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Cells In Sillico – Parallel Tissue Development Simulation

Berghoff, Marco

Abstract:

Insights in cell dynamics and tissue development are constantly changing our understanding of fundamental biological processes including embryogenesis, wound healing, and tumorigenesis. The availability of high-quality microscopy data and an increasing understanding of single-cell effects are speeding up discoveries. However, many computational models still describe either a few cells in high detail or larger cell ensembles and tissues in rather coarse detail. We combine these two scales, therefore we developed a highly parallel version of the cellular Potts model and provides an agent-based model for controlling cellular events. The model can be modularly extended to a multimodel simulation at both scales. Based on the NAStJA framework, we implemented a scalable version that runs efficiently on high-performance computing systems. Our model scales beyond 10,000 cores in an approximately linear manner, enabling the simulation of large three-dimensional tissues. The strictly modular design allows flexible configuration of arbitrary models and enables applications in a wide range of research questions. Cells in Silico can be easily adapted to different modeling assumptions and helps computational scientists to extend their simulations to a new area of tissue simulations. ... mehr


Volltext §
DOI: 10.5445/IR/1000135057
Veröffentlicht am 06.07.2021
Cover der Publikation
Zugehörige Institution(en) am KIT Steinbuch Centre for Computing (SCC)
Universität Karlsruhe (TH) – Zentrale Einrichtungen (Zentrale Einrichtungen)
Publikationstyp Vortrag
Publikationsdatum 16.06.2021
Sprache Englisch
Identifikator KITopen-ID: 1000135057
HGF-Programm 46.21.01 (POF IV, LK 01) Domain-Specific Simulation & SDLs and Research Groups
Veranstaltung Society for Mathematical Biology - Annual Meeting (SMB 2021), Online, 13.06.2021 – 17.06.2021
KIT – Die Forschungsuniversität in der Helmholtz-Gemeinschaft
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