自组装简单模型中的演化动力学
Evolutionary Dynamics in a Simple Model of Self-Assembly
摘要：
我们调查的演化动力学的一个理想化的模型强大的自组装的二维结构称为polyominoes。该模型包括对驱动自组装过程的正方形瓦片组之间的相互作用进行编码的规则。模型的规则集和其产生的自组装结构之间的关系可以被看作是一个基因型-表型图，并纳入遗传算法。规则集根据指定目标结构的选择而演变。相应的，复杂的适应度景观产生丰富的演化动力学作为参数的函数，如人口规模，搜索空间大小，突变率，重组的方法。此外，这些系统足够简单，在某些情况下，相关的模型基因组空间可以完全表征，揭示了演化动力学如何依赖于适应度景观的详细结构。最后，我们应用该模型来研究出现的偏好二面角的环状对称性观察同源蛋白质四聚体。
英文摘要：
We investigate the evolutionary dynamics of an idealised model for the robust self-assembly of two-dimensional structures called polyominoes. The model includes rules that encode interactions between sets of square tiles that drive the self-assembly process. The relationship between the model's rule set and its resulting self-assembled structure can be viewed as a genotype-phenotype map and incorporated into a genetic algorithm. The rule sets evolve under selection for specified target structures. The corresponding, complex fitness landscape generates rich evolutionary dynamics as a function of parameters such as the population size, search space size, mutation rate, and method of recombination. Furthermore, these systems are simple enough that in some cases the associated model genome space can be completely characterised, shedding light on how the evolutionary dynamics depends on the detailed structure of the fitness landscape. Finally, we apply the model to study the emergence of the preference for dihedral over cyclic symmetry observed for homomeric protein tetramers.
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