论文标题
使用标准化时空模式区分基准流量几何形状中基于个体的集体细胞运动模型
Discriminating between individual-based models of collective cell motion in a benchmark flow geometry using standardised spatiotemporal patterns
论文作者
论文摘要
共同协调的细胞迁移在组织胚胎发生，癌症，稳态和愈合中起作用。为了研究这些过程，已经开发了不同的基于细胞的建模方法，从基于晶格的细胞自动机到无晶格模型，这些模型将细胞视为点状颗粒或扩展的详细细胞形状轮廓。本着奥斯本等人的精神。 [PLOS计算生物学，（2017）13，1-34]对于细胞组织结构仿真模型，我们在这里比较了五个集体细胞迁移的模拟模型，该模型被选为越来越多的详细信息的代表性。它们是Vicsek-Grégoire的颗粒，Szabó样颗粒，自propelled Voronoi模型，细胞Potts模型和多颗粒细胞，每个模型都包含细胞运动。我们研究了这些模型在应用于相同的生物学问题时如何比较，以及由于不同的模型假设和抽象而引起的行为差异。为此，我们使用一个区分复杂材料流模型的基准，并且可以使用细胞培养物进行实验接近：圆形障碍物周围的通道内的流动，也就是说，在其历史1851年实验中使用的几何形状Stokes。对于每个模型，我们说明如何最好地实施它；各种细胞密度，吸引力和比对相互作用；画出所得的速度，密度和变形场的地图；并最终讨论其各自的优势和局限性。因此，我们提供了有关如何选择模型来回答给定问题的建议，并检查了运动颗粒和动感细胞的模型是否显示出相似的集体效果。
Collectively coordinated cell migration plays a role in tissue embryogenesis, cancer, homeostasis and healing. To study these processes, different cell-based modelling approaches have been developed, ranging from lattice-based cellular automata to lattice-free models that treat cells as point-like particles or extended detailed cell shape contours. In the spirit of what Osborne et al. [PLOS Computational Biology, (2017) 13, 1-34] did for cellular tissue structure simulation models, we here compare five simulation models of collective cell migration, chosen to be representative in increasing order of included detail. They are Vicsek-Grégoire particles, Szabó-like particles, self-propelled Voronoi model, cellular Potts model, and multiparticle cells, where each model includes cell motility. We examine how these models compare when applied to the same biological problem, and what differences in behaviour are due to different model assumptions and abstractions. For that purpose, we use a benchmark that discriminates between complex material flow models, and that can be experimentally approached using cell cultures: the flow within a channel around a circular obstacle, that is, the geometry Stokes used in his historical 1851 experiment. For each model we explain how to best implement it; vary cell density, attraction force and alignment interaction; draw the resulting maps of velocity, density and deformation fields; and eventually discuss its respective advantages and limitations. We thus provide a recommendation on how to select a model to answer a given question, and we examine whether models of motile particles and motile cells display similar collective effects.
