Abstract
ya||a is yet another parallel agent-based model for morphogenesis. It is several orders of magnitude faster than conventional models, because it runs on GPUs and because it has been designed for performance: Previously only complex and therefore computationally expensive models could simulate both mesenchyme and epithelium. We chose to extend the simple spheroid model by the addition of spin-like polarities to simulate epithelial sheets and tissue polarity. We also incorporate recently developed models for protrusions and migration. ya||a is written in concise, plain CUDA/C++ and available at github dot com/germannp/yalla under the MIT license.
Highlights
Embryonic tissues come in two basic states, epithelial and mesenchymal
Epithelial tissues are organized into sheets with stable neighborhoods and show a marked apicalbasal polarity across the depth of the sheet. Such sheets undergo complex 3D deformations by means of active cell behaviors, which result in folding, bending, or twisting of the sheet, or by means of passive mechanical forces exerted by the surrounding tissues (Honda, 2017)
Mesenchymal cells come in various shapes, which are typically highly dynamic because of the formation and retraction of protrusions
Summary
Embryonic tissues come in two basic states, epithelial and mesenchymal. Epithelial tissues are organized into sheets with stable neighborhoods and show a marked apicalbasal polarity across the depth of the sheet. Such sheets undergo complex 3D deformations by means of active cell behaviors, which result in folding, bending, or twisting of the sheet, or by means of passive mechanical forces exerted by the surrounding tissues (Honda, 2017). Mesenchymal cells, on the other hand, are typically looser 3D tissues with abundant extracellular matrix. Cell transitions from epithelial to mesenchymal type, and interactions between both tissue types, are common throughout disease and development. Limb bud development starts with an epithelial to mesenchymal transition (Gros and Tabin, 2014), and outgrowth is orchestrated by a feedback loop between epithelial and mesenchymal signals (Zeller et al, 2009)
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