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

Non-equilibrium raft-like membrane domains under continuous recycling

We present a model for the kinetics of spontaneous membrane domain (raft) assembly that includes the effect of membrane recycling ubiquitous in living cells. We show that the domains have a broad power-law distribution with an average radius that scales with the 1/4 power of the domain lifetime when the line tension at the domain edges is large. For biologically reasonable recycling and diffusion rates the average domain radius is in the tens of nm range, consistent with observations. This represents one possible link between signaling (involving rafts) and traffic (recycling) in cells. Finally, we present evidence that suggests that the average raft size may be the same for all scale-free recycling schemes.Comment: 8 pages, 5 figure

High-throughput pipeline for the de novo viral genome assembly and the identification of minority variants from Next-Generation Sequencing of residual diagnostic samples

Motivation: The underlying genomic variation of a large number of pathogenic viruses can give rise to drug resistant mutations resulting in treatment failure. Next generation sequencing (NGS) enables the identification of viral quasi-species and the quantification of minority variants in clinical samples; therefore, it can be of direct benefit by detecting drug resistant mutations and devising optimal treatment strategies for individual patients. / Results: The ICONIC (InfeCtion respONse through vIrus genomiCs) project has developed an automated, portable and customisable high-throughput computational pipeline to assemble de novo whole viral genomes, either segmented or non-segmented, and quantify minority variants using residual diagnostic samples. The pipeline has been benchmarked on a dedicated High-Performance Computing cluster using paired-end reads from RSV and Influenza clinical samples. The median length of generated genomes was 96% for the RSV dataset and 100% for each Influenza segment. The analysis of each set lasted less than 12 hours; each sample took around 3 hours and required a maximum memory of 10 GB. The pipeline can be easily ported to a dedicated server or cluster through either an installation script or a docker image. As it enables the subtyping of viral samples and the detection of relevant drug resistance mutations within three days of sample collection, our pipeline could operate within existing clinical reporting time frames and potentially be used as a decision support tool towards more effective personalised patient treatments. / Availability: The software and its documentation are available from https://github.com/ICONIC-UCL/pipeline / Contact: t.cassarino{at}ucl.ac.uk, pk5{at}sanger.ac.uk / Supplementary information: Supplementary data are available at Briefings in Bioinformatics online

The Retrosplenial Cortex: Intrinsic Connectivity and Connections with the (Para)Hippocampal Region in the Rat. An Interactive Connectome

A connectome is an indispensable tool for brain researchers, since it quickly provides comprehensive knowledge of the brain's anatomical connections. Such knowledge lies at the basis of understanding network functions. Our first comprehensive and interactive account of brain connections comprised the rat hippocampal–parahippocampal network. We have now added all anatomical connections with the retrosplenial cortex (RSC) as well as the intrinsic connections of this region, because of the interesting functional overlap between these brain regions. The RSC is involved in a variety of cognitive tasks including memory, navigation, and prospective thinking, yet the exact role of the RSC and the functional differences between its subdivisions remain elusive. The connectome presented here may help to define this role by providing an unprecedented interactive and searchable overview of all connections within and between the rat RSC, parahippocampal region and hippocampal formation

Soft X-ray emission lines of Fe XV in solar flare observations and the Chandra spectrum of Capella

Recent calculations of atomic data for Fe XV have been used to generate theoretical line ratios involving n = 3-4 transitions in the soft X-ray spectral region (52-83 A), for a wide range of electron temperatures and densities applicable to solar and stellar coronal plasmas. A comparison of these with solar flare observations from a rocket-borne spectrograph (XSST) reveals generally good agreement between theory and experiment. In particular, the 82.76 A emission line in the XSST spectrum is identified, for the first time to our knowledge in an astrophysical source. Most of the Fe XV transitions which are blended have had the species responsible clearly identified, although there remain a few instances where this has not been possible. The line ratio calculations are also compared with a co-added spectrum of Capella obtained with the Chandra satellite, which is probably the highest signal-to-noise observation achieved for a stellar source in the 25-175 A soft X-ray region. Good agreement is found between theory and experiment, indicating that the Fe XV lines are reliably detected in Chandra spectra, and hence may be employed as diagnostics to determine the temperature and/or density of the emitting plasma. However the line blending in the Chandra data is such that individual emission lines are difficult to measure accurately, and fluxes may only be reliably determined via detailed profile fitting of the observations. The co-added Capella spectrum is made available to hopefully encourage further exploration of the soft X-ray region in astronomical sources.Comment: 27 pages, 10 figures, Astrophysical Journal, in pres

Fluctuations and Correlations of net baryon number, electric charge, and strangeness: A comparison of lattice QCD results with the hadron resonance gas model

We calculate the quadratic fluctuations of net baryon number, electric charge and strangeness as well as correlations among these conserved charges in (2+1)-flavor lattice QCD at zero chemical potential. Results are obtained using calculations with tree level improved gauge and the highly improved staggered quark (HISQ) actions with almost physical light and strange quark masses at three different values of the lattice cut-off. Our choice of parameters corresponds to a value of 160 MeV for the lightest pseudo scalar Goldstone mass and a physical value of the kaon mass. The three diagonal charge susceptibilities and the correlations among conserved charges have been extrapolated to the continuum limit in the temperature interval 150 MeV <T < 250 MeV. We compare our results with the hadron resonance gas (HRG) model calculations and find agreement with HRG model results only for temperatures T<= 150 MeV. We observe significant deviations in the temperature range 160 MeV < T < 170 MeV and qualitative differences in the behavior of the three conserved charge sectors. At T < 160 MeV quadratic net baryon number fluctuations in QCD agree with HRG model calculations while, the net electric charge fluctuations in QCD are about 10% smaller and net strangeness fluctuations are about 20% larger. These findings are relevant to the discussion of freeze-out conditions in relativistic heavy ion collisions.Comment: 17 pages, 18 EPS-files, 5 tables, revised version includes continuum limit extrapolations of off-diagonal susceptibilities, to appear in Phys. Rev.

Relativistic coupled-cluster studies of ionization potentials, lifetimes and polarizabilities in singly ionized calcium

Using the relativistic coupled-cluster method, we have calculated ionization potentials, E1 matrix elements and dipole polarizabilities of many low-lying states of Ca$^+$. Contributions from the Breit interaction are given explicitly for these properties. Polarizabilities of the ground and the first excited d-states are determined by evaluating the wave functions that are perturbed to first order by the electric dipole operator and the black-body radiation shifts are estimated from these results. We also report the results of branching ratios and lifetimes of the first excited p-states using both the calculated and experimental wavelengths and compare them with their measured values.Comment: 10 pages, 1 figur

Energy levels and lifetimes of Gd IV and enhancement of the electron dipole moment

We have calculated energy levels and lifetimes of 4f7 and 4f6 5d configurations of Gd IV using Hartree-Fock and configuration interaction methods. This allows us to reduce significantly the uncertainty of the theoretical determination of the electron electric dipole moment (EDM) enhancement factor in this ion and, correspondingly, in gadolinium-containing garnets for which such measurements were recently proposed. Our new value for the EDM enhancement factor of Gd+3 is -2.2 +- 0.5. Calculations of energy levels and lifetimes for Eu~III are used to control the accuracy.Comment: Submitted to Phys. Rev. A 6 pages, 0 figures, 3 table

Light pseudoscalar decay constants, quark masses, and low energy constants from three-flavor lattice QCD

As part of our program of lattice simulations of three flavor QCD with improved staggered quarks, we have calculated pseudoscalar meson masses and decay constants for a range of valence quark masses and sea quark masses on lattices with lattice spacings of about 0.125 fm and 0.09 fm. We fit the lattice data to forms computed with staggered chiral perturbation theory. Our results provide a sensitive test of the lattice simulations, and especially of the chiral behavior, including the effects of chiral logarithms. We find: f_\pi=129.5(0.9)(3.5)MeV, f_K=156.6(1.0)(3.6)MeV, and f_K/f_\pi=1.210(4)(13), where the errors are statistical and systematic. Following a recent paper by Marciano, our value of f_K/f_\pi implies |V_{us}|=0.2219(26). Further, we obtain m_u/m_d= 0.43(0)(1)(8), where the errors are from statistics, simulation systematics, and electromagnetic effects, respectively. The data can also be used to determine several of the constants of the low energy effective Lagrangian: in particular we find 2L_8-L_5=-0.2(1)(2) 10^{-3} at chiral scale m_\eta. This provides an alternative (though not independent) way of estimating m_u; 2L_8-L_5 is far outside the range that would allow m_u=0. Results for m_s^\msbar, \hat m^\msbar, and m_s/\hat m can be obtained from the same lattice data and chiral fits, and have been presented previously in joint work with the HPQCD and UKQCD collaborations. Using the perturbative mass renormalization reported in that work, we obtain m_u^\msbar=1.7(0)(1)(2)(2)MeV and m_d^\msbar=3.9(0)(1)(4)(2)MeV at scale 2 GeV, with errors from statistics, simulation, perturbation theory, and electromagnetic effects, respectively.Comment: 86 pages, 22 figures. v3: Remarks about m_u=0 and the strong CP problem modified; reference added. Figs 5--8 modified for clarity. Version to be published in Phys. Rev. D. v2: Expanded discussion of finite volume effects, normalization in Table I fixed, typos and minor errors correcte