Allen group website - Former group members

Former group members

S. Lucas Black defended his PhD thesis in 2011. Lucas was jointly supervised by Rosalind and Dr. Bruce Ward. His work focused on the response of the enteric bacterium Escherichia coli and the marine bacterium Photobacterium profundum to hydrostatic and osmotic pressure. He also helped develop high resolution microscope pressure cells, together with Hugh Vass.

Rebecca Brouwers finished her PhD with Rosalind in 2019 and worked as a postdoc on our UKRI-funded project in 2019-20, with collaborators in Sheffield, Cambridge and Newcastle, to understand the biophysics of bacteria that are resistant to cell-wall targeting antibiotics. Rebecca's PhD work investigated the response of E. coli bacteria to cell wall-targeting antibiotics.

Timothy Bush finished his PhD with Rosalind in June 2015. In his PhD he used both theory and experiments to study the dynamics of microbial ecosystems, in particular oxic-anoxic transitions which can occur as a function of the environmental conditions. After his PhD Tim worked with Rosalind and Andrew Free as a postdoc and also worked as a postdoc at the University of Amsterdam with Gerard Muijzer and Jef Huisman.

Martin Carballo Pacheco worked as a postdoc with Rosalind and Bartek Waclaw, funded by our ERC grant, from 2016 to 2019. He used theory and simulations to understand how bacteria evolve resistance to antibiotics. Following a postdoc at Columbia University Martin returned to the UK where he is now a Computational Biologist at Hoxton Farms.

Luca Ciandrini was a SULSA-funded PhD student jointly supervised by Mamen Romano and Ian Stansfield in Aberdeen and by Rosalind. He defended his thesis in 2013. During his PhD, Luca used TASEP models to describe protein production in yeast, developing a new mean-field theory to predict the behaviour of multiple TASEPS coupled to a single reservoir, mimicking the intracellular competition of mRNAs for ribosomes. Luca now runs his own group at the University of Montpellier.

Steven Court defended his PhD in 2014. He worked with Rosalind and Richard Blythe on a “stacked contact process” statistical physics model for the spatial transmission of horizontally-transmitted traits. He also worked with Rosalind and Bartek Waclaw, using a computer algorithm to exhaustively search the biochemically allowed space of metabolic pathways. In this work, he discovered many alternative pathways to glycolysis, which is one of the most important and ancient processes in biology. This work sheds new light on how metabolic pathways might have evolved.

Tine Curk worked as a postdoc jointly between Edinburgh University and the Institute of Physics of the Chinese Academy of Sciences in Beijing, from 2017-2018. He was doing simulations to investigate possible methods for detecting bacterial infections, funded by a Royal Society GCRF Challenge grant. Tine is now a postdoc at Northwestern University.

Susana Direito is an impact acceleration associate (IAA) at the Edinburgh Complex Fluids Partnership and an NBIC research fellow. She works on establishing links with industrial partners and specialises in projects involving biofilms and bacterial sterilisation. Susana worked as a postdoc on our ERC project for a while but now conducts her own independent research. She is co-supervisor of Laura Confalonieri's and Ofelia Popescu's PhDs. She is also part of the outreach programme for our UKRI-funded project on the Physics of AMR.

Kym Eden defended his PhD in 2013. He worked with Cait MacPhee and Rosalind, using simulations to model the growth of amyloid fibrils. His work revealed new mechanisms for how insulin fibrils assemble, and also for what happens in the very early stages of fibril formation.

Philip Greulich was a DAAD fellow working with Rosalind and Martin Evans from 2010-2012. He used TASEP models to understand gene expression, in collaboration with Luca Ciandrini, Mamen Romano and Rosalind. He also collaborated with Rosalind and Bartek Waclaw on models for evolution in drug gradients (you can read about this in our PRL 2012 paper), and worked together with Rosalind, Martin Evans and Matt Scott on models for the effects of ribosome-targeting antibiotics on bacterial physiology. Philip now has his own group at the University of Southampton.

Darshana Joshi worked as a postdoc jointly with Rosalind and Erika Eiser in Cambridge, in 2017-18. She did experiments to investigate possible ways of detecting bacterial infections, funded by a Royal Society GCRF Challenge grant.

Line Jourdain worked with Rosalind and Cait MacPhee as a postdoc in 2006-2008, doing experiments and simulations on amyloid fibril nucleation.

Bhavin Khatri worked with Rosalind and Andrew Free as a postdoc, funded by the Leverhulme Trust and by EPSRC, constructing theoretical models for microbial ecosystems and developing a new method to analyse experimental DGGE data. Bhavin is now a research fellow in statistical genomics at Imperial College London.

Elin Lilja worked as a postdoc with Rosalind and Bartek Waclaw, funded by our ERC grant, from 2016 - 2020. She used evolution experiments to study how bacteria become resistant to antibiotics. Elin is now a postdoc with Bartek Waclaw at the Dioscuri Centre for Physics and Chemistry of Bacteria in Warsaw.

Juho Lintuvuori worked as a postdoc working with Rosalind, Kevin Stratford and Davide Marenduzzo, in 2011-2013, funded by our EPSRC grant "Rare event simulations via parallel forward flux sampling". He developed a software framework to allow the use of forward flux sampling with generic codes. Juho is now a CNRS researcher at the University of Bordeaux.

Tom Lion completed his PhD with Rosalind in 2013. He used Molecular Dynamics simulations to understand the physics behind osmotic pressure. In particular he simulated a model in which solute and solvent particles have identical short-ranged interaction potentials and the semi-permeable membrane is invisible to the solvent. This model seems simple but isn't! Tom also discovered that interesting physics can happen when the solutes are active particles such as swimming bacteria or Janus particles.

Diarmuid Lloyd did a PhD with Rosalind, finishing in 2014, and after that was a postdoc with Bartek Waclaw and Wilson Poon for 2 years, and also collaborated with our group. He was using microscopy experiments to understand how bacteria self-assemble when they are grown on soft agar surfaces.

Gavin Melaugh is a postdoc who worked on our HFSP collaboration (2012-6) on how spatial structure develops in microbial biofilms, and later on our EPSRC programme grant "design principles of soft materials", and on our ERC grant. Gavin uses computer simulations and experiments to understand the physics of bacterial aggregation and biofilm formation. Since 2018 he has transferred to the National Biofilms Innovation Centre research programme, led in Edinburgh by Professor Cait MacPhee, but he continues to be closely involved in the work of our group. In 2021 Gavin is setting up his own group as a Chancellor's Fellow at Edinburgh University.

Catherine Mills completed her PhD with Richard Blythe and Rosalind in May 2016. She developed models for species diversity in microbial systems, and in ecosystems more generally. Her work especially focused on the factors affecting the balance between specialist and generalist species. She later did a postdoc in Ecology at Monash University in Australia.

Nikola Ojkic worked as a postdoc with Rosalind and Bartek Waclaw from 2016-18, funded by our ERC grant. He investigated how antibiotics inhibit bacterial growth and how resistance evolves, using theoretical and computational approaches. Nikola went on to do a further postdoc with Shiladitya Banerjee at University College London.

Eulyn Pagaling is an environmental microbiologist who worked as a postdoc with Andrew Free and Rosalind, funded by the Leverhulme Trust and by EPSRC, in 2009-2012. She used advanced DNA-based techniques to study how microbial communities assemble, based on a model system of microcosms made from freshwater pond sediment and water.

Patrick Sinclair was a PhD student funded by the EPSRC National Productivity Investment Fund. His project was co-supervised by Chris Brackley and is in collaboration with Akzo Nobel, with our former postdoc Martin Carballo Pacheco and with Professor Nick Cogan at Florida State University. Patrick used computer simulations to understand how bacteria grow in gradients of antimicrobials, including close to surfaces coated with antifouling paint. He also developed a new theoretical model for stochastic initiation of bacterial biofilms. Patrick is now doing a postdoc at Glasgow University, modelling viral epidemics.

Joakim Stenhammar was a postdoc funded by a fellowship from the Swedish research council. He worked with Mike Cates, Davide Marenduzzo and Rosalind on simulations and theory for active Brownian particles, from 2012-2015. Joachim now has his own group at the University of Lund in Sweden.

Juraj Szavitz-Nossan was a postdoc funded by our group's EPSRC programme grant from 2013-2016. He worked with Martin Evans, Cait MacPhee and Rosalind on solving theoretical models to describe amyloid fibril formation kinetics. Juraj went on to be awarded independent Leverhulme Early Career Fellowship at the School of Physics in Edinburgh to work on TASEP models for protein production. He is now extending his work to model also RNA transcription.

Dan Taylor was a PhD student working with Simon Titmuss and Rosalind as part of the SOFI CDT. He used microfluidics experiments, as well as computer simulations, to investigate how bacteria grow in small fluid droplets. His work was in collaboration with Patrick Warren at Unilever. Dan submitted his thesis in March 2019.

Chantal Valeriani was a Marie Curie research fellow in the Edinburgh soft matter group, from 2008-2012. She collaborated with Rosalind and Davide Marenduzzo to simulate nonequilibrium colloidal "chuckers". Chantal now runs her own group at the Universidad Complutense de Madrid.

Juan Venegas-Ortiz completed his PhD in 2013, working with Martin Evans and Rosalind. He used theory and simulations to understand the dynamics of expanding microbial populations which undergo evolution by horizontal gene transfer. His work revealed that “coupled Fisher waves” may show different rules controlling their speed than the well-known standard Fisher wave.

Paolo Visco worked with Rosalind and Martin Evans as a postdoc, in 2006-2008, doing theoretical work and simulations on genetic switches and populations of switching cells in switching environments.

Ellen Young completed her PhD in 2020 and also worked as a postdoc in our group in 2020-21. She simulated bacterial biofilm formation, looking at how the roughness of a biofilm's surface depends on the key parameters in the system and linking this to well-known work in statistical physics on interface growth theory. Ellen was co-supervised by Rosalind and Gavin Melaugh.

Aniket Zodage was an MSc student at IISER Pune, in India. He did his MSc thesis under the supervision of myself and Martin Evans as external supervisors. Aniket is now doing a PhD at UC San Diego.