Peter Bolhuis is the director of the Van 't Hoff Institute for Molecular Sciences (HIMS). He is Professor Simulation of Biomolecular and Soft Matter Systems. His research is at the intersection of (bio) physical chemistry and statistical mechanics.
Many important chemical processes are activated, such as chemical reactions, biomolecular isomerization and nucleation phenomena. The high barriers involved make the process a rare but important event, determining kinetic rate constants as well as the mechanism. The study of rare events has always been a focal point in the field of molecular simulation, with most invented techniques relying on the identification of a coordinate that describes the progress of the transition. However, in complex molecular systems the a priori definition of a proper reaction coordinate is often impossible, constituting the heart of the rare event problem. Transition path sampling avoids this problem by focusing on dynamical pathways undergoing the activated event, providing the reaction coordinate as a result, that is extracted from the simulated transition pathways. Path sampling has elucidated the dynamics of important molecular processes, including electron transfer, biomolecular proton transfer, protein folding as well as nucleation events. The development of the OpenPathSampling framework has enabled easy and flexible use and implementation of novel path sampling algorithms on large systems.
In this presentation, I will give a brief overview of recent developments and discuss case studies on protein dissociation, DNA base pair rolling, and polymorph selection in methane hydrate nucleation. For the later we have explored novel machine learning approaches to investigate reaction coordinates.
Van 't Hoff Institute for Molecular Sciences (HIMS)/ University of Amsterdam.
Fundamentals and Methods of Chemistry
Scientific research done in the Computational Chemistry and Physics group
Wednesday 11 December
13:50 - 14:20h