We use experiments, computer simulations, and theoretical calculations to understand how physical laws affect living organisms.
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 EPSRC, BBSRC, DTI, Scottish 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).
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
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.
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.
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
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
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.
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
- Bacteria Motility in Complex Media
- Communal Living for Bacteria
- Evolution of antibiotic resistance in bacterial colonies
- How antibiotics work
- Microswimmers in Complex Fluids
- Multiple stable states in ecosystem development?
- Nutrient limitation in microorganisms
- Simulating how antibiotics kill persistent infections
- The physics of killing bacteria
- The use of mass spectrometry to probe the metamorphic protein Lymphotactin
- Using microfluidics to create highly parallelized biological physics experiments
- Virus Self-assembly: Structure, Dynamics and Mechanical Properties
- Why and How Proteins Stick to Each Other
People in Physics of Living Matter
|Name||Position||Email address||Telephone (UK)||Building||Room number|
|Graeme Ackland||Professor||g [dot] j [dot] ackland [at] ed [dot] ac [dot] uk||0131 650 5299||JCMB||2502|
|Rosalind Allen||Lecturer||rosalind [dot] allen [at] ed [dot] ac [dot] uk||0131 651 7197||JCMB||2507|
|Richard Blythe||Reader||r [dot] a [dot] blythe [at] ed [dot] ac [dot] uk||0131 650 5105||JCMB||2505|
|Charles Cockell||Professor of Astrobiology||c [dot] s [dot] cockell [at] ed [dot] ac [dot] uk||0131 650 2961||JCMB||1502|
|Martin Evans||Professor of Statistical Physics||m [dot] evans [at] ed [dot] ac [dot] uk||0131 650 5294||JCMB||2615|
|Cait MacPhee||Professor||cait [dot] macphee [at] ed [dot] ac [dot] uk||0131 650 5291||JCMB||2613|
|Davide Marenduzzo||Personal Chair in Computational Biophysics||dmarendu [at] ph [dot] ed [dot] ac [dot] uk||0131 650 5289||JCMB||2506|
|Alexander Morozov||Reader||alexander [dot] morozov [at] ed [dot] ac [dot] uk||0131 650 5882||JCMB||2616|
|Wilson Poon||Professor||w [dot] poon [at] ed [dot] ac [dot] uk||0131 650 5297||JCMB||2620|
|Simon Titmuss||Lecturer||simon [dot] titmuss [at] ed [dot] ac [dot] uk||0131 650 5267||JCMB||2504|
|Bartlomiej Waclaw||RSE Research Fellow||bwaclaw [at] staffmail [dot] ed [dot] ac [dot] uk||0131 651 7688||JCMB||2503|
|Name||Position||Email address||Telephone (UK)||Building||Room number|
|Matthew Blow||PDRA||mblow [at] staffmail [dot] ed [dot] ac [dot] uk||0131 650 5175||JCMB||1506|
|Chris Brackley||PDRA||cbrackle [at] ph [dot] ed [dot] ac [dot] uk||0131 650 8617||JCMB||2609|
|Aidan Brown||PDRA||abrown20 [at] staffmail [dot] ed [dot] ac [dot] uk||0131 651 3456||JCMB||2610|
|Delma Childers||PDRA||delma [dot] childers [at] ed [dot] ac [dot] uk||0131 650 6478||JCMB||1503|
|Angela Dawson||PDRA||angela [dot] dawson [at] ed [dot] ac [dot] uk||0131 650 7165||JCMB||2617|
|Steven Gardner||Postdoctoral Research Associate||steven [dot] gardner [at] ed [dot] ac [dot] uk||0131 651 7771||JCMB||1603|
|Alys Jepson||PDRA||ajepson2 [at] staffmail [dot] ed [dot] ac [dot] uk||0131 651 7742||JCMB||1505|
|Nick Koumakis||PDRA||nick [dot] koumakis [at] ed [dot] ac [dot] uk||0131 650 5883||JCMB||2621|
|Thomas Le Goff||Postdoctoral Research Associate||thomas [dot] le-goff [at] ed [dot] ac [dot] uk||0131 651 3455||JCMB||1509|
|Benno Liebchen||PDRA||benno [dot] liebchen [at] ed [dot] ac [dot] uk||0131 650 5175||JCMB||1506|
|Diarmuid Lloyd||PDRA||diarmuid [dot] lloyd [at] ed [dot] ac [dot] uk||0131 651 7742||JCMB||1505|
|Vincent Martinez||PDRA||vincent [dot] martinez [at] ed [dot] ac [dot] uk||0131 650 8617||JCMB||2609|
|Gavin Melaugh||PDRA||gmelaugh [at] ed [dot] ac [dot] uk||0131 651 3456||JCMB||1508|
|Davide Michieletto||PDRA||davide [dot] michieletto [at] ed [dot] ac [dot] uk||0131 651 7742||JCMB||1505|
|Marieke Schor||PDRA||mschor [at] ed [dot] ac [dot] uk||0131 650 7165||JCMB||2617|
|Jana Schwarz-Linek||PDRA||jslinek [at] staffmail [dot] ed [dot] ac [dot] uk||0131 650 8617||JCMB||2609|
|Petra Schwendner||PDRA||pschwend [at] staffmail [dot] ed [dot] ac [dot] uk||JCMB||1603|
|Adriano Tiribocchi||PDRA||atiriboc [at] staffmail [dot] ed [dot] ac [dot] uk||0131 65- 5175||JCMB||1506|
|Teun Vissers||Marie Curie Fellow||t [dot] vissers [at] ed [dot] ac [dot] uk||0131 650 5883||JCMB||2621|
|Tiffany Wood||Industrial Research Liaison||tiffany [dot] wood [at] ed [dot] ac [dot] uk||0131 651 7687||JCMB||2611|
|Name||Position||Email address||Telephone (UK)||Building||Room number|
|Siobhan Liddle||Tutor||s [dot] liddle [at] ed [dot] ac [dot] uk||0131 650 6799||JCMB||2510|
|Name||Email address||Telephone (UK)||Building||Room number|
|Giovanni Brandani||s1246659 [at] sms [dot] ed [dot] ac [dot] uk||0131 650 6799||JCMB||2510|
|Rebecca Brouwers||s1529080 [at] sms [dot] ed [dot] ac [dot] uk||JCMB||2618|
|Timothy Bush||s1118784 [at] sms [dot] ed [dot] ac [dot] uk||0131 650 6799||JCMB||2509|
|Giulio De Magistris||s1356442 [at] sms [dot] ed [dot] ac [dot] uk||0131 650 8603||JCMB||2501|
|Fred Farrell||s1042268 [at] sms [dot] ed [dot] ac [dot] uk||0131 651 7176||JCMB||1511|
|Milana Filatenkova||s1145105 [at] sms [dot] ed [dot] ac [dot] uk||0131 650 6799||JCMB||2510|
|Martina Foglino||mfoglino [at] staffmail [dot] ed [dot] ac [dot] uk||JCMB||1510|
|Joe Forth||s1115855 [at] sms [dot] ed [dot] ac [dot] uk||0131 651 3455||JCMB||1509|
|Mark Fox-Powell||m [dot] fox-powell [at] ed [dot] ac [dot] uk||0131 651 7774||JCMB||1607|
|Jay Gillam||j [dot] e [dot] gillam [at] sms [dot] ed [dot] ac [dot] uk||JCMB||2603|
|Tom Ives||s0935333 [at] sms [dot] ed [dot] ac [dot] uk||0131 650 8603||JCMB||2501|
|Hanna Landenmark||s1046113 [at] sms [dot] ed [dot] ac [dot] uk||0131 651 7176||JCMB||1511|
|Tao Li||s1165179 [at] sms [dot] ed [dot] ac [dot] uk||0131 650 6799||JCMB||2510|
|Benjamin Little||s0675186 [at] sms [dot] ed [dot] ac [dot] uk||0131 650 5263||JCMB||2603|
|Ioan Magdau||s1165169 [at] sms [dot] ed [dot] ac [dot] uk||0131 650 6799||JCMB||2510|
|Iva Manasi||s1374036 [at] sms [dot] ed [dot] ac [dot] uk||0131 651 7176||JCMB||2510|
|Vincent Margerin||vincent [dot] margerin [at] ed [dot] ac [dot] uk||0131 650 5284||JCMB||8206|
|Laura McKinley||l [dot] e [dot] mckinley [at] ed [dot] ac [dot] uk||0131 650 6799||JCMB||2510|
|Alexander McVey||a [dot] f [dot] mcvey [at] ed [dot] ac [dot] uk||0131 651 3454||G.25|
|Ryan Morris||ryan [dot] morris [at] ed [dot] ac [dot] uk||0131 650 6799||JCMB||1601|
|Jakub Pastuszak||s0789788 [at] sms [dot] ed [dot] ac [dot] uk||0131 650 6799||JCMB||1510|
|Chay Paterson||s1338295 [at] sms [dot] ed [dot] ac [dot] uk||0131 650 8603||JCMB||2501|
|Toby Samuels||s1360327 [at] sms [dot] ed [dot] ac [dot] uk||0131 651 7774||JCMB||1607|
|Alexander Slowman||s1271420 [at] sms [dot] ed [dot] ac [dot] uk||0131 650 8603||JCMB||2501|
|Daniel Taylor||daniel [dot] taylor [at] ed [dot] ac [dot] uk||JCMB||2510|
|Stuart Thomson||s0828679 [at] sms [dot] ed [dot] ac [dot] uk||0131 651 7176||JCMB||2510|
|Joshua Williams||s1461461 [at] sms [dot] ed [dot] ac [dot] uk||0131 651 7176||JCMB||2510|
|Xuemao Zhou||s1461318 [at] sms [dot] ed [dot] ac [dot] uk||0131 651 7176||JCMB||2510|