Compute Canada

We have calculated the effects of structural distortions of armchair carbon nanotubes on their electronic and electrical properties. We found that the bending of the nanotubes decreases their transmission function in certain energy ranges and leads to an increased electrical resistance. Electronic structure calculations show that these energy ranges contain localized states with significant $\ensuremath{\sigma}\ensuremath{-}\ensuremath{\pi}$ hybridization resulting from the increased curvature produced by bending. Twisting strongly affects the electronic structure of nanotubes (NTs). Normally metallic armchair $(n,n)$ NT's develop a band gap which initially scales linearly with twisting angle and then reaches a constant value. This saturation is associated with a structural transition to a flattened helical structure. The computed values of the twisting energy and of the band gap are strongly affected by allowing structural relaxation in the twisted structures. Finally, our calculations show that the large contact resistances observed for single-wall NT's are likely due to the weak coupling of the NT to the metal in side bonded NT-metal configurations.

Stellar evolution models of stars of 1.45 to 3.0 M fi have been calculated including the atomic diffusion of metals and radiative accelerations for all species in the OPAL opacities. As the abundances change, the opacities and radiative accelerations are continuously recalculated during evolution. These models develop iron peak convection zones centered at a temperature of approximately 200 000 K. If one then assumes that there is sufficient overshoot to homogenize the surface regions between the hydrogen, helium and iron peak convection zones, it is shown here that the surface abundances variations that are produced, without any arbitrary parameter, closely resemble the abundance anomalies of AmFm stars except that they are larger by a factor of about 3. Detailed evolutionary model calculations have been carried out varying the turbulence in the outer stellar regions in order to improve the agreement with the observed anomalies in AmFm stars. The outer mass mixed by turbule...

The solar evolution has been calculated including all the e ects of the di usion of helium and heavy elements. Monochromatic opacities are used to calculate radiative accelerations and Rosseland opacities at each evolution time step, taking into account the local abundance changes of all important (21) chemical elements. The OPAL monochromatic data are used for the opacities and the radiative accelerations. The Opacity Project data are needed to calculate how chemical species and electrons share the momentum absorbed from the radiation ux.

BACKGROUND: With the decreasing cost of sequencing and the rapid developments in genomics technologies and protocols, the need for validated bioinformatics software that enables efficient large-scale data processing is growing. FINDINGS: Here we present GenPipes, a flexible Python-based framework that facilitates the development and deployment of multi-step workflows optimized for high-performance computing clusters and the cloud. GenPipes already implements 12 validated and scalable pipelines for various genomics applications, including RNA sequencing, chromatin immunoprecipitation sequencing, DNA sequencing, methylation sequencing, Hi-C, capture Hi-C, metagenomics, and Pacific Biosciences long-read assembly. The software is available under a GPLv3 open source license and is continuously updated to follow recent advances in genomics and bioinformatics. The framework has already been configured on several servers, and a Docker image is also available to facilitate additional installations. CONCLUSIONS: GenPipes offers genomics researchers a simple method to analyze different types of data, customizable to their needs and resources, as well as the flexibility to create their own workflows.

This paper presents a new model for estimating optical flow based on the motion of planar regions plus local deformations. The approach exploits brightness information to organize and constrain the interpretation of the motion by using segmented regions of piecewise smooth brightness to hypothesize planar regions in the scene. Parametric flow models are estimated in these regions in a two step process which first computes a coarse fit and then estimates the appropriate parametrization of the motion of the region. The initial fit is refined using a generalization of the standard area-based regression approaches. Since the assumption of planarity is likely to be violated, we allow local deformations from the planar assumption in the same spirit as physically-based approaches which model shape using coarse parametric models plus local deformations. This parametric plus deformation model exploits the strong constraints of parametric approaches while retaining the adaptive nature of regularization approaches. Experimental results on a variety of images model produces accurate flow estimates while the incorporation of brightness segmentation boundaries.

Our recently developed method for the calculation of indirect nuclear spin–spin coupling constants is studied in more detail. For the couplings between nuclei other than N, O, and F (which have lone pairs) the method yields very reliable results. The results for 1J(Si–H) couplings are presented and their dependence on the basis set quality is analyzed. Also, 2J(H–H) and 1J(X–H) couplings (X=C, Si, Ge, Sn) in XH4 molecules are presented and the relativistic effects on 1J(X–H) are discussed. The limitations of the method, which is based on density functional theory, are connected with the inability of the present LDA and GGA exchange-correlation functionals to describe properly the spin-perturbations (through the Fermi-contact mechanism) on atoms to the right of the periodic table (containing lone pairs). However, the deviations from experiment of the calculated couplings for such nuclei are systematic, at least for one-bond couplings, and therefore these calculated couplings should still be useful for NMR structure determinations.

The density functional calculations using the Perdew nonlocal corrections to exchange and correlation have been carried out for a sequence of hydrated proton clusters. The optimized structures were obtained up to H13O+6. It is found that H3O+ is indeed the central unit in all the lowest energy structures we found. Our results support the argument that the structure with a four-coordinate first solvation shell is very unlikely in small hydrated proton clusters. The density functional calculations with the Perdew nonlocal corrections to exchange and correlation give somewhat shorter hydrogen bond lengths, but slightly longer chemical bond lengths as compared with the post-Hartree–Fock calculations. The harmonic vibrational frequencies and IR intensities of various vibrational modes have been generated for all the structures optimized. Results for small clusters are compared with the high resolution experimental spectroscopy studies of Yeh et al. and Begemann et al. Results for larger clusters are used to interpret the low resolution spectra of Schwartz. Very good accord with experimental results is obtained. The solvent effects on proton transfer energy barriers in clusters have been studied by designing a few model systems. The barrier is found to be very sensitive to the solvent configurations. When the solvent water is replaced by the classical partial charge model, a significant change of the barrier is observed, indicating that a quantitative treatment will ultimately require a good pseudopotential to properly account for the quantum nature of the solvent. A combined density functional and molecular dynamics simulation was used to calculate the proton transfer energy and free energy barrier in aqueous solution. The barrier is found to be 3 kcal/mol higher than in gas phase. Very large solvent fluctuation is observed which may have a significant influence on the reaction rate.

We review the behavior of the oscillating shear layer produced by gravity waves below the surface convection zone of the Sun. We show that, under asymmetric filtering produced by this layer, gravity waves of low spherical order, which are stochastically excited at the base of the convection zone of late type stars, can extract angular momentum from their radiative interior. The time-scale for this momentum extraction in a Sun-like star is of the order of 10^7 years. The process is particularly efficient in the central region, and it could produce there a slowly rotating core.

Stellar models, including all effects of atomic diffusion and radiative accelerations, are evolved from the pre-main sequence to the giant branch for stars of 1.3 to 4.0 M☉, with metallicity ranging from Z0 = 0.01 to 0.03. It is shown that radiative accelerations lead to the accumulation of iron-peak elements around 200,000 K; this increases the opacity and causes the appearance of Fe convection zones when macroscopic motions are not rapid enough to wipe out the effects of particle transport. The behavior of Fe convection zones and conditions for their appearance are studied in detail. Iron-peak convection zones appear naturally in all solar metallicity models more massive than 1.5 M☉. In the 1.5 M☉ model, it is present only for a fraction of the main-sequence lifetime, but in models without turbulence of 1.7 M☉ and more, the Fe convection zone rapidly develops after arrival on the main-sequence and remains until its end. For a metallicity of Z = 0.01, an Fe convection zone appears even in a 1.3 M☉ model. Moreover, the interaction between the diffusion velocities of different species leads to an accumulation of heavy elements around the convective core, causing semiconvection. A detached semiconvection zone develops in the 1.5 M☉ model. Finally, the surface abundances are calculated using a number of turbulence models and compared to observations of τ UMa in order to show how abundance anomalies may be used to test various turbulence models; the gravity at which abundance anomalies should be expected to disappear is determined. It is shown that in Am stars, the Ca underabundance should disappear during evolution at the same gravity as iron-peak overabundances.

Consistent stellar evolution models of F stars (1.1-1.5 M☉) are calculated with radiative forces, opacities, and diffusion for all elements included in OPAL's opacity tables. The opacities and radiative forces are continuously recomputed during evolution from OPAL's monochromatic data (~1.5 Gbyte) in order to include all effects of abundance changes due to diffusion and nuclear evolution. TOPbase is also used for radiative accelerations. Iron surface overabundances occur in stars more massive than 1.3 M☉. Local overabundances of iron peak elements increase the Rosseland opacity in a region at the base of the convection zone by a factor of 3-6; this increases the mass of the convective zone by up to a factor of 5. It is important to follow Cr, Mn, and Ni independently of Fe, since they peak at different temperatures within the star. The predicted abundance anomalies are much larger than observed in most F-type stars of open clusters. This suggests that atomic diffusion is not the only process responsible for the Li gap in open clusters. The predicted iron peak element overabundances indicate trends that are compatible with those observed in Fm stars. They however tend to be larger than the observed overabundances, leaving room for some perturbing hydrodynamical process. The present models, devoid of free parameters, are a necessary step in constraining the additional hydrodynamical processes required to better reproduce observed surface abundances. Since the abundances of 28 elements are calculated, one may have 27 constraints on stellar hydrodynamics, once the relative abundances of all species have been determined observationally.

Evolutionary models have been calculated for Pop II stars of 0.5 to 1.0$M_\\odot$ from the pre-main-sequence to the lower part of the giant branch. Rosseland opacities and radiative accelerations were calculated taking into account the concentration variations of 28 chemical species, including all species contributing to Rosseland opacities in the OPAL tables. The effects of radiative accelerations, thermal diffusion and gravitational settling are included. While models were calculated both for Z=0.00017 and 0.0017, we concentrate on models with Z=0.00017 in this paper. These are the first Pop II models calculated taking radiative acceleration into account. It is shown that, at least in a 0.8$M_\\odot$ star, it is a better approximation not to let Fe diffuse than to calculate its gravitational settling without including the effects of $g_{rad}(Fe)$. In the absence of any turbulence outside of convection zones, the effects of atomic diffusion are large mainly for stars more massive than 0.7$M_\\odot$. Overabundances are expected in some stars with $\\teff \\ge 6000K$. Most chemical species heavier than CNO are affected. At 12 Gyr, overabundance factors may reach 10 in some cases (e.g. for Al or Ni) while others are limited to 3 (e.g. for Fe). The calculated surface abundances are compared to recent observations of abundances in globular clusters as well as to observations of Li in halo stars. It is shown that, as in the case of Pop I stars, additional turbulence appears to be present.

Abstract The present paper is the second article in a three‐part series on anisotropic mesh adaptation and its application to (2‐D) structured and unstructured meshes. In the first article, the theory was presented, the methodology detailed and brief examples given of the application of the method to both types of grids. The second part details the application of the mesh adaptation method to structured grids. The adaptation operations are restricted to mesh movement in order to avoid the creation of hanging nodes. Being based on a spring analogy with no restrictive orthogonality constraint, a wide grid motion is allowed. The adaptation process is first validated on analytical test cases and its high efficiency is shown on relevant transonic and supersonic benchmarks. These latter test cases are also solved on adapted unstructured grids to provide a reference for comparison studies. The third part of the series will demonstrate the capability of the methodology on 2‐D unstructured test cases. Copyright © 2002 John Wiley & Sons, Ltd.

The topology of the molecular electrostatic potential of 18 molecules, calculated in the framework of Kohn–Sham density functional theory, is studied. For the location of the different kinds of critical points a newly developed search algorithm is applied. A chemical interpretation of the critical points in terms of lone pairs, π bonds, hybrid orbitals and other electronic structure elements is suggested. A Poincaré–Hopf relationship for the molecular electrostatic potential is derived, connecting electronic structure elements and electrostatic reactivity via the topology of the molecular electrostatic potential.

An ab initio molecular dynamics simulation technique is developed employing the Born–Oppenheimer (BO) approach in the framework of a Gaussian implementation of Kohn–Sham density functional theory (DFT). Simulation results for H5O2+ at 200 K are reported. The density profiles, autocorrelation functions and power spectra are presented. The anharmonic frequencies at 200 K are found to be close to the harmonic frequencies calculated directly from quantum methods at 0 K. Structures of large hydrated proton clusters are optimized. Simulated annealing techniques were employed to search for low energy structures and found to be very useful for clusters with 7–8 water molecules. A few very different structures with ground state energy 1–2 kcal/mol apart are shown. H3O+ is found to be the central unit of a few structures optimized. The ionic hydrogen bond was responsible for the stability of the H9O4+ unit in the large hydrated proton clusters. We also find structures with nascent H5O2+ units at the center whose energy is close to, sometimes even lower than that of the H3O+ centered structures. This can be used to explain the solvation facilitated proton transfer in clusters and in solution. The vibrational frequencies of the structures we optimized are tabulated and compared with the experimental results of Price et al. Questions are raised regarding their prediction of a new feature due to water molecules in the third solvation shell. Some new features have been observed for large clusters with heretofore unpredicted structures.

Abstract The present paper is the third article in a three‐part series on anisotropic mesh adaptation and its application to two‐ and three‐dimensional, structured and unstructured meshes. This third paper concerns the application of the full adaptation methodology to 2‐D unstructured meshes, including all four mesh modification strategies presented in Part I, i.e. refinement/coarsening, edge swapping and node movement. The mesh adaptation procedure is validated through a careful monitoring of a single adaptation step and of the solution–adaptation loop. Independence from the initial mesh and from the flow solver is illustrated. The efficiency of the overall methodology is investigated on relevant laminar and turbulent flow benchmarks. Copyright © 2002 John Wiley & Sons, Ltd.

Isochrones for ages between 12 and 18 Gyr have been derived from the evolutionary tracks presented in Paper I (Richard et al.) for masses from 0.5 to 1.0 M☉ and initial chemical abundances corresponding to (1) Y = 0.2352, Z = 1.69 × 10-4 ([Fe/H] = -2.31, [α/Fe] = 0.3) and (2) Y = 0.2370, Z = 1.69 × 10-3 ([Fe/H = -1.31, [α/Fe] = 0.3). These are the first models for Population II stars in which both gravitational settling and radiative accelerations have been taken into account. Allowance for these diffusive processes leads to a 10%-12% reduction in age at a given turnoff luminosity. However, in order for the diffusive models to satisfy the constraints from Li and Fe abundance data (see Paper I) and to reproduce the observed morphologies of globular cluster (GC) color-magnitude diagrams (CMDs) in a straightforward way, extra mixing just below the boundary of the convective envelope seems to be necessary. Indeed, when additional turbulent mixing is invoked, the resultant models are able to satisfy all of these constraints, as well as those provided by the CMDs of local subdwarfs, rather well. Moreover, they imply an age near 13.5 Gyr for M92, which is one of the most metal-deficient (and presumably one of the oldest) of the Galaxy's GCs, if the field subgiant HD 140283 is used to derive the cluster distance. Comparisons of field subdwarfs and subgiants with a recently published fiducial for M5 suggests that the cluster has [Fe/H] ≲ -1.4, in conflict with some estimates based on high-resolution spectroscopy, if the metallicities of the field stars are to be trusted. In addition, an age of ≈11.5 Gyr is found for M5, irrespective of whether diffusive or nondiffusive isochrones are employed in the analysis. The implications of our results for the extragalactic distance scale and for the Hubble constant are briefly discussed in the context of the presently favored ΩM ≈ 0.35, ΩΛ ≈ 0.65 cosmological model.

Evolutionary models have been calculated for Pop II stars of 0.5 to 1.0$M_\odot$ from the pre-main-sequence to the lower part of the giant branch. Rosseland opacities and radiative accelerations were calculated taking into account the concentration variations of 28 chemical species, including all species contributing to Rosseland opacities in the OPAL tables. The effects of radiative accelerations, thermal diffusion and gravitational settling are included. While models were calculated both for Z=0.00017 and 0.0017, we concentrate on models with Z=0.00017 in this paper. These are the first Pop II models calculated taking radiative acceleration into account. It is shown that, at least in a 0.8$M_\odot$ star, it is a better approximation not to let Fe diffuse than to calculate its gravitational settling without including the effects of $g_{rad}(Fe)$. In the absence of any turbulence outside of convection zones, the effects of atomic diffusion are large mainly for stars more massive than 0.7$M_\odot$. Overabundances are expected in some stars with $\teff \ge 6000K$. Most chemical species heavier than CNO are affected. At 12 Gyr, overabundance factors may reach 10 in some cases (e.g. for Al or Ni) while others are limited to 3 (e.g. for Fe). The calculated surface abundances are compared to recent observations of abundances in globular clusters as well as to observations of Li in halo stars. It is shown that, as in the case of Pop I stars, additional turbulence appears to be present.

The conformational equilibrium of gaseous glycine presents a severe challenge to quantum chemistry and, in particular, to density functional theory (DFT), due to the presence of internal hydrogen bonds. We present new DFT results for the structure and the energetics of glycine and malonaldehyde, using the recently developed nonlocal exchange-correlation functionals BLap1 and PLap1. A comparative analysis is made with the results of the generalized-gradient-approximation (GGA) schemes Becke–Perdew (BP86) and Becke–Lee–Yang–Parr (BLYP), the hybrid Hartree–Fock (HF)-DFT methods B3PW91 and B3LYP, with post-HF methods, and with the available experimental data. Our BLap1/TZVP and PLap1/TZVP values for the energy margin between the two lowest conformers of glycine (0.84 and 1.05 kcal/mol, respectively) are within the experimental error bars (1.0±0.5 kcal/mol). MP2 underestimates this energy difference by about 0.5 kcal/mol, BLYP and the hybrid methods are off by about 0.9 kcal/mol. The optimized geometry of malonaldehyde is improved with the Lap1 functionals, compared to the GGA results reported previously. Improvement over the GGA is also achieved for the energy barrier for the internal proton transfer in malonaldehyde. Recent high quality post-HF (G2) calculations of Barone and Adamo1 yield 4.4 kcal/mol. The best GGA (PP86) value of 2.1 kcal/mol is seriously underestimated. The best B3LYP estimate is 3.0 kcal/mol.1 Our BLap1/TZVP (3.28 kcal/mol) and PLap1/TZVP (4.56 kcal/mol) values are in the correct energy range, the latter being, in fact, very close to the G2 estimate.

Physicians and the general public are increasingly using web-based tools to find answers to medical questions. The field of rare diseases is especially challenging and important as shown by the long delay and many mistakes associated with diagnoses. In this paper we review recent initiatives on the use of web search, social media and data mining in data repositories for medical diagnosis. We compare the retrieval accuracy on 56 rare disease cases with known diagnosis for the web search tools google.com, pubmed.gov, omim.org and our own search tool findzebra.com. We give a detailed description of IBM's Watson system and make a rough comparison between findzebra.com and Watson on subsets of the Doctor's dilemma dataset. The recall@10 and recall@20 (fraction of cases where the correct result appears in top 10 and top 20) for the 56 cases are found to be be 29%, 16%, 27% and 59% and 32%, 18%, 34% and 64%, respectively. Thus, FindZebra has a significantly (p < 0.01) higher recall than the other 3 search engines. When tested under the same conditions, Watson and FindZebra showed similar recall@10 accuracy. However, the tests were performed on different subsets of Doctors dilemma questions. Advances in technology and access to high quality data have opened new possibilities for aiding the diagnostic process. Specialized search engines, data mining tools and social media are some of the areas that hold promise.

Première partie : le premier chapitre contient un exposé sommaire des définitions de la théorie du potentiel de Hunt ; le second introduit les fonctionnelles multiplicatives de Markov, les semi-groupes subordonnés, les temps terminaux, et établit l’équivalence de ces notions. Le chapitre III donne la caractérisation de certains semi-groupes subordonnés (dits “exacts”) qui possèdent une théorie du potentiel satisfaisante, et montre que tout semi-groupe subordonné diffère “peu” d’un tel semi-groupe exact. À l’aide de ces résultats, on peut établir au chapitre IV que toutes les fonctionnelles multiplicatives possèdent la “propriété forte de Markov”. Enfin, le chapitre V a pour objet la caractérisation des semi-groupes subordonnés exacts au moyen de leur résolvante. Seconde partie : le premier chapitre étudie les conséquences d’une nouvelle hypothèse [l’hypothèse (L)], particulièrement en ce qui concerne : les familles filtrantes croissantes et décroissantes de fonctions excessives ; les deux structures naturelles d’espace de Riesz sur l’espace des différences de fonctions excessives ; les ensembles semi-polaires et la topologie fine. Le second chapitre définit les principales classes de fonctions excessives : fonctions harmoniques, potentiels, fonctions régulières, fonctions de la classe (D). L’étude des fonctionnelles additives de Markov est abordée au chapitre III, poursuivie au chapitre IV : le résultat fondamental en est le théorème d’existence et d’unicité de la représentation d’un potentiel de la classe (D) comme potentiel d’une fonctionnelle additive de la “classe d’unicité”. Enfin, les chapitres V et VI contiennent, l’un des théorèmes de compacité (qui peuvent dans certains cas tenir lieu du théorème de compacité vague des ensembles bornés de mesures), l’autre des applications à la théorie “classique” du potentiel. Le chapitre VII, consacré aux changements aléatoires de temps, établit un lien entre les deux parties de ce travail, lorsque les fonctionnelles envisagées sont continues.