Towards Better Integrators for Dissipative Particle Dynamics Simulations

Coarse-grained models that preserve hydrodynamics provide a natural approach to study collective properties of soft-matter systems. Here, we demonstrate that commonly used integration schemes in dissipative particle dynamics give rise to pronounced artifacts in physical quantities such as the compressibility and the diffusion coefficient. We assess the quality of these integration schemes, including variants based on a recently suggested self-consistent approach, and examine their relative performance. Implications of integrator-induced effects are discussed.Comment: 4 pages, 3 figures, 2 tables, accepted for publication in Phys. Rev. E (Rapid Communication), tentative publication issue: 01 Dec 200

Momentum of an electromagnetic wave in dielectric media

Almost a hundred years ago, two different expressions were proposed for the energy--momentum tensor of an electromagnetic wave in a dielectric. Minkowski's tensor predicted an increase in the linear momentum of the wave on entering a dielectric medium, whereas Abraham's tensor predicted its decrease. Theoretical arguments were advanced in favour of both sides, and experiments proved incapable of distinguishing between the two. Yet more forms were proposed, each with their advocates who considered the form that they were proposing to be the one true tensor. This paper reviews the debate and its eventual conclusion: that no electromagnetic wave energy--momentum tensor is complete on its own. When the appropriate accompanying energy--momentum tensor for the material medium is also considered, experimental predictions of all the various proposed tensors will always be the same, and the preferred form is therefore effectively a matter of personal choice.Comment: 23 pages, 3 figures, RevTeX 4. Removed erroneous factor of mu/mu_0 from Eq.(44

Canonical and kinetic forms of the electromagnetic momentum in an ad hoc quantization scheme for a dispersive dielectric

An ad hoc quantization scheme for the electromagnetic field in a weakly dispersive, transparent dielectric leads to the definition of canonical and kinetic forms for the momentum of the electromagnetic field in a dispersive medium. The canonical momentum is uniquely defined as the operator that generates spatial translations in a uniform medium, but the quantization scheme suggests two possible choices for the kinetic momentum operator, corresponding to the Abraham or the Minkowski momentum in classical electrodynamics. Another implication of this procedure is that a wave packet containing a single dressed photon travels at the group velocity through the medium. The physical significance of the canonical momentum has already been established by considerations of energy and momentum conservation in the atomic recoil due to spontaneous emission, the Cerenkov effect, the Doppler effect, and phase matching in nonlinear optical processes. In addition, the data of the Jones and Leslie radiation pressure experiment is consistent with the assignment of one ?k unit of canonical momentum to each dressed photon. By contrast, experiments in which the dielectric is rigidly accelerated by unbalanced electromagnetic forces require the use of the Abraham momentum.Comment: 21 pages, 1 figure, aip style, submitted to PR

The MOSFIRE Deep Evolution Field (MOSDEF) Survey: Rest-Frame Optical Spectroscopy for ~1500 H-Selected Galaxies at 1.37 < z < 3.8

In this paper we present the MOSFIRE Deep Evolution Field (MOSDEF) survey. The MOSDEF survey aims to obtain moderate-resolution (R=3000-3650) rest-frame optical spectra (~3700-7000 Angstrom) for ~1500 galaxies at 1.37<z<3.80 in three well-studied CANDELS fields: AEGIS, COSMOS, and GOODS-N. Targets are selected in three redshift intervals: 1.37<z<1.70, 2.09<z<2.61, and 2.95<z<3.80, down to fixed H_AB (F160W) magnitudes of 24.0, 24.5 and 25.0, respectively, using the photometric and spectroscopic catalogs from the 3D-HST survey. We target both strong nebular emission lines (e.g., [OII], Hbeta, [OIII], 5008, Halpha, [NII], and [SII]) and stellar continuum and absorption features (e.g., Balmer lines, Ca-II H and K, Mgb, 4000 Angstrom break). Here we present an overview of our survey, the observational strategy, the data reduction and analysis, and the sample characteristics based on spectra obtained during the first 24 nights. To date, we have completed 21 masks, obtaining spectra for 591 galaxies. For ~80% of the targets we derive a robust redshift from either emission or absorption lines. In addition, we confirm 55 additional galaxies, which were serendipitously detected. The MOSDEF galaxy sample includes unobscured star-forming, dusty star-forming, and quiescent galaxies and spans a wide range in stellar mass (~10^9-10^11.5 Msol) and star formation rate (~10^0-10^3 Msol/yr). The spectroscopically confirmed sample is roughly representative of an H-band limited galaxy sample at these redshifts. With its large sample size, broad diversity in galaxy properties, and wealth of available ancillary data, MOSDEF will transform our understanding of the stellar, gaseous, metal, dust, and black hole content of galaxies during the time when the universe was most active.Comment: Accepted for publication in ApJS; 28 pages, 19 figures; MOSDEF spectroscopic redshifts available at http://mosdef.astro.berkeley.edu/Downloads.htm

The Halos and Environments of Nearby Galaxies (HERON) Survey

We have used dedicated 0.7m telescopes in California and Israel to image the halos of ~200 galaxies in the Local Volume to 29 mag/sq arcsec, the sample mainly drawn from the 2MASS Large Galaxy Atlas (LGA). We supplement the LGA sample with dwarf galaxies and more distant giant ellipticals. Low surface brightness halos exceeding 50 kpc in diameter are found only in galaxies more luminous than L* and classic interaction signatures are relatively infrequent. Halo diameter is correlated with total galaxy luminosity. Extended low surface brightness halos are present even in galaxies as faint as M_V=-18. Edge-on galaxies with boxy bulges tend to lack extended spheroidal halos, while those with large classical bulges exhibit extended round halos, supporting the notions that boxy or barlike bulges originate from disks. Most face-on spiral galaxies present features that appear to be irregular extensions of spiral arms, although rare cases show smooth boundaries with no sign of star formation. Although we serendipitously discovered a dwarf galaxy undergoing tidal disruption in the halo of NGC 4449, we found no comparable examples in our general survey. A search for similar examples in the Local Volume identified hcc087, a tidally disrupting dwarf galaxy in the Hercules Cluster, but we do not confirm an anomalously large half-light radius reported for the dwarf VCC 1661

Faecal volatile organic compounds analysis using field asymmetric ion mobility spectrometry : non-invasive diagnostics in paediatric inflammatory bowel disease

Inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), remains challenging to diagnose. Diagnostic work up carries a high burden, especially in paediatric patients, due to invasive endoscopic procedures. IBD is associated with alterations in intestinal microbiota composition. Faecal volatile organic compounds (VOCs) reflect gut microbiota composition. Aim of this study was to assess the diagnostic accuracy of faecal VOC profiling as non-invasive diagnostic biomarker for paediatric IBD

Gamma-Ray Bursts via the Neutrino Emission from Heated Neutron Stars

A model is proposed for gamma-ray bursts based upon a neutrino burst of about 10^52 ergs lasting a few seconds above a heated collapsing neutron star. This type of thermal neutrino burst is suggested by relativistic hydrodynamic studies of the compression, heating, and collapse of close binary neutron stars as they approach their last stable orbit, but may arise from other sources as well. We present a hydrodynamic simulation of the formation and evolution of the pair plasma associated with such a neutrino burst. This pair plasma leads to the production of ~10^51 - 10^52 ergs in gamma-rays with spectral and temporal properties consistent with observed gamma-ray bursts.Comment: Final version. 30 pages, 10 figures, 6 tables, accepted for publication in The Astrophysical Journa

Benchmarking laboratory processes to characterise low-biomass respiratory microbiota

Abstract The low biomass of respiratory samples makes it difficult to accurately characterise the microbial community composition. PCR conditions and contaminating microbial DNA can alter the biological profile. The objective of this study was to benchmark the currently available laboratory protocols to accurately analyse the microbial community of low biomass samples. To study the effect of PCR conditions on the microbial community profile, we amplified the 16S rRNA gene of respiratory samples using various bacterial loads and different number of PCR cycles. Libraries were purified by gel electrophoresis or AMPure XP and sequenced by V2 or V3 MiSeq reagent kits by Illumina sequencing. The positive control was diluted in different solvents. PCR conditions had no significant influence on the microbial community profile of low biomass samples. Purification methods and MiSeq reagent kits provided nearly similar microbiota profiles (paired Bray–Curtis dissimilarity median: 0.03 and 0.05, respectively). While profiles of positive controls were significantly influenced by the type of dilution solvent, the theoretical profile of the Zymo mock was most accurately analysed when the Zymo mock was diluted in elution buffer (difference compared to the theoretical Zymo mock: 21.6% for elution buffer, 29.2% for Milli-Q, and 79.6% for DNA/RNA shield). Microbiota profiles of DNA blanks formed a distinct cluster compared to low biomass samples, demonstrating that low biomass samples can accurately be distinguished from DNA blanks. In summary, to accurately characterise the microbial community composition we recommend 1. amplification of the obtained microbial DNA with 30 PCR cycles, 2. purifying amplicon pools by two consecutive AMPure XP steps and 3. sequence the pooled amplicons by V3 MiSeq reagent kit. The benchmarked standardized laboratory workflow presented here ensures comparability of results within and between low biomass microbiome studies

IPD-MHC 2.0:An improved inter-species database for the study of the major histocompatibility complex

The IPD-MHC Database project (http://www.ebi.ac.uk/ipd/mhc/) collects and expertly curates sequences of the major histocompatibility complex from non-human species and provides the infrastructure and tools to enable accurate analysis. Since the first release of the database in 2003, IPD-MHC has grown and currently hosts a number of specific sections, with more than 7000 alleles from 70 species, including non-human primates, canines, felines, equids, ovids, suids, bovins, salmonids and murids. These sequences are expertly curated and made publicly available through an open access website. The IPD-MHC Database is a key resource in its field, and this has led to an average of 1500 unique visitors and more than 5000 viewed pages per month. As the database has grown in size and complexity, it has created a number of challenges in maintaining and organizing information, particularly the need to standardize nomenclature and taxonomic classification, while incorporating new allele submissions. Here, we describe the latest database release, the IPD-MHC 2.0 and discuss planned developments. This release incorporates sequence updates and new tools that enhance database queries and improve the submission procedure by utilizing common tools that are able to handle the varied requirements of each MHC-group

Independent Ion Migration in Suspensions of Strongly Interacting Charged Colloidal Spheres

We report on sytematic measurements of the low frequency conductivity in aequous supensions of highly charged colloidal spheres. System preparation in a closed tubing system results in precisely controlled number densities between 1E16/m3 and 1E19/m^3 (packing fractions between 1E-7 and 1E-2) and electrolyte concentrations between 1E-7 and 1E-3 mol/l. Due to long ranged Coulomb repulsion some of the systems show a pronounced fluid or crystalline order. Under deionized conditions we find s to depend linearily on the packing fraction with no detectable influence of the phase transitions. Further at constant packing fraction s increases sublinearily with increasing number of dissociable surface groups N. As a function of c the conductivity shows pronounced differences depending on the kind of electrolyte used. We propose a simple yet powerful model based on independent migration of all species present and additivity of the respective conductivity contributions. It takes account of small ion macro-ion interactions in terms of an effectivly transported charge. The model successfully describes our qualitatively complex experimental observations. It further facilitates quantitative estimates of conductivity over a wide range of particle and experimental parameters.Comment: 32 pages, 17 figures, 2 tables, Accepted by Physical Review