Dust-acoustic Rogue Waves in Four-Component Plasmas

Plasma Physics Reports - A theoretical investigation has been made on modulational instability (MI) and dust-acoustic (DA) rogue waves (DARWs) in a four-component dusty plasma medium containing...     

Modulational Instability,Ion-Acoustic Envelope Solitons,and Rogue Waves in Four-Component Plasmas

Plasma Physics Reports - Modulational instability (MI) of ion-acoustic waves (IAWs) has been theoretically investigated in a plasma system which is composed of inertial warm adiabatic ions,...     

Heavy Ion-Acoustic Solitary Waves and Double Layers in a Multi-Ion Plasma

The formation and propagation of small-amplitude heavy-ion-acoustic (HIA) solitary waves and double layers in an unmagnetized collisionless multicomponent plasma system consisting of superthermal electrons, Boltzmann distributed light ions, and adiabatic positively charged inertial heavy ions are theoretically investigated. The reductive perturbation technique is employed to derive the modified Korteweg–de Vries (mKdV) and standard Gardner (SG) equations. The solitary wave (SW) solution of mKdV and SG equations, as well as double layers (DLs) solution of SG equation, is studied for analysis of higher order nonlinearity. It is found that the plasma system under consideration supports positive and negative potential Gardner solitons, but only positive potential mKdV solitons. In addition, it is shown that, the basic properties of HIA mKdV and Gardner solitons and DLs (viz. polarity, amplitude, width, and phase speed) are incomparably influenced by the adiabaticity effect of heavy ions and the superthermality effect of electrons. The relevance of the present findings to the system of space plasmas, as well as to the system of researchers interest, is specified.     

New Views of Multi-Ion Channels

The rate constants of acetylcholine receptor channels (AChR) desensitization and recovery were estimated from the durations and frequencies of clusters of single-channel currents. Diliganded-open AChR desensitize much faster than either unliganded- or diliganded-closed AChR, which indicates that the desensitization rate constant depends on the status of the activation gate rather than the occupancy of the transmitter binding sites. The desensitization rate constant does not change with the nature of the agonist, the membrane potential, the species of permeant cation, channel block by ACh, the subunit composition (ε or γ), or several mutations that are near the transmitter binding sites. The results are discussed in terms of cyclic models of AChR activation, desensitization, and recovery. In particular, a mechanism by which activation and desensitization are mediated by two distinct, but interrelated, gates in the ion permeation pathway is proposed.     

Quasiperiodic Route to Chaos for the Dust Ion Acoustic Waves in Magnetized Dusty Plasmas

Plasma Physics Reports - Quasiperiodic and chaotic features of the dust ion acoustic (DIA) waves in a magnetized dusty plasma is studied. Reductive perturbation technique (RPT) is used to derive...     

Rogue Sperm Indicate Sexually Antagonistic Coevolution in Nematodes

Intense reproductive competition often continues long after animals finish mating. In many species, sperm from one male compete with those from others to find and fertilize oocytes. Since this competition occurs inside the female reproductive tract, she often influences the outcome through physical or chemical factors, leading to cryptic female choice. Finally, traits that help males compete with each other are sometimes harmful to females, and female countermeasures may thwart the interests of males, which can lead to an arms race between the sexes known as sexually antagonistic coevolution. New studies from Caenorhabditis nematodes suggest that males compete with each other by producing sperm that migrate aggressively and that these sperm may be more likely to win access to oocytes. However, one byproduct of this competition appears to be an increased probability that these sperm will go astray, invading the ovary, prematurely activating oocytes, and sometimes crossing basement membranes and leaving the gonad altogether. These harmful effects are sometimes observed in crosses between animals of the same species but are most easily detected in interspecies crosses, leading to dramatically lowered fitness, presumably because the competitiveness of the sperm and the associated female countermeasures are not precisely matched. This mismatch is most obvious in crosses involving individuals from androdioecious species (which have both hermaphrodites and males), as predicted by the lower levels of sperm competition these species experience. These results suggest a striking example of sexually antagonistic coevolution and dramatically expand the value of nematodes as a laboratory system for studying postcopulatory interactions. On the Origin of Species focused almost exclusively on the role of natural selection in evolution [1], but Darwin realized that animals also compete for mates and described the process of sexual selection at length in a later book [2]. The simplest examples involve combat like that between male elephant seals fighting for access to females. However, sexual selection also includes many other types of interactions. For example, some male birds have elaborate plumage because females favor this trait when choosing mates (reviewed in [3]). In their simplest form, these interactions can be thought of as parts of a triangle—competition between two males forming the base and the interactions between each of the males and the female forming the two legs.     

Effects of Nonextensive Ions (Heavier and Lighter) on Ion Acoustic Solitary Waves in a Magnetized Five Component Cometary Plasma with Kappa Described Electrons

Plasma Physics Reports - We have investigated the propagation characteristics of Ion-Acoustic Solitary Waves (IASWs) in a magnetized, cometary plasma consisting of hydrogen ions, positively and...     

Polyhedral Geometry of Phylogenetic Rogue Taxa

It is well known among phylogeneticists that adding an extra taxon (e.g. species) to a data set can alter the structure of the optimal phylogenetic tree in surprising ways. However, little is known about this “rogue taxon” effect. In this paper we characterize the behavior of balanced minimum evolution (BME) phylogenetics on data sets of this type using tools from polyhedral geometry. First we show that for any distance matrix there exist distances to a “rogue taxon” such that the BME-optimal tree for the data set with the new taxon does not contain any nontrivial splits (bipartitions) of the optimal tree for the original data. Second, we prove a theorem which restricts the topology of BME-optimal trees for data sets of this type, thus showing that a rogue taxon cannot have an arbitrary effect on the optimal tree. Third, we computationally construct polyhedral cones that give complete answers for BME rogue taxon behavior when our original data fits a tree on four, five, and six taxa. We use these cones to derive sufficient conditions for rogue taxon behavior for four taxa, and to understand the frequency of the rogue taxon effect via simulation.     

3D Magnetic Holes in Collisionless Plasmas

Recent multispacecraft observations in the Earth’s magnetosphere have revealed an abundance of magnetic holes—localized magnetic field depressions. These magnetic holes are characterized by the plasma pressure enhancement and strongly localized currents flowing around the hole boundaries. There are several numerical and analytical models describing 2D configurations of magnetic holes, but the 3D distribution of magnetic fields and electric currents is studied poorly. Such a 3D magnetic field configuration is important for accurate investigation of charged particle dynamics within magnetic holes. Moreover, the 3D distribution of currents can be used for distant probing of magnetic holes in the magnetosphere. In this study, a 3D magnetic hole model using the single-fluid approximation and a spatial scale hierarchy with the distinct separation of gradients is developed. It is shown that such 3D holes can be obtained as a generalization of 1D models with the plasma pressure distribution adopted from the kinetic approach. The proposed model contains two magnetic field components and field-aligned currents. The magnetic field line configuration resembles the magnetic trap where hot charged particles bounce between mirror points. However, the approximation of isotropic pressure results in a constant plasma pressure along magnetic field lines, and the proposed magnetic hole model does not confine plasma along the field direction.     

Three-dimensional Nonlinear Structures in Magnetized Complex Plasmas

Plasma Physics Reports - A three-dimensional multi-component magneto-plasma system consisting of hybrid nonextensive-nonthermal-distributed electrons, positive ions, and immobile negatively charged...     

A Three-State Multi-Ion Kinetic Model for Conduction Properties of ClC-0 Chloride Channel

A three-state, multiion kinetic model was proposed to enable the conduction properties of the mammalian channel ClC-0 to be well characterized. Using this rate-theory based model, the current-voltage and conductance-concentration relations were obtained. The five parameters needed were determined by fitting the data of conduction experiments of the wild-type ClC-0 and its K519C mutant. The model was then tested against available calculation and simulation data, and the energy differences between distinct chloride-occupancy states computed agreed with an independent calculation on the binding free energies solved by using the Poisson-Boltzmann equation. The average ion number of conduction and the ion passing duration calculated closely resembled the values obtained from Brownian dynamics simulations. According to the model, the decrease of conductance caused by mutating residue K519 to C519 can be attributed to the effect of K519C mutation on translocation rate constants. Our study sets up a theoretical model for ion permeation and conductance in ClC-0. It provides a starting point for experimentalists to test the three-state model, and would help in understanding the conduction mechanism of ClC-0.     

Hybrid and Rogue Kinases Encoded in the Genomes of Model Eukaryotes

The highly modular nature of protein kinases generates diverse functional roles mediated by evolutionary events such as domain recombination, insertion and deletion of domains. Usually domain architecture of a kinase is related to the subfamily to which the kinase catalytic domain belongs. However outlier kinases with unusual domain architectures serve in the expansion of the functional space of the protein kinase family. For example, Src kinases are made-up of SH2 and SH3 domains in addition to the kinase catalytic domain. A kinase which lacks these two domains but retains sequence characteristics within the kinase catalytic domain is an outlier that is likely to have modes of regulation different from classical src kinases. This study defines two types of outlier kinases: hybrids and rogues depending on the nature of domain recombination. Hybrid kinases are those where the catalytic kinase domain belongs to a kinase subfamily but the domain architecture is typical of another kinase subfamily. Rogue kinases are those with kinase catalytic domain characteristic of a kinase subfamily but the domain architecture is typical of neither that subfamily nor any other kinase subfamily. This report provides a consolidated set of such hybrid and rogue kinases gleaned from six eukaryotic genomes–S.cerevisiae, D. melanogaster, C.elegans, M.musculus, T.rubripes and H.sapiens–and discusses their functions. The presence of such kinases necessitates a revisiting of the classification scheme of the protein kinase family using full length sequences apart from classical classification using solely the sequences of kinase catalytic domains. The study of these kinases provides a good insight in engineering signalling pathways for a desired output. Lastly, identification of hybrids and rogues in pathogenic protozoa such as P.falciparum sheds light on possible strategies in host-pathogen interactions.     

Optical Properties of Dense Plasmas

Plasma Physics Reports - The results of studies of optical properties of plasmas in the framework of the self-consistent method of moments, which are in satisfactory agreement with experimental...     

Multi-Ion Mechanism for Ion Permeation and Block in the Cystic Fibrosis Transmembrane Conductance Regulator Chloride Channel

The mechanism of Cl⁻ ion permeation through single cystic fibrosis transmembrane conductance regulator (CFTR) channels was studied using the channel-blocking ion gluconate. High concentrations of intracellular gluconate ions cause a rapid, voltage-dependent block of CFTR Cl⁻ channels by binding to a site ∼40% of the way through the transmembrane electric field. The affinity of gluconate block was influenced by both intracellular and extracellular Cl⁻ concentration. Increasing extracellular Cl⁻ concentration reduced intracellular gluconate affinity, suggesting that a repulsive interaction occurs between Cl⁻ and gluconate ions within the channel pore, an effect that would require the pore to be capable of holding more than one ion simultaneously. This effect of extracellular Cl⁻ is not shared by extracellular gluconate ions, suggesting that gluconate is unable to enter the pore from the outside. Increasing the intracellular Cl⁻ concentration also reduced the affinity of intracellular gluconate block, consistent with competition between intracellular Cl⁻ and gluconate ions for a common binding site in the pore. Based on this evidence that CFTR is a multi-ion pore, we have analyzed Cl⁻ permeation and gluconate block using discrete-state models with multiple occupancy. Both two- and three-site models were able to reproduce all of the experimental data with similar accuracy, including the dependence of blocker affinity on external Cl⁻ (but not gluconate) ions and the dependence of channel conductance on Cl⁻ concentration. The three-site model was also able to predict block by internal and external thiocyanate (SCN⁻) ions and anomalous mole fraction behavior seen in Cl⁻/SCN⁻ mixtures.     

Ion Selectivity of the KcsA Channel: A Perspective from Multi-Ion Free Energy Landscapes

Potassium (K⁺) channels are specialized membrane proteins that are able to facilitate and regulate the conduction of K⁺ through cell membranes. Comprising five specific cation binding sites (S₀-S₄) formed by the backbone carbonyl groups of conserved residues common to all K⁺ channels, the narrow selectivity filter allows fast conduction of K⁺ while being highly selective for K⁺ over Na⁺. To extend our knowledge of the microscopic mechanism underlying selectivity in K⁺ channels, we characterize the free energy landscapes governing the entry and translocation of a Na⁺ or a K⁺ from the extracellular side into the selectivity filter of KcsA. The entry process of an extracellular ion is examined in the presence of two additional K⁺ in the pore, and the three-ion potential of mean force is computed using extensive all-atom umbrella sampling molecular dynamics simulations. A comparison of the potentials of mean force yields a number of important results. First, the free energy minima corresponding to configurations with extracellular K⁺ or Na⁺ in binding site S₀ or S₁ are similar in depth, suggesting that the thermodynamic selectivity governed by the free energy minima for those two binding sites is insignificant. Second, the free energy barriers between stable multi-ion configurations are generally higher for Na⁺ than for K⁺, implying that the kinetics of ion conduction is slower when a Na⁺ enters the pore. Third, the region corresponding to binding site S₂ near the center of the narrow pore emerges as the most selective for K⁺ over Na⁺. In particular, while there is a stable minimum for K⁺ in site S₂, Na⁺ faces a steep free energy increase with no local free energy well in this region. Lastly, analysis shows that selectivity is not correlated with the overall coordination number of the ion entering the pore, but is predominantly affected by changes in the type of coordinating ligands (carbonyls versus water molecules). These results further highlight the importance of the central region near binding site S₂ in the selectivity filter of K⁺ channels.