Publications

Chemical Physics

2023

• E.J. Ratajczyk, P. Šulc, A.J. Turberfield, J.P.K. Doye and A.A. Louis, submitted
  Coarse-grained modelling of DNA-RNA hybrids
• I. Seet, T.E. Ouldridge and J.P.K. Doye, submitted
  Pipelined information flow in molecular mechanical circuits leads to increased error and irreversibility
• B. Najafi, K.G. Young, J. Bath, A.A. Louis, J.P.K. Doye and A.J. Turberfield, submitted
  Characterising DNA T-motifs by simulation and experiment
• J. S. Schreck, F. Romano, A.A. Louis and J.P.K. Doye, submitted
  Mechanisms of kinetic control in the self-assembly of DNA polyhedral nanostructures
• R.M. Harrison, F. Romano, T.E. Ouldridge, A.A. Louis and J.P.K. Doye, submitted
  Coarse-grained modelling of strong DNA bending I: Thermodynamics and comparison to an experimental “molecular vice”
• J.P.K. Doye, H. Fowler, D. Prešern, J. Bohlin, L. Rovigatti, F. Romano, P. Šulc, C.K. Wong, A.A. Louis, J.S. Schreck and M.C. Engel, M. Matthies, E. Benson, E. Poppleton, B.E.K. Snodin, Methods in Molecular Biology, DNA and RNA Origami: Methods and Protocols, Vol. 2639, 93-112 (2023)
  The oxDNA coarse-grained model as a tool to simulate DNA origami
• I. Seet, T.E. Ouldridge and J.P.K. Doye, Phys. Rev. E 107, 024134 (2023)
  Simulation of reversible molecular mechanical logic gates and circuits

2022

• I.G. Johnston, K. Dingle, S.F. Greenbury, C.Q. Camargo, J.P.K. Doye, S.E. Ahnert and A.A. Louis, Proc. Natl. Acad. USA, 119, e2205299119 (2022)
  Reply to Ocklenburg and Mundorf: The interplay of developmental bias and natural selection
• J.P.K. Doye, A.A. Louis, J.S. Schreck, F. Romano, R.M. Harrison, M. Mosayebi, M.C. Engel, T.E. Ouldridge, in Energy Landscapes of Nanoscale Systems, ed. D.J. Wales, Frontiers of Nanoscience Vol. 21 (Elsevier), Chapter 9, pp 195-210 (2022)
  Free-energy landscapes of DNA and its assemblies: Perspectives from coarse-grained modelling
• C.K. Wong and J.P.K. Doye, Appl. Sci. 12, 5875 (2022)
  The free-energy landscape of a mechanically bistable DNA origami
• X. Wang, S. Li, H. Jun, T. John, K. Zhang, H. Fowler, J.P.K. Doye, W. Chiu and M. Bathe, Sci. Adv. 8, eabn0039 (2022)
  Planar 2D wireframe DNA origami
• W. Lim, F. Randisi, J.P.K. Doye and Ard A. Louis, Nucleic Acids Res. 50, 2480-2492 (2022)
  The interplay of supercoiling and thymine dimers in DNA
• C.K. Wong, C. Tang, J.S. Schreck and J.P.K. Doye, Nanoscale, 14, 2638-2648 (2022)
  Characterizing the free-energy landscapes of DNA origamis
• I.G. Johnston, K. Dingle, S.F. Greenbury, C.Q. Camargo, J.P.K. Doye, S.E. Ahnert and A.A. Louis, Proc. Natl. Acad. USA, 119, e2113883119 (2022)
  Symmetry and simplicity spontaneously emerge from the algorithmic nature of evolution

2021

• H. Su, J.M. Brockman, Y. Duan, N. Sen, H. Chhabra, A. Bazrafshan, A.T. Blanchard, T. Meyer, B. Andrews, J.P.K. Doye, Y. Ke, R.B. Dyer and K. Salaita, J. Am. Chem. Soc. 43, 19466–19473 (2021)
  Massively parallelized molecular force manipulation with on demand thermal and optical control
• E.G. Noya, C.K. Wong, P. Llombart and J.P.K. Doye, Nature, 596, 367-371 (2021)
  How to design an icosahedral quasicrystal through directional bonding
• J.P.K. Doye and E.G. Noya, Proc. Natl. Acad. Sci. USA, 118, e2107024118 (2021)
  Computational explorations in the space of one-component crystals
• D.F. Tracey, E.G. Noya and J.P.K. Doye, J. Chem. Phys. 154, 194505 (2021)
  Programming patchy particles to form three-dimensional dodecagonal quasicrystals

2020

• J.F. Berengut, C.K. Wong, J.C. Berengut, J.P.K. Doye, T.E. Ouldridge and L.K. Lee, ACS Nano 14, 17428–17441 (2020)
  Self-limiting polymerization of DNA origami subunits with strain accumulation
• 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
• M.C. Engel, F. Romano, A.A. Louis and J.P.K. Doye, J. Chem. Theor. Comput. 16, 7764–7775 (2020)
  Measuring internal forces in single-stranded DNA: Application to a DNA force clamp
• 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
• M.M.C. Tortora, G. Mishra, D. Prešern and J.P.K. Doye, Sci. Adv. 6, eaaw8331 (2020)
  Chiral shape fluctuations and the origin of chirality in cholesteric phases of DNA origamis
• M. Heidenreich, J. Georgeson, E. Locatelli, L. Rovigatti, S.K. Nandi, A. Steinberg, Y. Nadav, E. Shimoni, S.A. Safran, J.P.K. Doye, E.D. Levy, Nat. Chem. Biol. 16, 939-945 (2020)
  Designer protein assemblies with tunable phase diagrams in living cells

2019

• D.F. Tracey, E.G. Noya and J.P.K. Doye, J. Chem. Phys. 151, 224506 (2019)
  Programming patchy particles to form complex periodic structures
• J.F. Berengut, J.C. Berengut, J.P.K. Doye, D. Prešern, A. Kawamoto, J. Ruan, M.J. Wainwright and L.K. Lee, Nucleic Acids Res. 47, 11963–11975 (2019)
  Design and synthesis of pleated DNA origami nanotubes with adjustable diameters
• 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.M. Harrison, F. Romano, T.E. Ouldridge, A.A. Louis and J.P.K. Doye, J. Chem. Theory Comput. 15, 4660-4672 (2019)
  Identifying physical causes of apparent enhanced cyclization of short DNA molecules with a coarse-grained model
• A. Suma, E. Poppleton, M. Matthies, P. Šulc, F. Romano, A.A. Louis, J.P.K. Doye, C. Micheletti, and L. Rovigatti, J. Comput. Chem. 40, 2586-2595 (2019)
  tacoxDNA: a user-friendly web server for simulations of complex DNA structures, from single strands to origami
• B. E. K. Snodin, J. S. Schreck, F. Romano, A.A. Louis and J.P.K. Doye, Nucleic Acids Res. 47, 1585-1597 (2019)
  Coarse-grained modelling of the structural properties of DNA origami

2018

• P. Šulc, J.P.K. Doye and A. A. Louis, in "Quantitative Biology: Theory, Computational Methods, and Models", ed. B. Munsky, W.S. Hlavacek and L.S. Tsimring (MIT Press, 2018), pp. 179-208
  Introduction to molecular simulation
• M.C. Engel, D. M. Smith, M.A. Jobst, M. Sajfutdinow, T. Liedl, F. Romano, L. Rovigatti, A.A. Louis and J.P.K. Doye, ACS Nano, 12, 6734-6747 (2018)
  Force-induced unravelling of DNA Origami
• M.M.C. Tortora and J.P.K. Doye, Mol. Phy. 116, 2773-2791 (2018)
  Incorporating particle flexibility in a density functional description of nematics and cholesterics
• P. Fonseca, F. Romano, J.S. Schreck, T.E. Ouldridge, J.P.K. Doye and A.A. Louis, J. Chem. Phys. 148, 134910 (2018)
  Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly
• Y. Gao, F. Romano, R.P.A. Dullens, J.P.K. Doye and D.G.A.L. Aarts, Phys. Rev. Materials 2, 015601 (2018)
  Directed self-assembly into low-density colloidal liquid crystal phases
• D.C. Khara, J.S. Schreck, T.E. Tomov, Y. Berger, T.E. Ouldridge, J.P.K. Doye and E. Nir, Nucleic Acids Res. 46, 1553-1561 (2018)
  DNA bipedal motor walking dynamics: An experimental and theoretical study of the dependency on step size
• B. Joffroy, Y.O. Uca, D. Prešern, J.P.K. Doye and T.L. Schmidt, Nucleic Acids Res. 46, 538-545 (2018)
  Rolling circle amplification shows a sinusoidal template length-dependent amplification bias

2017

• M.M.C. Tortora and J.P.K. Doye, J. Chem. Phys. 147, 224504 (2017)
  Hierarchical bounding structures for efficient virial computations: Towards a realistic molecular description of cholesterics
• 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
• M.M.C. Tortora and J.P.K. Doye, J. Chem. Phys. 146, 184504 (2017)
  Perturbative density functional methods for cholesteric liquid crystals
• A. Reinhardt, J.S. Schreck, F. Romano and J.P.K. Doye, J. Phys: Condens. Matter, 29, 014006 (2017).
  Self-assembly of two-dimensional binary quasicrystals: A possible route to a DNA quasicrystal

2016

• D. Palagin and J.P.K. Doye, Phys. Chem. Chem. Phys. 18, 22311-22322 (2016)
  DNA-stabilized Ag-Au bimetallic clusters: The effects of alloying and embedding on optical properties
• T. Sutthibutpong, C. Matek, C. Benham, G.G. Slade, A. Noy, C. Laughton, J.P.K. Doye, A.A. Louis and S.A. Harris, Nucleic Acids Res. 44, 9121-9130 (2016)
  Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation
• J. S. Schreck, F. Romano, M.H. Zimmer, A.A. Louis and J.P.K. Doye, ACS Nano, 10, 4236-4247 (2016)
  Characterizing DNA star-tile-based nanostructures using a coarse-grained model
• B.E.K. Snodin, F. Romano, L. Rovigatti, T.E. Ouldridge, A.A. Louis and J.P.K. Doye, ACS Nano, 10, 1724-1737 (2016)
  Direct simulation of the self-assembly of a small DNA origami
• V. Kočar, J.S. Schreck, S. Čeru, H. Gradišar, N. Bašić, T. Pisanski, J.P.K. Doye, and R. Jerala, Nat. Commun. 7, 10803 (2016)
  Design principles for rapid folding of knotted DNA nanostructures

2015

• M. Mosayebi, A.A. Louis, J.P.K. Doye and T.E. Ouldridge, ACS Nano, 9, 11993–12003 (2015)
  Force-induced rupture of a DNA duplex: From fundamentals to force sensors
• C. Matek, P. Šulc, F. Randisi, J.P.K. Doye and A.A. Louis, J. Chem. Phys. 143, 243122 (2015)
  Coarse-grained modelling of supercoiled RNA
• B.E.K. Snodin, F. Randisi, M. Mosayebi, P. Šulc, J.S. Schreck, F. Romano, T.E. Ouldridge, R. Tsukanov, E. Nir, A.A. Louis and J.P.K. Doye, J. Chem. Phys. 142, 234901 (2015)
  Introducing improved structural properties and salt dependence into a coarse-grained model of DNA
• D. Palagin and J.P.K. Doye, Phys. Chem. Chem. Phys. 17, 28010-28021 (2015)
  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. 142, 165101 (2015)
  Characterizing the bending and flexibility induced by bulges in DNA duplexes
• P. Šulc, 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, Nucleic Acids Res. 43, 6181-6190 (2015)
  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

2014

• 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. Šulc, 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. Šulc, 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

2013

• J.P.K. Doye, T.E. Ouldridge, A.A. Louis, F. Romano, P. Šulc, 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. Šulc, J. M. Schaeffer, B. Yurke, A.A. Louis, J.P.K. Doye and E. Winfree, Nucleic Acids Res. 41, 10641-10658 (2013)
  On the biophysics and kinetics of toehold-mediated DNA strand displacement
• T.E. Ouldridge, P. Šulc, F. Romano, J.P.K. Doye and A.A. Louis, Nucleic 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

2012

• A. Reinhardt, J.P.K. Doye, E.G. Noya and C. Vega, J. Chem. Phys. 137, 194504 (2012).
  Local order parameters for use in driving homogeneous ice nucleation with all-atom models of water
• P. Šulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye and A.A. Louis, J. Chem. Phys, 137, 135101 (2012)
  Sequence-dependent thermodynamics of a coarse-grained DNA model
• 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
• A. Reinhardt and J.P.K. Doye, J. Chem. Phys. 136, 054501 (2012).
  Free energy landscapes for homogeneous nucleation of ice for a monatomic model of water
• F. Calvo, J.P.K. Doye and D. J. Wales, Nanoscale, 4, 1085-1100 (2012)
  Energy landscapes of colloidal clusters: Thermodynamics and rearrangement mechanisms

2011

• I.G. Johnston, S.E. Ahnert, A.A. Louis and J.P.K. Doye, Phys. Rev. E 83, 066105 (2011)
  Evolutionary dynamics in a simple model of self-assembly
• A. Reinhardt, A.J. Williamson, J.P.K. Doye, J. Carrete, L.M. Varela and A.A. Louis, J. Chem. Phys. 134, 104905 (2011)
  Reentrant phase behaviour for systems with competition between phase separation and self-assembly
• T.E. Ouldridge, A.A. Louis and J.P.K. Doye, J. Chem. Phys, 134, 085101 (2011)
  Structural, mechanical and thermodynamic properties of a coarse-grained DNA model
• A.J. Williamson, A.W. Wilber, J.P.K. Doye and A.A. Louis, Soft Matter, 7, 3423-3431 (2011)
  Templated self-assembly of patchy particles

2010

• S.E. Ahnert, I.G. Johnston, T.M.A. Fink, J.P.K. Doye and A.A. Louis, Phys. Rev. E 82, 026117 (2010)
  Self-assembly, modularity and physical complexity
• 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 effect of scale-free topology on the robustness and evolvability of genetic regulatory networks
• E.G. Noya, C. Vega, J.P.K. Doye and A. A. Louis, J. Chem. Phys. 132, 234511 (2010)
  The stability of a crystal with diamond structure for patchy particles with tetrahedral symmetry
• T.E. Ouldridge, A.A. Louis and J.P.K. Doye, Phys. Rev. Lett. 104, 178101 (2010)
  DNA nanotweezers studied with a coarse-grained model of DNA
• 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
• T.E. Ouldridge, A.A. Louis and J.P.K. Doye, J. Phys.: Condens. Matter 22, 104102 (2010)
  Extracting bulk properties of self-assembling systems from small simulations

2009

• 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
• A.W. Wilber, J.P.K. Doye and A.A. Louis, J. Chem. Phys. 131, 175101 (2009)
  Self-assembly of monodisperse clusters: Dependence on target geometry
• 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)
  The self-assembly of DNA Holliday junctions studied with a minimal model

2008

• F. Calvo, D. J. Wales, J.P.K. Doye, R.S. Berry, P. Labastie and M. Schmidt, EPL 82, 43003 (2008)
  Comment on `Critical analysis of negative heat capacities in nanoclusters'

2007

• C.P. Massen and J.P.K. Doye, J. Chem. Phys. 127, 114306 (2007)
  Preferential attachment during the evolution of a potential energy landscape
• 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
• E.G. Noya, C. Vega, J.P.K. Doye and A. A. Louis, J. Chem. Phys. 127, 054501 (2007)
  Phase diagram of model anisotropic particles with octahedral symmetry
• 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
• E.G. Noya, J.P.K. Doye, D.J. Wales and A. Aguado, Eur. Phys. J. D 43, 57-60 (2007)
  Geometric magic numbers of sodium clusters: Interpretation of the melting behaviour
• 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
• C.P. Massen and J.P.K. Doye, Phys. Rev. E 75, 037101 (2007)
  Power-law distributions for the areas of the basins of attraction on a potential energy landscape
• C.P. Massen and J.P.K. Doye, Physica A 377, 351-362 (2007)
  A self-consistent approach to measure preferential attachment in networks and its application to an inherent structure network

2006

• C.P. Massen and J.P.K. Doye, cond-mat/0610077
  Thermodynamics of community structure
• J.P.K. Doye and L. Meyer, cond-mat/0604250
  The structure of binary Lennard-Jones clusters: The effects of atomic size ratio
• E.G. Noya and J.P.K. Doye, J. Chem. Phys. 124, 104503 (2006)
  Structural transitions in the 309-atom magic number Lennard-Jones cluster
• J.P.K. Doye and W.C.K. Poon, Curr. Opin. Colloid In. 11, 40-46 (2006)
  Protein Crystallization in vivo
• E.G. Noya, J.P.K. Doye and F. Calvo, Phys. Rev. B 73, 125407 (2006)
  Theoretical study of the melting of aluminum clusters
• J.P.K. Doye, Comp. Mater. Sci. 35, 227-231 (2006)
  Lead clusters: different potentials, different structures
• J.P.K. Doye, in `Global Optimization: Scientific and Engineering Case Studies' (Nonconvex Optimization and Its Applications Series: Vol. 85), ed. J.D. Pinter (Springer, 2006), pp. 103-139
  Physical perspectives on the global optimization of atomic clusters

2005

• J.P.K. Doye and L. Meyer, Phys. Rev. Lett. 95, 063401 (2005)
  Mapping the magic numbers in binary Lennard-Jones clusters
• J.P.K. Doye and C.P. Massen, in `Complexity, Metastability and Nonextensivity', ed. C. Beck, G. Benedek, A. Rapisarda and C. Tsallis (World Scientific, 2005), pp. 375-384
  Energy landscapes, scale-free networks and Apollonian packings
• C.P. Massen and J.P.K. Doye, Phys. Rev. E, 71, 046101 (2005)
  Identifying "communities" within energy landscapes
• J.P.K. Doye and C.P. Massen, J. Chem. Phys. 122, 084105 (2005)
  Characterizing the network topology of the energy landscapes of atomic clusters
• J.P.K. Doye and C.P. Massen, Phys. Rev. E 71, 016128 (2005)
  Self-similar disk packings as model spatial scale-free networks

2004

• J.P.K. Doye, A. A. Louis and M. Vendruscolo, Physical Biology 1, P9-P13 (2004)
  Inhibition of protein crystallization by evolutionary negative design
• F. Calvo and J.P.K. Doye, Phys. Rev. B 69, 125414 (2004)
  Pressure effects on the structure of nanoclusters
• J.P.K. Doye, R.H. Leary, M. Locatelli and F. Schoen, INFORMS J. Comput. 16, 371-379 (2004)
  Global optimization of Morse clusters by potential energy transformations

2003

• J.P.K. Doye and F. Calvo, J. Chem. Phys. 119, 12680-12681 (2003)
  Comment on "Strontium clusters: Many-body potential, energetics, and structural transitions"
• D.J. Wales and J.P.K. Doye, J. Chem. Phys. 119, 12409-12416 (2003)
  Stationary points and dynamics in high-dimensional systems
• J.P.K. Doye, Phys. Rev. B 68, 195418 (2003)
  Identifying structural patterns in 'disordered` metal clusters
• J.P.K. Doye, J. Chem. Phys., 119, 1136-1147 (2003)
  A model metal potential exhibiting polytetrahedral clusters
• F. Baletto, J.P.K. Doye, R. Ferrando and C. Mottet, Surf. Sci. 532-535, 898-904 (2003)
  Adsorption and diffusion on nanoclusters of C₆₀ molecules
• J.P.K. Doye and D.J. Wales, J. Chem. Phys. 118, 5263-5264 (2003)
  Comment on "Quasisaddles as relevant points of the potential energy surface in the dynamics of supercooled liquids"
• J.P.K. Doye, D.J. Wales, F.H.M. Zetterling and M. Dzugutov, J. Chem. Phys. 118, 2792-2799 (2003)
  The favoured cluster structures of model glass formers
• J.P.K. Doye and S.C. Hendy, Eur. Phys. J. D 22, 99-107 (2003)
  On the structure of small lead clusters

2002

• S.C. Hendy and J.P.K. Doye, Phys. Rev. B 66, 235402 (2002)
  Surface-reconstructed icosahedral structures for lead clusters
• F. Calvo, J.P.K. Doye and D.J. Wales, Chem. Phys. Lett. 366, 176-183 (2002)
  Equilibrium properties of clusters in the harmonic superposition approximation
• J.P.K. Doye, Phys. Rev. Lett. 88, 238701 (2002)
  The network topology of a potential energy landscape: A static scale-free network
• J.P.K. Doye and F. Calvo, J. Chem. Phys. 116, 8307-8317 (2002)
  Entropic effects on the structure of Lennard-Jones clusters
• J.P.K. Doye and D.J. Wales, J. Chem. Phys. 116, 3777-3788 (2002)
  Saddle points and dynamics of Lennard-Jones clusters, solids and supercooled liquids
• F. Baletto, J.P.K. Doye and R. Ferrando, Phys. Rev. Lett. 88, 075503 (2002)
  Evidence of kinetic trapping in clusters of C₆₀ molecules
• F. Calvo, J.P.K. Doye and D.J. Wales, J. Chem. Phys. 116, 2642-2649 (2002)
  Collapse of Lennard-Jones homopolymers: size effects and energy landscapes

2001

• J.P.K. Doye, D.J. Wales, W. Branz and F. Calvo, Phys. Rev. B 64, 235409 (2001)
  Modelling the structure of clusters of C₆₀ molecules
• F. Calvo, J.P.K. Doye and D.J. Wales, J. Chem. Phys. 115, 9627-9636 (2001)
  Characterization of anharmonicities on complex potential energy surfaces: Perturbation theory and simulation
• F. Calvo, J.P.K. Doye and D.J. Wales, Phys. Rev. Lett. 87, 119301 (2001)
  Comment on ``Effect of Potential Energy Distribution on the Melting of Clusters''
• J.P.K. Doye and D.J. Wales, Phys. Rev. Lett. 86, 5719-5722 (2001)
  Polytetrahedral clusters
• J.P.K. Doye, D.J. Wales and S.I. Simdyankin, Faraday Discuss. 118, 159-170 (2001)
  Global optimization and the energy landscapes of Dzugutov clusters
• D.J. Wales and J.P.K. Doye, Phys. Rev. B 63, 214204 (2001)
  Dynamics and thermodynamics of supercooled liquids and glasses from a model energy landscape
• F. Calvo, J.P.K. Doye and D.J. Wales, J. Chem. Phys. 114, 7312-7329 (2001)
  Quantum partition functions from classical distributions. Application to rare-gas clusters
• J.P.K. Doye and F. Calvo, Phys. Rev. Lett. 86, 3570-3573 (2001)
  Entropic effects on the size dependence of cluster structure
• F. Calvo and J.P.K. Doye, Phys. Rev. E 63, 010902(R) (2001)
  Entropic tempering: A method for overcoming quasi-ergodicity

2000

• J.P.K. Doye, Phys. Rev. E 62, 8753-8761 (2000)
  The effect of compression on the global optimization of atomic clusters
• D.J. Wales, J.P.K. Doye, M.A. Miller, P.N. Mortenson and T.R. Walsh, Adv. Chem. Phys. 115, 1-111 (2000)
  Energy Landscapes: From Clusters to Biomolecules
• J.P.K. Doye, Polymer 41, 8857-8867 (2000)
  Computer simulations of the mechanism of thickness selection in polymer crystals
• J.P.K. Doye and D. Frenkel, Polymer 41, 1519-1528 (2000) 
  The effect of temperature jumps during polymer crystallization

1999

• J.P.K. Doye and D.J. Wales, J. Chem. Phys. 111, 11070-11079 (1999)
  The dynamics of structural transitions in sodium chloride clusters
• R. H. Leary and J.P.K. Doye, Phys. Rev. E 60, R6320-R6322 (1999)
  Tetrahedral global minimum for the 98-atom Lennard-Jones cluster
• J.P.K. Doye, M.A. Miller and D.J. Wales, J. Chem. Phys. 111, 8417-8428 (1999)
  Evolution of the Potential Energy Surface with Size for Lennard-Jones Clusters
• M.A. Miller, J.P.K. Doye and D.J. Wales, Phys. Rev. E 60, 3701-3718 (1999)
  Structural relaxation in atomic clusters: Master equation dynamics
• J.P.K. Doye and D. Frenkel, J. Chem. Phys. 110, 7073-7086 (1999)
  The mechanism of thickness selection in the Sadler-Gilmer model of polymer crystallization
• J.P.K. Doye, M.A. Miller and D.J. Wales, J. Chem. Phys. 110, 6896-6906 (1999)
  The double-funnel energy landscape of the 38-atom Lennard-Jones cluster
• J.P.K. Doye and D. Frenkel, J. Chem. Phys. 110, 2692-2702 (1999)
  Kinetic Monte Carlo simulations of the growth of polymer crystals
• J.P.K. Doye and D.J. Wales, Phys. Rev. B 59, 2292-2300 (1999)
  Structural transitions and global minima of Sodium Chloride Clusters
• M.A. Miller, J.P.K. Doye and D.J. Wales, J. Chem. Phys. 110, 328-334 (1999)
  Structural relaxation in Morse clusters: Energy landscapes

1998

• J.P.K. Doye and D. Frenkel, J. Chem. Phys. 109, 10033-10041 (1998)
  Crystallization of a polymer on a surface
• J.P.K. Doye, D.J. Wales and M.A. Miller, J. Chem. Phys. 109, 8143-8153 (1998)
  Thermodynamics and the global optimization of Lennard-Jones clusters
• J.P.K. Doye and D. Frenkel, Phys. Rev. Lett. 81, 2160-2163 (1998)
  Mechanism of thickness determination in polymer crystals
• J.P.K. Doye and D.J. Wales, New J. Chem. 22, 733-744 (1998)
  Global minima for transition metal clusters described by Sutton-Chen potentials
• J.P.K. Doye and D.J. Wales, Phys. Rev. Lett. 80, 1357-1360 (1998)
  Thermodynamics of global optimization
• J.P.K. Doye, R.P. Sear and D. Frenkel, J. Chem. Phys. 108, 2134-2142 (1998)
  The effect of chain stiffness on the phase behaviour of isolated homopolymers

1997

• J.P.K. Doye and D.J. Wales, J. Chem. Soc., Faraday Trans. 93, 4233-4244 (1997) 
  Structural consequences of the range of the interatomic potential: a menagerie of clusters
• D.J. Wales and J.P.K. Doye, J. Phys. Chem. A, 101, 5111-5116 (1997)
  Global optimization by basin-hopping and the lowest energy structures of Lennard-Jones clusters containing up to 110 Atoms
• J.P.K. Doye, A. Dullweber and D.J. Wales, Chem. Phys. Lett. 269, 408-412 (1997) 
  Structural predictions for (C₆₀ )_N clusters with an all-atom potential
• D.J. Wales and J.P.K. Doye, J. Chem. Phys. 106, 5296 (1997)
  Comment on ``Relaxation of collective excitations in LJ-13 cluster'' [J. Chem. Phys. 105, 3679 (1996)] 
• J.P.K. Doye and D.J. Wales, Z. Phys. D, 40, 466-468 (1997)
  Thermally-induced surface reconstructions of Mackay icosahedra
• J.P.K. Doye and D.J. Wales, Z. Phys. D, 40, 194-197 (1997)
  Surveying a potential energy surface by eigenvector-following: Applications to global optimisation and the structural transformations of clusters

1996

• J.P.K. Doye, PhD Thesis (University of Cambridge, 1996)
  The structure, thermodynamics and dynamics of atomic clusters (html or postscript)
• J.P.K. Doye and D.J. Wales, J. Phys. B 29, 4859-4894 (1996)
  The effect of the range of the potential on the structure and stability of simple liquids: from clusters to bulk, from sodium to C₆₀
• J.P.K. Doye and D.J. Wales, Chem. Phys. Lett. 262, 167-174 (1996)
  The structure of (C₆₀ )_N clusters
• J.P.K. Doye and D.J. Wales, J. Chem. Phys. 105, 8428-8445 (1996)
  On potential energy surfaces and relaxation to the global minimum 
• D.J. Wales, L.J. Munro and J.P.K. Doye, J. Chem. Soc., Dalton Trans. 611-623 (1996)
  What can calculations employing empirical potentials teach us about bare transition metal clusters?
• J.P.K. Doye and D.J. Wales, Science 271, 484-487 (1996)
  The structure and stability of atomic liquids: from clusters to bulk
• D.J. Wales and J.P.K. Doye, in `Large Clusters of Atoms and Molecules' (NATO ASI Series E: Vol. 313), ed. T.P. Martin (Kluwer Academic, Dordrecht, 1996), pp. 241-279
  Theoretical predictions of structure and thermodynamics in the large cluster regime 

1995

• J.P.K. Doye and D.J. Wales, Chem. Phys. Lett. 247, 339-347 (1995)
  Magic numbers and growth sequences of small face-centred-cubic and decahedral clusters
• J.P.K. Doye, D.J. Wales and R.S. Berry, J. Chem. Phys. 103, 4234-4249 (1995)
  The effect of the range of the potential on the structures of clusters
• D.J. Wales and J.P.K. Doye, J. Chem. Phys. 103, 3061-3070 (1995)
  Coexistence and phase separation in clusters: From the small to the not-so-small regime
• J.P.K. Doye and D.J. Wales, J. Chem. Phys. 102, 9673-9688, (1995)
  An order parameter approach to coexistence in atomic clusters
• J.P.K. Doye and D.J. Wales, J. Chem. Phys. 102, 9659-9672 (1995)
  Calculation of thermodynamic properties of small Lennard-Jones clusters incorporating anharmonicity

1992

• J.P.K. Doye and D.J. Wales, J. Chem. Soc., Far. Trans. 88, 3295-3304 (1992)
  Systematic investigation of the structures and rearrangements of six-atom clusters bound by a model anisotropic potential

Other

• J.P.K. Doye, I.M.Goldby, C.M. Line, S.J. Lloyd, E.P.S. Shellard and D. Tricker, Science & Christian Belief, 7, 117-139 (1995)
  Contemporary perspectives on chance, providence and free will: A critique of some modern authors 

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