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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

Supercooled Lennard-Jones liquids and glasses:: a kinetic Monte Carlo approach
J Hernandez-Rojas, DJ Wales
– Journal of Non-Crystalline Solids
(2004)
336,
218
Some further applications of discrete path sampling to cluster isomerization
DJ Wales
– Molecular Physics
(2004)
102,
891
Comparison of kinetic Monte Carlo and molecular dynamics simulations of diffusion in a model glass former.
TF Middleton, DJ Wales
– The Journal of Chemical Physics
(2004)
120,
8134
A coarse-graining of energy landscape of proteins - Structural stability of the most stable states
K Hoshino, Y Matsunaga, M Miller, DJ Wales, T Komatsuzaki
– Aip Conference Proceedings
(2004)
708,
344
An ab initio study of tunneling splittings in the water dimer.
Y Watanabe, T Taketsugu, DJ Wales
– The Journal of Chemical Physics
(2004)
120,
5993
A doubly nudged elastic band method for finding transition states.
SA Trygubenko, DJ Wales
– J. Chem. Phys.
(2004)
120,
2082
Chemistry. Energy Landscapes: Applications to Clusters, Biomolecules and Glasses D. J. Wales
DC Clary
– Sci.
(2004)
305,
1108-1109
The dynamics of conformational isomerization in flexible biomolecules. II. Simulating isomerizations in a supersonic free jet with master equation dynamics
DA Evans, DJ Wales, BC Dian, TS Zwier
– The Journal of Chemical Physics
(2004)
120,
148
The dynamics of conformational isomerization in flexible biomolecules. II. Simulating isomerizations in a supersonic free jet with master equation dynamics
DA Evans, DJ Wales, BC Dian, TS Zwier
– J. Chem. Phys.
(2004)
120,
148-157
Some further applications of discrete path sampling to cluster isomerization
DJ Wales
– Mol. Phys.
(2004)
102,
891-908
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Research Group

Research Interest Groups

Telephone number

01223 336354

Email address

dw34@cam.ac.uk