Berlin 2024 – scientific programme

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BP: Fachverband Biologische Physik

BP 32: Tissue Mechanics II

BP 32.5: Talk

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

Topological Transformations in Graph Vertex Model — •Urban Železnik, Tanmoy Sarkar, and Matej Krajnc — Jožef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia

Vertex Model (VM) shows its reliability in modeling confluent biological tissues in two dimensions (2D). However, its application in three dimensions (3D) has been constrained by computational complexities, primarily stemming from managing topological changes during cell rearrangements. In the talk, I will demonstrate how the recently introduced Graph Vertex Model (GVM) successfully addresses the challenges posed by VM. GVM achieves this by exclusively storing topological data of cell networks within a Knowledge Graph (KG). The unique data structure of KG enables cell rearrangements and divisions to be equivalent to elementary graph transformations, which are also represented by graphs. Furthermore, cell rearrangements in 3D consist of graph transformations that correspond to more fundamental T1 transitions, thereby unifying topological transitions in both 2D and 3D space-filling packings. This implies that the GVM's graph data structure may be the most natural representation for cell aggregates and tissues.

Keywords: graph transformation; vertex model; topology; graph database; cell rearrangement