研究领域

Theoretical/Biological/Materials

The self-assembly of complex mesoscopic structures, the folding of proteins, and the complicated phenomenology of glasses are all manifestations of the underlying potential energy surface (PES). In each of these fields related ideas have emerged to explain and predict chemical and physical properties in terms of the PES. In studies of clusters and glasses the PES itself is often investigated directly, whereas for proteins and other biomolecules it is also common to define free energy surfaces, as the figure below illustrates for lysozyme. Applications of energy landscape theory in my group range from studies of tunnelling splitting patterns in small molecules to computer simulation of protein folding and misfolding, including aggregation of misfolded proteins. Other active research topics include global optimisation and investigation of how the thermodynamic and dynamic properties of glasses are related to the underlying PES. Two recent advances are now providing new insight into larger systems. Discrete path sampling enables dynamical properties to be obtained efficiently, and is being used to calculate folding rates for proteins. Unexpected connections between dynamics and thermodynamics have also been revealed by the application of catastrophe theory to energy landscapes, and new results are now being obtained to characterize phase transitions.

近期论文

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Benchmarks for Characterization of Minima, Transition States, and Pathways in Atomic, Molecular, and Condensed Matter Systems ST Chill, J Stevenson, V Ruehle, C Shang, P Xiao, JD Farrell, DJ Wales, G Henkelman – Journal of Chemical Theory and Computation (2014) 10, 5476 (DOI: 10.1021/ct5008718) Superposition-Enhanced Estimation of Optimal Temperature Spacings for Parallel Tempering Simulations. AJ Ballard, DJ Wales – Journal of Chemical Theory and Computation (2014) 10, 5599 (DOI: 10.1021/ct500797a) Energy landscapes, folding mechanisms, and kinetics of RNA tetraloop hairpins D Chakraborty, R Collepardo-Guevara, DJ Wales – Journal of the American Chemical Society (2014) 136, 18052 (DOI: 10.1021/ja5100756) The effect of dispersion damping functions on the structure of water clusters J Hernandez-Rojas, DJ Wales – Chemical Physics (2014) 444, 23 (DOI: 10.1016/j.chemphys.2014.09.013) Investigating the solid-liquid phase transition of water nanofilms using the generalized replica exchange method Q Lu, J Kim, JD Farrell, DJ Wales, JE Straub – The Journal of chemical physics (2014) 141, 18C525 (DOI: 10.1063/1.4896513) Large-Scale Density Functional Theory Transition State Searching in Enzymes G Lever, DJ Cole, R Lonsdale, KE Ranaghan, DJ Wales, AJ Mulholland, C-K Skylaris, MC Payne – The Journal of Physical Chemistry Letters (2014) 5, 3614 (DOI: 10.1021/jz5018703) Direct Observation of Intermediates in a Thermodynamically Controlled Solid-State Dynamic Covalent Reaction AM Belenguer, GI Lampronti, DJ Wales, JK Sanders – Journal of the American Chemical Society (2014) 136, 16156 (DOI: 10.1021/ja500707z) Structure prediction for multicomponent materials using biminima D Schebarchov, DJ Wales – Phys Rev Lett (2014) 113, 156102 (DOI: 10.1103/PhysRevLett.113.156102) Communication: Newton homotopies for sampling stationary points of potential energy landscapes. D Mehta, T Chen, JD Hauenstein, DJ Wales – The Journal of chemical physics (2014) 141, 121104 (DOI: 10.1063/1.4896657) Superposition enhanced nested sampling S Martiniani, JD Stevenson, DJ Wales, D Frenkel – Physical Review X (2014) 4, ARTN 031034 (DOI: 10.1103/PhysRevX.4.031034) Communication: optimal parameters for basin-hopping global optimization based on Tsallis statistics. C Shang, DJ Wales – The Journal of chemical physics (2014) 141, 071101 (DOI: 10.1063/1.4893344) Design principles for Bernal spirals and helices with tunable pitch. SN Fejer, D Chakrabarti, H Kusumaatmaja, DJ Wales – Nanoscale (2014) 6, 9448 (DOI: 10.1039/C4NR00324A) Energy landscapes of planar colloidal clusters JW Morgan, DJ Wales – Nanoscale (2014) 6, 10717 (DOI: 10.1039/c4nr02670e) Communication: Analysing kinetic transition networks for rare events JD Stevenson, DJ Wales – The Journal of chemical physics (2014) 141, 041104 (DOI: 10.1063/1.4891356) Structure and Properties of DNA in Apolar Solvents A Arcella, G Portella, R Collepardo-Guevara, D Chakraborty, DJ Wales, M Orozco – J Phys Chem B (2014) 118, 8540 (DOI: 10.1021/jp503816r) Certification and the potential energy landscape. D Mehta, JD Hauenstein, DJ Wales – The Journal of chemical physics (2014) 140, 224114 (DOI: 10.1063/1.4881638) Potential energy landscape of the two-dimensional XY model: Higher-index stationary points D Mehta, C Hughes, M Kastner, DJ Wales – The Journal of chemical physics (2014) 140, 224503 (DOI: 10.1063/1.4880417) An inversion-relaxation approach for sampling stationary points of spin model Hamiltonians. C Hughes, D Mehta, DJ Wales – The Journal of chemical physics (2014) 140, 194104 (DOI: 10.1063/1.4875697) Clusters of Coarse-Grained Water Molecules JD Farrell, DJ Wales – The journal of physical chemistry. A (2014) 118, 7338 (DOI: 10.1021/jp4119666) Chemistry, geometry, and defects in two dimensions. DJ Wales – ACS Nano (2014) 8, 1081 (DOI: 10.1021/nn500645r)