1. PolyHoop: Soft particle and tissue dynamics with topological transitions.
- Author
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Vetter, Roman, Runser, Steve V.M., and Iber, Dagmar
- Abstract
We present PolyHoop, a lightweight standalone C++ implementation of a mechanical model to simulate the dynamics of soft particles and cellular tissues in two dimensions. With only few geometrical and physical parameters, PolyHoop is capable of simulating a wide range of particulate soft matter systems: from biological cells and tissues to vesicles, bubbles, foams, emulsions, and other amorphous materials. The soft particles or cells are represented by continuously remodeling, non-convex, high-resolution polygons that can undergo growth, division, fusion, aggregation, and separation. With PolyHoop, a tissue or foam consisting of a million cells with high spatial resolution can be simulated on conventional laptop computers. Program Title: PolyHoop CPC Library link to program files: https://doi.org/10.17632/4jscxhkd2s.1 Licensing provisions: BSD 3-clause Programming language: C++11 Supplementary material: Figs. S1 and S2, Movies 1–7 Nature of problem: Various two-dimensional mechanical systems can be represented by elastic, tensile hoops marking the boundaries of fluidic domains. Examples include cellular tissues, vesicles, foams, emulsions, etc. PolyHoop efficiently solves the Newtonian dynamics of such systems, enabling the simulation of large ensembles with O (10 6) deformable particles on a single ordinary CPU. The simulated hoops can undergo a variety of topological transitions such as division and fusion. Solution method: The soft particles are represented by their boundary contours, discretized into high-resolution polygons. The polygon vertices are then propagated in time by solving Newtons's equation of motion with the semi-implicit Euler method, using conservative and dissipative nodal forces. To maintain high quality of the discretization even during large particle deformations, the particles automatically remodel their boundaries. For efficient collision detection, a spatial partitioning grid is used. Additional comments including restrictions and unusual features: The source code of PolyHoop is exceptionally compact, consisting of only about 720 commented lines in a single file. With no dependencies, it is highly portable and easy to handle, making it also suited for educational purposes. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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