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The design principles of discrete turing patterning systems
Journal of Theoretical Biology ( IF 2 ) Pub Date : 2021-09-13 , DOI: 10.1016/j.jtbi.2021.110901
Thomas Leyshon 1 , Elisa Tonello 2 , David Schnoerr 1 , Heike Siebert 2 , Michael P H Stumpf 3
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The formation of spatial structures lies at the heart of developmental processes. However, many of the underlying gene regulatory and biochemical processes remain poorly understood. Turing patterns constitute a main candidate to explain such processes, but they appear sensitive to fluctuations and variations in kinetic parameters, raising the question of how they may be adopted and realised in naturally evolved systems. The vast majority of mathematical studies of Turing patterns have used continuous models specified in terms of partial differential equations. Here, we complement this work by studying Turing patterns using discrete cellular automata models. We perform a large-scale study on all possible two-species networks and find the same Turing pattern producing networks as in the continuous framework. In contrast to continuous models, however, we find these Turing pattern topologies to be substantially more robust to changes in the parameters of the model. We also find that diffusion-driven instabilities are substantially weaker predictors for Turing patterns in our discrete modelling framework in comparison to the continuous case, in the sense that the presence of an instability does not guarantee a pattern emerging in simulations. We show that a more refined criterion constitutes a stronger predictor. The similarity of the results for the two modelling frameworks suggests a deeper underlying principle of Turing mechanisms in nature. Together with the larger robustness in the discrete case this suggests that Turing patterns may be more robust than previously thought.



中文翻译:

离散图灵图形系统的设计原则

空间结构的形成是发展过程的核心。然而,许多潜在的基因调控和生化过程仍然知之甚少。图灵模式是解释这些过程的主要候选者,但它们似乎对动力学参数的波动和变化很敏感,这就提出了如何在自然进化的系统中采用和实现它们的问题。图灵模式的绝大多数数学研究都使用了根据偏微分方程指定的连续模型。在这里,我们通过使用离散元胞自动机模型研究图灵模式来补充这项工作。我们对所有可能的两种网络进行了大规模研究,并找到了与连续框架中相同的图灵模式生成网络。然而,与连续模型相比,我们发现这些图灵模式拓扑对模型参数的变化更加稳健。我们还发现,与连续情况相比,在我们的离散建模框架中,扩散驱动的不稳定性对于图灵模式的预测要弱得多,因为不稳定的存在并不能保证在模拟中出现模式。我们表明,更精细的标准构成了更强的预测因子。两个建模框架结果的相似性暗示了自然界中图灵机制的更深层次的基本原理。连同离散情况下更大的稳健性,这表明图灵模式可能比以前认为的更稳健。我们还发现,与连续情况相比,在我们的离散建模框架中,扩散驱动的不稳定性对于图灵模式的预测要弱得多,因为不稳定的存在并不能保证在模拟中出现模式。我们表明,更精细的标准构成了更强的预测因子。两个建模框架结果的相似性暗示了自然界中图灵机制的更深层次的基本原理。连同离散情况下更大的稳健性,这表明图灵模式可能比以前认为的更稳健。我们还发现,与连续情况相比,在我们的离散建模框架中,扩散驱动的不稳定性对于图灵模式的预测要弱得多,因为不稳定的存在并不能保证在模拟中出现模式。我们表明,更精细的标准构成了更强的预测因子。两个建模框架结果的相似性暗示了自然界中图灵机制的更深层次的基本原理。连同离散情况下更大的稳健性,这表明图灵模式可能比以前认为的更稳健。从某种意义上说,不稳定的存在并不能保证模拟中出现模式。我们表明,更精细的标准构成了更强的预测因子。两个建模框架结果的相似性暗示了自然界中图灵机制的更深层次的基本原理。连同离散情况下更大的稳健性,这表明图灵模式可能比以前认为的更稳健。从某种意义上说,不稳定的存在并不能保证模拟中出现模式。我们表明,更精细的标准构成了更强的预测因子。两个建模框架结果的相似性暗示了自然界中图灵机制的更深层次的基本原理。连同离散情况下更大的稳健性,这表明图灵模式可能比以前认为的更稳健。

更新日期:2021-10-01
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