Connectivity percolation in suspensions of hard platelets

We present a study on connectivity percolation in suspensions of hard platelets by means of Monte Carlo simulation. We interpret our results using a contact-volume argument based on an effective single--particle cell model. It is commonly assumed that the percolation threshold of anisotropic objects scales as their inverse aspect ratio. While this rule has been shown to hold for rod-like particles, we find that for hard plate-like particles the percolation threshold is non-monotonic in the aspect ratio. It exhibits a shallow minimum at intermediate aspect ratios and then saturates to a constant value. This effect is caused by the isotropic-nematic transition pre-empting the percolation transition. Hence the common strategy to use highly anisotropic, conductive particles as fillers in composite materials in order to produce conduction at low filler concentration is expected to fail for plate-like fillers such as graphene and graphite nanoplatelets

Data from: Genotyping-by-Sequencing for Populus Population Genomics: An Assessment of Genome Sampling Patterns and Filtering Approaches

Continuing advances in nucleotide sequencing technology are inspiring a suite of genomic approaches in studies of natural populations. Researchers are faced with data management and analytical scales that are increasing by orders of magnitude. With such dramatic advances comes a need to understand biases and error rates, which can be propagated and magnified in large-scale data acquisition and processing. Here we assess genomic sampling biases and the effects of various population-level data filtering strategies in a genotyping-by-sequencing (GBS) protocol. We focus on data from two species of Populus, because this genus has a relatively small genome and is emerging as a target for population genomic studies. We estimate the proportions and patterns of genomic sampling by examining the Populus trichocarpa genome (Nisqually-1), and demonstrate a pronounced bias towards coding regions when using the methylation-sensitive ApeKI restriction enzyme in this species. Using population-level data from a closely related species (P. tremuloides), we also investigate various approaches for filtering GBS data to retain high-depth, informative SNPs that can be used for population genetic analyses. We find a data filter that includes the designation of ambiguous alleles resulted in metrics of population structure and Hardy-Weinberg equilibrium that were most consistent with previous studies of the same populations based on other genetic markers. Analyses of the filtered data (27,910 SNPs) also resulted in patterns of heterozygosity and population structure similar to a previous study using microsatellites. Our application demonstrates that technically and analytically simple approaches can readily be developed for population genomics of natural populations

Numerical loop quantum cosmology: an overview

A brief review of various numerical techniques used in loop quantum cosmology and results is presented. These include the way extensive numerical simulations shed insights on the resolution of classical singularities, resulting in the key prediction of the bounce at the Planck scale in different models, and the numerical methods used to analyze the properties of the quantum difference operator and the von Neumann stability issues. Using the quantization of a massless scalar field in an isotropic spacetime as a template, an attempt is made to highlight the complementarity of different methods to gain understanding of the new physics emerging from the quantum theory. Open directions which need to be explored with more refined numerical methods are discussed.Comment: 33 Pages, 4 figures. Invited contribution to appear in Classical and Quantum Gravity special issue on Non-Astrophysical Numerical Relativit

NNLO corrections to top-pair production at hadron colliders: the all-fermionic scattering channels

This is a second paper in our ongoing calculation of the next-to-next-to-leading order (NNLO) QCD correction to the total inclusive top-pair production cross-section at hadron colliders. In this paper we calculate the reaction $q\bar q \to t\bar t + q\bar q$ which was not considered in our previous work on $q\bar q \to t\bar t +X$ due to its phenomenologically negligible size. We also calculate all remaining fermion-pair-initiated partonic channels $qq', q\bar q'$ and $qq$ that contribute to top-pair production starting from NNLO. The contributions of these reactions to the total cross-section for top-pair production at the Tevatron and LHC are small, at the permil level. The most interesting feature of these reactions is their characteristic logarithmic rise in the high energy limit. We compute the constant term in the leading power behavior in this limit, and achieve precision that is an order of magnitude better than the precision of a recent theoretical prediction for this constant. All four partonic reactions computed in this paper are included in our numerical program Top++. The calculation of the NNLO corrections to the two remaining partonic reactions, $qg\to t\bar t+X$ and $gg\to t\bar t+X$, is ongoing.Comment: 1+16 pages; 3 figure

Suppression factors in diffractive photoproduction of dijets

After new publications of H1 data for the diffractive photoproduction of dijets, which overlap with the earlier published H1 data and the recently published data of the ZEUS collaboration, have appeared, we have recalculated the cross sections for this process in next-to-leading order (NLO) of perturbative QCD to see whether they can be interpreted consistently. The results of these calculations are compared to the data of both collaborations. We find that the NLO cross sections disagree with the data, showing that factorization breaking occurs at that order. If direct and resolved contributions are both suppressed by the same amount, the global suppression factor depends on the transverse-energy cut. However, by suppressing only the resolved contribution, also reasonably good agreement with all the data is found with a suppression factor independent of the transverse-energy cut.Comment: 28 pages, 11 figures, 3 table

The Cyprinodon variegatus genome reveals gene expression changes underlying differences in skull morphology among closely related species

Genes in durophage intersection set at 15 dpf. This is a comma separated table of the genes in the 15 dpf durophage intersection set. Given are edgeR results for each pairwise comparison. Columns indicating whether a gene is included in the intersection set at a threshold of 1.5 or 2 fold are provided. (CSV 13 kb

Exclusive diffractive processes and the quark substructure of mesons

Exclusive diffractive processes on the nucleon are investigated within a model in which the quark-nucleon interaction is mediated by Pomeron exchange and the quark substructure of mesons is described within a framework based on the Dyson-Schwinger equations of QCD. The model quark-nucleon interaction has four parameters which are completely determined by high-energy $\pi N$ and $K N$ elastic scattering data. The model is then used to predict vector-meson electroproduction observables. The obtained $\rho$- and $\phi$-meson electroproduction cross sections are in excellent agreement with experimental data. The predicted $q^2$ dependence of $J/\psi$-meson electroproduction also agrees with experimental data. It is shown that confined-quark dynamics play a central role in determining the behavior of the diffractive, vector-meson electroproduction cross section. In particular, the onset of the asymptotic $1/q^4$ behavior of the cross section is determined by a momentum scale that is set by the current-quark masses of the quark and antiquark inside the vector meson. This is the origin of the striking differences between the $q^2$ dependence of $\rho$-, $\phi$- and $J/\psi$-meson electroproduction cross sections observed in recent experiments.Comment: 53 pages, 23 figures, revtex and epsfig. Minor additions to tex

DNA damage alters nuclear mechanics through chromatin reorganization

AbstractDNA double-strand breaks drive genomic instability. However, it remains unknown how these processes may affect the biomechanical properties of the nucleus and what role nuclear mechanics play in DNA damage and repair efficiency. Here, we have used Atomic Force Microscopy to investigate nuclear mechanical changes, arising from externally induced DNA damage. We found that nuclear stiffness is significantly reduced after cisplatin treatment, as a consequence of DNA damage signalling. This softening was linked to global chromatin decondensation, which improves molecular diffusion within the organelle. We propose that this can increase recruitment for repair factors. Interestingly, we also found that reduction of nuclear tension, through cytoskeletal relaxation, has a protective role to the cell and reduces accumulation of DNA damage. Overall, these changes protect against further genomic instability and promote DNA repair. We propose that these processes may underpin the development of drug resistance

Loop Quantum Cosmology: A Status Report

The goal of this article is to provide an overview of the current state of the art in loop quantum cosmology for three sets of audiences: young researchers interested in entering this area; the quantum gravity community in general; and, cosmologists who wish to apply loop quantum cosmology to probe modifications in the standard paradigm of the early universe. An effort has been made to streamline the material so that, as described at the end of section I, each of these communities can read only the sections they are most interested in, without a loss of continuity.Comment: 138 pages, 15 figures. Invited Topical Review, To appear in Classical and Quantum Gravity. Typos corrected, clarifications and references adde

Moments of Nucleon Light Cone Quark Distributions Calculated in Full Lattice QCD

Moments of the quark density, helicity, and transversity distributions are calculated in unquenched lattice QCD. Calculations of proton matrix elements of operators corresponding to these moments through the operator product expansion have been performed on $16^3 \times 32$ lattices for Wilson fermions at $\beta = 5.6$ using configurations from the SESAM collaboration and at $\beta = 5.5$ using configurations from SCRI. One-loop perturbative renormalization corrections are included. At quark masses accessible in present calculations, there is no statistically significant difference between quenched and full QCD results, indicating that the contributions of quark-antiquark excitations from the Dirac Sea are small. Close agreement between calculations with cooled configurations containing essentially only instantons and the full gluon configurations indicates that quark zero modes associated with instantons play a dominant role. Naive linear extrapolation of the full QCD calculation to the physical pion mass yields results inconsistent with experiment. Extrapolation to the chiral limit including the physics of the pion cloud can resolve this discrepancy and the requirements for a definitive chiral extrapolation are described.Comment: 53 Pages Revtex, 26 Figures, 9 Tables. Added additional reference and updated referenced data in Table I