Projecting low and extensive dimensional chaos from spatio-temporal dynamics

We review the spatio-temporal dynamical features of the Ananthakrishna model for the Portevin-Le Chatelier effect, a kind of plastic instability observed under constant strain rate deformation conditions. We then establish a qualitative correspondence between the spatio-temporal structures that evolve continuously in the instability domain and the nature of the irregularity of the scalar stress signal. Rest of the study is on quantifying the dynamical information contained in the stress signals about the spatio-temporal dynamics of the model. We show that at low applied strain rates, there is a one-to-one correspondence with the randomly nucleated isolated bursts of mobile dislocation density and the stress drops. We then show that the model equations are spatio-temporally chaotic by demonstrating the number of positive Lyapunov exponents and Lyapunov dimension scale with the system size at low and high strain rates. Using a modified algorithm for calculating correlation dimension density, we show that the stress-strain signals at low applied strain rates corresponding to spatially uncorrelated dislocation bands exhibit features of low dimensional chaos. This is made quantitative by demonstrating that the model equations can be approximately reduced to space independent model equations for the average dislocation densities, which is known to be low-dimensionally chaotic. However, the scaling regime for the correlation dimension shrinks with increasing applied strain rate due to increasing propensity for propagation of the dislocation bands. The stress signals in the partially propagating to fully propagating bands turn to have features of extensive chaos.

Top polarization in stop production at the LHC

We survey the expected polarization of the top produced in the decay of a scalar top quark, t -> t((chi) over tildei)(0), i = 1 - 2. The phenomenology is quite interesting, since the expected polarization depends both on the mixing in the stop and neutralino sectors and on the mass differences between the stop and the neutralino. We find that a mixed stop behaves almost like a right-handed stop due to the larger hypercharge that enters the stop/top/gaugino coupling and that these polarisation effects disappear, when m((t) over tilde1) approximate to m(t) +m((chi) over tildei)(0). After a discussion on the expected top polarization from the decay of a scalar top quark, we focus on the interplay of polarization and kinematics at the LHC. We discuss different probes of the top polarization in terms of lab-frame observables. We find that these observables faithfully reflect the polarization of the parent top-quark, but also have a non-trivial dependence on the kinematics of the stop production and decay process. In addition, we illustrate the effect of top polarization on the energy and transverse momentum of the decay lepton in the laboratory frame. Our results show that both spectra are softened substantially in case of a negatively polarized top, particularly for a large mass difference between the stop and the neutralino. Thus, the search strategies, and the conclusions that can be drawn from them, depends not just on the mass difference m((t) over tilde) - m((chi) over tildei)(0) due to the usual kinematic effects but also on the effects of top polarization on the decay kinematics the extent of which depends in turn on the said mass difference.

A Hybrid Parallel Algorithm for Computing and Tracking Level Set Topology

The contour tree is a topological abstraction of a scalar field that captures evolution in level set connectivity. It is an effective representation for visual exploration and analysis of scientific data. We describe a work-efficient, output sensitive, and scalable parallel algorithm for computing the contour tree of a scalar field defined on a domain that is represented using either an unstructured mesh or a structured grid. A hybrid implementation of the algorithm using the GPU and multi-core CPU can compute the contour tree of an input containing 16 million vertices in less than ten seconds with a speedup factor of upto 13. Experiments based on an implementation in a multi-core CPU environment show near-linear speedup for large data sets.

Gap renormalization of molecular crystals from density-functional theory

Fundamental gap renormalization due to electronic polarization is a basic phenomenon in molecular crystals. Despite its ubiquity and importance, all conventional approaches within density-functional theory completely fail to capture it, even qualitatively. Here, we present a new screened range-separated hybrid functional, which, through judicious introduction of the scalar dielectric constant, quantitatively captures polarization-induced gap renormalization, as demonstrated on the prototypical organic molecular crystals of benzene, pentacene, and C-60. This functional is predictive, as it contains system-specific adjustable parameters that are determined from first principles, rather than from empirical considerations.

Subttractors

We consider extremal limits of the recently constructed ``subtracted geometry''. We show that extremality makes the horizon attractive against scalar perturbations, but radial evolution of such perturbations changes the asymptotics: from a conical-box to flat Minkowski. Thus these are black holes that retain their near-horizon geometry under perturbations that drastically change their asymptotics. We also show that this extremal subtracted solution (''subttractor'') can arise as a boundary of the basin of attraction for flat space attractors. We demonstrate this by using a fairly minimal action (that has connections with STU model) where the equations of motion are integrable and we are able to find analytic solutions that capture the flow from the horizon to the asymptotic region. The subttractor is a boundary between two qualitatively different flows. We expect that these results have generalizations for other theories with charged dilatonic black holes.

Topological saliency

Topological methods have been successfully used to identify features in scalar fields and to measure their importance. In this paper, we define a notion of topological saliency that captures the relative importance of a topological feature with respect to other features in its local neighborhood. Features are identified by extreme points of an input scalar field, and their importance measured by the so-called topological persistence. Computing the topological saliency of all features for varying neighborhood sizes results in a saliency plot that serves as a summary of relative importance of all topological features. We develop a convenient tool for users to interactively select and inspect features using the saliency plot. We demonstrate the use of topological saliency together with the rich information encoded in the saliency plot in several applications, including key feature identification, scalar field simplification, and feature clustering. (C) 2013 Elsevier Ltd. All rights reserved.

Beam polarization effects in the radiative production of lightest neutralinos in e(+)e(-) collisions in supersymmetric grand unified models

We study the production of the lightest neutralinos in the process e(+)e(-) -> chi(0)(1)chi(0)(1)gamma in supersymmetric grand unified models for the International Linear Collider energies with longitudinally polarized beams. We consider cases where the standard model gauge group is unified into the grand unified gauge groups SU(5), or SO(10). We have carried out a comprehensive study of this process in the SU(5) and SO(10) grand unified theories which includes the QED radiative corrections. We compare and contrast the dependence of the signal cross section on the grand unified gauge group, and on the different representations of the grand unified gauge group, when the electron and positron beams are longitudinally polarized. To assess the feasibility of experimentally observing the radiative production process, we have also considered in detail the background to this process coming from the radiative neutrino production process e(+)e(-)-> nu(nu) over bar gamma with longitudinally polarized electron and positron beams. In addition we have also considered the supersymmetric background coming from the radiative production of scalar neutrinos in the process e(+)e(-) -> (nu) over tilde(nu) over tilde*gamma with longitudinally polarized beams. The process can be a major background to the radiative production of neutralinos when the scalar neutrinos decay invisibly.

Structure constants of beta deformed super Yang-Mills

We study the structure constants of the N = 1 beta deformed theory perturbatively and at strong coupling. We show that the planar one loop corrections to the structure constants of single trace gauge invariant operators in the scalar sector is determined by the anomalous dimension Hamiltonian. This result implies that 3 point functions of the chiral primaries of the theory do not receive corrections at one loop. We then study the structure constants at strong coupling using the Lunin-Maldacena geometry. We explicitly construct the supergravity mode dual to the chiral primary with three equal U(1) R-charges in the Lunin-Maldacena geometry. We show that the 3 point function of this supergravity mode with semi-classical states representing two other similar chiral primary states but with large U(1) charges to be independent of the beta deformation and identical to that found in the AdS(5) x S-5 geometry. This together with the one-loop result indicate that these structure constants are protected by a non-renormalization theorem. We also show that three point function of U(1) R-currents with classical massive strings is proportional to the R-charge carried by the string solution. This is in accordance with the prediction of the R-symmetry Ward identity.

A matroidal framework for network-error correcting codes

Matroidal networks were introduced by Dougherty et al. and have been well studied in the recent past. It was shown that a network has a scalar linear network coding solution if and only if it is matroidal associated with a representable matroid. The current work attempts to establish a connection between matroid theory and network-error correcting codes. In a similar vein to the theory connecting matroids and network coding, we abstract the essential aspects of network-error correcting codes to arrive at the definition of a matroidal error correcting network. An acyclic network (with arbitrary sink demands) is then shown to possess a scalar linear error correcting network code if and only if it is a matroidal error correcting network associated with a representable matroid. Therefore, constructing such network-error correcting codes implies the construction of certain representable matroids that satisfy some special conditions, and vice versa.

Effects of initial height on the steady-state persistence probability of linear growth models

The effects of the initial height on the temporal persistence probability of steady-state height fluctuations in up-down symmetric linear models of surface growth are investigated. We study the (1 + 1)-dimensional Family model and the (1 + 1)-and (2 + 1)-dimensional larger curvature (LC) model. Both the Family and LC models have up-down symmetry, so the positive and negative persistence probabilities in the steady state, averaged over all values of the initial height h(0), are equal to each other. However, these two probabilities are not equal if one considers a fixed nonzero value of h(0). Plots of the positive persistence probability for negative initial height versus time exhibit power-law behavior if the magnitude of the initial height is larger than the interface width at saturation. By symmetry, the negative persistence probability for positive initial height also exhibits the same behavior. The persistence exponent that describes this power-law decay decreases as the magnitude of the initial height is increased. The dependence of the persistence probability on the initial height, the system size, and the discrete sampling time is found to exhibit scaling behavior.

DNA STRUCTURAL FEATURES AND ARCHITECTURE OF PROMOTER REGIONS PLAY A ROLE IN GENE RESPONSIVENESS OF S. CEREVISIAE

Gene expression is the most fundamental biological process, which is essential for phenotypic variation. It is regulated by various external (environment and evolution) and internal (genetic) factors. The level of gene expression depends on promoter architecture, along with other external factors. Presence of sequence motifs, such as transcription factor binding sites (TFBSs) and TATA-box, or DNA methylation in vertebrates has been implicated in the regulation of expression of some genes in eukaryotes, but a large number of genes lack these sequences. On the other hand, several experimental and computational studies have shown that promoter sequences possess some special structural properties, such as low stability, less bendability, low nucleosome occupancy, and more curvature, which are prevalent across all organisms. These structural features may play role in transcription initiation and regulation of gene expression. We have studied the relationship between the structural features of promoter DNA, promoter directionality and gene expression variability in S. cerevisiae. This relationship has been analyzed for seven different measures of gene expression variability, along with two different regulatory effect measures. We find that a few of the variability measures of gene expression are linked to DNA structural properties, nucleosome occupancy, TATA-box presence, and bidirectionality of promoter regions. Interestingly, gene responsiveness is most intimately correlated with DNA structural features and promoter architecture.

Charge and color breaking constraints in MSSM after the Higgs discovery at LHC

We revisit the constraints on the parameter space of the Minimal Supersymmetric Standard Model (MSSM), from charge and color breaking minima in the light of information on the Higgs from the LHC so far. We study the behavior of the scalar potential keeping two light sfermion fields along with the Higgs in the pMSSM framework and analyze the stability of the vacuum. We find that for lightest stops a parts per thousand(2) 1 TeV and small mu a parts per thousand(2) 500 GeV, the absolute stability of the potential can be attained only for . The bounds become stronger for larger values of the mu parameter. Note that this is approximately the value of Xt which maximizes the Higgs mass. Our bounds on the low scale MSSM parameters are more stringent than those reported earlier in literature. We reanalyze the stau sector as well, keeping both staus. We study the connections between the observed Higgs rates and vacuum (meta)stability. We show how a precision study of the ratio of signal strengths, (mu (gamma gamma) /mu (ZZ) ) can shed further light.

Sensitivity of Water Dynamics to Biologically Significant Surfaces of Monomeric Insulin: Role of Topology and Electrostatic Interactions

In addition to the biologically active monomer of the protein insulin circulating in human blood, the molecule also exists in dimeric and hexameric forms that are used as storage. The insulin monomer contains two distinct surfaces, namely, the dimer forming surface (DFS) and the hexamer forming surface (HFS), that are specifically designed to facilitate the formation of the dimer and the hexamer, respectively. In order to characterize the structural and dynamical behavior of interfacial water molecules near these two surfaces (DFS and HFS), we performed atomistic molecular dynamics simulations of insulin with explicit water. Dynamical characterization reveals that the structural relaxation of the hydrogen bonds formed between the residues of DFS and the interfacial water molecules is faster than those formed between water and that of the HFS. Furthermore, the residence times of water molecules in the protein hydration layer for both the DFS and HFS are found to be significantly higher than those for some of the other proteins studied so far, such as HP-36 and lysozyme. In particular, we find that more structured water molecules, with higher residence times (similar to 300-500 ps), are present near HFS than those near DFS. A significant slowing down is observed in the decay of associated rotational auto time correlation functions of O-H bond vector of water in the vicinity of HFS. The surface topography and the arrangement of amino acid residues work together to organize the water molecules in the hydration layer in order to provide them with a preferred orientation. HFS having a large polar solvent accessible surface area and a convex extensive nonpolar region, drives the surrounding water molecules to acquire predominantly an outward H-atoms directed, clathrate-like structure. In contrast, near the DFS, the surrounding water molecules acquire an inward H-atoms directed orientation owing to the flat curvature of hydrophobic surface and the interrupted hydrophilic residual alignment. We have followed escape trajectory of several such quasi-bound water molecules from both the surfaces that reveal the significant differences between the two hydration layers.

Linear filtering methods for fixed rate quantisation with noisy symmetric error channels

This study considers linear filtering methods for minimising the end-to-end average distortion of a fixed-rate source quantisation system. For the source encoder, both scalar and vector quantisation are considered. The codebook index output by the encoder is sent over a noisy discrete memoryless channel whose statistics could be unknown at the transmitter. At the receiver, the code vector corresponding to the received index is passed through a linear receive filter, whose output is an estimate of the source instantiation. Under this setup, an approximate expression for the average weighted mean-square error (WMSE) between the source instantiation and the reconstructed vector at the receiver is derived using high-resolution quantisation theory. Also, a closed-form expression for the linear receive filter that minimises the approximate average WMSE is derived. The generality of framework developed is further demonstrated by theoretically analysing the performance of other adaptation techniques that can be employed when the channel statistics are available at the transmitter also, such as joint transmit-receive linear filtering and codebook scaling. Monte Carlo simulation results validate the theoretical expressions, and illustrate the improvement in the average distortion that can be obtained using linear filtering techniques.

Role of DNA sequence based structural features of promoters in transcription initiation and gene expression

D Regulatory information for transcription initiation is present in a stretch of genomic DNA, called the promoter region that is located upstream of the transcription start site (TSS) of the gene. The promoter region interacts with different transcription factors and RNA polymerase to initiate transcription and contains short stretches of transcription factor binding sites (TFBSs), as well as structurally unique elements. Recent experimental and computational analyses of promoter sequences show that they often have non-B-DNA structural motifs, as well as some conserved structural properties, such as stability, bendability, nucleosome positioning preference and curvature, across a class of organisms. Here, we briefly describe these structural features, the differences observed in various organisms and their possible role in regulation of gene expression.