Energy-momentum conserving algorithm for nonlinear transient analysis within the framework of hybrid elements

This work deals with the formulation and implementation of an energy-momentum conserving algorithm for conducting the nonlinear transient analysis of structures, within the framework of stress-based hybrid elements. Hybrid elements, which are based on a two-field variational formulation, are much less susceptible to locking than conventional displacement-based elements within the static framework. We show that this advantage carries over to the transient case, so that not only are the solutions obtained more accurate, but they are obtained in fewer iterations. We demonstrate the efficacy of the algorithm on a wide range of problems such as ones involving dynamic buckling, complicated three-dimensional motions, et cetera.

Theoretical description of time-resolved pump/probe photoemission in TaS2: a single-band DFT+DMFT(NRG) study within the quasiequilibrium approximation

In this work, we theoretically examine recent pump/probe photoemission experiments on the strongly correlated charge-density-wave insulator TaS2.We describe the general nonequilibrium many-body formulation of time-resolved photoemission in the sudden approximation, and then solve the problem using dynamical mean-field theory with the numerical renormalization group and a bare density of states calculated from density functional theory including the charge-density-wave distortion of the ion cores and spin-orbit coupling. We find a number of interesting results: (i) the bare band structure actually has more dispersion in the perpendicular direction than in the two-dimensional planes; (ii) the DMFT approach can produce upper and lower Hubbard bands that resemble those in the experiment, but the upper bands will overlap in energy with other higher energy bands; (iii) the effect of the finite width of the probe pulse is minimal on the shape of the photoemission spectra; and (iv) the quasiequilibrium approximation does not fully describe the behavior in this system.

The interference environment of radio Noise froh4 lightning

The paper furnishes a review and air ovendepr "f radio noise *om lightning as rr so~irce of interference to analogue and digital Corn?tunicatioiz. The parameters of fhe different fornls < f, noise necessary .for pssessigth e interfering effect of the rloise are described. 4railublr irfjrncroiun thrr tndevstor71zs, thunder-clouds, convecrion cells and lightning are er ieveadn d their liizitatimsp ointed oui. Thew fol101r.s a descripiicn of how the source, popugafiona nd receiver chaacteristidse termine the sfrticture qf a/rnosplro.ic noise as receiwd at a point of observation. The tratrrral unit for this noise i.s the mise burst rtrising from o w complete lightning.flas4. The pmuneters of the nrise birrst as a 11.hole and its structure ctetennine the inrqfflrrence enrirnniient. A hisforic reriel$. qf t2sophericii oke .studies sho1(5 that it i. wrreirt(v of importance oldy in thc ropicarl egions of' the wr ldf i>rs hichf hc neailable data are wry defective. New data are ficnrished. The contribution of atmospheric noise for backgrouzd interference even in remote places ,for r.adicj astronomy at VHF is firrnished. The imporlance of aimcspizeric nctise cceurring ;vporadiea@ in high values fur slzort inier.als at VHF and higher frequencies in the tropics is brought out.

The evolution of loop structures in flux rings within the solar convection zone

Choudhuri and Gilman (1987) considered certain implications of the hypothesis that the magnetic flux within the Sun is generated at the bottom of the convection zone and then rises through it. Taking flux rings symmetric around the rotation axis and using reasonable values of different parameters, they found that the Coriolis force deflects these flux rings into trajectories parallel to the rotation axis so that they emerge at rather high latitudes. This paper looks into the question of whether the action of the Coriolis force is subdued when the initial configuration of the flux ring has non-axisymmetries in the form of loop structures. The results depend dramatically on whether the flux ring with the loops lies completely within the convection zone or whether the lower parts of it are embedded in the stable layers underneath the convection zone. In the first case, the Coriolis force supresses the non-axisymmetric perturbations so that the flux ring tends to remain symmetric and the trajectories are very similar to those of Choudhuri and Gilman (1987). In the second case, however, the lower parts of the flux ring may remain anchored underneath the bottom of the convection zone, but the upper parts of the loops still tend to move parallel to the rotation axis and emerge at high latitudes. Thus the problem of the magnetic flux not being able to come out at the sunspot latitudes still persists after the non-axisymmetries in the flux rings are taken into account.

Dynamics of Barrierless and Activated Chemical Reactions in a Dispersive Medium within the Fractional Diffusion Equation Approach

Barrierless chemical reactions have often been modeled as a Brownian motion on a one-dimensional harmonic potential energy surface with a position-dependent reaction sink or window located near the minimum of the surface. This simple (but highly successful) description leads to a nonexponential survival probability only at small to intermediate times but exponential decay in the long-time limit. However, in several reactive events involving proteins and glasses, the reactions are found to exhibit a strongly nonexponential (power law) decay kinetics even in the long time. In order to address such reactions, here, we introduce a model of barrierless chemical reaction where the motion along the reaction coordinate sustains dispersive diffusion. A complete analytical solution of the model can be obtained only in the frequency domain, but an asymptotic solution is obtained in the limit of long time. In this case, the asymptotic long-time decay of the survival probability is a power law of the Mittag−Leffler functional form. When the barrier height is increased, the decay of the survival probability still remains nonexponential, in contrast to the ordinary Brownian motion case where the rate is given by the Smoluchowski limit of the well-known Kramers' expression. Interestingly, the reaction under dispersive diffusion is shown to exhibit strong dependence on the initial state of the system, thus predicting a strong dependence on the excitation wavelength for photoisomerization reactions in a dispersive medium. The theory also predicts a fractional viscosity dependence of the rate, which is often observed in the reactions occurring in complex environments.

Functional Identification of Regulatory Elements within the Promoter Region of Platelet-Derived Growth Factor 2

Human platelet-derived growth factor (PDGF) is composed of two polypeptide chains, PDGF-1 and PDGF-2,the human homolog of the v-sis oncogene. Deregulation of PDGF-2 expression can confer a growth advantage to cells possessing the cognate receptor and, thus, may contribute to the malignant phenotype. We investigated the regulation of PDGF-2 mRNA expression during megakaryocytic differentiation of K562 cells. Induction by 12-O-tetradecanoylphorbol-13-acetate (TPA) led to a greater than 200-fold increase in PDGF-2 transcript levels in these cells. Induction was dependent on protein synthesis and was not enhanced by cycloheximide exposure.In our initial investigation of the PDGF-2 promoter, a minimal promoter region, which included sequences extending only 42 base pairs upstream of the TATA signal, was found to be as efficient as 4 kilobase pairs upstream of the TATA signal in driving expression of a reporter gene in uninduced K562 cells. We also functionally identified different regulatory sequence elements of the PDGF-2 promoter in TPA-induced K562 cells. One region acted as a transcriptional silencer, while another region was necessary for maximal activity of the promoter in megakaryoblasts. This region was shown to bind nuclear factors and was the target for trans-activation in normal and tumor cells. In one tumor cell line, which expressed high PDGF-2 mRNA levels, the presence of the positive regulatory region resulted in a 30-fold increase in promoter activity. However, the ability of the minimal PDGF-2 promoter to drive reporter gene expression in uninduced K562 cells and normal fibroblasts, which contained no detectable PDGF-2 transcripts, implies the existence of other negative control mechanisms beyond the regulation of promoter activity.

An EXAFS investigation of the Zn environment in K2ZnCl4 during solid-to-solid phase transformations

Extended X-ray absorption fine structure (EXAFS) spectroscopy is applied to an investigation of the structural environment around Zn in polycrystalline K2ZnCi4 over the temperature range associated with its solid-to-solid phase transformations at 127 degrees C and 282 degrees C. The results show a reversible increase in thermal disorder and in the tetrahedral distortion of the ZnCl42- anion upon transformation into the incommensurate phase.

Transient electric field distribution within the working volume of an NEMP simulator

Nuclear electro-magnetic pulse (NEMP) simulators which are used in the simulation of transient electromagnetic fields due to a high altitude nuclear detonation are generally excited with a double exponential high voltage pulse. This results in a current distribution on the wires of the simulator and hence a transient electric field in the working volume of the simulator where the test object is kept. It is found that for the simulator under study, the current distribution is non-uniform and so is the field distribution along the width of the simulator in the working volume. To make the current distribution uniform, several methods have been suggested and the results of these methods are analyzed and suitable conclusions are arrived at from those results.

Down-to-earth temperatures: The mechanics of the thermal environment

This lecture describes some recent attempts at unravelling the mechanics of the temperature distribution near ground, especially during calm, clear nights. In particular, a resolution is offered of the so-called Ramdas paradox, connected with observations of a temperature minimum some decimetres above bare soil on calm clear nights, in apparent defiance of the Rayleigh criterion for instability due to thermal convection. The dynamics of the associated temperature distribution is governed by radiative and convective transport and by thermal conduction, and is characterised by two time constants, involving respectively quick radiative adjustments and slow diffusive relaxation. The theory underlying the work described here suggests that surface parameters like ground emissivity and soil thermal conductivity can exert appreciable influence on the development of nocturnal inversions.

Role of water contamination within the GC column of a GasBench II peripheral on the reproducibility of O-18/O-16 ratios in water samples

The GasBench II peripheral along with MAT 253 combination provides a more sensitive platform for the determination of water isotope ratios. Here, we examined the role of adsorbed moisture within the gas chromatography (GC) column of the GasBench II on measurement uncertainties. The uncertainty in O-18/O-16 ratio measurements is determined by several factors, including the presence of water in the GC. The contamination of GC with water originating from samples as water vapour over a longer timeframe is a critical factor in determining the reproducibility of O-18/O-16 ratios in water samples. The shift in isotope ratios observed in the experiment under dry and wet conditions correlates strongly with the retention time of analyte CO2, indicating the effect of accumulated moisture. Two possible methods to circumvent or minimise the effect of adsorbed water on isotope ratios are presented here. The proposed methodology includes either the regular baking of the GC column at a higher temperature (120 degrees C) after analysis of a batch of 32 sample entries or conducting the experiment at a low GC column temperature (22.5 degrees C). The effects of water contamination on long-term reproducibility of reference water, with and without baking protocol, have been described.

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

Fine-tuning solid-state luminescence in NPIs (1,8-naphthalimides): impact of the molecular environment and cumulative interactions

An investigation of a series of seven angular ``V'' shaped NPIs (1-7) is presented. The effect of substitution of these structurally similar NPIs on their photophysical properties in the solution-state and the solid-state is presented and discussed in light of experimental and computational findings. Compounds 1-7 show negligible to intensely strong emission yields in their solid-state depending on the nature of substituents appended to the oxoaryl moiety. The solution and solid-state properties of the compounds can be directly correlated with their structural rigidity, nature of substituents and intermolecular interactions. The versatile solid-state structures of the NPI siblings are deeply affected by the pendant substituents. All of the NPIs (1-7) show antiparallel dimeric pi-pi stacking interactions in their solid-state which can further extend in a parallel, alternate, orthogonal or lateral fashion depending on the steric and electronic nature of the C-4' substituents. Structural investigations including Hirshfeld surface analysis methods reveal that where strongly interacting systems show weak to moderate emission in their condensed states, weakly interacting systems show strong emission yields under the same conditions. The nature of packing and extended structures also affects the emission colors of the NPIs in their solid-states. Furthermore, DFT computational studies were utilized to understand the molecular and cumulative electronic behaviors of the NPIs. The comprehensive studies provide insight into the condensed-state luminescence of aggregationprone small molecules like NPIs and help to correlate the structure-property relationships.

Sequence and conformational preferences at termini of alpha-helices in membrane proteins: Role of the helix environment

-helices are amongst the most common secondary structural elements seen in membrane proteins and are packed in the form of helix bundles. These -helices encounter varying external environments (hydrophobic, hydrophilic) that may influence the sequence preferences at their N and C-termini. The role of the external environment in stabilization of the helix termini in membrane proteins is still unknown. Here we analyze -helices in a high-resolution dataset of integral -helical membrane proteins and establish that their sequence and conformational preferences differ from those in globular proteins. We specifically examine these preferences at the N and C-termini in helices initiating/terminating inside the membrane core as well as in linkers connecting these transmembrane helices. We find that the sequence preferences and structural motifs at capping (Ncap and Ccap) and near-helical (N' and C') positions are influenced by a combination of features including the membrane environment and the innate helix initiation and termination property of residues forming structural motifs. We also find that a large number of helix termini which do not form any particular capping motif are stabilized by formation of hydrogen bonds and hydrophobic interactions contributed from the neighboring helices in the membrane protein. We further validate the sequence preferences obtained from our analysis with data from an ultradeep sequencing study that identifies evolutionarily conserved amino acids in the rat neurotensin receptor. The results from our analysis provide insights for the secondary structure prediction, modeling and design of membrane proteins. Proteins 2014; 82:3420-3436. (c) 2014 Wiley Periodicals, Inc.

Evidence for N-7 guanine methyl transferase activity encoded within the modular domain of RNA-dependent RNA polymerase L of a Morbillivirus

Post-transcriptional modification of viral mRNA is essential for the translation of viral proteins by cellular translation machinery. Due to the cytoplasmic replication of Paramyxoviruses, the viral-encoded RNA-dependent RNA polymerase (RdRP) is thought to possess all activities required for mRNA capping and methylation. In the present work, using partially purified recombinant RNA polymerase complex of rinderpest virus expressed in insect cells, we demonstrate the in vitro methylation of capped mRNA. Further, we show that a recombinant C-terminal fragment (1717-2183 aa) of L protein is capable of methylating capped mRNA, suggesting that the various post-transcriptional activities of the L protein are located in independently folding domains.