Information based clustering

In an age of increasingly large data sets, investigators in many different disciplines have turned to clustering as a tool for data analysis and exploration. Existing clustering methods, however, typically depend on several nontrivial assumptions about the structure of data. Here we reformulate the clustering problem from an information theoretic perspective which avoids many of these assumptions. In particular, our formulation obviates the need for defining a cluster "prototype", does not require an a priori similarity metric, is invariant to changes in the representation of the data, and naturally captures non-linear relations. We apply this approach to different domains and find that it consistently produces clusters that are more coherent than those extracted by existing algorithms. Finally, our approach provides a way of clustering based on collective notions of similarity rather than the traditional pairwise measures.Comment: To appear in Proceedings of the National Academy of Sciences USA, 11 pages, 9 figure

The Lemaitre-Schwarzschild Problem Revisited

The Lemaitre and Schwarzschild analytical solutions for a relativistic spherical body of constant density are linked together through the use of the Weyl quadratic invariant. The critical radius for gravitational collapse of an incompressible fluid is shown to vary continuously from 9/8 of the Schwarzschild radius to the Schwarzschild radius itself while the internal pressures become locally anisotropic.Comment: Final version as accepted by GR&G (to appear in vol. 34, september 2002

HUT observations of carbon monoxide in the coma of Comet Levy (1990c)

Observations of comet Levy (1990c) were made with the Hopkins Ultraviolet Telescope during the Astro-1 Space Shuttle mission on 10 Dec. 1990. The spectrum, covering the wavelength range 415 to 1850 A at a spectral emission of 3 A (in first order), shows the presence of carbon monoxide and atomic hydrogen, carbon, and sulfur in the coma. Aside from H I Lyman-beta, no cometary features are detected below 1200 A, although cometary O I and O II would be masked by the same emissions present in the day airglow spectrum. The 9.4 x 116 arcsec aperture corresponds to 12,000 x 148,000 km at the comet. The derived production rate of CO relative to water, 0.13 + or - 0.02, compared with the same ratio derived from IUE observations (made in Sep. 1990) which sample a much smaller region of the coma, 0.04 + or - 0.01, suggests the presence of an extended source of CO, as was found in comet Halley. Upper limits on Ne and Ar abundance are within an order of magnitude or solar abundances

Near Infrared Spectra of Type Ia Supernovae

We report near infrared (NIR) spectroscopic observations of twelve ``Branch-normal'' Type Ia supernovae (SNe Ia) which cover the wavelength region from 0.8-2.5 microns. Our sample more than doubles the number of SNe Ia with published NIR spectra within three weeks of maximum light. The epochs of observation range from thirteen days before maximum light to eighteen days after maximum light. A detailed model for a Type Ia supernovae is used to identify spectral features. The Doppler shifts of lines are measured to obtain the velocity and, thus, the radial distribution of elements. The NIR is an extremely useful tool to probe the chemical structure in the layers of SNe Ia ejecta. This wavelength region is optimal for examining certain products of the SNe Ia explosion that may be blended or obscured in other spectral regions. We identify spectral features from MgII, CaII, SiII, FeII, CoII, NiII and possibly MnII. We find no indications for hydrogen, helium or carbon in the spectra. The spectral features reveal important clues about the physical characteristics of SNe Ia. We use the features to derive upper limits for the amount of unburned matter, to identify the transition regions from explosive carbon to oxygen burning and from partial to complete silicon burning, and to estimate the level of mixing during and after the explosion.Comment: 44 pages, 7 figures, 3 tables, accepted by Ap

Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS

GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest supercomputers in the world. Here, we describe some of the ways we have been able to realize this through the use of parallelization on all levels, combined with a constant focus on absolute performance. Release 4.6 of GROMACS uses SIMD acceleration on a wide range of architectures, GPU offloading acceleration, and both OpenMP and MPI parallelism within and between nodes, respectively. The recent work on acceleration made it necessary to revisit the fundamental algorithms of molecular simulation, including the concept of neighborsearching, and we discuss the present and future challenges we see for exascale simulation - in particular a very fine-grained task parallelism. We also discuss the software management, code peer review and continuous integration testing required for a project of this complexity.Comment: EASC 2014 conference proceedin

Anisotropic static solutions in modelling highly compact bodies

Einstein field equations for anisotropic spheres are solved and exact interior solutions obtained. This paper extends earlier treatments to include anisotropic models which accommodate a wider variety of physically viable energy densities. Two classes of solutions are possible. The first class contains the limiting case $\mu\propto r^{-2}$ for the energy density which arises in many astrophysical applications. In the second class the singularity at the center of the star is not present in the energy density. The models presented in this paper allow for increasing and decreasing profiles in the behavior of the energy density.Comment: 9 pages, to appear in Pramana - J. Phy

Neutrino Trapping in a Supernova and Ion Screening

Neutrino-nucleus elastic scattering is reduced in dense matter because of correlations between ions. The static structure factor for a plasma of electrons and ions is calculated from Monte Carlo simulations and parameterized with a least squares fit. Our results imply a large increase in the neutrino mean free path. This strongly limits the trapping of neutrinos in a supernova by coherent neutral current interactions.Comment: 9 pages, 1 postscript figure using epsf.st

A pantothenate suxotroph of BCG rxpressing Gag confers enhanced HIV-specific immunogenicity compared to wildtype and perfingolysin expressing strains

In tuberculosis vaccine studies, perfingolysin expressing strains (pfo) of recombinant Mycobacterium bovis (rBCG) have been shown to enhance immunogenicity as compared to wildtype strains whilst pantothenate auxotrophic strains (ΔpanCD) have been shown to be safer and more immunogenic. Our group has recently shown that rBCGΔpanCD expressing HIV-1 Gag is more immunogenic than the wildtype Pasteur strain of BCG in the murine model. In this study, a wild type strain, a ΔpanCDstrain, a pfo strain and a ΔpanCD strain expressing perfringolysin (ΔpanCDpfo) of Danish BCG were used as vectors to express HIV-1 subtype C Gag. Gag specific immune responses induced by a prime with each rBCG-Gag vaccine and boost with modified vaccinia Ankara (MVA) were compared