Part II projects

• The self-assembly of monodisperse objects, such as viruses
• Modelling DNA self-assembly
• Protein and colloidal crystallization
• The structure of binary clusters
• The thermodynamics of large clusters
• The structure of large clusters
• Complex networks and energy landscapes

There is also the possibility of doing a summer internship in the group funded by NVIDIA as part of the Oxford NVIDIA CUDA Centre of Excellence.

To discuss any of these in more detail contact Jonathan Doye.

Project students that I have supervised or co-supervised have received the following prizes:

• Aleks Reinhardt won a Part II Thesis prize (Proxime Accesserunt in Physical & Theoretical Chemistry) in 2009
• Adam Levy won the 2009 Data Connection Prize for the best use of software in a Physics MPhys project.
• Gabriel Villar won the 2008 Data Connection Prize for the best use of software in a Physics MPhys project.
• Anna Lewis won the 2007 BP prize for best MPhys project in Theoretical Physics.
• Iain Johnston won the 2006 Tessela prize for the best computational project in Cambridge Physics.
• I-Chun Lin won the 2004 ICI prize for the best theoretical project in Cambridge Chemistry.

Research done by previous project students that I have supervised or co-supervised have contributed to the following publications:

• C.K. Wong, C. Tang, J.S. Schreck and J.P.K. Doye, Nanoscale, accepted (2022)
  Characterizing the free-energy landscapes of DNA origamis
• H. Chhabra, G. Mishra, Y. Cao, D. Prešern, E. Skoruppa, M.M.C. Tortora and J.P.K. Doye, J. Chem. Theor. Comput. 16, 7748–7763 (2020)
  Computing the elastic mechanical properties of rod-like DNA nanostructures
• K.G. Young, B. Najafi, W.M. Sant, S. Contera, A.A. Louis, J.P.K. Doye, A.J. Turberfield and J. Bath, Angew. Chem. Int. Ed. 59, 15942-15946 (2020)
  Reconfigurable T-junction DNA origami
• T.D. Craggs, M. Sustarsic, A. Plochowietz, M. Mosayebi, H. Kaju, A. Cuthbert, J. Hohlbein, L. Domicevica, P.C. Biggin, J.P.K. Doye and A.N. Kapanidis, Nucleic Acids Res. 47, 10788–10800 (2019)
  Substrate conformational dynamics facilitate structure-specific recognition of gapped DNA by DNA polymerase
• R. Sharma, J.S. Schreck, F. Romano, A.A. Louis and J.P.K. Doye, ACS Nano, 11, 12426–12435 (2017)
  Characterizing the motion of jointed DNA nanostructures using a coarse-grained model
• J. S. Schreck, F. Romano, M.H. Zimmer, A.A. Louis and J.P.K. Doye, ACS Nano, 10, 4236-4247 (2016)
  Characterizing DNAstar-tile-based nanostructures using a coarse-grained model
• J.S. Schreck, T.E. Ouldridge, F. Romano, L. Shaw, A.A. Louis and J.P.K. Doye, Nucl. Acids Res. 43, 6181-6190 (2015)
  DNA hairpins primarily promote duplex melting rather than inhibiting hybridization
• G. Fraux and J.P.K. Doye, J. Chem. Phys. 141, 216101 (2014)
  Heterogeneous ice nucleation on silver-iodide-like surfaces
• 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
• 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
• 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
• C. Matek, T.E. Ouldridge, A. Levy, J.P.K. Doye, and A.A. Louis, J. Phys. Chem. B, 116, 11616-11625 (2012)
  DNA cruciform arms nucleate through a correlated but asynchronous cooperative mechanism
• F. Romano, A. Hudson, J.P.K. Doye, T.E. Ouldridge and A.A. Louis, J. Chem. Phys. 136, 215102 (2012)
  The effect of topology on the structure and free energy landscapes of DNA kissing complexes
• M. N. van der Linden, J.P.K. Doye and A.A. Louis, J. Chem. Phys. 136, 054904 (2012)
  Formation of dodecagonal quasicrystals in two-dimensional systems of patchy particles
• S. F. Greenbury, I.G. Johnston, M. A. Smith, J.P.K. Doye and A.A. Louis, J. Theor. Biol. 267, 48-61 (2010)
  The effects of topology on robustness and evolvability in genetic regulatory networks
• I.G. Johnston, A.A. Louis and J.P.K. Doye, J. Phys.: Condens. Matter 22, 104101 (2010)
  Modelling the self-assembly of virus capsids
• A.W. Wilber, J.P.K. Doye, A.A. Louis and A.C.F. Lewis, J. Chem. Phys, 131, 175102 (2009)
  Monodisperse self-assembly in a model with protein-like interactions
• G. Villar, A.W. Wilber, A.J. Williamson, P. Thiara, J.P.K. Doye, A.A. Louis, M.N. Jochum, A.C.F. Lewis and E.D. Levy, Phys. Rev. Lett. 102, 118106 (2009)
  The self-assembly and evolution of homomeric protein complexes
• T.E. Ouldridge, I.G. Johnston, A.A. Louis and J.P.K. Doye, J. Chem. Phys. 130, 065101 (2009)
  Minimal models of DNA and the self-assembly of DNA nanostructures
• J.P.K. Doye and L. Meyer, submitted
  The structure of binary Lennard-Jones clusters: The effects of atomic size ratio
• A.W. Wilber, J.P.K. Doye, A.A. Louis, E.G. Noya, M.A. Miller, P. Wong, J. Chem. Phys. 127, 085106 (2007)
  Reversible self-assembly of patchy particles into monodisperse icosahedral clusters
• C.P. Massen, J.P.K. Doye and R.W. Nash, Physica A 382, 683-692 (2007)
  Exploring the origins of the power-law properties of energy landscapes: An egg-box model
• J.P.K. Doye, A.A. Louis, I-C. Lin, L.R. Allen, E.G. Noya, A.W. Wilber, H.C. Kok, R. Lyus, Phys. Chem. Chem. Phys. 9, 2197-2205 (2007)
  Controlling crystallization and its absence: Proteins, colloids and patchy models
• J.P.K. Doye and L. Meyer, Phys. Rev. Lett. 95, 063401 (2005)
  Mapping the magic numbers in binary Lennard-Jones clusters