Louis Group
Members
Research
Publications
MPhys projects
Positions available
Teaching
News

    Louis group research interests: Soft and Biological Systems

Research in our group is interdisciplinary, on the border between theoretical physics and chemistry, applied mathematics and biology. We study how complex behaviour emerges from the interactions between many individual objects. Specific topics of interest include biological systems such as virus self-assembly, DNA nano-structure self-assembly or the evolution of gene networks, as well as the properties of complex fluids/soft matter systems such as colloids polymers, or proteins in solution. We primarily use the tools of statistical mechanics -- especially analytic theories and computer simulations -- to better understand the behaviour of these fascinating systems. "Coarse-graining", where a subset of the (microscopic) degrees of freedom are integrated out to yield a simpler and more tractable problem, is a common theme in these descriptions. Here at Oxford, we work closely with members of the Theory of Soft and Biological Matter group, with whom we share many research interests. We're also members of the StoMP Network between mathematical modellers and microbiologists.

Research Projects in the Louis group

Here are some research projects that give a flavour of the work in our group. In practice, these projects always evolve, in part because research advances rapidly, and in part because we adapt the projects to the particular strengths and interests of the DPhil candidates or postdocs.

  • Self-Assembling DNA

    The ability to design nanostructures which accurately self-assemble from simple units is central to the goal of engineering objects and machines on the nanoscale. Without self-assembly, structures must be laboriously constructed in a step by step fashion. Double-stranded DNA (dsDNA) has the ideal properties for a nanoscale building block, and new DNA nanostructures are being published at an ever increasing rate. Here in the Clarendon the world-leading experimental group of Andrew Turberfield has created a number of intriguing nanostructures using physical self-assembly mechanisms. We have recently developed a new simplified theoretical model of DNA that appears to capture the dominant physics involved. In this project you would apply the model to study some simple nanostructures. You will mainly be using Monte Carlo simulations and statistical mechanical calculations to study these processes. A potential new direction for this project could also be to extend our new methods to study RNA nanostructures.

  • The physics of biological evolution

    "Nothing in Biology Makes Sense Except in the Light of Evolution." wrote the great naturalist Theodosius Dobzhansky , but to really understand evolution, a stochastic optimization process in a very high dimensional space, will require techniques from statistical physics. In this project you will use theoretical tools and computer simulations to study a number of simplified models we have been developing in our group to understand the physics of evolution. We are studynig the evolution of protein quaternary structure, RNA secondary structures, and how concepts from algorithmic information theory help explain how evolutionary search is so efficient at finding solutions.


    This project is in close collaboration with the group of Dr. Jonathan Doye.

  • Design Rules for Self-Assembly

    The remarkable ability of biological matter to robustly self-assemble into well defined composite objects excites the imagination. Viruses, for example, can be reversibly dissolved and re-assembled from their component parts simply by changing the solution pH. How does nature achieve this feat? Can we uncover the "positive design rules" for inter-particle interactions that allow the self-assembly of a particular desired 3-dimensional structure [1]? Can we use evolutionary algorithms to design these particles? Such understanding could have important implications for nanoscience, where objects are too small to directly manipulate, and instead must come together by self-assembly mechanisms.
    This project is in close collaboration with the group of Dr. Jonathan Doye.

    Here is a movie that Iain made about virus self-assembly:


    [1] Reversible self-assembly of patchy particles into monodisperse clusters
    Alex W. Wilber, Jonathan P. K. Doye, Ard A. Louis, Mark A. Miller, Eva G. Noya, Pauline Wong
    J. Chem. Phys. 127, 085106 (2007)
    | arxiv abstract | pdf reprint| Modelling the Self-Assembly of Virus Capsids


    Iain G. Johnston, Ard A. Louis and Jonathan P.K. Doye
    J. Phys.: Condensed Matter, 22 , 104101 (2010)
    | arxiv abstract | pdf reprint | (this paper was selected for journal cover and as one of the journal's Highlights of 2010)

  • The interplay of Brownian and hydrodynamic interactions in suspensions

    When suspended particles move in a background fluid, they experience random kicks (Brownian motion), but also generate long-ranged hydrodynamic flows. This project would use a new computer simulation method, stochastic rotation dynamics (SRD) that includes both these effects, to study flow properties of complex fluids. There is also scope for more mathematical approaches combining non-equilibrium statistical mechanics and hydrodynamics to explain some of the dramatic effects we are seeing. Examples of applications include dynamic lane formation, fluctuations during sedimentation, colloidal nano-pumps, and colloidal "explosions".

      To see the effect of hydrodynamic interactions, compare these two movies:
    • .

    • Or check out what happens when you have aggregation and sedimentation:

    This project would also work closely with the experimental groups of Dr Roel Dullens and Dr Dirk Aarts , and the theory group of Prof Julia Yeomans

    The effects of inter-particle attractions on colloidal sedimentation
    A. Moncho Jorda', A. A. Louis and J. T. Padding
    Phys. Rev. Lett. 104, 068301 (2010)
    | arxiv abstract | pdf reprint | (this paper was selected as an Editor's Suggestion" in PRL)

    The interplay between hydrodynamic and Brownian fluctuations in sedimenting colloidal suspensions
    J.T. Padding and A.A. Louis
    Phys. Rev. E 77, 011402 (2008) || pdf reprint |

    Hydrodynamic interactions and Brownian forces in colloidal suspensions: Coarse-graining over time and length-scales
    J.T. Padding and A.A. Louis
    Phys. Rev. E 74, 031402 (2006)
    | arxiv abstract | pdf reprint|

    Hydrodynamic and Brownian Fluctuations in Sedimenting Suspensions
    J.T. Padding and A. A. Louis, Phys. Rev. Lett. 93, 220601 (2004)
    | arxiv abstract | pdf reprint|

  • Fundamental questions in coarse-graining

    An important source of progress in statistical mechanics comes from better coarse-grained models, that is descriptions that are simpler and more tractable, but nevertheless retain the fundamental underlying physics that one is interested in investigating. It is intuitively obvious that these simplified descriptions throw some information away and that compromises are made. After all, there is no such thing as a free lunch. But how much are we paying, and what can we get away with? We have argued that good coarse-graining procedures are best interpreted in terms of the emergent properties that one is trying to model.

  • Here are two introductory papers:
Louis Group Members Research Publications Mphys projects Positions available Teaching News