Projects per year
I am an EPSRC Research Software Engineer (RSE) Fellow. My role is to help researchers develop more flexible, performant and sustainable software. I work in the Advanced Computing Research Centre and the School of Chemistry, and have developed a range of programming and computational chemistry teaching resources that are available here. I am a strong supporter of the campaign to recognise the importance of research software, and to improve career pathways for research software engineers and developers, and am one of the founding trustees of the Society of Research Software Engineering.
I now run the Research Software Engineering Group at the University of Bristol. In this position I collaborate on a range of projects across the University. These cover everything from developing infrastructure for cloud computing, through building interoperable frameworks for molecular simulations, using machine learning for image analysis to creating bespoke data visualisations for temporal social networks.
Prior to this, my computational chemistry research career focussed on the development of new methods and software for biomolecular simulation. I am particularly interested in developing novel Monte Carlo algorithms for sampling multiscale models, I have developed two major pieces of molecular simulation software; Sire, and ProtoMS. I use these programs to develop new methods to enhance the accuracy, speed and precision of biomolecular simulations.
I am particulary interested in modelling and predicting molecular recognitiion. To this end, I have developed the waterswap and ligandswap methods, that allows for direct calculation of absolute and relative protein-ligand binding free energies from a single simulation, together with decompositions to per-residue and per-water components. I have also developed new methods that allow for rapid Monte Carlo sampling of systems modelled using multiscale quantum mechanics / molecular mechanics (QM/MM) Hamiltonians, and am applying these ideas to the calculation of relative protein/ligand binding free energies, and to investigate the free energy profiles of enzyme-catalysed reactions.
Structured keywords and research groupings
4/07/16 → 3/07/21
4/07/21 → 30/09/21
1/05/21 → 30/04/24
Computer-aided whole-cell design: taking a holistic approach by integrating synthetic with systems biologyMarucci, L., Barberis, M., Karr, J., Ray, O., Race, P. R., de Souza Andrade, M., Grierson, C. S., Hoffmann, S. A., Landon, S., Rech, E., Rees-Garbutt, J. P., Seabrook, R., Shaw, W. & Woods, C. J., 7 Aug 2020, In: Frontiers in Bioengineering and Biotechnology. 8, 11 p., 942.
Research output: Contribution to journal › Article (Academic Journal) › peer-reviewOpen AccessFile45 Downloads (Pure)
Oliveira, A. S. F., Edsall, C. J., Woods, C. J., Bates, P., Nunez, G. V., Wonnacott, S., Bermudez, I., Ciccotti, G., Gallagher, T., Sessions, R. B. & Mulholland, A. J., 26 Dec 2019, In: Journal of the American Chemical Society. 141, 51, p. 19953-19958 6 p., 51.
Research output: Contribution to journal › Article (Academic Journal) › peer-reviewOpen AccessFile2 Citations (Scopus)18 Downloads (Pure)
Mulholland, A. J., Woods, C. J. & Michel, J., 22 Nov 2019, In: Journal of Open Source Software. 4, 1831.
Research output: Contribution to journal › Article (Academic Journal) › peer-reviewOpen AccessFile56 Downloads (Pure)