Research Guides

Department of Chemistry University of Oxford

Professor Jonathan Doye

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".

1. Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly, J. Chem. Phys. 148, 134910 (2018) 
2. Directed self-assembly into low-density colloidal liquid-crystal phases, Phys. Rev. Materials 2, 015601 (2018)  
3. DNA motor bipedal walking dynamics: An experimental and theoretical study of the dependence on step size, Nucl. Acids Res. 46, 1553 (2018) 
4. Rolling circle amplification shows a sinusoidal template-length dependent amplification bias, Nucl. Acids. Res. 46, 538 (2018)
5. Characterizing the motion of jointed DNA nanostructures with a coarse-grained model, ACS Nano 11, 12426 (2017)
6. Perturbative density functional methods for cholesteric liquid crystals, J. Chem. Phys. 146, 184504 (2017)
7. Direct simulation of the self-assembly of a small DNA origami, ACS Nano, 10, 1724 (2016)
8. Design principles for rapid folding of knotted DNA nanostructures, Nat. Commun. 7, 10803 (2016)
9. CO oxidation catalysed by Pd-based bimetallic nanoalloys, Phys. Chem. Chem. Phys. 17, 28010 (2015)
10. Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA, Scientific Reports 5, 7655 (2015)
11. A nucleotide-level coarse-grained model of RNA, J. Chem. Phys. 140, 235102 (2014)
12. Heterogeneous ice nucleation on silver-iodide-like surfaces, J. Chem. Phys. 141, 216101 (2014)
13. Coarse-graining DNA for simulations of DNA nanotechnology, Phys. Chem. Chem. Phys. 15, 20395 (2013)
14. On the biophysics and kinetics of toehold-mediated DNA strand displacement, Nucl. Acids Res. 41, 10641 (2013)
15. DNA hybridization kinetics: zippering, internal displacement and sequence dependence, Nucl. Acids Res. 41, 8886 (2013)
16. Computing phase diagrams for a quasicrystal-forming patchy-particle system, Phys. Rev. Lett. 110, 255503 (2013)
17. DNA nanotweezers studied with a coarse-grained model of DNA, Phys. Rev. Lett. 104, 178101 (2010)
18. The self-assembly and evolution of homomeric protein complexes, Phys. Rev. Lett. 102, 118106 (2009)
19. Controlling crystallization and its absence: Proteins, colloids and patchy models, Phys. Chem. Chem. Phys. 9, 2197 (2007)
20. Protein crystallization in vivo, Curr. Opin. Colloid In, 11, 40 (2006) 
21. Mapping the magic numbers in binary Lennard-Jones clusters, Phys. Rev. Lett. 95, 063401 (2005)
22. The network topology of a potential energy landscape: A static scale-free network, Phys. Rev. Lett. 88, 238701 (2002)
23. Global optimization by basin-hopping and the lowest-energy structures of Lennard-Jones clusters containing up to 110 atoms, J. Phys. Chem. A 101, 5111, (1997)