Broken-Symmetry Unrestricted Hybrid Density Functional Calculations on Nickel Dimer and Nickel Hydride

In the present work we investigate the adequacy of broken-symmetry unrestricted density functional theory (DFT) for constructing the potential energy curve of nickel dimer and nickel hydride, as a model for larger bare and hydrogenated nickel cluster calculations. We use three hybrid functionals: the popular B3LYP, Becke's newest optimized functional Becke98, and the simple FSLYP functional (50% Hartree-Fock and 50% Slater exchange and LYP gradient-corrected correlation functional) with two basis sets: all-electron (AE) Wachters+f basis set and Stuttgart RSC effective core potential (ECP) and basis set. We find that, overall, the best agreement with experiment, comparable to that of the high-level CASPT2, is obtained with B3LYP/AE, closely followed by Becke98/AE and Becke98/ECP. FSLYP/AE and B3LYP/ECP give slightly worse agreement with experiment, and FSLYP/ECP is the only method among the ones we studied that gives an unaceptably large error, underestimating the dissociation energy of nickel dimer by 28%, and being in the largest disagreement with the experiment and the other theoretical predictions.Comment: 17 pages, 7 tables, 7 figures; submitted to J. Chem. Phys.; Revtex4/LaTeX2e. v2 (8/5/04): New (and better) ECP results, without charge density fitting (which was found to give large errors). Subtracted the relativistic corrections from all experimental value

Wavelet Formulation of Path Integral Monte Carlo

A wavelet formulation of path integral Monte Carlo (PIMC)is constructed. Comparison with Fourier path integral Monte Carlo is presented using simple one-dimensional examples. Wavelet path integral Monte Carlo exhibits a few advantages over previous methods for PIMC. The efficiency of the current method is at least comparable to other techniques

Applications of sensitivity analysis for probit stochastic network equilibrium

Network equilibrium models are widely used by traffic practitioners to aid them in making decisions concerning the operation and management of traffic networks. The common practice is to test a prescribed range of hypothetical changes or policy measures through adjustments to the input data, namely the trip demands, the arc performance (travel time) functions, and policy variables such as tolls or signal timings. Relatively little use is, however, made of the full implicit relationship between model inputs and outputs inherent in these models. By exploiting the representation of such models as an equivalent optimisation problem, classical results on the sensitivity analysis of non-linear programs may be applied, to produce linear relationships between input data perturbations and model outputs. We specifically focus on recent results relating to the probit Stochastic User Equilibrium (PSUE) model, which has the advantage of greater behavioural realism and flexibility relative to the conventional Wardrop user equilibrium and logit SUE models. The paper goes on to explore four applications of these sensitivity expressions in gaining insight into the operation of road traffic networks. These applications are namely: identification of sensitive, ‘critical’ parameters; computation of approximate, re-equilibrated solutions following a change (post-optimisation); robustness analysis of model forecasts to input data errors, in the form of confidence interval estimation; and the solution of problems of the bi-level, optimal network design variety. Finally, numerical experiments applying these methods are reported

Neuronal pentraxins mediate synaptic refinement in the developing visual system

Peer reviewedPublisher PD

Insights into the Conformation of Aminofluorene-Deoxyguanine Adduct in a DNA Polymerase Active Site

The active site conformation of the mutagenic fluoroaminofluorene-deoxyguanine adduct (dG-FAF, N-(2′-deoxyguanosin-8-yl)-7-fluoro-2-aminofluorene) has been investigated in the presence of Klenow fragment of Escherichia coli DNA polymerase I (Kfexo−) and DNA polymerase β (pol β) using 19F NMR, insertion assay, and surface plasmon resonance. In a single nucleotide gap, the dG-FAF adduct adopts both a major-groove- oriented and base-displaced stacked conformation, and this heterogeneity is retained upon binding pol β. The addition of a non-hydrolysable 2′-deoxycytosine-5′-[(α,β)-methyleno]triphosphate (dCMPcPP) nucleotide analog to the binary complex results in an increase of the major groove conformation of the adduct at the expense of the stacked conformation. Similar results were obtained with the addition of an incorrect dAMPcPP analog but with formation of the minor groove binding conformer. In contrast, dG-FAF adduct at the replication fork for the Kfexo− complex adopts a mix of the major and minor groove conformers with minimal effect upon the addition of non-hydrolysable nucleotides. For pol β, the insertion of dCTP was preferred opposite the dG-FAF adduct in a single nucleotide gap assay consistent with 19F NMR data. Surface plasmon resonance binding kinetics revealed that pol β binds tightly with DNA in the presence of correct dCTP, but the adduct weakens binding with no nucleotide specificity. These results provide molecular insights into the DNA binding characteristics of FAF in the active site of DNA polymerases and the role of DNA structure and sequence on its coding potential

Conductance distribution between Hall plateaus

Mesoscopic fluctuations of two-port conductance and four-port resistance between Hall plateaus are studied within a realistic model for a two-dimensional electron gas in a perpendicular magnetic field and a smooth disordered potential. The two-port conductance distribution $P(g)$ is concave between $g=0$ and $g=1$ and is nearly flat between $g=0.2$ and $g=0.8$. These characteristics are consistent with recent observations. The distribution is found to be sharply peaked near the end-points $g=0$ and $g=1$. The distribution functions for the three independent resistances in a four-port Hall bar geometry are, on the other hand, characterized by a central peak and a relatively large width.Comment: 11 pages, 5 ps figures, submitted to Phys. Rev.

One-loop Vilkovisky-DeWitt Counterterms for 2D Gravity plus Scalar Field Theory

The divergent part of the one-loop off-shell effective action is computed for a single scalar field coupled to the Ricci curvature of 2D gravity ($c \phi R$), and self interacting by an arbitrary potential term $V(\phi)$. The Vilkovisky-DeWitt effective action is used to compute gauge-fixing independent results. In our background field/covariant gauge we find that the Liouville theory is finite on shell. Off-shell, we find a large class of renormalizable potentials which include the Liouville potential. We also find that for backgrounds satisfying $R=0$, the Liouville theory is finite off shell, as well.Comment: 19 pages, OKHEP 92-00

Epidemiology, genetics, and subtyping of preserved ratio impaired spirometry (PRISm) in COPDGene.

BackgroundPreserved Ratio Impaired Spirometry (PRISm), defined as a reduced FEV1 in the setting of a preserved FEV1/FVC ratio, is highly prevalent and is associated with increased respiratory symptoms, systemic inflammation, and mortality. Studies investigating quantitative chest tomographic features, genetic associations, and subtypes in PRISm subjects have not been reported.MethodsData from current and former smokers enrolled in COPDGene (n = 10,192), an observational, cross-sectional study which recruited subjects aged 45-80 with ≥10 pack years of smoking, were analyzed. To identify epidemiological and radiographic predictors of PRISm, we performed univariate and multivariate analyses comparing PRISm subjects both to control subjects with normal spirometry and to subjects with COPD. To investigate common genetic predictors of PRISm, we performed a genome-wide association study (GWAS). To explore potential subgroups within PRISm, we performed unsupervised k-means clustering.ResultsThe prevalence of PRISm in COPDGene is 12.3%. Increased dyspnea, reduced 6-minute walk distance, increased percent emphysema and decreased total lung capacity, as well as increased segmental bronchial wall area percentage were significant predictors (p-value <0.05) of PRISm status when compared to control subjects in multivariate models. Although no common genetic variants were identified on GWAS testing, a significant association with Klinefelter's syndrome (47XXY) was observed (p-value < 0.001). Subgroups identified through k-means clustering include a putative "COPD-subtype", "Restrictive-subtype", and a highly symptomatic "Metabolic-subtype".ConclusionsPRISm subjects are clinically and genetically heterogeneous. Future investigations into the pathophysiological mechanisms behind and potential treatment options for subgroups within PRISm are warranted.Trial registrationClinicaltrials.gov Identifier: NCT000608764