Computational biology, Systems biology, Morphogenesis, 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
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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 A.; and Alber, Mark S., "On Multiscale Approaches to 3-Dimensional Modeling of Morphogenesis" (2005). Mathematics. 60.