Software Pipelined Execution of Stream Programs on GPUs

The StreamIt programming model has been proposed to exploit parallelism in streaming applications on general purpose multi-core architectures. This model allows programmers to specify the structure of a program as a set of filters that act upon data, and a set of communication channels between them. The StreamIt graphs describe task, data and pipeline parallelism which can be exploited on modern Graphics Processing Units (GPUs), as they support abundant parallelism in hardware. In this paper, we describe the challenges in mapping StreamIt to GPUs and propose an efficient technique to software pipeline the execution of stream programs on GPUs. We formulate this problem - both scheduling and assignment of filters to processors - as an efficient Integer Linear Program (ILP), which is then solved using ILP solvers. We also describe a novel buffer layout technique for GPUs which facilitates exploiting the high memory bandwidth available in GPUs. The proposed scheduling utilizes both the scalar units in GPU, to exploit data parallelism, and multiprocessors, to exploit task and pipelin parallelism. Further it takes into consideration the synchronization and bandwidth limitations of GPUs, and yields speedups between 1.87X and 36.83X over a single threaded CPU.

Raman effect of corundum

The Raman effect of corundum (sapphire) was measured with an Ar+ laser source. The seven expected Raman active phonons were found and their symmetry characters determined. Assignment of the internal and external vibrations of the crystals was made and the effect of birefringence in the Raman selection rules is discussed.

ESR and optical absorption studies in copper diethyldithiocarbamate

ESR investigations at X band and optical-absorption measurements have been reported in single crystals of copper (n) diethyldithiocarbamate Cu[S 2CN(C2H5)2]2 diluted to 0.2% with the corresponding zinc complex. The measurements have been made both at room and liquid-oxygen temperatures. ESR measurements gave the following values for the parameters in spin Hamiltonian g11=2.1085, g=2.023(6), A63= 142.4×10-4 cm-1, A65 = 152.0×10-4 cm-1, B = 22.4×10-4 cm-1, Q~3×10-4 cm-1. Polarized optical absorption study has made possible a proper assignment of the absorption bands to their corresponding transitions. This has led to information regarding the ordering of the MO levels of the complex. The coefficients used in the MO description of the complex have been calculated from the observed parameters. The results show that the metal ligand BIσ bond is purely covalent and that the out-of-plane w bonding is appreciably covalent whereas the in-plane Π bonding is ionic. Further, it is noted that the metal ligand binding is more covalent with sulfur as ligand than with oxygen or nitrogen.

The Raman spectrum of cyclohexanol

The Raman spectrum of cyclohexanol has been studied in detail in the liquid state at 30° C. and at about 68° C. and in the solid state at about 13° C. The O-H stretching frequency of cyclohexanol has been found to extend from 3106-3571 cm.-1 in the liquid state at 30° C. and from 3204-3652 cm.-1 at 68° C. The 38 lines recorded in the present investigation have been following frequency shifts: 342, 408, 458, 478, 555, 653, 789, 834, 843, 863, 887, 920, 966, 978, 1024, 1047, 1070, 1139, 1173, 1184, 1210, 1235, 1252, 1301, 1329, 1346, 1362, 1438, 1448, 1464, 2660, 2684, 2710, 2854, 2896, 2925, 2940, 3106 to 3511 (band). Those lines which are italicized are the additional lines observed for the first time. The Raman lines at 966 cm.-1 and 1070 cm.-1 have been assigned to C-OH stretching vibrations of the axial and equatorial isomers. The ratio of the integrated intensity of the 1070 cm.-1 line to the 966 cm.-1 gave the equilibrium constant K as 2·896 at 30° C. and as 2·66 at 68° C. Knowing K, the free energy different Δ F was calculated and it was found to be 0·64 Kcal./mole at 30° C. and 0·66 Kcal./mole at about 68° C. Reasonable assignment has been made for most of the observed Raman lines.

HARMONY: a server for the assessment of protein structures

Protein structure validation is an important step in computational modeling and structure determination. Stereochemical assessment of protein structures examine internal parameters such as bond lengths and Ramachandran (phi, psi) angles. Gross structure prediction methods such as inverse folding procedure and structure determination especially at low resolution can sometimes give rise to models that are incorrect due to assignment of misfolds or mistracing of electron density maps. Such errors are not reflected as strain in internal parameters. HARMONY is a procedure that examines the compatibility between the sequence and the structure of a protein by assigning scores to individual residues and their amino acid exchange patterns after considering their local environments. Local environments are described by the backbone conformation, solvent accessibility and hydrogen bonding patterns. We are now providing HARMONY through a web server such that users can submit their protein structure files and, if required, the alignment of homologous sequences. Scores are mapped on the structure for subsequent examination that is useful to also recognize regions of possible local errors in protein structures. HARMONY server is located at http://caps.ncbs.res.in/harmony/

Infrared Spectra of Dimethylquinolines in the Gas Phase: Experiment and Theory

Infrared spectra of atmospherically important dimethylquinolines (DMQs), namely 2,4-DMQ, 2,6-DMQ, 2,7-DMQ, and 2,8-DMQ in the gas phase at 80 degrees C were recorded using a long variable path-length cell. DFT calculations were carried out to assign the bands in the experimentally observed spectra at the B3LYP/6-31G* level of theory. The spectral assignments particularly for the C-H stretching modes could not be made unambiguously using calculated anharmonic or scaled harmonic frequencies. To resolve this problem, a scaled force field method of assignment was used. Assignment of fundamental modes was confirmed by potential energy distributions (PEDs) of the normal modes derived by the scaled force fields using a modified version of the UMAT program in the QCPE package. We demonstrate that for large molecules such as the DMQs, the scaling of the force field is more effective in arriving at the correct assignment of the fundamentals for a quantitative vibrational analysis. An error analysis of the mean deviation of the calculated harmonic, anharmonic, and force field fitted frequencies from the observed frequency provides strong evidence for the correctness of the assignment.

Classification of Protein Kinases on the Basis of Both Kinase and Non-Kinase Regions

Background: Protein phosphorylation is a generic way to regulate signal transduction pathways in all kingdoms of life. In many organisms, it is achieved by the large family of Ser/Thr/Tyr protein kinases which are traditionally classified into groups and subfamilies on the basis of the amino acid sequence of their catalytic domains. Many protein kinases are multidomain in nature but the diversity of the accessory domains and their organization are usually not taken into account while classifying kinases into groups or subfamilies. Methodology: Here, we present an approach which considers amino acid sequences of complete gene products, in order to suggest refinements in sets of pre-classified sequences. The strategy is based on alignment-free similarity scores and iterative Area Under the Curve (AUC) computation. Similarity scores are computed by detecting common patterns between two sequences and scoring them using a substitution matrix, with a consistent normalization scheme. This allows us to handle full-length sequences, and implicitly takes into account domain diversity and domain shuffling. We quantitatively validate our approach on a subset of 212 human protein kinases. We then employ it on the complete repertoire of human protein kinases and suggest few qualitative refinements in the subfamily assignment stored in the KinG database, which is based on catalytic domains only. Based on our new measure, we delineate 37 cases of potential hybrid kinases: sequences for which classical classification based entirely on catalytic domains is inconsistent with the full-length similarity scores computed here, which implicitly consider multi-domain nature and regions outside the catalytic kinase domain. We also provide some examples of hybrid kinases of the protozoan parasite Entamoeba histolytica. Conclusions: The implicit consideration of multi-domain architectures is a valuable inclusion to complement other classification schemes. The proposed algorithm may also be employed to classify other families of enzymes with multidomain architecture.

Vibrational Spectra and Normal Coordinate Analysis of N-Methyl Thiourea

The infrared spectra of N-methylthiourea (NMTU) and its N-deuterated and S-methylated species were measured. Assignment of the infrared and Raman spectra of NMTU has been accomplished by correlation with thiourea and by use of infrared band shifts on N-deuteration as well as S-methylation. Normal coordinate analysis was performed for all the fundamentals of NMTU and NMTU-d3, the assignments obtained from the force field calculations being discussed in relation to those in other related thioureas and thioamides. The potential barriers to the internal rotations for the �NH2, �CH3, and �CN groups were estimated from the force constants.

Vibrational analysis of 1,3-thiazolidine-2-thione and its selenium analogue

The i.r. spectra of 1,3-thiazolidine-2-thione, ?2-selone and their N-deuteriated derivatives have been investigated in the region between 4000 and 20 cm?1. A complete assignment of the fundamental vibrational frequencies has been made based upon the normal coordinate analysis carried out using a simple Urey�Bradley force field supplemented by the valence force constants for the out-of-plane vibrations of the planar molecular skeleton. The proposed assignments are discussed in relation to the group frequencies in structurally related molecules and in terms of the computed potential energy distributions among the symmetry coordinates.

Roofed polyquinanes: synthesis and electronic structure

Starting from readily available norbornenobenzoquinone 7 and employing a photothermal metathesis reaction as the main strategy, novel "roofed" polyquinane bisenones 3 and 13 have been synthesized. Among these, the former is potentially serviceable for further elaboration to dodecahedrane 1. Catalytic hydrogenation of 3 provided the dione 12, which fully inscribes the circumference of dodecahedrane sphere. The "roofed" C-16-bisenone 3 has been successfully annulated to C19-bisenone 24 and C19-trisenone 26 by employing the Greene methodology and Pauson-Khand reaction, respectively. The molecular structures of 3 and 13 were computed using molecular mechanics and semiempirical MO methods. The nonbonded distances between the double bonds vary strongly with the method employed. The interactions between the pi-MO's were, therefore, probed by means of photoelectron (PE) spectroscopy. Comparison with the PE spectra of a series of model systems with increasing complexity enabled an unambiguous assignment of the observed peaks. The symmetric and antisymmetric combinations of the pi-MO's of the enone moieties of 3 and 13 show large splittings, characteristic of propano-bridged systems in which through-space and through-bond effects act in concert.

Hydrologic drought prediction under climate change: Uncertainty modeling with Dempster-Shafer and Bayesian approaches

Representation and quantification of uncertainty in climate change impact studies are a difficult task. Several sources of uncertainty arise in studies of hydrologic impacts of climate change, such as those due to choice of general circulation models (GCMs), scenarios and downscaling methods. Recently, much work has focused on uncertainty quantification and modeling in regional climate change impacts. In this paper, an uncertainty modeling framework is evaluated, which uses a generalized uncertainty measure to combine GCM, scenario and downscaling uncertainties. The Dempster-Shafer (D-S) evidence theory is used for representing and combining uncertainty from various sources. A significant advantage of the D-S framework over the traditional probabilistic approach is that it allows for the allocation of a probability mass to sets or intervals, and can hence handle both aleatory or stochastic uncertainty, and epistemic or subjective uncertainty. This paper shows how the D-S theory can be used to represent beliefs in some hypotheses such as hydrologic drought or wet conditions, describe uncertainty and ignorance in the system, and give a quantitative measurement of belief and plausibility in results. The D-S approach has been used in this work for information synthesis using various evidence combination rules having different conflict modeling approaches. A case study is presented for hydrologic drought prediction using downscaled streamflow in the Mahanadi River at Hirakud in Orissa, India. Projections of n most likely monsoon streamflow sequences are obtained from a conditional random field (CRF) downscaling model, using an ensemble of three GCMs for three scenarios, which are converted to monsoon standardized streamflow index (SSFI-4) series. This range is used to specify the basic probability assignment (bpa) for a Dempster-Shafer structure, which represents uncertainty associated with each of the SSFI-4 classifications. These uncertainties are then combined across GCMs and scenarios using various evidence combination rules given by the D-S theory. A Bayesian approach is also presented for this case study, which models the uncertainty in projected frequencies of SSFI-4 classifications by deriving a posterior distribution for the frequency of each classification, using an ensemble of GCMs and scenarios. Results from the D-S and Bayesian approaches are compared, and relative merits of each approach are discussed. Both approaches show an increasing probability of extreme, severe and moderate droughts and decreasing probability of normal and wet conditions in Orissa as a result of climate change. (C) 2010 Elsevier Ltd. All rights reserved.

Total synthesis of substituted (±)-6,6-dimethyl-B-norestra-1,3,5(10)-trien-17?-ols and their 9?-isomers

Total syntheses of (±)-1,4-dimethoxy-6,6-dimethyl-B-norestra-1,3,5(10)-trien-17?-ol(11a), (±)-2,3-dimethoxy-6,6-dimethyl-B-norestra-1,3,5(10)-trien-17?-ol (11b), and (±)-3-methoxy-6,6-dimethyl-B-norestra-1,3,5(10)trien-17?-ol (11c), have been carried out starting from 4,7-dimethoxy-3,3-dimethylindan-1-one (1), 5,6-dimethoxy-3,3-dimethylindan-1-one (2), and 4?-methoxy-3-methylbut-2-enophenone (4), respectively. Generally, it is found that the intermediate 6,6-dimethyl-B-norestra-1,3,5(10),8-tetraen-17?-ols (10), on lithium�liquid ammonia reduction, yield a mixture of 8?,9?- and 8?,9?-trienols, (11) and (12) respectively, in the ratio 1 : 1. This is due to the comparable stabilities of these two isomers. However, the reduction carried out in presence of aniline affords a higher percentage of the 8?,9?-trienol (11). The assignment of configurations is made by chemical and 1H n.m.r. analysis. Catalytic hydrogenation of the tetraenols (10) is shown to proceed via initial isomerisation to the corresponding 6,6-dimethyl-B-norestra-1,3,5(10),9(11)-tetraen-17?-ols (26), followed by hydrogenation from the ?-side to give, exclusively, the 8?,9?-trienols (12).

Determination of rational strategies for players in two-target games

This paper addresses some of the basic issues involved in the determination of rational strategies for players in two-target games. We show that unlike single-target games where the task of role assignment and selection of strategies is conceptually straightforward, in two-target games, many factors like the preference ordering of outcomes by players, the relative configuration of the target sets and secured outcome regions, the uncertainty about the parameters of the game, etc., also influence the rational selection of strategies by players. The importance of these issues is illustrated through appropriate examples.

Raman spectral studies of borate glasses

Raman spectroscopic measurements in borate glasses have been reviewe. The review shows that the technique is useful in identifying the structural groups present in the borate on the basis of the Krogh-Moe hypothesis. Vitreous B2O3 and alkali borates are extensvvely studied and a satisfactory assignment of bands is possible by a careful consideration of the literature. A cation effect on the borate netwoork is observed. Availaable measurements on binary borates other than alkali borates and on ternary borates are limited and more work is required to identify the structural modifications that take place with composition. Mixed alkali effect is reported only lithium-caesium borade and shows the formation of non-bridging oxygens, destroying the six-membered rings when Li2O is replaced by Cs2O. Fast ionic glasses (alkali borates containing alkali halides) yield the same Raman spectra as the alkali borates, except when the alkali is a fluoride.

Relationship between the controllability grammian and closed-loop eigenvalues: the single input case

The controllability grammian is important in many control applications. Given a set of closed-loop eigenvalues the corresponding controllability grammian can be obtained by computing the controller which assigns the eigenvalues and then by solving the Lyapunov equation that defines the grammian. The relationship between the controllability grammian, resulting from state feedback, and the closed-loop eigenvalues of a single input linear time invariant (LTI) system is obtained. The proposed methodology does not require the computation of the controller that assigns the specified eigenvalues. The closed-loop system matrix is obtained from the knowledge of the open-loop system matrix, control influence matrix and the specified closed-loop eigenvalues. Knowing the closed-loop system matrix, the grammian is then obtained from the solution of the Lyapunov equation that defines it. Finally the proposed idea is extended to find the state covariance matrix for a specified set of closed-loop eigenvalues (without computing the controller), due to impulsive input in the disturbance channel and to solve the eigenvalue assignment problem for the single input case.