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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

Energy Landscapes of Deoxyxylo- and Xylo-Nucleic Acid Octamers.
DJ Sharpe, K Röder, DJ Wales
– Journal of Physical Chemistry B
(2020)
124,
4062
From sticky-hard-sphere to Lennard-Jones-type clusters
L Trombach, RS Hoy, DJ Wales, P Schwerdtfeger
– Physical Review E
(2020)
97,
043309
Affinity-Selected Bicyclic Peptide G-Quadruplex Ligands Mimic a Protein-like Binding Mechanism.
KC Liu, K Röder, C Mayer, S Adhikari, DJ Wales, S Balasubramanian
– J Am Chem Soc
(2020)
142,
8367
Defining, Calculating, and Converging Observables of a Kinetic Transition Network.
TD Swinburne, DJ Wales
– J Chem Theory Comput
(2020)
16,
2661
Perspective: New insights from loss function landscapes of neural networks
SR Chitturi, PC Verpoort, AA Lee, DJ Wales
– Machine Learning: Science and Technology
(2020)
1,
023002
Counterion‐Trapped‐Molecules: From High Polarity and Enriched IR Spectra to Induced Isomerization
FY Naumkin, DJ Wales
– Chemphyschem : a European journal of chemical physics and physical chemistry
(2020)
21,
348
Multifunnel Energy Landscapes for Phosphorylated Translation Repressor 4E-BP2 and Its Mutants.
W Kang, F Jiang, Y-D Wu, DJ Wales
– Journal of Chemical Theory and Computation
(2020)
16,
800
A multifunnel energy landscape encodes the competing $\alpha$-helix and $\beta$-hairpin conformations for a designed peptide
D Chakraborty, Y Chebaro, DJ Wales
– Physical chemistry chemical physics : PCCP
(2020)
22,
1359
Flip rearrangement in the water pentamer: Analysis of electronic structure
T Xu, X Bin, SR Kirk, DJ Wales, S Jenkins
– International Journal of Quantum Chemistry
(2019)
120,
ARTN e26124
Nested Basin-Sampling
D Wales, M Griffiths
– Journal of Chemical Physics
(2019)
15,
6865
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Research Group

Research Interest Groups

Telephone number

01223 336354

Email address

dw34@cam.ac.uk