Organogenesis, Cell dynamics, Cellular Potts Model, Reaction-diffusion, Vertebrate limb, Multiscale models, Pattern formation, Monte Carlo simulations, Hybrid continuous-discrete models
In this paper we present the foundation of a unified, object-oriented, three-dimensional (3D) biomodeling environment, which allows us to integrate multiple submodels at scales from subcellular to tissues and organs. Our current implementation combines a modified discrete model from statistical mechanics, the Cellular Potts Model (CPM), with a continuum reaction-diffusion (RD) model and a state automaton with well-defined conditions for cell differentiation transitions to model genetic regulation. This environment allows us to rapidly and compactly create computational models of a class of complex developmental phenomena. To illustrate model development, we simulate a simplified version of the formation of the skeletal pattern in a growing embryonic vertebrate limb.
Journal of the Royal Society Interface
Required Publisher's Statement
Copyright © The Royal Society
This is the author's peer reviewed manuscript. To link to the published version: http://rsif.royalsocietypublishing.org/content/2/3/237
Chaturvedi, Rajiv; Huang, Chengbang; Kazmierczak, Bogdan; Schneider, T.; Izaguirre, Jesus A.; Glimm, Tilmann; Hentschel, H. George E.; Newman, Stuart (Stuart A.); Alber, Mark; and Glazier, James A., "On Multiscale Approaches to 3-Dimensional Modeling of Morphogenesis" (2005). Mathematics. 60.
Subjects - Topical (LCSH)
Computational biology; Systems biology--Mathematical models; Morphogenesis--Mathematical models; Extremities (Anatomy)--Mathematical models
Copying of this document in whole or in part is allowable only for scholarly purposes. It is understood, however, that any copying or publication of this document for commercial purposes, or for financial gain, shall not be allowed without the author’s written permission.