Genetic Characterization of the Tick-Borne Orbiviruses

The International Committee for Taxonomy of Viruses (ICTV) recognizes four species of tick-borne orbiviruses (TBOs): Chenuda virus, Chobar Gorge virus, Wad Medani virus and Great Island virus (genus Orbivirus, family Reoviridae). Nucleotide (nt) and amino acid (aa) sequence comparisons provide a basis for orbivirus detection and classification, however full genome sequence data were only available for the Great Island virus species. We report representative genome-sequences for the three other TBO species (virus isolates: Chenuda virus (CNUV); Chobar Gorge virus (CGV) and Wad Medani virus (WMV)). Phylogenetic comparisons show that TBOs cluster separately from insect-borne orbiviruses (IBOs). CNUV, CGV, WMV and GIV share low level aa/nt identities with other orbiviruses, in 'conserved' Pol, T2 and T13 proteins/genes, identifying them as four distinct virus-species. The TBO genome segment encoding cell attachment, outer capsid protein 1 (OC1), is approximately half the size of the equivalent segment from insect-borne orbiviruses, helping to explain why tick-borne orbiviruses have a ~1 kb smaller genome

Phase Transition in the Number Partitioning Problem

Number partitioning is an NP-complete problem of combinatorial optimization. A statistical mechanics analysis reveals the existence of a phase transition that separates the easy from the hard to solve instances and that reflects the pseudo-polynomiality of number partitioning. The phase diagram and the value of the typical ground state energy are calculated.Comment: minor changes (references, typos and discussion of results

Random Costs in Combinatorial Optimization

The random cost problem is the problem of finding the minimum in an exponentially long list of random numbers. By definition, this problem cannot be solved faster than by exhaustive search. It is shown that a classical NP-hard optimization problem, number partitioning, is essentially equivalent to the random cost problem. This explains the bad performance of heuristic approaches to the number partitioning problem and allows us to calculate the probability distributions of the optimum and sub-optimum costs.Comment: 4 pages, Revtex, 2 figures (eps), submitted to PR

Number partitioning as random energy model

Number partitioning is a classical problem from combinatorial optimisation. In physical terms it corresponds to a long range anti-ferromagnetic Ising spin glass. It has been rigorously proven that the low lying energies of number partitioning behave like uncorrelated random variables. We claim that neighbouring energy levels are uncorrelated almost everywhere on the energy axis, and that energetically adjacent configurations are uncorrelated, too. Apparently there is no relation between geometry (configuration) and energy that could be exploited by an optimization algorithm. This ``local random energy'' picture of number partitioning is corroborated by numerical simulations and heuristic arguments.Comment: 8+2 pages, 9 figures, PDF onl

Noise-induced switching between vortex states with different polarization in classical two-dimensional easy-plane magnets

In the 2-dimensional anisotropic Heisenberg model with XY-symmetry there are non-planar vortices which exhibit a localized structure of the z-components of the spins around the vortex center. We study how thermal noise induces a transition of this structure from one polarization to the opposite one. We describe the vortex core by a discrete Hamiltonian and consider a stationary solution of the Fokker-Planck equation. We find a bimodal distribution function and calculate the transition rate using Langer's instanton theory (1969). The result is compared with Langevin dynamics simulations for the full many-spin model.Comment: 15 pages, 4 figures, Phys. Rev. B., in pres

Alfalfa: Crop for the Future

Alfalfa use by dairy cattle has decreased in recent years because of excessive nonprotein nitrogen and low fiber digestibility. Ideal attributes for plant modification of alfalfa may include those that increase milk potential per acre and/or per ton, enhance digestible NDF, improve protein content and amino acid balance, improve agronomic traits for insect protection (safer forage supply), herbicide tolerance, virus resistance, drought tolerance, cold tolerance, improved mineral availability and enhanced yield. Progress in attaining these attributes will accelerate with the use of biotechnology. Livestock and hay enterprises will benefit from alfalfa that is less prone to contain mycotoxins or toxic weeds, or to induce bloat; have improved nutrient utilization for milk and meat production; and produce less animal wastes resulting in improved efficiency, profitability, and a better environment. Value-added traits of alfalfa are needed to provide farmers new high value profitable products. Processing alfalfa to obtain value added products includes three different fractionation methods: 1) wet fractionation; separation into juice fraction and a fiber fraction, 2) dry fractionation; separation into leaves and stems, and 3) fractionation by passage of the whole herbage through the digestive systems of ruminant animals, leaving a high fiber residue. Phytase from transgenic alfalfa has been tested in poultry and swine rations. Alfalfa hay can be fractionated to yield stems and leaf meal. Alfalfa leaf meal has been shown to be acceptable supplement to replace a portion of alfalfa hay and soybean meal in diets of lactating dairy cattle, replace protein supplement in beef cow diets, finishing steer diets and diets of growing turkeys. The fiber portion of alfalfa can produce lactic acid, ethanol or a bioadhesives for use in plywood

Optimal combinations of imperfect objects

We address the question of how to make best use of imperfect objects, such as defective analog and digital components. We show that perfect, or near-perfect, devices can be constructed by taking combinations of such defects. Any remaining objects can be recycled efficiently. In addition to its practical applications, our `defect combination problem' provides a novel generalization of classical optimization problems.Comment: 4 pages, 3 figures, minor change

Internal mode mechanism for collective energy transport in extended systems

We study directed energy transport in homogeneous nonlinear extended systems in the presence of homogeneous ac forces and dissipation. We show that the mechanism responsible for unidirectional motion of topological excitations is the coupling of their internal and translation degrees of freedom. Our results lead to a selection rule for the existence of such motion based on resonances that explains earlier symmetry analysis of this phenomenon. The direction of motion is found to depend both on the initial and the relative phases of the two harmonic drivings, even in the presence of noise.Comment: Final version, to appear in Physical Review Letter

Soliton ratchets in homogeneous nonlinear Klein-Gordon systems

We study in detail the ratchet-like dynamics of topological solitons in homogeneous nonlinear Klein-Gordon systems driven by a bi-harmonic force. By using a collective coordinate approach with two degrees of freedom, namely the center of the soliton, $X(t)$, and its width, $l(t)$, we show, first, that energy is inhomogeneously pumped into the system, generating as result a directed motion; and, second, that the breaking of the time shift symmetry gives rise to a resonance mechanism that takes place whenever the width $l(t)$ oscillates with at least one frequency of the external ac force. In addition, we show that for the appearance of soliton ratchets, it is also necesary to break the time-reversal symmetry. We analyze in detail the effects of dissipation in the system, calculating the average velocity of the soliton as a function of the ac force and the damping. We find current reversal phenomena depending on the parameter choice and discuss the important role played by the phases of the ac force. Our analytical calculations are confirmed by numerical simulations of the full partial differential equations of the sine-Gordon and $\phi^4$ systems, which are seen to exhibit the same qualitative behavior. Our results are in agreement with recent experimental work on dissipation induced symmetry breaking.Comment: Minor corrections, several references added, accepted for publication in Chao

Vortex motion in a finite-size easy-plane ferromagnet and application to a nanodot

We study the motion of a non-planar vortex in a circular easy-plane ferromagnet, which imitates a magnetic nanodot. Analysis was done using numerical simulations and a new collective variable theory which includes the coupling of Goldstone-like mode with the vortex center. Without magnetic field the vortex follows a spiral orbit which we calculate. When a rotating in-plane magnetic field is included, the vortex tends to a stable limit cycle which exists in a significant range of field amplitude B and frequency $\omega$ for a given system size L. For a fixed $\omega$, the radius R of the orbital motion is proportional to L while the orbital frequency $\Omega$ varies as 1/L and is significantly smaller than $\omega$. Since the limit cycle is caused by the interplay between the magnetization and the vortex motion, the internal mode is essential in the collective variable theory which then gives the correct estimate and dependency for the orbit radius $R\sim B L/\omega$. Using this simple theory we indicate how an ac magnetic field can be used to control vortices observed in real magnetic nanodots.Comment: 15 pages (RevTeX), 14 figures (eps