Interference Alignment as a Tool in Network Coding as Applied to Distributed Storage

In this paper, we outline an approach to the task of designing network codes in a non-multicast setting. Our approach makes use of the concept of interference alignment. As an example, we consider the distributed storage problem where the data is stored across the network in n nodes and where a data collector can recover the data by connecting to any k of the n nodes and where furthermore, upon failure of a node, a new node can replicate the data stored in the failed node while minimizing the repair bandwidth.

Structural Alignment based Kernels for Protein Structure Classification

Structural alignments are the most widely used tools for comparing proteins with low sequence similarity. The main contribution of this paper is to derive various kernels on proteins from structural alignments, which do not use sequence information. Central to the kernels is a novel alignment algorithm which matches substructures of fixed size using spectral graph matching techniques. We derive positive semi-definite kernels which capture the notion of similarity between substructures. Using these as base more sophisticated kernels on protein structures are proposed. To empirically evaluate the kernels we used a 40% sequence non-redundant structures from 15 different SCOP superfamilies. The kernels when used with SVMs show competitive performance with CE, a state of the art structure comparison program.

Interference Alignment Algorithms for the K User Constant MIMO Interference Channel

This paper considers the degrees of freedom (DOF) for a K user multiple-input multiple-output (MIMO) M x N interference channel using interference alignment (IA). A new performance metric for evaluating the efficacy of IA algorithms is proposed, which measures the extent to which the desired signal dimensionality is preserved after zero-forcing the interference at the receiver. Inspired by the metric, two algorithms are proposed for designing the linear precoders and receive filters for IA in the constant MIMO interference channel with a finite number of symbol extensions. The first algorithm uses an eigenbeamforming method to align sub-streams of the interference to reduce the dimensionality of the interference at all the receivers. The second algorithm is iterative, and is based on minimizing the interference leakage power while preserving the dimensionality of the desired signal space at the intended receivers. The improved performance of the algorithms is illustrated by comparing them with existing algorithms for IA using Monte Carlo simulations.

A generalized network alignment for three-source three-destination multiple unicast networks with delays

The concept of interference alignment when extended to three-source three-destination instantaneous multiple unicast network for the case where, each source-destination pair has a min-cut of 1 and zero-interference conditions are not satisfied, is known to achieve a rate of half for every source-destination pair under certain conditions [6]. This was called network alignment. We generalize this concept of network alignment to three-source three-destination multiple unicast (3S-3D-MU) networks with delays, without making use of memory at the intermediate nodes (i.e., nodes other than the sources and destinations) and using time varying Local Encoding Kernels (LEKs). This achieves half the rate corresponding to the individual source-destination min-cut for some classes of 3S-3D-MU network with delays which do not satisfy the zero-interference conditions.

Band alignment studies in InN/p-Si(100) heterojunctions by x-ray photoelectron spectroscopy

The band offsets in InN/p-Si heterojunctions are determined by high resolution x-ray photoemission spectroscopy. The valence band of InN is found to be 1.39 eV below that of Si. Given the bandgap of 0.7 eV for InN, a type-III heterojunction with a conduction band offset of 1.81 eV was found. Agreement between the simulated and experimental data obtained from the heterojunction spectra was found to be excellent, establishing that the method of determination was accurate. The charge neutrality level (CNL) model provided a reasonable description of the band alignment of the InN/p-Si interface and a change in the interface dipole by 0.06 eV was observed for InN/p-Si interface.

Studies towards synthesis, evolution and alignment characteristics of dense, millimeter long multiwalled carbon nanotube arrays

We report the synthesis of aligned arrays of millimeter long carbon nanotubes (CNTs), from benzene and ferrocene as the molecular precursor and catalyst respectively, by a one-step chemical vapor deposition technique. The length of the grown CNTs depends on the reaction temperature and increases from similar to 85 mu m to similar to 1.4 mm when the synthesis temperature is raised from 650 to 1100 degrees C, while the tube diameter is almost independent of the preparation temperature and is similar to 80 nm. The parallel arrangement of the CNTs, as well as their tube diameter can be verified spectroscopically by small angle X-ray scattering (SAXS) studies. Based on electron diffraction scattering (EDS) studies of the top and the base of the CNT films, a root growth process can be deduced.

Interference Alignment in Regenerating Codes for Distributed Storage: Necessity and Code Constructions

Regenerating codes are a class of recently developed codes for distributed storage that, like Reed-Solomon codes, permit data recovery from any arbitrary of nodes. However regenerating codes possess in addition, the ability to repair a failed node by connecting to any arbitrary nodes and downloading an amount of data that is typically far less than the size of the data file. This amount of download is termed the repair bandwidth. Minimum storage regenerating (MSR) codes are a subclass of regenerating codes that require the least amount of network storage; every such code is a maximum distance separable (MDS) code. Further, when a replacement node stores data identical to that in the failed node, the repair is termed as exact. The four principal results of the paper are (a) the explicit construction of a class of MDS codes for d = n - 1 >= 2k - 1 termed the MISER code, that achieves the cut-set bound on the repair bandwidth for the exact repair of systematic nodes, (b) proof of the necessity of interference alignment in exact-repair MSR codes, (c) a proof showing the impossibility of constructing linear, exact-repair MSR codes for d < 2k - 3 in the absence of symbol extension, and (d) the construction, also explicit, of high-rate MSR codes for d = k+1. Interference alignment (IA) is a theme that runs throughout the paper: the MISER code is built on the principles of IA and IA is also a crucial component to the nonexistence proof for d < 2k - 3. To the best of our knowledge, the constructions presented in this paper are the first explicit constructions of regenerating codes that achieve the cut-set bound.

Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies

Comparison of multiple protein structures has a broad range of applications in the analysis of protein structure, function and evolution. Multiple structure alignment tools (MSTAs) are necessary to obtain a simultaneous comparison of a family of related folds. In this study, we have developed a method for multiple structure comparison largely based on sequence alignment techniques. A widely used Structural Alphabet named Protein Blocks (PBs) was used to transform the information on 3D protein backbone conformation as a ID sequence string. A progressive alignment strategy similar to CLUSTALW was adopted for multiple PB sequence alignment (mulPBA). Highly similar stretches identified by the pairwise alignments are given higher weights during the alignment. The residue equivalences from PB based alignments are used to obtain a three dimensional fit of the structures followed by an iterative refinement of the structural superposition. Systematic comparisons using benchmark datasets of MSTAs underlines that the alignment quality is better than MULTIPROT, MUSTANG and the alignments in HOMSTRAD, in more than 85% of the cases. Comparison with other rigid-body and flexible MSTAs also indicate that mulPBA alignments are superior to most of the rigid-body MSTAs and highly comparable to the flexible alignment methods. (C) 2012 Elsevier Masson SAS. All rights reserved.

Weakly ordered chiral alignment medium derived from 5 `-GMP: guanosine

A novel weakly ordered chiral lyotropic alignment medium, derived by the self-assembly of guanosine 5'-monophosphate (5'-GMP) : guanosine for scaling RDCs to desired strengths and for the discrimination of enantiomers, is reported. The preparation of this inexpensive mesophase is straightforward, requires less time (1 h), and is sustainable, reversible and tunable over a wide range of temperature (280-330 K) and concentration.

Gap-Dependent Quasiparticle Dynamics and Coherent Acoustic Phonons in CaFe2As2 across Spin Density Wave Phase Transition

We report ultrafast quasiparticle (QP) dynamics and coherent acoustic phonons in undoped CaFe2As2 iron pnictide single crystals exhibiting spin-density wave (SDW) and concurrent structural phase transition at temperature T-SDW similar to 165K using femtosecond time-resolved pump-probe spectroscopy. The contributions in transient differential reflectivity arising from exponentially decaying QP relaxation and oscillatory coherent acoustic phonon mode show large variations in the vicinity of T-SDW. From the temperature-dependence of the QP recombination dynamics in the SDW phase, we evaluate a BCS-like temperature dependent charge gap with its zero-temperature value of similar to(1.6 perpendicular to 0.2)k(B)T(SDW), whereas, much above T-SDW, an electron-phonon coupling constant of similar to 0.13 has been estimated from the linear temperature-dependence of the QP relaxation time. The long-wavelength coherent acoustic phonons with typical time-period of similar to 100 ps have been analyzed in the light of propagating strain pulse model providing important results for the optical constants, sounds velocity and the elastic modulus of the crystal in the whole temperature range of 3 to 300 K.

Ultrafast quasiparticle relaxation dynamics in superconducting iron pnictide Ca(Fe0.944Co0.056)(2)As-2

Nonequilibrium quasiparticle relaxation dynamics is reported in superconducting Ca(Fe0.944Co0.056)(2)As-2 single crystals by measuring transient reflectivity changes using femtosecond time-resolved pump-probe spectroscopy. Large changes in the temperature-dependent differential reflectivity values in the vicinity of the spin density wave (T-SDW) and superconducting (T-SC) transition temperatures of the sample have been inferred to have charge gap opening at those temperatures. We have estimated the zero-temperature charge gap value in the superconducting state to be similar to 1.8k(B)T(SC) and an electron-phonon coupling constant lambda of similar to 0.1 in the normal state that signifies the weak coupling in iron pnictides. From the peculiar temperature-dependence of the quasiparticle dynamics in the intermediate temperature region between T-SC and T-SDW we infer a temperature scale where the charge gap associated with the spin ordered phase is maximum and closes on either side while approaching the two phase transition temperatures.

Multiobjective discrete particle swarm optimization for multisensor image alignment

A new technique is proposed for multisensor image registration by matching the features using discrete particle swarm optimization (DPSO). The feature points are first extracted from the reference and sensed image using improved Harris corner detector available in the literature. From the extracted corner points, DPSO finds the three corresponding points in the sensed and reference images using multiobjective optimization of distance and angle conditions through objective switching technique. By this, the global best matched points are obtained which are used to evaluate the affine transformation for the sensed image. The performance of the image registration is evaluated and concluded that the proposed approach is efficient.

On the feasibility of network alignment for three-source three-destination Multiple Unicast networks with delays

A transform approach to network coding was in-troduced by Bavirisetti et al. (arXiv:1103.3882v3 [cs.IT]) as a tool to view wireline networks with delays as k-instantaneous networks (for some large k). When the local encoding kernels (LEKs) of the network are varied with every time block of length k >1, the network is said to use block time varying LEKs. In this work, we propose a Precoding Based Network Alignment (PBNA) scheme based on transform approach and block time varying LEKs for three-source three-destination multiple unicast network with delays (3-S3-D MUN-D). In a recent work, Menget al. (arXiv:1202.3405v1 [cs.IT]) reduced the infinite set of sufficient conditions for feasibility of PBNA in a three-source three-destination instantaneous multiple unicast network as given by Das et al. (arXiv:1008.0235v1 [cs.IT]) to a finite set and also showed that the conditions are necessary. We show that the conditions of Meng et al. are also necessary and sufficient conditions for feasibility of PBNA based on transform approach and block time varying LEKs for 3-S3-D MUN-D.

On interference alignment for symmetrically connected interference networks with line of sight channels at finite powers

In this work, interference alignment for a class of Gaussian interference networks with general message demands, having line of sight (LOS) channels, at finite powers is considered. We assume that each transmitter has one independent message to be transmitted and the propagation delays are uniformly distributed between 0 and (L - 1) (L >; 0). If receiver-j, j ∈{1,2,..., J}, requires the message of transmitter-i, i ∈ {1, 2, ..., K}, we say (i, j) belongs to a connection. A class of interference networks called the symmetrically connected interference network is defined as a network where, the number of connections required at each transmitter-i is equal to ct for all i and the number of connections required at each receiver-j is equal to cr for all j, for some fixed positive integers ct and cr. For such networks with a LOS channel between every transmitter and every receiver, we show that an expected sum-spectral efficiency (in bits/sec/Hz) of at least K/(e+c1-1)(ct+1) (ct/ct+1)ct log2 (1+min(i, j)∈c|hi, j|2 P/WN0) can be achieved as the number of transmitters and receivers tend to infinity, i.e., K, J →∞ where, C denotes the set of all connections, hij is the channel gain between transmitter-i and receiver-j, P is the average power constraint at each transmitter, W is the bandwidth and N0 W is the variance of Gaussian noise at each receiver. This means that, for an LOS symmetrically connected interference network, at any finite power, the total spectral efficiency can grow linearly with K as K, J →∞. This is achieved by extending the time domain interference alignment scheme proposed by Grokop et al. for the k-user Gaussian interference channel to interference networks.

mulPBA: an efficient multiple protein structure alignment method based on a structural alphabet

The increasing number of available protein structures requires efficient tools for multiple structure comparison. Indeed, multiple structural alignments are essential for the analysis of function, evolution and architecture of protein structures. For this purpose, we proposed a new web server called multiple Protein Block Alignment (mulPBA). This server implements a method based on a structural alphabet to describe the backbone conformation of a protein chain in terms of dihedral angles. This sequence-like' representation enables the use of powerful sequence alignment methods for primary structure comparison, followed by an iterative refinement of the structural superposition. This approach yields alignments superior to most of the rigid-body alignment methods and highly comparable with the flexible structure comparison approaches. We implement this method in a web server designed to do multiple structure superimpositions from a set of structures given by the user. Outputs are given as both sequence alignment and superposed 3D structures visualized directly by static images generated by PyMol or through a Jmol applet allowing dynamic interaction. Multiple global quality measures are given. Relatedness between structures is indicated by a distance dendogram. Superimposed structures in PDB format can be also downloaded, and the results are quickly obtained. mulPBA server can be accessed at www.dsimb.inserm.fr/dsimb_tools/mulpba/.