CN108537000B - Milli-type state machine design method based on molecular calculation - Google Patents
Milli-type state machine design method based on molecular calculation Download PDFInfo
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Abstract
The invention discloses a method for designing a Milli state machine based on molecular calculation, which comprises the following steps: s1: drawing a corresponding state transition diagram aiming at a specific sequential logic function of the Milli type state machine; s2: determining an initial state of a state machine; s3: if only one input variable of the state machine exists, the input variable molecule converts the catalyst maintaining the current state into the catalyst corresponding to an arrow pointing from the current state to the next state through catalytic reaction; if the input variable of the state machine exceeds one, all input variable molecules are compressed into one molecule through a two-molecule reaction, and the compressed molecule converts the catalyst in the current state into the catalyst corresponding to an arrow pointing from the current state to the next state; s4: the converted catalyst updates the values of the state variables and the output variables according to the state transition diagram, and converts the input variables into substances unrelated to the whole chemical reaction network. The invention improves the feasibility of physical implementation of chemical reaction networks.
Description
Technical Field
The invention relates to a method for designing a Milli-type state machine based on molecular calculation.
Background
The chemical reaction network is formed by a series of forms
The set of elementary reactions (including reactants, products, reaction rate constants). The chemical reaction network is a modeling language of molecular calculation, and in order to realize logic functions by using the molecular calculation, reactants and products in the chemical reaction network represent digital logic variables in a form of dual-rail logic. For example, 2 logical values of a certain logical variable X are composed of 2 molecules X0、X1Represents, i.e.: if a certain concentration of X appears in the chemical reaction network0Represents a logical value of 0 for X; if a certain concentration of X appears in the chemical reaction network1And represents a logical value of 1 for X.
The physical realization carrier of chemical reaction network is chemical reaction in solution, wherein DNA strand displacement reaction has been theoretically proved to realize any chemical reaction network, provided that the chemical reaction network only comprises bimolecular reaction and monomolecular reaction. The prior art has proposed a clock-driven state machine method using a chemical reaction network design, which has the disadvantage that the implementation of the state machine needs to be driven by means of a clock generated by the chemical reaction network. Although the chemical reaction network can theoretically simulate the clock signal, the corresponding physical implementation (such as DNA strand displacement reaction) has great difficulty and has no related mature technology so far.
Disclosure of Invention
The purpose of the invention is as follows: the invention aims to provide a method for designing a Milli state machine based on molecular calculation without clock driving.
The technical scheme is as follows: in order to achieve the purpose, the invention adopts the following technical scheme:
the invention relates to a method for designing a Milli-type state machine based on molecular calculation, which comprises the following steps:
s1: drawing a corresponding state transition diagram aiming at a specific sequential logic function of the Milli state machine, wherein the state transition diagram comprises three logic variables of a state variable, an input variable and an output variable, and each logic variable is assigned with a specific chemical molecule to represent a logic value of the logic variable; the state transition diagram comprises a plurality of arrows, and each arrow represents the transition from one state to another state; setting a specific catalyst molecule for each state transition, wherein the catalyst molecule is used for updating or keeping the values of the state variable and the output variable to the state value and the output value corresponding to the arrow through catalytic reaction;
s2: determining an initial state of a state machine;
s3: if only one input variable of the state machine exists, the input variable molecule converts the catalyst maintaining the current state into the catalyst corresponding to an arrow pointing from the current state to the next state through catalytic reaction; if the input variable of the state machine exceeds one, all input variable molecules are compressed into one molecule through a two-molecule reaction, and the compressed molecule converts the catalyst in the current state into the catalyst corresponding to an arrow pointing from the current state to the next state;
s4: the converted catalyst updates the values of the state variables and the output variables according to the state transition diagram, and converts the input variables into substances unrelated to the whole chemical reaction network.
Further, the initial state in the step S2 is expressed by a state variable numerator and an output variable numerator, and the values of the state variable and the output variable are maintained by a catalytic reaction with a catalyst.
Has the advantages that: the invention discloses a method for designing a Milli state machine based on molecular calculation, which realizes the Milli state machine in the field of molecular calculation by constructing a chemical reaction network, so that the time sequence logic function in the field of molecular calculation can get rid of the dependence of a clock, and the feasibility of physical realization of the chemical reaction network is improved.
Drawings
FIG. 1 is a state transition diagram of a Milli state machine in accordance with an embodiment of the present invention;
FIG. 2 is a schematic representation of a plurality of input variable molecules being compressed into one molecule in accordance with an embodiment of the present invention;
FIG. 3 is a diagram illustrating a single state transition of a state machine according to an embodiment of the present invention.
Detailed Description
The technical solution of the present invention will be further described with reference to the following detailed description and accompanying drawings.
The specific embodiment discloses a method for designing a Milli state machine based on molecular calculation, which comprises the following steps:
s1: drawing a corresponding state transition diagram according to the specific time sequence logic function of the Milli state machine, wherein the state transition diagram comprises three logic variables of a state variable, an input variable and an output variable, and each logic variable is assigned with a specific chemical molecule to represent the logic of the logic variableEditing a value; the state transition diagram comprises a plurality of arrows, and each arrow represents the transition from one state to another state; for each state transition a specific catalyst molecule is set, which is used to update or maintain the values of the state variable and the output variable to the state value and the output value corresponding to the arrows by catalytic reaction. The state transition diagram is shown in FIG. 1, where X, Y is the state variable, M is the input variable, Z, C is the output variable, TiFor a catalyst molecule, i ═ 1,2, …, k, k is the total number of arrows in the state transition diagram.
S2: an initial state of the state machine is determined. The initial state is represented by a state variable numerator and an output variable numerator, and the values of the state variable and the output variable are maintained by a catalytic reaction with a catalyst.
S3: if only one input variable of the state machine exists, the input variable molecule converts the catalyst maintaining the current state into the catalyst corresponding to an arrow pointing from the current state to the next state through catalytic reaction; if the input variable of the state machine exceeds one, all input variable molecules are compressed into one molecule through a two-molecule reaction, and the compressed molecule converts the catalyst in the current state into the catalyst corresponding to an arrow pointing from the current state to the next state.
S4: the converted catalyst updates the values of the state variables and the output variables according to the state transition diagram, and in order to prevent the input molecules at the next moment from existing simultaneously with the current input molecules, the converted catalyst converts the current input variables (single input variables or compressed input variables) into substances independent of the whole chemical reaction network.
The input variable molecules can indirectly drive the state transition by driving the conversion of the catalyst, which frees the sequential logic from being dependent on the clock. The catalyst molecule consumes the current input variable molecule, and the ambiguity of the input value due to the existence of the current input variable molecule and the input variable molecule at the next time is prevented.
The catalytic reaction involved in the state transition is shown in formula (1), wherein Y1Which represents a logical value of 1 and,Y0representing a logical value of 0. The function performed by the reaction is the catalyst molecule TiThe value of the logical variable Y is converted from 0 to 1. If the initial state in the chemical reaction network is Y only1And TiPresent, then TiThe function of (2) is understood to be to maintain the value of Y at 1 and to prevent the value of Y from being inverted.
Y0+Ti→Y1+Ti (1)
FIG. 2 is an example of multiple input variable molecules compressed into 1 molecule, where Xi(I-1, 2 … 9) is 9 input variables, Ii(i-1, 2, …,7) is an intermediate product, L1The input variable molecules after compression. There are a total of 8 reactions in the figure, all with 2 reactants and 1 product, such as: the reaction equation corresponding to the bottom is: i is7+X1 9->L1。
Formula (2) represents a catalyst molecule TiSingle input variable or compressed input variable (all here using L)iExpressed) to a substance independent of the whole chemically reactive network (expressed with Φ).
Li+Ti→φ+Ti (2)
Fig. 3 is a single state transition diagram of a state machine. StatecRepresenting the current state value and output value; t isjIs the current state (state)c) The catalyst of (1); statenRepresenting the next state value and the output value; t iskIs the next state (state)n) The catalyst of (1); inputs represent a number of input variables; l isiRepresenting the input molecules after compression; Φ represents a substance independent of the entire chemically reactive network. The solid line represents the conversion of the substance and the dotted line represents the catalytic action.
Claims (2)
1. The method for designing the Milli state machine based on molecular calculation is characterized by comprising the following steps: the method comprises the following steps:
s1: drawing a corresponding state transition diagram aiming at a specific sequential logic function of the Milli state machine, wherein the state transition diagram comprises three logic variables of a state variable, an input variable and an output variable, and each logic variable is assigned with a specific chemical molecule to represent a logic value of the logic variable; the state transition diagram comprises a plurality of arrows, and each arrow represents the transition from one state to another state; setting a specific catalyst molecule for each state transition, wherein the catalyst molecule is used for updating or keeping the values of the state variable and the output variable to the state value and the output value corresponding to the arrow through catalytic reaction;
s2: determining an initial state of a state machine;
s3: if only one input variable of the state machine exists, the input variable molecule converts the catalyst maintaining the current state into the catalyst corresponding to an arrow pointing from the current state to the next state through catalytic reaction; if the input variable of the state machine exceeds one, all input variable molecules are compressed into one molecule through a two-molecule reaction, and the compressed molecule converts the catalyst in the current state into the catalyst corresponding to an arrow pointing from the current state to the next state;
s4: the converted catalyst updates the values of the state variables and the output variables according to the state transition diagram, and converts the input variables into substances unrelated to the whole chemical reaction network.
2. The method of claim 1, wherein the method comprises: the initial state in S2 is represented by a state variable numerator and an output variable numerator, and the values of the state variable and the output variable are maintained by a catalytic reaction with a catalyst.
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| WO2003042395A2 (en) * | 2001-11-14 | 2003-05-22 | Yeda Research And Development Co.Ltd. | Programmable and autonomous computing machine made of biomolecules |
| US10388404B2 (en) * | 2015-10-27 | 2019-08-20 | International Business Machines Corporation | Using machine-learning to perform linear regression on a DNA-computing platform |
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