Research On Analog DNA Strand Displacement Circuit

The advancement of science and technology require computer with higher computing speed and better performance.Computing speed and performance of traditional computer based on Si-based materials may be limited by waving of electron,tunnel effect and so on.New computer types,such as DNA molecular computation has drawn people's attention.DNA molecular computation based on biotechnology succeeds multiple strengths of DNA,such as compilability,high storability,nanoscale,low consumption and parallel processing.DNA strand displacement(DSD)has grown into a new means of technology and a novel method of DNA molecular computation gradually,because of spontaneous reaction under normal temperature,high output and easy operation.This dissertation mainly researches on the kinetic characteristics of many analog DSD circuits,and implementation of different function by DSD.The main contents summarize as follows:(1)Synchronization and projective synchronization of analog DSD circuits are realized.This dissertation explored error degradation of two species,and proposed synchronization or projective synchronization reaction module and new degradation reaction module,which can build ideal formal chemical reaction network(CRN).Synchronization and projective synchronization of two Lotka,Volterra oscillators with the same structures but different initial concentration are proved by Lyapunov stability theory.Numerical simulations indicate that,analog DSD is very good to approximate synchronization or projective synchronization of ideal formal CRN.(2)Coupling control and synchronization of analog DSD circuits are realized.Several DSD reaction modules with fluorophore and dark quencher are designed,because detection of luminous intensity is more accurate and convenient than concentration.Two dimensional Lotka-Volterra oscillator is extended to three dimensional Lotka-Volterra oscillator by coupling reaction module,and the coupling strength of system is controlled through coupling reaction module.Furthermore,three dimensional Lotka-Volterra oscillator is extended to N dimensional system by multiple coupling reaction modules.Take the three dimensional Lotka-Volterra oscillator for example,the coupling synchronization of two systems is realized by coupling reaction module according to Lyapunov stability theory.Numerical simulations indicate that,analog DSD circuit approximates coupling control and synchronization well.(3)Analog computation based on DSD is improved.Four analog DNA gates are designed including addition gate,subtraction gate,multiplication gate and division gate based on dual-rail principle against nonnegative property of DNA strand concentration.All of the analog gates can complete analog computation between two positive numbers,two negative numbers,a positive and a negative number,a negative and a positive number.Then,polynomial is computed by analog DSD circuits built by four gates due to the cascade and homogeneity of the four gates.The robust performances of four gates and analog circuit are demonstrated by simulation results.(4)Solution circuits based on DSD are proposed.Catalysis,degradation and annihilation reaction modules are designed,and these modules corresponding to different computation modules.Different equation or equations can divide into different computation modules,and different computation modules corresponding to different reaction modules,which can compose different CRNs.According to ordinary differential equations(ODE)of CRNs,equation or equations are solved when CRNs approached equilibrium.Comparing to ideal formal CRNs,analog DSD circuits realize the solution of ideal formal CRNs well.(5)Adaline based on analog DSD circuits is proposed.This dissertation designed catalysis,degradation and adjustment reaction modules according to the different part of Adaline.Then,a novel Adaline is proposed by the ODEs of ideal formal CRN built by reaction modules,the weights of Adaline are obtained when CRN has approached to equilibrium,and Adaline can fit a class of linear function.Through the analysis and assessment,DSD circuits can implement the learning ability of ideal formal CRN,and it is robust to DNA strand concentration,reaction rate and noise.