On multiscale approaches to three-dimensional modelling of morphogenesis

• Published in: Journal of the Royal Society interface Vol. 2; no. 3; pp. 237 - 253
• Main Authors: Chaturvedi, R, Huang, C, Kazmierczak, B, Schneider, T, Izaguirre, J.A, Glimm, T, Hentschel, H.G.E, Glazier, J.A, Newman, S.A, Alber, M.S
• Format: Journal Article
• Language: English
• Published: London The Royal Society 22-06-2005
• Subjects: Animals; Cattle; Cell Death; Cell Division; Cell Dynamics; Cell Physiological Phenomena; Cellular Potts Model; Computational Biology; Models, Biological; Morphogenesis; Morphogenesis - physiology; Organogenesis; Physiology - methods; Systems Biology
• ISSN: 1742-5689; 1742-5662
• DOI: 10.1098/rsif.2005.0033

In this paper we present the foundation of a unified, object-oriented, three-dimensional biomodelling environment, which allows us to integrate multiple submodels at scales from subcellular to those of tissues and organs. Our current implementation combines a modified discrete model from statistical mechanics, the Cellular Potts Model, with a continuum reaction-diffusion 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.