Soybean mosaic virus: A successful potyvirus with a wide distribution but restricted natural host range

Taxonomy. Soybean mosaic virus (SMV) is a species within the genus Potyvirus, family Potyviridae that includes almost a quarter of all known plant RNA viruses affecting agriculturally important plants. The Potyvirus genus is the largest of all genera of plant RNA viruses with 160 species. Particle. The filamentous particles of SMV, typical of potyviruses, are about 7,500 Å long and 120 Å in diameter with a central hole of about 15 Å in diameter. Coat protein residues are arranged in helice of about 34 Å pitch having slightly less than 9 subunits per turn. Genome. The SMV genome consists of a single-stranded positive-sense polyadenylated RNA of approximately 9.6 kb with a virus-encoded protein (VPg) linked at the 5\u27 terminus. The genomic RNA contains a single large open reading frame (ORF). The polypeptide produced from the large ORF is processed proteolytically by three viral-encoded proteinases to yield about 10 functional proteins. A small ORF, partially overlapping the P3 cistron, pipo, is encoded as a fusion protein in the N-terminus of P3 (P3N+PIPO). Biological properties. SMV’s host range is restricted mostly to two plant species of a single genus; Glycine max (cultivated soybean) and G. soja (wild soybean). SMV is transmitted by aphids non-persistently and by seeds. Variability of SMV is recognized by reactions on cultivars with dominant resistance (R) genes. Recessive resistance genes are not known. Geographical distribution and economic importance. As a consequence of its seed transmissibility, SMV is present in all soybean growing areas of the world. SMV infections can reduce significantly seed quantity and quality (e.g., mottled seed coats, reduced seed size and viability, and altered chemical composition). Control. The most effective means of managing losses from SMV are planting virus-free seeds and cultivars containing single or multiple R genes. Key attractions. The interactions of SMV with soybean genotypes containing different dominant R genes and understanding functional role(s) of SMV-encoded proteins in virulence, transmission and pathogenicity have been intensively investigated. The SMV-soybean pathosystem has become an excellent model for examining the genetics and genomics of uniquely complex gene-for-gene resistance model in a crop of worldwide importance

Linear "ship waves" generated in stationary flow of a Bose-Einstein condensate past an obstacle

Using stationary solutions of the linearized two-dimensional Gross-Pitaevskii equation, we describe the ``ship wave'' pattern occurring in the supersonic flow of a Bose-Einstein condensate past an obstacle. It is shown that these ``ship waves'' are generated outside the Mach cone. The developed analytical theory is confirmed by numerical simulations of the flow past body problem in the frame of the full non-stationary Gross-Pitaevskii equation.Comment: 5 pages, 4 figure

Whitham systems and deformations

We consider the deformations of Whitham systems including the "dispersion terms" and having the form of Dubrovin-Zhang deformations of Frobenius manifolds. The procedure is connected with B.A. Dubrovin problem of deformations of Frobenius manifolds corresponding to the Whitham systems of integrable hierarchies. Under some non-degeneracy requirements we suggest a general scheme of the deformation of the hyperbolic Whitham systems using the initial non-linear system. The general form of the deformed Whitham system coincides with the form of the "low-dispersion" asymptotic expansions used by B.A. Dubrovin and Y. Zhang in the theory of deformations of Frobenius manifolds.Comment: 27 pages, Late

The frustrated Brownian motion of nonlocal solitary waves

We investigate the evolution of solitary waves in a nonlocal medium in the presence of disorder. By using a perturbational approach, we show that an increasing degree of nonlocality may largely hamper the Brownian motion of self-trapped wave-packets. The result is valid for any kind of nonlocality and in the presence of non-paraxial effects. Analytical predictions are compared with numerical simulations based on stochastic partial differential equationComment: 4 pages, 3 figures

Strong Shock Waves and Nonequilibrium Response in a One-dimensional Gas: a Boltzmann Equation Approach

We investigate the nonequilibrium behavior of a one-dimensional binary fluid on the basis of Boltzmann equation, using an infinitely strong shock wave as probe. Density, velocity and temperature profiles are obtained as a function of the mixture mass ratio \mu. We show that temperature overshoots near the shock layer, and that heavy particles are denser, slower and cooler than light particles in the strong nonequilibrium region around the shock. The shock width w(\mu), which characterizes the size of this region, decreases as w(\mu) ~ \mu^{1/3} for \mu-->0. In this limit, two very different length scales control the fluid structure, with heavy particles equilibrating much faster than light ones. Hydrodynamic fields relax exponentially toward equilibrium, \phi(x) ~ exp[-x/\lambda]. The scale separation is also apparent here, with two typical scales, \lambda_1 and \lambda_2, such that \lambda_1 ~ \mu^{1/2} as \mu-->0$, while \lambda_2, which is the slow scale controlling the fluid's asymptotic relaxation, increases to a constant value in this limit. These results are discussed at the light of recent numerical studies on the nonequilibrium behavior of similar 1d binary fluids.Comment: 9 pages, 8 figs, published versio

Bogoliubov-Cerenkov radiation in a Bose-Einstein condensate flowing against an obstacle

We study the density modulation that appears in a Bose-Einstein condensate flowing with supersonic velocity against an obstacle. The experimental density profiles observed at JILA are reproduced by a numerical integration of the Gross-Pitaevskii equation and then interpreted in terms of Cerenkov emission of Bogoliubov excitations by the defect. The phonon and the single-particle regions of the Bogoliubov spectrum are respectively responsible for a conical wavefront and a fan-shaped series of precursors

Kinetic equation for a dense soliton gas

We propose a general method to derive kinetic equations for dense soliton gases in physical systems described by integrable nonlinear wave equations. The kinetic equation describes evolution of the spectral distribution function of solitons due to soliton-soliton collisions. Owing to complete integrability of the soliton equations, only pairwise soliton interactions contribute to the solution and the evolution reduces to a transport of the eigenvalues of the associated spectral problem with the corresponding soliton velocities modified by the collisions. The proposed general procedure of the derivation of the kinetic equation is illustrated by the examples of the Korteweg -- de Vries (KdV) and nonlinear Schr\"odinger (NLS) equations. As a simple physical example we construct an explicit solution for the case of interaction of two cold NLS soliton gases.Comment: 4 pages, 1 figure, final version published in Phys. Rev. Let

Dynamic Singularities in Cooperative Exclusion

We investigate cooperative exclusion, in which the particle velocity can be an increasing function of the density. Within a hydrodynamic theory, an initial density upsteps and downsteps can evolve into: (a) shock waves, (b) continuous compression or rarefaction waves, or (c) a mixture of shocks and continuous waves. These unusual phenomena arise because of an inflection point in the current versus density relation. This anomaly leads to a group velocity that can either be an increasing or a decreasing function of the density on either side of these wave singularities.Comment: 4 pages, 4 figures, 2 column revtex 4-1 format; version 2: substantially rewritten and put in IOP format, mail results unchanged; version 3: minor changes, final version for publication in JSTA

On the relationship between nonlinear equations integrable by the method of characteristics and equations associated with commuting vector fields

It was shown recently that Frobenius reduction of the matrix fields reveals interesting relations among the nonlinear Partial Differential Equations (PDEs) integrable by the Inverse Spectral Transform Method ($S$-integrable PDEs), linearizable by the Hoph-Cole substitution ($C$-integrable PDEs) and integrable by the method of characteristics ($Ch$-integrable PDEs). However, only two classes of $S$-integrable PDEs have been involved: soliton equations like Korteweg-de Vries, Nonlinear Shr\"odinger, Kadomtsev-Petviashvili and Davey-Stewartson equations, and GL(N,\CC) Self-dual type PDEs, like Yang-Mills equation. In this paper we consider the simple five-dimensional nonlinear PDE from another class of $S$-integrable PDEs, namely, scalar nonlinear PDE which is commutativity condition of the pair of vector fields. We show its origin from the (1+1)-dimensional hierarchy of $Ch$-integrable PDEs after certain composition of Frobenius type and differential reductions imposed on the matrix fields. Matrix generalization of the above scalar nonlinear PDE will be derived as well.Comment: 14 pages, 1 figur

Multiple hydrodynamical shocks induced by Raman effect in photonic crystal fibres

We theoretically predict the occurrence of multiple hydrodynamical-like shock phenomena in the propagation of ultrashort intense pulses in a suitably engineered photonic crystal fiber. The shocks are due to the Raman effect, which acts as a nonlocal term favoring their generation in the focusing regime. It is shown that the problem is mapped to shock formation in the presence of a slope and a gravity-like potential. The signature of multiple shocks in XFROG signals is unveiled