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

NamePositionContact detailsLocationPhoto
Academic staff
Graeme AcklandProfessor
JCMB
2502
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Rosalind AllenLecturer
JCMB
2507
Photo of Rosalind Allen
Richard BlytheReader
JCMB
2505
Photo of Richard Blythe
Aidan BrownChancellor's Fellow
JCMB
2610
Photo of Aidan Brown
Charles CockellProfessor of Astrobiology
JCMB
1502
Photo of Charles Cockell
Martin EvansProfessor of Statistical Physics
JCMB
2615
Photo of Martin Evans
Cait MacPheeProfessor
JCMB
2613
Photo of Cait MacPhee
Davide MarenduzzoPersonal Chair in Computational Biophysics
JCMB
2506
Photo of Davide Marenduzzo
Alexander MorozovReader
JCMB
2616
Photo of Alexander Morozov
Wilson PoonProfessor
JCMB
2620
Photo of Wilson Poon
Simon TitmussLecturer
JCMB
2504
Photo of Simon Titmuss
Bartlomiej WaclawRSE Research Fellow
JCMB
2503
Photo of Bartlomiej Waclaw
Research staff
Jochen ArltResearch Fellow
JCMB
2601
Photo of Jochen Arlt
Matthew BlowPDRA
JCMB
1506
Chris BrackleyPDRA
JCMB
2609
Photo of Chris Brackley
Angela DawsonPDRA
JCMB
2617
Photo of Angela Dawson
Niccolo De FrancescoResearch Assistant
JCMB
2612
Susana DireitoPDRA
JCMB
1603
Steven GardnerPostdoctoral Research Associate
JCMB
1603
Alys JepsonPDRA
JCMB
1505
Photo of Alys Jepson
Nick KoumakisPDRA
JCMB
2621
Thomas Le GoffPostdoctoral Research Associate
JCMB
1509
Benno LiebchenMarie Curie Fellow
JCMB
1506
Elin LiljaPDRA
JCMB
1510
Diarmuid LloydPDRA
JCMB
1505
Vincent MartinezPDRA
JCMB
2609
Photo of Vincent Martinez
Gavin MelaughPDRA
JCMB
1508
Davide MichielettoPDRA
JCMB
1505
Nikola OjkicPDRA
JCMB
1505
Marieke SchorPDRA
JCMB
2617
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Jana Schwarz-LinekPDRA
JCMB
2609
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Petra SchwendnerPDRA
JCMB
1603
Sharareh TavaddodPDRA
JCMB
1510
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Teun VissersMarie Curie Fellow
JCMB
2621
Tiffany WoodDirector of the Edinburgh Complex Fluids Partnership
JCMB
2611
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Research postgraduates
Giovanni BrandaniPostgraduate Student
JCMB
2510
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Rebecca BrouwersPostgraduate Student
JCMB
2618
Photo of Rebecca Brouwers
Francesco CagnettaPostgraduate Student
JCMB
1616
Photo of Francesco Cagnetta
Giulio De MagistrisPostgraduate Student
JCMB
2501
Milana FilatenkovaPostgraduate Student
JCMB
2510
Martina FoglinoEarly Stage Researcher
JCMB
2509
Photo of Martina Foglino
Mark Fox-PowellPostgraduate Student
JCMB
1607
Jay GillamPostgraduate Student
JCMB
2603
Photo of Jay Gillam
Tom IvesPostgraduate Student
JCMB
2501
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Hanna LandenmarkPostgraduate Student
JCMB
1511
Photo of Hanna Landenmark
Tao LiPostgraduate Student
JCMB
2510
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Benjamin LittlePostgraduate Student
JCMB
2603
Photo of Benjamin Little
Iva ManasiPostgraduate Student
JCMB
2510
Photo of Iva Manasi
Vincent MargerinPostgraduate Student
JCMB
8206
Laura McKinleyPostgraduate Student
JCMB
2510
Alexander McVeyPostgraduate Student
G.25
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Ryan MorrisPostgraduate Student
JCMB
1601
Francois MouvetVisitor
JCMB
1510
Eoin O'LaighleisPostgraduate Student
JCMB
1616
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Jakub PastuszakPostgraduate Student
JCMB
1510
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Chay PatersonPostgraduate Student
JCMB
2501
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Toby SamuelsPostgraduate Student
JCMB
1607
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Alexander SlowmanPostgraduate Student
JCMB
2501
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Daniel TaylorPostgraduate Student
JCMB
2510
Stuart ThomsonPostgraduate Student
JCMB
2510
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Joshua WilliamsPostgraduate Student
JCMB
2510
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Ellen YoungPostgraduate Student
JCMB
2618
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Xuemao ZhouPostgraduate Student
JCMB
2510
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