Abstract
Chemical reaction networks (CRNs) are a versatile language for describing the dynamical behaviour of chemical kinetics, capable of modelling a variety of digital and analogue processes. While CRN designs for synchronous sequential logic circuits have been proposed and their implementation in DNA demonstrated, a physical realisation of these devices is difficult because of their reliance on a clock. Asynchronous sequential logic, on the other hand, does not require a clock, and instead relies on handshaking protocols to ensure the temporal ordering of different phases of the computation. This paper provides novel CRN designs for the construction of asynchronous logic, arithmetic and control flow elements based on a bi-molecular reaction motif with catalytic reactions and uniform reaction rates. We model and validate the designs for the deterministic and stochastic semantics using Microsoft’s GEC tool and the probabilistic model checker PRISM, demonstrating their ability to emulate the function of asynchronous components under low molecular count.
Highlights
Chemical Reaction Networks (CRNs) are traditionally used to capture the behaviour of inorganic and organic chemical reactions in a well-mixed solution
This paper provides novel CRN designs for the construction of asynchronous logic, arithmetic and control flow elements based on a bi-molecular reaction motif with catalytic reactions and uniform reaction rates
A paradigm shift in the scientific community has seen the use of CRNs extend to that of a high-level programming language for molecular computing devices (Cook et al 2009), where the fundamental computational process differs from conventional digital electronics in that it involves transformation of input chemicals into output via reaction rules, as opposed to processing discrete signals interpreted as Boolean values
Summary
Chemical Reaction Networks (CRNs) are traditionally used to capture the behaviour of inorganic and organic chemical reactions in a well-mixed solution. The correctness of the behaviour of a circuit described by a finite CRN can be analysed by inspecting its stochastic and deterministic evolution over time. Techniques such as model checking can be employed to analyse the temporal ordering of events. An isochronous fork is a component which produces a fan-out of signals that reach the target at virtually the same time This assumption is difficult to achieve in conventional electronics, because of the need to make the wires the same length, but is straightforward in chemical kinetics because of the well-mixed assumption. This paper is an extended version of the conference paper Cardelli et al (2016)
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