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)

 

Stability of β-lactam antibiotics in bacterial growth media

 

Phenotypic delay: Mechanistic models and their implications for the evolution of resistance to antibiotics

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)

 

 

 

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)

 

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 117 (16) 8719-8726 (2020)

 

Growth-dependent drug susceptibility can prevent or enhance spatial expansion of a bacterial population

P. Sinclair, M. Carballo Pacheco* and R. J. Allen*

Physical Biology 16, 046001 (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)

 

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)

 

Bacterial growth: a statistical physicist's guide

R. J. Allen and B. Waclaw

Reports on Progress in Physics  82, 016601 (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)

 

Assembly of microbial communities in replicate nutrient-cycling model ecosystems follows divergent trajectories, leading to alternate stable states

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)

 

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

  

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)

 

Calcium sensitive fluorescent dyes Fluo-4 and Fura Red under pressure: investigation of fluorescence and buffer properties under hydrostatic pressures up to 200 MPa

D. Schneidereit, H. Vass, R. J. Allen and O. Friedrich PLoS One 11, e0164509 (2016)

 

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)

 

Challenges in microbial ecology: building predictive understanding of community function and dynamics

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.

 

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)

 

Competition for space during bacterial colonisation of a surface

D. P. Lloyd and R. J. Allen 

J. R. Soc. Interface 12, 20150608 (2015)

 

Redox regime shifts in microbially-mediated biogeochemical cycles

T. Bush, T. B. Butler, A. Free and R. J. Allen 

Biogeosciences 12, 3717-3724 (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).

 

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).

 

The role of mechanical forces in the planar-to-bulk transition in growing Escherichia coli microcolonies

M. A. A. Grant, B. Waclaw, R. J. Allen and P. Cicuta 

J. R. Soc. Interface 11, 20140400 (2014)

 

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)

 

Malliavin Weight Sampling: a Practical Guide

P. B. Warren and R. J. Allen 

Entropy 16, 221-232 (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).

 

Osmosis with active solutes

T. W. Lion and R. J. Allen 

Europhysics Letters 106, 34003 (2014)

 

Parasites on parasites: coupled fluctuations in stacked contact processes

S. J. Court, R. A. Blythe and R. J. Allen 

Europhys. Lett. 101, 50001 (2013)

 

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)

 

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).

 

Genes required for growth at high hydrostatic pressure in Escherichia coli K-12 identified by genome-wide screening

S. L. Black, A. Dawson, F. B. Ward and R. J. Allen 

PLoS One 8, e73995 (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)

 

Automatic, optimal interface placement in forward flux sampling simulations

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

J. Chem. Phys. 138, 164112 (2013).

 

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)

 

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).

 

Malliavin weight sampling for computing sensitivity coefficients in Brownian dynamics simulations

P. B. Warren and R. J. Allen 

Phys. Rev. Lett. 109, 250601 (2012).

 

Computing the local pressure in molecular dynamics simulations

T. W. Lion and R. J. Allen 

J. Phys. Condensed Matter 24, 284133 (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).

 

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)

 

Oscillating microbial dynamics driven by small populations, limited nutrient supply and high death rates

B. S. Khatri, A. Free and R. J. Allen 

J. Theor. Biol. 314, 120-129 (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)

 

Non-equilibrium dynamics of an active colloidal "chucker"

C. Valeriani, R. J. Allen* and D. Marenduzzo* 

J. Chem. Phys. 132, 204904 (2010) (*=equal contribution).

 

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).

 

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)

 

Modelling bacteriophage

R. Allen 

Microbiology Today, February 2010.

 

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)

 

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).

 

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

 

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)

 

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

 

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

 

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).

 

Electrostatic interactions of charges and dipoles near a polarizable membrane.

R. Allen and J.-P. Hansen. 

Mol. Phys. 101, 1575 (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

 

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).

 

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).

 

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