Modulated whistler wave packets associated with density perturbations

The parametric interaction between large amplitude whistlers and ponderomotively driven quasistationary density perturbations in plasmas is considered. A cubic nonlinear Schrodinger equation is derived and then solved analytically to show the occurrence of modulational instability as well as the existence of bright and dark envelope solitons, which are referred to as whistlerons. Explicit whistleron profiles are presented and the relevance to space and laboratory plasmas is discussed. (C) 2005 American Institute of Physics.

Modulated dust-acoustic wave packets in a plasma with non-isothermal electrons and ions

The Nonlinear self-modulation of dust acoustic waves is studied in the presence of non-thermal (non-Maxwellian) ion and electron populations. By employing a multiple scale technique, a nonlinear Schrodinger-type equation (NLSE) is derived for the wave amplitude. The influence of non-thermality, in addition to obliqueness (between the propagation and modulation directions), on the conditions for modulational instability to occur is discussed. Different types of localized solutions (envelope excitations) which may possibly occur are discussed, and the dependence of their characteristics oil physical parameters is traced. The ion deviation from a Maxwellian distribution comes out to be more important than the electron analogous deviation alone. Both yield a de-stabilizing effect oil (the amplitude of) DAWs propagating in a dusty plasma with negative dust grains, and thus favour the formation of bright- (rather than dark-) type envelope structures, (solitons) in the plasma. A similar tendency towards amplitude de-stabilization is found for the ease of the presence of positively charged dust in the plasma.

Exact theory for localized envelope modulated electrostatic wavepackets in space and dusty plasmas

Abundant evidence for the occurrence of modulated envelope plasma wave packets is provided by recent satellite missions. These excitations are characterized by a slowly varying localized envelope structure, embedding the fast carrier wave, which appears to be the result of strong modulation of the wave amplitude. This modulation may be due to parametric interactions between different modes or, simply, to the nonlinear (self-)interaction of the carrier wave. A generic exact theory is presented in this study, for the nonlinear self-modulation of known electrostatic plasma modes, by employing a collisionless fluid model. Both cold (zero-temperature) and warm fluid descriptions are discussed and the results are compared. The (moderately) nonlinear oscillation regime is investigated by applying a multiple scale technique. The calculation leads to a Nonlinear Schrodinger-type Equation (NLSE), which describes the evolution of the slowly varying wave amplitude in time and space. The NLSE admits localized envelope (solitary wave) solutions of bright(pulses) or dark- (holes, voids) type, whose characteristics (maximum amplitude, width) depend on intrinsic plasma parameters. Effects like amplitude perturbation obliqueness (with respect to the propagation direction), finite temperature and defect (dust) concentration are explicitly considered. Relevance with similar highly localized modulated wave structures observed during recent satellite missions is discussed.

Nonlinear propagation of modulated ion-acoustic plasma waves in the presence of an electron beam

Theoretical and numerical studies are presented of the amplitude modulation of ion-acoustic waves (IAWs) in a plasma consisting of warm ions, Maxwellian electrons, and a cold electron beam. Perturbations parallel to the carrier IAW propagation direction have been investigated. The existence of four distinct linear ion acoustic modes is shown, each of which possesses a different behavior from the modulational stability point of view. The stability analysis, based on a nonlinear Schrodinger equation (NLSE) reveals that the IAW may become unstable. The stability criteria depend on the IAW carrier wave number, and also on the ion temperature, the beam velocity and the beam electron density. Furthermore, the occurrence of localized envelope structures (solitons) is investigated, from first principles. The numerical analysis shows that the two first modes (essentially IAWs, modified due to the beam) present a complex behavior, essentially characterized by modulational stability for large wavelengths and instability for shorter ones. Dark-type envelope excitations (voids, holes) occur in the former case, while bright-type ones (pulses) appear in the latter. The latter two modes are characterized by an intrinsic instability, as the frequency develops a finite imaginary part for small ionic temperature values. At intermediate temperatures, both bright- and dark-type excitations may exist, although the numerical landscape is intertwined between stability and instability regions.(c) 2006 American Institute of Physics.

Modulated electrostatic modes in pair plasmas: Modulational stability profile and envelope excitations

A pair plasma consisting of two types of ions, possessing equal masses and opposite charges, is considered. The nonlinear propagation of modulated electrostatic wave packets is studied by employing a two-fluid plasma model. Considering propagation parallel to the external magnetic field, two distinct electrostatic modes are obtained, namely a quasiacoustic lower moddfe and a Langmuir-like, as optic-type upper one, in agreement with experimental observations and theoretical predictions. Considering small yet weakly nonlinear deviations from equilibrium, and adopting a multiple-scale technique, the basic set of model equations is reduced to a nonlinear Schrodinger equation for the slowly varying electric field perturbation amplitude. The analysis reveals that the lower (acoustic) mode is stable and may propagate in the form of a dark-type envelope soliton (a void) modulating a carrier wave packet, while the upper linear mode is intrinsically unstable, and may favor the formation of bright-type envelope soliton (pulse) modulated wave packets. These results are relevant to recent observations of electrostatic waves in pair-ion (fullerene) plasmas, and also with respect to electron-positron plasma emission in pulsar magnetospheres. (c) 2006 American Institute of Physics.

Nonlinearly modulated dust lattice wave packets in two-dimensional hexagonal dust crystals

The amplitude modulation of dust lattice waves (DLWs) propagating in a two-dimensional hexagonal dust crystal is investigated in a continuum approximation, accounting for the effect of dust charge polarization (dressed interactions). A dusty plasma crystalline configuration with constant dust grain charge and mass is considered. The dispersion relation and the group velocity for DLWs are determined for wave propagation in both longitudinal and transverse directions. The reductive perturbation method is used to derive a (2+1)-dimensional nonlinear Schrodinger equation (NLSE). New expressions for the coefficients of the NLSE are derived and compared, for a Yukawa-type potential energy and for a

Modulated transverse off-plane dust-lattice wave packets in hexagonal two-dimensional dusty plasma crystals

The propagation of nonlinear dust-lattice waves in a two-dimensional hexagonal crystal is investigated. Transverse (off-plane) dust grain oscillatory motion is considered in the form of a backward propagating wave packet whose linear and nonlinear characteristics are investigated. An evolution equation is obtained for the slowly varying amplitude of the first (fundamental) harmonic by making use of a two-dimensional lattice multiple scales technique. An analysis based on the continuum approximation (spatially extended excitations compared to the lattice spacing) shows that wave packets will be modulationally stable and that dark-type envelope solitons (density holes) may occur in the long wavelength region. Evidence is provided of modulational instability and of the occurrence of bright-type envelopes (pulses) at shorter wavelengths. The role of second neighbor interactions is also investigated and is shown to be rather weak in determining the modulational stability region. The effect of dissipation, assumed negligible in the algebra throughout the article, is briefly discussed.

A topological algorithm for identification of structural domains of proteins

Background: Identification of the structural domains of proteins is important for our understanding of the organizational principles and mechanisms of protein folding, and for insights into protein function and evolution. Algorithmic methods of dissecting protein of known structure into domains developed so far are based on an examination of multiple geometrical, physical and topological features. Successful as many of these approaches are, they employ a lot of heuristics, and it is not clear whether they illuminate any deep underlying principles of protein domain organization. Other well-performing domain dissection methods rely on comparative sequence analysis. These methods are applicable to sequences with known and unknown structure alike, and their success highlights a fundamental principle of protein modularity, but this does not directly improve our understanding of protein spatial structure.

Algorithmic computation of knot polynomials of secondary structure elements of proteins

The classification of protein structures is an important and still outstanding problem. The purpose of this paper is threefold. First, we utilize a relation between the Tutte and homfly polynomial to show that the Alexander-Conway polynomial can be algorithmically computed for a given planar graph. Second, as special cases of planar graphs, we use polymer graphs of protein structures. More precisely, we use three building blocks of the three-dimensional protein structure-alpha-helix, antiparallel beta-sheet, and parallel beta-sheet-and calculate, for their corresponding polymer graphs, the Tutte polynomials analytically by providing recurrence equations for all three secondary structure elements. Third, we present numerical results comparing the results from our analytical calculations with the numerical results of our algorithm-not only to test consistency, but also to demonstrate that all assigned polynomials are unique labels of the secondary structure elements. This paves the way for an automatic classification of protein structures.

Effect of antioxidants and ACE inhibition on chemical modification of proteins and progression of nephropathy in the streptozotocin diabetic rat

Aims/hypothesis. This study was designed to determine whether inhibition of formation of AGE and advanced lipoxidation end-products (ALE) is a mechanism of action common to a diverse group of therapeutic agents that limit the progress of diabetic nephropathy. We compared the effects of the ACE inhibitor enalapril, the antioxidant vitamin E, the thiol compound lipoic acid, and the AGE/ALE inhibitor pyridoxamine on the formation of AGE/ALE and protection against nephropathy in streptozotocin diabetic rats.

Increased endocytosis in retinal vascular endothelial cells grown in high glucose medium is modulated by inhibitors of nonenzymatic glycosylation

We sought to determine if hyperglycaemia is responsible for increased retinal vascular endothelial-cell (RVEC) endocytosis in diabetes and to assess the role of nonenzymatic glycosylation in mediation of this novel endothelial-cell pathology. RVECs were propagated in media containing either 5 or 25 mmol/l glucose for up to 10 days after which they were exposed to the protein tracer horseradish peroxidase for 30 min. The level of RVEC endocytosis was quantified in intact cell monolayers by electron microscopic stereology, and in cell lysates by a simple spectrophotometric method. The effect of the nonenzymatic glycosylation inhibitors, aminoguanidine and D-lysine, on high-glucose medium induced changes in RVEC endocytosis was tested by inclusion of these agents in the culture medium. RVECs exposed to 25 mmol/l glucose showed a stepwise increase in endocytosis of horseradish peroxidase culminating in a two- to threefold increase after 10 days. Endocytosis returned to normal levels after a further 10 days in 5 mmol/l glucose medium. The increase in RVEC endocytosis was markedly reduced, but not completely normalised, by aminoguanidine and D-lysine. Exposure of cultured RVECs to 25 mmol/l glucose causes an increase in endocytosis of similar magnitude to that experienced by RVEC in early diabetes, and implicates hyperglycaemia in the latter situation. A significant component of the increase in RVEC endocytosis appears to be mediated by nonenzymatic glycosylation.

Molecular identity and cellular distribution of advanced glycation endproduct receptors: relationship of p60 to OST-48 and p90 to 80K-H membrane proteins.

Advanced glycation endproducts (AGEs) are derivatives of nonenzymatic reactions between sugars and protein or lipids, and together with AGE-specific receptors are involved in numerous pathogenic processes associated with aging and hyperglycemia. Two of the known AGE-binding proteins isolated from rat liver membranes, p60 and p90, have been partially sequenced. We now report that the N-terminal sequence of p60 exhibits 95% identity to OST-48, a 48-kDa member of the oligosaccharyltransferase complex found in microsomal membranes, while sequence analysis of p90 revealed 73% and 85% identity to the N-terminal and internal sequences, respectively, of human 80K-H, a 80- to 87-kDa protein substrate for protein kinase C. AGE-ligand and Western analyses of purified oligosaccharyltransferase complex, enriched rough endoplasmic reticulum, smooth endoplasmic reticulum, and plasma membranes from rat liver or RAW 264.7 macrophages yielded a single protein of approximately 50 kDa recognized by both anti-p60 and anti-OST-48 antibodies, and also exhibited AGE-specific binding. Immunoprecipitated OST-48 from rat rough endoplasmic reticulum fractions exhibited both AGE binding and immunoreactivity to an anti-p60 antibody. Immune IgG raised to recombinant OST-48 and 80K-H inhibited binding of AGE-bovine serum albumin to cell membranes in a dose-dependent manner. Immunostaining and flow cytometry demonstrated the surface expression of OST-48 and 80K-H on numerous cell types and tissues, including mononuclear, endothelial, renal, and brain neuronal and glial cells. We conclude that the AGE receptor components p60 and p90 are identical to OST-48, and 80K-H, respectively, and that they together contribute to the processing of AGEs from extra- and intracellular compartments and in the cellular responses associated with these pathogenic substances.