Influences of the springtime northern Indian biomass burning over the central Himalayas

The influences of the springtime northern Indian biomass burning are shown for the first time over the central Himalayas by using three years (2007-2009) of surface and space based observations along with a radiative transfer model. Near-surface ozone, black carbon (BC), spectral aerosol optical depths (AODs) and the meteorological parameters are measured at a high altitude site Nainital (29.37 degrees N, 79.45 degrees E, 1958 m amsl) located in the central Himalayas. The satellite observations include the MODIS derived fire counts and AOD (0.55 mu m), and OMI derived tropospheric column NO(2), ultraviolet aerosol index and single scattering albedo. MODIS fire counts and BC observations are used to identify the fire-impacted periods (372 h during 2007-2009) and hence the induced enhancements in surface BC, AOD (0.5 mu m) and ozone are estimated to be 1802 ng m(-3) (similar to 145%), 0.3 (similar to 150%) and 19 ppbv (similar to 34%) respectively. Large enhancements (53-100%) are also seen in the satellite derived parameters over a 2 degrees x 2 degrees region around Nainital. The present analysis highlights the northern Indian biomass burning induced cooling at the surface (-27 W m(-2)) and top of the atmosphere (-8 W m(-2)) in the lesser polluted high altitude regions of the central Himalayas. This cooling leads to an additional atmospheric warming of 19 W m(-2) and increases the lower atmospheric heating rate by 0.8 K day(-1). These biomass burning induced changes over the central Himalayan atmosphere during spring may also lead to enhanced short-wave absorption above clouds and might have an impact on the monsoonal rainfall.

A simple numerical method for three-dimensional analysis of simple expansion chamber mufflers of rectangular as well as circular cross-section with a stationary medium

Three-dimensional effects are a primary source of discrepancy between the measured values of automotive muffler performance and those predicted by the plane wave theory at higher frequencies. The basically exact method of (truncated) eigenfunction expansions for simple expansion chambers involves very complicated algebra, and the numerical finite element method requires large computation time and core storage. A simple numerical method is presented in this paper. It makes use of compatibility conditions for acoustic pressure and particle velocity at a number of equally spaced points in the planes of the junctions (or area discontinuities) to generate the required number of algebraic equations for evaluation of the relative amplitudes of the various modes (eigenfunctions), the total number of which is proportional to the area ratio. The method is demonstrated for evaluation of the four-pole parameters of rigid-walled, simple expansion chambers of rectangular as well as circular cross-section for the case of a stationary medium. Computed values of transmission loss are compared with those computed by means of the plane wave theory, in order to highlight the onset (cutting-on) of various higher order modes and the effect thereof on transmission loss of the muffler. These are also compared with predictions of the finite element methods (FEM) and the exact methods involving eigenfunction expansions, in order to demonstrate the accuracy of the simple method presented here.

Preliminary X-ray crystallographic studies on acetate kinase (AckA) from Salmonella typhimurium in two crystal forms

Acetate kinase (AckA) catalyzes the reversible transfer of a phosphate group from acetyl phosphate to ADP, generating acetate and ATP, and plays a central role in carbon metabolism. In the present work, the gene corresponding to AckA from Salmonella typhimurium (StAckA) was cloned in the IPTG-inducible pRSET C vector, resulting in the attachment of a hexahistidine tag to the N-terminus of the expressed enzyme. The recombinant protein was overexpressed, purified and crystallized in two different crystal forms using the microbatch-under-oil method. Form I crystals diffracted to 2.70 angstrom resolution when examined using X-rays from a rotating-anode X-ray generator and belonged to the monoclinic space group C2, with unit-cell parameters a = 283.16, b = 62.17, c = 91.69 angstrom, beta = 93.57 degrees. Form II crystals, which diffracted to a higher resolution of 2.35 angstrom on the rotating-anode X-ray generator and to 1.90 angstrom on beamline BM14 of the ESRF, Grenoble, also belonged to space group C2 but with smaller unit-cell parameters (a = 151.01, b = 78.50, c = 97.48 angstrom, beta = 116.37 degrees). Calculation of Matthews coefficients for the two crystal forms suggested the presence of four and two protomers of StAckA in the asymmetric units of forms I and II, respectively. Initial phases for the form I diffraction data were obtained by molecular replacement using the coordinates of Thermotoga maritima AckA (TmAckA) as the search model. The form II structure was phased using a monomer of form I as the phasing model. Inspection of the initial electron-density maps suggests dramatic conformational differences between residues 230 and 300 of the two crystal forms and warrants further investigation.

Formulas for algorithmic computation of impedance matrix using general circuit constants

A set of formulas is derived from general circuit constants which facilitates formation of the impedance matrix of a power system by the bus-impedance method. The errors associated with the lumpedparameter representation of a transmission line are thereby eliminated. The formulas are valid for short lines also, if the relevant general circuit constants are employed. The mutual impedance between the added line and the existing system is not considered, but the approach suggested can well be extended to it.

Nonspecific Interaction between DNA and Protein allows for Cooperativity: A Case Study with Mycobacterium DNA Binding Protein

Different DNA-binding proteins have different interaction modes with DNA. Sequence-specific DNA protein interaction has been mostly associated with regulatory processes inside a cell, and as such extensive studies have been made. Adequate data is also available on nonspecific DNA protein interaction, as an intermediate to protein's search for its cognate partner. Multidomain nonspecific DNA protein interaction involving physical sequestering of DNA has often been implicated to regulate gene expression indirectly. However, data available on this type of interaction is limited. One such interaction is the binding of DNA with mycobacterium DNA binding proteins. We have used the Langmuir-Blodgett technique to evaluate for the first time the kinetics and thermodynamics of Mycobacterium smegmatis Dps 1 binding to DNA. By immobilizing one of the interacting partners, we have shown that, when a kinetic bottleneck is applied, the binding mechanism showed cooperative binding (n = 2.72) at lower temperatures, but the degree of cooperativity gradually reduces (n = 1.38) as the temperature was increased We have also compared the kinetics and thermodynamics of sequence-specific and nonspecific DNA protein interactions under the same set of conditions.

Mercury Segregation and Diselenide Self-Assembly on Gold

We have investigated the self-assembly of didecyldiselenide on gold containing mercury using X-ray photoelectron spectroscopy, cyclic voltammetry and infrared spectroscopy. The analysis of intensity and chemical shift of selected Se, Hg, and Au photoelectron lines on samples with increasing Hg content, show that didecyldiselenide adsorption strongly contributed to segregation of bulk Hg to the surface. The voltammetry results support this conclusion and suggest the formation of Hg-Au surface amalgam. The Hg surface segregation effect must be related to the restructuring of the surface following initial adsorption, and to the strong selenophilicity of Hg. The reflectance absorbance infrared spectroscopy studies show that the molecular layer on Hg-Au substrates lacks good order.

Electrochemical Integration of Graphene with Light-Absorbing Copper-Based Thin Films

We present an electrochemical route for the integration of graphene with light-sensitive copper-based alloys used in optoelectronic applications. Graphene grown using chemical vapor deposition (CVD) transferred to glass is found to be a robust substrate on which photoconductive CuxS films of 1-2 mu m thickness can be deposited. The effect of growth parameters on the morphology and photoconductivity of CuxS films is presented. Current-voltage (I-V) characterization and photoconductivity decay experiments are performed with graphene as one contact and silver epoxy as the other.

Study on the structure and vibrational spectra of efavirenz conformers using DFT: Comparison to experimental data

Efavirenz, (S)-6-chloro-4-(cyclopropylethynyl)-1,4-dihydro-4-(trifluoromethyl)-2H-3 ,1-benzoxazin-2-one, is an anti HIV agent belonging to the class of the non-nucleoside inhibitors of the HIV-1 virus reverse transcriptase. A systematic quantum chemical study of the possible conformations, their relative stabilities and vibrational spectra of efavirenz has been reported. Structural and spectral characteristics of efavirenz have been studied by vibrational spectroscopy and quantum chemical methods. Density functional theory (DFT) calculations for potential energy curve, optimized geometries and vibrational spectra have been carried out using 6-311++G(d,p) basis sets and B3LYP functionals. Based on these results, we have discussed the correlation between the vibrational modes and the crystalline structure of the most stable form of efavirenz. 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 infrared and the Raman spectra of the molecule based on OFT calculations show reasonable agreement with the experimental results. The calculated HOMO and LUMO energies shows that charge transfer occur within the molecule. (C) 2011 Elsevier B.V. All rights reserved.

Free Energy Barriers for Escape of Water Molecules from Protein Hydration Layer

Free energy barriers separating interfacial water molecules from the hydration layer at the surface of a protein to the bulk are obtained by using the umbrella sampling method of free energy calculation. We consider hydration layer of chicken villin head piece (HP-36) which has been studied extensively by molecular dynamics simulations. The free energy calculations reveal a strong sensitivity to the secondary structure. In particular, we find a region near the junction of first and second helix that contains a cluster of water molecules which are slow in motion, characterized by long residence times (of the order of 100 ps or more) and separated by a large free energy barrier from the bulk water. However, these ``slow'' water molecules constitute only about 5-10% of the total number of hydration layer water molecules. Nevertheless, they play an important role in stabilizing the protein conformation. Water molecules near the third helix (which is the important helix for biological function) are enthalpically least stable and exhibit the fastest dynamics. Interestingly, barrier height distributions of interfacial water are quite broad for water surrounding all the three helices (and the three coils), with the smallest barriers found for those near the helix-3. For the quasi-bound water molecules near the first and second helices, we use well-known Kramers' theory to estimate the residence time from the free energy surface, by estimating the friction along the reaction coordinate from the diffusion coefficient by using Einstein relation. The agreement found is satisfactory. We discuss the possible biological function of these slow, quasi-bound (but transient) water molecules on the surface.

Layer-by-Layer Assembled Thin Film of Albumin Nanoparticles for Delivery of Doxorubicin

Protein nanoparticles (NPs) have found significant applications in drug delivery due to their inherent biocompatibility, which is attributed to their natural origin. In this study, bovine serum abumin (BSA) nanoparticles were introduced in multilayer thin film via layer-by-layer self-assembly for localized delivery of the anticancer drug Doxorubicin (Dox). BSA nanoparticles (similar to 100 nm) show a high negative zeta potential in aqueous medium (-55 mV) and form a stable dispersion in water without agglomeration for a long period. Hence, BSA NPs can be assembled on a substrate via layer-by-layer approach using a positively charged polyelectrolyte (chitosan in acidic medium). The protein nature of these BSA nanoparticles ensures the biocompatibility of the film, whereas the availability of functional groups on this protein allows one to tune the property of the self-assembly to have a pH-dependent drug release profile. The growth of multilayer thin film was monitored by UV-visible spectroscopy, and the films were further characterized by atomic force microscopy (AFM) and field emission scanning electron microscopy (FESEM). The drug release kinetics of these BSA nanoparticles and their self-assembled thin film has been compared at a physiological pH of 7.4 and an acidic pH of 6.4.

First-Principles Study of the Effect of Organic Ligands on the Crystal Structure of CdS Nanoparticles

We show with the aid of first-principles electronic structure calculations that suitable choice of the capping ligands may be an important control parameter for crystal structure engineering of nanoparticles. Our calculations on CdS nanocrystals reveal that the binding energy of model trioctylphosphine molecules on the (001) facets of zincblende nanocrystals is larger compared to that on wurtzite facets. Similarly, the binding energy of model cis-oleic acid is found to be dominant for the (10 (1) over bar0) facets of wurtzite structure. As a consequence, trioctylphosphine as a capping agent stabilizes the zincblende structure while cis-oleic acid stabilizes the wurtzite phase by influencing the surface energy, which has a sizable contribution to the energetics of a nanocrystal. Our detailed analysis suggests that the binding of molecules on the nanocrystalline facets depends on the surface topology of the facets, the coordination of the surface atoms where the capping molecule is likely to attach, and the conformation of the capping molecule.

Structural Transformations, Composition Anomalies and a Dramatic Collapse of Linear Polymer Chains in Dilute Ethanol-Water Mixtures

Water-ethanol mixtures exhibit many interesting anomalies, such as negative excess partial molar volume of ethanol, excess sound absorption coefficient at low concentrations, and positive deviation from Raoult's law for vapor pressure, to mention a few. These anomalies have been attributed to different, often contradictory origins, but a quantitative understanding is still lacking. We show by computer simulation and theoretical analyses that these anomalies arise from the sudden emergence of a bicontinuous phase that occurs at a relatively low ethanol concentration of x(eth) approximate to 0.06-0.10 (that amounts to a volume fraction of 0.17-0.26, which is a significant range!). The bicontinuous phase is formed by aggregation of ethanol molecules, resulting in a weak phase transition whose nature is elucidated. We find that the microheterogeneous structure of the mixture gives rise to a pronounced nonmonotonic composition dependence of local compressibility and nonmonotonic dependence in the peak value of the radial distribution function of ethyl groups. A multidimensional free energy surface of pair association is shown to provide a molecular explanation of the known negative excess partial volume of ethanol in terms of parallel orientation and hence better packing of the ethyl groups in the mixture due to hydrophobic interactions. The energy distribution of the ethanol molecules indicates additional energy decay channels that explain the excess sound attenuation coefficient in aqueous alcohol mixtures. We studied the dependence of the solvation of a linear polymer chain on the composition of the water-ethanol solvent. We find that there is a sudden collapse of the polymer at x(eth) approximate to 0.05-a phenomenon which we attribute to the formation of the microheterogeneous structures in the binary mixture at low ethanol concentrations. Together with recent single molecule pulling experiments, these results provide new insight into the behavior of polymer chain and foreign solutes, such as enzymes, in aqueous binary mixtures.

Spectroscopic Characterization and Modeling of Quadrupolar Charge-Transfer Dyes with Bulky Substituents

Joint experimental and theoretical work is presented on two quadrupolar D-pi-A-pi-D chromophores characterized by the same bulky donor (D) group and two different central cores. The first chromophore, a newly synthesized species with a malononitrile-based acceptor (A) group, has a V-shaped structure that makes its absorption spectrum very broad, covering most of the visible region. The second chromophore has a squaraine-based core and therefore a linear structure, as also evinced from its absorption spectra. Both chromophores show an anomalous red shift of the absorption band upon increasing solvent polarity, a feature that is ascribed to the large, bulky structure of the moleCules. For these molecules, the basic description of polar solvation in terms of a uniform reaction field fails. Indeed, a simple extension of the model to account for two independent reaction fields associated with the two molecular arms quantitatively reproduces the observed linear absorption and fluorescence as well as fluorescence anisotropy spectra, fully rationalizing their nontrivial dependence on solvent polarity. The model derived from the analysis of linear spectra is adopted to predict nonlinear spectra and specifically hyper-Rayleigh scattering and two-photon absorption spectra. In polar solvents, the V-shaped chromophore is predicted to have a large HRS response in a wide spectral region (approximately 600-1300 nm). Anomalously large and largely solvent-dependent HRS responses for the linear chromophores are ascribed to symmetry lowering induced by polar solvation and amplified in this bulky system by the presence of two reaction fields.