A MODELING AND SIMULATION LANGUAGE FOR BIOLOGICAL CELLS WITH COUPLED MECHANICAL AND CHEMICAL PROCESSES

Area of Science:

• Computational Biology
• Biophysics
• Active Matter Physics

Background:

• Biological cells exhibit complex behaviors in response to environmental stimuli, involving coupled mechanical, chemical, and electrical processes.
• Modeling these dynamic cellular phenomena presents significant computational challenges, requiring specialized languages and efficient simulation engines.

Purpose of the Study:

• To develop a spatial hybrid systems modeling language and simulation engine tailored for biological cell dynamics.
• To enable domain experts to create physically motivated models using biologically relevant constructs.
• To efficiently simulate the time evolution of coupled cellular processes in dynamic environments.

Main Methods:

• Development of a novel spatial hybrid systems modeling language.
• Implementation of a compiler to translate biologically motivated descriptions into executable models.
• Creation of a mesh-free Lagrangian-based simulation engine for efficient computation.

Main Results:

• The developed system allows for the natural representation of complex intra- and extra-cellular spatial structures.
• It supports the simulation of coupled mechanical, chemical, and electrical processes within and around cells.
• The engine efficiently handles a time-varying number of cells and their environment, capturing dynamic phenomena.

Conclusions:

• The proposed modeling language, compiler, and simulation engine effectively address the computational challenges in modeling cellular dynamics.
• Domain experts can now define and simulate complex biological systems using intuitive, biologically motivated terms.
• This approach facilitates a deeper understanding of active matter behavior at the cellular level.