## A Framework for Three-Dimensional Simulation of Morphogenesis (2004)

Citations: | 19 - 10 self |

### BibTeX

@MISC{Cickovski04aframework,

author = {Trevor Cickovski and Chengbang Huang and Rajiv Chaturvedi and Tilmann Glimm and H.G.E. Hentschel and Mark Alber and James A. Glazier and Stuart A. Newman and Jesus A. Izaguirre},

title = {A Framework for Three-Dimensional Simulation of Morphogenesis},

year = {2004}

}

### OpenURL

### Abstract

We present COMPUCELL3D, a software framework for three-dimensional simulation of morphogenesis in different organisms. COMPUCELL3D employs biologically relevant models for cell clustering, growth, and interaction with chemical fields. COMPUCELL3D uses design patterns for speed, efficient memory management, extensibility, and flexibility, permitting the simulation of various organisms. We verify COMPUCELL3D by building a model of growth and skeletal pattern formation in the avian (chicken) limb bud. Binaries and source code are available, along with documentation and input files for sample simulations, at http://www.nd.edu/lcls/compucell.

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Citation Context ...rm [53] and spatially nonuniform [22] growth on biological development. Dillon and Othmer implemented a domain-growth model of the shaping of the developing vertebrate limb using a continuum approach =-=[25]-=-. COMPUCELL3D includes a 3D density-dependent growth algorithm. Navier-Stokes, reaction-advection-diffusion (RAD) equation solvers, have also reproduced two-dimensional (2D) patterns and simulated gro... |

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Citation Context ...CPM Hamiltonian allow the CPM to model highly polar cells, e.g., [94], [93], [62]. Some of the many studies using the CPM include Mombach and Glazier’s [67] study of chicken retinal cells and Marée’s =-=[55]-=-, [57], [58], [56] study of Dictyostelium discoideum. Many of these studies include direct, quantitative validation of the CPM results against experiments. The idea that cell-cell interactions depend ... |

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Citation Context ...orm of the equations of Hentschel et al. [38] which we implemented in COMPUCELL3D. We kept only the two dominant equations and added two terms baðca casÞ 3 and biðci cisÞ 3 to enforce stability [29], =-=[1]-=-. As noted above, these equations represent known biological interactions in the chick limb. We used them to generate the chemical field in our verification simulations. The emergence of the sequence ... |

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Citation Context ...ave improved the engine’s efficiency through better data structures and algorithms, and its extensibility through a more thoroughly object-oriented design, which uses scientific design patterns [79], =-=[14]-=-. Specifically, COMPUCELL consumed too much memory when running 3D simulations. For example, we could not extend the technique of representing grid space as a 2D array to 3D because of the quantity of... |

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Citation Context ...evelopment, reaction-diffusion, cellular automata, morphogenesis, Extensible Markup Language (XML). 1 INTRODUCTION THIS paper presents COMPUCELL3D, a three-dimensional (3D), cell-centered, multiscale =-=[17]-=- framework for modeling morphogenesis. Morphogenesis is the structural development of an organism and its organs, involving cell differentiation, growth and migration, bulk changes in tissue shape, an... |

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Citation Context ... goes back well before Thompson, who was one of the first to attempt a semiquantitative comparison [84]. Steinberg then developed this idea into his Differential Adhesion Hypothesis [80], [81], [30], =-=[26]-=-. Experimental studies on cell sorting in vitro [30], [26] and, more recently, in vivo [33], [34], [36], support this approach to tissue morphogenesis based on consideration of surface forces akin to ... |

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Citation Context ...in none of the cases we treat here is long-range force transduction significant. In the quasifluid environment of soft tissues, we have established that the flows the CPM predicts are realistic [46], =-=[47]-=-, [9], [45]. For the purposes of developmental modeling, because movements are so slow and deformations so small, in most cases the exertion of force against the fixed underlying lattice is an adequat... |

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Citation Context ...s: First, we obtain cell-behavior data from the scientific literature and experiments. In our verification simulation, we assume an irregular mesenchymal cell morphology and obtain mitosis rates from =-=[54]-=-, define an activator signal which we identify with TGF- [63], a putative inhibitor [59], [64], [85], andan ECM componentwhich the cell secretes, which we identify with fibronectin [38], [50]. We assu... |

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Citation Context ...ian allow the CPM to model highly polar cells, e.g., [94], [93], [62]. Some of the many studies using the CPM include Mombach and Glazier’s [67] study of chicken retinal cells and Marée’s [55], [57], =-=[58]-=-, [56] study of Dictyostelium discoideum. Many of these studies include direct, quantitative validation of the CPM results against experiments. The idea that cell-cell interactions depend on surface-t... |

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Citation Context ...he cytoskeleton. It models mesenchymal cells, which are relatively isotropic, without requiring further extensions. Extra terms in the CPM Hamiltonian allow the CPM to model highly polar cells, e.g., =-=[94]-=-, [93], [62]. Some of the many studies using the CPM include Mombach and Glazier’s [67] study of chicken retinal cells and Marée’s [55], [57], [58], [56] study of Dictyostelium discoideum. Many of the... |