All publications
Urine production rate is critical in a model for catheter-associated urinary tract infection
F. Bull, S. Tavaddod, N. Bommer, M. Perry, C. A. Brackley and R. J. Allen
BioRxiv 10.1101/2022.10.31.514508 (2022)
Dynamic diatom-bacteria consortia in synthetic plankton communities
Y. Deng, M. Mauri, M. Vallet, M. Staudinger, R. J. Allen and G. Pohnert
Applied and Environmental Microbiology (2022)
Model for quorum-sensing mediated stochastic biofilm formation
P. Sinclair, C. A. Brackley, M. Carballo-Pacheco and R. J. Allen
Physical Review Letters (2022)
Reviewed in Nature Reviews Physics: "Fluctuating into a biofilm" by Zoe Budrikis (2022)
Lineage dynamics in growing biofilms: spatial patterns of standing vs. de novo diversity
E. Young and R. J. Allen
Frontiers in Microbiology 13 915095 (2022)
A computational model for microbial colonisation of an antifouling surface
P. Sinclair, J. Longyear, K. Reynolds, A. A. Finnie, C. A. Brackley, M. Carballo-Pacheco and R. J. Allen
Frontiers in Microbiology 13 920014 (2022)
Tracking the stochastic growth of bacterial populations in microfluidic droplets
Daniel Taylor, Nia Verdon, Peter Lomax, Rosalind J Allen and Simon Titmuss
Physical Biology 19, 026003 (2022)
Computational design of probes to detect bacterial genomes by multivalent binding
T. Curk, C. A. Brackley, J. D. Farrell, Z. Xing, D. Joshi, S. Direito, U. Bren, S. Angioletti-Uberti, J. Dobnikar, E. Eiser, D. Frenkel and R. J. Allen
Proc. Natl. Acad. Sci. USA
Staff and student perceptions of a community urinary catheter nursing service
F. Oswald, E. Young, F. Denison, R. J. Allen and M. Perry
International Journal of Urological Nursing 1-9 (2020)
Stability of β-lactam antibiotics in bacterial growth media
M. Carballo-Pacheco, M. D. Nicholson, E. Lilja, R. J. Allen and B. Waclaw
PLoS Computational Biology 16, e1007930 (2020)
Predictable properties of fitness landscapes induced by adaptational tradeoffs
S. G. Das, S. O. L. Direito, B. Waclaw, R. J. Allen and J. Krug
eLife 9, e55155 (2020)
A roadblock-and-kill model explains the action of the DNA-targeting antibiotic
ciprofloxacin
N. Ojkic, E. Lilja, S. Direito, R. J. Allen and B. Waclaw
Antimicrobial Agents and Chemotherapy 64, e02487-19 (2020)
P. Sinclair, M. Carballo Pacheco* and R. J. Allen*
Physical Biology 16, 046001 (2019)
Bacterial growth: a statistical physicist's guide
R. J. Allen and B. Waclaw
Reports on Progress in Physics 82, 016601 (2019)
Resource spectrum engineering by specialist species can shift the specialist-generalist balance
C. G. Mills, R. J. Allen* and R. A. Blythe*
Theoretical Ecology 1-15 (2019)
A simulation study of aggregation mediated by production of cohesive molecules
G. Melaugh, D. Marenduzzo, A. Morozov and R. J. Allen
Soft Matter 15, 9120 (2019)
Trajectory reweighting for non-equilibrium steady states
- P. B. Warren and R. J. Allen
Molecular Physics 116, 3103-3113 (2018)
Predicting the dynamics of bacterial growth inhibition by ribosome-targeting antibiotics
P. Greulich*, J. Dolezal*, M. Scott, M. R. Evans and R. J. Allen (* = equal contribution)
Physical Biology 14, 6 (2017). This article is part of the special issue on antimicrobial resistance co-edited by Bartek Waclaw and me.
Oxic-anoxic regime shifts induced by biogeochemical feedbacks in microbial communities
T. Bush, M. Diao, R. J. Allen, R. Sinnige, G. Muyzer and J. Huisman
Nature Communications 8, 789 (2017)
E. Pagaling, K. Vassileva, C. G. Mills, T. Bush, R. A. Blythe, J. Schwarz-Linek, F. Strathdee, R. J. Allen and A. Free
Environmental Microbiology 19: 3374–3386 (2017)
The Pseudomonas aeruginosa polysaccharide PSL is a social but non-cheatable trait in biofilms
Y. Irie, A. Roberts, K. Kragh, V. Gordon, J. Hutchison, R. Allen, G. Melaugh, T. Bjarnsholt, S. West and S. Diggle
mBio 8, e00374-17 (2017)
Antibiotic resistance: a physicist's view
R. J. Allen and B. Waclaw
Physical Biology 13 045001 (2016)
This article introduces a special issue on antimicrobial resistance co-edited by Bartek Waclaw and myself
- S. Widder, R. J. Allen et al.
ISME Journal 10, 2557-2568 (2016)
- This review article results from a 4-month programme "Understanding Microbial Communities" at the Isaac Newton Institute, Cambridge University, which I co-organised in August-December 2014.
Role of pre-formed aggregates during Pseudomonas aeruginosa biofilm development
- K. Kragh*, J. Hutchison*, G. Melaugh*, C. Rodesney, A. Roberts, Y. Irie, P. Jensen, S. Diggle, R. J. Allen**, V. D. Gordon** and T. Bjarnsholt** (*, ** = equal contribution)
mBio 7, e00237-16 (2016)
Shaping the growth behaviour of biofilms initiated from bacterial aggregates
- G. Melaugh, J. Hutchison, K. Kragh, Y. Irie, A. Roberts, T. Bjarnsholt, S. Diggle, V. Gordon and R. J. Allen
Plos One 11, e0149683 (2016)
D. Schneidereit, H. Vass, R. J. Allen and O. Friedrich PLoS One 11, e0164509 (2016)
Growth-dependent bacterial susceptibility to ribosome-targeting antibiotics
- P. Greulich*, M. Scott*, M. R. Evans and R. J. Allen
Molecular Systems Biology 11, 796 (2015) (* = equal contribution)
Lower glycolysis carries a higher flux than any biochemically possible alternative
- S. J. Court, B. Waclaw* and R. J. Allen*
Nature Communications 6, 8427 (2015) (* = equal contribution)
Redox regime shifts in microbially-mediated biogeochemical cycles
- T. Bush, T. B. Butler, A. Free and R. J. Allen
Biogeosciences 12, 3717-3724 (2015)
Competition for space during bacterial colonisation of a surface
- D. P. Lloyd and R. J. Allen
J. R. Soc. Interface 12, 20150608 (2015)
A kinetic study of ovalbumin fibril formation: the importance of fragmentation and end-joining
- J. M. D. Kalapothakis, J. Szavits-Nossan, R. J. Morris, K. Eden, S. Colvill, S. Tabor, J. Gillam, P. E. Barran, R. J. Allen and C. E. MacPhee
Biophysical Journal 108, 2300-2311 (2015)
Competition between primary nucleation and autocatalysis in amyloid fibril self-assembly
- K. Eden, R. Morris, C. E. MacPhee and R. J. Allen
Biophysical Journal 108, 632-643 (2015).
Speed of invasion of an expanding population by a horizontally-transmitted trait
- J. Venegas-Ortiz, R. J. Allen* and M. R. Evans*
Genetics 196, 497-507 (2014) (* = equal contribution)
- M. A. A. Grant, B. Waclaw, R. J. Allen and P. Cicuta
J. R. Soc. Interface 11, 20140400 (2014)
Inherent variability in the kinetics of autocatalytic protein self-assembly
- J. Szavitz-Nossan, K. Eden, R. J. Morris, C. E. MacPhee, M. R. Evans and R. J. Allen
Phys. Rev. Lett. 113, 098101 (2014).
Phase behaviour of active Brownian particles: The role of dimensionality
- J. Stenhammar, D. Marenduzzo, R. J. Allen and M. E. Cates
Soft Matter 10, 1489-1499 (2014).
Scalar phi^4 theories for active-particle phase separation
- R. Wittkowski, A. Tiribocchi, J. Stenhammar, R. J. Allen, D. Marenduzzo and M. E. Cates
Nature Communications 5, 4351 (2014).
Malliavin Weight Sampling: a Practical Guide
- P. B. Warren and R. J. Allen
Entropy 16, 221-232 (2014).
- T. W. Lion and R. J. Allen
Europhysics Letters 106, 34003 (2014)
Selection history affects the predictability of microbial ecosystem development
- E. Pagaling, F. Strathdee, B. Spears, M. E. Cates, R. J. Allen* and A. Free*
ISME J. 8, 19-30 (2013) (*=equal contribution)
Parasites on parasites: coupled fluctuations in stacked contact processes
- S. J. Court, R. A. Blythe and R. J. Allen
Europhys. Lett. 101, 50001 (2013)
Mechanistic and environmental control of the prevalence and lifetime of amyloid oligomers
- R. Morris*, K. Eden*, R. Yarwood, L. Jourdain, R. J. Allen and C. E. MacPhee
Nature Communications 4, 1891 (2013) (* = equal contribution)
A continuum theory of phase separation kinetics for active Brownian particles
- J. Stenhammar, A. Tiribocchi, R. J. Allen, D. Marenduzzo and M. E. Cates
Phys. Rev. Lett.,111, 145702 (2013)
Single-molecule imaging at high hydrostatic pressure
- H. Vass*, S. L. Black*, C. Flors, D. P. Lloyd, F. B. Ward and R. J. Allen
Applied Physics Letters 102, 154103 (2013) (* = equal contribution).
- S. L. Black, A. Dawson, F. B. Ward and R. J. Allen
PLoS One 8, e73995 (2013).
Automatic, optimal interface placement in forward flux sampling simulations
- K. Kratzer, A. Arnold and R. J. Allen
J. Chem. Phys. 138, 164112 (2013).
- B. S. Khatri, A. Free and R. J. Allen
J. Theor. Biol. 314, 120-129 (2012)
Mutational pathway determines whether drug gradients accelerate evolution of drug-resistant cells
- P. Greulich*, B. Waclaw* and R. J. Allen
Phys. Rev. Lett. 109, 088101 (2012) (*=equal contribution)
Selected as editor's choice and featured in a viewpoint article "Bacteria Evolve to Go Against the Grain" by Oskar Hallatschek, Physics 5, 93 (2012)
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)
Osmosis in a minimal model system
- T. W. Lion and R. J. Allen
J. Chem. Phys. 137, 244911 (2012).
Computing the local pressure in molecular dynamics simulations
- T. W. Lion and R. J. Allen
J. Phys. Condensed Matter 24, 284133 (2012).
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).
Effects of macromolecular crowding on genetic switches
- M. J. Morelli, R. J. Allen and P. R. ten Wolde,
Biophys. J. 101, 2882-2891 (2011)
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)
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)
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).
Non-equilibrium dynamics of an active colloidal "chucker"
- C. Valeriani, R. J. Allen* and D. Marenduzzo*
J. Chem. Phys. 132, 204904 (2010) (*=equal contribution).
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
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).
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).
- R. J. Allen, C. Valeriani, S. Tanase-Nicola, P. R. ten Wolde and D. Frenkel
J. Chem. Phys. 129, 134704 (2008)
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)
- 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
- 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
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
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).
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
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!