Abstract

I will discuss methods for spatio-temporal modelling in molecular and cell biology, including all-atom and coarse-grained molecular dynamics (MD) and stochastic reaction-diffusion models, with the aim of developing and analysing multiscale methods which use MD simulations in parts of the computational domain and (less-detailed) stochastic reaction-diffusion approaches in the remainder of the domain. The main goal of this multiscale methodology is to use a detailed modelling approach in localized regions of particular interest (in which accuracy and microscopic details are important) and a less detailed model in other regions in which accuracy may be traded for simulation efficiency. Applications using all-atom MD include intracellular dynamics of ions and ion channels. Applications using coarse-grained MD include protein binding to receptors on the cellular membrane, where modern stochastic reaction-diffusion simulators of intracellular processes can be used in the bulk and a ccurately coupled with a (more detailed) MD model of protein binding which is used close to the membrane.

References:
[1] Radek Erban, “Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics”, Proceedings of the Royal Society A, Volume 472, Number 2186, 20150556 (2016)
[2] Radek Erban, “From molecular dynamics to Brownian dynamics”, Proceedings of the Royal Society A, Volume 470, Number 2167, 20140036 (2014)

Related Links

• http://rspa.royalsocietypublishing.org/content/472/2186/20150556 – Reference [1]
• http://rspa.royalsocietypublishing.org/content/470/2167/20140036 – Reference [2]
• http://people.maths.ox.ac.uk/erban/ – Preprints