PolyHoop: Soft particle and tissue dynamics with topological transitions

Review this paper

Submitted by rvetter

June 4, 2024, 4:35 p.m.

PolyHoop: Soft particle and tissue dynamics with topological transitions

Roman Vetter, Steve V. M. Runser, Dagmar Iber
Computer Physics Communications 299, 109128 (2024)
DOI:  10.1016/j.cpc.2024.109128        

Number of reviews:   1

Brief Description
The paper introduces a very compact C++ program to simulate high-resolution tissue dynamics in 2D. It is exceptionally easy to use, fast and portable, which makes it accessible also to programming novices. The paper showcases the diverse systems that can be simulated and includes a computational benchmark demonstrating the numerical performance in terms of runtime and memory usage. The full source code consists of just one file and can be freely downloaded from the paper website. To reproduce the results shown, the parameters listed in Table 3 need to be set at the top of the source code file, it needs to be compiled (one-liner given in the paper) and run (also a one-liner) from a unix terminal.
Why should we reproduce your paper?
There is a numerical benchmark reported in Fig. 4 with absolute runtimes and memory usages that can directly be reproduced with the provided source code. The benchmark was performed on the author's computer, and since numerical performance and parallel scaling can be somewhat hardware-dependent, it would be of interest to see whether a performance that is comparable to the one reported in the paper can be reproduced by others on their own computers in practice. The benchmark simulates a growing tissue from one to 10,000 cells in just ten minutes, so this offers an easy entry point into tissue modeling and simulation. No input data is needed to reproduce the output. The program has no dependencies.
What should reviewers focus on?


Associated event