Ordered dusty structures in the plasma of an RF electrodeless gas discharge

Results are presented from the experimental studies and numerical simulations of the behavior of dust grains in the plasma of an inductive RF discharge. The experiments were carried out with neon at a pressure of 25–500 Pa and with 1.87-μm melamine formaldehyde grains. The discharge was excited by a ring inductor supplied from a generator operating at a 100-MHz frequency. The effective dust-grain interaction potential used in numerical simulations involved the spatial dependence of the grain charge on the plasma floating potential, grain-interaction anisotropy resulting from the focusing of the drift ion current by the negatively charged grains, and specific features of the shielding of the dust grains by the plasma electrons and ions recombining both in the plasma bulk and on the grain surface. The results of Monte Carlo simulations show that the dust grains form specific filament structures observed experimentally in the plasma of an inductive electrodeless discharge. __________ Translated from Fizika Plazmy, Vol. 26, No. 5, 2000, pp. 445–454. Original Russian Text Copyright ? 2000 by Zobnin, Nefedov, Sinel’shchikov, Sinkevich, Usachev, Filinov, Fortov.     

Screening of the dust grain charge in a nonequilibrium plasma with two positive ion species

The screening of the grain charge in a nonequilibrium plasma is studied with allowance for electron and ion fluxes to the grain surface and the bulk processes of production and loss of charged particles in an argon plasma. The objective of the paper is to investigate how the conversion of monatomic Ar⁺ ions into diatomic Ar₂⁺ ions influences the screening of the dust grain charge in a plasma produced by an external gas ionization source. It is found that the conversion of positive ions leads to the onset of a second ion species in the plasma and, as a consequence, to a three-exponential screening of the grain charge; moreover, in a certain range of plasma parameters, all three screening constants are of the same order of magnitude. Analytical results are compared with the data of numerical simulations carried out based on the drift-diffusion approximation.     

The Role of Grain Boundaries on Ionic Defect Migration in Metal Halide Perovskites

Halide perovskites are emerging as revolutionary materials for optoelectronics. Their ionic nature and the presence of mobile ionic defects within the crystal structure have a dramatic influence on the operation of thin‐film devices such as solar cells, light‐emitting diodes, and transistors. Thin films are often polycrystalline and it is still under debate how grain boundaries affect the migration of ions and corresponding ionic defects. Laser excitation during photoluminescence (PL) microscopy experiments leads to formation and subsequent migration of ionic defects, which affects the dynamics of charge carrier recombination. From the microscopic observation of lateral PL distribution, the change in the distribution of ionic defects over time can be inferred. Resolving the PL dynamics in time and space of single crystals and thin films with different grain sizes thus, provides crucial information about the influence of grain boundaries on the ionic defect movement. In conjunction with experimental observations, atomistic simulations show that defects are trapped at the grain boundaries, thus inhibiting their diffusion. Hence, with this study, a comprehensive picture highlighting a fundamental property of the material is provided while also setting a theoretical framework in which the interaction between grain boundaries and ionic defect migration can be understood.     

Effect of microwave radiation on a dusty plasma

The effect of microwave radiation on a complex plasma produced by an external ionizer is studied using numerical simulations. It is shown that, as the radiation intensity increases, the scattering of the incident radiation by charged metal grains is enhanced and radiation at the second harmonic of the incident radiation appears in the scattered spectrum. This effect is associated with the grain charge oscillations caused by the nonlinear action of the microwave field. It is found that, under the action of strong microwave radiation, the grain charge can increase by one order of magnitude. It is shown that, when the microwave intensity is high enough, the distribution of the electric field near a dust grain is shown to change so radically that the field component normal to the grain surface can even change its sign.     

Charging of Dust Grains in a Nuclear-Induced Plasma at High Pressures

The process of dust-grain charging in plasmas produced by radioactive decay products or spontaneous fission fragments in air and xenon at high pressures is studied numerically in the hydrodynamic approximation. It is shown that, at sufficiently high rates of gas ionization, the dust grains in air are charged by electrons rather than ions, so that the grain charge in air is comparable to that in electropositive gases. The results of numerical calculations based on a complete model agree well with the experimental data. The time evolution of the grain charge is investigated, and the characteristic time scales on which the grains acquire an electric charge are established. The validity of approximate theories of dust-grain charging in electropositive and electronegative gases at high pressures is examined.     

Dust grain charges in a nuclear-track plasma and the formation of dynamic vortex dust structures

Results are presented from Monte Carlo calculations of the electric charge of dust grains in a plasma produced during the slowing down of the radioactive decay products of californium nuclei in neon. The dust grain charging is explained for the first time as being due to the drift of electrons and ions in an external electric field. It is shown that the charges of the grains depend on their coordinates and strongly fluctuate with time. The time-averaged grain charges agree with the experimental data obtained on ordered liquidlike dust structures in a nuclear-track plasma. The time-averaged dust grain charges are used to carry out computer modeling of the formation of dynamic vortex structures observed in experiments. Evidence is obtained of the fact that the electrostatic forces experienced by the dust grains are potential in character.     

Behavior of a dust grain in the double layer of an electric probe in a gas-discharge plasma

Equations for the motion of an individual dust grain in the double layer of a negatively charged cylindrical probe in a glow discharge plasma are derived and solved numerically. The distribution of the electric potential near the probe is determined, and the grain charge is calculated as a function of the distance from the probe for different probe potentials. The trajectories of grains with different initial energies are traced. An analysis of the grain trajectories shows that, at a certain distance from the probe, high-energy grains may be recharged; i.e., the grain charge may change sign. The grains are found to have no direct effect on the probe current in a dusty plasma of a glow discharge.     

Development of a self-consistent model of dust grain charging at elevated pressures using the method of moments

A model of dust grain charging is constructed using the method of moments. The dust grain charging process in a weakly ionized helium plasma produced by a 100-keV electron beam at atmospheric pressure is studied theoretically. In simulations, the beam current density was varied from 1 to 10⁶ μA/cm². It is shown that, in a He plasma, dust grains of radius 5 μm and larger perturb the electron temperature only slightly, although the reduced electric field near the grain reaches 8 Td, the beam current density being 10⁶ μA/cm². It is found that, at distances from the grain that are up to several tens or hundreds of times larger than its radius, the electron and ion densities are lower than their equilibrium values. Conditions are determined under which the charging process may be described by a model with constant electron transport coefficients. The dust grain charge is shown to be weakly affected by secondary electron emission. In a beam-produced helium plasma, the dust grain potential calculated in the drift-diffusion model is shown to be close to that calculated in the orbit motion limited model. It is found that, in the vicinity of a body perturbing the plasma, there may be no quasineutral plasma presheath with an ambipolar diffusion of charged particles. The conditions for the onset of this presheath in a beam-produced plasma are determined. __________ Translated from Fizika Plazmy, Vol. 29, No. 3, 2003, pp. 214–226. Original Russian Text Copyright ? 2003 by Filippov, Dyatko, Pal’, Starostin.     

Charge and potential of a dust grain versus the intergrain distance and establishment of the latter in a low-pressure plasma

Results from experimental studies of ordered dust structures in plasma are reviewed. The experimental conditions and the data on the grain size and intergrain distance in plasma dust crystals are analyzed. It is shown that intergrain distance is a function of the grain size. The range of the ratio of the dust grain size to the Debye radius within which plasma dust crystals can form is determined. A volume cell surrounding a dust grain in plasma is considered. It is found that the potential and charge of the grain depend substantially on the intergrain distance. The charge, potential, and potential energy of a dust grain in a plasma dust crystal, as well as the electrostatic force exerted by the plasma field on the grain, are calculated by the method of molecular dynamics as functions of the intergrain distance. The corresponding analytic approximations and the criterion for the establishment of a steady-state intergrain distance are proposed.     

Empirical approximation for the ion current to the surface of a dust grain in a weakly ionized gas-discharge plasma

The results from numerical simulation of the dust grain charging process in a weakly ionized gasdischarge plasma are analyzed. An empirical approximate formula for the ion current to the grain surface under conditions close to those in laboratory experiments with dusty plasmas is derived. Investigations show that the approximation proposed greatly simplifies determination of the grain charge by avoiding laborious calculations for different grain sizes and different parameters of the surrounding plasma.     

Excitation energy transfer and charge separation in photosystem II membranes revisited

We have performed time-resolved fluorescence measurements on photosystem II (PSII) containing membranes (BBY particles) from spinach with open reaction centers. The decay kinetics can be fitted with two main decay components with an average decay time of 150 ps. Comparison with recent kinetic exciton annihilation data on the major light-harvesting complex of PSII (LHCII) suggests that excitation diffusion within the antenna contributes significantly to the overall charge separation time in PSII, which disagrees with previously proposed trap-limited models. To establish to which extent excitation diffusion contributes to the overall charge separation time, we propose a simple coarse-grained method, based on the supramolecular organization of PSII and LHCII in grana membranes, to model the energy migration and charge separation processes in PSII simultaneously in a transparent way. All simulations have in common that the charge separation is fast and nearly irreversible, corresponding to a significant drop in free energy upon primary charge separation, and that in PSII membranes energy migration imposes a larger kinetic barrier for the overall process than primary charge separation.     

Ion-acoustic solitons in dusty plasma

The dynamics of dust ion-acoustic solitons is analyzed in a wide range of dusty plasma parameters. The cases of both a positive dust grain charge arising due to the photoelectric effect caused by intense electromagnetic radiation and a negative grain charge established in the absence of electromagnetic radiation are considered. The ranges of plasma parameters and Mach numbers in which ??conservative?? (nondissipative) solitons can exist are determined. It is shown that, in dusty plasma with negatively charged dust grains, both compression and rarefaction solitons can propagate, whereas in plasma with positively charged dust grains, only compression solitons can exist. The evolution of soliton-like compression and rarefaction perturbations is studied by numerically solving the hydrodynamic equations for ions and dust grains, as well as the equation for dust grain charging. The main dissipation mechanisms, such as grain charging, ion absorption by dust grains, momentum exchange between ions and dust grains, and ion-neutral collisions are taken into account. It is shown that the amplitudes of soliton-like compression and rarefaction perturbations decrease in the course of their evolution and their velocities (the Mach numbers) decrease monotonically in time. At any instant of time, the shape of an evolving soliton-like perturbation coincides with the shape of a conservative soliton corresponding to the current value of the Mach number. It is shown that, after the interaction between any types of soliton-like perturbations, their velocities and shapes are restored (with a certain phase shift) to those of the corresponding perturbations propagating without interaction; i.e., they are in fact weakly dissipative solitons.     

Parametric dependence on shear viscosity of SPC/E water from equilibrium and non-equilibrium molecular dynamics simulations

A parametric dependent study is crucial for the accurate determination of transport coefficients such as shear viscosity. In this study, we calculate the shear viscosity of extended simple point charge water using a transverse current auto-correlation function (TCAF) from equilibrium molecular dynamics (EMD) and the periodic perturbation method from non-equilibrium molecular dynamics (NEMD) simulations for varying coupling time and system sizes. Results show that the shear viscosity calculated using EMD simulations with different thermostats varies significantly with coupling times and system size. The use of Berendsen and velocity-rescale thermostats in NEMD simulations generates a significant drift from the target temperature and results in an inconsistent shear viscosity with coupling time and system size. The use of Nosé–Hoover thermostat in NEMD simulations offers thermodynamic stability which results in a consistent shear viscosity for various coupling times and system sizes.     

Quantifying uncertainty in molecular dynamics simulations of grain boundary migration

Molecular dynamics simulations of simple bicrystal systems have been much used as a tool to explore how the migration of grain boundaries varies with their structure and with experimental conditions. In order to permit the exploration of a large parameter space, many studies are forced to rely on a small number of simulations (often a single simulation) for each configuration. The motion of a grain boundary is inherently statistical and any variability in the measured grain boundary velocity should be taken into account in subsequent analysis of trends in grain boundary mobility. Here we present the results of large numbers of simulations of equivalent boundaries, which show that this variability can be large, particularly when small systems are simulated. We show how a bootstrap resampling approach can be used to characterise the statistical uncertainty in boundary velocity using the information present in a single simulation. We show that the approach is robust across a variety of system sizes, temperatures and driving force strengths and types, and provides a good order-of-magnitude measure of the population standard deviation across multiple equivalent simulations.     

Phosphorylation tunes elongation propensity and cohesiveness of INCENP’s intrinsically disordered region

The inner centromere protein, INCENP, is crucial for correct chromosome segregation during mitosis. It connects the kinase Aurora B to the inner centromere allowing this kinase to dynamically access its kinetochore targets. However, the function of its central, 440-residue long intrinsically disordered region (IDR) and its multiple phosphorylation sites is unclear. Here, we determined the conformational ensemble of INCENP’s IDR, systematically varying the level of phosphorylation, using all-atom and coarse-grain molecular dynamics simulations. Our simulations show that phosphorylation expands INCENP’s IDR, both locally and globally, mainly by increasing its overall net charge. The disordered region undergoes critical globule-to-coil conformational transitions and the transition temperature non-monotonically depends on the degree of phosphorylation, with a mildly phosphorylated case of neutral net charge featuring the highest collapse propensity. The IDR transitions from a multitude of globular states, accompanied by several specific internal contacts that reduce INCENP length by loop formation, to weakly interacting and highly extended coiled conformations. Phosphorylation critically shifts the population between these two regimes. It thereby influences cohesiveness and phase behavior of INCENP IDR assemblies, a feature presumably relevant for INCENP’s function in the chromosomal passenger complex. Overall, we propose the disordered region of INCENP to act as a phosphorylation-regulated and length-variable component, within the previously defined “dog-leash” model, that thereby regulates how Aurora B reaches its targets for proper chromosome segregation.     

Theoretical investigation of infrared spectra and pocket dynamics of photodissociated carbonmonoxy myoglobin

Molecular dynamics simulations of the photodissociated state of carbonmonoxy myoglobin (MbCO) are presented using a fluctuating charge model for CO. A new three-point charge model is fitted to high-level ab initio calculations of the dipole and quadrupole moment functions taken from the literature. The infrared spectrum of the CO molecule in the heme pocket is calculated using the dipole moment time autocorrelation function and shows good agreement with experiment. In particular, the new model reproduces the experimentally observed splitting of the CO absorption spectrum. The splitting of 3-7 cm(-1) (compared to the experimental value of 10 cm(-1)) can be directly attributed to the two possible orientations of CO within the docking site at the edge of the distal heme pocket (the B states), as previously suggested on the basis of experimental femtosecond time-resolved infrared studies. Further information on the time evolution of the position and orientation of the CO molecule is obtained and analyzed. The calculated difference in the free energy between the two possible orientations (Fe...CO and Fe...OC) is 0.3 kcal mol(-1) and agrees well with the experimentally estimated value of 0.29 kcal mol(-1). A comparison of the new fluctuating charge model with an established fixed charge model reveals some differences that may be critical for the correct prediction of the infrared spectrum and energy barriers. The photodissociation of CO from the myoglobin mutant L29F using the new model shows rapid escape of CO from the distal heme pocket, in good agreement with recent experimental data. The effect of the protein environment on the multipole moments of the CO ligand is investigated and taken into account in a refined model. Molecular dynamics simulations with this refined model are in agreement with the calculations based on the gas-phase model. However, it is demonstrated that even small changes in the electrostatics of CO alter the details of the dynamics.     

Photoelectric charging of dust grains

Photoemission from the surface of a dust grain in vacuum is considered. It is shown that the cutoff in the energy spectrum of emitted electrons leads to the formation of a steady-state electron cloud. The equation describing the distribution of the electric potential in the vicinity of a dust grain is solved numerically. The dust grain charge is found as a function of the grain size.     

Simulations of the Effect of Currently Used Grenade Harpoons for the Killing of Whales Using a Pig-Model

Physical model experiments, as well as simulations of the effects of grenade harpooning on anaesthetized pigs fully immersed in water suggest that the shock effect of the blast from the currently used grenades is relatively minor. Also the animals are not stunned to death, but loose consciousness and subsequently die from hemorrhage. Survival time is therefore very short if the animals are hit in the thorax, and is likely to be further reduced if the charge which is currently used is increased, or, even better, if shrapnel (fragment scattering) grenades are used instead of blast grenades.     

Effect of ion collisions on the parameters of dust-plasma structures

A study is made of how collisions of ions with gas atoms affect the parameters of an ion flow and the interaction between dust grains, as well as their interaction with the flow. The ion velocity distribution in a gas discharge is analyzed with allowance for both resonant charge exchange of the ions with parent gas atoms and polarizing collisions. The interaction forces between a dust grain and an ion flow and among the grains due to the charge exchange of ions with gas atoms near the grain are examined.     

Recent progress in biological charge transfer: Theory and simulation

In this contribution, we discuss three recent developments in atomistic biological charge transfer theory. First, in the context of Marcus' classical theory of charge transfer, key quantities of the theory such as driving forces and reorganization enthalpies are now accessible by thermodynamic integration schemes within standard molecular dynamics simulations at high accuracy. Second, direct simulations of charge transfer enable the computation of fast charge transfer reaction rates without having to resort to Marcus' theory. Finally, exploring the electronic structure beyond that of hitherto presumed centers of localization helps to identify new stepping stones of charge transfer reactions. This article is part of a Special Issue entitled: 17th European Bioenergetics Conference (EBEC 2012).