Conformational Basis for Substrate Recruitment in Protein Tyrosine Phosphatase 10D

The coordinated activity of protein tyrosine phosphatases (PTPs) is crucial for the initiation, modulation, and termination of diverse cellular processes. The catalytic activity of this protein depends on a nucleophilic cysteine at the active site that mediates the hydrolysis of the incoming phosphotyrosine substrate. While the role of conserved residues in the catalytic mechanism of PTPs has been extensively examined, the diversity in the mechanisms of substrate recognition and modulation of catalytic activity suggests that other, less conserved sequence and structural features could contribute to this process. Here we describe the crystal structures of Drosophila melanogaster PTP10D in the apo form as well as in a complex with a substrate peptide and an inhibitor. These studies reveal the role of aromatic ring stacking interactions at the boundary of the active site of PTPs in mediating substrate recruitment. We note that phenylalanine 76, of the so-called KNRY loop, is crucial for orienting the phosphotyrosine residue toward the nucleophilic cysteine. Mutation of phenylalanine 76 to leucine results in a 60-fold decrease in the catalytic efficiency of the enzyme. Fluorescence measurements with a competitive inhibitor, p-nitrocatechol sulfate, suggest that Phe76 also influences the formation of the enzyme-substrate intermediate. The structural and biochemical data for PTP10D thus highlight the role of relatively less conserved residues in PTP domains in both substrate recruitment and modulation of reaction kinetics.

On Convergence of Differential Evolution Over a Class of Continuous Functions With Unique Global Optimum

Differential evolution (DE) is arguably one of the most powerful stochastic real-parameter optimization algorithms of current interest. Since its inception in the mid 1990s, DE has been finding many successful applications in real-world optimization problems from diverse domains of science and engineering. This paper takes a first significant step toward the convergence analysis of a canonical DE (DE/rand/1/bin) algorithm. It first deduces a time-recursive relationship for the probability density function (PDF) of the trial solutions, taking into consideration the DE-type mutation, crossover, and selection mechanisms. Then, by applying the concepts of Lyapunov stability theorems, it shows that as time approaches infinity, the PDF of the trial solutions concentrates narrowly around the global optimum of the objective function, assuming the shape of a Dirac delta distribution. Asymptotic convergence behavior of the population PDF is established by constructing a Lyapunov functional based on the PDF and showing that it monotonically decreases with time. The analysis is applicable to a class of continuous and real-valued objective functions that possesses a unique global optimum (but may have multiple local optima). Theoretical results have been substantiated with relevant computer simulations.

Composite instantaneous comparators basis for design and their transient performance

Principles of design of composite instantaneous comparators (a combination of amplitude- and phase- comparison techniques) are laid out to provide directional, directional-reactance, nonoffset-resistance and conductance characteristices. The respective signals provided by the voltage transformer and the current transformer are directly used as relaying signals without resorting to any form of mixing. Phase shifts required, are obtained by using magnetic ferrite cores in a novel manner. Sampling units employing a combination of ferrite cores and semiconductor devices provide highly reliable designs. Special attention is paid to the choice of relaying signals, to eliminate the need for any synchronisation or modification and to avoid `image¿ characteristics. These factors have resulted in a considerable simplification of the practical circuitry. A thyristor AND circuit is employed in dual comparator units to provide the final tripping, and leads to a circuit which is much less sensitive to extraneous signals than a single-thyristor unit.

The radiation resistance of off-set series slots in microstrip line

The radiation resistance of off-set series slots has been calculated for microstrip lines using the method proposed by Breithaupt for strip lines. A suitable transformation is made to allow for the difference in structure. Curves relating the slot resistance to the microstrip length, width and off-set distance have been obtained. Microstrip slot antenna arrays are becoming important in applications where size and weight are of significance. The radiation resistance is a very significant parameter is the design of such arrays. Oliner first calculated the radiation conductance of centered series slots in strip transmission lines and that analysis was extended by Breithaupt to the off-set series slots in stripline. The radiation resistance of off-set series slots in microstrip lines is calculated in this paper and data are obtained for different slot lengths, slot widths and off-set values. An example of the use of these data in array antenna design in shown.

Dynamic shear modulus as affected by displacement amplitude

The realistic estimation of the dynamic characteristics for a known set of loading conditions continues to be difficult despite many contributions in the past. The design of a machine foundation is generally made on the basis of limiting amplitude or resonant frequency. These parameters are in turn dependent on the dynamic characteristics of soil viz., the shear modulus/stiffness and damping. The work reported herein is an attempt to relate statistically the shear modulus of a soil to its resonant amplitude under a known set of static and dynamic loading conditions as well as wide ranging soil conditions. The two parameters have been statistically related with a good correlation coefficient and low standard error of estimate.

The Role of Tool Design in Influencing the Mechanism for the Formation of Friction Stir Welds in Aluminum Alloy 7020

Design of the required tool is a key and important parameter in the technique of friction stir welding (FSW). This is so because tool design does exert a close control over the quality of the weld. In an attempt to optimize tool design and its selection, it is essential and desirable to understand the mechanisms governing the formation of the weld. In this research study, few experiments were conducted to systematically analyze the intrinsic mechanisms governing the formation of the weld and to effectively utilize the analysis to establish a logical basis for design of the tool. For this purpose, the experiments were conducted using different geometries of the shoulder and pin of the rotating tool in such a way that only tool geometry had an intrinsic influence on formation of the weld. The results revealed that for a particular diameter of the pin there is an optimum diameter of the shoulder. Below this optimum shoulder diameter, the weld does not form while above the optimum diameter the overall symmetry of the weld is lost. Based on experimental results, a mechanism for the formation of friction stir weld is proposed. A synergism of the experimental results with the proposed mechanism is helpful in establishing the set of welding parameters for a given material.

Fuzzy Expert Approach with Curtailed Controllers for Improved Reactive Power Dispatch

This paper addresses the problem of curtailing the number of control actions using fuzzy expert approach for voltage/reactive power dispatch. It presents an approach using fuzzy set theory for reactive power control with the purpose of improving the voltage profile of a power system. To minimize the voltage deviations from pre-desired values of all the load buses, using the sensitivities with respect to reactive power control variables form the basis of the proposed Fuzzy Logic Control (FLC). Control variables considered are switchable VAR compensators, On Load Tap Changing (OLTC) transformers and generator excitations. Voltage deviations and controlling variables are translated into fuzzy set notations to formulate the relation between voltage deviations and controlling ability of controlling devices. The developed fuzzy system is tested on a few simulated practical Indian power systems and modified IEEE-30 bus system. The performance of the fuzzy system is compared with conventional optimization technique and results obtained are encouraging. Results obtained for a modified IEEE-30 bus test system and a 205-node equivalent EHV system a part of Indian southern grid are presented for illustration purposes. The proposed fuzzy-expert technique is found suitable for on-line applications in energy control centre as the solution is obtained fast with significant speedups with few number of controllers.

Bases and Ideal Generators for Projective Monomial Curves

In this article we study bases for projective monomial curves and the relationship between the basis and the set of generators for the defining ideal of the curve. We understand this relationship best for curves in P-3 and for curves defined by an arithmetic progression. We are able to prove that the latter are set theoretic complete intersections.

Network properties of protein-decoy structures

Convergence of the vast sequence space of proteins into a highly restricted fold/conformational space suggests a simple yet unique underlying mechanism of protein folding that has been the subject of much debate in the last several decades. One of the major challenges related to the understanding of protein folding or in silico protein structure prediction is the discrimination of non-native structures/decoys from the native structure. Applications of knowledge-based potentials to attain this goal have been extensively reported in the literature. Also, scoring functions based on accessible surface area and amino acid neighbourhood considerations were used in discriminating the decoys from native structures. In this article, we have explored the potential of protein structure network (PSN) parameters to validate the native proteins against a large number of decoy structures generated by diverse methods. We are guided by two principles: (a) the PSNs capture the local properties from a global perspective and (b) inclusion of non-covalent interactions, at all-atom level, including the side-chain atoms, in the network construction accommodates the sequence dependent features. Several network parameters such as the size of the largest cluster, community size, clustering coefficient are evaluated and scored on the basis of the rank of the native structures and the Z-scores. The network analysis of decoy structures highlights the importance of the global properties contributing to the uniqueness of native structures. The analysis also exhibits that the network parameters can be used as metrics to identify the native structures and filter out non-native structures/decoys in a large number of data-sets; thus also has a potential to be used in the protein `structure prediction' problem.

Reducing convergence times of self-propelled swarms via modified nearest neighbor rules

Vicsek et al. proposed a biologically inspired model of self-propelled particles, which is now commonly referred to as the Vicsek model. Recently, attention has been directed at modifying the Vicsek model so as to improve convergence properties. In this paper, we propose two modification of the Vicsek model which leads to significant improvements in convergence times. The modifications involve an additional term in the heading update rule which depends only on the current or the past states of the particle's neighbors. The variation in convergence properties as the parameters of these modified versions are changed are closely investigated. It is found that in both cases, there exists an optimal value of the parameter which reduces convergence times significantly and the system undergoes a phase transition as the value of the parameter is increased beyond this optimal value. (C) 2012 Elsevier B.V. All rights reserved.

An operator-splitting Galerkin/SUPG finite element method for population balance equations : stability and convergence

We present a heterogeneous finite element method for the solution of a high-dimensional population balance equation, which depends both the physical and the internal property coordinates. The proposed scheme tackles the two main difficulties in the finite element solution of population balance equation: (i) spatial discretization with the standard finite elements, when the dimension of the equation is more than three, (ii) spurious oscillations in the solution induced by standard Galerkin approximation due to pure advection in the internal property coordinates. The key idea is to split the high-dimensional population balance equation into two low-dimensional equations, and discretize the low-dimensional equations separately. In the proposed splitting scheme, the shape of the physical domain can be arbitrary, and different discretizations can be applied to the low-dimensional equations. In particular, we discretize the physical and internal spaces with the standard Galerkin and Streamline Upwind Petrov Galerkin (SUPG) finite elements, respectively. The stability and error estimates of the Galerkin/SUPG finite element discretization of the population balance equation are derived. It is shown that a slightly more regularity, i.e. the mixed partial derivatives of the solution has to be bounded, is necessary for the optimal order of convergence. Numerical results are presented to support the analysis.

On maximum entropy and minimum KL-divergence optimization by Grobner basis methods

In this paper we study constrained maximum entropy and minimum divergence optimization problems, in the cases where integer valued sufficient statistics exists, using tools from computational commutative algebra. We show that the estimation of parametric statistical models in this case can be transformed to solving a system of polynomial equations. We give an implicit description of maximum entropy models by embedding them in algebraic varieties for which we give a Grobner basis method to compute it. In the cases of minimum KL-divergence models we show that implicitization preserves specialization of prior distribution. This result leads us to a Grobner basis method to embed minimum KL-divergence models in algebraic varieties. (C) 2012 Elsevier Inc. All rights reserved.

Extracting Three Dimensional Surface Model of Human Kidney from the Visible Human Data Set using Free Software

Three dimensional digital model of a representative human kidney is needed for a surgical simulator that is capable of simulating a laparoscopic surgery involving kidney. Buying a three dimensional computer model of a representative human kidney, or reconstructing a human kidney from an image sequence using commercial software, both involve (sometimes significant amount of) money. In this paper, author has shown that one can obtain a three dimensional surface model of human kidney by making use of images from the Visible Human Data Set and a few free software packages (ImageJ, ITK-SNAP, and MeshLab in particular). Images from the Visible Human Data Set, and the software packages used here, both do not cost anything. Hence, the practice of extracting the geometry of a representative human kidney for free, as illustrated in the present work, could be a free alternative to the use of expensive commercial software or to the purchase of a digital model.

Electrical properties of buckled multiwalled carbon nanotube arrays in the diffusive regime

We report the geometrical effect of graded buckled multiwalled carbon nanotube arrays on the electrical transport properties in the diffusive regime, via successive breakdown caused by the Joule heating. This breakdown occurs in the straighter region. Empirical relations involving the current-carrying ability, resistance, breakdown power, threshold voltage, diameter and length of carbon nanotube arrays are discussed on the basis of an extensive set of experimental data along with justification. The experimental results are corroborated by the density functional tight-binding calculations of electronic band structure. The band gap decreases as buckleness increases leading to the enhancement in the current-carrying ability and elucidating the role of buckleness in carbon nanotubes. Copyright (c) EPLA, 2012