Computational Model Design And Application Research Based On DNA Strand Displacement Circuits

Due to the high programmability and storability of DNA circuits,they have been widely used in biocomputing.DNA strand displacement reaction is popular among scholars and abroad as an implementation method of DNA strand displacement circuits.Currently,logarithmic functions,linear equations and polynomials have been solved based on DNA strand displacement reactions.For solutions of nonlinear equations,exponential functions and state transfer matrix are still relatively rare.In order to realize the solution of nonlinear equations,exponential functions and state transfer matrix,different DNA strand displacement reaction modules are designed and DNA strand displacement integrated circuits are constructed in this paper based on DNA strand displacement reactions.Higher-order systems of simultaneous equations,exponential function polynomials,and state transfer matrices are solved by cascading different DNA strand displacement reaction modules and DNA circuits.The main works of this paper are as follows.Research on DNA biocomputing has focused on the problem of implementing solutions to nonlinear equations.The catalysis reaction module,degradation reaction module,annihilation reaction module and adjusted reaction module are designed according to the different functions of the solved computations.The cascade of different reaction modules and the mass action kinetics are used to build a model for the simultaneous equations of higher order.The solution of higher order equations is achieved.Compared with the solution of the linear equation in the previous paper,it is not only extended to the nonlinear domain,but also considers the effect of reaction rate error on the DNA strand displacement reaction,which improves the robustness of the overall reaction.It provides a reference for future solutions of nonlinear equations based on DNA strand displacement reactions.Research on DNA biocomputing has focused on the problem of implementing polynomial solutions for exponential functions and has designed addition,subtraction,multiplication,division,n-order and 1/n-order gates depending on the computational function.The DNA integrated circuits are formed by combining different gates.The model of the exponential function polynomial is built,and the solution of the exponential function polynomial is realized,and the error accuracy is controlled to within 0.02.The proposed of n-order gate as well as 1/norder gate can reduce the number of DNA strands used and improve the computational speed of DNA integrated circuits.It provides a reference for the future implementation of large-scale DNA strand displacement integrated circuits.Research on DNA biocomputing has focused on the problem of implementing state transfer matrix solutions,a method of matrix solving based on DNA strand displacement circuits is proposed.The computation module is combined with DNA analog gates to form the summation reaction module,subtraction reaction module,multiplication reaction module,division reaction module,and exponential reaction module.The different reaction modules are cascaded and the model of state transfer matrixes is built by mass action kinetics.Finally,the solutions of state transfer matrixes are realized by the DNA strand displacement circuits,extending the computation of DNA molecules to the matrix domain.It provides a reference for future solutions of the matrixes based on the DNA strand displacement circuits.The computational results of this research are based on the simulation class software Visual DSD and Matlab for comparison and validation.The order of this research is the study of nonlinear equation solving,the study of exponential function polynomial solving,and the study of state transfer matrix solving.Finally,the accuracy of this research is verified by comparing the experimental results.