From multiscale intracellular kinetics to scalable models of stochastic cell-cell interaction
speaker: Andreas Hellander (Uppsala)abstract: Multiscale simulation of intracellular kinetics using hybrid methods that blends hard-sphere based microscopic simulations with on-lattice mesoscopic descriptions can be an e ective way of simulating multiscale systems with large disparity in the degree of di usion control of reactions. However, a priori knowledge about the system dynamics is usually needed to partition the system, and this limits the usefulness of hybrid methods as black-box simulation tools. We here introduce one recent approach to address this problem with a priori automatic system partitioning based on our previous work on multiscale reaction-rates for the reaction-di usion master equation. One of the great challenges ahead is to develop tools that can help analyze the e ects of single-cell gene regulation on system level phenomena in multicellular systems, without sacri cing the capability of analyzing stochastic and spatial e ects from molecular interactions. We will brie y address the challenges of scaling up stochastic models of intracellular kinetics to multiple interacting cells using bottom-up multiscale modeling. We also introduce Orchestral, a lightweight framework for combining di erent models and software at di erent scales into a highly horizontally scalable parallel simulation of detailed multicellular signalling, designed to leverage cloud infrastructure in a seamless manner.
timetable:
Mon 1 Oct, 16:45 - 18:00, Aula Dini
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