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Iain Johnston


My work employs computer simulations to model biological self-assembly and evolutionary processes. Self-assembly is an amazing tool in Nature's workshop, bringing together materials on all scales, galaxies to molecules, to construct order from chaos and symmetry from randomness. Biological evolution is the mechanism by which Darwin's "endless forms most beautiful" have emerged from the simple chemistry of prehistoric Earth.

Two walks on landscapes:
symmetry evolves quickly;
structures build themselves.

- my research in Haiku.

I hold an M.Sci. in Natural Sciences from Cambridge University, and my research is funded by the EPSRC. My fourth-year undergraduate project on virus capsid assembly was awarded the Tessella Prize for Innovative Use of Software. I am currently in the 4th Year of D.Phil. research in Theoretical Physics at Oxford University, supervised by Dr. A. Louis.

Pictured: Coarse-grained model assembly of T=1 and T=3 virus capsids, an evolved 'zoo' of icosominoes demonstrating modularity and symmetry, and a graph representation of the full dynamics of the core of a network evolved to produce a period-10 cyclic output.

Some self-assembly videos related to my work:

  • Polyominoes: http://www.youtube.com/watch?v=Si0b8EnMhVw
  • Snowflakes: http://www.youtube.com/watch?v=u4PtD6xvnT4
  • Viruses: http://www.youtube.com/watch?v=Ozg--zPRj0Q

  • Current areas of investigation include:

    Complexity and biological evolution:
    The quantitative study of complex systems, where interactions between simple components lead to complicated emergent behaviour, is a rapidly advancing field. Living organisms demonstrate immense complexity. How does this complexity arise from the process of biological evolution? We aim to show the key features of a biological environment that facilitate the evolution of complexity.

    Reversible self-assembly of virus capsids:
    Modelling the formation of protein coats that surround a virus' genetic information. These structures self-assemble from a number of identical subunits within the cell, and self-assemble reversibly, so that, for example, on changing the pH of the system the structure can be dissembled then reassembled. My work aims to provide a model for this process, complimenting recent energy landscape analysis and investigate the thermodynamics and mechanisms of the assembly, with possible applications in medicine and nanotechnology.

    Deterministic assembly of polyomino structures:
    Using 'building blocks' of patchy particles on a 2D lattice and a 'genome' of instructions on how these blocks interact allows large and complex structures to be grown from a small number of nucleus points. A well-defined complexity value can be assigned to structures assembled in this way. Genetic algorithms can be used to determine the correct genome for a particular structure, providing a flexible framework for modelling evolution with a non-trivial genotype-phenotype map. 2D self-assembly processes may also prove useful in creating structures like electric circuits on the nanoscale.


    Other areas of interest:

  • Evolutionary landscape topology:
    Biological evolution may be pictured as a stochastic search process on a complicated, high-dimensional landscape defined by a genotype-phenotype map. Recent work has shown that the structure of this landscape may be used to infer properties of phenotypes in an evolving system, including robustness, evolvability, and the probability of a given phenotype being found in an evolutionary simulation. I am interested in the topology and interconnectedness of neutral spaces in evolutionary landscapes, particularly those (necessarily corresponding to simple systems) which can be exhaustively searched.
  • Modelling biological networks:
    The study of simplified models of biological networks, for example, gene regulatory networks (GRNs). Our work has shown that such model networks can display considerable stability with respect to noise and perturbations, and simultaneously exhibit robustness to mutation and evolvability. We also study the 'core' structures responsible for driving the dynamics of these networks.
  • Power spectra in evolutionary dynamics:
    The distribution of many evolutionary statistics (including species ages, stasis times in punctuated equilibrium, extinction sizes and phylogenetic tree sizes) are often found to display power-law behaviour, with exponents comparable across a wide range of systems. We investigate this ubiquitous phenomenon with analytic and numerical evolutionary models.


    Publications:
    Self-assembly, modularity, and physical complexity
    Phys. Rev. E 82, 026117 (2010)
    Sebastian E. Ahnert, Iain G. Johnston, Thomas M. A. Fink, Jonathan P. K. Doye, Ard A. Louis

    The effect of scale-free topology on the robustness and evolvability of genetic regulatory networks
    J. Theor. Biol. 267, 48 (2010)
    Sam F. Greenbury, Iain G. Johnston, Matthew A. Smith, Jonathan P. K. Doye, Ard A. Louis

    Modelling the Self-Assembly of Virus Capsids
    J. Phys.: Condens. Matter 22, 104101 (2010) [front cover]
    Iain G. Johnston, Ard A. Louis, Jonathan P. K. Doye

    The Self-Assembly of DNA Holliday Junctions Studied with a Minimal Model
    J. Chem. Phys. 130, 065101 (2009)
    Thomas E. Ouldridge, Iain G. Johnston, Ard A. Louis, Jonathan P. K. Doye

    Evolutionary Dynamics in a Simple Model of Self-Assembly
    (in preparation)
    Iain G. Johnston, Sebastian E. Ahnert, Ard A. Louis, Jonathan P. K. Doye
    Conferences Attended:
    MOLSIM 2007
    SOCOBIM 2007
    (poster: "Positive Design in Self-Assembly of Virus Capsids")
    Oxford Mesoscale Modelling 2007
    Physics By The Lake 2007
    IOP Physics Meets Biology 2008
    (poster: "Walking on Fitness Landscapes: Modelling Evolution, Complexity and Deterministic 2D Assembly")
    IOP Complex Fluids Winter School 2009
    CeCAM Workshop on Colloids 2009


    My other interests include martial arts, gymnastics, photography, music (both performance and appreciation, especially metal, funk, rock, folk and feel-good summer music!), walking on Dartmoor and my beautiful home county of Devon.

    Links:
    Tavistock, my hometown.
    Bilang, a martial arts tricks website.
    Dartmoor Photographs by Tony Howell.
    Gouranga, my old band in Cambridge.
    36 Crazyfists, my all-time favourite band.
    Rodney Mullen, the best skateboarder in the world.
    Michael Angelo Batio doing frankly silly things with a guitar.
    Toy Science Links:
    Fractal Forest Applet
    Map of Metal Music
    Termination of a Number Game