Insights into the Fold Organization of TIM Barrel from Interaction Energy Based Structure Networks

There are many well-known examples of proteins with low sequence similarity, adopting the same structural fold. This aspect of sequence-structure relationship has been extensively studied both experimentally and theoretically, however with limited success. Most of the studies consider remote homology or ``sequence conservation'' as the basis for their understanding. Recently ``interaction energy'' based network formalism (Protein Energy Networks (PENs)) was developed to understand the determinants of protein structures. In this paper we have used these PENs to investigate the common non-covalent interactions and their collective features which stabilize the TIM barrel fold. We have also developed a method of aligning PENs in order to understand the spatial conservation of interactions in the fold. We have identified key common interactions responsible for the conservation of the TIM fold, despite high sequence dissimilarity. For instance, the central beta barrel of the TIM fold is stabilized by long-range high energy electrostatic interactions and low-energy contiguous vdW interactions in certain families. The other interfaces like the helix-sheet or the helix-helix seem to be devoid of any high energy conserved interactions. Conserved interactions in the loop regions around the catalytic site of the TIM fold have also been identified, pointing out their significance in both structural and functional evolution. Based on these investigations, we have developed a novel network based phylogenetic analysis for remote homologues, which can perform better than sequence based phylogeny. Such an analysis is more meaningful from both structural and functional evolutionary perspective. We believe that the information obtained through the ``interaction conservation'' viewpoint and the subsequently developed method of structure network alignment, can shed new light in the fields of fold organization and de novo computational protein design.

Quantum capacitance in bilayer graphene nanoribbon

We address a physically based analytical model of quantum capacitance (C-Q) in a bilayer graphene nanoribbon (BGN) under the application of an external longitudinal static bias. We demonstrate that as the gap (Delta) about the Dirac point increases, a phenomenological population inversion of the carriers in the two sets of subbands occurs. This results in a periodic and composite oscillatory behavior in the C-Q with the channel potential, which also decreases with increase in Delta. We also study the quantum size effects on the C-Q, which signatures heavy spatial oscillations due to the occurrence of van Hove singularities in the total density-of-states function of both the sets of subbands. All the mathematical results as derived in this paper converge to the corresponding well-known solution of graphene under certain limiting conditions and this compatibility is an indirect test of our theoretical formalism. (C) 2012 Elsevier By. All rights reserved.

Constraining form factors with the method of unitarity bounds

The availability of a reliable bound on an integral involving the square of the modulus of a form factor on the unitarity cut allows one to constrain the form factor at points inside the analyticity domain and its shape parameters, and also to isolate domains on the real axis and in the complex energy plane where zeros are excluded. In this lecture note, we review the mathematical techniques of this formalism in its standard form, known as the method of unitarity bounds, and recent developments which allow us to include information on the phase and modulus along a part of the unitarity cut. We also provide a brief summary of some results that we have obtained in the recent past, which demonstrate the usefulness of the method for precision predictions on the form factors.

Flavored co-annihilations

Neutralino dark matter in supersymmetric models is revisited in the presence of flavor violation in the soft supersymmetry breaking sector. We focus on flavor violation the sleptonic sector and study the implications for the co-annihilation regions. Flavor is introduced by a single (mu) over tilde (R) - (T) over tilde (R) insertion in the slepton mass matrix. Limits on insertion from BR(tau -> mu + gamma) are weak in some regions of the parameter space where happen within the amplitudes. We look for overlaps in parameter space where the co-annihilation condition as well as the cancellations within the amplitudes occur. mSUGRA, such overlap regions are not existent, whereas they are present in models non-universal Higgs boundary conditions (NUHM). The effect of flavor violation is fold: (a) it shifts the co-annihilation regions towards lighter neutralino masses (b) co-annihilation cross sections would be modified with the inclusion of flavor violating which can contribute significantly. Even if flavor violation is within the presently limits, this is sufficient to modify the thermally averaged cross-sections by about 15)% in mSUGRA and (20{30)% in NUHM, depending on the parameter space. In overlap regions, the flavor violating cross sections become comparable and in some even dominant to the flavor conserving ones. A comparative study of the channels is for mSUGRA and NUHM cases.

Postcards from oases in the desert: phenomenology of SUSY with intermediate scales

The presence of new matter fields charged under the Standard Model gauge group at intermediate scales below the Grand Unification scale modifies the renormalization group evolution of the gauge couplings. This can in turn significantly change the running of the Minimal Supersymmetric Standard Model parameters, in particular the gaugino and the scalar masses. In the absence of new large Yukawa couplings we can parameterise all the intermediate scale models in terms of only two parameters controlling the size of the unified gauge coupling. As a consequence of the modified running, the low energy spectrum can be strongly affected with interesting phenomenological consequences. In particular, we show that scalar over gaugino mass ratios tend to increase and the regions of the parameter space with neutralino Dark Matter compatible with cosmological observations get drastically modified. Moreover, we discuss some observables that can be used to test the intermediate scale physics at the LHC in a wide class of models.

Interaction Signatures Stabilizing the NAD(P)-Binding Rossmann Fold: A Structure Network Approach

The fidelity of the folding pathways being encoded in the amino acid sequence is met with challenge in instances where proteins with no sequence homology, performing different functions and no apparent evolutionary linkage, adopt a similar fold. The problem stated otherwise is that a limited fold space is available to a repertoire of diverse sequences. The key question is what factors lead to the formation of a fold from diverse sequences. Here, with the NAD(P)-binding Rossmann fold domains as a case study and using the concepts of network theory, we have unveiled the consensus structural features that drive the formation of this fold. We have proposed a graph theoretic formalism to capture the structural details in terms of the conserved atomic interactions in global milieu, and hence extract the essential topological features from diverse sequences. A unified mathematical representation of the different structures together with a judicious concoction of several network parameters enabled us to probe into the structural features driving the adoption of the NAD(P)-binding Rossmann fold. The atomic interactions at key positions seem to be better conserved in proteins, as compared to the residues participating in these interactions. We propose a ``spatial motif'' and several ``fold specific hot spots'' that form the signature structural blueprints of the NAD(P)-binding Rossmann fold domain. Excellent agreement of our data with previous experimental and theoretical studies validates the robustness and validity of the approach. Additionally, comparison of our results with statistical coupling analysis (SCA) provides further support. The methodology proposed here is general and can be applied to similar problems of interest.

Electrical transport characteristics of ZnO-Bi2O3-B2O3 glasses

Optically clear glasses in the ZnO-Bi2O3-B2O3 (ZBBO) system were fabricated via the conventional melt-quenching technique. Dielectric constant and loss measurements carried out on ZBBO glasses unraveled nearly frequency (1 kHz-10 MHz)-independent dielectric characteristics associated with significantly low loss (D = 0.004). However, weak temperature response was found with temperature coefficient of dielectric constant 18 +/- 4 ppm A degrees C-1 in the 35-250 A degrees C temperature range. The conduction and relaxation phenomena were rationalized using universal AC conductivity power law and modulus formalism respectively. The activation energy for relaxation determined using imaginary parts of modulus peaks was 2.54 eV which was close to that of the DC conduction implying the involvement of similar energy barriers in both the processes. Stretched and power exponents were temperature dependent. The relaxation and conduction in these glasses were attributed to the hoping and migration of Bi3+ cations in their own and different local environment.

Implication of a Higgs boson at 125 GeV within the stochastic superspace framework

We revisit the issue of considering stochasticity of Grassmannian coordinates in N = 1 superspace, which was analyzed previously by Kobakhidze et al. In this stochastic supersymmetry (SUSY) framework, the soft SUSY breaking terms of the minimal supersymmetric Standard Model (MSSM) such as the bilinear Higgs mixing, trilinear coupling, as well as the gaugino mass parameters are all proportional to a single mass parameter xi, a measure of supersymmetry breaking arising out of stochasticity. While a nonvanishing trilinear coupling at the high scale is a natural outcome of the framework, a favorable signature for obtaining the lighter Higgs boson mass m(h) at 125 GeV, the model produces tachyonic sleptons or staus turning to be too light. The previous analyses took Lambda, the scale at which input parameters are given, to be larger than the gauge coupling unification scale M-G in order to generate acceptable scalar masses radiatively at the electroweak scale. Still, this was inadequate for obtaining m(h) at 125 GeV. We find that Higgs at 125 GeV is highly achievable, provided we are ready to accommodate a nonvanishing scalar mass soft SUSY breaking term similar to what is done in minimal anomaly mediated SUSY breaking (AMSB) in contrast to a pure AMSB setup. Thus, the model can easily accommodate Higgs data, LHC limits of squark masses, WMAP data for dark matter relic density, flavor physics constraints, and XENON100 data. In contrast to the previous analyses, we consider Lambda = M-G, thus avoiding any ambiguities of a post-grand unified theory physics. The idea of stochastic superspace can easily be generalized to various scenarios beyond the MSSM. DOI: 10.1103/PhysRevD.87.035022

Proposal for generalised supersymmetry Les Houches Accord for see-saw models and PDG numbering scheme

The SUSY Les Houches Accord (SLHA) 2 extended the first SLHA to include various generalisations of the Minimal Supersymmetric Standard Model (MSSM) as well as its simplest next-to-minimal version. Here, we propose further extensions to it, to include the most general and well-established see-saw descriptions (types I/II/III, inverse, and linear) in both an effective and a simple gauged extension of the MSSM framework. In addition, we generalise the PDG numbering scheme to reflect the properties of the particles. (c) 2012 Elsevier B.V. All rights reserved.

Renormalization of noncommutative quantum field theories

We report on a comprehensive analysis of the renormalization of noncommutative phi(4) scalar field theories on the Groenewold-Moyal plane. These scalar field theories are twisted Poincare invariant. Our main results are that these scalar field theories are renormalizable, free of UV/IR mixing, possess the same fixed points and beta-functions for the couplings as their commutative counterparts. We also argue that similar results hold true for any generic noncommutative field theory with polynomial interactions and involving only pure matter fields. A secondary aim of this work is to provide a comprehensive review of different approaches for the computation of the noncommutative S-matrix: noncommutative interaction picture and noncommutative Lehmann-Symanzik-Zimmermann formalism. DOI: 10.1103/PhysRevD.87.064014

Supersymmetry of classical solutions in Chern-Simons higher spin supergravity

We construct and study classical solutions in Chern-Simons supergravity based on the superalgebra sl(N vertical bar N = 1). The algebra for the N = 3 case is written down explicitly using the fact that it arises as the global part of the super conformal W-3 superalgebra. For this case we construct new classical solutions and study their supersymmetry. Using the algebra we write down the Killing spinor equations and explicitly construct the Killing spinor for conical defects and black holes in this theory. We show that for the general sl(N|N - 1) theory the condition for the periodicity of the Killing spinor can be written in terms of the products of the odd roots of the super algebra and the eigenvalues of the holonomy matrix of the background. Thus the supersymmetry of a given background can be stated in terms of gauge invariant and well defined physical observables of the Chern-Simons theory. We then show that for N >= 4, the sl(N|N - 1) theory admits smooth supersymmetric conical defects.

k.p based closed form energy band gap and transport electron effective mass model for 100] and 110] relaxed and strained Silicon nanowire

In this paper, we address a physics based closed form model for the energy band gap (E-g) and the transport electron effective mass in relaxed and strained 100] and 110] oriented rectangular Silicon Nanowire (SiNW). Our proposed analytical model along 100] and 110] directions are based on the k.p formalism of the conduction band energy dispersion relation through an appropriate rotation of the Hamiltonian of the electrons in the bulk crystal along 001] direction followed by the inclusion of a 4 x 4 Luttinger Hamiltonian for the description of the valance band structure. Using this, we demonstrate the variation in Eg and the transport electron effective mass as function of the cross-sectional dimensions in a relaxed 100] and 110] oriented SiNW. The behaviour of these two parameters in 100] oriented SiNW has further been studied with the inclusion of a uniaxial strain along the transport direction and a biaxial strain, which is assumed to be decomposed from a hydrostatic deformation along 001] with the former one. In addition, the energy band gap and the effective mass of a strained 110] oriented SiNW has also been formulated. Using this, we compare our analytical model with that of the extracted data using the nearest neighbour empirical tight binding sp(3)d(5)s* method based simulations and has been found to agree well over a wide range of device dimensions and applied strain. (C) 2012 Elsevier Ltd. All rights reserved.

Bilateral smoothing of gradient vector field and application to image segmentation

Medical image segmentation finds application in computer-aided diagnosis, computer-guided surgery, measuring tissue volumes, locating tumors, and pathologies. One approach to segmentation is to use active contours or snakes. Active contours start from an initialization (often manually specified) and are guided by image-dependent forces to the object boundary. Snakes may also be guided by gradient vector fields associated with an image. The first main result in this direction is that of Xu and Prince, who proposed the notion of gradient vector flow (GVF), which is computed iteratively. We propose a new formalism to compute the vector flow based on the notion of bilateral filtering of the gradient field associated with the edge map - we refer to it as the bilateral vector flow (BVF). The range kernel definition that we employ is different from the one employed in the standard Gaussian bilateral filter. The advantage of the BVF formalism is that smooth gradient vector flow fields with enhanced edge information can be computed noniteratively. The quality of image segmentation turned out to be on par with that obtained using the GVF and in some cases better than the GVF.

Performance limits of transition metal dichalcogenide (MX2) nanotube surround gate ballistic field effect transistors

We theoretically analyze the performance of transition metal dichalcogenide (MX2) single wall nanotube (SWNT) surround gate MOSFET, in the 10 nm technology node. We consider semiconducting armchair (n, n) SWNT of MoS2, MoSe2, WS2, and WSe2 for our study. The material properties of the nanotubes are evaluated from the density functional theory, and the ballistic device characteristics are obtained by self-consistently solving the Poisson-Schrodinger equation under the non-equilibrium Green's function formalism. Simulated ON currents are in the range of 61-76 mu A for 4.5 nm diameter MX2 tubes, with peak transconductance similar to 175-218 mu S and ON/OFF ratio similar to 0.6 x 10(5)-0.8 x 10(5). The subthreshold slope is similar to 62.22 mV/decade and a nominal drain induced barrier lowering of similar to 12-15 mV/V is observed for the devices. The tungsten dichalcogenide nanotubes offer superior device output characteristics compared to the molybdenum dichalcogenide nanotubes, with WSe2 showing the best performance. Studying SWNT diameters of 2.5-5 nm, it is found that increase in diameter provides smaller carrier effective mass and 4%-6% higher ON currents. Using mean free path calculation to project the quasi-ballistic currents, 62%-75% reduction from ballistic values in drain current in long channel lengths of 100, 200 nm is observed.

Warped alternatives to Froggatt-Nielsen models

We consider the Randall-Sundrum (RS) setup to be a theory of flavor, as an alternative to Froggatt-Nielsen models instead of as a solution to the hierarchy problem. The RS framework is modified by taking the low-energy brane to be at the grand unified theory (GUT) scale. This also alleviates constraints from flavor physics. Fermion masses and mixing angles are fit at the GUT scale. The ranges of the bulk mass parameters are determined using a chi(2) fit taking into consideration the variation in O(1) parameters. In the hadronic sector, the heavy top quark requires large bulk mass parameters localizing the right-handed top quark close to the IR brane. Two cases of neutrino masses are considered: (a) Planck scale lepton number violation and (b) Dirac neutrino masses. Contrary to the case of weak scale RS models, both these cases give reasonable fits to the data, with the Planck scale lepton number violation fitting slightly better compared to the Dirac case. In the supersymmetric version, the fits are not significantly different except for the variation in tan beta. If the Higgs superfields and the supersymmetry breaking spurion are localized on the same brane, then the structure of the sfermion masses are determined by the profiles of the zero modes of the hypermultiplets in the bulk. Trilinear terms have the same structure as the Yukawa matrices. The resultant squark spectrum is around similar to 2-3 TeV required by the light Higgs mass to be around 125 GeV and to satisfy the flavor violating constraints.