Controlling the occurrence sequence of reaction modules through biochemical relaxation oscillators

2024/01/04 by Xiaopeng Shi, Shi, Xiaopeng, Chuanhou Gao +3 · 2 citations
Biochemistry, Genetics and Molecular Biology · Engineering · #Dynamical Systems (math.DS) #FOS: Biological sciences #FOS: Mathematics #Gene Regulatory Network Analysis #Molecular Networks (q-bio.MN) #Semiconductor Lasers and Optical Devices #Slime Mold and Myxomycetes Research

paper · pdf · doi:10.48550/arxiv.2401.02061

openalex publication_date 2024/01/04 · openalex created_date 2024/01/10 · openalex updated_date 2026/07/28

Abstract

Embedding sequential computations in biochemical environments is challenging because the computations are carried out by chemical reactions, which are inherently disordered. In this paper we apply modular design to specific calculations through chemical reactions and provide a design scheme of biochemical oscillator models in order to generate periodical species for the order regulation of these reaction modules. We take the case of arbitrary multi-module regulation into consideration, analyze the main errors in the regulation process under mass-action kinetics and demonstrate our design scheme under existing synthetic biochemical oscillator models.

Cited by

• Structure-conditioned input-to-state stability for layer-by-layer molecular computations in parallel chemical reaction networks
• Structure and input-to-state stability for composable computations in chemical reaction networks

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