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BP: Fachverband Biologische Physik

BP 32: Tissue Mechanics II

BP 32.4: Talk

Thursday, March 21, 2024, 15:45–16:00, H 2032

Vertex Model Challenges Meet Knowledge Graph Solutions — •Tanmoy Sarkar and Matej Krajnc — Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia

Vertex model (VM) shows its credibility in modeling confluent biological tissues in two dimensions. However, due to computational complexities, only a few studies have been reported since the introduction of the first three-dimensional (3D) vertex model almost two decades ago. Most of the challenges lie in handling the changes in topology during dynamic cell rearrangements, which justifies the absence of a proper algorithmic form of topological transformations so far. This issue is often viewed in the community as a complex engineering problem. In the talk, I will demonstrate a possible solution to this outstanding problem using a new approach called the Graph Vertex Model (GVM). GVM is founded on the concept of representing the topology of the cell network using a Knowledge Graph (KG), effectively rendering topological transformations both intuitive and mathematically well-defined. Furthermore, I will highlight the enhanced credibility and utility of the KG by introducing the GRAPh Embryo project (GRAPE). GRAPE is an online database designed to facilitate interactive analyses of an entire fly embryo, showcasing the practical applications and benefits of this approach.

Keywords: vertex model; 3D cell aggregate; graph vertex model; knowledge graph