EC Math TP CH 17


Hybrid reaction-diffusion-Markov-state model of systems with many interaction molecules


Freie Universität Berlin



Financial support:

Einstein Center for Mathematics


Jun 01, 2017 — Dec 31, 2018

While simulations of detailed molecular structure, e.g. using atomistic or coarse- grained MD simulation is able to describe the evolution of molecular systems at length/timescales of nanometers/milliseconds, we require a way to bridge from the molecular scale to large-scale/long-time evolutions of molecular superstructures such as actin networks on the scale of micrometers/hours. Such time- and lengthscales while still maintaining some structural, and importantly single-molecule resolution, can be covered by particle-based reaction-diffusion simulations. Molecular kinetic models of small parts of the overall machinery (single molecules and small complexes) can be parametrized with high-throughput MD simulations, enhanced sampling simu- lations, possibly by incorporating constraints from experimental data. In order to ex- plore the long-range and long-time behavior of mixtures and superstructures of many molecules, we set out ot develop a rigorous and computationally efficient coupling be- tween molecular kinetics models and particle-based reaction-diffusion dynamics