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Large Scale Tissue Morphogenesis Simulation on Heterogenous Systems Based on a Flexible Biomechanical Cell Model

机译:基于柔性生物力学细胞模型的异质系统大规模组织形态发生模拟

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The complexity of biological tissue morphogenesis makes simulations of such system very interesting in order to gain a better understanding of the underlying mechanisms ruling the development of multicellular tissues. This complexity is mainly due to two elements: firstly, biological tissues comprise a large amount of cells; secondly, these cells exhibit complex interactions and behaviors. To address these two issues, we propose two tools: the first one is a virtual cell model that comprise two main elements: firstly, a mechanical structure (membrane, cytoskeleton, and cortex) and secondly, the main behaviors exhibited by biological cells, i.e., mitosis, growth, differentiation, molecule consumption, and production as well as the consideration of the physical constraints issued from the environment. An artificial chemistry is also included in the model. This virtual cell model is coupled to an agent-based formalism. The second tool is a simulator that relies on the OpenCL framework. It allows efficient parallel simulations on heterogenous devices such as micro-processors or graphics processors. We present two case studies validating the implementation of our model in our simulator: cellular proliferation controlled by cell signalling and limb growth in a virtual organism.
机译:生物组织形态发生的复杂性使这种系统的仿真变得非常有趣,以便更好地了解主导多细胞组织发展的潜在机制。这种复杂性主要归因于两个因素:第一,生物组织包含大量细胞;第二,生物组织包含大量细胞。其次,这些细胞表现出复杂的相互作用和行为。为了解决这两个问题,我们提出了两种工具:第一种是虚拟细胞模型,它包含两个主要元素:首先是机械结构(膜,细胞骨架和皮层),其次,生物细胞表现出的主要行为,即,有丝分裂,生长,分化,分子消耗和生产,以及对环境发出的物理限制的考虑。人造化学也包括在模型中。该虚拟单元模型耦合到基于代理的形式主义。第二个工具是依赖于OpenCL框架的模拟器。它允许在异构设备(例如微处理器或图形处理器)上进行高效的并行仿真。我们提供了两个案例研究来验证我们的模型在模拟器中的实现:受细胞信号传导控制的细胞增殖和虚拟生物中肢体的生长。

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