Review of the initial validation and characterization of a chicken 3K SNP array.

In 2004 the chicken genome sequence and more than 2.8 million single nucleotide polymorphisms (SNPs) were reported. This information greatly enhanced the ability of poultry scientists to understand chicken biology, especially with respect to identification of quantitative trait loci (QTL) and genes that control simple and complex traits. To validate and address the quality of the reported SNPs, assays for 3072 SNPS were developed and used to genotype 2576 DNAs isolated from commercial and experimental birds. Over 90% of the SNPs were valid based on the criterion used for segregating, and over 88% had a minor allele frequency of 2% or greater. As the East Lansing (EL) and Wageningen University (WAU) reference panels were genotyped, 1933 SNPs were added to the chicken genetic map, which was used in the second chicken genome sequence assembly. It was also discovered that linkage disequilibrium varied considerably between commercial layers and broilers; with the latter having haplotype blocks averaging 10 to 50 kb in size. Finally, it was estimated that commercial lines have lost 70% or more of their genetic diversity, with the majority of allele loss attributable to the limited number of chicken breeds used

Effects of electrojet turbulence on a magnetosphere-ionosphere simulation of a geomagnetic storm

Ionospheric conductance plays an important role in regulating the response of the magnetosphere‐ionosphere system to solar wind driving. Typically, models of magnetosphere‐ionosphere coupling include changes to ionospheric conductance driven by extreme ultraviolet ionization and electron precipitation. This paper shows that effects driven by the Farley‐Buneman instability can also create significant enhancements in the ionospheric conductance, with substantial impacts on geospace. We have implemented a method of including electrojet turbulence (ET) effects into the ionospheric conductance model utilized within geospace simulations. Our particular implementation is tested with simulations of the Lyon‐Fedder‐Mobarry global magnetosphere model coupled with the Rice Convection Model of the inner magnetosphere. We examine the impact of including ET‐modified conductances in a case study of the geomagnetic storm of 17 March 2013. Simulations with ET show a 13% reduction in the cross polar cap potential at the beginning of the storm and up to 20% increases in the Pedersen and Hall conductance. These simulation results show better agreement with Defense Meteorological Satellite Program observations, including capturing features of subauroral polarization streams. The field‐aligned current (FAC) patterns show little differences during the peak of storm and agree well with Active Magnetosphere and Planetary Electrodynamics Response Experiment (AMPERE) reconstructions. Typically, the simulated FAC densities are stronger and at slightly higher latitudes than shown by AMPERE. The inner magnetospheric pressures derived from Tsyganenko‐Sitnov empirical magnetic field model show that the inclusion of the ET effects increases the peak pressure and brings the results into better agreement with the empirical model.This material is based upon work supported by NASA grants NNX14AI13G, NNX13AF92G, and NNX16AB80G. The National Center for Atmospheric Research is sponsored by the National Science Foundation. This work used the XSEDE and TACC computational facilities, supported by National Science Foundation grant ACI-1053575. We would like to acknowledge high-performance computing support from Yellowstone (ark:/85065/d7wd3xhc) provided by NCAR's Computational and Information Systems Laboratory, sponsored by the National Science Foundation. We thank the AMPERE team and the AMPERE Science Center for providing the Iridium derived data products. All model output, simulation codes, and analysis routines are being preserved on the NCAR High-Performance Storage System and will be made available upon written request to the lead author of this publication. (NNX14AI13G - NASA; NNX13AF92G - NASA; NNX16AB80G - NASA; National Science Foundation; ACI-1053575 - National Science Foundation

Entanglement in spin-1/2 dimerized Heisenberg systems

We study entanglement in dimerized Heisenberg systems. In particular, we give exact results of ground-state pairwise entanglement for the four-qubit model by identifying a Z_2 symmetry. Although the entanglements cannot identify the critical point of the system, the mean entanglement of nearest-neighbor qubits really does, namely, it reaches a maximum at the critical point.Comment: Four pages, three figures, accepted in Communications in Theoretical Physic

Chiral effect in plane isotropic micropolar elasticity and its application to chiral lattices

In continuum mechanics, the non-centrosymmetric micropolar theory is usually used to capture the chirality inherent in materials. However when reduced to a two dimensional (2D) isotropic problem, the resulting model becomes non-chiral. Therefore, influence of the chiral effect cannot be properly characterized by existing theories for 2D chiral solids. To circumvent this difficulty, based on reinterpretation of isotropic tensors in a 2D case, we propose a continuum theory to model the chiral effect for 2D isotropic chiral solids. A single material parameter related to chirality is introduced to characterize the coupling between the bulk deformation and the internal rotation which is a fundamental feature of 2D chiral solids. Coherently, the proposed continuum theory is also derived for a triangular chiral lattice from a homogenization procedure, from which the effective material constants of the lattice are analytically determined. The unique behavior in the chiral lattice is demonstrated through the analyses of a static tension problem and a plane wave propagation problem. The results, which cannot be predicted by the non-chiral model, are validated by the exact solution of the discrete model.Comment: 33 pages, 7 figure

Event-based security control for discrete-time stochastic systems

This study is concerned with the event-based security control problem for a class of discrete-time stochastic systems with multiplicative noises subject to both randomly occurring denial-of-service (DoS) attacks and randomly occurring deception attacks. An event-triggered mechanism is adopted with hope to reduce the communication burden, where the measurement signal is transmitted only when a certain triggering condition is violated. A novel attack model is proposed to reflect the randomly occurring behaviours of the DoS attacks as well as the deception attacks within a unified framework via two sets of Bernoulli distributed white sequences with known conditional probabilities. A new concept of mean-square security domain is put forward to quantify the security degree. The authors aim to design an output feedback controller such that the closed-loop system achieves the desired security. By using the stochastic analysis techniques, some sufficient conditions are established to guarantee the desired security requirement and the control gain is obtained by solving some linear matrix inequalities with nonlinear constraints. A simulation example is utilised to illustrate the usefulness of the proposed controller design scheme.This work was supported in part by Royal Society of the UK, the National Natural Science Foundation of China under Grants 61329301, 61573246 and 61374039, the Shanghai Rising-Star Programme of China under Grant 16QA1403000, the Program for Capability Construction of Shanghai Provincial Universities under Grant 15550502500 and the Alexander von Humboldt Foundation of Germany

Spin Squeezing in the Ising Model

We analyze the collective spin noise in interacting spin systems. General expressions are derived for the short time behaviour of spin systems with general spin-spin interactions, and we suggest optimum experimental conditions for the detection of spin squeezing. For Ising models with site dependent nearest neighbour interactions general expressions are presented for the spin squeezing parameter for all times. The reduction of collective spin noise can be used to verify the entangling powers of quantum computer architectures based on interacting spins.Comment: 7 pages, including 3 figure

Penetration depth anisotropy in two-band superconductors

The anisotropy of the London penetration depth is evaluated for two-band superconductors with arbitrary inter- and intra-band scattering times. If one of the bands is clean and the other is dirty in the absence of inter-band scattering, the anisotropy is dominated by the Fermi surface of the clean band and is weakly temperature dependent. The inter-band scattering also suppress the temperature dependence of the anisotropy

Predicted Infrared and Raman Spectra for Neutral Ti_8C_12 Isomers

Using a density-functional based algorithm, the full IR and Raman spectra are calculated for the neutral Ti_8C_12 cluster assuming geometries of Th, Td, D2d and C3v symmetry. The Th pentagonal dodecahedron is found to be dynamically unstable. The calculated properties of the relaxed structure having C3v symmetry are found to be in excellent agreement with experimental gas phase infrared results, ionization potential and electron affinity measurements. Consequently, the results presented may be used as a reference for further experimental characterization using vibrational spectroscopy.Comment: 6 pages, 5 figures. Physical Review A, 2002 (in press

The effect of loading direction and Sn alloying on the deformation modes of Zr: An in-situ neutron diffraction study

Deformation modes (slip and twining) in a strongly textured model hcp alloy system (Zr–Sn) have been investigated using in-situ neutron diffraction and deformation along with complementary electron microscopy. Analysis of the evolution of the intergranular strain evolutions and intensity of specific reflections from neutron diffraction show differential influence of Sn on the extent of twinning too, depending on the deformation direction. While Sn displayed very noticeable influence on twin activity when samples were compressed along a direction that predominantly activates prismatic slip, this effect was not seen when samples were compressed along other different directions. These experimental observations were successfully simulated using a CPFE (crystal plasticity finite element) model that incorporates composition sensitive CRSS (critical resolved shear stress) for slip and composition insensitive CRSS activation of twinning. The success of the CPFE model in capturing the experimental observations with respect to twin evolution suggests that the twinning in Zr is chiefly governed by the initial crystallographic texture and the associated intergranular stress state generated during plastic deformation