Mechanism for ion acceleration along the normal to the axis of a beam-plasma discharge in a weak magnetic field

The mechanism responsible for the previously discovered phenomenon of acceleration of an ion flow along the normal to the axis of a beam-plasma discharge in a weak magnetic field is investigated. It is suggested that the ions are accelerated in the field of a helicon wave excited in the discharge plasma column. It is shown theoretically that, under actual experimental conditions, a helicon wave can be excited at the expense of the energy of an electron beam. The spectral parameters and spatial structure of the waves excited in a beam-plasma discharge in the frequency ranges of Langmuir and helicon waves are studied experimentally and are shown to be related to the parameters of the ion flow. Theoretical estimates are found to agree well with the experimental results.     

Helical structures in complex plasma I: Noncollective interaction

The conditions for the formation and stability of helical quasi-crystals in a complex plasma containing dust grains of equal size are investigated. A study is made of both the confinement of such helical structures in a direction transverse to the cylinder axis by means of an external parabolic potential well and the possibility of their self-confinement. Computer simulations of the helical dust structures were carried for two cases: for a structure of infinite length along the symmetry axis (or a closed structure in toroidal geometry) and for a structure of finite length. The dust grains were assumed to interact through a potential that is a superposition of the non-Debye nonlinear screened potential and the nonscreened noncollective attractive potential (the Lesage effect). Molecular dynamics simulations showed that, in the presence of dissipation, any initial random distribution of the dust grains interacting through such a potential in cylindrical geometry evolves to an equilibrium helical structure. When the external control parameter was varied smoothly, the pitch angle of the helix was observed to bifurcate (i.e., to undergo sharp jumps). The structure of the helix was also observed to bifurcate when the external parameter was varied: a helix changed into two interwoven helices, which then changed into three interwoven helices, etc. The smaller the confinement parameter (and, accordingly, the larger the radius of the helical structures) and the stronger the attractive forces between the grains, the larger the number of bifurcations. The results of analytical calculations of the parameters of the equilibrium structures and of their energies are in complete agreement with numerical results. It is also shown that noncollective attraction between dust grains makes it probable that helical structures will exists when the external confinement parameter is zero or even when it is negative. Bifurcations in such systems may provide the possibility of creating new types of memory elements.     

Excitation of waves in an inhomogeneous plasma

The evolution of initial perturbations in a spatially inhomogeneous cold electron plasma in the absence of an external magnetic field is considered. The excitation of both continuous-spectrum bulk plasma waves and surface plasma waves with a discrete frequency spectrum is investigated. Analytic solutions are obtained in the long-wavelength limit, and the excitation of waves of arbitrary length is analyzed numerically. The local, integral, and spatial spectra are calculated, as well as the field structures and dispersion properties of waves in waveguides filled nonuniformly with a plasma. It is shown that, in a plasma with a smooth boundary, there also exist surface waves with a discrete spectrum (although with somewhat different properties as compared to those in a plasma with a sharp boundary), which are excited together with continuous-spectrum bulk waves during the evolution of the initial perturbation.     

Stability analysis of the time delay in a host-parasitoid model

The effect of a time delay on the local stability of a host-parasitoid model is analyzed. The delay is between the time of parasitization of the host and the emergence of the parasitoid from the host. Both analytic methods and computer simulations are used in this study. By linearizing and transforming the original equations, sufficient conditions for the local stability are found. In the case of the parameters considered, the results illustrate the destabilizing effect of the time delay. As the lag increases the number of stable points decreases and the points become more scattered in the parameter space. Simulations of the original model are also produced. The region of stability indicated by the simulations is greater than that predicted by the use of the analytic technique. The analysis also reveals the impact of the population parameters upon the stability of the time delay model.The importance of understanding time lags is discussed with reference to population regulation.     

Excitation of helicons by current antennas

Depending on the angle θ between the wave vector and the magnetic field, helicons are conventionally divided into two branches: proper helicons (H mode), propagating at small θ, and Trivelpiece–Gould waves (TG mode), propagating at large θ. The latter are close to potential waves and have a significant electric component along the external magnetic field. It is believed that it is these waves that provide electron heating in helicon discharges. There is also commonly believed that current antennas, widely used to ignite helicon discharges, excite essentially nonpotential Н modes, which then transform into TG modes due to plasma inhomogeneity. In this work, it is demonstrated that electromagnetic energy can also be efficiently introduced in plasma by means of TG modes.     

Effect of Long-Wavelength Magnetic Field Disturbances on the Generation of Auroral Kilometric Radiation

The effect of long-wavelength magnetic field disturbances typical of the Earth’s auroral region on the generation of auroral kilometric radiation in a narrow three-dimensional plasma cavity in which a weakly relativistic electron flow propagates against the background of cold low-density plasma is analyzed. The dynamics of the propagation and amplification of fluctuation waves with initial group velocities directed toward the higher magnetic field is considered in the geometrical optics approximation. Analysis of wave trajectories shows that the wave amplification coefficients depend on the magnetic field gradient in the reflection region. If the wave reflection point lies in the region where the gradient of the disturbed magnetic field is less than that of the undisturbed dipole field, then the wave amplification coefficients exceed those of waves propagating in the undisturbed field, and vice versa. Thus, the shape of the spectrum of generated waves changes in the presence of long-wavelength disturbances of the dipole magnetic field in such a way that segments with different curvatures can form in the spectrum.     

Effect of the shear flow in the generation and self-organization of internal gravity wave structures in the dissipative ionosphere

A linear mechanism for the generation and amplification of internal gravity waves and their further nonlinear dynamics in the stably stratified dissipative ionosphere in the presence of an inhomogeneous zonal wind (shear flow) is studied. For shear flows, the operators of linear problems are non-self-conjugate and the corresponding eigenfunctions are nonorthogonal. Therefore, the canonical modal approach is poorly applicable to study such motions. In this case, the so-called nonmodal mathematical analysis is more adequate. Dynamic equations and equations for the energy transport of internal gravity perturbations in the ionosphere with shear flows are derived on the basis of the nonmodal approach. Exact analytic solutions of linear and nonlinear equations are found. The growth rate of the shear instability of internal gravity waves is determined. It is revealed that perturbations grow in time according to a power law, rather than exponentially. The frequency and wavenumber of the generated internal gravity modes depend on time; hence, a wide spectrum of wave perturbations caused by linear effects (rather than nonlinear turbulent ones) forms in the ionosphere with shear flows. The efficiency of the linear mechanism for the amplification of internal gravity waves during their interaction with the inhomogeneous zonal wind is analyzed. A criterion for the development of the shear instability of such waves in the ionospheric plasma is obtained. It is shown that, in the presence of shear instability, internal gravity waves extract the shear flow energy in the initial (linear) stage of their evolution, due to which their amplitude and, accordingly, energy increase substantially (by an order of magnitude). As the amplitude increases, the mechanism of nonlinear self-localization comes into play and the process terminates with the self-organization of strongly localized solitary nonlinear internal gravity vortex structures. As a result, a new degree of freedom of the system and a new way of the evolution of perturbations in a medium with a shear flow appear. Inductive and viscous dampings limit the lifetime of vortex internal gravity structures in the ionosphere; nevertheless, their lifetime is long enough for them to strongly affect the dynamic properties of the medium. It is revealed on the basis of the analytic solution of a set of time-independent nonlinear dynamic equations that, depending on the velocity profile of the shear flow, the nonlinear internal gravity structures can take the form of a purely monopole vortex, a dipole cyclone-anticyclone pair, a transverse vortex chain, or a longitudinal vortex path against the background of the inhomogeneous zonal wind. The accumulation of such vortices in the ionosphere can result in a strongly turbulent state.     

Surface Plasmon Polariton Emission Prompted by Organic Nanofibers on Thin Gold Films

The excitation of surface plasmon polaritons (SPP) at a gold?Cvacuum interface by femtosecond light pulses mediated by organic nanofiber-induced dielectric perturbations is observed using interferometric time-resolved photoemission electron microscopy. The experimental data are quantitatively reproduced by analytic simulations, where the nanofibers are considered as superior source of the SPP emission. The flexibility and tuneability of phenylene-based nanofibers in their morphology and intrinsic optical properties open up future applications to fabricate custom-designed nanoscale sources of SPP.     

Electron energy balance and ionization in the channel of a stationary plasma thruster

The paper presents results of numerical simulations of the electron dynamics in the field of the azimuthal and longitudinal waves excited in the channel of a stationary plasma thruster (SPT). The simulations are based on the experimentally determined wave characteristics. The simulation results show that the azimuthal wave displayed as ionization instability enhances electron transport along the thruster channel. It is established that the electron transport rate in the azimuthal wave increases as compared to the rate of diffusion caused by electron scattering from neutral atoms in proportion to the ratio between the times of electron? neutral collisions responsible for ionization and elastic electron scattering, respectively. An expression governing the plasma conductivity is derived with allowance for electron interaction with the azimuthal wave. The Hall parameter, the electron component of the discharge current, and the electron heating power in the thruster channel are calculated for two model SPTs operating with krypton and xenon. The simulation results agree well with the results of experimental studies of these two SPTs.     

Current generation by helicons and lower hybrid waves in modern tokamaks and reactors ITER and DEMO. Scenarios, modeling and antennae

The innovative concept and 3D full-wave code modeling the off-axis current drive by radio-frequency (RF) waves in large-scale tokamaks, ITER and DEMO, for steady-state operation with high efficiency is proposed. The scheme uses the helicon radiation (fast magnetosonic waves at high (20–40) ion cyclotron frequency harmonics) at frequencies of 500–700 MHz propagating in the outer regions of the plasmas with a rotational transform. It is expected that the current generated by helicons, in conjunction with the bootstrap current, ensure the maintenance of a given value of the total current in the stability margin q(0) ≥ 2 and q(a) ≥ 4, and will help to have regimes with a negative magnetic shear and internal transport barrier to ensure stability at high normalized plasma pressure β _N > 3 (the so-called advanced scenarios) of interest for the commercial reactor. Modeling with full-wave three-dimensional codes PSTELION and STELEC showed flexible control of the current profile in the reactor plasmas of ITER and DEMO, using multiple frequencies, the positions of the antennae and toroidal wave slow down. Also presented are the results of simulations of current generation by helicons in the DIII-D, T-15MD, and JT-60AS tokamaks. Commercially available continuous-wave klystrons of the MW/tube range are promising for commercial stationary fusion reactors. The compact antennae of the waveguide type are proposed, and an example of a possible RF system for today’s tokamaks is given. The advantages of the scheme (partially tested at lower frequencies in tokamaks) are a significant decline in the role of parametric instabilities in the plasma periphery, the use of electrically strong resonator-waveguide type antennae, and substantially greater antenna-plasma coupling.     

Emission of alfvén waves from a nonuniform MHD waveguide

The efficiency of the wave energy loss from a nonuniform MHD waveguide due to the conversion of the trapped magnetosonic waveguide modes into runaway Alfvén waves is estimated theoretically. It is shown that, if the waveguide parameters experience a jumplike change along the waveguide axis, the interaction between the waveguide modes and Alfvén waves occurs precisely at this “jump.” This effect is incorporated into the boundary conditions. A set of coupled integral equations with a singular kernel is derived in order to determine the transmission and reflection coefficients for the waveguide modes. The poles in the kernels of the integral operators correspond to the surface waves. When the jump in the waveguide parameters is small, analytic expressions for the frequency dependence of the transformation coefficients are obtained by using a model profile of the Alfvén velocity along the magnetic field. For the jump characterized by the small parameter value ε=0.3, the wave-amplitude transformation coefficient can amount to 5–10%. Under the phase synchronization condition (when the phase velocities of the waveguide modes on both sides of the jump are the same), the wave-energy transformation coefficient is much higher: it increases from a fraction of one percent to tens of percent. The transformation of fast magnetosonic waves into Alfvén waves is resonant in character, which ensures the frequency and wavelength filteringof the emitted Alfvén perturbations.     

Spectral properties of an N-pole helical structure consisting of like-charged equal-size dust grains

The oscillations and stability of an N-pole helical structure that consists of like-charged equal-size dust grains and is confined in a plasma in an axisymmetric potential well are studied theoretically. Self-confining structures, as well as their linear collective modes corresponding to three coupled types of grain displacements (change in the radius of the structure, change in the distance between neighboring lattice planes of the structure, and angular displacements in the lattice planes), are found. On the whole, the coupled oscillations have the form of wormlike perturbations. Dispersion relations for the oscillation modes of helical structures composed of N interwoven helices are derived and solved numerically.     

Statistical prediction and molecular dynamics simulation

We describe a statistical approach to the validation and improvement of molecular dynamics simulations of macromolecules. We emphasize the use of molecular dynamics simulations to calculate thermodynamic quantities that may be compared to experimental measurements, and the use of a common set of energetic parameters across multiple distinct molecules. We briefly review relevant results from the theory of stochastic processes and discuss the monitoring of convergence to equilibrium, the obtaining of confidence intervals for summary statistics corresponding to measured quantities, and an approach to validation and improvement of simulations based on out-of-sample prediction. We apply these methods to replica exchange molecular dynamics simulations of a set of eight helical peptides under the AMBER potential using implicit solvent. We evaluate the ability of these simulations to quantitatively reproduce experimental helicity measurements obtained by circular dichroism. In addition, we introduce notions of statistical predictive estimation for force-field parameter refinement. We perform a sensitivity analysis to identify key parameters of the potential, and introduce Bayesian updating of these parameters. We demonstrate the effect of parameter updating applied to the internal dielectric constant parameter on the out-of-sample prediction accuracy as measured by cross-validation.     

Order through disorder: hyper-mobile C-terminal residues stabilize the folded state of a helical peptide. a molecular dynamics study

Conventional wisdom has it that the presence of disordered regions in the three-dimensional structures of polypeptides not only does not contribute significantly to the thermodynamic stability of their folded state, but, on the contrary, that the presence of disorder leads to a decrease of the corresponding proteins' stability. We have performed extensive 3.4 μs long folding simulations (in explicit solvent and with full electrostatics) of an undecamer peptide of experimentally known helical structure, both with and without its disordered (four residue long) C-terminal tail. Our simulations clearly indicate that the presence of the apparently disordered (in structural terms) C-terminal tail, increases the thermodynamic stability of the peptide's folded (helical) state. These results show that at least for the case of relatively short peptides, the interplay between thermodynamic stability and the apparent structural stability can be rather subtle, with even disordered regions contributing significantly to the stability of the folded state. Our results have clear implications for the understanding of peptide energetics and the design of foldable peptides.     

Quantum theory of Cherenkov beam instabilities in plasma

A quantum theory of stimulated Cherenkov emission of longitudinal waves by an electron beam in an isotropic plasma is presented. The emitted radiation is interpreted as instability due to the decay of the de Broglie wave of a beam electron. Nonrelativistic and relativistic nonlinear quantum equations for Cherenkov beam instabilities are obtained. A linear approximation is used to derive quantum dispersion relations and to determine the instability growth rates. The mechanisms for nonlinear saturation of quantum Cherenkov beam instabilities are investigated, and the corresponding analytic solutions are found.     

Collective movement of ions in the cytoplasm

A theoretical model of propagation in the cytoplasm of self-consistent electromagnetic waves of the millimeter-infrared range has been developed, cytoplasmic ions surrounded by water ??coats?? being the main carriers of these waves. It has been discovered that not only own long-wavelength transverse oscillations, but also longitudinal waves that cannot leave the cytoplasm can exist in tissues of living organisms. Frequencies and logarithmic decrements of such perturbations have been found, and it is shown that these frequencies are close to those of ion oscillations inside the ??coats.?? Passage of laser radiation in bioobjects at the indicated frequencies has been analyzed, revealing bands of body impenetrability for waves. A new mechanism of swinging of cytoplasm own oscillations is proposed, based on the existence of an extreme border of the ion movement area. It has been shown that with this mechanism, the electric field amplitude for the longitudinal waves is six to seven orders of magnitude greater than the Planck fluctuation level.     

Parameter domains for instability of uniform states in systems with many delays

 We present a computational method for determining regions in parameter space corresponding to linear instability of a spatially uniform steady state solution of any system of two coupled reaction-diffusion equations containing up to four delay terms. At each point in parameter space the required stability properties of the linearised system are found using mainly the Principle of the Argument. The method is first developed for perturbations of a particular wavenumber, and then generalised to allow arbitrary perturbations. Each delay term in the system may be of either a fixed or a distributed type, and spatio-temporal delays are also allowed. Received 19 September 1995; received in revised form 4 September 1996     

3D Burgers Equation in Relativistic Plasma in the Presence of Electron and Negative Ion Trapping: Evolution of Shock Wave

The characteristics of shock waves in a relativistic plasma in the presence of nonisothermal electrons and nonisothermal negative ions is investigated by deriving the evolution equation in terms of a modified 3D Burgers equation, or trapped 3D Burgers equation. The solution of this equation is examined analytically to study the salient characteristics of shock waves in such plasma. The nonlinear coefficient is found to have the lowest (highest) value when the negative ions move toward thermal equilibrium with a dip-shaped electron distribution (when both electrons and negative ions follow a dip-shaped distribution) for a particular value of relativistic factor, and it remains in an intermediate state when both electrons and negative ions follow a flat-topped distribution. On the other hand, the dissipative coefficient is found to decrease (increase) with increasing relativistic parameter (viscous parameter). A profound effect of the trapped state of both electrons and negative ions and the temperature ratio between positive ions and electrons (negative ions and electrons) on the structure of the shock wave is also seen. However, it has been noticed that the trapped parameter of electrons has a dominating control over the shock potential profile than the trapped parameter of negative ions.     

Transition from an excitable to an oscillatory state in dictyostelium discoideum

Under conditions of starvation, populations of the amoebae Dictyostelium discoideum aggregate are mediated by chemical excitation waves of cAMP. Two types of waves can be observed, either spiral or circular-shaped ones. We investigate transitions from rotating spirals to circular shaped waves (target patterns). Two different experiments demonstrating this phenomenon are presented. In the first case a continuous transition from the spiral type pattern to target waves was observed at the later stages of aggregation. In the second case the transition was induced by annihilation of waves by a spatially homogeneous cAMP pulse. Instead of the originally present spiral waves, oscillating spots bearing target patterns emerged. On the basis of a model for Dictyostelium aggregation, we provide a theoretical explanation for such transitions. It is shown that cell density can be an effective bifurcation parameter. Under certain conditions, the system is shifted from the excitable to the oscillatory state while the frequency of oscillations is proportional to the square root of the cell density. Thus, the regions with the highest cell density during the early stages of the spatial rearrangement of the cells become pacemakers and produce target patterns. The analytic results were confirmed in numerical simulations of the model.     

Deep-subwavelength Guiding and Superfocusing of Spoof Surface Plasmon Polaritons on Helically Grooved Metal Wire

Deep-subwavelength guiding and superfocusing of spoof surface plasmon polaritons (SSPPs) realized on a helically grooved metal wire at microwave frequencies are presented in this paper. Two smooth bridges with gradient helical grooves decorated on the cylindrical and conical metal wire are proposed and designed, respectively. High-efficiency and broadband mode conversion from the traditional guided waves to the SSPPs and superfocusing of SSPPs are reported. Numerical simulations quantitatively show that the amplitudes of electric field at the tip of the conical wire with gradient helical grooves can be magnified 50 times more than that of the input signal in broadband. Moreover, the second transition structure ensures that the depth of helical groove can be tuned flexibly and arbitrarily, making it compatible with all kinds of N-type coaxial connectors. Strong field concentration and superfocusing of these two structures can be easily extended to terahertz (THz) frequencies by tuning the geometrical parameters and can find important applications in sensing, spectroscopy and near-field imaging in the microwave and THz frequencies.