Surface plasmon resonance imaging (SPRi) as an alternative technique for rapid and quantitative screening of small molecules, useful in drug discovery

Surface plasmon resonance imaging (SPRi) is a label free technology for biomolecular interaction, which gives access to binding kinetic parameters from real time acquisition. It offers the possibility to test in a single run a large number of interactions, allowing rapid identification of the most suitable compounds toward a given biological entity. Until now, this technique has proven to be relevant for interaction between relatively large molecules (protein, antibodies, DNA) but has not been challenged yet for the screening of small molecules that can be of interested in the field of drug discovery. As a proof a principle, we have used SPRi to screen for interaction of several small molecules, referred to as G4-ligands on G-quadruplex DNA. This technology allowed to easy discrimination of the binding properties of four G4-ligands on quadruplex DNA models.     

Selective voltammetric determination of electroactive neuromodulating species in biological samples using iron(II) phthalocyanine modified multi-wall carbon nanotubes paste electrode

Iron(II) phthalocyanine (FePc) modified multi-wall carbon nanotubes paste electrodes (MWCNTPEs) were used as voltammetric sensors to selectively detect dopamine (DA) in the presence of serotonin (5-HT). The electrochemical behavior of DA at the new modified electrode was investigated using CV. The enhanced current response of DA indicates that FePc modification of the MWCNTPE surface results in a high catalytic activity for the redox reaction of DA. Differential pulse voltammetry was applied in detection of DA and 5-HT at FePc-MWCNTPE. The method parameters were optimized. Detection limit of 2.05 × 10⁻⁷ M was obtained for DA by using the electrocatalytic oxidation signal corresponding to the Fe^II/Fe^III redox process. The separation between the peak potentials of DA and 5-HT is 170 mV which is large enough for the simultaneously, selective determination of the two chemical species in their mixtures. There was no electrochemical response for ascorbic acid (AA) added in the sample. The monoamine neurotransmitter measuring method has been tested in analyzing deproteinized serum samples.     

STRINGVACUA. A Mathematica package for studying vacuum configurations in string phenomenology

We give a simple tutorial introduction to the Mathematica package STRINGVACUA, which is designed to find vacua of string-derived or inspired four-dimensional N=1 supergravities. The package uses powerful algebro-geometric methods, as implemented in the free computer algebra system Singular, but requires no knowledge of the mathematics upon which it is based. A series of easy-to-use Mathematica modules are provided which can be used both in string theory and in more general applications requiring fast polynomial computations. The use of these modules is illustrated throughout with simple examples.

Program summary

Program title: STRINGVACUACatalogue identifier: AEBZ_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBZ_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: GNU GPLNo. of lines in distributed program, including test data, etc.: 31 050No. of bytes in distributed program, including test data, etc.: 163 832Distribution format: tar.gzProgramming language: “Mathematica” syntaxComputer: Home and office spec desktop and laptop machines, networked or stand aloneOperating system: Windows XP (with Cygwin), Linux, Mac OS, running Mathematica V5 or aboveRAM: Varies greatly depending on calculation to be performedClassification: 11.1External routines: Linux: The program “Singular” is called from Mathematica. Windows: “Singular” is called within the Cygwin environment from Mathematica.Nature of problem: A central problem of string-phenomenology is to find stable vacua in the four-dimensional effective theories which result from compactification.Solution method: We present an algorithmic method, which uses techniques of algebraic geometry, to find all of the vacua of any given string-phenomenological system in a huge class.Running time: Varies greatly depending on calculation requested.     

A mathematical model and a computer tool for the Tower of Hanoi and Tower of London puzzles

We propose a mathematical model for the Towers of Hanoi and London based on state graphs. The analysis of this model allows to address questions like equivalence of puzzles, difficulty of tasks and optimality of solutions using topological, metric and symmetry properties of the corresponding graphs.The mathematical model serves as a base for a computer program to administer tower puzzles in a variety of psychological test situations. It is suitable for bedside use and is equipped with numerous devices for post-processing of recorded data. Among these features is the graphical representation of the projection of the path taken by a test person onto the state graph.     

A geostatistical algorithm to reproduce lateral gradual facies transitions: Description and implementation

Valid representations of geological heterogeneity are fundamental inputs for quantitative models used in managing subsurface activities. Consequently, the simulation of realistic facies distributions is a significant aim. Realistic facies distributions are typically obtained by pixel-based, object-based or process-based methods. This work presents a pixel-based geostatistical algorithm suitable for reproducing lateral gradual facies transitions (LGFT) between two adjacent sedimentary bodies. Lateral contact (i.e. interfingering) between distinct depositional facies is a widespread geometric relationship that occurs at different scales in any depositional system. The algorithm is based on the truncation of the sum of a linear expectation trend and a random Gaussian field, and can be conditioned to well data. The implementation introduced herein also includes subroutines to clean and geometrically characterize the obtained LGFT. The cleaned sedimentary body transition provides a more appropriate and realistic facies distribution for some depositional settings. The geometric measures of the LGFT yield an intuitive measure of the morphology of the sedimentary body boundary, which can be compared to analogue data. An example of a LGFT obtained by the algorithm presented herein is also flow simulated, quantitatively demonstrating the importance of realistically reproducing them in subsurface models, if further flow-related accurate predictions are to be made.     

SDP-based approximation of stabilising solutions for periodic matrix Riccati differential equations

Numerically finding stabilising feedback control laws for linear systems of periodic differential equations is a nontrivial task with no known reliable solutions. The most successful method requires solving matrix differential Riccati equations with periodic coefficients. All previously proposed techniques for solving such equations involve numerical integration of unstable differential equations and consequently fail whenever the period is too large or the coefficients vary too much. Here, a new method for numerical computation of stabilising solutions for matrix differential Riccati equations with periodic coefficients is proposed. Our approach does not involve numerical solution of any differential equations. The approximation for a stabilising solution is found in the form of a trigonometric polynomial, matrix coefficients of which are found solving a specially constructed finite-dimensional semidefinite programming (SDP) problem. This problem is obtained using maximality property of the stabilising solution of the Riccati equation for the associated Riccati inequality and sampling technique. Our previously published numerical comparisons with other methods shows that for a class of problems only this technique provides a working solution. Asymptotic convergence of the computed approximations to the stabilising solution is proved below under the assumption that certain combinations of the key parameters are sufficiently large. Although the rate of convergence is not analysed, it appeared to be exponential in our numerical studies.     

Efficient classical simulation of the Deutsch–Jozsa and Simon’s algorithms

A long-standing aim of quantum information research is to understand what gives quantum computers their advantage. This requires separating problems that need genuinely quantum resources from those for which classical resources are enough. Two examples of quantum speed-up are the Deutsch–Jozsa and Simon’s problem, both efficiently solvable on a quantum Turing machine, and both believed to lack efficient classical solutions. Here we present a framework that can simulate both quantum algorithms efficiently, solving the Deutsch–Jozsa problem with probability 1 using only one oracle query, and Simon’s problem using linearly many oracle queries, just as expected of an ideal quantum computer. The presented simulation framework is in turn efficiently simulatable in a classical probabilistic Turing machine. This shows that the Deutsch–Jozsa and Simon’s problem do not require any genuinely quantum resources, and that the quantum algorithms show no speed-up when compared with their corresponding classical simulation. Finally, this gives insight into what properties are needed in the two algorithms and calls for further study of oracle separation between quantum and classical computation.     

State synchronization of linear and nonlinear agents in time‐varying networks

This paper studies state synchronization of homogeneous time‐varying networks with diffusive full‐state coupling or partial‐state coupling. In the case of full‐state coupling, linear agents as well as a class of nonlinear time‐varying agents are considered. In the case of partial‐state coupling, we only consider linear agents, but, in contrast with the literature, we do not require the agents in the network to be minimum phase or at most weakly unstable. In both cases, the network is time‐varying in the sense that the network graph switches within an infinite set of graphs with arbitrarily small dwell time. A purely decentralized linear static protocol is designed for agents in the network with full‐state coupling. For partial‐state coupling, a linear dynamic protocol is designed for agents in the network while using additional communication among controller variables using the same network. In both cases, the design is based on a high‐gain methodology. Copyright © 2017 John Wiley & Sons, Ltd.     

A numerical framework for load identification and regularization with application to rolling disc problem

Indirect identification methods are applied when direct measurement is unfeasible. One example is the measurement of the contact force between wheel and rail in railway traffic. This paper focuses on optimization-based methods for the identification of contact forces with the aim of developing a reliable and robust load identification scheme. A particular issue discussed here is the choice of discretization in space–time, enabling the sampling instances of the measurements, the parameterization of the sought input and the discretization of the pertinent state equations to be decoupled, in contrast to traditional methods such as, e.g. dynamic programming.In the present preliminary study where a 2-D disc is considered as a representative of a train wheel, a radial concentrated force rotates around the disc’s perimeter, representing the contact force acting on the rim of the wheel, while radial strains are measured on a set of points corresponding to the strain gauges position. The strain history data is then used in the identification procedure where the applied force is sought to minimize the discrepancy between the predicted and measured strain history. In particular the convergence of the results with respect to the temporal discretization of the model and the time parameterization of the sought loading history are investigated under the influence of noise. It is seen that choosing a discretization of the sought load that is coarser than that of the state variable gives a more robust scheme. The traditional Tikhonov regularization can also be added within the current framework. Furthermore, with the aid of a sensitivity analysis, the influence of measurement noise can be quantified.     

Homotopy-based surface reconstruction with application to?acoustic signals

This work introduces a new algorithm for surface reconstruction in ℝ³ from spatially arranged one-dimensional cross sections embedded in ℝ³. This is generally the case with acoustic signals that pierce an object non-destructively. Continuous deformations (homotopies) that smoothly reconstruct information between any pair of successive cross sections are derived. The zero level set of the resulting homotopy field generates the desired surface. Four types of homotopies are suggested that are well suited to generate a smooth surface. We also provide derivation of necessary higher order homotopies that can generate a C ² surface. An algorithm to generate surface from acoustic sonar signals is presented with results. Reconstruction accuracies of the homotopies are compared by means of simulations performed on basic geometric primitives.