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Yusuf Hamied Department of Chemistry

 
Portrait of dw34

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

Numerical analysis of first-passage processes in finite Markov chains exhibiting metastability
DJ Sharpe, DJ Wales
– Physical Review E
(2021)
104,
015301
Graph transformation and shortest paths algorithms for finite Markov chains
DJ Sharpe, DJ Wales
– Physical Review E: Statistical, Nonlinear, and Soft Matter Physics
(2021)
103,
063306
Side-Chain Polarity Modulates the Intrinsic Conformational Landscape of Model Dipeptides.
D Chakraborty, A Banerjee, DJ Wales
– The Journal of Physical Chemistry B: Biophysical Chemistry, Biomaterials, Liquids, and Soft Matter
(2021)
125,
5809
Surface Chirality Influences Molecular Rotation upon Desorption.
SC Matysik, DJ Wales, SJ Jenkins
– Phys Rev Lett
(2021)
126,
166101
Crystal structure prediction for benzene using basin-hopping global optimization
A Banerjee, D Jasrasaria, SP Niblett, DJ Wales
– The Journal of Physical Chemistry A
(2021)
125,
3776
Development of ReaxFF Reactive Force Field for Aqueous Iron–Sulfur Clusters with Applications to Stability and Reactivity in Water
E Moerman, D Furman, DJ Wales
– J Chem Inf Model
(2021)
61,
1204
Optimal dimensionality reduction of Markov chains using graph transformation.
D Kannan, DJ Sharpe, TD Swinburne, DJ Wales
– J Chem Phys
(2020)
153,
244108
Energy Landscapes for Electronic Structure.
HGA Burton, DJ Wales
– Journal of chemical theory and computation
(2020)
17,
151
Systematic Evaluation of ReaxFF Reactive Force Fields for Biochemical Applications
E Moerman, D Furman, DJ Wales
– Journal of chemical theory and computation
(2020)
17,
497
Rare events and first passage time statistics from the energy landscape.
TD Swinburne, D Kannan, DJ Sharpe, DJ Wales
– J Chem Phys
(2020)
153,
134115
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Research Group

Research Interest Groups

Telephone number

01223 336354

Email address

dw34@cam.ac.uk