Idiosyncracies in Multi-Spatial Modeling

Henning, Philipp and Köster, Till and Uhrmacher, Adelinde M. (2017) Idiosyncracies in Multi-Spatial Modeling. In: 15th Conference on Computational Methods in Systems Biology (CMSB 2017), 27-29 Sep 2017, Darmstadt, Germany. Poster.

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Abstract

A plethora of different approaches have recently been developed allow for simulating of cell biological systems at different spatial resolutions. However, to move from one spatial resolution to the next requires some careful treatment and often additional information. Thus, we investigate the transformation of a deterministic, non-spatial regime, such as ordinary differential equations, over several steps, for example reaction diffusion master equation, to a more realistic, particle-based regime with particle-particle interaction potentials. We show how the required knowledge about the system changes in the different regimes and how this affects the dynamics of the generic reversible reaction A+B <-> C. The treatment of such a reaction is a common problem [1] in particle-based approaches and it’s not trivial to reproduce the correct equilibrium. Based on the particle-particle interaction potentials and the resulting forces in our particle-based approach [2] we developed a new method to handle backward-reactions and generate the right equilibrium. Furthermore, this approach also allows us to add external forces to particles to simulate directed processes, which is often the case in cells (e.g. by a transport molecule). In a pure Brownian system such a process cannot be simulated [3].