On multiscale approaches to three-dimensional modelling of morphogenesis

Chaturvedi, Rajiv; Huang, Chengbang; Kaźmierczak, Bogdan; Schneider, Tobias; Izaguirre, Jesús A.; Glimm, Tilmann; Hentschel, H. G. E.; Glazier, James A.; Newman, Stuart A.; Alber, Mark

doi:10.1098/rsif.2005.0033

Cited by 124 publications

(90 citation statements)

References 56 publications

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“…Extensive comparisons between experiments and GGH simulations have validated GGH methods (Mareé and Hogeweg, 2001;Zeng et al, 2004;Chaturvedi et al, 2005;Poplawski et al, 2007; for multicell morphogenesis modeling.…”

Section: A the Glazier-graner-hogeweg Modelmentioning

confidence: 99%

Coordinated Action of N-CAM, N-cadherin, EphA4, and ephrinB2 Translates Genetic Prepatterns into Structure during Somitogenesis in Chick

Glazier¹,

Zhang²,

Swat³

et al. 2008

Current Topics in Developmental Biology

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During gastrulation in vertebrates, mesenchymal cells at the anterior end of the pre-somitic mesoderm (PSM) periodically compact, transiently epithelialize and detach from the posterior PSM to form somites. In the prevailing clock-and-wavefront model of somitogenesis, periodic gene expression, particularly of Notch and Wnt, interacts with an FGF8-based thresholding mechanism to determine cell fates. However, this model does not explain how cell determination and subsequent differentiation translates into somite morphology. In this paper, we use computer simulations of chick somitogenesis to show that experimentally-observed temporal and spatial patterns of adhesive N-CAM and N-cadherin and repulsive EphA4-ephrinB2 pairs suffice to reproduce the complex dynamic morphological changes of somitogenesis in wild-type and N-cadherin (−/−) chick, including intersomitic separation, boundary-shape evolution and sorting of misdifferentiated cells across compartment boundaries. Since different models of determination yield the same, experimentallyobserved, distribution of adhesion and repulsion molecules, the patterning is independent of the details of this mechanism.

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Section: A the Glazier-graner-hogeweg Modelmentioning

confidence: 99%

Coordinated Action of N-CAM, N-cadherin, EphA4, and ephrinB2 Translates Genetic Prepatterns into Structure during Somitogenesis in Chick

Glazier¹,

Zhang²,

Swat³

et al. 2008

Current Topics in Developmental Biology

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“…CPM has been used as a part of other models to simulate the rearrangement of cells during morphogenesis (Chaturvedi et al, 2005;Glazier and Graner, 1993) and to model avascular tumor growth (Jiang et al, 2005). A discussion of how cell-centered simulations like CPM can help to explain aspects of developmental biology can be found in Merks and Glazier (2005).…”

Section: Previous Workmentioning

confidence: 99%

“…The hybrid approach has been used to simulate morphogenesis, organism motility, and chemotaxis. It also has been extended to 3-D to create simple geometric structures (Fleischer, 1995), and has found limited use in modeling more complex biological processes and systems (Chaturvedi et al, 2005).…”

Section: Previous Workmentioning

confidence: 99%

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A computational model of chemotaxis-based cell aggregation

et al. 2008

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We present a computational model that successfully captures the cell behaviors that play important roles in 2-D cell aggregation. A virtual cell in our model is designed as an independent, discrete unit with a set of parameters and actions. Each cell is defined by its location, size, rates of chemoattractant emission and response, age, life cycle stage, proliferation rate and number of attached cells. All cells are capable of emitting and sensing a chemoattractant chemical, moving, attaching to other cells, dividing, aging and dying. We validated and fine-tuned our in silico model by comparing simulated 24-hour aggregation experiments with data derived from in vitro experiments using PC12 pheochromocytoma cells. Quantitative comparisons of the aggregate size distributions from the two experiments are produced using the Earth Mover's Distance (EMD) metric. We compared the two size distributions produced after 24 hours of in vitro cell aggregation and the corresponding computer simulated process. Iteratively modifying the model's parameter values and measuring the difference between the in silico and and in vitro results allow us to determine the optimal values that produce simulated aggregation outcomes closely matched to the PC12 experiments. Simulation results demonstrate the ability of the model to recreate large-scale aggregation behaviors seen in live cell experiments.

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“…Examples of these models can be found in. [22][23][24][25][26][27][28][29][30][31][32][33][34][35][36][37][38][39] In the agent based approach, we design fundamental rules for neighboring agents (cells in the context of aggregates) to interact with neighboring cells or particles. These probabilistic rules coupled with the fluctuation dynamics can lead to the desired collective or mesoscopic dynamics.…”

Section: Mathematical Modelsmentioning

confidence: 99%

In-Silico Analysis on 3D Biofabrication Using Kinetic Monte Carlo Simulations

Sun

Wang

2017

ATROA

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We present a three-dimensional (3D) lattice model based on the differential adhesion hypothesis (DAH) to study self-assembly and fusion of multicellular aggregates, which forms the foundation for the scaffold-less biofabrication of tissues and organs, known as "bio-printing". In this new technology, live multicellular aggregates are used as bio-ink to make tissue or organ constructs via the layer-by-layer deposition technique in biocompatible hydrogels; the printed bio-constructs embedded in the hydrogels are then placed in bioreactors to undergo the fusion process to form the desired functional tissue or organ products. Our in-silico approach is an agent-based method, which uses the kinetic Monte Carlo (KMC) algorithm to evolve the cellular system on a 3D lattice. In this model, the cells and the hydrogel media, in which cells are embedded, are coarse-grained to material's points on the lattice, where the cellcell and cell-medium interaction are quantified by adhesion and cohesion energies. In a multicellular aggregate system with a fixed number of cells and fixed amount of hydrogel media, the effect of cell differentiation, proliferation, and death are tactically neglected in the current model, which can be readily included in the model, and the interaction s primarily dictated by the interfacial energy between cell and cell as well as between cells and medium particles on the lattice, respectively. The KMC method is applicable to transient simulations of fusion of multicellular aggregates at the time and length scale appropriate to biofabrication. Numerical experiments are presented to demonstrate fusion and cell sorting during tissue and organ maturation processes.

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On multiscale approaches to three-dimensional modelling of morphogenesis

Cited by 124 publications

References 56 publications

Coordinated Action of N-CAM, N-cadherin, EphA4, and ephrinB2 Translates Genetic Prepatterns into Structure during Somitogenesis in Chick

Coordinated Action of N-CAM, N-cadherin, EphA4, and ephrinB2 Translates Genetic Prepatterns into Structure during Somitogenesis in Chick

A computational model of chemotaxis-based cell aggregation

In-Silico Analysis on 3D Biofabrication Using Kinetic Monte Carlo Simulations

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