Molecular dynamics and computational biochemistry

Molecular dynamics (MD) approaches, based on the rules of classical mechanics, are commonly used to study the behaviour of complex biomolecules in biological applications. They are given as systems of ordinary or stochastic differential equations for the time evolution of positions and velocities of particles, representing either individual atoms or groups of atoms, describing parts of a biomolecule. At much coarser level, biomolecules and their interactions can also be modelled by Brownian dynamics (BD) approaches and other stochastic reaction-diffusion models.

In the WCMB, we investigate connections between MD and BD, focusing on limiting theorems guaranteeing convergence of an MD model to a coarser stochastic description, given by the (generalized) Langevin dynamics written in terms of a relatively low-dimensional stochastic dynamical system. Understanding of this limiting process helps us to develop and analyze multi-resolution methods for spatio-temporal modelling of intracellular processes. These methods use detailed MD simulations in localized regions of particular interest (in which accuracy and microscopic details are important) and a coarser (less-detailed) model in other regions where  accuracy may be traded for simulation efficiency. 

Key contact: Radek Erban - @email
References:
  • R. Erban and S. J. Chapman (2019). Stochastic Modelling of Reaction-Diffusion Processes, Cambridge Texts in Applied Mathematics, Cambridge University Press, ISBN 9781108498128
  • R. Gunaratne, D. Wilson, M. Flegg and R. Erban (2019). Multi-resolution dimer models in heat baths with short-range and long-range interactions, Interface Focus 9: rsfs.2018.0070
  • R. Erban (2016). Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics. Proceedings of the Royal Society A472: 20150556
  • R. Erban (2014). From molecular dynamics to Brownian dynamics. Proceedings of the Royal Society A470: 20140036
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