Solitary and compact-like shear waves in the bulk of solids

We show that a model proposed by Rubin, Rosenau, and Gottlieb [J. Appl. Phys. 77 (1995) 4054], for dispersion caused by an inherent material characteristic length, belongs to the class of simple materials. Therefore, it is possible to generalize the idea of Rubin, Rosenau, and Gottlieb to include a wide range of material models, from nonlinear elasticity to turbulence. Using this insight, we are able to fine-tune nonlinear and dispersive effects in the theory of nonlinear elasticity in order to generate pulse solitary waves and also bulk travelling waves with compact support

The Mating System of the Wild-to-Domesticated Complex of Gossypium hirsutum L. Is Mixed

The domestication syndrome of many plants includes changes in their mating systems. The evolution of the latter is shaped by ecological and genetic factors that are particular to an area. Thus, the reproductive biology of wild relatives must be studied in their natural distribution to understand the mating system of a crop species as a whole. Gossypium hirsutum (upland cotton) includes both domesticated varieties and wild populations of the same species. Most studies on mating systems describe cultivated cotton as self-pollinated, while studies on pollen dispersal report outcrossing; however, the mating system of upland cotton has not been described as mixed and little is known about its wild relatives. In this study we selected two wild metapopulations for comparison with domesticated plants and one metapopulation with evidence of recent gene flow between wild relatives and the crop to evaluate the mating system of cotton’s wild-to-domesticated complex. Using classic reproductive biology methods, our data demonstrate that upland cotton presents a mixed mating system throughout the complex. Given cotton’s capacity for outcrossing, differences caused by the domestication process in cultivated individuals can have consequences for its wild relatives. This characterization of the diversity of the wild relatives in their natural distribution, as well as their interactions with the crop, will be useful to design and implement adequate strategies for conservation and biosecurity

A probabilistic model for gene content evolution with duplication, loss, and horizontal transfer

We introduce a Markov model for the evolution of a gene family along a phylogeny. The model includes parameters for the rates of horizontal gene transfer, gene duplication, and gene loss, in addition to branch lengths in the phylogeny. The likelihood for the changes in the size of a gene family across different organisms can be calculated in O(N+hM^2) time and O(N+M^2) space, where N is the number of organisms, $h$ is the height of the phylogeny, and M is the sum of family sizes. We apply the model to the evolution of gene content in Preoteobacteria using the gene families in the COG (Clusters of Orthologous Groups) database

Close Packing of Atoms, Geometric Frustration and the Formation of Heterogeneous States in Crystals

To describe structural peculiarities in inhomogeneous media caused by the tendency to the close packing of atoms a formalism based on the using of the Riemann geometry methods (which were successfully applied lately to the description of structures of quasicrystals and glasses) is developed. Basing on this formalism we find in particular the criterion of stability of precipitates of the Frank-Kasper phases in metallic systems. The nature of the ''rhenium effect'' in W-Re alloys is discussed.Comment: 14 pages, RevTex, 2 PostScript figure

Shock Wave Structure in a Strongly Nonlinear Granular Lattice with Viscous Dissipation

The shock wave structure in a one-dimensional lattice (e.g. granular chain) with a power law dependence of force on displacement between particles with viscous dissipation is considered and compared to the corresponding long wave approximation. A dissipative term depending on the relative velocity between neighboring particles is included in the discrete model to investigate its influence on the shape of steady shock profiles. The critical viscosity coefficient is obtained from the long-wave approximation for arbitrary values of the exponent n and denotes the transition from an oscillatory to a monotonic shock profile in stronly nonlinear systems. The expression for the critical viscosity coefficient converges to the known equation for the critical viscosity in the weakly nonlinear case. Values of viscosity based on this expression are comparable to the values obtained in the numerical analysis of a discrete particle lattice with a Herzian contact interaction corresponding to n = 3/2. An initial disturbance in a discrete system approaches a stationary shock profile after traveling a short distance that is comparable to the width of the leading pulse of a stationary shock front. The shock front width is minimized when the viscosity is equal to its critical value.Comment: 20 pages, 6 figure

Radiation temperature measurements in laser-heated hohlraums

Two x-ray spectrographs have been used on the Trident laser at LANL to monitor the radiation temperature of small Au hohlraums. The cylindrical targets are smaller than 1 mm. The x radiation produced by {approximately} 400 J of 0.53-{micro}m laser light is detected with a 7-channel VNIIEF soft-x-ray spectrometer. Each channel employs a multi-layer mirror and a filter to limit the channel bandwidth to 1--3% of the channel energy. X rays are detected with calibrated Al x-ray diodes. A second spectrometer is based on a free-standing Au transmission grating for spectral dispersion and a multi-channel diamond photo-conductive device detector. The small hohlraum results are consistent with radiation temperatures exceeding 100 eV. Simple computer modeling shows that late in the plasma discharge, radiation of this temperature is emitted from the target

Automatically extracting functionally equivalent proteins from SwissProt

In summary, FOSTA provides an automated analysis of annotations in UniProtKB/Swiss-Prot to enable groups of proteins already annotated as functionally equivalent, to be extracted. Our results demonstrate that the vast majority of UniProtKB/Swiss-Prot functional annotations are of high quality, and that FOSTA can interpret annotations successfully. Where FOSTA is not successful, we are able to highlight inconsistencies in UniProtKB/Swiss-Prot annotation. Most of these would have presented equal difficulties for manual interpretation of annotations. We discuss limitations and possible future extensions to FOSTA, and recommend changes to the UniProtKB/Swiss-Prot format, which would facilitate text-mining of UniProtKB/Swiss-Prot

2-{[2,8-Bis(trifluoro­meth­yl)quinolin-4-yl](hy­droxy)meth­yl}piperidin-1-ium 3-amino-5-nitro­benzoate sesquihydrate

The asymmetric unit of the title salt solvate, C17H17F6N2O+·C7H5N2O4 −·1.5H2O, comprises a piperidin-1-ium cation, a 3-amino-5-nitro­benzoate anion, and three fractionally occupied [i.e. 0.414 (3), 0.627 (6) and 0.459 (5)] disordered water mol­ecules of solvation. The cation has an L shape with a C—C—C—C torsion angle of −102.9 (3)° for the atoms linking the quinolinyl group to the rest of the cation. In the anion, the carboxyl­ate and nitro groups are essentially coplanar with the benzene ring [O—C—C—C torsion angle = 179.7 (2)° and O—N—C—C torsion angle = −3.9 (3)°]. In the crystal, extensive O—H⋯O, O—H⋯F and N—H⋯·O hydrogen bonding leads to the formation of a layer in the ab plane