Self-replication and Mutation of Polymeric Molecules Simulated by Simplified Chemistry
Self-replication and Mutation of Polymeric Molecules Simulated by Simplified Chemistry
复制标题
简化化学模拟聚合物分子的自我复制和突变
DOI：
10.1109/candarw57323.2022.00083
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发表时间：
2022
期刊：
影响因子：
--
通讯作者：
Murata Satoshi
中科院分区：
文献类型：
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作者：
Mori Taisei;Kawamata Ibuki;Murata Satoshi
在本文中，我们考虑了一个简化的化学模型的自我复制和突变过程的DNA类聚合物分子。到目前为止，已经尝试了各种元胞自动机模型来表示自复制过程，其中仅将分子的化学性质的变化表示为离散状态变化。在该模型中，考虑了分子的大小和形状，通过引入物理相互作用的元素表示为弹簧质量阻尼器。元素具有像元胞自动机一样的离散状态，在连续空间中移动，并且当元素接近某个邻域时经历状态转换。在这里，我们设计了一个规则集的状态转换，实现自我复制的任何序列编码的聚合物字符串，如单链DNA。通过布朗动力学模拟研究了分子的密度和分子间的局部相互作用对自复制过程的影响，特别是对突变率的影响。
In this paper, we consider a simplified chemical model of self-replication and mutation processes of DNA-like polymeric molecules. Various cellular automaton models have been attempted to represent the self-replication process so far, in which only changes of chemical properties of the molecules are represented as discrete state changes. In the proposed model, the size and shape of molecules are taken into account, by introducing physical interactions among the elements represented as spring-mass-damper. Elements have discrete states like cellular automata, move in a continuous space, and undergo state transitions when an element approaches a certain neighborhood. Here, we designed a rule set for state transitions which realizes self-replication of any sequence encoded in a polymeric string such as single-stranded DNA. Brownian dynamics simulations were conducted to study how the density of the elements and local interactions among elements affect the self-replication process, especially mutation rate.