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Article overview
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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 | Abstract: | Biological 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 | Services: | Forum | Review | PDF | Favorites |
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