Development of a Method for Modeling Cell Dynamics Considering the Microenvironment Based on Cellular Potts Model
Olesya S. Kuznetsova1, Artur D. Nasyrov1, Leonid Y. Polynkin1, Stanislav O. Yurchenko1, Nikita P. Kryuchkov1; 1 Center for Soft Matter and Physics of Fluids, Bauman Moscow State Technical University, Moscow, Russia
Abstract
The development of realistic models of multicellular systems requires considering not only cell–cell interactions and spatial organization, but also the influence of physical factors shaping the cellular microenvironment. In particular, convective transport caused by external fluid flow can significantly affect the distribution of nutrients and metabolites, while it is often neglected in standard Cellular Potts Model implementations. In this work, a method for modeling cell dynamics with consideration of hydrodynamic effects based on the Cellular Potts Model was developed. The approach integrates the Cellular Potts Model implemented in CompuCell3D with hydrodynamic flow simulations and convective-diffusive metabolite transport calculations in OpenFOAM. Bidirectional data exchange between the models was established: the three-dimensional cellular geometry and local metabolic parameters are transferred from CompuCell3D to OpenFOAM, where the fluid velocity field and metabolite concentration distribution are calculated. The updated concentration field is then returned to the cellular model. A three-dimensional cell spheroid exposed to external hydrodynamic flow was considered as a test case. Cell behavior was described using a stochastic Cellular Potts Model including cell growth, division, hypoxia transition, and cell death depending on local oxygen availability. Software modules and Python scripts were developed to automate geometry export, STL conversion, preparation of metabolite fields, OpenFOAM simulations, and result import into CompuCell3D. The proposed method accounts for the dynamically changing geometry of a cellular ensemble and its impact on surrounding physical processes. It can be adapted for various multicellular systems, including microfluidic devices and organ-on-a-chip models.
Speaker
Olesia Kuznetsova
Center for Soft Matter and Physics of Fluids, Bauman Moscow State Technical University, Moscow, Russia
Russia
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