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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

Go-Kit: A Tool To Enable Energy Landscape Exploration of Proteins.
S Neelamraju, DJ Wales, S Gosavi
– Journal of chemical information and modeling
(2019)
acs.jcim.9b00007
Dynamics of an adenine-adenine RNA conformational switch from discrete path sampling.
D Chakraborty, DJ Wales
– Journal of Chemical Physics
(2019)
150,
125101
Energy Landscapes for Proteins: From Single Funnels to Multifunctional Systems
K Röder, JA Joseph, BE Husic, DJ Wales
– Advanced Theory and Simulations
(2019)
2,
1800175
Energy Landscape for Fold-Switching in Regulatory Protein RfaH.
JA Joseph, D Chakraborty, DJ Wales
– J Chem Theory Comput
(2018)
15,
731
Computational Investigation of RNA A-Bulges Related to the Microtubule-Associated Protein Tau Causing Frontotemporal Dementia and Parkinsonism.
DJ Wales, MD Disney, I Yildirim
– Journal of Physical Chemistry B
(2019)
123,
57
Intrinsically Disordered Landscapes for Human CD4 Receptor Peptide
JA Joseph, DJ Wales
– J Phys Chem B
(2018)
122,
11906
Evolved Minimal Frustration in Multifunctional Biomolecules.
K Röder, DJ Wales
– The Journal of Physical Chemistry B
(2018)
122,
10989
Mapping Surface Hydrophobicity of α-Synuclein Oligomers at the Nanoscale
J-E Lee, JC Sang, M Rodrigues, AR Carr, MH Horrocks, S De, MN Bongiovanni, P Flagmeier, CM Dobson, DJ Wales, SF Lee, D Klenerman
– Nano letters
(2018)
18,
7494
Mutational Basin-Hopping: Combined Structure and Sequence Optimization for Biomolecules
K Röder, DJ Wales
– The Journal of Physical Chemistry Letters
(2018)
9,
6169
Analysis of the Ub to Ub-CR transition in ubiquitin
K Röder, DJ Wales
– Biochemistry
(2018)
57,
6180
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Research Group

Research Interest Groups

Telephone number

01223 336354

Email address

dw34@cam.ac.uk