Dehydrophenylalanine zippers: strong helix-helix clamping through a network of weak interactions

A decapeptide Boc-L-Ala-(DeltaPhe)(4)-L-Ala-(DeltaPhe)(3)-Gly-OMe (Peptide I) was synthesized to study the preferred screw sense of consecutive alpha,beta-dehydrophenylalanine (DeltaPhe) residues. Crystallographic and CD studies suggest that, despite the presence of two L-Ala residues in the sequence, the decapeptide does not have a preferred screw sense. The peptide crystallizes with two conformers per asymmetric unit, one of them a slightly distorted right-handed 3(10)-helix (X) and the other a left-handed 3(10)-helix (Y) with X and Y being antiparallel to each other. An unanticipated and interesting observation is that in the solid state, the two shape-complement molecules self-assemble and interact with an extensive network of C-H...O hydrogen bonds and pi-pi interactions, directed laterally to the helix axis with amazing regularity. Here, we present an atomic resolution picture of the weak interaction mediated mutual recognition of two secondary structural elements and its possible implication in understanding the specific folding of the hydrophobic core of globular proteins and exploitation in future work on de novo design.

Strong ground motion at Bhuj city during the Kutch earthquake

In the absence of near field strong motion records, the level of ground motion during the devastating 26 January 2001 earthquake has to be found by indirect means. For the city of Bhuj, three broad band velocity time histories have been recorded by India Meteorological Department. In this paper these data are processed to obtain an estimate of strong ground motion at Bhuj. It is estimated that the peak ground acceleration at Bhuj was of the order of 0.38 g. Ground motion in the surrounding region is indirectly found using available spectral response recorder (SRR) data. These instrument-based results are compared with analytical results obtained from a half-space regional model.

Mitigation of Alkali Induced Heave in Rectorite Soil with Fly Ash

Mechanisms that control the volume changes behavior of foundation soils are well understood. The changes that occur in the behavior of soil due to migration of pollutants are not well understood. The extent of changes that occur in the presence of small concentration of contaminants can be predicted based on changes in the thickness of double layer and associated fabric changes. Interactions that occur with strong contaminants depends on the type of soil, type and concentration of contamination and duration of interaction etc It has been shown that different concentrations (1N and 4N) of sodium hydroxide solution causes abnormal changes on volume change behaviour of soil due to mineralogical changes. An attempt is made in this paper to stabilize contaminated soil using fly ash, after establishing its stability in alkali solutions. It was found that the effectiveness of fly ash to control the alkali induced heave increases with fly ash content incorporated into the soil. X-ray diffraction studies reveal that the mineralogical changes that occur in soil due to alkali interaction are inhibited by the presence of fly ash.

Impact of Sulphate counter ion in the migration of sodium ion through soils

Laboratory advection-diffusion tests are performed on two regional soils-Brown Earth and Red Earth-in order to assess their capacity to control contaminant migration with synthetic contaminant solution of sodium sulphate with sodium concentration of 1000 mg/L. The test was designed to study the transport/attenuation behaviour of sodium in the presence of sulphate. Effective diffusion coefficient (De) that takes into consideration of attenuation processes is used. Cation exchange capacity is an important factor for the attenuation of cationic species. Monovalent sodium ion cannot usually replace other cations and the retention of sodium ion is very less. This is particularly true when chloride is anion is solution. However, sulphate is likely to play a role in the attenuation of sodium. Cation exchange capacity and type of exchangeable ions of soils are likely to play an important role. The effect of sulphate ions on the effective diffusion coefficient of sodium, in two different types of soils, of different cation exchange capacity has been studied. The effective diffusion coefficients of sodium ion for both the soils were calculated using Ogata Bank’s equation. It was shown that effective diffusion coefficient of sodium in the presence of sulphate is lower for Brown Earth than for Red Earth due to exchange of sodium with calcium ions from the exchangeable complex of clay. The soil with the higher cation exchange retained more sodium. Consequently, the breakthrough times and the number of pore volumes of sodium ion increase with the cation exchange capacity of soil.

Strong electron correlation of Re 5d electrons in Ca2FeReO6

We have investigated the electronic structure of a double perovskite Ca2FeReO6 using photoemission spectroscopy and LDA+U bandstructure calculations. Small spectral weight at the Fermi level observed above the metal–insulator transition temperature, gradually disappears with decreasing T, forming a small (≤50 meV) energy gap. To reproduce this small energy gap, we require a very large effective U (Ueff) for Re (4 eV) in addition to Ueff of 4 eV for Fe. From simple calculations in terms of the ionic radii, we demonstrate that the Fe–Re bandwidth is smaller than that of Fe–Mo in Ca2FeMoO6, which should yield a strong electron correlation in the Re 5d bands.

On the two dimensional effective electron mass in quantum wells, inversion layers and NIPI superlattices of Kane type semiconductors in the presence of strong light waves: Simplified theory and relative comparison

An attempt is made to study the two dimensional (2D) effective electron mass (EEM) in quantum wells (Qws), inversion layers (ILs) and NIPI superlattices of Kane type semiconductors in the presence of strong external photoexcitation on the basis of a newly formulated electron dispersion laws within the framework of k.p. formalism. It has been found, taking InAs and InSb as examples, that the EEM in Qws, ILs and superlattices increases with increasing concentration, light intensity and wavelength of the incident light waves, respectively and the numerical magnitudes in each case is band structure dependent. The EEM in ILs is quantum number dependent exhibiting quantum jumps for specified values of the surface electric field and in NIPI superlattices; the same is the function of Fermi energy and the subband index characterizing such 2D structures. The appearance of the humps of the respective curves is due to the redistribution of the electrons among the quantized energy levels when the quantum numbers corresponding to the highest occupied level changes from one fixed value to the others. Although the EEM varies in various manners with all the variables as evident from all the curves, the rates of variations totally depend on the specific dispersion relation of the particular 2D structure. Under certain limiting conditions, all the results as derived in this paper get transformed into well known formulas of the EEM and the electron statistics in the absence of external photo-excitation and thus confirming the compatibility test. The results of this paper find three applications in the field of microstructures. (C) 2011 Elsevier Ltd. All rights reserved.

Bose-Hubbard model in a strong effective magnetic field: Emergence of a chiral Mott insulator ground state

Motivated by experiments on Josephson junction arrays, and cold atoms in an optical lattice in a synthetic magnetic field, we study the ``fully frustrated'' Bose-Hubbard model with half a magnetic flux quantum per plaquette. We obtain the phase diagram of this model on a two-leg ladder at integer filling via the density matrix renormalization group approach, complemented by Monte Carlo simulations on an effective classical XY model. The ground state at intermediate correlations is consistently shown to be a chiral Mott insulator (CMI) with a gap to all excitations and staggered loop currents which spontaneously break time-reversal symmetry. We characterize the CMI state as a vortex supersolid or an indirect exciton condensate, and discuss various experimental implications.

Incremental Cycle Detection, Topological Ordering, and Strong Component Maintenance

We present two online algorithms for maintaining a topological order of a directed n-vertex acyclic graph as arcs are added, and detecting a cycle when one is created. Our first algorithm handles m arc additions in O(m(3/2)) time. For sparse graphs (m/n = O(1)), this bound improves the best previous bound by a logarithmic factor, and is tight to within a constant factor among algorithms satisfying a natural locality property. Our second algorithm handles an arbitrary sequence of arc additions in O(n(5/2)) time. For sufficiently dense graphs, this bound improves the best previous bound by a polynomial factor. Our bound may be far from tight: we show that the algorithm can take Omega(n(2)2 root(2lgn)) time by relating its performance to a generalization of the k-levels problem of combinatorial geometry. A completely different algorithm running in Theta (n(2) log n) time was given recently by Bender, Fineman, and Gilbert. We extend both of our algorithms to the maintenance of strong components, without affecting the asymptotic time bounds.

Nanoindentation as a probe for mechanically-induced molecular migration in layered organic donor-acceptor complexes

Nanoindentation and scratch experiments on 1:1 donor-acceptor complexes, 1 and 2, of 1,2,4,5-tetracyanobenzene with pyrene and phenanthrene, respectively, reveal long-range molecular layer gliding and large interaction anisotropy. Due to the layered arrangements in these crystals, these experiments that apply stress in particular directions result in the breaking of interlayer interactions, thus allowing molecular sheets to glide over one another with ease. Complex 1 has a layered crystal packing wherein the layers are 68° skew under the (002) face and the interlayer space is stabilized by van der Waals interactions. Upon indenting this surface with a Berkovich tip, pile-up of material was observed on just one side of the indenter due to the close angular alignment of the layers with the half angle of the indenter tip (65.35°). The interfacial differences in the elastic modulus (21 ) and hardness (16 ) demonstrate the anisotropic nature of crystal packing. In 2, the molecular stacks are arranged in a staggered manner; there is no layer arrangement, and the interlayer stabilization involves C-H�N hydrogen bonds and ��� interactions. This results in a higher modulus (20 ) for (020) as compared to (001), although the anisotropy in hardness is minimal (4 ). The anisotropy within a face was analyzed using AFM image scans and the coefficient of friction of four orthogonal nanoscratches on the cleavage planes of 1 and 2. A higher friction coefficient was obtained for 2 as compared to 1 even in the cleavage direction due to the presence of hydrogen bonds in the interlayer region making the tip movement more hindered. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantum corrections to screening at strong coupling

We compute a certain class of corrections to (specific) screening lengths in strongly coupled non-abelian plasmas using the AdS/CFT correspondence. In this holographic framework, these corrections arise from various higher curvature interactions modifying the leading Einstein gravity action. The changes in the screening lengths are perturbative in inverse powers of the `t Hooft coupling or of the number of colors, as can be made precise in the context where the dual gauge theory is superconformal. We also compare the results of these holographic calculations to lattice results for the analogous screening lengths in QCD. In particular, we apply these results within the program of making quantitative comparisons between the strongly coupled quark-gluon plasma and holographic descriptions of conformal field theory. (c) 2012 Elsevier B.V. All rights reserved.

Regulation of S100A2 expression by TGF-beta-induced MEK/ERK signalling and its role in cell migration/invasion

S100A2, an EF hand calcium-binding protein, is a potential biomarker in several cancers and is also a TGF-beta (transforming growth factor-beta)-regulated gene in melanoma and lung cancer cells. However, the mechanism of S100A2 regulation by TGF-beta and its significance in cancer progression remains largely unknown. In the present study we report the mechanism of S100A2 regulation by TGF-beta and its possible role in TGF-beta-mediated tumour promotion. Characterization of the S100A2 promoter revealed an AP-1 (activator protein-1) element at positions -1161 to -1151 as being the most critical factor for the TGF-beta 1 response. Chromatin immunoprecipitation and electrophoretic mobility-shift assays confirmed the functional binding of the AP-1 complex, predominantly JunB, to the S100A2 promoter in response to TGF-beta 1 in HaCaT keratinocytes. JunB overexpression markedly stimulated the S100A2 promoter which was blocked by the dominant-negative JunB and MEK1 MAPK (mitogen-activated protein kinase)/ERK (extracellular-signal-regulated kinase) kinase 1] inhibitor, PD98059. Intriguingly, despite the presence of a putative SMAD-binding element, S100A2 regulation by TGF-beta 1 was found to be SMAD3 independent. Interestingly, p53 protein and TGF-beta 1 show synergistic regulation of the S100A2 promoter. Finally, knockdown of S100A2 expression compromised TGF-beta 1-induced cell migration and invasion of Hep3B cells. Together our findings highlight an important link between the TGF-beta 1-induced MAPK and p53 signalling pathways in the regulation of S100A2 expression and pro-tumorigenic actions.

Capacity region of K-user discrete memoryless interference channels with a mixed strong-very strong interference

The capacity region of the 3-user Gaussian Interference Channel (GIC) with mixed strong-very strong interference was established in [1]. The mixed strong-very strong interference conditions considered in [1] correspond to the case where, at each receiver, one of the interfering signals is strong and the other is very strong. In this paper, we derive the capacity region of K-user (K ≥ 3) Discrete Memoryless Interference Channels (DMICs) with a mixed strong-very strong interference. This corresponds to the case where, at each receiver one of the interfering signals is strong and the other (K - 2) interfering signals are very strong. This includes, as a special case, the 3-user DMIC with mixed strong-very strong interference. The proof is specialized to the 3-user GIC case and hence an alternative derivation for the capacity region of the 3-user GIC with mixed strong-very strong interference is provided.

Hypernuclear matter in strong magnetic field

Compact stars with strong magnetic fields (magnetars) have been observationally determined to have surface magnetic fields of order of 10(14)-10(15) G, the implied internal field strength being several orders larger. We study the equation of state and composition of dense hypernuclear matter in strong magnetic fields in a range expected in the interiors of magnetars. Within the non-linear Boguta-Bodmer-Walecka model we find that the magnetic field has sizable influence on the properties of matter for central magnetic field B >= 10(17) G, in particular the matter properties become anisotropic. Moreover, for the central fields B >= 10(18) G, the magnetized hypernuclear matter shows instability, which is signalled by the negative sign of the derivative of the pressure parallel to the field with respect to the density, and leads to vanishing parallel pressure at the critical value B-cr congruent to 10(19) G. This limits the range of admissible homogeneously distributed fields in magnetars to fields below the critical value B-cr. (c) 2012 Elsevier B.V. All rights reserved.

Evidence for the role of Mycobacteriumtuberculosis RecG helicase in DNA repair and recombination

In order to survive and replicate in a variety of stressful conditions during its life cycle, Mycobacteriumtuberculosis must possess mechanisms to safeguard the integrity of the genome. Although DNA repair and recombination related genes are thought to play key roles in the repair of damaged DNA in all organisms, so far only a few of them have been functionally characterized in the tubercle bacillus. In this study, we show that M.tuberculosis RecG (MtRecG) expression was induced in response to different genotoxic agents. Strikingly, expression of MtRecG in Escherichiacoli recG mutant strain provided protection against mitomycin C, methyl methane sulfonate and UV induced cell death. Purified MtRecG exhibited higher binding affinity for the Holliday junction (HJ) compared with a number of canonical recombinational DNA repair intermediates. Notably, although MtRecG binds at the core of the mobile and immobile HJs, and with higher binding affinity for the immobile HJ, branch migration was evident only in the case of the mobile HJ. Furthermore, immobile HJs stimulate MtRecG ATPase activity less efficiently than mobile HJs. In addition to HJ substrates, MtRecG exhibited binding affinity for a variety of branched DNA structures including three-way junctions, replication forks, flap structures, forked duplex and a D-loop structure, but demonstrated strong unwinding activity on replication fork and flap DNA structures. Together, these results support that MtRecG plays an important role in processes related to DNA metabolism under normal as well as stress conditions.