Implicit and multigrid procedures for steady-state computations with upwind algorithms

A computational study for the convergence acceleration of Euler and Navier-Stokes computations with upwind schemes has been conducted in a unified framework. It involves the flux-vector splitting algorithms due to Steger-Warming and Van Leer, the flux-difference splitting algorithms due to Roe and Osher and the hybrid algorithms, AUSM (Advection Upstream Splitting Method) and HUS (Hybrid Upwind Splitting). Implicit time integration with line Gauss-Seidel relaxation and multigrid are among the procedures which have been systematically investigated on an individual as well as cumulative basis. The upwind schemes have been tested in various implicit-explicit operator combinations such that the optimal among them can be determined based on extensive computations for two-dimensional flows in subsonic, transonic, supersonic and hypersonic flow regimes. In this study, the performance of these implicit time-integration procedures has been systematically compared with those corresponding to a multigrid accelerated explicit Runge-Kutta method. It has been demonstrated that a multigrid method employed in conjunction with an implicit time-integration scheme yields distinctly superior convergence as compared to those associated with either of the acceleration procedures provided that effective smoothers, which have been identified in this investigation, are prescribed in the implicit operator.

A linear programming approach for estimating the structure of a sparse linear genetic network from transcript profiling data

Background: A genetic network can be represented as a directed graph in which a node corresponds to a gene and a directed edge specifies the direction of influence of one gene on another. The reconstruction of such networks from transcript profiling data remains an important yet challenging endeavor. A transcript profile specifies the abundances of many genes in a biological sample of interest. Prevailing strategies for learning the structure of a genetic network from high-dimensional transcript profiling data assume sparsity and linearity. Many methods consider relatively small directed graphs, inferring graphs with up to a few hundred nodes. This work examines large undirected graphs representations of genetic networks, graphs with many thousands of nodes where an undirected edge between two nodes does not indicate the direction of influence, and the problem of estimating the structure of such a sparse linear genetic network (SLGN) from transcript profiling data. Results: The structure learning task is cast as a sparse linear regression problem which is then posed as a LASSO (l1-constrained fitting) problem and solved finally by formulating a Linear Program (LP). A bound on the Generalization Error of this approach is given in terms of the Leave-One-Out Error. The accuracy and utility of LP-SLGNs is assessed quantitatively and qualitatively using simulated and real data. The Dialogue for Reverse Engineering Assessments and Methods (DREAM) initiative provides gold standard data sets and evaluation metrics that enable and facilitate the comparison of algorithms for deducing the structure of networks. The structures of LP-SLGNs estimated from the INSILICO1, INSILICO2 and INSILICO3 simulated DREAM2 data sets are comparable to those proposed by the first and/or second ranked teams in the DREAM2 competition. The structures of LP-SLGNs estimated from two published Saccharomyces cerevisae cell cycle transcript profiling data sets capture known regulatory associations. In each S. cerevisiae LP-SLGN, the number of nodes with a particular degree follows an approximate power law suggesting that its degree distributions is similar to that observed in real-world networks. Inspection of these LP-SLGNs suggests biological hypotheses amenable to experimental verification. Conclusion: A statistically robust and computationally efficient LP-based method for estimating the topology of a large sparse undirected graph from high-dimensional data yields representations of genetic networks that are biologically plausible and useful abstractions of the structures of real genetic networks. Analysis of the statistical and topological properties of learned LP-SLGNs may have practical value; for example, genes with high random walk betweenness, a measure of the centrality of a node in a graph, are good candidates for intervention studies and hence integrated computational – experimental investigations designed to infer more realistic and sophisticated probabilistic directed graphical model representations of genetic networks. The LP-based solutions of the sparse linear regression problem described here may provide a method for learning the structure of transcription factor networks from transcript profiling and transcription factor binding motif data.

A Jacobian-Based Algorithm for Planning Attitude Maneuvers Using Forward and Reverse Rotations

Algorithms for planning quasistatic attitude maneuvers based on the Jacobian of the forward kinematic mapping of fully-reversed (FR) sequences of rotations are proposed in this paper. An FR sequence of rotations is a series of finite rotations that consists of initial rotations about the axes of a body-fixed coordinate frame and subsequent rotations that undo these initial rotations. Unlike the Jacobian of conventional systems such as a robot manipulator, the Jacobian of the system manipulated through FR rotations is a null matrix at the identity, which leads to a total breakdown of the traditional Jacobian formulation. Therefore, the Jacobian algorithm is reformulated and implemented so as to synthesize an FR sequence for a desired rotational displacement. The Jacobian-based algorithm presented in this paper identifies particular six-rotation FR sequences that synthesize desired orientations. We developed the single-step and the multiple-step Jacobian methods to accomplish a given task using six-rotation FR sequences. The single-step Jacobian method identifies a specific FR sequence for a given desired orientation and the multiple-step Jacobian algorithm synthesizes physically feasible FR rotations on an optimal path. A comparison with existing algorithms verifies the fast convergence ability of the Jacobian-based algorithm. Unlike closed-form solutions to the inverse kinematics problem, the Jacobian-based algorithm determines the most efficient FR sequence that yields a desired rotational displacement through a simple and inexpensive numerical calculation. The procedure presented here is useful for those motion planning problems wherein the Jacobian is singular or null.

Broadband Suspended Microstrip Antenna For Circular Polarization

In this paper we propose a circularly polarized (CP) microstrip antenna on a suspended substrate with a coplanar capacitive feed and a slot within the rectangular patch. The antenna has an axial ratio bandwidth (< 3 dB) of 7.1%. The proposed antenna exhibits a much higher impedance bandwidth of about 49% (S11 < -10 dB) and also yields return loss better than -15 dB in the useful range of circular polarization. Measured characteristics of the antenna are in good agreement with the simulated results. The radiation patterns indicate good cross polarization rejection and low back lobe radiations. The design proposed here can be scaled to any frequency of interest.

trans-Dichloro-bis-(arylazoimidazole)palladium(II): Synthesis, Structure, Photoisomerization, and DFT Calculation

Reaction between PdCl2 and 1-alkyl-2-(arylazo)imidazole (RaaiR') or 1-alkyl-2-(naphthyl-alpha/beta-azo)imidazole (alpha/beta-NaiR') under reflux in ethanol has isolated complexes of compositions Pd(RaaiR')(2)Cl-2 (5, 6) and Pd(alpha/beta-NaiR')(2)Cl-2 (7, 8). The X-ray structure determination of one of the molecules, Pd(alpha-NaiBz)(2)Cl-2 (7c), has reported a trans-PdCl2 configuration, and alpha-NaiBz acts as monodentate N(imidazole) donor ligand. The spectral (IR, UV-vis, H-1 NMR) data support the structure. UV light irradiation (light source: Perkin-Elmer LS 55 spectrofluorimeter, Xenon discharge lamp, lambda = 360-396 nm) in a MeCN solution of the complexes shows E-to-Z isomerization of the coordinated azoimidazole unit. The reverse transformation, Z-to-E, is very slow with visible light irradiation. Quantum yields (phi(E-Z)) of E-to-Z isomerization are calculated, and phi is lower than that of the free ligand but comparable with those of Cd(II) and Hg(II) complexes of the same ligand. The Z-to-E isomerization is a thermally induced process. The activation energy (E-a) of Z-to-E isomerization is calculated by controlled-temperature experimentation. cis-Pd(azoimidazole)Cl-2 complexes (azomidazole acts as N(imidazole) and N(azo) Chelating ligand) do not respond upon light irradiation, which supports the idea that the presence of noncoordinated azo-N to make free azo (-N=N-) function is important to reveal photochromic activity. DFT calculation of Pd(alpha-NaiBz)(2)Cl-2 (7c) has suggested that the HOMO of the molecule is constituted of Pd (32%) and Cl (66%), and hence photo excitation may use the energy of Pd and Cl instead of that of the photofunctional -N=N-Ar motif; thus, the rate of photoisomerization and quantum yield decrease versus the free ligand values.

Frictional response of fatty acids on steel

Self-assembled monolayers of fatty acids were formed on stainless steel by room-temperature solution deposition. The acids are covalently bound to the Surface as carboxylate in a bidentate manner. To explore the effect Of Saturation in the carbon backbone on friction in sliding tribology, we Study the response of saturated stearic acid (SA) and unsaturated linoleic acid (LA) as self-assembled monolayers using lateral force microscopy and nanotribometry and when the molecules are dispersed in hexadecane, using pin-on-disc tribometry. Over a very wide range (10 MPa-2.5 GPa) of contact pressures it is consistently demonstrated that the unsaturated linoleic acid molecules yield friction which is significantly lower than that of the saturated stearic acid. it is argued, using density functional theory predictions and XPS of slid track, that when the molecular backbone of unsaturated fatty acids are tilted and pressed strongly by a probe, in tribological contact, the high charge density of the double bond region of the backbone allows coupling with the steel Substrate. The interaction yields a low friction carboxylate soap film on the substrate. The saturated fatty acid does not show this effect.

On optimum stratification with proportional allocation for a class of pareto distributions

Cum ./LSTA_A_8828879_O_XML_IMAGES/LSTA_A_8828879_O_ILM0001.gif rule [Singh (1975)] has been suggested in the literature for finding approximately optimum strata boundaries for proportional allocation, when the stratification is done on the study variable. This paper shows that for the class of density functions arising from the Wang and Aggarwal (1984) representation of the Lorenz Curve (or DBV curves in case of inventory theory), the cum ./LSTA_A_8828879_O_XML_IMAGES/LSTA_A_8828879_O_ILM0002.gif rule in place of giving approximately optimum strata boundaries, yields exactly optimum boundaries. It is also shown that the conjecture of Mahalanobis (1952) “. . .an optimum or nearly optimum solutions will be obtained when the expected contribution of each stratum to the total aggregate value of Y is made equal for all strata” yields exactly optimum strata boundaries for the case considered in the paper.

Disulfide luminescence. Emission characteristics of cyclic tetrapeptide disulfides

Luminescence has been detected in cyclic tetrapeptide disulfides containing only nonaromatic residues. Excitation of the S-S- n-cr transition between 280 and 290 nm leads to.ernission in the region 300-340 nm. The position and intensity of the emission band depends on the stereochemistry of the peptide and polarity of the solvent. Quantum yields ranging from 0.002 to 0.026 have been determined. Disulfide luminescence is quenched by oxygen and enhanced in solutions saturated with nitrogen. Contributions from disulfide linkages should be considered, when analysing the emission spectra of proteins, lacking tryptophan but having a high cystine content.

Singlet emission studies on porphyrins appended with heterocyclic bases

Porphyrins appended in the meso positions with 1,2-diazole, indole and quinoline are shown to exhibit enhanced fluorescence quantum yields relative to meso tetraphenyl porphyrin. The singlet emission yields decrease with the number of appended heterocyclic bases. An intramolecular charge transfer resonance mechanism has been advanced to interpret these results.

Dialkyl (3-Aryl- 1,2,4-oxadiazol-5-yl)phosphonates: Synthesis and Thermal Behavior-Evidence for Monomeric Alkyl Metaphosphate

Dialkyl (3-aryl-l,2,4-oxadiazol-5-yl)phosphonate6sa -h have been obtained by 1,3-dipolar cycloaddition of arenenitrile oxides 5a-f to dialkyl phosphorocyanidates (4a and 4b) in yields ranging between 30% and 58%. A standardized method for obtaining cyanidates 4a and 4b has been established. The diethyl thiophosphorocyanidate (4c) is less reactive than 4a and 4b, only the 3-(4'-nitrophenyl) derivative 6i being obtainable. While the IR and NMFt spectra of 6a-i were unexceptional, their UV spectra showed evidence of conjugative interaction in high degrees between the phosphonate and heterocyclic moieties as well as a varying conjugative interaction between the heterocyclic and aryl moieties. The oxadiazoles 6a-h are thermally labile and yield trialkyl phosphates 7 as the only identifiable products. A mechanism based on the intermediacy of monomeric alkyl metaphosphate 11 in the formation of trialkyl phosphate was postulated, and supportive evidence in the form of trapping the metaphosphate with acetophenone has been obtained.

Short-lived triplets of aliphatic thioketenes

The photophysical behavior of the triplets of three aliphatic thioketenes, namely di-tert-butylthioketene (1), 2,6-di-tert-butylcyclohexylthioketene (2) and 2,2,6,6-tetramethylcyclohexylthioketene, has been studied in fluid solutions at room temperature by nanosecond laser flash photolysis. Upon 532 nm laser excitation into the S1 state, the thioketenes in concentrated benzene solutions produce very short-lived transient absorptions (τ < 5 ns; λmax ≈ 450 nm) attributable to their triplets. The photogeneration of the latter under S1 excitation has also been established by energy transfer to all-trans-1,6-diphenyl-1,3,5-hexatriene. The factors which render the triplet lifetimes short are shown to be intrinsic in origin (rather than self-quenching). Unlike thiocarbonyl compounds in general, the thioketenes posses low intersystem crossing yields (less than 0.1 in benzene). From the kinetics of the quenching of a series of sensitizer triplets by 1 and 2, the thioketene triplet energies are estimated to be 43 – 44 kcal mol−1.

A laser flash photolysis study of pivalothiophenone triplets: steric and electronic effects in thione photoreaction kinetics

Upon laser pulse excitation (Aex = 532 nm) into the lowest-lying '(n,a*) band system, pivalothiophenones in benzene solutions give rise to short-lived triplets (Ama: = 325-335 nm, em: = (1 1-15) X lo3 M-' cm-I) with quantitative intersystem crossing efficiencies. The triplet yields decrease slightly (by 10-30%) upon changing A, to 308 nm (Le., upon excitation into S2). Kinetic data are presented for intrinsic triplet lifetimes, self-quenching, and quenching by oxygen, di-tert-butylnitroxy radical, and various reagents capable of interacting with the triplets via energy, electron, or hydrogen-atom transfer and by biradical formation (possibly leading to cycloaddition). The mechanisms of the quenching processes are discussed. Relative to rigid aromatic thiones, namely, xanthione and thiocoumarin, the interaction of pivalothiophenone triplets with most of the quenchers are kinetically inefficient. This is interpreted primarily as a manifestation of the steric crowding at positions a to the thiocarbonyl group.

Adsorption isitherms for neutral organic compounds-A hierarchy in modelling: Part IV. Charge of maximum adsorption-Statistical mechanical basis

The charge at which adsorption of orgamc compounds attains a maximum ( \sigma MAX M) at an electrochenucal interface is analysed using several multi-state models in a hierarchical manner The analysis is based on statistical mechamcal results for the following models (A) two-state site parity, (B) two-state muhl-slte, and (C) three-state site parity The coulombic interactions due to permanent and reduced dipole effects (using mean field approximation), electrostatic field effects and specific substrate interactions have been taken into account. The simplest model in the hierarchy (two-state site parity) yields the exphcit dependence of ( \sigma MAX M) on the permanent dipole moment, polarizability of the solvent and the adsorbate, lattice spacing, effective coordination number, etc Other models in the baerarchy bring to hght the influence of the solvent structure and the role of substrate interactions, etc As a result of this approach, the "composition" of oM.x m terms of the fundamental molecular constants becomes clear. With a view to use these molecular results to maxamum advantage, the derived results for ( \sigma MAX M) have been converted into those involving experimentally observable parameters lake Co, C 1, E N, etc Wherever possible, some of the earlier phenomenologlcal relations reported for ( \sigma MAX M), notably by Parsons, Damaskm and Frumkln, and Trasattl, are shown to have a certain molecular basis, vlz a simple two-state sate panty model.As a corollary to the hxerarcbacal modelling, \sigma MAX M and the potential corresponding to at (Emax) are shown to be constants independent of 0max or Corg for all models The lmphcatlon of our analysis f o r OmMa x with respect to that predicted by the generalized surface layer equation (which postulates Om~ and Ema x varlaUon with 0) is discussed in detail Finally we discuss an passing o M. and the electrosorptlon valency an this context.

Bismuth tungsten-oxide bronzes - a study of intergrowth phases and related aspects

Reaction of bismuth metal with WO$_3$ in the absence of oxygen yields interesting bronze-like phases. From analytical electron microscopy and X-ray photoelectron spectroscopy, the product phases are found to have the general composition Bi$_x$ WO$_3$ with bismuth in the 3+ state. Structural investigations made with high resolution electron micrscopy and cognate techniques reveal that when x < 0.02, a perovskite bronze is formed. When x $\geqslant$ 0.02, however, intergrowth tungsten bronzes (i.t.b.) containing varying widths of the WO$_3$ slab are formed, the lattice periodicity being in the range 2.3-5.1 nm in a direction perpendicular to the WO$_3$ slabs. Image-matching studies indicate that the bismuth atoms are in the tunnels of the hexagonal tungsten bronze (h.t.b.) strips and the h.t.b. strips always remain one-tunnel wide. Annealed samples show a satellite structure around the superlattice spots in the electron diffraction patterns, possibly owing to ordering of the bismuth atoms in the tunnels. The i.t.b. phases show recurrent intergrowths extending up to 100 nm in several crystals. The periodicity varies considerably within the same crystal wherever there is disordered intergrowth, but unit cell dimensions can be assigned from X-ray and electron diffraction patterns. The maximum value of x in the i.t.b. phases is ca. 0.07 and there is no evidence for the i.t.b. phase progressively giving way to the h.t.b. phase with increase in x. Hexagonal tungsten bronzes that contain bismuth with x up to 0.02 can be formed by starting from hexagonal WO$_3$, but the h.t.b. phase seems to be metastable. Optical, magnetic and electron transport properties of the i.t.b. phases have been measured and it appears that the electrons become itinerant when x > 0.05.

Use of 45° pulse pair as a filter for pure-phase two-dimensional NMR spectroscopy

Conventionally two-dimensional NMR spectra are recorded in the absolute-intensity mode (1-4). It has recently been demonstrated that absorption-mode 2D spectra have much higher resolution and are the preferred mode of presentation, especially for 2D spectra of biomolecules (5-7). Indeed, any experimental scheme which yields phasemixed lineshapes is subject to modification to yield pure-phase spectra, even at the expense of intensity and anomalous multiplet structure (8-10). For this purpose two types of filters are already known: the z filter (9, 20) and the purging pulse (8, 10). In this note, we propose a 45” pulse pair as a filter for obtaining pure-phase 2D spectra, mainly for experiments in which the above filters do not yield pure-phase spectra.