Reaction Systems and Synchronous Digital Circuits

Abstract

A reaction system is a modeling framework for investigating the functioning of the living cell, focused on capturing cause–effect relationships in biochemical environments. Biochemical processes in this framework are seen to interact with each other by producing the ingredients enabling and/or inhibiting other reactions. They can also be influenced by the environment seen as a systematic driver of the processes through the ingredients brought into the cellular environment. In this paper, the first attempt is made to implement reaction systems in the hardware. We first show a tight relation between reaction systems and synchronous digital circuits, generally used for digital electronics design. We describe the algorithms allowing us to translate one model to the other one, while keeping the same behavior and similar size. We also develop a compiler translating a reaction systems description into hardware circuit description using field-programming gate arrays (FPGA) technology, leading to high performance, hardware-based simulations of reaction systems. This work also opens a novel interesting perspective of analyzing the behavior of biological systems using established industrial tools from electronic circuits design.

Quantitative extensions of reaction systems based on SOS semantics

“…We believe that optimisation of asynchronous circuits could be an interesting challenge for applying our framework. We also note that the work in [10] shows a tight relationship of reaction systems and synchronous circuits, while our extension with delay and duration might open the way to show a relationship of our extension with asynchronous circuits.…”

“…The behaviour of a RS is hence defined as a discrete time interactive process consisting of a context sequence (the sets of entities received at each unit of time from the environment), a result sequence (the sets of entities produced at each unit of time by reactions) and a state sequence (the join of the context sequence with the result sequence). Since their introduction, RSs have shown to be a quite general computation model whose application ranges from the modelling of biological phenomena [3][4][5][6] and molecular chemistry [7] to theoretical foundations of computing [8][9][10].…”

Simulation of reaction systems by the strictly minimal ones

“…Meanwhile, the study on the complexity of problems pertaining to the dynamicsof reaction systems has also received remarkable amount of interest [2,10,18]. Furthermore, physical simulation of reaction systems on the hardware has alsobeen initiated [19,23,29]. On top of these, various ingenious extended frameworks have been proposed notably recently, for example [7,13,20].…”