Topological data analysis approaches to uncovering the timing of ring structure onset in filamentous networks

TL;DR

This paper introduces a topological data analysis method to detect and analyze the formation timing of ring structures in filamentous networks within cells, using simulated data to overcome experimental visualization limitations.

Contribution

The paper develops a novel TDA-based algorithm for identifying and visualizing dynamic ring structures in cellular filament networks from simulated data.

Findings

Successfully detects ring structure formation over time in simulated data.

Provides visualization tools for dynamic topological feature analysis.

Offers insights into how molecular interactions influence network organization.

Abstract

Improvements in experimental and computational technologies have led to significant increases in data available for analysis. Topological data analysis (TDA) is an emerging area of mathematical research that can identify structures in these data sets. Here we develop a TDA method to detect physical structures in a cell that persist over time. In most cells, protein filaments (actin) interact with motor proteins (myosins) and organize into polymer networks and higher-order structures. An example of these structures are ring channels that maintain constant diameters over time and play key roles in processes such as cell division, development, and wound healing. The interactions of actin with myosin can be challenging to investigate experimentally in living systems, given limitations in filament visualization \textit{in vivo}. We therefore use complex agent-based models that simulate mechanical and chemical interactions of polymer proteins in cells. To understand how filaments organize into structures, we propose a TDA method that assesses effective ring generation in data consisting of simulated actin filament positions through time. We analyze the topological structure of point clouds sampled along these actin filaments and propose an algorithm for connecting significant topological features in time. We introduce visualization tools that allow the detection of dynamic ring structure formation. This method provides a rigorous way to investigate how specific interactions and parameters may impact the timing of filamentous network organization.