Research Guides

Department of Chemistry University of Oxford

Professor Jonathan Doye

In my research I typically use molecular simulation techniques to probe simple models that capture the essential physics and chemistry of the system of interest. Applications span a diverse range of fields including DNA nanotechnology, nucleic acid biophysics, cholesteric liquid crystals, colloidal self-assembly, ice nucleation, polymer and protein crystallization, clusters and complex networks.

We have developed oxDNA, a nucleotide-level coarse-grained model of DNA that is particularly suited to studying DNA biophysics and DNA nanotechnology.  The picture below shows snapshots from simulations of twisting a long DNA duplex, and of a 2D DNA origami. Our simulation code for the model is available at http://dna.physics.ox.ac.uk.
 
We are increasingly collaborating with experimental DNA groups to interpret their data. For example, oxDNA has been used to explain the dependence of the rate of toehold-mediated strand displacement on toehold length and the presence of mismatches; why rolling circle amplification shows a sinusoidal template-length amplification bias; the effect of substrate conformational dynamics on the binding of a DNA polymerase to its gapped duplex substrate,  the physical origins of the dependence of the dynamics of DNA walkers on step size; the kinetic constraints on the self-assembly of a single strand into a highly-knotted pyramidal structure, the mechanisms underlying the complex force-induced unravelling of DNA origamis, and to measure the internal forces in origami force sensors.

We are also interested in cholesteric liquid crystals, in particular the relationship between the chiral structure of the liquid-crystal forming particles and the chirality of the cholesteric phase. The figure illustrates how the preferred close packing of a pair of chiral screw-like particles can be left or right-handed depending on the angle of the thread. We have developed an efficient classical density functional theory approach that enables the properties of realistic chiral particles to be predicted for the first time. Combined with oxDNA we can apply this approach to a variety of DNA liquid-crystal forming systems. This work has highlighted the potential role of the particle's chiral shape fluctuations in determining the cholesteric behaviour.

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)