Profile

Career

2008 -	Senior Lecturer	Department of Biology, University of York
2002 - 2008	Lecturer in Structural Bioinformatics	Department of Biology, University of York
1997 - 2002	Lecturer in Computational Chemistry	Department of Chemistry, University of York
1994 - 1997	Teaching & Research Fellow	Department of Chemistry, University of York
1991 - 1994	NATO/SERC Postdoctoral Research Fellow	Department of Chemistry, Harvard University
1989 - 1990	Postdoctoral Research Fellow	Department of Chemistry, University of York
1985 - 1989	DPhil	Department of Chemistry, University of York
1982 - 1985	BSc (Hons)	Department of Chemistry, University of Birmingham

Research

Overview

Modelling & Simulation of Complex Systems: simulation of complex biosystems. e.g. biomolecular self-assembly processes; emergent properties of artificial chemistries. Data Science: methods & tools for exploratory data analysis and visualisation for biosystems. Discoveries Complexity pervades.

Current projects

• Alastair Droop, Post Doc project: Analysis of gene expression patterns in human cancer (with Prof. Norman Maitland)
• Karim ElSawy, Post Doc Project: Computer simulation of biomolecular assembly processes (with Prof. Reidun Twarock)
• Self-assembly of biomolecules – an energy landscape approach (with Dr. Reidun Twarock, Maths/Biology) ( Funding body: Leverhulme)
• The TRANSIT Programme – Discipline Bridging at the University of York (Funding body: EPSRC)
• Artificial Biochemical Networks: Computational Models and Architectures (Funding body: EPSRC)
• Large-scale analysis of multiple microarray datasets to identify correlated gene expression patterns in human cancer (with Prof. Norman Maitland) (Funding body: Yorkshire Cancer Research)

Research group(s)

Status	Name	Project
Post doctoral fellow	Alastair Droop	Modelling reserve mobilisation and germination in oilseeds (joint with Prof. I. Graham, CNAP)
Post doctoral fellow	Dr Karim M ElSawy	Energy landscapes of biomolecular systems (with Dr. Reidun Twarock)
Research student	Adam Faulconbridge	Artificial Chemistry for Artificial Life (joint with Prof. S. Stepney, Computer Science and Dr. Julian Miller, Electronics

    
       

Available PhD research projects

Dynamics of biomolecular association processes (for 2011-12)
How life emerges from complex molecular interactions is a key question for modern biology. Complex biosystems arise from the orchestrated production of many biomolecules, which then associate to form intricate networks that involve both transient interactions and/or stable assemblies. We seek to study the details of biomolecular interaction processes ranging from long-range diffusional encounters, to the details of how native complexes form after the initial encounter. In collaboration with mathematicians and experimental bioscientists we will use computer simulation techniques (such as Brownian Dynamics, Molecular Dynamics) to study the detailed structural and energetic aspects of biomolecular association. Of particular interest is the study of the spontaneous self-assembly of viral capsids from their protein building blocks in collaboration with Prof. Reidun Twarock.

Publications

Selected publications

Elsawy KM, Caves LSD, Twarock R (2010) The Impact of Viral RNA on the Association Rates of Capsid Protein Assembly: Bacteriophage MS2 as a Case Study. J Mol Biol 368 1231-1248

B. R. Brooks et al (2009) CHARMM: The biomolecular simulation programme Journal of Computational Chemistry 30(10): 1545-1614

Elsawy KM, Caves LSD and Twarock R (2008) Polyomaviridae assembly polymorphism from an energy landscape perspective Computational and Mathematical Methods in Medicine 9: 245-256

Danks GB Stepney S and Caves LSD (2008) Protein Folding with Stochastic L-Systems in Artificial Life XI: Proceeds. of the 11th Int. Conf. on the Simulation and Synthesis of Living Systems (MIT Press,): 50-157

Grant BJ, McCammon JA, Caves LSD and Cross R (2007) Multivariate analysis of conserved sequence-structure relationships in kinesins: coupling of the active site and a tubulin-binding subdomain J. Mol. Biol. 368: 1231-1248

Danks GB, Stepney S and Caves LSD (2007) Folding Protein-Like Structures with Open L-Systems Lecture Notes In Computer Science 4648: 1100-1109

External activities

Memberships

• Member, Management Group Collaborative Computational Project in Biomolecular Simulation (CCPB)