Undergraduate Tutorial for Simulating Flocking with the Vicsek Model

A. Tabatabai, Macquarrie Thomson, Reece Keller
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Abstract

There are many instances of collective behaviors in the natural world. For example, eukaryotic cells coordinate their motion to heal wounds; bacteria swarm during colony expansion; defects in alignment in growing bacterial populations lead to biofilm growth; and birds move within dynamic flocks. Although the details of how these groups behave vary across animals and species, they share the same qualitative feature: they exhibit collective behaviors that are not simple extensions of details associated with the motion of an individual. To learn more about these biological systems, we propose studying these systems through the lens of the foundational Vicsek model. Here, we present the process of building this computational model from scratch in a tutorial format that focuses on building the appropriate skills of an undergraduate student. In doing so, an undergraduate student should be able to work alongside this article, the corresponding tutorial, and the original manuscript of the Vicsek model to build their own model. We conclude by summarizing some of the current work involving computational modeling of flocking with Vicsek-type models.
用Vicsek模型模拟群集的本科生教程
自然界中有许多集体行为的例子。例如,真核细胞协调它们的运动来愈合伤口;菌落扩张过程中的细菌群;生长中的细菌种群的排列缺陷导致生物膜生长;鸟类在充满活力的群中活动。尽管这些群体行为的细节因动物和物种而异,但它们有着相同的定性特征:它们表现出的集体行为并不是与个体运动相关细节的简单延伸。为了了解更多关于这些生物系统的信息,我们建议通过基本的Vicsek模型来研究这些系统。在这里,我们以教程的形式介绍了从头开始构建这个计算模型的过程,重点是培养本科生的适当技能。在这样做的过程中,本科生应该能够与这篇文章、相应的教程和Vicsek模型的原始手稿一起构建自己的模型。最后,我们总结了目前使用Vicsek型模型进行植绒计算建模的一些工作。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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