Computational modeling and topological data analysis for biological ring channels

Veronica Ciocanel (May 8, 2020)

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Abstract

Contractile rings are cellular structures made of actin filaments that are important in development, wound healing, and cell division. In the reproductive system of the roundworm C. elegans, ring channels allow nutrient exchange between developing egg cells and the worm and are regulated by forces exerted by myosin motor proteins.

In this work, we use an agent-based modeling and data analysis framework for the interactions between actin filaments and myosin motor proteins inside cells. This approach may provide key insights for the mechanistic differences between two motors that are believed to maintain the rings at a constant diameter. In particular, we propose tools from topological data analysis to understand time-series data of filamentous network interactions. Our proposed methods clearly reveal the impact of certain parameters on significant topological circle formation, thus giving insight into ring channel formation and maintenance.