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Yusuf Hamied Department of Chemistry

 

Professor of Chemical Physics

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.

Publications

Computational investigation of RNA CUG repeats responsible for myotonic dystrophy 1.
I Yildirim, D Chakraborty, MD Disney, DJ Wales, GC Schatz
– J Chem Theory Comput
(2015)
11,
4943
Mapping Structural Changes in Electrode Materials: Application of the Hybrid Eigenvector-Following Density Functional Theory (DFT) Method to Layered Li0.5MnO2
ID Seymour, S Chakraborty, DS Middlemiss, DJ Wales, CP Grey
– Chemistry of Materials
(2015)
27,
5550
Markov state modeling and dynamical coarse-graining via discrete relaxation path sampling
B Fačkovec, E Vanden-Eijnden, DJ Wales
– J Chem Phys
(2015)
143,
044119
Hydroxyproline Ring Pucker Causes Frustration of Helix Parameters in the Collagen Triple Helix
WY Chow, D Bihan, CJ Forman, DA Slatter, DG Reid, DJ Wales, RW Farndale, MJ Duer
– Sci Rep
(2015)
5,
12556
Energy landscapes of a hairpin peptide including NMR chemical shift restraints
JM Carr, CS Whittleston, DC Wade, DJ Wales
– Phys Chem Chem Phys
(2015)
17,
20250
Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory
Z Cournia, TW Allen, I Andricioaei, B Antonny, D Baum, G Brannigan, N-V Buchete, JT Deckman, L Delemotte, C Del Val, R Friedman, P Gkeka, H-C Hege, J Hénin, MA Kasimova, A Kolocouris, ML Klein, S Khalid, MJ Lemieux, N Lindow, M Roy, J Selent, M Tarek, F Tofoleanu, S Vanni, S Urban, DJ Wales, JC Smith, A-N Bondar
– Journal of Membrane Biology
(2015)
248,
611
Intrinsically Disordered Energy Landscapes
Y Chebaro, AJ Ballard, D Chakraborty, DJ Wales
– Scientific reports
(2015)
5,
10386
Exploring the potential energy landscape of the Thomson problem via Newton homotopies.
D Mehta, T Chen, JWR Morgan, DJ Wales
– The Journal of chemical physics
(2015)
142,
194113
Quasi-combinatorial energy landscapes for nanoalloy structure optimisation
D Schebarchov, DJ Wales
– Physical Chemistry Chemical Physics
(2015)
17,
28331
Equilibrium Molecular Thermodynamics from Kirkwood Sampling
S Somani, Y Okamoto, AJ Ballard, DJ Wales
– The Journal of Physical Chemistry B
(2015)
119,
6155
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Research Group

Research Interest Groups

Telephone number

01223 336354

Email address

dw34@cam.ac.uk