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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

Free energy surfaces from an extended harmonic superposition approach and kinetics for alanine dipeptide
B Strodel, DJ Wales
– Chem. Phys. Lett.
(2008)
466,
105
Energy landscapes for diffusion: Analysis of cage-breaking processes (13 pages).
VK de Souza, DJ Wales
– Journal of Chemical Physics
(2008)
129,
164507
PHYS 96-Protein folding using basin-hopping and energy landscapes
MC Prentiss, DJ Wales, PG Wolynes
– ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY
(2008)
236,
Folding pathways and rates for the three-stranded β-sheet peptide Beta3s using discrete path sampling
JM Carr, DJ Wales
– Journal of Physical Chemistry B
(2008)
112,
8760
Characterizing the first steps of amyloid formation for the ccβ peptide
B Strodel, AW Fitzpatrick, M Vendruscolo, CM Dobson, DJ Wales
– Journal of Physical Chemistry B
(2008)
112,
9998
Protein structure prediction using basin-hopping
MC Prentiss, DJ Wales, PG Wolynes
– The Journal of chemical physics
(2008)
128,
225106
Structural trends in clusters of quadrupolar spheres
MA Miller, JJ Shepherd, DJ Wales
– Molecular Physics
(2008)
106,
1655
Energy landscape of a model discotic liquid crystal
D Chakrabarti, DJ Wales
– Phys. Rev. E
(2008)
77,
051709
Comment on "Critical analysis of negative heat capacities in nanoclusters" by Michaelian K. and Santamaria-Holek I.
F Calvo, DJ Wales, JPK Doye, RS Berry, P Labastie, M Schmidt
– Europhys. Lett.
(2008)
82,
43003
Relaxation of caloric curves on complex potential energy surfaces.
F Calvo, DJ Wales
– Journal of Chemical Physics
(2008)
128,
154501
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Research Group

Research Interest Groups

Telephone number

01223 336354

Email address

dw34@cam.ac.uk