A physically-motivated quantisation of the electromagnetic field on curved spacetimes

Recently, Bennett et al. [Eur. J. Phys. 37:014001, 2016] presented a physically-motivated and explicitly gauge-independent scheme for the quantisation of the electromagnetic field in flat Minkowski space. In this paper we generalise this field quantisation scheme to curved spacetimes.Working within the standard assumptions of quantum field theory and only postulating the physicality of the photon, we derive the Hamiltonian, H, and the electric and magnetic field observables, E and B, without having to invoke a specific gauge. As an example, we quantise the electromagnetic field in the spacetime of an accelerated Minkowski observer, Rindler space, and demonstrate consistency with other field quantisation schemes by reproducing the Unruh effect

Cavity optomechanics with Si3N4 membranes at cryogenic temperatures

We describe a cryogenic cavity-optomechanical system that combines Si3N4 membranes with a mechanically-rigid Fabry-Perot cavity. The extremely high quality-factor frequency products of the membranes allow us to cool a MHz mechanical mode to a phonon occupation of less than 10, starting at a bath temperature of 5 kelvin. We show that even at cold temperatures thermally-occupied mechanical modes of the cavity elements can be a limitation, and we discuss methods to reduce these effects sufficiently to achieve ground state cooling. This promising new platform should have versatile uses for hybrid devices and searches for radiation pressure shot noise.Comment: 19 pages, 5 figures, submitted to New Journal of Physic

Metabolic flexibility as a major predictor of spatial distribution in microbial communities

A better understand the ecology of microbes and their role in the global ecosystem could be achieved if traditional ecological theories can be applied to microbes. In ecology organisms are defined as specialists or generalists according to the breadth of their niche. Spatial distribution is often used as a proxy measure of niche breadth; generalists have broad niches and a wide spatial distribution and specialists a narrow niche and spatial distribution. Previous studies suggest that microbial distribution patterns are contrary to this idea; a microbial generalist genus (Desulfobulbus) has a limited spatial distribution while a specialist genus (Methanosaeta) has a cosmopolitan distribution. Therefore, we hypothesise that this counter-intuitive distribution within generalist and specialist microbial genera is a common microbial characteristic. Using molecular fingerprinting the distribution of four microbial genera, two generalists, Desulfobulbus and the methanogenic archaea Methanosarcina, and two specialists, Methanosaeta and the sulfate-reducing bacteria Desulfobacter were analysed in sediment samples from along a UK estuary. Detected genotypes of both generalist genera showed a distinct spatial distribution, significantly correlated with geographic distance between sites. Genotypes of both specialist genera showed no significant differential spatial distribution. These data support the hypothesis that the spatial distribution of specialist and generalist microbes does not match that seen with specialist and generalist large organisms. It may be that generalist microbes, while having a wider potential niche, are constrained, possibly by intrageneric competition, to exploit only a small part of that potential niche while specialists, with far fewer constraints to their niche, are more capable of filling their potential niche more effectively, perhaps by avoiding intrageneric competition. We suggest that these counter-intuitive distribution patterns may be a common feature of microbes in general and represent a distinct microbial principle in ecology, which is a real challenge if we are to develop a truly inclusive ecology

Cooperativity and Frustration in Protein-Mediated Parallel Actin Bundles

We examine the mechanism of bundling of cytoskeletal actin filaments by two representative bundling proteins, fascin and espin. Small-angle X-ray studies show that increased binding from linkers drives a systematic \textit{overtwist} of actin filaments from their native state, which occurs in a linker-dependent fashion. Fascin bundles actin into a continuous spectrum of intermediate twist states, while espin only allows for untwisted actin filaments and fully-overtwisted bundles. Based on a coarse-grained, statistical model of protein binding, we show that the interplay between binding geometry and the intrinsic \textit{flexibility} of linkers mediates cooperative binding in the bundle. We attribute the respective continuous/discontinous bundling mechanisms of fascin/espin to differences in the stiffness of linker bonds themselves.Comment: 5 pages, 3 figures, figure file has been corrected in v

Manifestation of classical wave delays in a fully quantized model of the scattering of a single photon

We consider a fully quantized model of spontaneous emission, scattering, and absorption, and study propagation of a single photon from an emitting atom to a detector atom both with and without an intervening scatterer. We find an exact quantum analog to the classical complex analytic signal of an electromagnetic wave scattered by a medium of charged oscillators. This quantum signal exhibits classical phase delays. We define a time of detection which, in the appropriate limits, exactly matches the predictions of a classically defined delay for light propagating through a medium of charged oscillators. The fully quantized model provides a simple, unambiguous, and causal interpretation of delays that seemingly imply speeds greater than c in the region of anomalous dispersion.Comment: 18 pages, 4 figures, revised for clarity, typos corrrecte

Lines, Circles, Planes and Spheres

Let $S$ be a set of $n$ points in $\mathbb{R}^3$, no three collinear and not all coplanar. If at most $n-k$ are coplanar and $n$ is sufficiently large, the total number of planes determined is at least $1 + k \binom{n-k}{2}-\binom{k}{2}(\frac{n-k}{2})$. For similar conditions and sufficiently large $n$, (inspired by the work of P. D. T. A. Elliott in \cite{Ell67}) we also show that the number of spheres determined by $n$ points is at least $1+\binom{n-1}{3}-t_3^{orchard}(n-1)$, and this bound is best possible under its hypothesis. (By $t_3^{orchard}(n)$, we are denoting the maximum number of three-point lines attainable by a configuration of $n$ points, no four collinear, in the plane, i.e., the classic Orchard Problem.) New lower bounds are also given for both lines and circles.Comment: 37 page

Genetic Variability and the Classification of Hepatitis E Virus (vol 87, pg 4161, 2013)

The classification of hepatitis E virus (HEV) variants is currently in transition without agreed definitions for genotypes and sub-types or for deeper taxonomic groupings into species and genera that could incorporate more recently characterized viruses as-signed to theHepeviridae family that infect birds, bats, rodents, and fish. These conflicts arise because of differences in the vi-ruses and genomic regions compared and in the methodology used. We have reexamined published sequences and found that synonymous substitutions were saturated in comparisons between and within virus genotypes. Analysis of complete genome sequences or concatenated ORF1/ORF2 amino acid sequences indicated that HEV variants most closely related to those infecting humans can be consistently divided into six genotypes (types 1 to 4 and two additional genotypes fromwild boar). Variants iso-lated from rabbits, closely related to genotype 3, occupy an intermediate position. No consistent criteria could be defined for the assignment of virus subtypes. Analysis of amino acid sequences from these viruses with the more divergent variants from chick

One-loop divergences in the two-dimensional non-anticommutative supersymmetric sigma-model

We discuss the structure of the non-anticommutative N=2 non-linear sigma-model in two dimensions, constructing differential operators which implement the deformed supersymmetry generators and using them to reproduce the classical action. We then compute the one-loop quantum corrections and express them in a more compact form using the differential operators.Comment: 20pp, 8 figures, uses LaTeX. Title expanded to clarify conten

Genetic variability and the classification of hepatitis E virus

The classification of hepatitis E virus (HEV) variants is currently in transition without agreed definitions for genotypes and subtypes or for deeper taxonomic groupings into species and genera that could incorporate more recently characterized viruses assigned to the Hepeviridae family that infect birds, bats, rodents, and fish. These conflicts arise because of differences in the viruses and genomic regions compared and in the methodology used. We have reexamined published sequences and found that synonymous substitutions were saturated in comparisons between and within virus genotypes. Analysis of complete genome sequences or concatenated ORF1/ORF2 amino acid sequences indicated that HEV variants most closely related to those infecting humans can be consistently divided into six genotypes (types 1 to 4 and two additional genotypes from wild boar). Variants isolated from rabbits, closely related to genotype 3, occupy an intermediate position. No consistent criteria could be defined for the assignment of virus subtypes. Analysis of amino acid sequences from these viruses with the more divergent variants from chickens, bats, and rodents in three conserved subgenomic regions (residues 1 to 452 or 974 to 1534 of ORF1 or residues 105 to 458 of ORF2) provided consistent support for a division into 4 groups, corresponding to HEV variants infecting humans and pigs, those infecting rats and ferrets, those from bats, and those from chickens. This approach may form the basis for a future genetic classification of HEV into four species, with the more divergent HEV-like virus from fish (cutthroat trout virus) representing a second genus

Isotropic-nematic phase transition in suspensions of filamentous virus and the neutral polymer Dextran

We present an experimental study of the isotropic-nematic phase transition in an aqueous mixture of charged semi-flexible rods (fd virus) and neutral polymer (Dextran). A complete phase diagram is measured as a function of ionic strength and polymer molecular weight. At high ionic strength we find that adding polymer widens the isotropic-nematic coexistence region with polymers preferentially partitioning into the isotropic phase, while at low ionic strength the added polymer has no effect on the phase transition. The nematic order parameter is determined from birefringence measurements and is found to be independent of polymer concentration (or equivalently the strength of attraction). The experimental results are compared with the existing theoretical predictions for the isotropic-nematic transition in rods with attractive interactions.Comment: 8 Figures. To be published in Phys. Rev. E. For more information see http://www.elsie.brandeis.ed