Study of molecular structure and vibrational spectra of poly (beta,-1-malic acid) PMLA] using DFT approach

Poly (beta-L-malic acid) (PMLA) is a biodegradable polymer and it has various important applications in the biomedical field. In the present work the structural and spectral characteristics of PMLA have been studied by methods of infrared. Raman spectroscopy and quantum chemistry. Electrostatic potential surface, optimized geometry, harmonic vibrational frequencies, infrared intensities and activities of Raman scattering were calculated by density functional theory (DFT) using oligomeric approach employing B3LYP with complete relaxation in the potential energy surface using 6-311++G (d, p) basis set. Based on results, we have discussed the correlation between the vibrational modes and the structure of the PMLA. A complete analysis of the experimental infrared and Raman spectra has been reported on the basis of wavenumber of the vibrational bands and potential energy distribution. The calculated HOMO and LUMO energies shows that charge transfer occur within the molecule. The calculated infrared and the Raman spectra of the polymer based on DFT calculations show reasonable agreement with the experimental results. (c) 2012 Elsevier Ltd. All rights reserved.

Extent of Structural Asymmetry in Homodimeric Proteins: Prevalence and Relevance

Most homodimeric proteins have symmetric structure. Although symmetry is known to confer structural and functional advantage, asymmetric organization is also observed. Using a non-redundant dataset of 223 high-resolution crystal structures of biologically relevant homodimers, we address questions on the prevalence and significance of asymmetry. We used two measures to quantify global and interface asymmetry, and assess the correlation of several molecular and structural parameters with asymmetry. We have identified rare cases (11/223) of biologically relevant homodimers with pronounced global asymmetry. Asymmetry serves as a means to bring about 2:1 binding between the homodimer and another molecule; it also enables cellular signalling arising from asymmetric macromolecular ligands such as DNA. Analysis of these cases reveals two possible mechanisms by which possible infinite array formation is prevented. In case of homodimers associating via non-topologically equivalent surfaces in their tertiary structures, ligand-dependent mechanisms are used. For stable dimers binding via large surfaces, ligand-dependent structural change regulates polymerisation/depolymerisation; for unstable dimers binding via smaller surfaces that are not evolutionarily well conserved, dimerisation occurs only in the presence of the ligand. In case of homodimers associating via interaction surfaces with parts of the surfaces topologically equivalent in the tertiary structures, steric hindrance serves as the preventive mechanism of infinite array. We also find that homodimers exhibiting grossly symmetric organization rarely exhibit either perfect local symmetry or high local asymmetry. Binding of small ligands at the interface does not cause any significant variation in interface asymmetry. However, identification of biologically relevant interface asymmetry in grossly symmetric homodimers is confounded by the presence of similar small magnitude changes caused due to artefacts of crystallisation. Our study provides new insights regarding accommodation of asymmetry in homodimers.

Local Structural Differences in Homologous Proteins: Specificities in Different SCOP Classes

The constant increase in the number of solved protein structures is of great help in understanding the basic principles behind protein folding and evolution. 3-D structural knowledge is valuable in designing and developing methods for comparison, modelling and prediction of protein structures. These approaches for structure analysis can be directly implicated in studying protein function and for drug design. The backbone of a protein structure favours certain local conformations which include alpha-helices, beta-strands and turns. Libraries of limited number of local conformations (Structural Alphabets) were developed in the past to obtain a useful categorization of backbone conformation. Protein Block (PB) is one such Structural Alphabet that gave a reasonable structure approximation of 0.42 angstrom. In this study, we use PB description of local structures to analyse conformations that are preferred sites for structural variations and insertions, among group of related folds. This knowledge can be utilized in improving tools for structure comparison that work by analysing local structure similarities. Conformational differences between homologous proteins are known to occur often in the regions comprising turns and loops. Interestingly, these differences are found to have specific preferences depending upon the structural classes of proteins. Such class-specific preferences are mainly seen in the all-beta class with changes involving short helical conformations and hairpin turns. A test carried out on a benchmark dataset also indicates that the use of knowledge on the class specific variations can improve the performance of a PB based structure comparison approach. The preference for the indel sites also seem to be confined to a few backbone conformations involving beta-turns and helix C-caps. These are mainly associated with short loops joining the regular secondary structures that mediate a reversal in the chain direction. Rare beta-turns of type I' and II' are also identified as preferred sites for insertions.

Thermoelectricity in graphene: Effects of a gap and magnetic fields

We calculate the thermopower of monolayer graphene in various circumstances. We consider acoustic phonon scattering which might be the operative scattering mechanism in freestanding films and predict that the thermopower will be linear in any induced gap in the system. Further, the thermopower peaks at the same value of chemical potential (tunable by gate voltage) independent of the gap. We show that in the semiclassical approximation, the thermopower in a magnetic field saturates at high field to a value which can be calculated exactly and is independent of the details of the scattering. This effect might be observable experimentally. We also note that a Yukawa scattering potential can be used to fit experimental data for the thermopower for reasonable values of the screening length parameter.

Performance and variability trade-off with gate-to-source/drain overlap length

The impact of gate-to-source/drain overlap length on performance and variability of 65 nm CMOS is presented. The device and circuit variability is investigated as a function of three significant process parameters, namely gate length, gate oxide thickness, and halo dose. The comparison is made with three different values of gate-to-source/drain overlap length namely 5 nm, 0 nm, and -5 nm and at two different leakage currents of 10 nA and 100 nA. The Worst-Case-Analysis approach is used to study the inverter delay fluctuations at the process corners. The drive current of the device for device robustness and stage delay of an inverter for circuit robustness are taken as performance metrics. The design trade-off between performance and variability is demonstrated both at the device level and circuit level. It is shown that larger overlap length leads to better performance, while smaller overlap length results in better variability. Performance trades with variability as overlap length is varied. An optimal value of overlap length of 0 nm is recommended at 65 nm gate length, for a reasonable combination of performance and variability.

A Linear S-N Curve with Load Dependent Variance and Explicit Failure Probability

We reconsider standard uniaxial fatigue test data obtained from handbooks. Many S-N curve fits to such data represent the median life and exclude load-dependent variance in life. Presently available approaches for incorporating probabilistic aspects explicitly within the S-N curves have some shortcomings, which we discuss. We propose a new linear S-N fit with a prespecified failure probability, load-dependent variance, and reasonable behavior at extreme loads. We fit our parameters using maximum likelihood, show the reasonableness of the fit using Q-Q plots, and obtain standard error estimates via Monte Carlo simulations. The proposed fitting method may be used for obtaining S-N curves from the same data as already available, with the same mathematical form, but in cases in which the failure probability is smaller, say, 10 % instead of 50 %, and in which the fitted line is not parallel to the 50 % (median) line.

Parameter estimation of a two-horizon soil profile by combining crop canopy and surface soil moisture observations using GLUE

Estimation of soil parameters by inverse modeling using observations on either surface soil moisture or crop variables has been successfully attempted in many studies, but difficulties to estimate root zone properties arise when heterogeneous layered soils are considered. The objective of this study was to explore the potential of combining observations on surface soil moisture and crop variables - leaf area index (LAI) and above-ground biomass for estimating soil parameters (water holding capacity and soil depth) in a two-layered soil system using inversion of the crop model STICS. This was performed using GLUE method on a synthetic data set on varying soil types and on a data set from a field experiment carried out in two maize plots in South India. The main results were (i) combination of surface soil moisture and above-ground biomass provided consistently good estimates with small uncertainity of soil properties for the two soil layers, for a wide range of soil paramater values, both in the synthetic and the field experiment, (ii) above-ground biomass was found to give relatively better estimates and lower uncertainty than LAI when combined with surface soil moisture, especially for estimation of soil depth, (iii) surface soil moisture data, either alone or combined with crop variables, provided a very good estimate of the water holding capacity of the upper soil layer with very small uncertainty whereas using the surface soil moisture alone gave very poor estimates of the soil properties of the deeper layer, and (iv) using crop variables alone (else above-ground biomass or LAI) provided reasonable estimates of the deeper layer properties depending on the soil type but provided poor estimates of the first layer properties. The robustness of combining observations of the surface soil moisture and the above-ground biomass for estimating two layer soil properties, which was demonstrated using both synthetic and field experiments in this study, needs now to be tested for a broader range of climatic conditions and crop types, to assess its potential for spatial applications. (C) 2012 Elsevier B.V. All rights reserved.

Bromenium-Catalysed Tandem Ring Opening/Cyclisation of Vinylcyclopropanes and Vinylcyclobutanes: A Metal-Free 3+2+1]/4+2+1] Cascade for the Synthesis of Chiral Amidines and Computational Investigation

We present a detailed study of a 3+2+1] cascade cyclisation of vinylcyclopropanes (VCP) catalysed by a bromenium species (Brd+?Xd-) generated in situ, which results in the synthesis of chiral bicyclic amidines in a tandem one-pot operation. The formation of amidines involves the ring-opening of VCPs with Br?X, followed by a Ritter-type reaction with chloramine-T and a tandem cyclisation. The reaction has been further extended to vinylcyclobutane systems and involves a 4+2+1] cascade cyclisation with the same reagents. The versatility of the methodology has been demonstrated by careful choice of VCPs and VCBs to yield bicyclo4.3.0]-, -4.3.1]- and -4.4.0]amidines in enantiomerically pure form. On the basis of the experimental observations and DFT calculations, a reasonable mechanism has been put forth to account for the formation of the products and the observed stereoselectivity. We propose the existence of a p-stabilised homoallylic carbocation at the cyclopropane carbon as the reason for high stereoselectivity. DFT studies at B3LYP/6-311+G** and M06-2X/6-31+G* levels of theory in gas-phase calculations suggest the ring-opening of VCP is initiated at the p-complex stage (between the double bond and Br?X). This can be clearly perceived from the solution-phase (acetonitrile) calculations using the polarisable continuum model (PCM) solvation model, from which the extent of the ring opening of VCP was found to be noticeably high. Studies also show that the formation of zero-bridge bicyclic amidines is favoured over other bridged bicyclic amidines. The energetics of competing reaction pathways is compared to explain the product selectivity.

A spring-mass-lever model, stiffness and inertia maps for single-input, single-output compliant mechanisms

A spring-mass-lever (SML) model is introduced in this paper for a single-input-single-output compliant mechanism to capture its static and dynamic behavior. The SML model is a reduced-order model, and its five parameters provide physical insight and quantify the stiffness and inertia(1) at the input and output ports as well as the transformation of force and displacement between the input and output. The model parameters can be determined with reasonable accuracy without performing dynamic or modal analysis. The paper describes two uses of the SML model: computationally efficient analysis of a system of which the compliant mechanism is a part; and design of compliant mechanisms for the given user-specifications. During design, the SML model enables determining the feasible parameter space of user-specified requirements, assessing the suitability of a compliant mechanism to meet the user-specifications and also selecting and/or re-designing compliant mechanisms from an existing database. Manufacturing constraints, material choice, and other practical considerations are incorporated into this methodology. A micromachined accelerometer and a valve mechanism are used as examples to show the effectiveness of the SML model in analysis and design. (C) 2012 Published by Elsevier Ltd.

Identification of mycobacterial lectins from genomic data

Sixty-four sequences containing lectin domains with homologs of known three-dimensional structure were identified through a search of mycobacterial genomes. They appear to belong to the -prism II, the C-type, the Microcystis virdis (MV), and the -trefoil lectin folds. The first three always occur in conjunction with the LysM, the PI-PLC, and the -grasp domains, respectively while mycobacterial -trefoil lectins are unaccompanied by any other domain. Thirty heparin binding hemagglutinins (HBHA), already annotated, have also been included in the study although they have no homologs of known three-dimensional structure. The biological role of HBHA has been well characterized. A comparison between the sequences of the lectin from pathogenic and nonpathogenic mycobacteria provides insights into the carbohydrate binding region of the molecule, but the structure of the molecule is yet to be determined. A reasonable picture of the structural features of other mycobacterial proteins containing one or the other of the four lectin domains can be gleaned through the examination of homologs proteins, although the structure of none of them is available. Their biological role is also yet to be elucidated. The work presented here is among the first steps towards exploring the almost unexplored area of the structural biology of mycobacterial lectins. Proteins 2013. (c) 2012 Wiley Periodicals, Inc.

Evaluation of isopentane, R-245fa and their mixtures as working fluids for organic Rankine cycles

Low grade thermal energy from sources such as solar, geothermal and industrial waste heat in the temperature range of 380-425 K can be converted to electrical energy with reasonable efficiency using isopentane and R-245fa. While the former is flammable and the latter has considerable global warming potential, their mixture in 0.7/0.3 mole fraction is shown to obviate these disadvantages and yet retain dominant merits of each fluid. A realistic thermodynamic analysis is carried out wherein the possible sources of irreversibilities such as isentropic efficiencies of the expander and the pump and entropy generation in the regenerator, boiler and condenser are accounted for. The performance of the system in the chosen range of heat source temperatures is evaluated. A technique of identifying the required source temperature for a given output of the plant and the maximum operating temperature of the working fluid is developed. This is based on the pinch point occurrence in the boiler and entropy generation in the boiling and superheating regions of the boiler. It is shown that cycle efficiencies of 10-13% can be obtained in the range investigated at an optimal expansion ratio of 7-10. (C) 2012 Elsevier Ltd. All rights reserved.

Electron rich supramolecular polymers as fluorescent sensors for nitroaromatics

Three pi-electron rich fluorescent supramolecular polymers (1-3) have been synthesized incorporating 2-methyl-3-butyn-2-ol groups in reasonable yield by employing Sonagashira coupling. They were characterized by multinuclear NMR (H-1, C-13), ESI-MS and single crystal X-ray diffraction analyses 1 = 1( 2-methyl-3-butyn-2-ol) pyrene; 2 = 9,10-bis(2-methyl-3-butyn-2-ol) anthracene; 3 = 1,3,6,8-tetrakis(2methyl- 3-butyn-2-ol) pyrene]. Single crystal structures of 1-3 indicated that the incorporation of hydroxy (-OH) groups on the peripheral of the fluorophores helps them to self-associate into an infinite supramolecular polymeric network via intermolecular hydrogen bonding interactions between the adjacent discrete fluorophore units. All these compounds showed fluorescence characteristics in chloroform solution due to the extended pi-conjugation and were used as selective fluorescent sensors for the detection of electron deficient nitroaromatics. The changes in photophysical properties of fluorophores (1-3) upon complex formation with electron deficient nitroaromatic explosives were studied in chloroform solution by using fluorescence spectroscopy. All these fluorophores showed the largest quenching response with moderate selectivity for nitroaromatics over various other electron deficient/ rich aromatic compounds tested (Chart 1). Analysis of the fluorescence titration profile of 9,10-bis(2-methyl-3butyn- 2-ol) anthracene fluorophore (2) with 1,3,5-trinitrotoluene/ 2,4-dinitrotoluene provided evidence that this particular fluorophore detects nitroaromatics in the nanomolar range 2.0 ppb for TNT, 13.7 ppb for DNT]. Moreover, sharp visual color change was observed upon mixing nitroaromatic (DNT) with fluorophores (1-3) both in solution as well as in solid phase. Furthermore, the vapor-phase sensing study of thin film of fluorophores (1-3) showed efficient quenching responses for DNT and this sensing process is reproducible. Selective fluorescence quenching response including a sharp visual color change for nitroaromatics make these tested fluorophores (1-3) as potential sensors for nitroaromatic compounds with a detection limit of ppb level.

Thermoelectric properties of PbTe with encapsulated bismuth secondary phase

Lead Telluride (PbTe) with bismuth secondary phase embedded in the bulk has been prepared by matrix encapsulation technique. X-Ray Diffraction results indicated crystalline PbTe, while Rietveld analysis showed that Bi did not substitute at either Pb or Te site, which was further confirmed by Raman and X-Ray Photoelectron Spectroscopy. Scanning Electron Microscopy showed the expected presence of a secondary phase, while Energy Dispersive Spectroscopy results showed a slight deficiency of tellurium in the PbTe matrix, which might have occurred during synthesis due to higher vapor pressure of Te. Transmission Electron Microscopy results did not show any nanometer sized Bi phase. Seebeck coefficient (S) and electrical conductivity (sigma) were measured from room temperature to 725 K. A decrease in S and sigma with increasing Bi content showed an increased scattering of electrons from PbTe-Bi interfaces, along with a possible electron acceptor role of Bi secondary phase. An overall decrease in the power factor was thus observed. Thermal conductivity, measured from 400K to 725K, was smaller at starting temperature with increasing Bi concentration, and almost comparable to that of PbTe at higher temperatures, indicating a more important role of electrons as compared to phonons at PbTe-Bi interfaces. Still, a reasonable zT of 0.8 at 725K was achieved for undoped PbTe, but no improvement was found for bismuth added samples with micrometer inclusions. (C) 2013 American Institute of Physics. http://dx.doi.org/10.1063/1.4796148]

Mixing enhancement in a compact trapped vortex combustor

Previous studies on a single-cavity, compact trapped vortex combustor concept showed good flame stability for a wide range of flow conditions. However, achieving good mixing between cavity products and mainstream flow was still a major challenge. In the present study, a passive mixing enhancement strategy of using inclined struts along with a flow guide vane is presented and experimentally tested at atmospheric pressure conditions. Results show excellent mixing and consequently low values of the combustor exit pattern factor in the range of 0.1 and small flame lengths (57 times the main-duct depth). The pressure drop is small in the range of 0.35%, and NOx levels of the order of 12ppm are achieved. The flame stability is excellent, and combustion efficiency is reasonable in the range of 96%. The effectiveness of the proposed strategy is explained on the basis of in-situ OH chemiluminescence images and prior numerical simulations of the resulting complex flow field. The flow guide vane is observed to lead to a counterclockwise cavity vortex, which is conducive to the rise of cavity combustion products along the inclined struts and subsequent mixing with the mainstream flow.

Assessing future rainfall projections using multiple GCMs and a multi-site stochastic downscaling model

Impact of global warming on daily rainfall is examined using atmospheric variables from five General Circulation Models (GCMs) and a stochastic downscaling model. Daily rainfall at eleven raingauges over Malaprabha catchment of India and National Center for Environmental Prediction (NCEP) reanalysis data at grid points over the catchment for a continuous time period 1971-2000 (current climate) are used to calibrate the downscaling model. The downscaled rainfall simulations obtained using GCM atmospheric variables corresponding to the IPCC-SRES (Intergovernmental Panel for Climate Change - Special Report on Emission Scenarios) A2 emission scenario for the same period are used to validate the results. Following this, future downscaled rainfall projections are constructed and examined for two 20 year time slices viz. 2055 (i.e. 2046-2065) and 2090 (i.e. 2081-2100). The model results show reasonable skill in simulating the rainfall over the study region for the current climate. The downscaled rainfall projections indicate no significant changes in the rainfall regime in this catchment in the future. More specifically, 2% decrease by 2055 and 5% decrease by 2090 in monsoon (HAS) rainfall compared to the current climate (1971-2000) under global warming conditions are noticed. Also, pre-monsoon (JFMAM) and post-monsoon (OND) rainfall is projected to increase respectively, by 2% in 2055 and 6% in 2090 and, 2% in 2055 and 12% in 2090, over the region. On annual basis slight decreases of 1% and 2% are noted for 2055 and 2090, respectively.