Dynamic path profile aided recompilation in a JAVA just-in-time compiler

Just-in-Time (JIT) compilers for Java can be augmented by making use of runtime profile information to produce better quality code and hence achieve higher performance. In a JIT compilation environment, the profile information obtained can be readily exploited in the same run to aid recompilation and optimization of frequently executed (hot) methods. This paper discusses a low overhead path profiling scheme for dynamically profiling AT produced native code. The profile information is used in recompilation during a subsequent invocation of the hot method. During recompilation tree regions along the hot paths are enlarged and instruction scheduling at the superblock level is performed. We have used the open source LaTTe AT compiler framework for our implementation. Our results on a SPARC platform for SPEC JVM98 benchmarks indicate that (i) there is a significant reduction in the number of tree regions along the hot paths, and (ii) profile aided recompilation in LaTTe achieves performance comparable to that of adaptive LaTTe in spite of retranslation and profiling overheads.

Enhanced aerosol loading over Arabian Sea during the pre-monsoon season: Natural or anthropogenic?

[1] Recent experiments conducted over the oceanic regions adjacent to the Indian sub continent have revealed the presence of anthropogenic aerosol haze during January to March. It has been suggested that the major source of this aerosol is South and Southeast Asia. Here we show from long term, multi-station and ship borne observations that aerosols transported from regions northwest of Indian subcontinent especially Arabian and Saharan regions (mostly natural dust) along with the locally produced sea-salt aerosols by sea-surface winds constitute a more significant source of aerosols during April-May period. The radiative forcing due to Arabian/Saharan aerosols (mostly natural) during April May period is comparable and often exceed (as much as 1.5 times) the forcing due to anthropogenic aerosols during January to March period. The presence of dust load over the Arabian Sea can influence the temperature profile and radiative balance in this region.

Evaluation of bearing capacity improvement using composite grids

Recently, composite reinforcements in which combinations of materials and material forms such as strips, grids, and strips and anchors, depending on requirements have proven to be effective in various ground improvement applications. Composite geogrids studied in this paper belong to the category of composite reinforcements and are useful for bearing capacity improvement. The paper presents evaluation of results of bearing capacity tests conducted oil a composite geogrid, made of composite reinforcement consisting of steel and cement mortar. The study shows that the behavior of composite reinforcements follows the general trends observed in the case of conventional geogrids, with reference to the depth of first layer below the footing, number of layers of reinforcement, and vertical spacing of the reinforcement. Results show that the performance is comparable to that of a conventional polymer geogrid.

DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins

Depth measures the extent of atom/residue burial within a protein. It correlates with properties such as protein stability, hydrogen exchange rate, protein-protein interaction hot spots, post-translational modification sites and sequence variability. Our server, DEPTH, accurately computes depth and solvent-accessible surface area (SASA) values. We show that depth can be used to predict small molecule ligand binding cavities in proteins. Often, some of the residues lining a ligand binding cavity are both deep and solvent exposed. Using the depth-SASA pair values for a residue, its likelihood to form part of a small molecule binding cavity is estimated. The parameters of the method were calibrated over a training set of 900 high-resolution X-ray crystal structures of single-domain proteins bound to small molecules (molecular weight < 1.5 KDa). The prediction accuracy of DEPTH is comparable to that of other geometry-based prediction methods including LIGSITE, SURFNET and Pocket-Finder (all with Matthew's correlation coefficient of similar to 0.4) over a testing set of 225 single and multi-chain protein structures. Users have the option of tuning several parameters to detect cavities of different sizes, for example, geometrically flat binding sites. The input to the server is a protein 3D structure in PDB format. The users have the option of tuning the values of four parameters associated with the computation of residue depth and the prediction of binding cavities. The computed depths, SASA and binding cavity predictions are displayed in 2D plots and mapped onto 3D representations of the protein structure using Jmol. Links are provided to download the outputs. Our server is useful for all structural analysis based on residue depth and SASA, such as guiding site-directed mutagenesis experiments and small molecule docking exercises, in the context of protein functional annotation and drug discovery.

Adsorption of 1,1,1,2-Tetrafluoroethane on Activated Charcoal

This paper presents adsorption isotherms for HFC-134a on activated charcoal, in the temperature range of 273-353 K and for pressures up to 0.65 MPa, measured using the volumetric method. Three samples of charcoals with widely varying surface areas were chosen. The shapes of the isotherms,obtained from the experimental data were similar in all cases and comparable to those reported in the literature. Adsorption parameters were evaluated from the isotherms using the Dubinin-Astakhov (DA) equation. The concentration dependence of the isosteric enthalpies of adsorption is extracted from the data.

Real-time kinetic analysis of hCG-monoclonal antibody interaction using radiolabeled hCG probe: presence of two forms of Ag-mAb complex as revealed by solid phase dissociation studies

Real-time kinetics of ligand-ligate interaction has predominantly been studied by either fluorescence or surface plasmon resonance based methods. Almost all such studies are based on association between the ligand and the ligate. This paper reports our analysis of dissociation data of monoclonal antibody-antigen (hCG) system using radio-iodinated hCG as a probe and nitrocellulose as a solid support to immobilize mAb. The data was analyzed quantitatively for a one-step and a two-step model. The data fits well into the two-step model. We also found that a fraction of what is bound is non-dissociable (tight-binding portion (TBP)). The TBP was neither an artifact of immobilization nor does it interfere with analysis. It was present when the reaction was carried out in homogeneous solution in liquid phase. The rate constants obtained from the two methods were comparable. The work reported here shows that real-time kinetics of other ligand-ligate interaction can be studied using nitrocellulose as a solid support. (C) 2002 Elsevier Science B.V. All rights reserved.

Modified kinetic flux vector splitting (m-KFVS) method for compressible flows

To resolve many flow features accurately, like accurate capture of suction peak in subsonic flows and crisp shocks in flows with discontinuities, to minimise the loss in stagnation pressure in isentropic flows or even flow separation in viscous flows require an accurate and low dissipative numerical scheme. The first order kinetic flux vector splitting (KFVS) method has been found to be very robust but suffers from the problem of having much more numerical diffusion than required, resulting in inaccurate computation of the above flow features. However, numerical dissipation can be reduced by refining the grid or by using higher order kinetic schemes. In flows with strong shock waves, the higher order schemes require limiters, which reduce the local order of accuracy to first order, resulting in degradation of flow features in many cases. Further, these schemes require more points in the stencil and hence consume more computational time and memory. In this paper, we present a low dissipative modified KFVS (m-KFVS) method which leads to improved splitting of inviscid fluxes. The m-KFVS method captures the above flow features more accurately compared to first order KFVS and the results are comparable to second order accurate KFVS method, by still using the first order stencil. (C) 2011 Elsevier Ltd. All rights reserved.

Manipulation of the Hydration Levels in Minerals of Sodium Cadmium Bisulfate toward the Design of Functional Materials

Several variants of hydrated sodium cadmium bisulfate, Na(2)Cd(2)(SO(4))(3) center dot 3H(2)O, Na(2)Cd(SO(4))(2) center dot 2H(2)O, and Na(2)Cd(SO(4))(2) center dot 4H(2)O have been synthesized, and their thermal properties followed by phase transitions have been invesigated. The formation of these phases depends on the stochiometry and the time taken for crystallization from water. Na(2)Cd(2)(SO(4))(3)center dot 3H(2)O, which crystallizes in the trigonal system, space group P3c, is grown from the aqueous solution in about four weeks. The krohnkite type mineral Na(2)Cd(SO(4))(2) center dot 2H(2)O and the mineral astrakhanite, also known as blodite, Na(2)Cd (SO(4))(2)center dot 4H(2)O, crystallize concomittantly in about 24 weeks. Both these minerals belong to the monoclinic system(space group P2(1)/c). Na(2)Cd(2)(SO(4))(3)center dot 3H(2)O loses water completely when heated to 250 degrees C and transforms to a dehydrated phase (cubic system, space group I (4) over bar 3d) whose structure has been established using ab initio powder diffration techniques. Na(2)Cd(SO(4))(2)center dot 2H(2)O transforms to alpha-Na(2)Cd(SO(4))(2) (space group C2/c) on heating to 150 degrees C which is a known high ionic conductor and remains intact over prolonged periods of exposure to moisture (over six months). However, when alpha-Na(2)Cd(SO(4))(2) is heated to 570 degrees C followed by sudden quenching in liquid nitrogen beta-Na(2)Cd(SO(4))(2) (P2(1)/c) is formed. beta-Na(2)Cd(SO(4))(2) takes up water from the atmosphere and gets converted completely to the krohnkite type mineral in about four weeks. Further, beta-Na(2)Cd(SO(4))(2) has a conductivity behavior comparable to the a-form up to 280 degrees C, the temperature required for the transformation of the beta- to alpha-form. These experiments demonstrate the possibility of utilizing the abundantly available mineral sources as precursors to design materials with special properties.

Ab initio, DFT and transition state theory calculations on 1,2-HF, HCI and CIF elimination reactions from CH2F-CH2Cl

This paper reports ab intio, DFT and transition state theory (TST) calculations on HF, HCI and CIF elimination reactions from CH2Cl-CH2F molecule. Both the ground state and the transition state for HX elimination reactions have been optimized at HF, MP2 and DFT calculations with 6-31G*, 6-31G** and 6-311++G** basis sets. In addition, CCSD(T) single point calculations were carried out with MP2/6-311++G** optimized geometry for more accurate determination of the energies of the minima and transition state, compared to the other methods employed here. Classical barriers are converted to Arrhenius activation energy by TST calculations for comparisons with experimental results. The pre-exponential factors, A, calculated at all levels of theory are significantly larger than the experimental values. For activation energy, E-a DFT gives good results for HF elimination, within 4-8 W mol(-1) from experimental values. None of the methods employed, including CCSD(T), give comparable results for HCI elimination reactions. However, rate constants calculated by CCSD(T) method are in very good agreement with experiment for HCI elimination and they are in reasonable agreement for HF elimination reactions. Due to the strong correlation between A and E., the rate constants could be fit to a lower A and E-a (as given by experimental fitting, corresponding to a tight TS) or to larger A and E-a (as given by high level ab initio calculations, corresponding to a loose TS). The barrier for CIF elimination is determined to be 607 U mol(-1) at HF level and it is unlikely to be important for CH2FCH2Cl. Results for other CH2X-CH2Y (X,Y = F/Cl) are included for comparison.

AlignHUSH: Alignment of HMMs using structure and hydrophobicity information

Background: Sensitive remote homology detection and accurate alignments especially in the midnight zone of sequence similarity are needed for better function annotation and structural modeling of proteins. An algorithm, AlignHUSH for HMM-HMM alignment has been developed which is capable of recognizing distantly related domain families The method uses structural information, in the form of predicted secondary structure probabilities, and hydrophobicity of amino acids to align HMMs of two sets of aligned sequences. The effect of using adjoining column(s) information has also been investigated and is found to increase the sensitivity of HMM-HMM alignments and remote homology detection. Results: We have assessed the performance of AlignHUSH using known evolutionary relationships available in SCOP. AlignHUSH performs better than the best HMM-HMM alignment methods and is observed to be even more sensitive at higher error rates. Accuracy of the alignments obtained using AlignHUSH has been assessed using the structure-based alignments available in BaliBASE. The alignment length and the alignment quality are found to be appropriate for homology modeling and function annotation. The alignment accuracy is found to be comparable to existing methods for profile-profile alignments. Conclusions: A new method to align HMMs has been developed and is shown to have better sensitivity at error rates of 10% and above when compared to other available programs. The proposed method could effectively aid obtaining clues to functions of proteins of yet unknown function. A web-server incorporating the AlignHUSH method is available at http://crick.mbu.iisc.ernet.in/similar to alignhush/

Epitaxial Growth of Co3O4 Films by Low Temperature, Low Pressure Chemical Vapor Deposition

The growth of strongly oriented or epitaxial thin films of metal oxides generally requires relatively high growth temperatures or infusion of energy to the growth surface through means such as ion bombardment. We have grown high quality epitaxial thin films of Co3O4 on different substrates at a temperature as low as 450°C by low-pressure metal-organic chemical vapor deposition (MOCVD) using cobalt(II) acetylacetonate as the precursor. With oxygen as the reactant gas, polycrystalline Co3O4 films are formed on glass and Si(100) in the temperature range 350-550°C. Under similar conditions of growth, highly oriented films of Co3O4 are formed on SrTiO3(100) and LaAlO3(100). The film on LaAlO3(100) grown at 450°C show a rocking curve FWHM of 1.61°, which reduces to 1.32° when it is annealed in oxygen at 725°C. The film on SrTiO3(100) has a FWHM of 0.330 (as deposited) and 0.29° (after annealing at 725°C). The ø-scan analysis shows cube-on-cube epitaxy on both these substrates. The quality of epitaxy on SrTiO3(100) is comparable to the best of the pervoskite-based oxide thin films grown at significantly higher temperatures.

Denaturant mediated unfolding of both native and molten globule states of maltose binding protein are accompanied by large [Delta]Cp's

Maltose binding protein (MBP) is a large, monomeric two domain protein containing 370 amino acids. In the absence of denaturant at neutral pH, the protein is in the native state, while at pH 3.0 it forms a molten globule. The molten globule lacks a tertiary circular dichroism signal but has secondary structure similar to that of the native state. The molten globule binds 8-anilino-1-naphthalene sulfonate (ANS). The unfolding thermodynamics of MBP at both pHs were measured by carrying out a series of isothermal urea melts at temperatures ranging from 274–329 K. At 298 K, values of [Delta]G°, [Delta]Cp, and Cm were 3.1 ± 0.2 kcal mol−1, 5.9 ± 0.8 kcal mol−1 K−1 (15.9 cal (mol-residue)−1 K−1), and 0.8 M, respectively, at pH 3.0 and 14.5 ± 0.4 kcal mol−1, 8.3 ± 0.7 kcal mol−1 K−1 (22.4 kcal (mol-residue)−1 K−1), and 3.3 M, respectively, at pH 7.1. Guanidine hydrochloride denaturation at pH 7.1 gave values of [Delta]G° and [Delta]Cp similar to those obtained with urea. The m values for denaturation are strongly temperature dependent, in contrast to what has been previously observed for small globular proteins. The value of [Delta]Cp per mol-residue for the molten globule is comparable to corresponding values of [Delta]Cp for the unfolding of typical globular proteins and suggests that it is a highly ordered structure, unlike molten globules of many small proteins. The value of [Delta]Cp per mol-residue for the unfolding of the native state is among the highest currently known for any protein.

Properties of concrete containing ultra-fine fly ash

Fly ash and silica fume are two pozzolans that have been widely used for improved concrete strength and durability. Silica fume displays a greater pozzolanic reactivity than fly ash primarily due to its finer particle size. The reactivity of fly ash can be improved by reducing its particle size distribution. This paper discusses the fresh and hardened properties of concrete made with an ultra-fine fly ash (UFFA) produced by air classification. Durability testing for chloride diffusivity, rapid chloride permeability, alkali-silica reaction (ASR), and sulfate attack was also conducted It was found that at a given workability and water content, concrete containing UFFA could be produced with only 50% of the high-range water-reducer dosage required for comparable silica fume concrete. Similar early strengths and durability measures as silica fume concrete were observed when a slightly higher dosage of UFFA was used with a small reduction (10%) in water content.

Role of interface states associated with transitional nanophase precipitates in the photoluminescence enhancement of SrTiO3 : Pr3+,Al3+

SrTiO3:Pr3+,Al3+ phosphor samples with varying ratios of Sr/Ti/Al were prepared by the gel-carbonate method and the mechanism of enhancement of the red photoluminescence intensity therein was investigated. The photoluminescence (PL) spectra of SrTiO3:Pr3+ show both D-1(2) --> H-3(4) and P-3(0) --> H-3(4) emission in the red and blue spectral regions, respectively, with comparable intensity. The emission intensity of D-1(2) --> H-3(4) is drastically enhanced by the incorporation of Al3+ and excess Ti4+ in the compositional range Sr(Ti,Al-y)(O3+3y/2):Pr3+ (0.2 less than or equal to y less than or equal to 0.4) and SrTi1+xAlyO3+z:Pr3+ (0.2 less than or equal to x less than or equal to 0.5; 0.05 less than or equal to y less than or equal to 0.1; z = 2x + 3y/2) with the complete disappearance of the blue band. This cannot be explained by the simple point defect model as the EPR studies do not show any evidence for the presence of electron or hole centers. TEM investigations show the presence of exsolved nanophases of SrAl12O19 and/or TiO2 in the grain boundary region as well as grain interiors as lamellae which, in turn, form the solid-state defects, namely, dislocation networks, stacking faults and crystallographic shear planes whereby the framework of corner shared TiO6 octehedra changes over to edge-sharing TiO5-AlO5 strands as indicated from the Al-27 MAS NMR studies. The presence of transitional nanophases and the associated defects modify the excitation-emission processes by way of formation of electronic sub-levels at 3.40 and 4.43 eV, leading to magnetic-dipole related red emission with enhanced intensity. This is evidenced by the fact that SrAl12O19:Pr3+,Ti4+ shows bright red emission whereas SrAl12O19:Pr3+ does not show red photoluminescence.

Some salient features of the atmosphere observed over the north Bay of Bengal during BOBMEX

This paper describes the near surface characteristics and vertical variations based on the observations made at 17.5degreesN and 89degreesE from ORV Sagar Kanya in the north Bay of Bengal during the Bay of Bengal Monsoon Experiment (BOBMEX) carried out in July-August 1999. BOBMEX captured both the active and weak phases of convection. SST remained above the convection threshold throughout the BOBMEX. While the response of the SST to atmospheric forcing was clearly observed, the response of the atmosphere to SST changes was not clear. SST decreased during periods of large scale precipitation, and increased during a weak phase of convection. It is shown that the latent heat flux at comparable wind speeds was about 25-50% lower over the Bay during BOBMEX compared to that over the Indian Ocean during other seasons and tropical west Pacific. On the other hand, the largest variations in the surface daily net heat flux are observed over the Bay during BOBMEX. SST predicted using observed surface fluxes showed that 1-D heat balance model works sometime but not always, and horizontal advection is important. The high resolution Vaisala radiosondes launched during BOBMEX could clearly bring out the changes in the vertical structure of the atmosphere between active and weak phases of convection. Convective Available Potential Energy of the surface air decreased,by 2-3 kJ kg(-1) following convection, and recovered in a time period of one or two days. The mid tropospheric relative humidity and water vapor content, and wind direction show the major changes between the active and weak phases of convection.