Physics of Living Matter

We use experiments, computer simulations, and theoretical calculations to understand how physical laws affect living organisms.

Overview

Our research in this area spans many length and time scales: from aqueous solutions of small bioactive molecules through proteins and DNA to single cells, cell-cell interactions, and collection of organisms in ecosystems, studying phenomena occurring at picoseconds to millions of years. Many experiments use optical techniques made available through COSMIC. In our wet labs (biological hazard containment level 1 and 2) we routinely work with bacteria such as E. coli, B. subtilis, and P. aeruginosa, as well as extremophile microbes that can survive at extremes of temperature, or pressure and can even eat rocks! We also use microfluidics and plate readers for high-throughput experiments, and neutron scattering for subcellular-resolution experiments.

Among the powerful resources accessed by our computer simulators and theorists is the computer cluster Eddie hosted by The Edinburgh Compute and Data Facility ECDF as well as the supercomputer ARCHER, and BlueGene-Q hosted by the Edinburgh Parallel Computing Centre (EPCC).

Much of the research is closely tied to our programme on soft matter and statistical physics and complexity. Funding comes from EPSRCBBSRCDTIScottish Enterprise, Wellcome Trust, The Royal Society, and the Royal Society of Edinburgh.

Physics of Living Matter forms part of the Scottish Universities Physics Alliance (SUPA) Physics and Life Sciences (PaLS) theme. The SUPA Graduate School offers annual Prize Studentships for PhD study (the typical deadline is end of January for entry in September).

Research interests

Protein self-assembly

All life is made of proteins - long chains of polymerized aminoacids which fold into complicated 3d structures with various shapes and functions. In order to function properly, a protein must fold into an appropriate configuration, otherwise it will not function properly and may result ina disease. Alzheimer's disease, Parkinson's disease are just two examples of what happens when a protein folds incorrectly. We use experiments and molecular dynamics simulations to investigate this self-assembly process of proteins. We are particularly interested in how this process can be affected by environmental factors. Besides proteins implicated in human diseases we investigate bacterial proteins which enable microbes to form "coats" protecting them from external stresses such as antibiotics.

DNA folding and transcription regulation

Simulations of the folding of the alpha globin locus in the mouse chromosome

DNA is arguably one of the most important biopolymers, as its sequence encodes the genetic instructions needed in the development and functioning of living organisms. Within human nuclei, DNA is organised into chromatin, a fiber made up by histone proteins around which the DNA wraps essentially due to electrostatic interactions. Little is known either about the higher order structure of chromatin in the cell, or even how it self-assembles dynamically within the nucleus or even in the test tube.

Within ICMCS, we model DNA, chromatin and chromosomes at different levels of detail. Current projects involve modelling at different levels of resolution of chromosomes, or fractions thereof, in yeast, Drosophila (the fruit fly), and human. Finally, we plan to study the dynamics of such structures, and how the structures change when the genes are transcriptionally active or inactive.

Protein films & shells

Viruses have unique mechanical properties: they have to be strong enough to withstand the stresses involved in reaching their target in a host but fragile enough that disassembly and release of genetic material can be triggered by physicochemical stimulli on reaching the target. We are investigating the physical principles behind these mechanical properties using a combination of neutron spin echo spectroscopy. We also use our armoury of neutron & x-ray techniques to investigate the assembly of protein & peptide films at fluid interfaces.

Cell membranes

Simon Titmuss compressing a self-assembed peptide film on a Langmuir trough mounted on the OFFSPEC reflectometer at ISIS.

Bacterial resistance to antibiotics has in 2013 been placed on the National Risk Register and we use neutron & x-ray reflectivity to identify unifying physical principles in the way in which peptides involved in controlling bacterial growth and cell division interact with bacterial membranes and how this is modulated by the cell's metabolic state via membrane potential. The molecular-scale experimental information is nicely complemented by coarse-grained molecular dynamics simulations.

Cellular motility

Many cells are motile: unicellular organisms move around searching for food or evading toxic chemicals and predators, whereas eukaryotic (animal) cells such as the sperm or macrophages (white blood cells) search for the egg or invading microbes. We are interested how cytoskeleton dynamics (animal cells) or the rotation of the flagella (bacteria) is translated into the motion of the cell. This process involves physical interactions (hydrodynamics, adhesion) between the cell and its environment. We therefore investigate bacterial and sperm motility in different media using differential dynamic microscopy (DDM). We also develop theoretical and computer models of cellular motility.

We also use motile bacteria and algae as model 'active colloids' to study the physics of systems of self propelled particles. Current statistical mechanics offers no general recipe for determining the collective behaviour of such 'active matter', and experiments using well defined suspensions of motile microorganisms constitute a good source of data to guide theory development. 

Bacterial colonies and biofilms

Microcolony of E. coli. Colours represent different orientations of cells.
Microcolony of E. coli. Colours represent different orientations of cells

Bacteria often attach to surfaces and form colonies and biofilms. Surface-growing microbes are important in medicine (tooth plaque, infected catheters or implants) and industry (growth on food or in water distribution systems). Colonies of rod-shaped bacteria can also be viewed as the active nematics - an interesting counterpart to nematic liquid crystals. We are interested in how physical properties of bacterial cells and their environment affect how such colonies grow. We use experiments (microscopy) and computer simulations to address a variety of questions: what determined the shape of colonies and the orientation of cells in a growing colony, how colonies form multiple layers of cells, and how these processes affect the fate of new mutant bacteria occurring spontaneously in the colony. We also use agent-based simulations to predict the structure of bacterial biofilms under a variety of environmental conditions.

Microbial growth and evolution

Microbes (micro-size unicellular organisms such as bacteria) are able to grow in a wide range of conditions and utilize many different nutrients. Microbes can also grow in the presence of harmful chemicals such as antibiotics. We are interested in how physics and chemistry limit these capabilities. In particular, we investigate how bacteria respond and evolve resistance to antibiotics. In our research we use a combination of macro- and microfluidics experiments, computer simulations, and analytical calculations.

Life in Extreme Environments

All environments subject organisms to various combinations of physical and chemical stressors. We are interested in how life adapts to extreme conditions, for example in the deep subsurface or in newly available habitats, and how it copes with multiple extremes and energy limitation in such places. This work is primarily laboratory based as well as using environmental microbiology and modelling. Our work also involves studying what determines microbial community structure in extreme environments. This work has applications to understanding the limits of life on Earth and assessing the habitability of extreme environments on Earth and potentially elsewhere. For more details see UK Centre for Astrobiology.

Statistical-physics models of living systems

Simple cultural evolutionary model where linguistic behaviour is replicated and transmitted between agents
Simple cultural evolutionary model where linguistic behaviour is replicated and transmitted between agents

We use techniques borrowed from equlibrium and non-equilibrium statistical mechanics to study how complex systems of living organisms evolve in time and space. Among the systems we study are simple models of cultural evolution, the evolution of language, Darwinian evolution of spatially heterogeneous populations. See Statistical Physics and Complexity for more details.

Techniques

Below is a list of some of the techniques we use in our research:

  • Optical microscopy: brightfield, fluorescence, confocal
  • Neutron scattering and reflectivity
  • Molecular/Brownian dynamics/agent-based simulations
  • Mathematical modelling: ordinary and partial differential equations, stochastic models

PhD project opportunities in Physics of Living Matter

People in Physics of Living Matter

Academic staff
Name Position Contact details Location Photo
Graeme Ackland Professor 0131 650 5299
JCMB
2502
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Rosalind Allen Lecturer 0131 651 7197
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2507
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Richard Blythe Reader 0131 650 5105
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Charles Cockell Professor of Astrobiology 0131 650 2961
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1502
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Martin Evans Professor of Statistical Physics 0131 650 5294
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2615
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Cait MacPhee Professor 0131 650 5291
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Davide Marenduzzo Personal Chair in Computational Biophysics 0131 650 5289
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Alexander Morozov Reader 0131 650 5882
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Wilson Poon Professor 0131 650 5297
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Simon Titmuss Lecturer 0131 650 5267
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Bartlomiej Waclaw RSE Research Fellow 0131 651 7688
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Research staff
Name Position Contact details Location Photo
Jochen Arlt Research Fellow 0131 650 5121
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Matthew Blow PDRA 0131 650 5175
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1506
Chris Brackley PDRA 0131 650 8617
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Aidan Brown PDRA 0131 651 3456
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Steven Court Postdoctoral Research Assistant 0131 650 8603
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Angela Dawson PDRA 0131 650 7165
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Niccolo De Francesco Research Assistant
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Joe Forth PDRA
N/A
Steven Gardner Postdoctoral Research Associate 0131 651 7771
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Alys Jepson PDRA 0131 651 7742
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Nick Koumakis PDRA 0131 650 5883
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Thomas Le Goff Postdoctoral Research Associate 0131 651 3455
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Benno Liebchen PDRA 0131 650 5175
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Diarmuid Lloyd PDRA 0131 651 7742
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Vincent Martinez PDRA 0131 650 8617
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Gavin Melaugh PDRA 0131 651 3456
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Davide Michieletto PDRA 0131 651 7742
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Marieke Schor PDRA 0131 650 7165
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Jana Schwarz-Linek PDRA 0131 650 8617
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Petra Schwendner PDRA
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Teun Vissers Marie Curie Fellow 0131 650 5883
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Tiffany Wood Industrial Research Liaison 0131 651 7687
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Other staff
Name Position Contact details Location Photo
Siobhan Liddle Tutor 0131 650 6799
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Research postgraduates
Name Position Contact details Location Photo
Giovanni Brandani Postgraduate Student 0131 650 6799
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Rebecca Brouwers Postgraduate Student
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Timothy Bush Postgraduate Student 0131 650 6799
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2509
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Giulio De Magistris Postgraduate Student 0131 650 8603
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2501
Milana Filatenkova Postgraduate Student 0131 650 6799
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2510
Martina Foglino Early Stage Researcher
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1510
Mark Fox-Powell Postgraduate Student 0131 651 7774
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Jay Gillam Postgraduate Student
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Tom Ives Postgraduate Student 0131 650 8603
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Hanna Landenmark Postgraduate Student 0131 651 7176
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Tao Li Postgraduate Student 0131 650 6799
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Benjamin Little Postgraduate Student 0131 650 5263
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Ioan Magdau Postgraduate Student 0131 650 6799
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Iva Manasi Postgraduate Student 0131 651 7176
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Vincent Margerin Postgraduate Student 0131 650 5284
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Laura McKinley Postgraduate Student 0131 650 6799
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Alexander McVey Postgraduate Student 0131 651 3454
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Ryan Morris Postgraduate Student 0131 650 6799
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Francois Mouvet Visitor
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Jakub Pastuszak Postgraduate Student 0131 650 6799
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Chay Paterson Postgraduate Student 0131 650 8603
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Toby Samuels Postgraduate Student 0131 651 7774
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Alexander Slowman Postgraduate Student 0131 650 8603
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2501
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Daniel Taylor Postgraduate Student
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2510
Stuart Thomson Postgraduate Student 0131 651 7176
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Joshua Williams Postgraduate Student 0131 651 7176
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Xuemao Zhou Postgraduate Student 0131 651 7176
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2510
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