Method for calculating second-order Markov chain by using chemical reaction network

Abstract

The present invention discloses a method for calculating a second-order Markov chain by using a chemical reaction network. The method comprises the following steps: S1: designing a chemical reaction network to represent different states in a target second-order Markov chain with different reactant species, and setting the initial concentration of the corresponding reactants according to the initial probability distribution of the states of the target second-order Markov chain; S2: implementing transition of each state transition of the target second-order Markov chain through a bimolecular reaction, wherein each reactant represents two states before the transition, and the product represents the two states after the transition; S3: using the rate constant of each reaction to represent thetransition probability of the corresponding state transition, and setting the rate constant according to the value of the transition probability; S4 : removing the invalid reaction in the reaction network; and S5: calculating the steady-state distribution of the target second-order Markov chain, wherein the steady-state concentration of all the reactants after the reaction ends is the probabilityvalue of the steady-state distribution. The method disclosed by the present invention can implement the calculation of a second-order Markov chain.

Description

technical field [0001] The invention relates to the field of molecular calculations, in particular to a method for calculating second-order Markov chains using chemical reaction networks. Background technique [0002] Since Moore's law is no longer applicable to materials smaller than 5nm, molecular computing, as a new computing method, has attracted the attention of many researchers. The chemical reaction network can express a variety of dynamic characteristics, so it can be used as a programmable language. Among the existing research results, DNA reactions, RNA and polymerized proteins have been used to realize computer computing functions such as digital logic. Formal chemical reaction networks have been used to realize relatively complete digital circuits, analog circuits, signal processing, etc. Soloveichik, D., Seelig, G., and Winfree, E. Design precise DNA strand replacement in Proceedings of the National Academy of Sciences (PNAS) 107, 5393–5398, "DNA as a universa...

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Problems solved by technology

But no one has considered the design of higher-order Markov chains and the calculation of steady-state distributions

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