Head(s): Prof. Dr. Felix Höfling (FU Berlin), Prof. Dr. Frank Noé (FU Berlin), Prof. Dr. Christof Schütte (FU Berlin)
Project member(s): Dr. Rainald Ehrig, Katarina Elez, Dr. Daniela Frömberg, Dr. Arthur Straube, Dr. Stefanie Winkelmann
Participating institution(s): FU Berlin, ZIB

Project Summary

Chemical reactions cover many length scales from the formation of chemical bonds at the atomistic scale up to the physiological response of a whole cell or the size of a chemical reactor. Concomitantly, copy numbers may vary drastically between molecular species and as a function of time, covering many orders of magnitude. In biological and technological applications, complex geometrical landscapes may arise from cellular crowding or nanoporous grains. Simulations of such situations are thus facing a number of challenges, which need to be overcome by efficient modelling.
In C03 we want to push the methodological boundaries of modelling reaction kinetics in different regimes of the scaling cascades (low and high particle concentrations, fast and slow diffusion), and the scaling transitions between them. In the first funding period, significant progress has been achieved regarding models for different levels of resolution (mathematical foundations, new hybrid models coupling different levels, and their algorithmic realisation and practical use).
In the subsequent funding period, we aim at (i) a seamless integration of models for specific scaling regimes into hybrid models for real-life systems where population numbers may vary dramatically; (ii) developing rigorous particle-based reaction dynamics schemes with particle interaction forces and characterising the effect of molecular crowding on reaction kinetics; (iii) derive effective particle-based reaction dynamics schemes that account for crowded media and establish the coarse-graining transition to the spatiotemporal Master equation; (iv) bridging particle-based reaction dynamics with molecular dynamics (MD), both in order to obtain kinetic parameters for the reaction dynamics simulation, and to form a multiscale simulation method.

Publications C03