Parallel molecular computations of pairwise exclusive-or (XOR) using DNA "string tile" self-assembly

Self-assembling DNA nanostructures are an efficient means of executing parallel molecular computations. However, previous experimental demonstrations of computations by DNA tile self-assembly only allowed for one set of distinct input to be processed at a time. Here, we report the multibit, parallel computation of pairwise exclusive-or (XOR) using DNA "string tile" self-assembly. A set of DNA tiles encoding the truth table for the XOR logical operation was constructed. Parallel tile self-assembly and ligation led to the formation of reporter DNA strands which encoded both the input and the output of the computations. These reporter strands provided a molecular look-up table containing all possible pairwise XOR calculations up to a certain input size. The computation was readout by sequencing the cloned reporter strands. This is the first experimental demonstration of a parallel computation by DNA tile self-assembly in which a large number of distinct input were simultaneously processed.     

NMR implementation of adiabatic SAT algorithm using strongly modulated pulses

NMR implementation of adiabatic algorithms face severe problems in homonuclear spin systems since the qubit selective pulses are long and during this period, evolution under the Hamiltonian and decoherence cause errors. The decoherence destroys the answer as it causes the final state to evolve to mixed state and in homonuclear systems, evolution under the internal Hamiltonian causes phase errors preventing the initial state to converge to the solution state. The resolution of these issues is necessary before one can proceed to implement an adiabatic algorithm in a large system where homonuclear coupled spins will become a necessity. In the present work, we demonstrate that by using "strongly modulated pulses" (SMPs) for the creation of interpolating Hamiltonian, one can circumvent both the problems and successfully implement the adiabatic SAT algorithm in a homonuclear three qubit system. This work also demonstrates that the SMPs tremendously reduce the time taken for the implementation of the algorithm, can overcome problems associated with decoherence, and will be the modality in future implementation of quantum information processing by NMR.     

Semidirect parallel self-consistent field: the load balancing problem in the input/output intensive self-consistent field iterations

The full capacity of contemporary parallel computers can, in the context of iterative ab initio procedures like, for example, self-consistent field (SCF) and multiconfigurational SCF, only be utilized if the disk and input/output (I/O) capacity are fully exploited before the implementation turns to an integral direct strategy. In a recent report on parallel semidirect SCF http://www.tc.cornell.edu/er/media/1996/collabrate.html, http://www.fp.mcs.anl.gd/grand-challenges/chem/nondirect/index.html it was demonstrated that super-linear speedups are achievable for algorithms that exploit scalable parallel I/O. In the I/O-intensive SCF iterations of this implementation a static load balancing, however, was employed, dictated by the initial iteration in which integral evaluation dominates the central processing unit activity and thus determines the load balancing. In the present paper we present the first implementation in which load balancing is achieved throughout the whole SCF procedure, i.e. also in subsequent iterations. The improved scalability of our new algorithm is demonstrated in some test calculations, for example, for 63-node calculation a speedup of 104 was observed in the computation of the two-electron integral contribution to the Fock matrix.Contribution to the Björn Roos Honorary Issue Acknowledgement.We thank J. Nieplocha for valuable help and making the toolkit (including ChemIO) available to us. R.L. acknowledges the Intelligent Modeling Laboratory and the University of Tokyo for financial support during his stay in Japan.     

Vibrational computing: simulation of a full adder by optimal control

Within the context of vibrational molecular quantum computing, we investigate the implementation of a full addition of two binary digits and a carry that provides the sum and the carry out. Four qubits are necessary and they are encoded into four different normal vibrational modes of a molecule. We choose the bromoacetyl chloride molecule because it possesses four bright infrared active modes. The ground and first excited states of each mode form the one-qubit computational basis set. Two approaches are proposed for the realization of the full addition. In the first one, we optimize a pulse that implements directly the entire addition by a single unitary transformation. In the second one, we decompose the full addition in elementary quantum gates, following a scheme proposed by Vedral et al. [Phys. Rev. A 54, 147 (1996)]. Four elementary quantum gates are necessary, two two-qubit CNOT gates (controlled NOT) and two three-qubit TOFFOLI gates (controlled-controlled NOT). All the logic operations consist in one-qubit flip. The logic implementation is therefore quasiclassical and the readout is based on a population analysis of the vibrational modes that does not take the phases into account. The fields are optimized by the multitarget extension of the optimal control theory involving all the transformations among the 2(4) qubit states. A single cycle of addition without considering the preparation or the measure or copy of the result can be carried out in a very competitive time, on a picosecond time scale.     

Synthesis and spectral investigations of a new dyad with spiropyran and fluorescein units: toward information processing at the single molecular level

A new dyad 1 with two spiropyran units as the photochromic acceptors and one fluorescein unit as the fluorescent donor was synthesized and characterized. External inputs (ultraviolet light, visible light, and proton) induce the reversible changes of the structure and, concomitantly, the absorption spectrum of dyad 1 due to the presence of two spiropyran units. Only the absorption spectrum of the ME form of the spiropyran units in dyad 1 has large spectral overlap with the fluorescence spectrum of the fluorescein unit. Thus, the fluorescence intensity of dyad 1 is modulated by reversible conversion among the three states of the photochromic spiropyran units and the fluorescence resonance energy transfer (FRET) between the ME form and the fluorescein unit. Based on the fact that dyad 1 could "read out" three external input signals (ultraviolet light, visible ligh,t and proton) and "write" a compatible specific output signal (fluorescence intensity), dyad 1 described here can be considered to perform an integrated circuit function with one OR and one AND interconnected logic gates. The present results demonstrate an efficient strategy for elaborating and transmitting information at the single molecular level.     

High-resolution iterative frequency identification for NMR as a general strategy for multidimensional data collection

We describe a novel approach to the rapid collection and processing of multidimensional NMR data: "high-resolution iterative frequency identification for NMR" (HIFI-NMR). As with other reduced dimensionality approaches, HIFI-NMR collects n-dimensional data as a set of two-dimensional (2D) planes. The HIFI-NMR algorithm incorporates several innovative features. (1) Following the initial collection of two orthogonal 2D planes, tilted planes are selected adaptively, one-by-one. (2) Spectral space is analyzed in a rigorous statistical manner. (3) An online algorithm maintains a model that provides a probabilistic representation of the three-dimensional (3D) peak positions, derives the optimal angle for the next plane to be collected, and stops data collection when the addition of another plane would not improve the data model. (4) A robust statistical algorithm extracts information from the plane projections and is used to drive data collection. (5) Peak lists with associated probabilities are generated directly, without total reconstruction of the 3D spectrum; these are ready for use in subsequent assignment or structure determination steps. As a proof of principle, we have tested the approach with 3D triple-resonance experiments of the kind used to assign protein backbone and side-chain resonances. Peaks extracted automatically by HIFI-NMR, for both small and larger proteins, included approximately 98% of real peaks obtained from control experiments in which data were collected by conventional 3D methods. HIFI-NMR required about one-tenth the time for data collection and avoided subsequent data processing and peak-picking. The approach can be implemented on commercial NMR spectrometers and is extensible to higher-dimensional NMR.     

"Spectral implementation" for creating a labeled pseudo-pure state and the Bernstein-Vazirani algorithm in a four-qubit nuclear magnetic resonance quantum processor

A quantum circuit is introduced to describe the preparation of a labeled pseudo-pure state by multiplet-component excitation scheme which has been experimentally implemented on a 4-qubit nuclear magnetic resonance quantum processor. Meanwhile, we theoretically analyze and numerically investigate the low-power selective single-pulse implementation of a controlled-rotation gate, which manifests its validity in our experiment. Based on the labeled pseudo-pure state prepared, a 3-qubit Bernstein-Vazirani algorithm has been experimentally demonstrated by spectral implementation. The "answers" of the computations are identified from the split peak positions in the spectra of the observer spin, which are equivalent to projective measurements required by the algorithms.     

Encoding and Processing of Alphanumeric Information by Chemical Mixtures

A novel infochemical device that is based on ¹H NMR readout of chemical information is presented. This chemical encoding system utilizes two measurable parameters of homogeneous mixtures, chemical shift and peak integration, for three different applications: 1) a text‐encoding device that is based on spectral representation of a sequence of symbols, 2) encoding of 21‐digit binary numbers, each represented by an NMR spectrum, and their algebraic manipulations, such as addition and subtraction, and 3) encoding of 21‐digit decimal numbers. The first application enables molecular information storage and encryption. The relative concentration of each component, as measured by the relevant peak integration, can represent a symbol. The second application of this system, in addition to its obvious memory capability, enables mathematical operations. The NMR spectrum of a given mixture represents a 21‐digit binary number where each of the peaks encodes for a specific digit. In any of the input mixtures (numbers) each compound is either present or absent, representing either 1 or 0, respectively. We used the various binary numbers to carry out addition operations by combining two or more solutions (numbers). Subtraction operations were also preformed by digital processing of the information. The third application is the representation of decimal numbers. As before, each of the peaks encodes for a specific digit. In any of the input mixtures each compound is present in one of 10 different relative concentrations, representing the 10 digits of a decimal number.     

Heuristic extraction of rules in pruned artificial neural networks models used for quantifying highly overlapping chromatographic peaks

The suitability of an approach for extracting heuristic rules from trained artificial neural networks (ANNs) pruned by a regularization method and with architectures designed by evolutionary computation for quantifying highly overlapping chromatographic peaks is demonstrated. The ANN input data are estimated by the Levenberg-Marquardt method in the form of a four-parameter Weibull curve associated with the profile of the chromatographic band. To test this approach, two N-methylcarbamate pesticides, carbofuran and propoxur, were quantified using a classic peroxyoxalate chemiluminescence reaction as a detection system for chromatographic analysis. Straightforward network topologies (one and two outputs models) allow the analytes to be quantified in concentration ratios ranging from 1:7 to 5:1 with an average standard error of prediction for the generalization test of 2.7 and 2.3% for carbofuran and propoxur, respectively. The reduced dimensions of the selected ANN architectures, especially those obtained after using heuristic rules, allowed simple quantification equations to be developed that transform the input variables into output variables. These equations can be easily interpreted from a chemical point of view to attain quantitative analytical information regarding the effect of both analytes on the characteristics of chromatographic bands, namely profile, dispersion, peak height, and residence time.     

An integrated microfluidic processor for single nucleotide polymorphism-based DNA computing

An integrated microfluidic processor is developed that performs molecular computations using single nucleotide polymorphisms (SNPs) as binary bits. A complete population of fluorescein-labeled DNA "answers" is synthesized containing three distinct polymorphic bases; the identity of each base (A or T) is used to encode the value of a binary bit (TRUE or FALSE). Computation and readout occur by hybridization to complementary capture DNA oligonucleotides bound to magnetic beads in the microfluidic device. Beads are loaded into sixteen capture chambers in the processor and suspended in place by an external magnetic field. Integrated microfluidic valves and pumps circulate the input DNA population through the bead suspensions. In this example, a program consisting of a series of capture/rinse/release steps is executed and the DNA molecules remaining at the end of the computation provide the solution to a three-variable, four-clause Boolean satisfiability problem. The improved capture kinetics, transfer efficiency, and single-base specificity enabled by microfluidics make our processor well-suited for performing larger-scale DNA computations.     

A Self-consistent Reaction Field Model of Solvation Using Distributed Multipoles. II: Second Energy Derivatives and Application to Vibrational Spectra

The use of distributed multipoles in the formalism of the reaction field factors allowed us to develop a computational scheme adapted to quantum chemical computations on a molecule solvated by a dielectric continuum. The algorithm used to compute the second energy derivatives is developed and, after its implementation in a quantum chemical computational code, permits the computation of the vibrational frequencies of the solute. This approach has been tested successfully on two test molecules and applied to the study of the solvent effect on the structure and the vibrational spectrum of a series of parasubstituted benzonitriles.     

Multiple expression of molecular information: enforced generation of different supramolecular inorganic architectures by processing of the same ligand information through specific coordination algorithms

The multisubunit ligand 2 combines two complexation substructures known to undergo, with specific metal ions, distinct self-assembly processes to form a double-helical and a grid-type structure, respectively. The binding information contained in this molecular strand may be expected to generate, in a strictly predetermined and univocal fashion, two different, well-defined output inorganic architectures depending on the set of metal ions, that is, on the coordination algorithm used. Indeed, as predicted, the self-assembly of 2 with eight CuII and four CuI yields the intertwined structure D1. It results from a crossover of the two assembly subprograms and has been fully characterized by crystal structure determination. On the other hand, when the instructions of strand 2 are read out with a set of eight CuI and four MII (M = Fe, Co, Ni, Cu) ions, the architectures C1-C4, resulting from a linear combination of the two subprograms, are obtained, as indicated by the available physico-chemical and spectral data. Redox interconversion of D1 and C4 has been achieved. These results indicate that the same molecular information may yield different output structures depending on how it is processed, that is, depending on the interactional (coordination) algorithm used to read it. They have wide implications for the design and implementation of programmed chemical systems, pointing towards multiprocessing capacity, in a one code/ several outputs scheme, of potential significance for molecular computation processes and possibly even with respect to information processing in biology.     

基于稀疏模型的气相色谱-质谱数据解析及其在严重重叠峰解析中的应用

提出一种气相色谱-质谱（GC-MS）数据解析算法。以色谱峰顶点处的质谱作为待测谱,在谱库中检索一定量相关参考谱,求解关于各纯组分色谱响应值的方程。质谱检索采取分步策略,先利用质谱碎片规律建立高速索引进行粗选,然后使用强峰高概率出峰准则和耐挤压性准则排除无关质谱。为求解色谱响应值方程,提出基于稀疏模型的回归算法,相比传统算法,稀疏算法利于提取待测谱的主要结构,避免"过拟合"。实验结果表明,该质谱检索算法具有较高的精度和规模较小的剩余参考谱集,而所提稀疏模型算法可有效解析严重重叠峰。该算法可作为GC-MS重叠峰解析,特别是严重重叠峰解析的一种有效解决方案。     

Chemical sensor based on nonlinearity: principle and application.

Novel chemical sensors based on a time-dependent nonlinear response are reviewed. The strategy is to artificially mimic information transduction in living organisms. In taste and olfaction, information of chemical structure and concentration is transformed into nervous impulses in the nervous cell, i.e., time-dependent multi-dimensional information. Because the excitation and pulse generation in the nervous cell are typically nonlinear phenomena, it may be worthwhile to utilize the nonlinearity as the multi-dimensional information for molecular recognition. The principle of a "nonlinear" sensor is that a sinusoidal modulation is applied to a system, and the output signal is analyzed. The output signal of the sensor is characteristically deformed from the sinusoidal input depending on the chemical structure and concentration of the chemical stimuli. The characteristic nonlinear responses to chemical stimuli are discussed in relation to the kinetics of chemical compounds on the sensor surface. As a practical application, we introduced electrochemical sensors based on the differential capacitance, semiconductor gas sensors under the application of sinusoidal temperature or diffusion change, and a chemical sensor based on the spatio-temporal information. We demonstrated that mutli-dimensional information based on nonlinearity can provide quite useful information for the analysis of chemical species, even in the presence of another analyte or an interference with a single detector.     

Molecular conformation search by distance matrix perturbations

Three-dimensional molecular structure is fundamental in chemical function identification and computer-aided drug design. The enumeration of a small number of feasible conformations provides a rigorous way to determine the optimal or a few acceptable conformations. Our contribution concerns a heuristic enhancement of a method based on distance geometry, typically in relation with experiments of the NMR type. Distance geometry has been approached by different viewpoints; ours is expected to help in several subtasks arising in the process that determines 3D structure from distance information. More precisely, the input to our algorithm consists of a set of approximate distances of varying precision; some are specified by the covalent structure and others by Nuclear Magnetic Resonance (NMR) experiments (or X-ray crystallography which, however, requires crystallization). The output is a valid tertiary structure in a specified neighborhood of the input. Our approach should help in detecting outliers of the NMR experiments, and handles inputs with partial information. Moreover, our technique is able to bound the number of degrees of freedom of the conformation manifold. We have used numerical linear algebra algorithms for reasons of speed, and because they are well-implemented, fully documented and widely available. Our main tools include, besides distance matrices, structure-preserving matrix perturbations for minimizing singular values. Our MATLAB (or SCILAB) implementation is described and illustrated.AMS subject Classification: 92E10 Molecular structure, 92C40 Biochemistry, molecular biology, 65F15 Eigenvalues, eigenvectors, 15A18 Eigenvalues, singular values, and eigenvectors     

Connecting Ruthenium Photocatalysis to 1,2-Dioxetane-Mediated Chemiluminescence: a Versatile Combination for Optical Detection and Read-Out

Optical storage and photon quantification systems based on sensitive photoreactions have numerous applications. Herein, we report a highly efficient photocatalytic reaction, in which ruthenium photoredox catalysis is combined with a 1,2-dioxetane from which chemiluminescence can be triggered. In this system, blue light irradiation as optical input enables a defined inverse correlation with base-triggered, blue light emission as optical output. Comparison of readout by ¹H NMR and chemiluminescence, relative to previous optical input, underlines the reliability and usefulness of the ruthenium-dioxetane system for optical storage, sensing and ruthenium detection.     

Tuning the CD spectrum and optical rotation value of a new binaphthalene molecule with two spiropyran units: mimicking the function of a molecular "AND" logic gate and a new chiral molecular switch

With the view to developing new chiral molecular switches and logic gates, a new binaphthalene molecule with two spiropyran units (1) was synthesized and characterized. Absorption and 1H NMR spectral studies of 1 after reaction with acid/base indicate acidichromism can occur to compound 1. The synergistic actions of acid and UV light irradiation result in a remarkable change for the CD spectrum of the relatively dilute solution of 1, mimicking the behavior of a chiral "AND" gate, since the "ouput" is the CD signal. Furthermore, the optical rotation value of the relatively concentrated solution of 1 can be reversibly tuned after sequential reactions with acid and base, and thus a chiral molecular switch with nondestructive "output" signal is realized. The present results not only add a new example of chiral molecular switch with nondestructive readout but also provide a chiral "AND" gate based on the axial chiral binaphthalene to which switchable units are linked.     

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.     

Molecular photonic logic gates

The possibility of performing logical operations at the molecular level is being actively investigated at present with the aim of developing molecular logic gates, which can be used in information technologies. In this minireview, the design algorithm of molecular logic gates is considered and the requirements on molecular systems for use as logic gates are specified. Examples of molecular logic gates performing different logical operations are given. Attention is focused on all-photonic molecular logic gates, in which light is used as an input signal for transferring the system from one state to another and for reading the output signal by absorption or luminescence. In addition, optoelectronic devices with light as the input signal and electric current as the output signal are briefly discussed.     

Towards biochemical filters with a sigmoidal response to pH changes: buffered biocatalytic signal transduction

We realize a biochemical filtering process by introducing a buffer in a biocatalytic signal-transduction logic system based on the function of an enzyme, esterase. The input, ethyl butyrate, is converted into butyric acid--the output signal, which in turn is measured by the drop in the pH value. The developed approach offers a versatile "network element" for increasing the complexity of biochemical information processing systems. Evaluation of an optimal regime for quality filtering is accomplished in the framework of a kinetic rate-equation model.