A network representation of protein structures: Implications for protein stability

This study views each protein structure as a network of noncovalent connections between amino acid side chains. Each amino acid in a protein structure is a node, and the strength of the noncovalent interactions between two amino acids is evaluated for edge determination. The protein structure graphs (PSGs) for 232 proteins have been constructed as a function of the cutoff of the amino acid interaction strength at a few carefully chosen values. Analysis of such PSGs constructed on the basis of edge weights has shown the following: 1), The PSGs exhibit a complex topological network behavior, which is dependent on the interaction cutoff chosen for PSG construction. 2), A transition is observed at a critical interaction cutoff, in all the proteins, as monitored by the size of the largest cluster (giant component) in the graph. Amazingly, this transition occurs within a narrow range of interaction cutoff for all the proteins, irrespective of the size or the fold topology. And 3), the amino acid preferences to be highly connected (hub frequency) have been evaluated as a function of the interaction cutoff. We observe that the aromatic residues along with arginine, histidine, and methionine act as strong hubs at high interaction cutoffs, whereas the hydrophobic leucine and isoleucine residues get added to these hubs at low interaction cutoffs, forming weak hubs. The hubs identified are found to play a role in bringing together different secondary structural elements in the tertiary structure of the proteins. They are also found to contribute to the additional stability of the thermophilic proteins when compared to their mesophilic counterparts and hence could be crucial for the folding and stability of the unique three-dimensional structure of proteins. Based on these results, we also predict a few residues in the thermophilic and mesophilic proteins that can be mutated to alter their thermal stability.

A Proportional plus Multiresonant Controller for Three-Phase Four-Wire High-Frequency Link Inverter

A new solution for unbalanced and nonlinear loads in terms of power circuit topology and controller structure is proposed in this paper. A three-phase four-wire high-frequency ac-link inverter is adopted to cater to such loads. Use of high-frequency transformer results in compact and light-weight systems. The fourth wire is taken out from the midpoint of the isolation transformer in order to avoid the necessity of an extra leg. This makes the converter suitable for unbalanced loads and eliminates the requirements of bulky capacitor in half-bridge inverter. The closed-loop control is carried out in stationary reference frame using proportional + multiresonant controller (three separate resonant controller for fundamental, fifth and seventh harmonic components). The limitations on improving steady-state response of harmonic resonance controllers is investigated and mitigated using a lead-lag compensator. The proposed voltage controller is used along with an inner current loop to ensure excellent performance of the power converter. Simulation studies and experimental results with 1 kVA prototype under nonlinear and unbalanced loading conditions validate the proposed scheme.

STBC's from representation of extended Clifford Algebras

A set of sufficient conditions to construct lambda-real symbol Maximum Likelihood (ML) decodable STBCs have recently been provided by Karmakar et al. STBCs satisfying these sufficient conditions were named as Clifford Unitary Weight (CUW) codes. In this paper, the maximal rate (as measured in complex symbols per channel use) of CUW codes for lambda = 2(a), a is an element of N is obtained using tools from representation theory. Two algebraic constructions of codes achieving this maximal rate are also provided. One of the constructions is obtained using linear representation of finite groups whereas the other construction is based on the concept of right module algebra over non-commutative rings. To the knowledge of the authors, this is the first paper in which matrices over non-commutative rings is used to construct STBCs. An algebraic explanation is provided for the 'ABBA' construction first proposed by Tirkkonen et al and the tensor product construction proposed by Karmakar et al. Furthermore, it is established that the 4 transmit antenna STBC originally proposed by Tirkkonen et al based on the ABBA construction is actually a single complex symbol ML decodable code if the design variables are permuted and signal sets of appropriate dimensions are chosen.

A generalized mathematical theory and experimental verification of proportional notches

A theory and generalized synthesis procedure is advocated for the design of weir notches and orifice-notches having a base in any given shape, to a depth a, such that the discharge through it is proportional to any singular monotonically-increasing function of the depth of flow measured above a certain datum. The problem is reduced to finding an exact solution of a Volterra integral equation in Abel form. The maximization of the depth of the datum below the crest of the notch is investigated. Proof is given that for a weir notch made out of one continuous curve, and for a flow proportional to the mth power of the head, it is impossible to bring the datum lower than (2m − 1)a below the crest of the notch. A new concept of an orifice-notch, having discontinuity in the curve and a division of flow into two distinct portions, is presented. The division of flow is shown to have a beneficial effect in reducing the datum below (2m − 1)a from the crest of the weir and still maintaining the proportionality of the flow. Experimental proof with one such orifice-notch is found to have a constant coefficient of discharge of 0.625. The importance of this analysis in the design of grit chambers is emphasized.

Gas amplification in proportional counters

The variation of gas amplification with applied voltage is an important characteristic of a proportional counter. Results of studies on gas amplification for gas fillings of argon quenched with ethane and carbon dioxide are given. The effects of (a) pressure, (b) quenching agent and (c) concentration on A are discussed briefly.

Anti-windup Schemes for Proportional Integral and Proportional Resonant Controller

Problems like windup or rollover arise in a PI controller working under saturation. Hence anti-windup schemes are necessary to minimize performance degradation.Similar situation may occur in a Proportional Resonant(PR)controller in the presence of a sustained error input.Several methods can be employed based on existing knowledge on PI controller to counter this problem.In this paper few such schemes are proposed and implemented in FPGA and MATLAB and from the obtained results their possible use and limitations have been studied.

Inverted V-Notch: Practical Proportional Weir

This paper presents a practical linear proportional weir of simple geometric shape in the form of an inverted V-notch or inward trapezium. The flow through this weir, of half-width w and altitude d, for depths above 0.22d is proportional to the depth of flow measured above a reference plane situated at 0.08d for all heads in the range 0.22d<=h<=0.94d, with a maximum percentage deviation of ±1.5 from the theoretical discharge. The linear relationship between head and discharge is based on numerical optimization procedures. Nearly 75% of the depth of inverted V-notch can be used effectively as the measuring range. Experiments with four weirs, with different vertex angles, show excellent agreement with the theory by giving an average coefficient of discharge for each weir varying from 0.61–0.62.

Hamilton’s theory of turns and a new geometrical representation for polarization optics

Hamilton’s theory of turns for the group SU(2) is exploited to develop a new geometrical representation for polarization optics. While pure polarization states are represented by points on the Poincaré sphere, linear intensity preserving optical systems are represented by great circle arcs on another sphere. Composition of systems, and their action on polarization states, are both reduced to geometrical operations. Several synthesis problems, especially in relation to the Pancharatnam-Berry-Aharonov-Anandan geometrical phase, are clarified with the new representation. The general relation between the geometrical phase, and the solid angle on the Poincaré sphere, is established.

An improved representation of vehicle incompatibility in frontal NCAP tests using a modified rigid barrier

With the objective of better understanding the significance of New Car Assessment Program (NCAP) tests conducted by the National Highway Traffic Safety Administration (NHTSA), head-on collisions between two identical cars of different sizes and between cars and a pickup truck are studied in the present paper using LS-DYNA models. Available finite element models of a compact car (Dodge Neon), midsize car (Dodge Intrepid), and pickup truck (Chevrolet C1500) are first improved and validated by comparing theanalysis-based vehicle deceleration pulses against corresponding NCAP crash test histories reported by NHTSA. In confirmation of prevalent perception, simulation-bascd results indicate that an NCAP test against a rigid barrier is a good representation of a collision between two similar cars approaching each other at a speed of 56.3 kmph (35 mph) both in terms of peak deceleration and intrusions. However, analyses carried out for collisions between two incompatible vehicles, such as an Intrepid or Neon against a C1500, point to the inability of the NCAP tests in representing the substantially higher intrusions in the front upper regions experienced by the cars, although peak decelerations in cars arc comparable to those observed in NCAP tests. In an attempt to improve the capability of a front NCAP test to better represent real-world crashes between incompatible vehicles, i.e., ones with contrasting ride height and lower body stiffness, two modified rigid barriers are studied. One of these barriers, which is of stepped geometry with a curved front face, leads to significantly improved correlation of intrusions in the upper regions of cars with respect to those yielded in the simulation of collisions between incompatible vehicles, together with the yielding of similar vehicle peak decelerations obtained in NCAP tests.

Design of Constant Accuracy Linear Proportional Weir

Five different shaped weirs were designed and pertinent data for their use are given. One of these weir shapes had the least “sharp edge” at the junction of the base weir and “complementary weir.” Two other types of weirs had equal slopes at the junction of the base weir and complementary weir. Another shape, for which neither the indication accuracy was constant nor the slope was equal at the junction of the base weir and complementary weir, was also tested. The results of the four weir shapes hydraulically tested give consistent values for the coefficient of discharge varying between 0.625 to 0.631. The indication accuracies of all the previously designed linear proportional weirs (includig Sutro weir) are neither constant nor unity, as is believed.

Representation of Thermodynamic Properties of Dilute Multi-Component Solutions--Options and Constraints

The different formalisms for the representation of thermodynamic data on dilute multicomponent solutions are critically reviewed. The thermodynamic consistency of the formalisms are examined and the interrelations between them are highlighted. The options are constraints in the use of the interaction parameter and Darken's quadratic formalisms for multicomponent solutions are discussed in the light of the available experimental data. Truncatred Maclaurin series expansion is thermodynamically inconsistent unless special relations between interaction parameters are invoked. However, the lack of strict mathematical consistency does not affect the practical use of the formalism. Expressions for excess partial properties can be integrated along defined composition paths without significant loss of accuracy. Although thermodynamically consistent, the applicability of Darken's quadratic formalism to strongly interacting systems remains to be established by experiment.

Structure and representation of correlation functions and the density matrix for a statistical wave field in optics

A systematic structure analysis of the correlation functions of statistical quantum optics is carried out. From a suitably defined auxiliary two‐point function we are able to identify the excited modes in the wave field. The relative simplicity of the higher order correlation functions emerge as a byproduct and the conditions under which these are made pure are derived. These results depend in a crucial manner on the notion of coherence indices and of unimodular coherence indices. A new class of approximate expressions for the density operator of a statistical wave field is worked out based on discrete characteristic sets. These are even more economical than the diagonal coherent state representations. An appreciation of the subtleties of quantum theory obtains. Certain implications for the physics of light beams are cited.

A field-consistent and variationally correct representation of transverse shear strains in the nine-noded plate element

We present a biquadratic Lagrangian plate bending element with consistent fields for the constrained transverse shear strain functions. A technique involving expansion of the strain interpolations in terms of Legendre polynomials is used to redistribute the kinematically derived shear strain fields so that the field-consistent forms (i.e. avoiding locking) are also variationally correct (i.e. do not violate the variational norms). Also, a rational method of isoparametric Jacobian transformation is incorporated so that the constrained covariant shear strain fields are always consistent in whatever general quadrilateral form the element may take. Finally the element is compared with another formulation which was recently published. The element is subjected to several robust bench mark tests and is found to pass all the tests efficiently.

Parts based representation for pedestrian using NMF with robustness to partial occlusion

Computer Vision has seen a resurgence in the parts-based representation for objects over the past few years. The parts are usually annotated beforehand for training. We present an annotation free parts-based representation for the pedestrian using Non-Negative Matrix Factorization (NMF). We show that NMF is able to capture the wide range of pose and clothing of the pedestrians. We use a modified form of NMF i.e. NMF with sparsity constraints on the factored matrices. We also make use of Riemannian distance metric for similarity measurements in NMF space as the basis vectors generated by NMF aren't orthogonal. We show that for 1% drop in accuracy as compared to the Histogram of Oriented Gradients (HOG) representation we can achieve robustness to partial occlusion.