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28 March 2024
 
  » arxiv » 1701.0317

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A modeling and simulation language for biological cells with coupled mechanical and chemical processes
Endre Somogyi ; James A. Glazier ;
Date 2 Jan 2017
AbstractBiological cells are the preeminent active matter. Cells sense and respond to mechanical, chemical or electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical properties, changes in chemical uptake or secretion, cell differentiation, proliferation, death, or migration.
Modeling and simulation of such dynamic phenomena poses a number of computational challenges. A modeling language must first be able to naturally represent both the complex intra and extra-cellular spatial structures, and their coupled dynamics of mechanical, chemical and electrical objects and processes. In order to be useful to domain experts, a modeling language should be based on mechanical and chemical constructs native to the problem domain. A compiler must then be able to generate an executable model from this physically motivated description. Finally, an executable model must efficiently calculate the time evolution of such dynamic and inhomogeneous phenomena.
We present a spatial hybrid systems modeling language, compiler and mesh-free Lagrangian based simulation engine which will enable domain experts to define models using natural, biologically motivated constructs and to simulate time evolution of coupled cellular, mechanical and chemical processes acting on a time varying number of cells and their environment.
Source arXiv, 1701.0317
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