Reversible OR Logic Gate Design Using DNA
01 Jan 2013-pp 355-366
TL;DR: The design of two-input OR gate with E6 deoxyribozyme whose internal loop is not fixed is proposed, which helps to express Boolean expression in Sum of Product (SOP) form and sometimes it uses to minimize the Boolean function.
Abstract: In today’s world DNA technology is promoted as an alternative approach for advancement over silicon technology. The DNA technology is also used to detect diseases. It needs some molecular computation for which the development of basic circuit unit is required. Basic circuit comprises the AND, OR and NOT gate. In this paper we proposed the design of two-input OR gate with E6 deoxyribozyme whose internal loop is not fixed. OR logic helps to express Boolean expression in Sum of Product (SOP) form and sometimes it uses to minimize the Boolean function. The DNA technology can be used as a substitute method not only for lower time complexity and low power consumption but also this technology is reversible in nature.
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TL;DR: Enhanced logic properties have been observed for ssDNA after H adsorption due to improved electronic transmission and current-voltage characteristics confirm the formation of various Boolean logic gate operations.
Abstract: Molecular logic gate has been proposed using single-strand DNA (ssDNA) consisting of basic four nucleobases. In this study, density functional theory and non-equilibrium Green's function based first principle approach is applied to investigate the electronic transmission characteristics of ssDNA chain. The heavily hydrogen-doped-ssDNA (H-ssDNA) chain is connected with gold electrode to achieve enhanced quantum-ballistic transmission along 〈1 1 1〉 direction. Logic gates OR, Ex-OR, NXOR have been implemented using this analytical model of H-ssDNA device. Enhanced logic properties have been observed for ssDNA after H adsorption due to improved electronic transmission. Dense electron cloud is considered as logic `high' (1) output in presence of hydrogen molecule and on the contrary sparse cloud indicate logic `low' (0) in the absence of hydrogen molecule. Device current is significantly increased from 0.2 nA to 2.4 μA (approx.) when ssDNA chain is heavily doped with hydrogen molecule. The current-voltage characteristics confirm the formation of various Boolean logic gate operations.
7 citations
TL;DR: An asymmetrical element based on Au-DNA-Ag has been proposed and designed to play the role of a DNA memristor and it has been shown that the asymmetrical design causes a sharp decrease in flow and thus power consumption.
Abstract: An asymmetrical element based on Au-DNA-Ag has been proposed and designed to play the role of a DNA memristor. The role of the DNA length here is to decrease the power and size of the memristor. In fact, according to the context and simulation results, the combination of metal–DNA–metal can play the role of a memristor and produce a similar behavior as a memristor. It has been shown that the asymmetrical design, i.e., two different metals, causes a sharp decrease in flow and thus power consumption. With this element, a ternary logic has been designed and simulated with much less power in comparison with similar circuits. With the help of this device, a new, efficient and ternary reversible logic gate has been proposed and designed. With the help of this proposed gate, all logic circuits with minimum quantum cost, garbage output, power consumption and delay were proposed and designed. In fact, in this research, a reversible logic was proposed that has much less quantum cost, garbage output, power consumption and delay than previous designs.
5 citations
TL;DR: In this article, a universal reversible gate library (URGL) was proposed for synthesizing n-bit reversible circuits using DNA to reduce the average length and cost of the constructed circuits when compared with previous methods.
Abstract: DNA computers and quantum computers are gaining attention as alternatives to classical digital computers. DNA is a biological material that can be reprogrammed to perform computing functions. Quantum computing performs reversible computations by nature based on the laws of quantum mechanics. In this paper, DNA computing and reversible computing are combined to propose novel theoretical methods to implement reversible gates and circuits in DNA computers based on strand displacement reactions, since the advantages of reversible logic gates can be exploited to improve the capabilities and functionalities of DNA computers. This paper also proposes a novel universal reversible gate library (URGL) for synthesizing n-bit reversible circuits using DNA to reduce the average length and cost of the constructed circuits when compared with previous methods. Each n-bit URGL contains building blocks to generate all possible permutations of a symmetric group of degree n. Our proposed group (URGL) in the paper is a permutation group. The proposed implementation methods will improve the efficiency of DNA computer computations as the results of DNA implementations are better in terms of quantum cost, DNA cost, and circuit length.
TL;DR: In this paper, the electronic properties of a single-strand DNA chain are investigated to form the logic gate and the property of resistivity proves the law of Boolean logic of AND gate and universal logic gate.
Abstract: One of the emerging areas of today's research arena is molecular modeling and molecular computing. The molecular logic gate can be theoretically implemented from single-strand DNA which consists of four basic nucleobases. In this study, the electronic transmission characteristics of DNA chain are investigated to form the logic gate. This biomolecular single-strand DNA chain is passed through an electrically doped gallium-arsenide nano-pore to achieve reasonably improved transmission along direction. Current-voltage characteristic and device density of states with HOMO-LUMO plot of the device are explained along with the conductivity of the device to confirm the characteristics of some important logic gates like a universal gate. Ultimately the property of resistivity proves the law of Boolean logic of AND gate and universal logic gate, viz., NAND and NOR gate. All the electronic properties of the Boolean logic gate are explored based on the first principle approach by non-equilibrium Green's function coupled with density functional theory in room temperature.
References
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TL;DR: This experiment demonstrates the feasibility of carrying out computations at the molecular level by solving an instance of the directed Hamiltonian path problem with standard protocols and enzymes.
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4,266 citations
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2,148 citations
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1,411 citations
TL;DR: The design and experimental implementation of DNA-based digital logic circuits using single-stranded nucleic acids as inputs and outputs are reported, suggesting applications in biotechnology and bioengineering.
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1,374 citations
TL;DR: Diverse molecular self-assembly and disassembly pathways are program using a ‘reaction graph’ abstraction to specify complementarity relationships between modular domains in a versatile DNA hairpin motif.
Abstract: In nature, self-assembling and disassembling complexes of proteins and nucleic acids bound to a variety of ligands perform intricate and diverse dynamic functions. In contrast, attempts to rationally encode structure and function into synthetic amino acid and nucleic acid sequences have largely focused on engineering molecules that self-assemble into prescribed target structures, rather than on engineering transient system dynamics. To design systems that perform dynamic functions without human intervention, it is necessary to encode within the biopolymer sequences the reaction pathways by which self-assembly occurs. Nucleic acids show promise as a design medium for engineering dynamic functions, including catalytic hybridization, triggered self-assembly and molecular computation. Here, we program diverse molecular self-assembly and disassembly pathways using a 'reaction graph' abstraction to specify complementarity relationships between modular domains in a versatile DNA hairpin motif. Molecular programs are executed for a variety of dynamic functions: catalytic formation of branched junctions, autocatalytic duplex formation by a cross-catalytic circuit, nucleated dendritic growth of a binary molecular 'tree', and autonomous locomotion of a bipedal walker.
1,259 citations