On the duality between rate and power optimizations

Sequence design problems are considered in this paper. The problem of sum power minimization in a spread spectrum system can be reduced to the problem of sum capacity maximization, and vice versa. A solution to one of the problems yields a solution to the other. Subsequently, conceptually simple sequence design algorithms known to hold for the white-noise case are extended to the colored noise case. The algorithms yield an upper bound of 2N - L on the number of sequences where N is the processing gain and L the number of non-interfering subsets of users. If some users (at most N - 1) are allowed to signal along a limited number of multiple dimensions, then N orthogonal sequences suffice.

Study of gas cavity size hysteresis in a packed bed using DEM

When a high velocity gas jet is introduced into a packed bed a cavity is formed. The size of the cavity shows hysteresis on increasing and decreasing gas flow rates. This hysteresis leads to different cavity sizes at same gas flow rate depending on the bed history. The size of cavity affects the gas flow profiles in the packed bed. In this study the cavity size hysteresis phenomenon has been modeled using discrete element method along with turbulent gas flow. A reasonable agreement has been found between computed and experimental results on cavity size ysteresis. The effect of various parameters, such as nozzle height from the bed bottom and packing height, on the cavity size hysteresis has been studied. It is found that inter-particle interaction forces along with gas drag and bed porosity play an important role in describing the cavity size hysteresis. The injection of gas flow allows the particles to go to an unconstrained state than they were previously in, and their ability to remain in that state, even under decreased gas drag force, leads to the phenomenon of cavity size hysteresis. (c) 2007 Elsevier Ltd. All rights reserved.

Surface instability of confined elastic bilayers: Theory and simulations

The surface of a soft elastic film becomes unstable and forms a self-organized undulating pattern because of adhesive interactions when it comes in contact proximity with a rigid surface. For a single film, the pattern length scale lambda, which is governed by the minimization of the elastic stored energy, gives lambda similar to 3h, where h is the film thickness. Based on a linear stability analysis and simulations of adhesion and debonding, we consider the contact instability of an elastic bilayer, which provides greater flexibility in the morphological control of interfacial instability. Unlike the case of a single film, the morphology of the contact instability patterns, debonding distance, and debonding force in a bilayer can be controlled in a nonlinear way by varying the thicknesses and shear moduli of the films. Interestingly, the pattern wavelength in a bilayer can be greatly increased or decreased compared to a single film when the adhesive contact is formed by the stiffer or the softer of the two films, respectively. In particular, lambda as small as 0.5h can be obtained. This indicates a new strategy for pattern miniaturization in elastic contact lithography.

A novel approach for large-scale polypeptide folding based on elastic networks using continuous optimization

We present a new computationally efficient method for large-scale polypeptide folding using coarse-grained elastic networks and gradient-based continuous optimization techniques. The folding is governed by minimization of energy based on Miyazawa–Jernigan contact potentials. Using this method we are able to substantially reduce the computation time on ordinary desktop computers for simulation of polypeptide folding starting from a fully unfolded state. We compare our results with available native state structures from Protein Data Bank (PDB) for a few de-novo proteins and two natural proteins, Ubiquitin and Lysozyme. Based on our simulations we are able to draw the energy landscape for a small de-novo protein, Chignolin. We also use two well known protein structure prediction software, MODELLER and GROMACS to compare our results. In the end, we show how a modification of normal elastic network model can lead to higher accuracy and lower time required for simulation.

Maximum compatible classes from compatibility matrices

A fast algorithm for the computation of maximum compatible classes (mcc) among the internal states of an incompletely specified sequential machine is presented in this paper. All the maximum compatible classes are determined by processing compatibility matrices of progressingly diminishing order, whose total number does not exceed (p + m), where p is the largest cardinality among these classes, and m is the number of such classes. Consequently the algorithm is specially suitable for the state minimization of very large sequential machines as encountered in vlsi circuits and systems.

SPSA algorithms with measurement reuse

Four algorithms, all variants of Simultaneous Perturbation Stochastic Approximation (SPSA), are proposed. The original one-measurement SPSA uses an estimate of the gradient of objective function L containing an additional bias term not seen in two-measurement SPSA. As a result, the asymptotic covariance matrix of the iterate convergence process has a bias term. We propose a one-measurement algorithm that eliminates this bias, and has asymptotic convergence properties making for easier comparison with the two-measurement SPSA. The algorithm, under certain conditions, outperforms both forms of SPSA with the only overhead being the storage of a single measurement. We also propose a similar algorithm that uses perturbations obtained from normalized Hadamard matrices. The convergence w.p. 1 of both algorithms is established. We extend measurement reuse to design two second-order SPSA algorithms and sketch the convergence analysis. Finally, we present simulation results on an illustrative minimization problem.

Explicit Construction of Optimal Exact Regenerating Codes for Distributed Storage

Erasure coding techniques are used to increase the reliability of distributed storage systems while minimizing storage overhead. Also of interest is minimization of the bandwidth required to repair the system following a node failure. In a recent paper, Wu et al. characterize the tradeoff between the repair bandwidth and the amount of data stored per node. They also prove the existence of regenerating codes that achieve this tradeoff. In this paper, we introduce Exact Regenerating Codes, which are regenerating codes possessing the additional property of being able to duplicate the data stored at a failed node. Such codes require low processing and communication overheads, making the system practical and easy to maintain. Explicit construction of exact regenerating codes is provided for the minimum bandwidth point on the storage-repair bandwidth tradeoff, relevant to distributed-mail-server applications. A sub-space based approach is provided and shown to yield necessary and sufficient conditions on a linear code to possess the exact regeneration property as well as prove the uniqueness of our construction. Also included in the paper, is an explicit construction of regenerating codes for the minimum storage point for parameters relevant to storage in peer-to-peer systems. This construction supports a variable number of nodes and can handle multiple, simultaneous node failures. All constructions given in the paper are of low complexity, requiring low field size in particular.

Computer modelling approach to study the modes of binding of alpha- and beta-anomers of D-galactose, D-fucose and D-glucose to L-arabinose-binding protein

The modes of binding of alpha- and beta-anomers of D-galactose, D-fucose and D-glucose to L-arabinose-binding protein (ABP) have been studied by energy minimization using the low resolution (2.4 A) X-ray data of the protein. These studies suggest that these sugars preferentially bind in the alpha-form to ABP, unlike L-arabinose where both alpha- and beta-anomers bind almost equally. The best modes of binding of alpha- and beta-anomers of D-galactose and D-fucose differ slightly in the nature of the possible hydrogen bonds with the protein. The residues Arg 151 and Asn 232 of ABP from bidentate hydrogen bonds with both L-arabinose and D-galactose, but not with D-fucose or D-glucose. However in the case of L-arabinose, Arg 151 forms hydrogen bonds with the hydroxyl group at the C-4 atom and the ring oxygen, whereas in case of D-galactose it forms bonds with the hydroxyl groups at the C-4 and C-6 atoms of the pyranose ring. The calculated conformational energies also predict that D-galactose is a better inhibitor than D-fucose and D-glucose, in agreement with kinetic studies. The weak inhibitor D-glucose binds preferentially to one domain of ABP leading to the formation of a weaker complex. Thus these studies provide information about the most probable binding modes of these sugars and also provide a theoretical explanation for the observed differences in their binding affinities.

Origin of the Enhanced Photoluminescence from Semiconductor CdSeS Nanocrystals

Internal structures of extraordinarily luminescent semiconductor nanoparticles are probed with photoelectron spectroscopy, establishing a gradient alloy structure as an essential ingredient for the observed phenomenon. Comparative photoluminescence lifetime measurements provide direct evidence for a minimization of nonradiative decay channels because of the removal of interfacial defects due to a progressive change in the lattice parameters in such graded structures, exhibiting a nearly single exponential decay Quantum mechanical, calculations suggest a differential extent of spatial collapse of the electron and the hole wave functions in a way that helps to enhance the photoluminescence efficiency, while at the same time increasing the lifetime of the excited state, as observed in the experiments.

Modified linear prediction method for directions of arrival estimation of narrow-band plane waves

A modified linear prediction (MLP) method is proposed in which the reference sensor is optimally located on the extended line of the array. The criterion of optimality is the minimization of the prediction error power, where the prediction error is defined as the difference between the reference sensor and the weighted array outputs. It is shown that the L2-norm of the least-squares array weights attains a minimum value for the optimum spacing of the reference sensor, subject to some soft constraint on signal-to-noise ratio (SNR). How this minimum norm property can be used for finding the optimum spacing of the reference sensor is described. The performance of the MLP method is studied and compared with that of the linear prediction (LP) method using resolution, detection bias, and variance as the performance measures. The study reveals that the MLP method performs much better than the LP technique.

Design of an HA2-based Escherichia coli expressed influenza immunogen that protects mice from pathogenic challenge

Influenza HA is the primary target of neutralizing antibodies during infection, and its sequence undergoes genetic drift and shift in response to immune pressure. The receptor binding HA1 subunit of HA shows much higher sequence variability relative to the metastable, fusion-active HA2 subunit, presumably because neutralizing antibodies are primarily targeted against the former in natural infection. We have designed an HA2-based immunogen using a protein minimization approach that incorporates designed mutations to destabilize the low pH conformation of HA2. The resulting construct (HA6) was expressed in Escherichia coli and refolded from inclusion bodies. Biophysical studies and mutational analysis of the protein indicate that it is folded into the desired neutral pH conformation competent to bind the broadly neutralizing HA2 directed monoclonal 12D1, not the low pH conformation observed in previous studies. HA6 was highly immunogenic in mice and the mice were protected against lethal challenge by the homologous A/HK/68 mouse-adapted virus. An HA6-like construct from another H3 strain (A/Phil/2/82) also protected mice against A/HK/68 challenge. Regions included in HA6 are highly conserved within a subtype and are fairly well conserved within a clade. Targeting the highly conserved HA2 subunit with a bacterially produced immunogen is a vaccine strategy that may aid in pandemic preparedness.

Partially conserved axial-vector current inS-matrix theory

Mandelstam�s argument that PCAC follows from assigning Lorentz quantum numberM=1 to the massless pion is examined in the context of multiparticle dual resonance model. We construct a factorisable dual model for pions which is formulated operatorially on the harmonic oscillator Fock space along the lines of Neveu-Schwarz model. The model has bothm ? andm ? as arbitrary parameters unconstrained by the duality requirement. Adler self-consistency condition is satisfied if and only if the conditionm?2?m?2=1/2 is imposed, in which case the model reduces to the chiral dual pion model of Neveu and Thorn, and Schwarz. The Lorentz quantum number of the pion in the dual model is shown to beM=0.

Investigation of the effect of nonlocal scale on ultrasonic wave dispersion characteristics of a monolayer graphene

In this article, an ultrasonic wave propagation in graphene sheet is studied using nonlocal elasticity theory incorporating small scale effects. The graphene sheet is modeled as an isotropic plate of one-atom thick. For this model, the nonlocal governing differential equations of motion are derived from the minimization of the total potential energy of the entire system. An ultrasonic type of wave propagation model is also derived for the graphene sheet. The nonlocal scale parameter introduces certain band gap region in in-plane and flexural wave modes where no wave propagation occurs. This is manifested in the wavenumber plots as the region where the wavenumber tends to infinite or wave speed tends to zero. The frequency at which this phenomenon occurs is called the escape frequency. The explicit expressions for cutoff frequencies and escape frequencies are derived. The escape frequencies are mainly introduced because of the nonlocal elasticity. Obviously these frequencies are function of nonlocal scaling parameter. It has also been obtained that these frequencies are independent of y-directional wavenumber. It means that for any type of nanostructure, the escape frequencies are purely a function of nonlocal scaling parameter only. It is also independent of the geometry of the structure. It has been found that the cutoff frequencies are function of nonlocal scaling parameter (e(0)a) and the y-directional wavenumber (k(y)). For a given nanostructure, nonlocal small scale coefficient can be obtained by matching the results from molecular dynamics (MD) simulations and the nonlocal elasticity calculations. At that value of the nonlocal scale coefficient, the waves will propagate in the nanostructure at that cut-off frequency. In the present paper, different values of e(o)a are used. One can get the exact e(0)a for a given graphene sheet by matching the MD simulation results of graphene with the results presented in this paper. (C) 2010 Elsevier B.V. All rights reserved.

Stereochemistry of collagen

This review article, based on a lecture delivered in Madras in 1985, is an account of the author's experience in the working out of the molecular structure and conformation of the collagen triple-helix over the years 1952–78. It starts with the first proposal of the correct triple-helix in 1954, but with three residues per turn, which was later refined in 1955 into a coiled-coil structure with approximately 3.3 residues per turn. The structure readily fitted proline and hydroxyproline residues and required glycine as every third residue in each of the three chains. The controversy regarding the number of hydrogen bonds per tripeptide could not be resolved by X-ray diffraction or energy minimization, but physicochemical data, obtained in other laboratories during 1961–65, strongly pointed to two hydrogen bonds, as suggested by the author. However, it was felt that the structure with one straight NH … O bond was better. A reconciliation of the two was obtained in Chicago in 1968, by showing that the second hydrogen bond is via a water molecule, which makes it weaker, as found in the physicochemical studies mentioned above. This water molecule was also shown, in 1973, to take part in further cross-linking hydrogen bonds with the OH group of hydroxyproline, which occurred always in the location previous to glycine, and is at the right distance from the water. Thus, almost all features of the primary structure, X-ray pattern, optical and hydrodynamic data, and the role of hydroxyproline in stabilising the triple helical structure, have been satisfactorily accounted for. These also lead to a confirmation of Pauling's theory that vitamin C improves immunity to diseases, as explained in the last section.

Regenerating Codes for Distributed Storage Networks

In a storage system where individual storage nodes are prone to failure, the redundant storage of data in a distributed manner across multiple nodes is a must to ensure reliability. Reed-Solomon codes possess the reconstruction property under which the stored data can be recovered by connecting to any k of the n nodes in the network across which data is dispersed. This property can be shown to lead to vastly improved network reliability over simple replication schemes. Also of interest in such storage systems is the minimization of the repair bandwidth, i.e., the amount of data needed to be downloaded from the network in order to repair a single failed node. Reed-Solomon codes perform poorly here as they require the entire data to be downloaded. Regenerating codes are a new class of codes which minimize the repair bandwidth while retaining the reconstruction property. This paper provides an overview of regenerating codes including a discussion on the explicit construction of optimum codes.