Chaotic oscillation system based on DNA chemical reaction network

Abstract

The present application relates to the technical field of molecular computing and information security, in particular to a chaotic oscillation system based on DNA chemical reaction network, which mainly comprises a catalytic reaction module, a degradation reaction module, an annihilation reaction module and a synchronization reaction module; the present application takes DNA reaction network as a research starting point, designs a chaotic oscillation system based on DNA chemical reaction network, and constructs idealized CRN by the catalytic reaction module, the degradation reaction module, the annihilation reaction module and the synchronization reaction module designed by Visual DSD software, solves linear equations, monomial quadratic equations and linear equation groups through the differential equations of idealized CRN, and constructs DSD simulation circuit, so as to realize the construction of logic circuit and information encryption through the constructed DSD simulation circuit.

Description

Technical Field

[0001] This invention relates to the fields of molecular computing and information security technology, specifically to a chaotic oscillation system based on a DNA chemical reaction network. Background Technology

[0002] Chemical reaction equations and mass action kinetics provide a powerful mathematical language for describing and analyzing chemical systems, and the realization of chemical reaction networks can offer an effective programming paradigm for complex molecular systems. DNA-based chemical reaction networks consist of a series of cascaded DNA strand substitution reactions, hybridization chain reactions, molecular self-assembly, polymerase chain reactions, and ligase chain reactions. Compared to artificial reaction networks, DNA reaction networks can directly participate in information processing in fields such as molecular computing, biological detection, and medical diagnostics.

[0003] However, computational DNA reaction networks still have shortcomings. Currently, operations such as DNA encoding and DNA sequence addition and subtraction have become important means in image encryption schemes, but sequence operations based on DNA diversity are rarely involved in image encryption schemes. DNA strand substitution reaction networks are often used in logic operations, probabilistic reasoning, and equation solving, but the application of reaction networks in complex mathematical problems is still limited. Computational DNA reaction networks are currently used more in Boolean matrix operations, but research on solving matrix multiplication problems in algebra is still very limited. In some high-level logic circuits built based on DNA reaction networks (such as XOR gates and half-adders), the input signals are exhausted before entering the logic operation, which will result in the loss of upstream logic output, making it difficult for downstream cascade reactions to continue, thus affecting the cascade scale of logic circuits. Traditional DNA molecular logic circuit models lack good scalability, making it very difficult to expand and integrate large-scale molecular logic circuits. Constructing DNA molecular logic circuits that are easy to implement and have good scalability is also a major challenge.

[0004] In view of this, in order to overcome the above-mentioned technical problems, the present invention proposes a chaotic oscillation system based on DNA chemical reaction network, which solves the above-mentioned technical problems. Summary of the Invention

[0005] To overcome the shortcomings of existing technologies, this invention utilizes biotechnologies such as DNA strand substitution and hybridization chain reactions to construct DNA reaction networks and form chaotic oscillation systems, exploring their applications in image encryption, solving complex mathematical problems, and constructing logic circuits. This invention proposes a chaotic oscillation system based on a DNA chemical reaction network.

[0006] The present invention discloses a chaotic oscillation system based on a DNA chemical reaction network, which mainly includes:

[0007] Catalytic reaction module, degradation reaction module, annihilation reaction module and simultaneous reaction module;

[0008] The catalytic reaction module, degradation reaction module, annihilation reaction module, and synchronous reaction module construct a DSD analog circuit to realize the construction of logic circuits, information encryption, and the solution of complex mathematical problems.

[0009] Preferably, the chemical reaction network of the catalytic reaction module is described by the formula X1→2X1.

[0010] Preferably, the chemical reaction network of the catalytic reaction module is implemented by the following DNA strand substitution reaction network:

[0011]

[0012]

[0013] Preferably, in the chemical reaction network of the catalytic reaction module It is a single chain. Both `waste` and `waste` are complex chains.

[0014] Preferably, the chemical reaction network of the degradation reaction module is described by the formula X1→X2+X3.

[0015] Preferably, the chemical reaction network of the degradation reaction module is implemented by the following formula:

[0016] X1+G i →O i +q i ;

[0017] O i +T i →X2+X3+waste.

[0018] Preferably, in the chemical reaction network of the degradation reaction module, X1 and O i X2 and X3 are all single-chain, G i q i T i Both `waste` and `waste` are complex chains.

[0019] Preferably, the idealized reaction of the annihilation reaction module is:

[0020]

[0021] Preferably, the idealized reaction of the synchronous reaction module is:

[0022]

[0023] Preferably, the system includes the following steps:

[0024] S1: Construct the DNA chemical reaction network of the chaotic system and the DNA chemical reaction network of the DSD simulation circuit based on the basic principles of the four-variable chaotic oscillation system and the basic principles of the DSD simulation circuit, respectively.

[0025] S2: The DNA chemical reaction network of the four-variable chaotic oscillation system is divided into a catalytic reaction module, a degradation reaction module, an annihilation reaction module, and a synchronous reaction module;

[0026] S3: Construct the DNA base sequence of the chaotic system and the DNA strand substitution reaction equation of the chaotic system based on the DNA chemical reaction network of the chaotic system; construct the DNA base sequence of the DSD simulation circuit and the DNA strand substitution reaction equation of the DSD simulation circuit based on the DNA chemical reaction network of the DSD simulation circuit.

[0027] S4: The catalytic reaction module, degradation reaction module, annihilation reaction module and synchronization reaction module in the DNA chemical reaction network of the chaotic oscillation system are mapped to DSD simulation circuits, and the catalytic reaction module, degradation reaction module, annihilation reaction module and synchronization reaction module designed by Visual DSD software are used to construct an idealized CRN.

[0028] The beneficial effects of this invention are as follows:

[0029] This invention takes DNA reaction networks as its starting point and designs a chaotic oscillation system based on DNA chemical reaction networks. It constructs an idealized CRN by using catalytic reaction modules, degradation reaction modules, annihilation reaction modules, and synchronous reaction modules designed with Visual DSD software. The linear equations, quadratic equations, and systems of linear equations are solved by using the differential equations of the idealized CRN. A DSD simulation circuit is also constructed, and the logic circuit and information encryption are realized through the constructed DSD simulation circuit. Attached Figure Description

[0030] The present invention will be further described below with reference to the accompanying drawings and embodiments.

[0031] Figure 1 This is a flowchart of the present invention;

[0032] Figure 2 This is a reaction process diagram of the catalytic reaction module in this invention;

[0033] Figure 3 This is a reaction process diagram of the degradation reaction module in this invention. Detailed Implementation

[0034] To make the technical means, creative features, objectives and effects of this invention easier to understand, the invention will be further described below in conjunction with specific embodiments.

[0035] like Figures 1 to 3 As shown, the present invention discloses a chaotic oscillation system based on a DNA chemical reaction network, which mainly includes:

[0036] Catalytic reaction module, degradation reaction module, annihilation reaction module and simultaneous reaction module;

[0037] The catalytic reaction module, degradation reaction module, annihilation reaction module, and synchronous reaction module construct a DSD analog circuit to realize the construction of logic circuits, information encryption, and the solution of complex mathematical problems.

[0038] During operation, an idealized CRN is constructed by designing catalytic reaction modules, degradation reaction modules, annihilation reaction modules, and simultaneous reaction modules using Visual DSD software. Linear equations, quadratic equations, and systems of linear equations are then solved using the differential equations of the idealized CRN. Furthermore, Visual DSD software is used to... The DSD software-designed catalytic reaction module, degradation reaction module, annihilation reaction module, and synchronization reaction module construct DSD analog circuits. These DSD analog circuits enable the construction of logic circuits and information encryption. Specifically, the catalytic reaction module, degradation reaction module, annihilation reaction module, and synchronization reaction module can be freely combined to build more complex analog circuits. Since input and output results are represented by concentration in analog circuits, and concentration is non-negative, the input and output values ​​can only be non-negative. However, the annihilation reaction module can extend the input and output results to negative values, thus enabling the construction of richer logic circuits. Furthermore, the DNA molecule logic gates and the logic circuits they construct are binary circuits, meaning the circuit takes values ​​of "0" or "1". The principle is that when the concentration of the DNA strand is higher than a threshold, the logic expression is "1", and vice versa, it is "0". Therefore, it has strong anti-interference capabilities and achieves information encryption.

[0039] As a specific embodiment of the present invention, the chemical reaction network of the catalytic reaction module is described by the formula X1→2X1;

[0040] The chemical reaction network of the catalytic reaction module is implemented by the following DNA strand displacement reaction network:

[0041]

[0042]

[0043] In the chemical reaction network of the catalytic reaction module It is a single chain. Both `waste` and `waste` are complex chains.

[0044] During operation, the chemical reaction network of the catalytic reaction module is realized by the following DNA strand substitution reaction network:

[0045]

[0046] The specific reaction process is as follows: Figure 2 As shown:

[0047] In this reaction, DNA single strands Permutation complex chain Generating complex chains and DNA single strand Complex chains For discarded strands, single-stranded DNA As an intermediate product, complex chain Auxiliary strand; DNA single strand Re-permutation of complex chains Generate two DNA single strands Complex chains For auxiliary chain; q i and q max The reaction rate is indicated; the above reaction achieves the transformation X1→2X1.

[0048] As a specific embodiment of the present invention, the chemical reaction network of the degradation reaction module is described by the formula X1→X2+X3;

[0049] The chemical reaction network of the degradation reaction module is implemented by the following formula:

[0050] X1+G i →O i +q i ;

[0051] O i +T i →X2+X3+waste;

[0052] In the chemical reaction network of the degradation reaction module, X1 and O i X2 and X3 are all single-chain, G i q i T i Both `waste` and `waste` are complex chains.

[0053] During operation, the chemical reaction network of the degradation reaction module is implemented by the following formula:

[0054] X1+G i →O i +q i ;

[0055] O i +T i →X2+X3+waste; the specific reaction process is as follows: Figure 3 As shown;

[0056] In this reaction, single-stranded DNA X1 replaces complex strand G. i Generate complex chain q i and DNA single-stranded O i The complex chain q i For discarded strands, single-stranded DNA O i As an intermediate product, complex chain G i For auxiliary strand; DNA single strand O i Re-permutation of complex chain T i Two single-stranded DNA molecules, X2 and X3, are generated, with the complex strand T... i As an auxiliary chain, the above reaction achieves the transformation X1→2X1.

[0057] As a specific embodiment of the present invention, the idealized reaction of the annihilation reaction module is:

[0058]

[0059] During operation, consistent with the catalytic reaction module and the degradation reaction module, two auxiliary chains are added to this reaction respectively. as well as The auxiliary chain is reversibly consumed, generating a single chain and an auxiliary chain. The generated single chain and the auxiliary chain react to generate a discard chain, completing the annihilation reaction.

[0060] As a specific embodiment of the present invention, the idealized reaction of the synchronous reaction module is:

[0061]

[0062] During work, the reaction is as follows:

[0063]

[0064]

[0065]

[0066] Two complex DNA strands are added simultaneously to the reaction. as well as as well as quilt as well as Simultaneously perform reversible permutations to generate single chains. as well as as well as They were then respectively and Displacement, in the above reaction, and As an auxiliary chain, as well as It is an intermediate product; therefore as well as They exhibit synchronous concentration, thus completing a synchronous reaction.

[0067] As a specific embodiment of the present invention, the system includes the following steps:

[0068] S1: Construct the DNA chemical reaction network of the chaotic system and the DNA chemical reaction network of the DSD simulation circuit based on the basic principles of the four-variable chaotic oscillation system and the basic principles of the DSD simulation circuit, respectively.

[0069] S2: The DNA chemical reaction network of the four-variable chaotic oscillation system is divided into a catalytic reaction module, a degradation reaction module, an annihilation reaction module, and a synchronous reaction module;

[0070] S3: Construct the DNA base sequence of the chaotic system and the DNA strand substitution reaction equation of the chaotic system based on the DNA chemical reaction network of the chaotic system; Construct the DNA base sequence of the DSD simulation circuit and the DNA strand substitution reaction equation of the DSD simulation circuit based on the DNA chemical reaction network of the DSD simulation circuit.

[0071] S4: The catalytic reaction module, degradation reaction module, annihilation reaction module and synchronization reaction module in the DNA chemical reaction network of the chaotic oscillation system are mapped to DSD simulation circuits, and the catalytic reaction module, degradation reaction module, annihilation reaction module and synchronization reaction module designed by Visual DSD software are used to construct an idealized CRN.

Claims

1. A chaotic oscillation system based on a DNA chemical reaction network, characterized in that: The system mainly includes, Catalytic reaction module, degradation reaction module, annihilation reaction module and simultaneous reaction module; The catalytic reaction module, degradation reaction module, annihilation reaction module, and synchronous reaction module construct an idealized CRN. The logic circuit is constructed, information is encrypted, and complex mathematical problems are solved by solving linear equations, quadratic equations, and systems of linear equations through the differential equations of the idealized CRN and the DSD simulation circuit. The chemical reaction network of the catalytic reaction module is described by the formula X1→2X1; The chemical reaction network of the catalytic reaction module is implemented by the following DNA strand displacement reaction network: In the chemical reaction network of the catalytic reaction module It is a single chain. Both waste and DNA single strands are complex strands; in this reaction, a single DNA strand replaces a complex strand to generate a complex strand, and a single DNA strand, where the complex strand is the discarded strand, the single DNA strand is the intermediate product, and the complex strand is the auxiliary strand; the single DNA strand then replaces the complex strand to generate two single DNA strands, where the complex strand is the auxiliary strand. The chemical reaction network of the degradation reaction module is described by the formula X1→X2+X3; The chemical reaction network of the degradation reaction module is implemented by the following formula: X1+G i →O i +q i ; O i +T i →X2+X3+waste; The annihilation reaction module can be used to extend the input and output results to negative values, thus enabling the construction of richer logic circuits. Secondly, the DNA molecule logic gate and the logic circuit constructed therefrom are binary circuits, that is, the value in the circuit is "0" or "1". The principle is: when the concentration of DNA strands is higher than the threshold, the logic expression is "1", and otherwise it is "0". Therefore, it has strong anti-interference ability and realizes information encryption.

2. The chaotic oscillation system based on a DNA chemical reaction network according to claim 1, characterized in that: In the chemical reaction network of the degradation reaction module, X1 and O i X2 and X3 are all single-chain, G i q i T i Both `waste` and `waste` are complex chains.

3. The chaotic oscillation system based on a DNA chemical reaction network according to claim 1, characterized in that: The idealized reaction of the annihilation reaction module is:

4. The chaotic oscillation system based on a DNA chemical reaction network according to claim 1, characterized in that: The ideal reaction of the synchronous reaction module is:

5. The chaotic oscillation system based on a DNA chemical reaction network according to claim 1, characterized in that: The system includes the following steps: S1: Construct the DNA chemical reaction network of the chaotic system and the DNA chemical reaction network of the DSD simulation circuit based on the basic principles of the four-variable chaotic oscillation system and the basic principles of the DSD simulation circuit, respectively. S2: The DNA chemical reaction network of the four-variable chaotic oscillation system is divided into a catalytic reaction module, a degradation reaction module, an annihilation reaction module, and a synchronous reaction module; S3: Construct the DNA base sequence of the chaotic system and the DNA strand substitution reaction equation of the chaotic system based on the DNA chemical reaction network of the chaotic system; construct the DNA base sequence of the DSD simulation circuit and the DNA strand substitution reaction equation of the DSD simulation circuit based on the DNA chemical reaction network of the DSD simulation circuit. S4: The catalytic reaction module, degradation reaction module, annihilation reaction module and synchronization reaction module in the DNA chemical reaction network of the chaotic oscillation system are mapped to DSD simulation circuits, and the catalytic reaction module, degradation reaction module, annihilation reaction module and synchronization reaction module designed by Visual DSD software are used to construct an idealized CRN.

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