Residual based adaptivity and PWDG methods for the Helmholtz equation

We present a study of two residual a posteriori error indicators for the Plane Wave Discontinuous Galerkin (PWDG) method for the Helmholtz equation. In particular we study the h-version of PWDG in which the number of plane wave directions per element is kept fixed. First we use a slight modification of the appropriate a priori analysis to determine a residual indicator. Numerical tests show that this is reliable but pessimistic in that the ratio between the true error and the indicator increases as the mesh is refined. We therefore introduce a new analysis based on the observation that sufficiently many plane waves can approximate piecewise linear functions as the mesh is refined. Numerical results demonstrate an improvement in the efficiency of the indicators

Accelerated motion and the self-force in Schwarzschild spacetime

We provide expansions of the Detweiler-Whiting singular field for motion along arbitrary, planar accelerated trajectories in Schwarzschild spacetime. We transcribe these results into mode-sum regularization parameters, computing previously unknown terms that increase the convergence rate of the mode-sum. We test our results by computing the self-force along a variety of accelerated trajectories. For non-uniformly accelerated circular orbits we present results from a new 1+1D discontinuous Galerkin time-domain code which employs an effective-source. We also present results for uniformly accelerated circular orbits and accelerated bound eccentric orbits computed within a frequency-domain treatment. Our regularization results will be useful for computing self-consistent self-force inspirals where the particle's worldline is accelerated with respect to the background spacetime.Comment: 19 pages, 6 figures (accepted CQG special issue article version

Complementing the shape group method : assessing chirality

The Shape Group method is a powerful tool in the analysis of the shape of molecules, and in the correlation of molecular shape features to molecular properties in Quantitative Shape-Activity Relationship (QShAR) studies. However, the main disadvantage inherent in the method is that mirror image molecules are considered to be "exactly" similar. As such, the method requires a complementary chirality measure to allow for complete analysis where chirality is involved. In this work, two methods of creating chirality measures to complement the Shape Group method are presented. The first is based upon the assigning of handedness values to each array point of the computer file that contains specific property information and uses the parallels between a lattice animal inscribed in a Jordan curve, and the array points inscribed in an isodensity contour. Each array point can then be treated as a face-labelled cube, which is often a chiral object that can have an assigned handedness value. Grouping of these handedness values allows for the creation of chirality measures. In the second method, the Shape Group method is applied to electron density representations created by subtracting one fragmentary electron density from others and analysing the shape similarities of the resultant difference densities. With both methods, chirality information that is already embedded within the shape descriptions of electron density representations is emphasized. The Shape Group method and the developed chirality measures are then used to simply correlate the shape and chirality of the stereogenic carbon of molecules to optical rotation and rotational strengths of various classes of molecules

Spin-Polarized Electrons in Monolayer MoS2_2

The optical susceptibility is a local, minimally-invasive and spin-selective probe of the ground state of a two-dimensional electron gas. We apply this probe to a gated monolayer of MoS$_2$. We demonstrate that the electrons are spin polarized. Of the four available bands, only two are occupied. These two bands have the same spin but different valley quantum numbers. We argue that strong Coulomb interactions are a key aspect of this spontaneous symmetry breaking. The Bohr radius is so small that even electrons located far apart in phase space interact, facilitating exchange couplings to align the spins

Compassionate versus consequentialist conservation

Ethical treatment of wildlife and consideration of animal welfare have become important themes in conservation, but ethical perspectives on how best to protect wild animals and promote their welfare are diverse. There are advantages to the consequentialist harms ethical framework applied in managing wild herbivores for conservation purposes. To minimize harms while achieving conservation goals, we argue that overabundant wild herbivores should in many cases be managed through consumptive in situ killing. Advantages of this policy are that the negative welfare states imposed on animals last only a short time; remaining animals are not deprived of positive welfare states (e.g., linked to rearing offspring); poor welfare states of animals in overabundant populations are avoided (e.g., starvation); negative welfare impacts on heterospecifics through resource depletion (i.e., competition) are prevented; harvesting meat reduces the number of (agricultural) animals raised to supply meat; and minimal costs maximize funding for other wildlife management and conservation priorities. Alternative ethical approaches to our consequentialist framework include deontology (containing animal rights) and virtue ethics, some of which underpin compassionate conservation. These alternative ethical approaches emphasize the importance of avoiding intentional killing of animals but, if no population reduction occurs, are likely to impose considerable unintentional harms on overabundant wildlife and indirectly harm heterospecifics through ineffective population reduction. If nonlethal control is used, it is likely that overabundant animals would be deprived of positive welfare states and economic costs would be prohibitive. We encourage conservation stakeholders to consider animal-welfare consequentialism as an ethical approach to minimize harms to the animals under their care as well as other animals that policies may affect while at the same time pursuing conservation goals

Quantum confined Stark effect in a MoS2_2 monolayer van der Waals heterostructure

The optics of dangling-bond-free van der Waals heterostructures containing transition metal dichalcogenides are dominated by excitons. A crucial property of a confined exciton is the quantum confined Stark effect (QCSE). Here, such a heterostructure is used to probe the QCSE by applying a uniform vertical electric field across a molybdenum disulfide (MoS$_2$) monolayer. The photoluminescence emission energies of the neutral and charged excitons shift quadratically with the applied electric field provided the electron density remains constant, demonstrating that the exciton can be polarized. Stark shifts corresponding to about half the homogeneous linewidth were achieved. Neutral and charged exciton polarizabilities of (7.8~\pm~1.0)\times 10^{-10}~\tr{D~m~V}^{-1} and (6.4~\pm~0.9)\times 10^{-10}~\tr{D~m~V}^{-1} at relatively low electron density (8 \times 10^{11}~\tr{cm}^{-2}) have been extracted, respectively. These values are one order of magnitude lower than the previously reported values, but in line with theoretical calculations. The methodology presented here is versatile and can be applied to other semiconducting layered materials as well

A paucity of heterochromatin at functional human neocentromeres

<p>Abstract</p> <p>Background</p> <p>Centromeres are responsible for the proper segregation of replicated chromatids during cell division. Neocentromeres are fully functional ectopic human centromeres that form on low-copy DNA sequences and permit analysis of centromere structure in relation to the underlying DNA sequence. Such structural analysis is not possible at endogenous centromeres because of the large amounts of repetitive alpha satellite DNA present.</p> <p>Results</p> <p>High-resolution chromatin immunoprecipitation (ChIP) on CHIP (microarray) analysis of three independent neocentromeres from chromosome 13q revealed that each neocentromere contained ~100 kb of centromere protein (CENP)-A in a two-domain organization. Additional CENP-A domains were observed in the vicinity of neocentromeres, coinciding with CpG islands at the 5' end of genes. Analysis of histone H3 dimethylated at lysine 4 (H3K4me2) revealed small domains at each neocentromere. However, these domains of H3K4me2 were also found in the equivalent non-neocentric chromosomes. A surprisingly minimal (~15 kb) heterochromatin domain was observed at one of the neocentromeres, which formed in an unusual transposon-free region distal to the CENP-A domains. Another neocentromere showed a distinct absence of nearby significant domains of heterochromatin. A subtle defect in centromere cohesion detected at these neocentromeres may be due to the paucity of heterochromatin domains.</p> <p>Conclusions</p> <p>This high-resolution mapping suggests that H3K4me2 does not seem sufficiently abundant to play a structural role at neocentromeres, as proposed for endogenous centromeres. Large domains of heterochromatin also do not appear necessary for centromere function. Thus, this study provides important insight into the structural requirements of human centromere function.</p

Analysis of the largest tandemly repeated DNA families in the human genome

<p>Abstract</p> <p>Background</p> <p>Tandemly Repeated DNA represents a large portion of the human genome, and accounts for a significant amount of copy number variation. Here we present a genome wide analysis of the largest tandem repeats found in the human genome sequence.</p> <p>Results</p> <p>Using Tandem Repeats Finder (TRF), tandem repeat arrays greater than 10 kb in total size were identified, and classified into simple sequence e.g. GAATG, classical satellites e.g. alpha satellite DNA, and locus specific VNTR arrays. Analysis of these large sequenced regions revealed that several "simple sequence" arrays actually showed complex domain and/or higher order repeat organization. Using additional methods, we further identified a total of 96 additional arrays with tandem repeat units greater than 2 kb (the detection limit of TRF), 53 of which contained genes or repeated exons. The overall size of an array of tandem 12 kb repeats which spanned a gap on chromosome 8 was found to be 600 kb to 1.7 Mbp in size, representing one of the largest non-centromeric arrays characterized. Several novel megasatellite tandem DNA families were observed that are characterized by repeating patterns of interspersed transposable elements that have expanded presumably by unequal crossing over. One of these families is found on 11 different chromosomes in >25 arrays, and represents one of the largest most widespread megasatellite DNA families.</p> <p>Conclusion</p> <p>This study represents the most comprehensive genome wide analysis of large tandem repeats in the human genome, and will serve as an important resource towards understanding the organization and copy number variation of these complex DNA families.</p

Order-disorder transition in nanoscopic semiconductor quantum rings

Using the path integral Monte Carlo technique we show that semiconductor quantum rings with up to six electrons exhibit a temperature, ring diameter, and particle number dependent transition between spin ordered and disordered Wigner crystals. Due to the small number of particles the transition extends over a broad temperature range and is clearly identifiable from the electron pair correlation functions.Comment: 4 pages, 5 figures, For recent information on physics of small systems see http://www.smallsystems.d