Molecular beacon-based half-adder and half-subtractor

This work demonstrates two DNA-based logic circuits that behave as a half-adder and a half-subtractor. A half-adder is composed of an AND gate and an XOR gate, whereas a half-subtractor consists of an INH gate and an XOR gate. The proposed designs are inspired by molecular beacons.     

All-photonic molecular half-adder

One molecule acts as both an AND and an XOR Boolean logic gate that share the same two photonic inputs. The molecule comprises a half-adder, adding two binary digits with only light as inputs and outputs, and consists of three covalently linked photochromic moieties, a spiropyran and two quinoline-derived dihydroindolizines. The AND function is based on the absorption properties of the molecule, whereas the XOR function is based on an off-on-off response of the fluorescence to the inputs that results from interchromophore excited-state quenching interactions. The half-adder is simple to operate and can be cycled many times.     

Reconfigurable three-dimensional DNA nanostructures for the construction of intracellular logic sensors

Right out of the (logic) gate: Logic gates made from 3D DNA nanotetrahedra were constructed that are responsive to various ions, small molecules, and short strands of DNA. By including dynamic sequences in one or more edges of the tetrahedra, a FRET signal can be generated in the manner of AND, OR, XOR, and INH logic gates, as well as a half-adder circuit. These DNA logic gates were also applied to intracellular detection of ATP.     

Logic gates and elementary computing by enzymes

Different selected enzymes, glucose oxidase (GOx), catalase (Cat), glucose dehydrogenase (GDH), horseradish peroxidase (HRP), and formaldehyde dehydrogenase (FDH), are used alone or coupled to construct eight different logic gates. The added substrates for the respective enzymes, glucose and H(2)O(2), act as the gate inputs, while the biocatalytically generated gluconic acid or NADH are the output signals that follow the operation of the gates. Different enzyme-based gates are XOR, INHIBIT A, INHIBIT B, AND, OR, NOR, Identity and Inverter gates. By combining the AND and XOR or the XOR and INHIBIT A gates, the half-adder and half-subtractor are constructed, respectively, opening the way to elementary computing by the use of enzymes.     

A multifunctional arithmetical processor model integrated inside a single molecule

Improving the processing power of molecules remains the challenge for molecular logic and computation. Here we report a 2-phenylimidazo[4,5-f][1,10]phenanthroline (PIPH)-based three-state molecular switch by controlling its unique emission and absorption spectra in the acid and base condition. On one hand, PIPH can perform simultaneously the functions of an "AND" gate and an "XOR" gate, capable of operating as a half-adder, and the "off-on-off" function as well as comparison function by monitoring its fluorescent spectral changes. On the other hand, the molecule can also implement in parallel the functions of an "XOR" gate and two "INH" gates by monitoring its absorption spectral changes, which constructs two half-subtractors. The cooperative operation of comparator and half-subtractor makes general subtraction operation become possible, which is discussed conceptually in the report.     

All-photonic multifunctional molecular logic device

Photochromes are photoswitchable, bistable chromophores which, like transistors, can implement binary logic operations. When several photochromes are combined in one molecule, interactions between them such as energy and electron transfer allow design of simple Boolean logic gates and more complex logic devices with all-photonic inputs and outputs. Selective isomerization of individual photochromes can be achieved using light of different wavelengths, and logic outputs can employ absorption and emission properties at different wavelengths, thus allowing a single molecular species to perform several different functions, even simultaneously. Here, we report a molecule consisting of three linked photochromes that can be configured as AND, XOR, INH, half-adder, half-subtractor, multiplexer, demultiplexer, encoder, decoder, keypad lock, and logically reversible transfer gate logic devices, all with a common initial state. The system demonstrates the advantages of light-responsive molecules as multifunctional, reconfigurable nanoscale logic devices that represent an approach to true molecular information processing units.     

A differential ICT based molecular probe for multi-ions and multifunction logic circuits

This paper presents anthraquinone and benzimidazole based hybrid molecular architect as the state of the art for multifunctional molecular logic circuits. The moleculator exhibits differential output behavior towards F(-), Zn(2+) and Cu(2+) ions to provide opportunities for elaboration of XOR, INHIBIT, XNOR, AND, OR, NOR, logic functions and their integrated logic functions half-adder, half-subtractor and comparator within a single molecule. These integral logic functions can be reprogrammed by self-annihilation or by another additional input in the same cell. This single molecule behaves uniquely where different logic functions can be operated and reset by using different inputs and outputs.     

两种DNA分子同时检测的逻辑门及半加器的构建

本研究利用滴涂法和电沉积法构建了氧化石墨烯/金纳米粒子复合膜修饰电极(GCE/GO/AuNPs),基于目标DNA和探针结合前后探针在电极表面构型的变化导致电化学信号变化,实现对大肠杆菌(E.coli)DNA和沙门氏菌(Sal)DNA的智能识别。以目标物为输入信号,分别以Σ|ΔI|和|ΔIMB/ΔIFc|为输出,构建了"AND"型和"XOR"型DNA分子逻辑门,提出了一种新型的可用于逻辑运算的半加器模型。采用方波伏安法(SWV)检测两种标记探针电流变化值Σ|ΔI|,其与E.coli DNA和Sal DNA浓度的对数值在1.0×10~(-13)~1.0×10~(-8) mol·L~(-1)范围内呈现良好的线性关系,检出限(S/N=3)分别为3.2×10~(-14) mol·L~(-1)和1.7×10~(-14) mol·L~(-1)。     

Large and ultrafast third-order optical nonlinearity of novel copolymers containing fluorene and tetraphenyldiaminobiphenyl units in backbones

A femtosecond time-resolved optical Kerr gate method, using 115 fs laser pulses at 830 nm, has been applied to investigate the third-order nonlinearity of two novel copolymers containing fluorene and tetraphenyldiaminobiphenyl units in their backbones. Ultrafast off-resonant optical Kerr responses have been observed and the magnitude of the second-order hyperpolarizability was measured as large as 10⁻³⁰ esu. The origin of the extraordinary large value was explored and compared to other organic materials.     

Connectable DNA Logic Gates: OR and XOR Logics

Modern computer processors are based on semiconductor logic gates connected to each other in complex circuits. This study contributes to the development of a new class of connectable logic gates made of DNA in which the transfer of oligonucleotide fragments as input/output signals occurs upon hybridization of DNA sequences. The DNA strands responsible for a logic function form associates containing immobile DNA four‐way junction structures when the signal is high and dissociate into separate strands when the signal is low. A basic set of logic gates (NOT, AND, and OR) was designed. Two NOT gates, two AND gates, and an OR gate were connected in a network that corresponds to an XOR logic function. The design of the logic gates presented here may contribute to the development of the first biocompatible molecular computer.     

Defining and measuring optical frequencies: the optical clock opportunity--and more (Nobel lecture).

Four long-running currents in laser technology met and merged in 1999-2000. Two of these were the quest toward a stable repetitive sequence of ever-shorter optical pulses and, on the other hand, the quest for the most time-stable, unvarying optical frequency possible. The marriage of ultrafast- and ultrastable lasers was brokered mainly by two international teams and became exciting when a special "designer" microstructure optical fiber was shown to be nonlinear enough to produce "white light" from the femtosecond laser pulses, such that the output spectrum embraced a full optical octave. Then, for the first time, one could realize an optical frequency interval equal to the comb's lowest frequency, and count out this interval as a multiple of the repetition rate of the femtosecond pulse laser. This "gear-box" connection between the radiofrequency standard and any/all optical frequency standards came just as sensitivity-enhancing ideas were maturing. The four-way union empowered an explosion of accurate frequency measurement results in the standards field and prepared the way for refined tests of some of our cherished physical principles, such as the time-stability of some of the basic numbers in physics (e.g. the "fine-structure" constant, the speed of light, certain atomic mass ratios), and the equivalence of time-keeping by clocks based on different physics. The stable laser technology also allows time-synchronization between two independent femtosecond lasers so exact they can be made to appear as if the source were a single laser. By improving pump-probe experiments, one important application will be in bond-specific spatial scanning of biological samples. This next decade in optical physics should be a blast!     

Deoxyribozyme-based logic gates

We report herein a set of deoxyribozyme-based logic gates capable of generating any Boolean function. We construct basic NOT and AND gates, followed by the more complex XOR gate. These gates were constructed through a modular design that combines molecular beacon stem-loops with hammerhead-type deoxyribozymes. Importantly, as the gates have oligonucleotides as both inputs and output, they open the possibility of communication between various computation elements in solution. The operation of these gates is conveniently connected to a fluorescent readout.     

Transient phenomena in time- and frequency-gated spontaneous emission

The effect of overlapping pump and gate pulses on time- and frequency-gated spontaneous emission spectra is explored for a model of material dynamics that accounts for strong nonadiabatic and electron-vibrational coupling effects, vibrational relaxation, and optical dephasing, thus representing characteristic features of photoinduced excited-state dynamics in large molecules in the gas phase or in condensed phases. The behaviors of the sequential, coherent, and doorway-window contributions to the spontaneous emission spectrum are studied separately. The interrelation between the sequential and coherent contributions is demonstrated to be sensitive to the carrier frequencies of the pump and gate pulses and also to the optical dephasing rate, opening the possibility of an experimental determination of the latter. The coherent contribution is shown to dominate the spectrum at specific emission frequencies.     

Laser-Induced Breakdown Spectroscopy in open-path configuration for the analysis of distant objects

A review of recent results on stand-off Laser-Induced Breakdown Spectroscopy (LIBS) analysis and applications is presented. Stand-off LIBS was suggested for elemental analysis of materials located in environments where any physical access was not possible but optical access could be envisaged. This review only refers to the use of the open-path LIBS configuration in which the laser beam and the returning plasma light are transmitted through the atmosphere. It does not present the results obtained with a transportation of the laser pulses to the target through an optical fiber. Open-path stand-off LIBS has mainly been used with nanosecond laser pulses for solid sample analysis at distances of tens of meters. Liquid samples have also been analyzed at distances of a few meters. The distances achievable depend on many parameters including the laser characteristics (pulse energy and power, beam divergence, spatial profile) and the optical system used to focus the pulses at a distance. A large variety of laser focusing systems have been employed for stand-off analysis comprising refracting or reflecting telescope. Efficient collection of the plasma light is also needed to obtain analytically useful signals. For stand-off LIBS analysis, a lens or a mirror is required to increase the solid angle over which the plasma light can be collected. The light collection device can be either at an angle from the laser beam path or collinear with the optical axis of the system used to focus the laser pulses on the target surface. These different configurations have been used depending on the application such as rapid sorting of metal samples, identification of material in nuclear industry, process control and monitoring in metallurgical industry, applications in future planetary missions, detection of environmental contamination or cleaning of objects of cultural heritage. Recent stand-off analyses of metal samples have been reported using femtosecond laser pulses to extend LIBS capabilities to very long distances. The high-power densities achievable with these laser pulses can also induce self-guided filaments in the atmosphere which produce LIBS excitation of a sample. The first results obtained with remote filament-induced breakdown spectroscopy predict sample analysis at kilometer ranges.     

Modular multi-level circuits from immobilized DNA-based logic gates

One of the fundamental goals of molecular computing is to reproduce the tenets of digital logic, such as component modularity and hierarchical circuit design. An important step toward this goal is the creation of molecular logic gates that can be rationally wired into multi-level circuits. Here we report the design and functional characterization of a complete set of modular DNA-based Boolean logic gates (AND, OR, and AND-NOT) and further demonstrate their wiring into a three-level circuit that exhibits Boolean XOR (exclusive OR) function. The approach is based on solid-supported DNA logic gates that are designed to operate with single-stranded DNA inputs and outputs. Since the solution-phase serves as the communication medium between gates, circuit wiring can be achieved by designating the DNA output of one gate as the input to another. Solid-supported logic gates provide enhanced gate modularity versus solution-phase systems by significantly simplifying the task of choosing appropriate DNA input and output sequences used in the construction of multi-level circuits. The molecular logic gates and circuits reported here were characterized by coupling DNA outputs to a single-input REPORT gate and monitoring the resulting fluorescent output signals.     

Implementation of quantum gate operations in molecules with weak laser fields

We numerically propose a way to perform quantum computations by combining an ensemble of molecular states and weak laser pulses. A logical input state is expressed as a superposition state (a wave packet) of molecular states, which is initially prepared by a designed femtosecond laser pulse. The free propagation of the wave packet for a specified time interval leads to the specified change in the relative phases among the molecular basis states, which corresponds to a computational result. The computational results are retrieved by means of quantum interferometry. Numerical tests are implemented in the vibrational states of the B state of I2 employing controlled-NOT gate, and 2 and 3 qubits Fourier transforms. All the steps involved in the computational scheme, i.e., the initial preparation, gate operation, and detection steps, are achieved with extremely high precision.     

Deoxyribozyme-based half-adder

We have constructed a solution-phase array of three deoxyribozyme-based logic gates that behaves as a half-adder. Two deoxyribozymes mimic i(1)ANDNOTi(2) and i(2)ANDNOTi(1) gates that cleave a fluorogenic substrate, reporting through an increase in fluorescence emission at 570 nm. The third deoxyribozyme mimics an i(1)ANDi(2) gate and cleaves the other fluorogenic substrate, reporting through an increase in fluorescence emission at 520 nm. Together, this system represents the first example of a decision-making enzymatic network with two inputs and two outputs. Similar systems could be applied to control autonomous therapeutic and diagnostic devices.     

A Reversible DNA Logic Gate Platform Operated by One‐ and Two‐Photon Excitations

We demonstrate the use of two different wavelength ranges of excitation light as inputs to remotely trigger the responses of the self‐assembled DNA devices (D‐OR). As an important feature of this device, the dependence of the readout fluorescent signals on the two external inputs, UV excitation for 1 min and/or near infrared irradiation (NIR) at 800 nm fs laser pulses, can mimic function of signal communication in OR logic gates. Their operations could be reset easily to its initial state. Furthermore, these DNA devices exhibit efficient cellular uptake, low cytotoxicity, and high bio‐stability in different cell lines. They are considered as the first example of a photo‐responsive DNA logic gate system, as well as a biocompatible, multi‐wavelength excited system in response to UV and NIR. This is an important step to explore the concept of photo‐responsive DNA‐based systems as versatile tools in DNA computing, display devices, optical communication, and biology.     

Picosecond Time Resolved Hard X-Ray Diffraction from Laser Heated Metallic Crystals

We report the development of a novel hard X-ray diffraction system with picosecond time resolution. Picosecond X-ray pulses are produced by excitation of an X-ray diode with picosecond ultraviolet light pulses at a repetition rate of 300 Hz. The X-ray pulses are synchronized to the optical pulses with picosecond accuracy. The system has been utilized in picosecond time resolved X-ray diffraction of laser pulse heated gold and platinum single crystals.     

Simultaneous optimization by neuro-genetic approach for analysis of plant materials by laser induced breakdown spectroscopy

A simultaneous optimization strategy based on a neuro-genetic approach is proposed for selection of laser induced breakdown spectroscopy operational conditions for the simultaneous determination of macro-nutrients (Ca, Mg and P), micro-nutrients (B, Cu, Fe, Mn and Zn), Al and Si in plant samples. A laser induced breakdown spectroscopy system equipped with a 10 Hz Q-switched Nd:YAG laser (12 ns, 532 nm, 140 mJ) and an Echelle spectrometer with intensified coupled-charge device was used. Integration time gate, delay time, amplification gain and number of pulses were optimized. Pellets of spinach leaves (NIST 1570a) were employed as laboratory samples. In order to find a model that could correlate laser induced breakdown spectroscopy operational conditions with compromised high peak areas of all elements simultaneously, a Bayesian Regularized Artificial Neural Network approach was employed. Subsequently, a genetic algorithm was applied to find optimal conditions for the neural network model, in an approach called neuro-genetic. A single laser induced breakdown spectroscopy working condition that maximizes peak areas of all elements simultaneously, was obtained with the following optimized parameters: 9.0 µs integration time gate, 1.1 µs delay time, 225 (a.u.) amplification gain and 30 accumulated laser pulses. The proposed approach is a useful and a suitable tool for the optimization process of such a complex analytical problem.