Alan Mark

We use computer based modelling techniques to understand and predict the the structural and dynamic properties of (bio)molecules including proteins and lipid aggregates.

Born in 1961, I obtained a BSc (Hon 1) at the University of Sydney in 1982. I obtained my PhD in 1986 from the John Curtin School of Medical Research, Australian National University (ANU), on the "Binding Responses Associated with Self-Interacting Ligands: Studies on the Self-Association and Receptor binding of Insulin”. After holding postdoctoral positions at the ANU, University of Groningen, The Netherlands and the Federal Institute of Technology (ETH), Zurich, Switzerland I was appointed Professor of Biophysical Chemistry (Molecular Simulation) University of Groningen, in 1998. In 1998 I also received the Swiss Ruzicka Prize for research in Chemistry for work on simulating peptide folding. In 2004 I was awarded an ARC Federation Fellowship and in February 2005 an honorary chair (Bijzonder Hoogleraar) at the University of Groningen, The Netherlands. I have given over 90 invited lectures at conferences and academic Institutions around the world as well as at a range of summer and winter schools on advanced simulation techniques.

In my research I have performed pioneering simulations of a variety of important biological phenomena, including some of the first atomic simulations of protein unfolding and the first simulations of reversible peptide folding in a realistic environment. In recent years my group performed some of the first atomic and near atomic simulations of the spontaneous aggregation of surfactant and lipid systems into micelles, bilayers and vesicles. These have enabled us, amongst other things, to elucidate the mechanism by which pores are induced within biological membranes in unprecedented detail. Over the last decade I have been intimately involved in the development of the GROMOS force field which is specifically tuned for protein and peptide folding simulations and as well as the development of models for a range of solvents including methanol and trifluoroethanol. I have also been responsible for the development of methodology for the calculations of the thermodynamic properties of biomolecular systems such as free energies of binding and hydration, as well as estimating entropic effects from simulations. Most recently, I have been responsible for the development of novel approaches to promote structure formation in protein folding simulations that can be used for the refinement of protein structures generated by ab initio or by homology methods. Finally, I am associated with two, internationally recognised, (bio)molecular simulation packages the GROningen Molecular Simulation library (GROMOS) and the GROningen Machine for Chemical Simulations (GROMACS).