Fundamental building blocks for molecular biowire based forward error-correcting biosensors

This paper describes the fabrication, characterization and modeling of fundamental logic gates that can be used for designing biosensors with embedded forward error-correction (FEC). The proposed logic gates (AND and OR) are constructed by patterning antibodies at different spatial locations along the substrate of a lateral flow immunosensor assay. The logic gates operate by converting binding events between an antigen and an antibody into a measurable electrical signal using polyaniline nanowires as the transducer. In this study, B.?cereus and E.?coli have been chosen as model pathogens. The functionality of the AND and OR logic gates has been validated using conductance measurements with different pathogen concentrations. Experimental results show that the change in conductance across the gates can be modeled as a log-linear response with respect to varying pathogen concentration. Equivalent circuits models for AND and OR logic gates have been derived based on measured results.     

Performing Logical Operations with Stimuli‐Responsive Building Blocks

Chemical logic gates can be fabricated by synthesizing molecules that have the ability to detect external stimuli (e.g., temperature or pH) and provide logical outputs. It is, however, challenging to fabricate a system that consists of many logic gates using this method: complex molecules can be difficult to synthesize and these logic gates typically cannot be integrated together. Here, we fabricated different types of logic gates by assembling a combination of different types of stimuli‐responsive hydrogels that change their size under the influence of one type of stimulus. Importantly, the preparation of these stimuli‐responsive hydrogels is widely reported and technically simple. Through designing the geometry of the systems, we fabricated the YES, NOT, OR, AND, NOR, and NAND gates. Although the hydrogels respond to different types of stimuli, their outputs are the same: a change in size of the hydrogel. Hence, we show that the logic gates can be integrated easily (e.g., by connecting an AND gate to an OR gate). In addition, we fabricated a standalone system with the size of a normal drug tablet (i.e., a “smart tablet”) that can analyze (or diagnose) different stimuli and control the release of a chemical (or drug) via the logic gates.     

Design of synthetic biological logic circuits based on evolutionary algorithm

The construction of an artificial biological logic circuit using systematic strategy is recognised as one of the most important topics for the development of synthetic biology. In this study, a real‐structured genetic algorithm (RSGA), which combines general advantages of the traditional real genetic algorithm with those of the structured genetic algorithm, is proposed to deal with the biological logic circuit design problem. A general model with the cis ‐regulatory input function and appropriate promoter activity functions is proposed to synthesise a wide variety of fundamental logic gates such as NOT, Buffer, AND, OR, NAND, NOR and XOR. The results obtained can be extended to synthesise advanced combinational and sequential logic circuits by topologically distinct connections. The resulting optimal design of these logic gates and circuits are established via the RSGA. The in silico computer‐based modelling technology has been verified showing its great advantages in the purpose.Inspec keywords: biocomputing, biological techniques, combinational circuits, genetic algorithms, logic design, logic gates, sequential circuitsOther keywords: in silico computer‐based modelling, RSGA, sequential logic circuits, XOR gates, NOR gates, NAND gates, OR gates, AND gates, Buffer gates, NOT gates, fundamental logic gates, cis‐regulatory input function, real‐structured genetic algorithm, artiflcial biological logic circuit design     

Flexible logic gates composed of high performance GaAs-nanowire-based MESFETs with MHz-dynamic operations

High performance NOT, NAND and NOR logic gates composed of GaAs-nanowire (NW)-based metal-semiconductor field-effect transistors (MESFETs) were constructed on flexible plastics through a noble top-down route. The representative GaAs-NW-based MESFETs exhibited superior electrical characteristics such as a high mobility (～3300 cm(2) V(-) s(-1)), large I(on)/I(off) ratio (～10(8)) and small subthreshold swing (～70 mV/dec). The NOT, NAND and NOR logic gates showed a maximum voltage gain of 108 and logic swings of 97-99%. All of the logic gates successfully retained their electrical characteristics during 2000 bending cycles. Furthermore, the logic gates were well operated by square-wave signals of up to 100 MHz under various strain conditions. The high performances demonstrated in this study open the way to the realization of high speed flexible logic devices.     

Sensitive photonic crystal phase logic gates

Total optical phase logic gates are reported in this paper. They are constructed by coupled-defect photonic crystal after two problems are overcome by a heterostructure or an asymmetric structure. Both half and all-phase logic gates are discussed. The sensitivity of these total optical phase logic gates not only are two orders sensitive than those using amplitude-signal, but also have many other advantages: such as very low energy cost. By using such phase logic gates, only a continued wave laser with one frequency is sufficient to operate the phase logic gate or the whole optical integrated circuit.     

Cold trapped ions as quantum information processors

In this tutorial we review the physical implementation of quantum computing using a system of cold trapped ions. We discuss systematically all the aspects for making the implementation possible. Firstly, we go through the loading and confining of atomic ions in the linear Paul trap, then we describe the collective vibrational motion of trapped ions. Further, we discuss interactions of the ions with a laser beam. We treat the interactions in the travelling-wave and standing-wave configuration for dipole and quadrupole transitions. We review different types of laser cooling techniques associated with trapped ions. We address Doppler cooling, sideband cooling in and beyond the Lamb-Dicke limit, sympathetic cooling and laser cooling using electromagnetically induced transparency. After that we discuss the problem of state detection using the electron shelving method. Then quantum gates are described. We introduce single-qubit rotations, two-qubit controlled-NOT and multi-qubit controlled-NOT gates. We also comment on more advanced multiple-qubit logic gates. We describe how quantum logic networks may be used for the synthesis of arbitrary pure quantum states. Finally, we discuss the speed of quantum gates and we also give some numerical estimations for them. A discussion of dynamics on off-resonance transitions associated with a qualitative estimation of the weak-coupling regime is included in Appendix A and of the Lamb-Dicke regime in Appendix B.     

Reversible-logic design with online testability

Conventional digital circuits dissipate a significant amount of energy because bits of information are erased during the logic operations. Thus, if logic gates are designed such that the information bits are not destroyed, the power consumption can be reduced dramatically. The information bits are not lost in case of a reversible computation. This has led to the development of reversible gates. This paper proposes three new reversible logic gates; two of the proposed gates can be employed to design online testable reversible logic circuits. Furthermore, they can be used to implement any Boolean logic function. The application of the reversible gates in implementing several benchmark functions has been presented.     

Spatial soliton angular deflection logic gates

A generalized interaction geometry between orthogonally polarized optical spatial solitons is presented in which a weak signal soliton induces a small angular deflection of a stronger power supply, or pump, soliton, resulting in a spatially resolved shift of the pump at the gate output. This geometry allows for the all-optical realization of true three-terminal, inverting and restoring logic devices with gain, which can serve as building blocks for more complex logic operations. In addition, the effects of linear and nonlinear material absorption, which degrades the performance of the angular deflection gates, are considered. Even in the presence of realistic absorption, the angular deflection logic gates can still produce large-signal gain (>2) sufficient for general logic. Finally, by use of a modified gate transfer function approach, these optical logic gates are shown to possess large noise margins for robust operation.     

Simple,fast, label-free,and nanoquencher-free system for operating multivalued DNA logic gates using polythymine templated CuNPs as signal reporters

Boolean logic devices play a key role in both traditional and nontraditional molecular logic circuits.This kind of binary logic,in which each bit is coded by (0,1),has only two output states—on or off (or high/low).Because of the finite computing capacity and variation,it is facing challenges from multivalued logic gates while processing high-density or uncertain/imprecise information.However,a low-cost,simple,and universal system that can perform different multivalued logic computations has not yet been developed,and remains a concept for further study.Herein,taking the ternary OR and INHIBIT logic gates as model devices,we present the fabrication of a novel simple,fast,label-free,and nanoquencher-free system for multivalued DNA logic gates using poly-thymine (T) templated copper nanoparticles (CuNPs) as signal reporters.The mixture of Cu2+ and ascorbic acid (AA) is taken as a universal platform for all ternary logic gates.Different kinds of poly-T strands and delicately designed complementary poly-adenine (A) strands are alternatively applied as ternary inputs to exhibit the ternary output states (low/0,medium/1,high/2).Notably,there are no nanoquenchers in this platform as poly-A strands can function as not only inputs but also efficient inhibitors of poly-T templated CuNPs.Moreover,all DNA are unlabeled single-strand DNA that do not need sophisticated labeling procedures or sequence design.The above design greatly reduces the operating time,costs,and complexity.More importantly,the ternary logic computations can be completed within 20 min because of the fast formation of CuNPs,and all of them share the same threshold values.     

Multi‐threshold and multi‐input DNA logic design style for profiling the microRNA biomarkers of real cancers

Early detection of cancer is very critical because it can reduce the treatment risk and cost. MicroRNAs (miRNAs) have been introduced in recent years as an efficient class of biomarkers for cancer early detection. Now, real‐time polymerase chain reaction has been used to profile the miRNA expression, which is costly, time consuming and low accuracy. Most recently, DNA logic gates are used to detect the miRNA expression level that is more accurate and faster than previous methods. The DNA‐based logic gates face with serious challenges such as the large complexity and low scalability. In this study, the authors proposed a methodology to design multi‐threshold and multi‐input DNA‐based logic gates in response to specific miRNA inputs in live mammalian cells. The proposed design style can simultaneously recognise multiple miRNAs with different rising and falling thresholds. The design style has been evaluated on the lung cancer biomarkers and the experimental results show the efficiency of the proposed method in terms of accuracy, efficiency and speed.Inspec keywords: DNA, logic design, biocomputing, RNA, molecular biophysics, logic gates, lung, genetics, cellular biophysics, cancer, biology computing, enzymes, biosensorsOther keywords: falling thresholds, specific miRNA inputs, multiinput DNA‐based logic gates, low scalability, DNA‐based logic gates face, miRNA expression level, DNA logic gates, low accuracy, time consuming, real‐time polymerase chain reaction, cancer early detection, treatment risk, cancers, microRNA biomarkers, multiinput DNA logic design style, multithreshold, lung cancer biomarkers     

All-optical logic gates based on photoinduced anisotropy of bacteriorhodopsin film

All-optical logic gates based on photoinduced anisotropy of bacteriorhodopsin (BR) film are proposed. The photoinduced anisotropy in BR film, which arises from the selective absorption of BR molecules to polarized light, can be controlled by changing the amplitudes and polarizations of exiting beams. As a consequence, the polarization of the probe light passing through the BR film can be controlled by the polarization of the exiting beam. Based on this property, a novel scheme of all-optical logic gates, such as AND, OR, XOR and NOT, has been implemented via the pump-probe technique. A theoretical model for the all-optical logic gates is proposed, and the theoretical predictions are demonstrated with the experimental results.     

Implementation of high speed optical universal logic gates using the electro-optic effect-based Mach–Zehnder interferometer structures

The universal logic gates are the most important logic gates responsible for optimized design of different types of complex digital logic circuits. It is of great interest to implement the function of universal logic gates such as NAND and NOR logic gates using the concepts of electro-optic effect. The smart use of electro-optic effect can provide very effective optical power switching devices. The implementation of universal logic gates operation in the optical domain can improve the performance of the devices and includes the advantages of the optical communication system. The proper configuration of Mach–Zehnder interferometer working on the principle of electro-optic effect can provide the optical responses equivalent to the NAND and NOR logic gates. The proposed devices can be analyzed to check the various performance affecting parameters in order to specify the physical parameters.     

Josephson address control unit IC for a 4-bit microcomputerprototype

The authors describe the design and operation of a Josephson address control unit IC (integrated circuit), which will be used for controlling the instruction sequence of an experimental 4-bit Josephson microcomputer prototype system. The IC is composed of three sets of 7- to 10-bit-wide registers and combinational logic circuits driven by a two-phase monopolar power supply. 593 four-function logic gates have been used in the circuit and fabricated using 2.5-μm NbN/oxide/NbN junction technology with Mo resistors and SiO₂ insulation. The operation of the circuit has been successfully tested for all the instructions which control the program sequence of the computer system     

Simple and universal platform for logic gate operations based on molecular beacon probes

A new platform technology is herein described with which to construct molecular logic gates by employing the hairpin-structured molecular beacon probe as a basic work unit. In this logic gate operation system, single-stranded DNA is used as the input to induce a conformational change in a molecular beacon probe through a sequence-specific interaction. The fluorescent signal resulting from the opening of the molecular beacon probe is then used as the output readout. Importantly, because the logic gates are based on DNA, thus permitting input/output homogeneity to be preserved, their wiring into multi-level circuits can be achieved by combining separately operated logic gates or by designing the DNA output of one gate as the input to the other. With this novel strategy, a complete set of two-input logic gates is successfully constructed at the molecular level, including OR, AND, XOR, INHIBIT, NOR, NAND, XNOR, and IMPLICATION. The logic gates developed herein can be reversibly operated to perform the set-reset function by applying an additional input or a removal strand. Together, these results introduce a new platform technology for logic gate operation that enables the higher-order circuits required for complex communication between various computational elements.     

Illuminating Diverse Concomitant DNA Logic Gates and Concatenated Circuits with Hairpin DNA-Templated Silver Nanoclusters as Universal Dual-Output Generators

Exquisite administration of a new type of hairpin DNA-templated silver nanoclusters (H-AgNCs) as universal dual-output generators in DNA-based logic systems is reported. Diverse concomitant contrary logic gates (CCLGs) with opposite functions (YES^{^}NOT, OR^{^}NOR, INHIBIT^{^}IMPLICATION, XOR^{^}XNOR, and MAJORITY^{^}MINORITY) and extended concatenated logic circuits are presented and some of them perform specific functions, such as parity generators and checkers. The introduction of H-AgNCs as noncovalent signal reporters avoids tedious and high-cost labeling procedures. Of note, the concomitant feature of CCLGs attributed to the dual-emitter AgNCs conduces to reducing the time and cost to devise multiple logic gates. As compared to previous ones, this design eliminates numerous substances (e.g., organic dyes) and unstable components (hydrogen peroxide), which not only decreases the complexity of logic performs and improves repeatability of operation, but also makes it convenient to connect distinct DNA-based logic gates. It is worthy to anticipate that the cost-effective strategy will inspire researchers to develop much more complex logic systems and contribute to the field of molecular computing.     

First principle approach towards logic design using hydrogen‐doped single‐strand DNA

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.Inspec keywords: molecular electronics, Green''s function methods, hydrogen, logic gates, density functional theory, adsorption, DNA, logic design, logic circuitsOther keywords: hydrogen molecule, contrary sparse cloud, current–voltage characteristics, Boolean logic gate operations, first principle approach, logic design, hydrogen‐doped single‐strand DNA, molecular logic gate, density functional theory, electronic transmission characteristics, H, analytical model, NXOR logic gates, Ex‐OR logic gates, OR logic gates, hydrogen‐doped‐ssDNA chain, nonequilibrium Green''s function, nucleobases, dense electron cloud, improved electronic transmission, enhanced logic properties, H‐ssDNA device, enhanced quantum‐ballistic transmission, gold electrode     

数字电路可测性设计的一种故障定位方法

在逻辑函数ReedMuller模式的电路可测性设计方面，文章采用AND门阵列和XOR门树结构来设计电路，提出了一种设计方案，可实现任意逻辑函数的功能，而且所得电路具有通用测试集和完全可故障定位的特点。给出了进行故障定位的方法，并可把它应用于其他相关电路的可测性设计。     

Smart Universal Multiple-Valued Logic Gates by Transferring Single Electrons

This paper proposes smart universal multiple-valued (MV) logic gates by transferring single electrons (${rm SE{bf s}}$). The logic gates are based on mosfet based SE turnstiles that can accurately transfer ${rm SE{bf s}}$ with high speed at high temperature. The number of electrons transferred per cycle by the SE turnstile is a quantized function of its gate voltage, and this characteristic is fully exploited to compactly finish MV logic operations. First, we build arbitrary MV literal gates by using pairs of SE turnstiles. Then, we propose universal MV logic-to-value conversion gates and MV analog–digital conversion circuits. We propose a SPICE model to describe the behavior of the mosfet based SE turnstile. We simulate the performances of the proposed gates. The MV logic gates have small number of transistors and low power dissipations.      

Construction of a Fuzzy and Boolean Logic Gates Based on DNA

Logic gates are devices that can perform logical operations by transforming a set of inputs into a predictable single detectable output. The hybridization properties, structure, and function of nucleic acids can be used to make DNA‐based logic gates. These devices are important modules in molecular computing and biosensing. The ideal logic gate system should provide a wide selection of logical operations, and be integrable in multiple copies into more complex structures. Here we show the successful construction of a small DNA‐based logic gate complex that produces fluorescent outputs corresponding to the operation of the six Boolean logic gates AND, NAND, OR, NOR, XOR, and XNOR. The logic gate complex is shown to work also when implemented in a three‐dimensional DNA origami box structure, where it controlled the position of the lid in a closed or open position. Implementation of multiple microRNA sensitive DNA locks on one DNA origami box structure enabled fuzzy logical operation that allows biosensing of complex molecular signals. Integrating logic gates with DNA origami systems opens a vast avenue to applications in the fields of nanomedicine for diagnostics and therapeutics.     

Nucleic Acids and Smart Materials: Advanced Building Blocks for Logic Systems

Logic gates can convert input signals into a defined output signal, which is the fundamental basis of computing. Inspired by molecular switching from one state to another under an external stimulus, molecular logic gates are explored extensively and recognized as an alternative to traditional silicon‐based computing. Among various building blocks of molecular logic gates, nucleic acid attracts special attention owing to its specific recognition abilities and structural features. Functional materials with unique physical and chemical properties offer significant advantages and are used in many fields. The integration of nucleic acids and functional materials is expected to bring about several new phenomena. In this Progress Report, recent progress in the construction of logic gates by combining the properties of a range of smart materials with nucleic acids is introduced. According to the structural characteristics and composition, functional materials are categorized into three classes: polymers, noble‐metal nanomaterials, and inorganic nanomaterials. Furthermore, the unsolved problems and future challenges in the construction of logic gates are discussed. It is hoped that broader interests in introducing new smart materials into the field are inspired and tangible applications for these constructs are found.