Gunji Yukio Pegio, Adamatzky Andrew
Department of Intermedia Art and Science, School of Fundamental Science and Technology, Waseda University, Ohkubo 3-4-1, Shinjuku-ku, Tokyo 169-8555, Japan.
Unconventional Computing Laboratory, University of the West of England, Bristol BS16 1QY, UK.
Biomimetics (Basel). 2024 Jul 16;9(7):432. doi: 10.3390/biomimetics9070432.
A chemical reaction and its reaction environment are intrinsically linked, especially within the confines of narrow cellular spaces. Traditional models of chemical reactions often use differential equations with concentration as the primary variable, neglecting the density heterogeneity in the solution and the interaction between the reaction and its environment. We model the interaction between a chemical reaction and its environment within a geometrically confined space, such as inside a cell, by representing the environment through the size of molecular clusters. In the absence of fluctuations, the interplay between cluster size changes and the activation and inactivation of molecules induces oscillations. However, in unstable environments, the system reaches a fluctuating steady state. When an enzyme is introduced to this steady state, oscillations akin to action potential spike trains emerge. We examine the behavior of these spike trains and demonstrate that they can be used to implement logic gates. We discuss the oscillations and computations that arise from the interaction between a chemical reaction and its environment, exploring their potential for contributing to chemical intelligence.
化学反应与其反应环境本质上是相互关联的，尤其是在狭窄的细胞空间范围内。传统的化学反应模型通常使用以浓度为主要变量的微分方程，而忽略了溶液中的密度异质性以及反应与其环境之间的相互作用。我们通过分子簇的大小来表示环境，从而对化学反应与其在几何受限空间（如细胞内部）内的环境之间的相互作用进行建模。在没有波动的情况下，簇大小变化与分子的激活和失活之间的相互作用会引发振荡。然而，在不稳定的环境中，系统会达到一个波动的稳态。当向这个稳态引入一种酶时，类似于动作电位尖峰序列的振荡就会出现。我们研究了这些尖峰序列的行为，并证明它们可用于实现逻辑门。我们讨论了由化学反应与其环境之间的相互作用所产生的振荡和计算，探索它们对化学智能做出贡献的潜力。
