Precise charm to strange mass ratio and light quark masses from full lattice QCD

By using a single formalism to handle charm, strange and light valence quarks in full lattice QCD for the first time, we are able to determine ratios of quark masses to 1%. For $m_c/m_s$ we obtain 11.85(16), an order of magnitude more precise than the current PDG average. Combined with 1% determinations of the charm quark mass now possible this gives $\bar{m}_s(2{\rm GeV}) =$ 92.4(1.5) MeV. The MILC result for $m_s/m_l = 27.2(3)$ yields $\bar{m}_l(2{\rm GeV})$ = 3.40(7) MeV for the average of $u$ and $d$ quark masses.Comment: 4 pages, 2 figures. Version accepted by Physical Review Letters. Changes include modifying the title, using the MILC value for m_s/m_l which changes slightly the resulting up and down quark masses and their average, adding some references and making other small adjustments to the text for space reasons

A Prediction of the B*_c mass in full lattice QCD

By using the Highly Improved Staggered Quark formalism to handle charm, strange and light valence quarks in full lattice QCD, and NRQCD to handle bottom valence quarks we are able to determine accurately ratios of the B meson vector-pseudoscalar mass splittings, in particular, (m(B*_c)-m(B_c))/(m(B*_s)-m(B_s)). We find this ratio to be 1.15(15), showing the `light' quark mass dependence of this splitting to be very small. Hence we predict m(B_c*) = 6.330(7)(2)(6) GeV where the first two errors are from the lattice calculation and the third from existing experiment. This is the most accurate prediction of a gold-plated hadron mass from lattice QCD to date.Comment: 4 pages, 2 figure

Semiclassical Description of Exotic Nuclear Shapes

Exotic nuclear structures such as bubbles and tori are analyzed through semiclassical extended Thomas-Fermi calculations with the Skyrme force SkM$^*$. The variational equations for neutron and proton densities are solved fully self-consistently in spherical (bubbles) and cylindrical (tori) symmetries. The possible existence of bubble configurations in some astrophysical scenarios is discussed. The stability of toroidal structures against change of quadrupole moment is studied. A global minimum of the energy is found in heavyComment: 13 pages, 6 figures, Contribution to XIV Nuclear Physics Workshop at Kazimierz Dolny, Poland, Sept. 26-29, 200

Scaling studies of QCD with the dynamical HISQ action

We study the lattice spacing dependence, or scaling, of physical quantities using the highly improved staggered quark (HISQ) action introduced by the HPQCD/UKQCD collaboration, comparing our results to similar simulations with the asqtad fermion action. Results are based on calculations with lattice spacings approximately 0.15, 0.12 and 0.09 fm, using four flavors of dynamical HISQ quarks. The strange and charm quark masses are near their physical values, and the light-quark mass is set to 0.2 times the strange-quark mass. We look at the lattice spacing dependence of hadron masses, pseudoscalar meson decay constants, and the topological susceptibility. In addition to the commonly used determination of the lattice spacing through the static quark potential, we examine a determination proposed by the HPQCD collaboration that uses the decay constant of a fictitious "unmixed s bar s" pseudoscalar meson. We find that the lattice artifacts in the HISQ simulations are much smaller than those in the asqtad simulations at the same lattice spacings and quark masses.Comment: 36 pages, 11 figures, revised version to be published. Revisions include discussion of autocorrelations and several clarification

A convenient band-gap interpolation technique and an improved band line-up model for InGaAlAs on InP

The band-gap energy and the band line-up of InGaAlAs quaternary compound material on InP are essential information for the theoretical study of physical properties and the design of optoelectronics devices operating in the long-wavelength communication window. The band-gap interpolation of In1-x-y Ga (x) Al (y) As on InP is known to be a challenging task due to the observed discrepancy of experimental results arising from the bowing effect. Besides, the band line-up results of In1-x-y Ga (x) Al (y) As on InP based on previously reported models have limited success by far. In this work, we propose an interpolation solution using the single-variable surface bowing estimation interpolation method for the fitting of experimentally measured In1-x-y Ga (x) Al (y) As band-gap data with various degree of bowing using the same set of input parameters. The suggested solution provides an easier and more physically interpretable way to determine not only lattice matched, but also strained band-gap energy of In1-x-y Ga (x) Al (y) As on InP based on the experimental results. Interpolated results from this convenient method show a more favourable match to multiple independent experiment data sets measured under different temperature conditions as compared to those obtained from the commonly used weighted-sum approach. On top of that, extended framework of the model-solid theory for the band line-up of In1-x-y Ga (x) Al (y) As/InP heterostructure is proposed. Our model-solid theory band line-up result using the proposed extended framework has shown an improved accuracy over those without the extension. In contrast to some previously reported works, it is worth noting that the band line-up result based on our proposed extended model-solid theory has also shown to be more accurate than those given by Harrison's mode

A transcriptomic snapshot of early molecular communication between Pasteuria penetrans and Meloidogyne incognita

© The Author(s). 2018Background: Southern root-knot nematode Meloidogyne incognita (Kofoid and White, 1919), Chitwood, 1949 is a key pest of agricultural crops. Pasteuria penetrans is a hyperparasitic bacterium capable of suppressing the nematode reproduction, and represents a typical coevolved pathogen-hyperparasite system. Attachment of Pasteuria endospores to the cuticle of second-stage nematode juveniles is the first and pivotal step in the bacterial infection. RNA-Seq was used to understand the early transcriptional response of the root-knot nematode at 8 h post Pasteuria endospore attachment. Results: A total of 52,485 transcripts were assembled from the high quality (HQ) reads, out of which 582 transcripts were found differentially expressed in the Pasteuria endospore encumbered J2 s, of which 229 were up-regulated and 353 were down-regulated. Pasteuria infection caused a suppression of the protein synthesis machinery of the nematode. Several of the differentially expressed transcripts were putatively involved in nematode innate immunity, signaling, stress responses, endospore attachment process and post-attachment behavioral modification of the juveniles. The expression profiles of fifteen selected transcripts were validated to be true by the qRT PCR. RNAi based silencing of transcripts coding for fructose bisphosphate aldolase and glucosyl transferase caused a reduction in endospore attachment as compared to the controls, whereas, silencing of aspartic protease and ubiquitin coding transcripts resulted in higher incidence of endospore attachment on the nematode cuticle. Conclusions: Here we provide evidence of an early transcriptional response by the nematode upon infection by Pasteuria prior to root invasion. We found that adhesion of Pasteuria endospores to the cuticle induced a down-regulated protein response in the nematode. In addition, we show that fructose bisphosphate aldolase, glucosyl transferase, aspartic protease and ubiquitin coding transcripts are involved in modulating the endospore attachment on the nematode cuticle. Our results add new and significant information to the existing knowledge on early molecular interaction between M. incognita and P. penetrans.Peer reviewedFinal Published versio

Genome-wide signatures of convergent evolution in echolocating mammals

Evolution is typically thought to proceed through divergence of genes, proteins, and ultimately phenotypes(1-3). However, similar traits might also evolve convergently in unrelated taxa due to similar selection pressures(4,5). Adaptive phenotypic convergence is widespread in nature, and recent results from a handful of genes have suggested that this phenomenon is powerful enough to also drive recurrent evolution at the sequence level(6-9). Where homoplasious substitutions do occur these have long been considered the result of neutral processes. However, recent studies have demonstrated that adaptive convergent sequence evolution can be detected in vertebrates using statistical methods that model parallel evolution(9,10) although the extent to which sequence convergence between genera occurs across genomes is unknown. Here we analyse genomic sequence data in mammals that have independently evolved echolocation and show for the first time that convergence is not a rare process restricted to a handful of loci but is instead widespread, continuously distributed and commonly driven by natural selection acting on a small number of sites per locus. Systematic analyses of convergent sequence evolution in 805,053 amino acids within 2,326 orthologous coding gene sequences compared across 22 mammals (including four new bat genomes) revealed signatures consistent with convergence in nearly 200 loci. Strong and significant support for convergence among bats and the dolphin was seen in numerous genes linked to hearing or deafness, consistent with an involvement in echolocation. Surprisingly we also found convergence in many genes linked to vision: the convergent signal of many sensory genes was robustly correlated with the strength of natural selection. This first attempt to detect genome-wide convergent sequence evolution across divergent taxa reveals the phenomenon to be much more pervasive than previously recognised