4,006 research outputs found
Pursuing Parameters for Critical Density Dark Matter Models
We present an extensive comparison of models of structure formation with
observations, based on linear and quasi-linear theory. We assume a critical
matter density, and study both cold dark matter models and cold plus hot dark
matter models. We explore a wide range of parameters, by varying the fraction
of hot dark matter , the Hubble parameter and the spectral
index of density perturbations , and allowing for the possibility of
gravitational waves from inflation influencing large-angle microwave background
anisotropies. New calculations are made of the transfer functions describing
the linear power spectrum, with special emphasis on improving the accuracy on
short scales where there are strong constraints. For assessing early object
formation, the transfer functions are explicitly evaluated at the appropriate
redshift. The observations considered are the four-year {\it COBE} observations
of microwave background anisotropies, peculiar velocity flows, the galaxy
correlation function, and the abundances of galaxy clusters, quasars and damped
Lyman alpha systems. Each observation is interpreted in terms of the power
spectrum filtered by a top-hat window function. We find that there remains a
viable region of parameter space for critical-density models when all the dark
matter is cold, though must be less than 0.5 before any fit is found and
significantly below unity is preferred. Once a hot dark matter component is
invoked, a wide parameter space is acceptable, including . The
allowed region is characterized by \Omega_\nu \la 0.35 and 0.60 \la n \la
1.25, at 95 per cent confidence on at least one piece of data. There is no
useful lower bound on , and for curious combinations of the other parameters
it is possible to fit the data with as high as 0.65.Comment: 19 pages LaTeX file (uses mn.sty). Figures *not* included due to
length. We strongly recommend obtaining the full paper, either by WWW at
http://star-www.maps.susx.ac.uk/papers/lsstru_papers.html (UK) or
http://www.bartol.udel.edu/~bob/papers (US), or by e-mailing ARL. Final
version, to appear MNRAS. Main revision is update to four-year COBE data.
Miscellaneous other changes and reference updates. No significant changes to
principal conclusion
TeV cosmic-ray proton and helium spectra in the myriad model
Recent measurements of cosmic ray proton and helium spectra show a hardening
above a few hundreds of GeV. This excess is hard to understand in the framework
of the conventional models of Galactic cosmic ray production and propagation.
We propose here to explain this anomaly by the presence of local sources
(myriad model). Cosmic ray propagation is described as a diffusion process
taking place inside a two-zone magnetic halo. We calculate the proton and
helium fluxes at the Earth between 50 GeV and 100 TeV. Improving over a similar
analysis, we consistently derive these fluxes by taking into account both local
and remote sources for which a unique injection rate is assumed. We find cosmic
ray propagation parameters compatible with B/C measurements and for which the
proton and helium spectra remarkably agree with the PAMELA and CREAM
measurements over four decades in energy.Comment: 5 pages, 3 figure
An automatic method for assessing structural importance of amino acid positions
Background: A great deal is known about the qualitative aspects of the sequence-structure relationship, for example that buried residues are usually more conserved between structurally similar homologues, but no attempts have been made to quantitate the relationship between evolutionary conservation at a sequence position and change to global tertiary structure. In this paper we demonstrate that the Spearman correlation between sequence and structural change is suitable for this purpose.
Results:
Buried residues, bends, cysteines, prolines and leucines were significantly more likely to occupy positions highly correlated with structural change than expected by chance. Some buried residues were found to be less informative than expected, particularly residues involved in active sites and the binding of small molecules.
Conclusion:
The correlation-based method generates predictions of structural importance for superfamily positions which agree well with previous results of manual analyses, and may be of use in automated residue annotation piplines. A PERL script which implements the method is provided
Recent results from lattice calculations
Recent results from lattice QCD calculations relevant to particle physics
phenomenology are reviewed. They include the calculations of strong coupling
constant, quark masses, kaon matrix elements, and D and B meson matrix
elements. Special emphasis is on the recent progress in the simulations
including dynamical quarks.Comment: 13 pages, 8 figures, plenary talk at the 32nd International
Conference on High-Energy Physics (ICHEP 2004), August 16-22, 2004, Beijing,
Chin
On a generalization of the Jensen-Shannon divergence and the JS-symmetrization of distances relying on abstract means
The Jensen-Shannon divergence is a renown bounded symmetrization of the
unbounded Kullback-Leibler divergence which measures the total Kullback-Leibler
divergence to the average mixture distribution. However the Jensen-Shannon
divergence between Gaussian distributions is not available in closed-form. To
bypass this problem, we present a generalization of the Jensen-Shannon (JS)
divergence using abstract means which yields closed-form expressions when the
mean is chosen according to the parametric family of distributions. More
generally, we define the JS-symmetrizations of any distance using generalized
statistical mixtures derived from abstract means. In particular, we first show
that the geometric mean is well-suited for exponential families, and report two
closed-form formula for (i) the geometric Jensen-Shannon divergence between
probability densities of the same exponential family, and (ii) the geometric
JS-symmetrization of the reverse Kullback-Leibler divergence. As a second
illustrating example, we show that the harmonic mean is well-suited for the
scale Cauchy distributions, and report a closed-form formula for the harmonic
Jensen-Shannon divergence between scale Cauchy distributions. We also define
generalized Jensen-Shannon divergences between matrices (e.g., quantum
Jensen-Shannon divergences) and consider clustering with respect to these novel
Jensen-Shannon divergences.Comment: 30 page
Accelerated X-ray Structure Elucidation of a 36 kDa Muramidase/Transglycosylase Using wARP
The X-ray structure of the 36kDa soluble lytic transglycosylase from Escherichia coli has been determined starting with the multiple isomorphous replacement method with inclusion of anomalous scattering at 2.7 Å resolution. Subsequently, before any model building was carried out, phases were extended to 1.7 Å, resolution with the weighted automated refinement procedure wARP, which gave a dramatic improvement in the phases. The electron-density maps from wARP were of outstanding quality for both the main chain and the side chains of the protein, which allowed the time spent on the tracing, interpretation and building of the X-ray structure to be substantially shortened. The structure of the soluble lyric transglycosylase was refined at 1.7 Å, resolution with X-PLOR to a final crystallographic R factor of 18.9%. Analysis of the wARP procedure revealed that the use of the maximum-likelihood refinement in wARP gave much better phases than least-squares refinement, provided that the ratio of reflections to protein atom parameters was approximately 1.8 or higher. Furthermore, setting aside 5% of the data for an Rfree test set had a negative effect on the phase improvement. The mean WwARP, a weight determined at the end of the wARP procedure and based on the variance of structure factors from six individually refined wARP models, proved to be a better indicator than the Rfree factor to judge different phase improvement protocols. The elongated Slt35 structure has three domains named the alpha, beta and core domains. The alpha domain contains mainly α-helices, while the beta domain consists of a five-stranded antiparallel β-sheet flanked by a short α-helix. Sandwiched between the alpha and beta domains is the core domain, which bears some resemblance to the fold of the catalytic domain of the previously elucidated 70 kDa soluble lytic transglycosylase from E. coli. The putative active site is at the bottom of a large deep groove in the core domain.
First Results from the DRIFT-IIa Dark Matter Detector
Data from the DRIFT-IIa directional dark matter experiment are presented,
collected during a near continuous 6 month running period. A detailed
calibration analysis comparing data from gamma-ray, x-ray and neutron sources
to a GEANT4 Monte Carlo simulations reveals an efficiency for detection of
neutron induced recoils of 94+/-2(stat.)+/-5(sys.)%. Software-based cuts,
designed to remove non-nuclear recoil events, are shown to reject 60Co
gamma-rays with a rejection factor of better than 8x10-6 for all energies above
threshold. An unexpected event population has been discovered and is shown here
to be due to the alpha-decay of 222Rn daughter nuclei that have attached to the
central cathode. A limit on the flux of neutrons in the Boulby Underground
Laboratory is derived from analysis of unshielded and shielded data.Comment: 43 pages, 14 figures, submitted to Astroparticle Physic
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