Nonlocal elastic compliance for soft solids: theory, simulations, and experiments

The nonlocal elastic response function is crucial for understanding many properties of soft solids. This may be obtained by measuring strain-strain autocorrelation functions. We use computer simulations as well as video microscopy data of superparamagnetic colloids to obtain these correlations for two-dimensional triangular solids. Elastic constants and elastic correlation lengths are extracted by analyzing the correlation functions. We show that to explain our observations displacement fluctuations in a soft solid need to contain affine (strain) as well as nonaffine components

Crystal nuclei and structural correlations in two-dimensional colloidal mixtures: experiment versus simulation

We examine binary mixtures of superparamagnetic colloidal particles confined to a two-dimensional water-air interface both by real-space experiments and Monte-Carlo computer simulations at high coupling strength. In the simulations, the interaction is modelled as a pairwise dipole-dipole repulsion. While the ratio of magnetic dipole moments is fixed, the interaction strength governed by the external magnetic field and the relative composition is varied. Excellent agreement between simulation and experiment is found for the partial pair distribution functions including the fine structure of the neighbour shells at high coupling. Furthermore local crystal nuclei in the melt are identified by bond-orientational order parameters and their contribution to the pair structure is discussed

Dynamics of particles and cages in an experimental 2D glass former

We investigate the dynamics of a glass forming 2D colloidal mixture and show the existence of collective motions of the particles. We introduce a mean square displacement MSD with respect to the nearest neighbors which shows remarkable deviations from the usual MSD quantifying the individual motion of our particles. Combined with the analysis of the self part of the Van Hove function this indicates a coupled motion of particles with their cage as well as intra cage hopping processes.Comment: Submitted to EP

Highly sensitive quantitative PCR for the detection and differentiation of Pseudogymnoascus destructans and other Pseudogymnoascus species

White-nose syndrome is a fungal disease that has decimated bat populations across eastern North America. Identification of the etiologic agent, Pseudogymnoascus destructans (formerly Geomyces destructans), in environmental samples is essential to proposed management plans. A major challenge is the presence of closely related species, which are ubiquitous in many soils and cave sediments and often present in high abundance. We present a dual-probe real-time quantitative PCR assay capable of detecting and differentiating P. destructans from closely related fungi in environmental samples from North America. The assay, based on a single nucleotide polymorphism (SNP) specific to P. destructans, is capable of rapid low-level detection from various sampling media, including sediment, fecal samples, wing biopsy specimens, and skin swabs. This method is a highly sensitive, high-throughput method for identifying P. destructans, other Pseudogymnoascus spp., and Geomyces spp. in the environment, providing a fundamental component of research and risk assessment for addressing this disease, as well as other ecological and mycological work on related fungi

A new approach to in silico SNP detection and some new SNPs in the Bacillus anthracis genome

<p>Abstract</p> <p>Background</p> <p><it>Bacillus anthracis </it>is one of the most monomorphic pathogens known. Identification of polymorphisms in its genome is essential for taxonomic classification, for determination of recent evolutionary changes, and for evaluation of pathogenic potency.</p> <p>Findings</p> <p>In this work three strains of the <it>Bacillus anthracis </it>genome are compared and previously unpublished single nucleotide polymorphisms (SNPs) are revealed. Moreover, it is shown that, despite the highly monomorphic nature of <it>Bacillus anthracis</it>, the SNPs are (1) abundant in the genome and (2) distributed relatively uniformly across the sequence.</p> <p>Conclusions</p> <p>The findings support the proposition that SNPs, together with indels and variable number tandem repeats (VNTRs), can be used effectively not only for the differentiation of perfect strain data, but also for the comparison of moderately incomplete, noisy and, in some cases, unknown <it>Bacillus anthracis </it>strains. In the case when the data is of still lower quality, a new DNA sequence fingerprinting approach based on recently introduced markers, based on combinatorial-analytic concepts and called cyclic difference sets, can be used.</p

Optical polarization of neutron-rich sodium isotopes and β\beta-NMR measurements of quadrupole moments

The nuclear quadrupole moments of neutron-rich sodium isotopes are being investigated with the help of in-beam polarization by optical pumping in combination with $\beta$-NMR techniques. First measurements have yielded the quadrupole splittings of NMR signals in the lattice of LiNbO$_{3}$ for the isotopes $^{26}$Na, $^{27}$Na and $^{28}$Na. Interaction constants and ratios of the electric quadrupole moments are derived. In view of future experiments, $\beta$-decay asymmetries for the sequence of isotopes up to the $N$=20 neutron shell closure, $^{26-31}$Na, have been measured

Tracing melioidosis back to the source: using whole-genome sequencing to investigate an outbreak originating from a contaminated domestic water supply

Melioidosis, a disease of public health importance in Southeast Asia and northern Australia, is caused by the Gram-negative soil bacillus Burkholderia pseudomallei. Melioidosis is typically acquired through environmental exposure, and case clusters are rare, even in regions where the disease is endemic. B. pseudomallei is classed as a tier 1 select agent by the Centers for Disease Control and Prevention; from a biodefense perspective, source attribution is vital in an outbreak scenario to rule out a deliberate release. Two cases of melioidosis within a 3-month period at a residence in rural northern Australia prompted an investigation to determine the source of exposure. B. pseudomallei isolates from the property's groundwater supply matched the multilocus sequence type of the clinical isolates. Whole-genome sequencing confirmed the water supply as the probable source of infection in both cases, with the clinical isolates differing from the likely infecting environmental strain by just one single nucleotide polymorphism (SNP) each. For the first time, we report a phylogenetic analysis of genomewide insertion/deletion (indel) data, an approach conventionally viewed as problematic due to high mutation rates and homoplasy. Our whole-genome indel analysis was concordant with the SNP phylogeny, and these two combined data sets provided greater resolution and a better fit with our epidemiological chronology of events. Collectively, this investigation represents a highly accurate account of source attribution in a melioidosis outbreak and gives further insight into a frequently overlooked reservoir of B. pseudomallei. Our methods and findings have important implications for outbreak source tracing of this bacterium and other highly recombinogenic pathogens

Quadrupole moments and mean-square charge radii in the bismuth isotope chain

Isotope shifts and hyperfine structures of the $^{205, 206, 208, 210, 210m, 212, 213}$Bi isotopes have been studied on the 306.7nm line using gas cell laser spectroscopy. The neutron-rich isotopes are the first isotones of Pb to be measured immediately above the N=126 shell closure. The ground state quadrupole moments of the even--N isotopes increase as neutrons are added or removed from the N=126 shell, but no corresponding increase is observed in the charge radii

Molecular Epidemiology of Anthrax Cases Associated with Recreational Use of Animal Hides and Yarn in the United States

To determine potential links between the clinical isolate to animal products and their geographic origin, we genotyped (MLVA-8, MVLA-15, and canSNP analysis) 80 environmental and 12 clinical isolates and 2 clinical specimens from five cases of anthrax (California in 1976 [n = 1], New York in 2006 [n = 1], Connecticut in 2007 [n = 2], and New Hampshire in 2009[n = 1]) resulting from recreational handling of animal products. For the California case, four clinical isolates were identified as MLVA-8 genotype (GT) 76 and in the canSNP A.Br.Vollum lineage, which is consistent with the Pakistani origin of the yarn. Twenty eight of the California isolates were in the A.Br.Vollum canSNP lineage and one isolate was in the A.Br. 003/004 canSNP sub-group. All 52 isolates and both clinical specimens related to the New York and Connecticut cases were MLVA-8 GT 1. The animal products associated with the NY and CT cases were believed to originate from West Africa, but no isolates from this region are available to be genotyped for comparison. All isolates associated with the New Hampshire case were identical and had a new genotype (GT 149). Isolates from the NY, CT and NH cases diverge from the established canSNP phylogeny near the base of the A.Br.011/009. This report illustrates the power of the current genotyping methods and the dramatically different epidemiological conditions that can lead to infections (i.e., contamination by a single genotype versus widespread contamination of numerous genotypes). These cases illustrate the need to acquire and genotype global isolates so that accurate assignments can be made about isolate origins

Measurement of the magnetic moment of the one-neutron halo nucleus 11^{11}Be

The magnetic moment of $^{11}$Be was measured by detecting nuclear magnetic resonance signals in a beryllium crystal lattice. The experimental technique applied to a $^{11}$Be$^+$ ion beam from a laser ion source includes in-beam optical polarization, implantation into a metallic single crystal and observation of rf resonances in the asymmetric angular distribution of the $\beta$-decay ($\beta$-NMR). The nuclear magnetic moment $\mu(^{11}{\rm Be}) = -1.6816(8)\,\mu_N$ provides a stringent test for theoretical models describing the structure of the 1/2$^+$ neutron halo state