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Department of Chemistry

 

My research is concerned with the construction and analysis of kinetic transition networks for complex transitions in biomolecules and especially of DNA and RNA. Representing the dynamics of a biomolecular system as a kinetic transition network is desirable, since the network allows for retaining the full dimensionality of the system, rather than having to project onto a small number of order parameters. Furthermore, the geometry optimisation approach to constructing a network avoids explicit dependence on time, making the method a powerful tool for studying processes with long experimental timescales due to the existence of high energetic barriers, as is the case for protein and DNA folding.

Kinetic transition networks contain all thermodynamic and kinetic information of the system they represent. I am interested in implementing algorithms to analyse kinetic transition networks, with the aim of better understanding the fundamental features of biomolecular transitions. Algorithms to probe the existence of competing pathways, the identification of conformational ensembles, and the determination of dynamic bottlenecks are all valuable tools for gaining insight into the behaviour of biomolecules and the importance of such features to their biological function.

I previously studied at Van Mildert College, Durham University, obtaining a 1st class (Hons.) MChem degree and being awarded the Vice Chancellor’s Scholarship and Prize for Mastership of chemistry. I am a recipient of a Vice Chancellor’s Scholarship Award to study for a PhD at the University of Cambridge.

Publications

Energy Landscapes and Hybridization Pathways for DNA Hexamer Duplexes
S Xiao, DJ Sharpe, D Chakraborty, DJ Wales
– The Journal of Physical Chemistry Letters
(2019)
10,
6771
Identifying mechanistically distinct pathways in kinetic transition networks
DJ Sharpe, DJ Wales
– Journal of Chemical Physics
(2019)
151,
124101
Approximating the Shifted Hartree-Exchange-Correlation Potential in Direct Energy Kohn–Sham Theory
DJ Sharpe, M Levy, DJ Tozer
– J Chem Theory Comput
(2018)
14,
684
Energy landscapes and dynamics of xylo-nucleic acids
DJ Sharpe, K Roeder, DJ Wales

Research Group

Telephone number

01223 336350 (shared)

Email address

djs244@cam.ac.uk