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Yusuf Hamied Department of Chemistry

 

My research is concerned with the development of algorithms for the efficient simulation and analysis of Markov chain dynamics. Finite Markov chains are discrete-state stochastic models that are used to represent the dynamics of many processes. Examples of tangible applications include modeling financial markets and the distribution of species populations in an ecosystem. Markov chains are also commonly used as representations of the dynamics of condensed matter, biophysical, and biochemical systems. The analysis and simulation of Markov chains representing realistic processes, which typically feature a "rare event" that is of particular interest, is plagued by numerical and efficiency issues. To obtain the rare event trajectories and analyse characteristic features of the transition of interest, special enhanced sampling methodologies and numerically stable algorithms must be used.

I am the developer of the DISCOTRESS (DIscrete Time COntinuous State Rare Event Simulation Suite) for simulation and analysis of the dynamics for arbitrary Markov chains. Visit github.com/danieljsharpe

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

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
(2021)
103,
063306
Optimal dimensionality reduction of Markov chains using graph transformation
D Kannan, DJ Sharpe, TD Swinburne, DJ Wales
– J Chem Phys
(2020)
153,
244108
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
Efficient and exact sampling of transition path ensembles on Markovian networks
DJ Sharpe, DJ Wales
– The Journal of Chemical Physics
(2020)
153,
024121
Energy Landscapes and Hybridization Pathways for DNA Hexamer Duplexes
S Xiao, DJ Sharpe, D Chakraborty, DJ Wales
– Journal of Physical Chemistry Letters
(2019)
10,
6771
Identifying mechanistically distinct pathways in kinetic transition networks
DJ Sharpe, DJ Wales
– The 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
– Journal of chemical theory and computation
(2018)
14,
684
Energy landscapes and dynamics of xylo-nucleic acids
DJ Sharpe, K Roeder, DJ Wales

Research Group

Telephone number

01223 336350 (shared)