Small-amplitude shock waves and double layers in dusty plasmas with opposite polarity charged dust grains

Theoretical investigation is carried out for understanding the properties of nonlinear dust-acoustic (DA) waves in an unmagnetized dusty plasma whose constituents are massive, micron-sized, positive and negatively charged inertial dust grains along with q (nonextensive) distributed electrons and ions. The reductive perturbation method is employed in order to derive two types of nonlinear dynamical equations, namely, Burgers equation and modified Gardner equation (Gardner equation with dissipative term). They are also numerically analyzed to investigate the basic features (viz., polarity, amplitude, width, etc.) of shock waves and double layers. It has been observed that the effects of nonextensivity, opposite polarity charged dust grains, and different dusty plasma parameters have significantly modified the fundamental properties of shock waves and double layers. The results of this investigation may be used for researches of the nonlinear wave propagation in laboratory and space plasmas.     

Collective motion from local attraction

Many animal groups, for example schools of fish or flocks of birds, exhibit complex dynamic patterns while moving cohesively in the same direction. These flocking patterns have been studied using self-propelled particle models, most of which assume that collective motion arises from individuals aligning with their neighbours. Here, we propose a self-propelled particle model in which the only social force between individuals is attraction. We show that this model generates three different phases: swarms, undirected mills and moving aligned groups. By studying our model in the zero noise limit, we show how these phases depend on the relative strength of attraction and individual inertia. Moreover, by restricting the field of vision of the individuals and increasing the degree of noise in the system, we find that the groups generate both directed mills and three dynamically moving, ‘rotating chain’ structures. A rich diversity of patterns is generated by social attraction alone, which may provide insight into the dynamics of natural flocks.     

Experimental studies of the dynamics of dust grains in gas-discharge plasmas

Results of the experimental studies of the dynamics of dust grains in the plasmas of an rf capacitive discharge and a dc glow discharge are presented. The dusty plasma of a dc glow discharge was investigated in both ground-based experiments and experiments carried out under microgravity conditions (on board the Mir space station). The pair correlation function, temperature, and diffusion coefficient of dust grains are measured in a wide range of the dusty-plasma parameters. Dimensionless parameters responsible for the microscopic transport of dust-grains in a gas-discharge plasma are determined. A nonintrusive diagnostic technique for determining the dust-grain charges and screening lengths under the assumption of screened interaction between the grains is proposed. This technique is used to estimate the surface potential of dust grains of different size in a gas-discharge plasma.     

Formation of ordered structures in systems of charged thin cylindrical grains

Conditions for the formation of various orientational and spatial configurations of charged cylindrical particles in an external electric field are investigated both analytically and numerically. Analytical expressions allowing one to determine the tilt angle of cylinders relative to the symmetry axis/plane of the electric trap are proposed. A new algorithm for numerical modeling of the dynamics of interacting nonspherical particles is developed. Conditions for correct modeling of uniformly charged cylinders by means of “bipoles” consisting of two coupled point charges of the same sign are determined. The studies have been performed in a wide range of parameters close to those typical of laboratory experiments with dusty plasmas.     

Effect of dust size distribution on ion-acoustic solitons in dusty plasmas with different dust grains

Theoretical studies are carried out for ion acoustic solitons in multicomponent nonuniform plasma considering the dust size distribution. The Korteweg?de Vries equation for ion acoustic solitons is given by using the reductive perturbation technique. Two special dust size distributions are considered. The dependences of the width and amplitude of solitons on dust size parameters are shown. It is found that the properties of a solitary wave depend on the shape of the size distribution function of dust grains.     

Formation of chain structures in systems of charged grains interacting via isotropic pair potentials

Conditions for the formation of chain structures of charged grains confined in the gravitational field by external electric fields are studied analytically and numerically. The relationships between the parameters of the pair interaction potential, the number of grains, and the electric field gradient in the trap are found. A criterion for the violation of stable equilibrium in a quasi-one-dimensional chain of grains and the formation of a new configuration in the system is proposed.     

Longitudinal low-frequency waves in the flows of self-gravitating charged dust grains in an electron-ion plasma

A study is made of the features of wave processes in the individual flows of self-gravitating dust grains in a plasma and the electric and gravitational interactions in a system of several dusty plasma flows. It is shown that, in a dusty plasma, Debye screening can substantially weaken the electric coupling between the beams of self-gravitating grains, without affecting the gravitational forces between them, and that the electrostatic perturbations are exchanged between the grain flows via gravitational fields, as happens in vacuum.     

Positive column of a glow discharge in neon with charged dust grains (a review)

The effect of charged micron-size dust grains (microparticles) on the electric parameters of the positive column of a low-pressure dc glow discharge in neon has been studied experimentally and numerically. Numerical analysis is carried out in the diffusion-drift approximation with allowance for the interaction of dust grains with metastable neon atoms. In a discharge with a dust grain cloud, the longitudinal electric field increases. As the number density of dust grains in an axisymmetric cylindrical dust cloud rises, the growth of the electric field saturates. It is shown that the contribution of metastable atoms to ionization is higher in a discharge with dust grains, in spite of the quenching of metastable atoms on dust grains. The processes of charging of dust grains and the dust cloud are considered. As the number density of dust grains rises, their charge decreases, while the space charge of the dust cloud increases. The results obtained can be used in plasma technologies involving microparticles.     

Current filaments in plasmas

Possible configurations of current filaments in Z-pinch and tokamak plasmas are analyzed. A thin current-carrying beam injected in a plasma should be surrounded by a halo of countercurrents, in which case the resulting configuration may resemble a tubular structure. A.B. Kukushkin and V.A. Rantsev-Kartinov pointed out the existence of specific plasma structures of the squirrel-cage type and interpreted them as “wild cables of solid-state nanotubes.” It is shown that these structures can also be attributed to the fundamental mode of the conventional magnetic filamentation in the form of a “hexagonal parquet.” Also, a study is made of the phenomena governing the pattern of plasma structures, namely, tearing filamentation, two types of longitudinal beam bunching, and self-organization of the filaments.     

<Emphasis Type="Italic">l</Emphasis>=1 diocotron instability of single charged plasmas

The linear stability analysis of the l=1 diocotron perturbations in a low density single charged plasma confined in a cylindrical Penning trap is critically revisited. Particular attention is devoted to the instability due to the presence of one or more stationary points in the radial profile of the azimuthal rotation frequency. The asymptotic analysis of Smith and Rosenbluth for the case of a single-bounded plasma column (algebraic instability proportional to t^1/2) is generalized in a few respects. In particular, the existence of unperturbed density profiles that give rise to l=1 algebraic instabilities growing with time proportionally to t^1?1/m, m≥ 3 being the order of a stationary point in the rotation frequency profile, and even proportionally to t, is pointed out. It is also shown that smoothing the density jumps of a multistep density profile can convert algebraically growing perturbations into exponentially decaying modes. The relevant damping rates are computed. The asymptotic analysis (t → ∞) of the fundamental diocotron perturbations is then generalized to the case of a cylindrical Penning trap with an additional coaxial inner conductor. It is shown that the algebraic instability found in the case of a single-bounded plasma column becomes exponential at longer times. The relevant linear growth rate is computed by a suitable inverse Laplace transform (contour integral in the complex plane). In the particular case of an uncharged inner conductor of radius a, the growth rate is shown to scale as a^4/3 for a → 0. The theoretical results are compared with the numerical solution of the linearized two-dimensional drift Poisson equations.     

The attraction of paleomagnetism

The majority of fossil primates and human archeological sites are recovered from sedimentary rocks, but obtaining radioisotopic dates directly from rocks of this type is generally difficult. Paleomagnetism offers an alternative dating approach. Specific applications of paleomagnetism in the field of anthropology range from dating late Eocene fossil anthropoids to determining human archeological site use and occupation. This single dating technique is not restricted to a specific time range, but can be used across the entire span of primate evolution. When linked with other dating techniques, such as radioisotopic or astrochronologic methods, paleomagnetism offers a high level of temporal resolution in unraveling questions of the past.     

Collective Behaviour without Collective Order in Wild Swarms of Midges

Collective behaviour is a widespread phenomenon in biology, cutting through a huge span of scales, from cell colonies up to bird flocks and fish schools. The most prominent trait of collective behaviour is the emergence of global order: individuals synchronize their states, giving the stunning impression that the group behaves as one. In many biological systems, though, it is unclear whether global order is present. A paradigmatic case is that of insect swarms, whose erratic movements seem to suggest that group formation is a mere epiphenomenon of the independent interaction of each individual with an external landmark. In these cases, whether or not the group behaves truly collectively is debated. Here, we experimentally study swarms of midges in the field and measure how much the change of direction of one midge affects that of other individuals. We discover that, despite the lack of collective order, swarms display very strong correlations, totally incompatible with models of non-interacting particles. We find that correlation increases sharply with the swarm''s density, indicating that the interaction between midges is based on a metric perception mechanism. By means of numerical simulations we demonstrate that such growing correlation is typical of a system close to an ordering transition. Our findings suggest that correlation, rather than order, is the true hallmark of collective behaviour in biological systems.     

Sex attraction specificity in the Tortricidae

Sex attraction by pheromones seems general among the Tortricidae. Using virgin live females, female gland extracts or synthetic chemicals similar to known tortricid pheromones, it is shown that the species are attracted very specifically to their own pheromones. However, because of differences in seasonal cycles, circadian rhythms and secondary chemicals, many species may use the same primary attractant, without much interspecific attraction. There is some correlation between taxonomic groupings and pheromone structures.

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Résumé L'attraction sexuelle par les phéromones semble être la règle chez les Tortricidae. L'attraction interspécifique a été étudiée dans la nature au moyen de femelles vierges vivantes, et de produits chimiques synthétiques semblables aux phéromones de Tortricidae dont la structure chimique a été élucidée. En général, les mâles d'une espèce donnée sont attirés très spécifiquement par un produit ou par un mélange qui, à leur égard, a valeur de phéromone.Cependant, le même produit attractif est souvent utilisé par plusieurs espèces. Il existe dans ce cas des différences de cycle saisonnier, de rythme circadien ou de produit chimique additionnel servant à l'attraction, de sorte que l'attraction interspécifique demeure un évènement rare. On observe une corrélation entre les groupements taxonomiques et la structure chimique des phéromones: dans la sous-famille des Olethreutinae, il y a surtout des alcools insaturés à 12 carbones et leurs acetates; dans la sous-famille des Tortricinae, surtout des alcools à `4 carbones et leurs acetates, généralement avec une double liaison en position 11.

     

End-to-end attraction of duplex DNA

Recent experiments [Nakata, M. et al., End-to-end stacking and liquid crystal condensation of 6 to 20 basepair DNA duplexes. Science 2007; 318:1276-1279] have demonstrated spontaneous end-to-end association of short duplex DNA fragments into long rod-like structures. By means of extensive all-atom molecular dynamic simulations, we characterized end-to-end interactions of duplex DNA, quantitatively describing the forces, free energy and kinetics of the end-to-end association process. We found short DNA duplexes to spontaneously aggregate end-to-end when axially aligned in a small volume of monovalent electrolyte. It was observed that electrostatic repulsion of 5'-phosphoryl groups promoted the formation of aggregates in a conformation similar to the B-form DNA double helix. Application of an external force revealed that rupture of the end-to-end assembly occurs by the shearing of the terminal base pairs. The standard binding free energy and the kinetic rates of end-to-end association and dissociation processes were estimated using two complementary methods: umbrella sampling simulations of two DNA fragments and direct observation of the aggregation process in a system containing 458 DNA fragments. We found the end-to-end force to be short range, attractive, hydrophobic and only weakly dependent on the ion concentration. The relation between the stacking free energy and end-to-end attraction is discussed as well as possible roles of the end-to-end interaction in biological and nanotechnological systems.     

Heterotachy and long-branch attraction in phylogenetics

Background  

Probabilistic methods have progressively supplanted the Maximum Parsimony (MP) method for inferring phylogenetic trees. One of the major reasons for this shift was that MP is much more sensitive to the Long Branch Attraction (LBA) artefact than is Maximum Likelihood (ML). However, recent work by Kolaczkowski and Thornton suggested, on the basis of simulations, that MP is less sensitive than ML to tree reconstruction artefacts generated by heterotachy, a phenomenon that corresponds to shifts in site-specific evolutionary rates over time. These results led these authors to recommend that the results of ML and MP analyses should be both reported and interpreted with the same caution. This specific conclusion revived the debate on the choice of the most accurate phylogenetic method for analysing real data in which various types of heterogeneities occur. However, variation of evolutionary rates across species was not explicitly incorporated in the original study of Kolaczkowski and Thornton, and in most of the subsequent heterotachous simulations published to date, where all terminal branch lengths were kept equal, an assumption that is biologically unrealistic.     

A review of long-branch attraction

The history of long‐branch attraction, and in particular methods suggested to detect and avoid the artifact to date, is reviewed. Methods suggested to avoid LBA‐artifacts include excluding long‐branch taxa, excluding faster evolving third codon positions, using inference methods less sensitive to LBA such as likelihood, the Aguinaldo et al. approach, sampling more taxa to break up long branches and sampling more characters especially of another kind, and the pros and cons of these are discussed. Methods suggested to detect LBA are numerous and include methodological disconcordance, RASA, separate partition analyses, parametric simulation, random outgroup sequences, long‐branch extraction, split decomposition and spectral analysis. Less than 10 years ago it was doubted if LBA occurred in real datasets. Today, examples are numerous in the literature and it is argued that the development of methods to deal with the problem is warranted. A 16 kbp dataset of placental mammals and a morphological and molecular combined dataset of gall waSPS are used to illustrate the particularly common problem of LBA of problematic ingroup taxa to outgroups. The preferred methods of separate partition analysis, methodological disconcordance, and long branch extraction are used to demonstrate detection methods. It is argued that since outgroup taxa almost always represent long branches and are as such a hazard towards misplacing long branched ingroup taxa, phylogenetic analyses should always be run with and without the outgroups included. This will detect whether only the outgroup roots the ingroup or if it simultaneously alters the ingroup topology, in which case previous studies have shown that the latter is most often the worse. Apart from that LBA to outgroups is the major and most common problem; scanning the literature also detected the ill advised comfort of high support values from thousands of characters, but very few taxa, in the age of genomics. Taxon sampling is crucial for an accurate phylogenetic estimate and trust cannot be put on whole mitochondrial or chloroplast genome studies with only a few taxa, despite their high support values. The placental mammal example demonstrates that parsimony analysis will be prone to LBA by the attraction of the tenrec to the distant marsupial outgroups. In addition, the murid rodents, creating the classic “the guinea‐pig is not a rodent” hypothesis in 1996, are also shown to be attracted to the outgroup by nuclear genes, although including the morphological evidence for rodents and Glires overcomes the artifact. The gall wasp example illustrates that Bayesian analyses with a partition‐specific GTR + Γ + I model give a conflicting resolution of clades, with a posterior probability of 1.0 when comparing ingroup alone versus outgroup rooted topologies, and this is due to long‐branch attraction to the outgroup. © The Willi Hennig Society 2005.