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C03 - Multiscale modelling and simulation for spatiotemporal master equations

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

Project Summary

In the preceding funding periods we analyzed various techniques for modeling spatio-temporal cellular processes with cascades of scales in time, space and population size [9]. 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 [WZS21] and/or stochastic partial differential equations [HDCD+21] or coupling PBRD models with molecular kinetics like conformational changes or membrane dynamics [1, 2, 7]. Efficient algorithms for numerical simulations were proposed and their superior performance (in comparison to non-hybrid models) was demonstrated for various real-life applications [3, 5], [RSS20].
In the potential third funding period we plan to make the decisive final step: we plan to 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 m-receptor diffusion, co-localization, and kinetic interaction on the membrane surface of neurons. For this process, brand-new experimental data with single-molecule resolution in time and space is available [MIS+20] that 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