TopoSPAM: Topology grounded Simulation Platform for morphogenesis and biological Active Matter

Preprint, 2025

Abstract:

We present a topology grounded, multiscale simulation platform for morphogenesis and biological active matter. Morphogenesis and biological active matter represent keystone problems in biology with additional, far-reaching implications across the biomedical sciences. Addressing these problems will require flexible, cross-scale models of tissue shape, development, and dysfunction that can be tuned to understand, model, and predict relevant individual cases. Current approaches to simulating anatomical or cellular subsystems tend to rely on static, assumed shapes. Meanwhile, the potential for topology to provide natural dimensionality reduction and organization of shape and dynamical outcomes is not fully exploited. TopoSPAM combines ease of use with powerful simulation algorithms and methodological advances, including active nematic gels, topological-defect-driven shape dynamics, and an active 3D vertex model of tissues. It is capable of determining emergent flows and shapes across scales.

Recommended citation: "TopoSPAM: Topology grounded Simulation Platform for morphogenesis and biological Active Matter", A. Singh, A. Krishna, A. Amiri, A. Materne, P. Incardona, C. Duclut, C. M. Duque, A. Szałapak, M. Bahadorian, S. K. T. Veettil, P. H. Suhrcke, F. Jülicher, I. F. Sbalzarini, C. D. Modes, arXiv:2509.24905 (2025). https://arxiv.org/abs/2509.24905