PolyHoop: Soft particle and tissue dynamics with topological transitions
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Date
2023-07-27
Publication Type
Working Paper
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yes
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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.
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Publication status
published
Editor
Book title
Journal / series
Volume
Pages / Article No.
2307.15006
Publisher
Cornell University
Event
Edition / version
v1
Methods
Software
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Date collected
Date created
Subject
Soft Condensed Matter (cond-mat.soft); Biological Physics (physics.bio-ph); Computational Physics (physics.comp-ph); FOS: Physical sciences; Soft particle; Foam; Bubble; Cell; Tissue; Polygon
Organisational unit
03791 - Iber, Dagmar / Iber, Dagmar
Notes
Funding
170930 - A 3D Cell-Based Simulation Framework for Morphogenetic Problems (SNF)
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