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A Method for Realizing m/n Duty Cycle Clock Signals Based on Unimolecular and Bimolecular Chemical Reaction Networks

A chemical reaction network and clock signal technology, applied in the field of DNA computing, can solve the problems of the high cost of the reaction rate and the difficulty of realizing the trimolecular reaction, and achieve the effect of easy realization.

Active Publication Date: 2020-04-24
SOUTHEAST UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

Therefore, in a real DNA scene, a reactant such as R+2G→3G in Table 1 has a three-molecular reaction, that is, a three-molecular reaction will become more difficult to achieve
Moreover, although these reactions can be decomposed into cascade reactions with no more than two reactants, the complexity and especially the reaction rate penalty will become very large

Method used

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  • A Method for Realizing m/n Duty Cycle Clock Signals Based on Unimolecular and Bimolecular Chemical Reaction Networks
  • A Method for Realizing m/n Duty Cycle Clock Signals Based on Unimolecular and Bimolecular Chemical Reaction Networks
  • A Method for Realizing m/n Duty Cycle Clock Signals Based on Unimolecular and Bimolecular Chemical Reaction Networks

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Embodiment 1

[0055] This embodiment is specific steps for realizing a clock signal with a duty ratio of 1 / 2.

[0056] In order to realize a clock signal with a duty ratio of 1 / 2, a total of 32 chemical reactions are required, and the chemical reaction equations are shown in formulas (1)-(9). Let the clock state species of the 1 / 2 duty cycle clock signal be E 0 and E 1 , E0s and E1s are intermediate species, and the state transition of the whole molecular system is four species according to E 0 →E0s→E 1 →E1s→E 0 The form is repeated. Force signal species F 0 , F 1 ,M 0 and M 1 The generation of can be regarded as a delay unit, while the subsequent triggered chemical reaction shows the conversion of clock signal state species.

[0057] A chemical reaction network that implements a 1 / 2 duty cycle clock signal can be implemented with the aid of a square diagram, such as figure 1 shown. The square plot actually reveals the trajectory of species transfer in the cycle. Among them, eac...

Embodiment 2

[0080] For the clock signal with M / N duty ratio of N≠2, its realization is based on the clock signal with 1 / 2 duty ratio. Let the clock state species be RE 0 and RE 1 , representing the "low" and "high" logic states, respectively. The core idea of ​​the clock signal implementation method of M / N duty ratio is to "record" the E in the phase clock signal of 1 / 2 duty ratio 0 and E 1 The number of transformations, i.e. with a set of reactants CTR i to record each transition of the clock signal, where i is an integer from 1 to N. i.e. the entire 1 / 2 duty cycle clock signal will be "packed" into segments. Each segment contains the E 0 and E 1 N conversions between, which indicates the denominator N of the duty cycle. Molecule M is realized by clock state species RE 0 and RE 1 Constructed, that is, split N conversions into two parts, one containing N-M conversions, and the other containing M conversions. Therefore, the target M / N duty cycle clock signal can be determined by...

Embodiment 3

[0089] According to the method where N is an even number, it is natural to record N transitions of the state of the original 1 / 2 duty cycle clock signal when N is an odd number. However, the two are very different in choosing the "record reactant" to change the target clock state. The main reason is that if the method of N being an even number is still used, then the next cycle (from CTR 1 to CTR N ) will not proceed. Aiming at this problem, the present invention discloses a feasible solution to the situation that N is an odd number, that is, to carry out a new cycle, which includes two steps from CTR 1 to CTR N basic cycle. Thus this new cycle can "record" 2N transitions of the 1 / 2 clock signal. Reactants that trigger clock state changes include CTR N-M 、CTR N 、CTR 2N-M and CTR 2N . The specific steps to obtain the corresponding CRNs are shown in Table 3.

[0090] Table 3 Design of M / N duty cycle clock signal when N is an odd number

[0091]

[0092] In Table 3...

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Abstract

The invention discloses a method for realizing an M / N duty cycle clock signal based on monomolecular and bimolecular chemical reaction networks. The method comprises the following processes: if N is an even number, cyclically executing step 1: recording the transfer number of state species of N continuous 1 / 2 duty cycle clock signals, and when the N continuous 1 / 2 duty cycle clock signals are shifted from the species E0 to E1 for the N-Mth time and the Nth time, shifting the state of the M / N duty cycle clock signals, wherein E0 and E1 are the clock state species of the 1 / 2 duty cycle clock signals; and if N is an odd number, cyclically executing step 2: recording the transfer number of the state species of 2N continuous 1 / 2 duty cycle clock signals, and when the 2N continuous 1 / 2 duty cycle clock signals are shifted from the species E0 to E1 for the N-Mth time, the Nth time, the 2N-Mth time and the 2Nth time, shifting the state of the M / N duty cycle clock signals. The method disclosed by the invention only adopts monomolecular and bimolecular chemical reactions, does not need the aid of an N-phase oscillator, and is easy to implement.

Description

technical field [0001] The invention belongs to the field of DNA computing and is the basic front end of DNA complex design. Background technique [0002] In 2010, David Soloveichik and others proposed "DNA as a universal substrate for chemical kinetics", which proved to a certain extent theoretically that for any formal chemical reaction network (Chemical Reaction Networks, hereinafter referred to as CRNs), it is always possible to find its corresponding The physical realization of DNA. That is to say, any CRNs we designed can be mapped to the DNA molecular chain replacement reaction; and the DNA molecular chain replacement reaction can be abstracted as A CRN composed of a series of elementary reactions of the form A+B→C+D simplifies the design. [0003] In 2013, Jiang Hua et al. proposed "Digital Logic with Molecular Reactions". For a single bit such as X, it can be represented by a group of three chemical reactions in formula (A), and thus proposed a bistable state base...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): H03K3/017
CPCH03K3/017
Inventor 温栋林张川戈璐璐尤肖虎
Owner SOUTHEAST UNIV
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