The role of microscopic plasma instabilities in the current sheet in the violation of the ideal magnetohydrodynamic (MHD) condition is investigated by means of a $2\frac{1}{2}$-dimensional explicit particle simulation code. Two instabilities, lower hybrid drift instabilities (LHDIs) and drift kink instabilities (DKIs) are found to evolve in the current sheet. In the LHDI growing phase, nonlinear coupling of the fluctuations of the electric field and particle density generates the outward flow and deforms the current sheet profile. The DC electric field leading to the magnetic flux reduction and the damping of equilibrium current are observed in the DKI growing phase. The force balance between the averaged electric force term and the additional wavy component associated with the fluctuations of magnetic field and current density holds at the neutral sheet. This suggests that the DKI can contribute to creating anomalous resistivity and triggering the collisionless magnetic reconnection.

We have developed a new shell model for the Hall magnetohydrodynamic (MHD) system to investigate the spectral properties of the plasma turbulence. Through the numerical simulation of the shell model, in the Hall MHD case, we find that the energy spectral index of the flow field indicates $-\frac53$ in the whole inertial range, while the energy spectral index of the magnetic field indicates $-\frac{5}{3}$($-\frac{7}{3}$) in the large- (small-)scale region of the inertial range. The simulation of the conventional MHD case was also carried out, and we find that the energy spectral index of both the flow and magnetic fields indicate $-\frac{5}{3}$.

A comprehensive particle based integrated code including atomic and relaxation processes has been developed. By using the code, we have investigated the lightning process of compressed neon gas that in a uniformly applied electric field. After a long time interval, streamers are slowly developed from a tiny ionization spot that is initially set. Then a complicated branching is suddenly and also explosively triggered, leading to fine net-like structures or sprites. Electromagnetic radiations are emitted from the sprite and show a low-power wave number spectrum, suggesting that the sprite exhibits a fractal nature.

The characteristic of the electrostatic mode excited in non-neutral plasma in the equilibrium state is closely related to the internal state of plasma. This relationship has been used for non-destructive diagnosis of non-neutral plasma. Under the present conditions, this diagnosis is only supported by simplified theory. We employ numerical simulation reflecting actual experimental conditions and examine the characteristic of this electrostatic mode.

Three-dimensional magnetohydrodynamics of the Solar coronal plasma is investigated by numerical simulation, aiming to understand the mechanisms of the Solar flare onset. It is demonstrated by the simulations that the resistive tearing mode instability growing on the magnetic shear inversion layer can drive the large-scale eruption through the mutual excitation of double reconnections. It is also revealed that the instability is able to cause the magnetohydrodynamic energy relaxation, in which the typical sigmoidal structure is self-organized prior to the onset of eruption. The simulation results predict that both the formation of sigmoids and the onset of flares should occur around the electric current sheet where the magnetic shear is steeply reversed. It is consistent with the reversed-shear flare model and the vector magnetograph observations.

Analytical expressions for the TE10 mode fields and the acceleration gradient for an electron are obtained in a plasma filled rectangular waveguide under the effect of an obliquely applied external magnetic field. The lower and upper cutoff frequencies for the mode propagation and the acceleration gradient for the electron are evaluated under the effect of various parameters. The acceleration gradient is increased with the microwave frequency and angle of magnetic field. It becomes reduced for the higher plasma density and stronger magnetic field. The larger acceleration of electron is achieved when $\omega_{\rm p}> \omega_{\rm c}$.

Three-dimensional electrostatic particle simulations are performed in order to investigate the effects of ion flow parallel to magnetic-field lines and their velocity shears on low-frequency plasma instabilities in detail. In the case where the ion drift speed is so small that the low-frequency instabilities cannot take place, the ion-acoustic wave is destabilized by introducing the ion-flow velocity shear. The ion-acoustic wave is locally destabilized in the large velocity shear region. On the other hand, the ion-cyclotron instability is also destabilized when the ion drift speed exceeds a certain threshold. The flow velocity shear enhances not only the fundamental mode but also the high harmonic modes. As a result, the spiky fluctuations in the time domain are locally observed in the velocity shear region, which are caused by the simultaneous existence of several coherent ion-cyclotron harmonics.

The structure of radiofrequency (rf) discharges of SF6, which includes electrons, positive ions, negative ions, and gas molecules, is examined using the particle-in-cell/Monte Carlo simulation. Electron–neutral collisions, ion–neutral collisions, and positive–negative ion recombination are taken into consideration. An improved ion–molecule collision model is proposed, the use of which reproduces the measured swarm parameters. Results show the double-layer structure typical of the discharge of electronegative gases. Only a small quantity of electrons are involved in SF6 rf discharges and the main negative species are the negative ions. The loss of negative ions is solely determined by positive–negative ion recombination. The electron temperature in the plasma bulk takes a relatively high value of 5–6 eV.

The instability of a high-frequency wave, such as the Langmuir wave (LW) is studied using a Vlasov-kinetic model in streaming and irradiated dusty plasma with dust charge fluctuation. In irradiated dusty plasma, dust charge fluctuation is considered to be due to the combined effect of LW perturbation and photoelectron emission. It is found that the dust charge fluctuation makes the LW unstable and this instability linearly adds to the Landau effect. Growth rate of the instability of LW is discussed. Discussion is also given to justify the theory and to verify it in the laboratory experiment.

In a previous study (2005 Comput. Phys. Commun.169, 139–143), we clarified the dependence of the phase structure on the hydrophilicity of an amphiphilic molecule by varying the interaction potential between the hydrophilic molecule and water ($a_{\rm AW}$) in a dissipative particle dynamics (DPD) simulation using the Jury model. In the present paper, we perform another DPD simulation using the previous model to investigate the dependence of the interaction potential between adjacent hydrophilic groups on the phase structure. By varying the coefficient of the interaction potential between adjacent hydrophilic groups $a_{\rm AA}$ ($a_{\rm AA}=15,25,40$ and 250) at a dimensionless temperature of $T=0.5$ and a concentration of amphiphilic molecules in water of $\phi=50$%, hexagonal ($a_{\rm AA}=14,25,40$) and micellar ($a_{\rm AA}=250$) phases were observed. In comparison with the previous results, the dependence of the A–B dimer's shape on $a_{\rm AA}$ was determined to be weaker than that on $a_{\rm AW}$. Therefore, it is concluded that the solvent water ${\rm W}$ plays an important role in aggregation of the A–B dimers.

A highly accurate self-consistent Monte Carlo method including charged and neutral particle motion and resonance photon transport is developed and applied to the simulation of the positive column of Argon discharge. The distribution of power loss across the tube is investigated. It is shown that negative slope of the current–voltage gradient curve can not be explained by only one factor. Diffusion of metastable atoms to the tube wall in the case of low current (0.2–3 mA) is responsible for the most part of negative slope. For the high currents the variation of radiation power loss makes a main contribution to the amplitude of the negative slope.

The micelle formation in amphiphilic solution is investigated by means of a molecular dynamics simulation of coarse-grained amphiphilic molecules with explicit solvent molecules. A random configuration of amphiphilic molecules in solution at high temperature is quenched to a lower temperature. Our simulations show that the micellar shapes change from a cylindrical micelle to a planar bilayer as the number density increases. At higher densities, we also find the following characteristic features. (1) The potential energy relaxes in a stepwise manner. (2) The radius of gyration Rg of the largest micelles increases with time in a stepwise fashion. (3) The sharp bumps in Rg occur during coalescence of micelles.

The induced charge of a spherical conducting dust particle on a plasma-facing wall is studied analytically. An external non-uniform electric field is approximated by the polynomial of the axial coordinate and the bipolar coordinate is introduced in order to employ the boundary condition. The result is applied to the dust in the non-uniform electric field in the Debye sheath in front of the conducting wall. The results are useful for analyzing the shielding effects of the plasma surrounding a dust particle.

Maxwell equations were numerically solved by the finite-difference time-domain method in order to confirm and understand the effectiveness of observing thin surface nanostructures using a polarization near-field scanning optical microscope (NSOM), which was first indicated in an experiment by Sakai et al. (2004 Nanotechnology15, S362–S364). A method that requires small computational resources to reproduce polarization NSOMs has been developed.

The effect of radiation trapping is included in the standard collisional-radiative model for atomic hydrogen under a typical condition of divertor plasmas. The population of the first excited level of the ionizing plasma component is strongly enhanced by the absorption of resonance line photons produced by the recombining plasma component, and the effective ionization rate coefficient is also strongly enhanced.

The microscopic properties and the electrical conductivity of a dense semiclassical plasma are calculated by the molecular dynamics simulation method.

The methods and applications that integrate electron microscopic density maps and comparative atomic coordinates to generate atomic models of protein complexes and their assemblies have recently advanced. Here, we also report on a newly developed tool for integration between density maps at a spatial resolution of about one nanometer and atomic coordinates by introducing the spatial constraints into a molecular dynamics calculation, which we call spatially restricted molecular dynamics. We, successfully, constructed the atomic models well-fitted to the density maps generated from nine different atomic coordinates of proteins. The method will give us the useful, refined, and presumable atomic structure of macromolecules to elucidate the relationship between their structure and functions.

A Hermite finite-elements approach with adaptive mesh refinement for the solution of a set of second-order ordinary differential equations is described. The main advantage of the method is its usability for stiff equations with boundary conditions. For cases where exponentially growing solutions can exist, the method overcomes the common problems of initial value solvers. The method was successfully used for the full-wave solution of wave propagation in inhomogeneous plasma where the mode conversion process between ordinary, extraordinary and electron Bernstein waves occurs.

First- and second-order accurate implicit difference schemes for the numerical solution of the nonlinear generalized Charney–Obukhov and Hasegawa–Mima equations with scalar nonlinearity are constructed. On the basis of numerical calculations accomplished by means of these schemes, the dynamics of two-dimensional nonlinear solitary vortical structures are studied. The problem of stability for the first-order accurate semi-discrete scheme is investigated. The dynamic relation between solutions of the generalized Charney–Obukhov and Hasegawa–Mima equations is established. It is shown that, contrary to existing opinion, the scalar nonlinearity in the case of the generalized Hasegawa–Mima equation develops monopolar anticyclone, while in case of the generalized Charney–Obukhov equation it develops monopolar cyclone.

A numerical method for a nonlinear system is presented. Formulation of the electromagnetic behavior of the shielding current density in high-Tc superconductors (HTS) gives a system of time-dependent integro-differential equations. The behavior can be determined by solving the initial-boundary-value problem of the system using the element-free Galerkin (EFG) method and the complete implicit difference method. After discretizing the problem, we obtain a nonlinear equation. In the present study, the shielding current density in HTS is calculated by applying the deaccelerated Newton method (DNM) and adaptively deaccelerated Newton method (ADNM) for the solution of the nonlinear system. The results of computation show that the DNM does not give a convergent solution in some cases. On the other hand, the ADNM gives a convergent solution in a few iterations.