2008)

Complexation and phase behavior of oppositely charged polyelectrolyte/macroion systems
R. J. Allen and P. B. Warren, Langmuir 20, 1997 (2004).

Phase behaviour of oppositely charged polymer/surfactant mixtures
R. J. Allen and P. B. Warren, Europhys. Lett. 64, 468 (2003).

C12E2 reverse micelle: A molecular dynamics study.
R. Allen, S. Bandyopadhyay and M. L. Klein Langmuir 16, 10547 (2000).

Sedimentation equilibria of colloidal hard rod dispersions.
R. Allen, D. Goulding and J.-P. Hansen. PhysChemComm 2, 30 (1999).

Ion channels and pores

Kinetic models of ion transport through a nanopore,
J. Piasecki, R. J. Allen and J.-P. Hansen, Phys. Rev. E 70, 021105 (2004).
reprinted in Virtual Journal of Biological Physics Research and Virtual Journal of Nanoscale Science & Technology

Electric field-controlled water permeation coupled to ion transport through a nanopore
J. Dzubiella, R. J. Allen and J.-P. Hansen, J. Chem. Phys. 120, 5001 (2004).
reprinted in Virtual Journal of Biological Physics Research

A Molecular Dynamics investigation of water permeation through nanopores.
R. Allen, J.-P. Hansen and S. Melchionna, J. Chem. Phys. 119, 3905 (2003).
reprinted in Virtual Journal of Biological Physics Research and Virtual Journal of Nanoscale Science & Technology

Permeation of nanopores by water: the effects of channel polarization. (Conference Proceeding)
R. Allen, S. Melchionna and J.-P. Hansen. J. Phys. Condensed Matter 15, S297 (2003).

Intermittent permeation of cylindrical nanopores by water.
R. Allen, S. Melchionna and J.-P. Hansen Phys. Rev. Lett. 89, 175502 (2002).
reprinted in Virtual Journal of Biological Physics Research and Virtual Journal of Nanoscale Science & Technology

Electrostatics

Electrostatic interactions of charges and dipoles near a polarizable membrane.
R. Allen and J.-P. Hansen. Mol. Phys. 101, 1575 (2003).

Density functional approach to the effective interaction between charges within dielectric cavities.
R. Allen and J.-P. Hansen. J. Phys. Condensed Matter 14, 11981 (2002).

Electrostatic potential inside ionic solutions confined by dielectrics: a variational approach.
R. Allen, J.-P. Hansen and S. Melchionna. Phys. Chem. Chem. Phys. 3, 4177 (2001).

Non-refereed publications

Modelling bacteriophage
R. Allen Microbiology Today February 2010.