Novel noninvasive in situ probe of protein structure and dynamics

7-Amtryptophan is an ideal noninvasive in situ probe of protein structure and dynamics and provides an alternative to the use of ,tryptophan. 7-Azatryptophan affords a single-exponential fluorescence decay in aqueous solution, unlike tryptophan. Its absorption and fluorescence spectra are distinguishable from those of tryptophan. Its fluorescence spectrum and lifetime are sensitive to the environment. It can be used in peptide synthesis, and it can be incorporated into bacterial protein. These facts render 7-azatryptophan a unique probe that has the potential for widespread use

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

Renormalized waves and thermalization of the Klein-Gordon equation: What sound does a nonlinear string make?

We study the thermalization of the classical Klein-Gordon equation under a u^4 interaction. We numerically show that even in the presence of strong nonlinearities, the local thermodynamic equilibrium state exhibits a weakly nonlinear behavior in a renormalized wave basis. The renormalized basis is defined locally in time by a linear transformation and the requirement of vanishing wave-wave correlations. We show that the renormalized waves oscillate around one frequency, and that the frequency dispersion relation undergoes a nonlinear shift proportional to the mean square field. In addition, the renormalized waves exhibit a Planck like spectrum. Namely, there is equipartition of energy in the low frequency modes described by a Boltzmann distribution, followed by a linear exponential decay in the high frequency modes.Comment: 13 pages, 13 figure

Modeling M-Theory Vacua via Gauged S-Duality

We construct a model of M-theory vacua using gauged S-duality and the Chan-Paton symmetries by introducing an infinite number of open string charges. In the Bechi-Rouet-Stora-Tyutin formalism, the local description of the gauged S-duality on its moduli space of vacua is fully determined by one physical state condition on the vacua. We introduce the string probe of the spatial degrees of freedom and define the increment of the cosmic time. The dimensionality of space-time and the gauge group of the low energy effective theory originate in the symmetries (with or without their breakdown) in our model. This modeling leads to the derived category formulation of the quantum mechanical world including gravity and to the concept of a non-linear potential of gauged and affinized S-duality which specifies the morphism structure of this derived category.Comment: 31 pages, version reflecting the erratum. arXiv admin note: substantial text overlap with arXiv:1102.460

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

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

Wave-vortex interaction

We present an experimental study on the effect of a electromagneticaly generated vortex flow on parametrically amplified waves at the surface of a fluid. The underlying vortex flow, generated by a periodic Lorentz force, creates spatio-temporal fluctuations that interact nonlinearly with the standing surface waves. We characterize the bifurcation diagram and measure the power spectrum density (PSD) of the local surface wave amplitude. We show that the parametric instability threshold increases with increasing intensity of the vortex flow.Comment: 8 pages, 10 figures, submitted to Phys. Rev.

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

Thermodynamic phase transitions and shock singularities

We show that under rather general assumptions on the form of the entropy function, the energy balance equation for a system in thermodynamic equilibrium is equivalent to a set of nonlinear equations of hydrodynamic type. This set of equations is integrable via the method of the characteristics and it provides the equation of state for the gas. The shock wave catastrophe set identifies the phase transition. A family of explicitly solvable models of non-hydrodynamic type such as the classical plasma and the ideal Bose gas are also discussed.Comment: revised version, 18 pages, 6 figure

Optical supercavitation in soft-matter

We investigate theoretically, numerically and experimentally nonlinear optical waves in an absorbing out-of-equilibrium colloidal material at the gelification transition. At sufficiently high optical intensity, absorption is frustrated and light propagates into the medium. The process is mediated by the formation of a matter-shock wave due to optically induced thermodiffusion, and largely resembles the mechanism of hydrodynamical supercavitation, as it is accompanied by a dynamic phase-transition region between the beam and the absorbing material.Comment: 4 pages, 5 figures, revised version: corrected typos and reference