Paper Info
Title
A modeling and simulation language for biological cells with coupled mechanical and chemical processes.
Abstract
Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of mechanistic responses, including dynamic changes in morphology and mechanical properties, chemical uptake and secretion, cell differentiation, proliferation, death, and migration. Modeling and simulation of such dynamic phenomena pose a number of computational challenges. A modeling language describing cellular dynamics must naturally represent complex intra and extra-cellular spatial structures and coupled mechanical, chemical and electrical processes. A compiler must then be able to generate a computational model from this physically motivated description. Finally, a simulator must efficiently evaluate the time evolution of the computational model to generate simulation results. We present the Mechanica modeling language, compiler, and particle-based simulation engine. Mechanica enables construction and simulation of mechanistic models of natural phenomena which couple mechanical and chemical processes, using natural, physically and biologically motivated constructs.
Year
Venue
Keywords
2017
Proceedings of the Symposium on Theory of Modeling & Simulation
Biological Systems Modeling,Simulation,Spatial Hybrid Systems
DocType
Volume
Citations 
Conference
abs/1701.00317
0
PageRank 
References 
Authors
0.34
6
2
Name
Order
Citations
PageRank
Endre T. Somogyi100.34
James Glazier29314.35