Multi-Scale Modeling of Tissues Using CompuCell3D

Swat, Maciej; Thomas, Gilberto L.; Belmonte, Julio M.; Shirinifard, Abbas; Hmeljak, Dimitrij; Glazier, James A.

doi:10.1016/b978-0-12-388403-9.00013-8

Cited by 480 publications

(557 citation statements)

References 63 publications

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“…We built a computational model of the growth zone using the cellbased CompuCell3D simulation software (compucell3d.org) 45 . The initial conditions for our modelled growth zone were chosen to match the measured dimensions and cell counts in the growth zone in 18-h Tribolium embryos (Fig.…”

Section: Resultsmentioning

confidence: 99%

Changing cell behaviours during beetle embryogenesis correlates with slowing of segmentation

Nakamoto

Hester²,

Constantinou

et al. 2015

Nat Commun

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Segmented animals are found in major clades as phylogenetically distant as vertebrates and arthropods. Typically, segments form sequentially in what has been thought to be a regular process, relying on a segmentation clock to pattern budding segments and posterior mitosis to generate axial elongation. Here we show that segmentation in Tribolium has phases of variable periodicity during which segments are added at different rates. Furthermore, elongation during a period of rapid posterior segment addition is driven by high rates of cell rearrangement, demonstrated by differential fates of marked anterior and posterior blastoderm cells. A computational model of this period successfully reproduces elongation through cell rearrangement in the absence of cell division. Unlike current models of steady-state sequential segmentation and elongation from a proliferative growth zone, our results indicate that cell behaviours are dynamic and variable, corresponding to differences in segmentation rate and giving rise to morphologically distinct regions of the embryo.

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Section: Resultsmentioning

confidence: 99%

Changing cell behaviours during beetle embryogenesis correlates with slowing of segmentation

Nakamoto

Hester²,

Constantinou

et al. 2015

Nat Commun

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“…Therefore, it is possible to perform large-scale parameter sweeps and sensitivity analyses with CPM-based models [128,129]. Furthermore, open source software CPM modeling is readily available [130][131][132] which makes it easy to implement and simulate models using the CPM. However, there are some major disadvantages to the CPM.…”

Section: Cellular Automaton With Many Lattice Sites Per Cell (Type C;mentioning

confidence: 99%

Simulating tissue mechanics with agent-based models: concepts, perspectives and some novel results

et al. 2015

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In this paper we present an overview of agentbased models that are used to simulate mechanical and physiological phenomena in cells and tissues, and we discuss underlying concepts, limitations, and future perspectives of these models. As the interest in cell and tissue mechanics increase, agent-based models are becoming more common the modeling community. We overview the physical aspects, complexity, shortcomings, and capabilities of the major agent-based model categories: lattice-based models (cellular automata, lattice gas cellular automata, cellular Potts models), off-lattice models (center-based models, deformable cell models, vertex models), and hybrid discrete-continuum models. In this way, we hope to assist future researchers in choosing a model for the phenomenon they want to model and understand. The article also contains some novel results.

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“…changes in position and shape of tissues) also needs to be subject to testing for emergent properties with computational models. Mechanical and statistical modeling approaches are already underway to dissect tissue morphogenesis with computational tools (Brodland et al, 2007;Czirok and Isai, 2014;Mehes and Vicsek, 2014;Mones et al, 2015;Newman, 2008;Steimel et al, 2016;Swat et al, 2012;Voiculescu et al, 2014). However, inclusive and falsifiable models for morphogenetic movements that incorporate ECM motility, in addition to cell motility, are scarce.…”

Section: Mesogleamentioning

confidence: 99%

Extracellular matrix motion and early morphogenesis

et al. 2016

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For over a century, embryologists who studied cellular motion in early amniotes generally assumed that morphogenetic movement reflected migration relative to a static extracellular matrix (ECM) scaffold. However, as we discuss in this Review, recent investigations reveal that the ECM is also moving during morphogenesis. Time-lapse studies show how convective tissue displacement patterns, as visualized by ECM markers, contribute to morphogenesis and organogenesis. Computational image analysis distinguishes between cell-autonomous (active) displacements and convection caused by large-scale (composite) tissue movements. Modern quantification of large-scale 'total' cellular motion and the accompanying ECM motion in the embryo demonstrates that a dynamic ECM is required for generation of the emergent motion patterns that drive amniote morphogenesis.

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Multi-Scale Modeling of Tissues Using CompuCell3D

Cited by 480 publications

References 63 publications

Changing cell behaviours during beetle embryogenesis correlates with slowing of segmentation

Changing cell behaviours during beetle embryogenesis correlates with slowing of segmentation

Simulating tissue mechanics with agent-based models: concepts, perspectives and some novel results

Extracellular matrix motion and early morphogenesis

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