Physical & Theoretical Chemistry

In my research I typically use computer simulation techniques to probe simple models that capture the essential physics and chemistry of the system of interest with a particular emphasis on the role played by the underlying potential or free energy landscapes. Applications span a diverse range of fields including clusters, polymer, protein and colloidal crystallization, supercooled liquids and the glass transition, complex networks, biological self-assembly, DNA and evolution.

In my research I am increasingly addressing questions of biological interest. For example, I am trying to understand why proteins are hard to crystallize, how proteins can self assemble into monodisperse objects such as virus capsids and the evolutionary origins of the symmetry possessed by most homomeric protein complexes. Below are four snapshots from a simulation where 72 model particles self assemble to form six hollow icosahedra

We have also recently developed a coarse-grained model of DNA that we are using to visualize the self-assembly of DNA nanostructures and the action of DNA nanodevices. The picture below shows snapshots from the action cycle of DNA "nanotweezers" which can be made to close and open by the addition of single-stranded DNA. DNA nanotweezers In my work on cluster structure I have gone beyond the usual consideration of structures that are based on close-packing, to elucidate the types of structures that might be observed for materials that form quasicrystals or Frank-Kasper phases in the bulk. An example of a particularly stable binary metal cluster is shown right. I have also gone beyond the usual "energy-only" approach to structural stability by emphasising the role played by vibrational entropy in determining the thermodynamically most stable structure, and illustrated how the growth of clusters of C60 molecules leads to structures that are "kinetic products".

M. Mosayebi, A.A. Louis, J.P.K. Doye and T.E. Ouldridge, submitted Force-induced rupture of a DNA duplex D. Palagin and J.P.K. Doye, Phys. Chem. Chem. Phys. accepted CO Oxidation Catalysed by Pd-based Bimetallic Nanoalloys J. S. Schreck, T.E. Ouldridge, F. Romano, A.A. Louis and J.P.K. Doye, J. Chem. Phys. submitted Characterizing the bending and flexibility induced by bulges in DNA duplexes P. Sulc, T.E. Ouldridge, F. Romano, J.P.K. Doye and A.A. Louis, Biophys J. 108, 1238-1247 (2015) Modelling toehold-mediated RNA strand displacement J.S. Schreck, T.E. Ouldridge, F. Romano, L. Shaw, A.A. Louis and J.P.K. Doye, submitted DNA hairpins primarily promote duplex melting rather than inhibiting hybridization C. Matek, T.E. Ouldridge, J.P.K. Doye and A.A. Louis, Scientific Reports, 5, 7655 (2015) Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA M. Mosayebi, F. Romano, T.E. Ouldridge, A.A. Louis and J.P.K. Doye, J. Phys. Chem. B 118, 14326-14335 (2014) The role of loop stacking in the dynamics of DNA hairpin formation D. Palagin and J.P.K. Doye, J. Chem. Phys. 141, 214302 (2014) Ni-based nanoalloys: Towards thermally stable highly magnetic materials G. Fraux and J.P.K. Doye, J. Chem. Phys. 141, 216101 (2014) Heterogeneous ice nucleation on silver-iodide-like surfaces A. Reinhardt and J.P.K. Doye, J. Chem. Phys. 141, 084501 (2014) Effects of surface interactions on heterogeneous ice nucleation for a monatomic water model P. Sulc, F. Romano, T.E. Ouldridge, J.P.K. Doye and A.A. Louis, J. Chem. Phys. 140, 235102 (2014) A nucleotide-level coarse-grained model of RNA P. Sulc, T.E. Ouldridge, F. Romano, J.P.K. Doye and A.A. Louis, Natural Computing, 13, 535-547 (2014) Simulating a burnt-bridges DNA motor with a coarse-grained DNA model J.P.K. Doye, T.E. Ouldridge, A.A. Louis, F. Romano, P. Sulc, C. Matek, B.E.K. Snodin, L. Rovigatti, J.S. Schreck, R.M. Harrison, and W.P. Smith, Phys. Chem. Chem. Phys. 15, 20395-20414 (2013) Coarse-graining DNA for simulations of DNA nanotechnology A. Reinhardt and J.P.K. Doye, J. Chem. Phys. 139, 096102 (2013) Homogeneous TIP4P/2005 ice nucleation at low supercooling N. Srinivas, T.E. Ouldridge, P. Sulc, J. M. Schaeffer, B. Yurke, A.A. Louis, J.P.K. Doye and E. Winfree, Nucl. Acids Res. 41, 10641-10658 (2013) On the biophysics and kinetics of toehold-mediated DNA strand displacement T.E. Ouldridge, P. Sulc, F. Romano, J.P.K. Doye and A.A. Louis, Nucl. Acids Res. 41, 8886-8895 (2013) DNA hybridization kinetics: zippering, internal displacement and sequence dependence A. Reinhardt, F. Romano and J.P.K. Doye, Phys. Rev. Lett. 110, 255503 (2013) Computing phase diagrams for a quasicrystal-forming patchy-particle system T.E. Ouldridge, R. Hoare, A.A. Louis, J.P.K. Doye, J. Bath and A.J. Turberfield, ACS Nano 7, 2479-2490 (2013) Optimizing DNA nanotechnology through coarse-grained modelling: A two-footed DNA walker F. Romano, D. Chakraborty, J.P.K. Doye, T.E. Ouldridge and A.A. Louis, J. Chem. Phys. 138, 085101 (2013).

Coarse-grained simulations of DNA overstretching