Use of protein A gene fusions for the analysis of structure-function relationship of the transactivator protein C of bacteriophage Mu

A sensitive dimerization assay for DNA binding proteins has been developed using gene fusion technology. For this purpose, we have engineered a gene fusion using protein A gene of Staphylococcus aureus and C gene, the late gene transactivator of bacteriophage Mu. The C gene was fused to the 3' end of the gene for protein A to generate an A- C fusion. The overexpressed fusion protein was purified in a single step using immunoglobulin affinity chromatography. Purified fusion protein exhibits DNA binding activity as demonstrated by electrophoretic mobility shift assays. When the fusion protein A-C was mixed with C and analyzed for DNA binding, in addition to C and A-C specific complexes, a single intermediate complex comprising of a heterodimer of C and A-C fusion proteins was observed. Further, the protein A moiety in the fusion protein A-C does not contribute to DNA binding as demonstrated by proteolytic cleavage and circular dichroism (CD) analysis. The assay has also been applied to analyze the DNA binding domain of C protein by generating fusions between protein A and N- and C-terminal deletion mutants of C. The results indicate a role for the region towards the carboxy terminal of the protein in DNA binding. The general applicability of this method is discussed.

On generating optimal signal probabilities for random tests: A genetic approach

Genetic Algorithms are robust search and optimization techniques. A Genetic Algorithm based approach for determining the optimal input distributions for generating random test vectors is proposed in the paper. A cost function based on the COP testability measure for determining the efficacy of the input distributions is discussed, A brief overview of Genetic Algorithms (GAs) and the specific details of our implementation are described. Experimental results based on ISCAS-85 benchmark circuits are presented. The performance pf our GA-based approach is compared with previous results. While the GA generates more efficient input distributions than the previous methods which are based on gradient descent search, the overheads of the GA in computing the input distributions are larger. To account for the relatively quick convergence of the gradient descent methods, we analyze the landscape of the COP-based cost function. We prove that the cost function is unimodal in the search space. This feature makes the cost function amenable to optimization by gradient-descent techniques as compared to random search methods such as Genetic Algorithms.

Point Spread Function Engineering for Super-Resolution Single-Photon and Multiphoton Fluorescence Microscopy

Super-resolution imaging techniques are of paramount interest for applications in bioimaging and fluorescence microscopy. Recent advances in bioimaging demand application-tailored point spread functions. Here, we present some approaches for generating application-tailored point spread functions along with fast imaging capabilities. Aperture engineering techniques provide interesting solutions for obtaining desired system point spread functions. Specially designed spatial filters—realized by optical mask—are outlined both in a single-lens and 4Pi configuration. Applications include depth imaging, multifocal imaging, and super-resolution imaging. Such an approach is suitable for fruitful integration with most existing state-of-art imaging microscopy modalities.

Clusters of bound particles in the derivative delta-function Bose gas

In this paper we discuss a novel procedure for constructing clusters of bound particles in the case of a quantum integrable derivative delta-function Bose gas in one dimension. It is shown that clusters of bound particles can be constructed for this Bose gas for some special values of the coupling constant, by taking the quasi-momenta associated with the corresponding Bethe state to be equidistant points on a single circle in the complex momentum plane. We also establish a connection between these special values of the coupling constant and some fractions belonging to the Farey sequences in number theory. This connection leads to a classification of the clusters of bound particles associated with the derivative delta-function Bose gas and allows us to study various properties of these clusters like their size and their stability under the variation of the coupling constant. (C) 2013 Elsevier B.V. All rights reserved.

Bearing capacity of circular footings over rock mass by using axisymmetric quasi lower bound finite element limit analysis

The ultimate bearing capacity of a circular footing, placed over rock mass, is evaluated by using the lower bound theorem of the limit analysis in conjunction with finite elements and nonlinear optimization. The generalized Hoek-Brown (HB) failure criterion, but by keeping a constant value of the exponent, alpha = 0.5, was used. The failure criterion was smoothened both in the meridian and pi planes. The nonlinear optimization was carried out by employing an interior point method based on the logarithmic barrier function. The results for the obtained bearing capacity were presented in a non-dimensional form for different values of GSI, m(i), sigma(ci)/(gamma b) and q/sigma(ci). Failure patterns were also examined for a few cases. For validating the results, computations were also performed for a strip footing as well. The results obtained from the analysis compare well with the data reported in literature. Since the equilibrium conditions are precisely satisfied only at the centroids of the elements, not everywhere in the domain, the obtained lower bound solution will be approximate not true. (C) 2015 Elsevier Ltd. All rights reserved.

Optimal bounded control of first-passage failure of quasi-integrable Hamiltonian systems with wide-band random excitation

The optimal bounded control of quasi-integrable Hamiltonian systems with wide-band random excitation for minimizing their first-passage failure is investigated. First, a stochastic averaging method for multi-degrees-of-freedom (MDOF) strongly nonlinear quasi-integrable Hamiltonian systems with wide-band stationary random excitations using generalized harmonic functions is proposed. Then, the dynamical programming equations and their associated boundary and final time conditions for the control problems of maximizinig reliability and maximizing mean first-passage time are formulated based on the averaged It$\ddot{\rm o}$ equations by applying the dynamical programming principle. The optimal control law is derived from the dynamical programming equations and control constraints. The relationship between the dynamical programming equations and the backward Kolmogorov equation for the conditional reliability function and the Pontryagin equation for the conditional mean first-passage time of optimally controlled system is discussed. Finally, the conditional reliability function, the conditional probability density and mean of first-passage time of an optimally controlled system are obtained by solving the backward Kolmogorov equation and Pontryagin equation. The application of the proposed procedure and effectiveness of control strategy are illustrated with an example.

First-passage failure and its feedback minimization of quasi-partially integrable Hamiltonian systems

An n degree-of-freedom Hamiltonian system with r (1¡r¡n) independent 0rst integrals which are in involution is calledpartially integrable Hamiltonian system. A partially integrable Hamiltonian system subject to light dampings andweak stochastic excitations is called quasi-partially integrable Hamiltonian system. In the present paper, the procedures for studying the 0rst-passage failure and its feedback minimization of quasi-partially integrable Hamiltonian systems are proposed. First, the stochastic averaging methodfor quasi-partially integrable Hamiltonian systems is brie4y reviewed. Then, basedon the averagedIt ˆo equations, a backwardKolmogorov equation governing the conditional reliability function, a set of generalized Pontryagin equations governing the conditional moments of 0rst-passage time and their boundary and initial conditions are established. After that, the dynamical programming equations and their associated boundary and 0nal time conditions for the control problems of maximization of reliability andof maximization of mean 0rst-passage time are formulated. The relationship between the backwardKolmogorov equation andthe dynamical programming equation for reliability maximization, andthat between the Pontryagin equation andthe dynamical programming equation for maximization of mean 0rst-passage time are discussed. Finally, an example is worked out to illustrate the proposed procedures and the e9ectiveness of feedback control in reducing 0rst-passage failure.

First-passage failure of quasi-integrable Hamiltonian systems

The first-passage failure of quasi-integrable Hamiltonian si-stems (multidegree-of-freedom integrable Hamiltonian systems subject to light dampings and weakly random excitations) is investigated. The motion equations of such a system are first reduced to a set of averaged Ito stochastic differential equations by using the stochastic averaging method for quasi-integrable Hamiltonian systems. Then, a backward Kolmogorov equation governing the conditional reliability function and a set of generalized Pontryagin equations governing the conditional moments of first-passage time are established. Finally, the conditional reliability function, and the conditional probability density and moments of first-passage time are obtained by solving these equations with suitable initial and boundary conditions. Two examples are given to illustrate the proposed procedure and the results from digital simulation are obtained to verify the effectiveness of the procedure.

Statistical-theory of multiphoton excitation of polyatomic-molecules based on the wigner function

This paper is aimed at establishing a statistical theory of rotational and vibrational excitation of polyatomic molecules by an intense IR laser. Starting from the Wigner function of quantum statistical mechanics, we treat the rotational motion in the classical approximation; the vibrational modes are classified into active ones which are coupled directly with the laser and the background modes which are not coupled with the laser. The reduced Wigner function, i.e., the Wigner function integrated over all background coordinates should satisfy an integro-differential equation. We introduce the idea of ``viscous damping'' to handle the interaction between the active modes and the background. The damping coefficient can be calculated with the aid of the well-known Schwartz–Slawsky–Herzfeld theory. The resulting equation is solved by the method of moment equations. There is only one adjustable parameter in our scheme; it is introduced due to the lack of precise knowledge about the molecular potential. The theory developed in this paper explains satisfactorily the recent absorption experiments of SF6 irradiated by a short pulse CO2 laser, which are in sharp contradiction with the prevailing quasi-continuum theory. We also refined the density of energy levels which is responsible for the muliphoton excitation of polyatomic molecules.

New methods for generating populations in Markov network based EDAs: Decimation strategies and model-based template recombination

Methods for generating a new population are a fundamental component of estimation of distribution algorithms (EDAs). They serve to transfer the information contained in the probabilistic model to the new generated population. In EDAs based on Markov networks, methods for generating new populations usually discard information contained in the model to gain in efficiency. Other methods like Gibbs sampling use information about all interactions in the model but are computationally very costly. In this paper we propose new methods for generating new solutions in EDAs based on Markov networks. We introduce approaches based on inference methods for computing the most probable configurations and model-based template recombination. We show that the application of different variants of inference methods can increase the EDAs’ convergence rate and reduce the number of function evaluations needed to find the optimum of binary and non-binary discrete functions.

A measurement of inclusive quasi-elastic electron scattering cross sections at high momentum transfer

We have measured inclusive electron-scattering cross sections for targets of ^(4)He, C, Al, Fe, and Au, for kinematics spanning the quasi-elastic peak, with squared, four­ momentum transfers (q^2) between 0.23 and 2.89 (GeV/c)^2. Additional data were measured for Fe with q^2's up to 3.69 (GeV/c)^2 These cross sections were analyzed for the y-scaling behavior expected from a simple, impulse-approximation model, and are found to approach a scaling limit at the highest q^2's. The q^2 approach to scaling is compared with a calculation for infinite nuclear matter, and relationships between the scaling function and nucleon momentum distributions are discussed. Deviations from perfect scaling are used to set limits on possible changes in the size of nucleons inside the nucleus.

Energy spectrum of ground state and excitation spectrum of quasi-particle for hard-core boson in optical lattices

We investigate the energy spectrum of ground state and quasi-particle excitation spectrum of hard-core bosons, which behave very much like spinless noninteracting fermions, in optical lattices by means of the perturbation expansion and Bogoliubov approach. The results show that the energy spectrum has a single band structure, and the energy is lower near zero momentum; the excitation spectrum gives corresponding energy gap, and the system is in Mott-insulating state at Tonks limit. The analytic result of energy spectrum is in good agreement with that calculated in terms of Green's function at strong correlation limit.

Changes in the coherence of quasi-monochromatic electromagnetic Gaussian Schell-model beams propagating through turbulent atmosphere

Based on the extended Huygens-Fresnel principle, the mutual coherence function of quasi-monochromatic electromagnetic Gaussian Schell-model (EGSM) beams propagating through turbulent atmosphere is derived analytically. By employing the lateral and the longitudinal coherence length of EGSM beams to characterize the spatial and the temporal coherence of the beams, the behavior of changes in the spatial and the temporal coherence of those beams is studied. The results show that with a fixed set of beam parameters and under particular atmospheric turbulence model, the lateral coherence of an EGSM beam reaches its maximum value as the beam propagates a certain distance in the turbulent atmosphere, then it begins degrading and keeps decreasing along with the further distance. However, the longitudinal coherence length of an EGSM beam keeps unchanging in this propagation. Lastly, a qualitative explanation is given to these results. (c) 2007 Elsevier B.V. All rights reserved.

Intensity-moments characterization of general pulsed paraxial beams with the Wigner distribution function

On the basis of the space-time Wigner distribution function (STWDF), we use the matrix formalism to study the propagation laws for the intensity moments of quasi-monochromatic and polychromatic pulsed paraxial beams. The advantages of this approach are reviewed. Also, a least-squares fitting method for interpreting the physical meaning of the effective curvature matrix is described by means of the STWDF. Then the concept is extended to the higher-order situation, and what me believe is a novel technique for characterizing the beam phase is presented. (C) 1999 Optical Society of America [S0740-3232(99)001009-1].

When will a flame describing function approach to thermoacoustics work well?

In any thermoacoustic analysis, it is important not only to predict linear frequencies and growth rates, but also the amplitude and frequencies of any limit cycles. The Flame Describing Function (FDF) approach is a quasi-linear analysis which allows the prediction of both the linear and nonlinear behaviour of a thermoacoustic system. This means that one can predict linear growth rates and frequencies, and also the amplitudes and frequencies of any limit cycles. The FDF achieves this by assuming that the acoustics are linear and that the flame, which is the only nonlinear element in the thermoacoustic system, can be adequately described by considering only its response at the frequency at which it is forced. Therefore any harmonics generated by the flame's nonlinear response are not considered. This implies that these nonlinear harmonics are small or that they are sufficiently filtered out by the linear dynamics of the system (the low-pass filter assumption). In this paper, a flame model with a simple saturation nonlinearity is coupled to simple duct acoustics, and the success of the FDF in predicting limit cycles is studied over a range of flame positions and acoustic damping parameters. Although these two parameters affect only the linear acoustics and not the nonlinear flame dynamics, they determine the validity of the low-pass filter assumption made in applying the flame describing function approach. Their importance is highlighted by studying the level of success of an FDF-based analysis as they are varied. This is achieved by comparing the FDF's prediction of limit-cycle amplitudes to the amplitudes seen in time domain simulations.