Logic reversibility and thermodynamic irreversibility demonstrated by DNAzyme-based Toffoli and Fredkin logic gates (original) (raw)
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Symmetry, 2021
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) i...
Journal of the American Chemical Society, 2004
A conceptually new logic gate based on DNA has been devised. Methoxybenzodeazaadenine (MD A), an artificial nucleobase which we recently developed for efficient hole transport through DNA, formed stable base pairs with T and C. However, a reasonable hole-transport efficiency was observed in the reaction for the duplex containing an MD A/T base pair, whereas the hole transport was strongly suppressed in the reaction using a duplex where the base opposite MD A was replaced by C. The influence of complementary pyrimidines on the efficiency of hole transport through MD A was quite contrary to the selectivity observed for hole transport through G. The orthogonality of the modulation of these hole-transport properties by complementary pyrimidine bases is promising for the design of a new molecular logic gate. The logic gate system was executed by hole transport through short DNA duplexes, which consisted of the "logic gate strand", containing hole-transporting nucleobases, and the "input strand", containing pyrimidines which modulate the hole-transport efficiency of logic bases. A logic gate strand containing multiple MD A bases in series provided the basis for a sharp AND logic action. On the other hand, for OR logic and combinational logic, conversion of Boolean expressions to standard sum-of-product (SOP) expressions was indispensable. Three logic gate strands were designed for OR logic according to each product term in the standard SOP expression of OR logic. The hole-transport efficiency observed for the mixed sample of logic gate strands exhibited an OR logic behavior. This approach is generally applicable to the design of other complicated combinational logic circuits such as the full-adder.
ChemPhysChem, 2003
Miniaturization has been an essential ingredient in the outstanding progress of information technology over the past fifty years. The next, perhaps ultimate, limit of miniaturization is that of molecules, which are the smallest entities with definite size, shape, and properties. Recently, great effort has been devoted to design and investigate molecular-level systems that are capable of transferring, processing, and storing information in binary form. Some of these nanoscale devices can, in fact, perform logic operations of remarkable complexity. This research-although far from being transferred into technology-is attracting interest, as the nanometer realm seems to be out of reach for the ™top-down∫ techniques currently available to microelectronics industry. Moreover, such studies introduce new concepts in the ™old∫ field of chemistry and stimulate the ingenuity of researchers engaged in the ™bottom-up∫ approach to nanotechnology.
Quantum Logic Gates Based on DNAtronics, RNAtronics, and Proteintronics
Advanced Intelligent Systems, 2021
A quantum computer (QC) [1-3] implements quantum bits (qubits) and qudits [4] (e.g., qutrits [5] and ququarts [6]) to conduct computations instead of a traditional digital computer built from a transistor in which a binary bit is represented by either 1 or 0. Based on the Church-Turing-Deutch principle, a computing machine conducts simulations of every physical process and behaves as a universal QC. [7-9] Unlike a classical bit, the basic unit of a qubit is the superposition c 0 j0i þ c 1 j1i of two qubit states, j0i and j1i, where c 0 and c 1 denote complex numbers. [10] However, the operation of a QC with a relatively large number of qubits for conducting universal computations has attracted considerable attention. [11] Using quantum algorithms such as Shor's algorithm, [12] a quantum many-body simulation [10] and Simon's algorithm, [13] a large-scale QC could tackle problems faster than a classical computer. Until now, present quantum algorithms have been implemented by superconducting flux qubits (D-wave systems), [14] nuclear magnetic resonance (NMR) techniques, [15,16] photonic QCs, [17] and ion-trap systems. [18,19] For NMR techniques, Shor's factorizing algorithm, [20] which uses seven qubits, has been applied. The qubits are encoded in mixed states, and the output is a result of an ensemble measurement. Hence, NMR QCs are not scalable. [21] For a trapped-ion QC, the qubits are stored in the electronic states of ions and are controllable in long-lived internal states, and their quantum states can be detected with a very high efficiency close to 100%. [19,22,23] These characteristics permit the manipulation of pure states to build a scalable and universal QC. [24] Nevertheless, no quantum logic gate has been executed with a subnano-scaled molecular transistor to date. Classical computers operate with a microprocessor that consists of semiconductor logic gates with electronic input and output signals of a binary digital nature. The output can be only one of the two states, on or off, corresponding to logic 1 or 0, respectively. Consequently, the signal pattern can be described by a truth table based on Boolean algebra. [25] This critical feature in constructing computers could be conducted by a single-molecule transistor as a future classical computer. [26,27] However, accomplishing concerted arrays of molecular transistors remains an intrinsic challenge. [28,29] Recently, several experiments have shown the feasibility of conducting computations at the molecular level. For example, DNA is a reliable biomolecule and can be used to build molecular computation systems; however, it was used as a classical liquid computer to solve the Hamiltonian path problem. [30] DNA-based logic gates [25,31] have been designed by deoxyribozyme ligases. [32,33] It is possible to integrate the logic gates into simple circuits using a series of deoxyribozyme ligases communicating via a deoxyribozyme phosphodiesterase. [28] Meanwhile, NOT and two-input AND gates were integrated into an INHIBIT logic gate, and signal transduction was mediated by the association of several DNA strands.
Chemical communications (Cambridge, England), 2015
This feature article addresses the implementation of catalytic nucleic acids as functional units for the construction of logic gates and computing circuits, and discusses the future applications of these systems. The assembly of computational modules composed of DNAzymes has led to the operation of a universal set of logic gates, to field programmable logic gates and computing circuits, to the development of multiplexers/demultiplexers, and to full-adder systems. Also, DNAzyme cascades operating as logic gates and computing circuits were demonstrated. DNAzyme logic systems find important practical applications. These include the use of DNAzyme-based systems for sensing and multiplexed analyses, for the development of controlled release and drug delivery systems, for regulating intracellular biosynthetic pathways, and for the programmed synthesis and operation of cascades.
Reversible Molecular Logic: A Photophysical Example of a Feynman Gate
ChemPhysChem, 2009
The demand of modern information technology for ever more powerful microprocessors has to pass the bottleneck of miniaturization. Moore's law predicts a duplication of transistor density every 18-24 months. However, conventional lithographic technology is at a cross-roads regarding its spatial resolution capacity and the semiconductor industry is struggling to keep up with Moore's forecast. Currently, diverse efforts are pursued in the chemistry community to overcome obstacles of this top-down approach by substituting it with a bottom-up strategy based on first principles of supramolecular chemistry and clever design of functional molecular building blocks. [3] Especially photoactive (supra)molecular devices, whose behavior integrates logic gate functionality, have received growing interest. On the other hand, increasing the density of functional units on a chip creates different problems, one of them being the dissipation of heat. According to Landauer, every irreversible logic operation leads to minimum heat generation in the order of kT ln 2, as the result of information loss. In reversible logic, where input and output vectors are connected through a one-to-one mapping function, this is avoided. Thus, reversible logic gates have attracted growing interest for applications in conventional computing, DNA computing, [6] and quantum computing. However, photoactive molecular logic systems so far reported are logically irreversible, disregarding trivial cases such as the NOT gate. In a recent report, some of us predicted that reversible logic at the molecular level is an important future challenge. However, the therein realized XOR/INH combination is not a fully reversible logic operation. Herein, we now describe the first realization of this goal. It should be kept in mind that the reversibility we are referring to is logic reversibility and not chemical reversibility, used by others for resetting molecular logic operations. The truth table of a two-input XOR gate, shown in Scheme 1 a, contains the same output for different input combinations, that is, output O = 0 for the input vectors 00 and 11 and output O = 1 for the input combinations 01 and 10. Hence, it is impossible to assign the corresponding input vector based on the knowledge of the output only, implying that the operation is logically irreversible. The dilemma can be solved by adding another output column (output O1), as in Scheme 1 b, which combines with the XOR output O2 in such a way that exactly four different combinations are obtained. Now it is straightforward to identify any input or output based on its assigned counterpart. For two outputs, 24 different permutative combinations of four distinguished output vectors (i.e. 00, 01, 10, 11) are possible, each combination corresponding to a reversible logic gate. The particular situation shown in Scheme 1 b is described by the integration of a YES gate and an XOR gate, and is also known as controlled-NOT gate (CNOT) or Feynman gate. A straightforward molecular implementation of the CNOT gate could rely on two entities, which operate independently from each other as YES and XOR gates, triggered by common inputs. The readily available fluorophores ANAP and MAA (Scheme 2) are molecular switches, which can be addressed by protons and anions and deliver two spectrally well-separated Scheme 1. Representation of a) an XOR gate and its truth table and b) a controlled-NOT gate (CNOT or Feynman gate) as combination of an XOR and a YES gate and corresponding truth table.
Nuclease-containing media for resettable operation of DNA logic gates
Chemical communications (Cambridge, England), 2015
We designed and tested a system that allows DNA logic gates to respond multiple times to the addition of oligonucleotide inputs. After producing an output signal, the system spontaneously resets to the background state. This system does not require any operator action to achieve reset of a DNA logic gate, and may become useful for construction of reusable DNA-based computational devices.
Enzymatic AND Logic Gates Operated Under Conditions Characteristic of Biomedical Applications
2010
Experimental and theoretical analyses of the lactate dehydrogenase and glutathione reductase based enzymatic AND logic gates in which the enzymes and their substrates serve as logic inputs are performed. These two systems are examples of the novel, previously unexplored, class of biochemical logic gates that illustrate potential biomedical applications of biochemical logic. They are characterized by input concentrations at logic