Head(s): Prof. Dr. Christof Schütte (FU Berlin, ZIB), Dr. Stefanie Winkelmann (ZIB), Prof. Dr. Roland Netz (FU Berlin)
Project member(s): Katarina Elez, Nathalie Wehlitz
Participating institution(s): FU Berlin, ZIB

Project Summary

This project is concerned with the modeling and analysis of spatio-temporal cellular processes that comprise cascades of scales in time, space and population size. We successfully constructed several new hybrid models that seamlessly couple different resolutions for different molecular species and spatial locations within the cell, e.g., integrating particle-based reactions diffusion (PBRD) models with spatio-temporal master equations and/or stochastic partial differential equations, or coupling PBRD models with molecular kinetics like conformational changes or membrane dynamics. Efficient algorithms for numerical simulations were proposed and their superior performance (in comparison to non-hybrid models) was demonstrated for various real-life applications.
In the third funding period we make the decisive final step: we refine our methods further and integrate external progress in the field in order to construct a hybrid model and appropriate simulation algorithms for investigating the process of receptor diffusion, co-localization, and kinetic interaction on the membrane surface of neurons. For this process, experimental data with single-molecule resolution in time and space indicates surprising cluster formation of receptors. Modeling this process requires coupling of receptor conformation kinetics with diffusion, mediated by the interaction with the membrane, and bi-molecular interaction, making it into a prototype for the interaction across a cascade of scales.

Publications C03

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See below:

Image 1: Structural overview of mathematical modeling approaches for chemical reaction kinetics. In project C03, the relation between the approaches (dashed arrows) and their recombination to hybrid models (solid blue arrows) are investigated.

Image 2: In vitro studies show spatial clustering effects of receptors on the surface of living neural cells. These clustering dynamics are modeled and analyzed in Project C03.