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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

Tilted and helical columnar phases for an axially symmetric discoidal system.
D Chakrabarti, DJ Wales
– Physical review letters
(2008)
100,
127801
Implicit Solvent Models and the Energy Landscape for Aggregation of the Amyloidogenic KFFE Peptide
B Strodel, DJ Wales
– Journal of chemical theory and computation
(2008)
4,
657
Pathways for Conformational Change in Nitrogen Regulatory Protein C from Discrete Path Sampling
M Khalili, DJ Wales
– J Phys Chem B
(2008)
112,
2456
Pathways for Conformational Change in Nitrogen Regulatory Protein C from Discrete Path Sampling.
M Khalili, DJ Wales
– J. Phys. Chem. B
(2008)
112,
2456-2465
Structural trends in clusters of quadrupolar spheres.
M Miller, J Shepherd, D Wales
– Mol. Phys.
(2008)
106,
1655-1664
Implicit solvent models and the energy landscape for aggregation of the amyloidogenic KFFE peptide
B Strodel, DJ Wales
– J. Chem. Theor. Comput.
(2008)
4,
657-672
Protein structure prediction using basin-hopping (9 pages).
MC Prentiss, DJ Wales, PG Wolynes
– J. Chem. Phys.
(2008)
128,
225106
Relaxation of caloric curves on complex potential energy surfaces (10 pages).
F Calvo, DJ Wales
– J. Chem. Phys.
(2008)
128,
154501
Geometry optimization for peptides and proteins: Comparison of Cartesian and internal coordinates
EF Koslover, DJ Wales
– The Journal of Chemical Physics
(2007)
127,
234105
Thermodynamics and kinetics of aggregation for the GNNQQNY peptide
B Strodel, CS Whittleston, DJ Wales
– Journal of the American Chemical Society
(2007)
129,
16005
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Research Group

Research Interest Groups

Telephone number

01223 336354

Email address

dw34@cam.ac.uk