Computation implemented by the interaction of chemical reaction, clustering, and de-clustering of molecules

Gunji, Yukio Pegio; Adamatzky, Andrew

Abstract

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 behaviour 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.

Citation

Gunji, Y. P., & Adamatzky, A. (2024). Computation implemented by the interaction of chemical reaction, clustering, and de-clustering of molecules. Biomimetics, 9(7), Article 432. https://doi.org/10.3390/biomimetics9070432

• Journal Article Type: Article
• Acceptance Date: Jul 13, 2024
• Online Publication Date: Jul 16, 2024
• Publication Date: Jul 16, 2024
• Deposit Date: Jul 31, 2024
• Publicly Available Date: Jul 31, 2024
• Journal: Biomimetics
• Electronic ISSN: 2313-7673
• Publisher: MDPI
• Peer Reviewed: Peer Reviewed
• Volume: 9
• Issue: 7
• Article Number: 432
• DOI: https://doi.org/10.3390/biomimetics9070432
• Public URL: https://uwe-repository.worktribe.com/output/12712186