Hydrodynamic Electron Research Articles

Forced oscillations of a viscous incompressible plasma with allowance for the electron inertia in a circular tube

The forced oscillations of a plasma column resulting from harmonic oscillations of the total current at a frequency ω are investigated analytically and numerically. The column plasma is assumed to be quasi-neutral two-component viscous and electroconducting, the electron inertia and the displacement current being completely taken into account. The electrons and ions are considered to be incompressible interpenetrating fluids. It is shown that the oscillations of the total current lead to the appearance of colliding plasma flows in the column, and, as the oscillation frequency ω increases, a skin layer with respect to main plasma parameters (current density, electromagnetic field, and hydrodynamic electron and ion velocities) develops on the boundary of the column. A comparison with the MHD theory is carried out and the role of the electron inertia and the displacement current in the generation of forced oscillations is investigated. The results obtained are used to analyze the plasma compression in apparatuses such as z-pinch and plasma focus.

Electrical excitation of shock and soliton‐like waves in high‐electron‐mobility transistor structures

AbstractAbstract

Subunit Conformations and Assembly States of a DNA-translocating Motor: The Terminase of Bacteriophage P22

Bacteriophage P22, a podovirus infecting strains of Salmonella typhimurium, packages a 42-kbp genome using a headful mechanism. DNA translocation is accomplished by the phage terminase, a powerful molecular motor consisting of large and small subunits. Although many of the structural proteins of the P22 virion have been well characterized, little is known about the terminase subunits and their molecular mechanism of DNA translocation. We report here structural and assembly properties of ectopically expressed and highly purified terminase large and small subunits. The large subunit (gp2), which contains the nuclease and ATPase activities of terminase, exists as a stable monomer with an α/β fold. The small subunit (gp3), which recognizes DNA for packaging and may regulate gp2 activity, exhibits a highly α-helical secondary structure and self-associates to form a stable oligomeric ring in solution. For wild-type gp3, the ring contains nine subunits, as demonstrated by hydrodynamic measurements, electron microscopy, and native mass spectrometry. We have also characterized a gp3 mutant (Ala 112→Thr) that forms a 10-subunit ring, despite a subunit fold indistinguishable from wild type. Both the nonameric and decameric gp3 rings exhibit nonspecific DNA-binding activity, and gp2 is able to bind strongly to the DNA/gp3 complex but not to DNA alone. We propose a scheme for the roles of P22 terminase large and small subunits in the recruitment and packaging of viral DNA and discuss the model in relation to proposals for terminase-driven DNA translocation in other phages.

Plasma oscillations in two-dimensional electron channel of a ring diode

We present an analytical approach based on the boundary conditions and complete set of orthonormal functions applied to Poisson’s equation coupled with the hydrodynamic electron transport equations for calculating the spectra of the plasma oscillations in two-dimensional electron channel diodes with slot and ring geometries.

Ultrastructure of Human Erythrocyte GLUT1

This study was undertaken to examine GLUT1 quaternary structure. Independent but complementary methodologies were used to investigate the influence of membrane-solubilizing detergents on GLUT1/lipid/detergent micelle hydrodynamic radii. Hydrodynamic size analysis and electron microscopy of GLUT1/lipid/detergent micelles and freeze-fracture electron microscopy of GLUT1 proteoliposomes support the hypothesis that the glucose transporter is a multimeric (probably tetrameric) complex of GLUT1 proteins. GLUT1 forms a multimeric complex in octyl glucoside that dissociates upon addition of reductant. Some detergents (e.g., CHAPS and dodecyl maltoside) promote the dissociation of GLUT1 oligomers into smaller aggregation states (dimers or monomers). These complexes do not reassemble as larger oligomers when dissociating detergents are subsequently replaced with nondissociating detergents such as octyl glucoside or cholic acid. When dissociating detergents are replaced with lipids, the resulting proteoliposomes catalyze protein-mediated sugar transport, and the subsequent addition of solubilizing, nondissociating detergents generates higher (tetrameric) GLUT1 aggregation states. These findings suggest that some detergents stabilize while others destabilize GLUT1 quaternary structure. GLUT1 does not appear to exchange rapidly between protein/lipid/detergent micelles but is able to self-associate in the plane of the lipid bilayer.

Three-dimensional structure of the myosin V inhibited state by cryoelectron tomography

Unconventional myosin V (myoV) is an actin-based molecular motor that has a key function in organelle and mRNA transport, as well as in membrane trafficking. MyoV was the first member of the myosin superfamily shown to be processive, meaning that a single motor protein can 'walk' hand-over-hand along an actin filament for many steps before detaching. Full-length myoV has a low actin-activated MgATPase activity at low [Ca2+], whereas expressed constructs lacking the cargo-binding domain have a high activity regardless of [Ca2+] (refs 5-7). Hydrodynamic data and electron micrographs indicate that the active state is extended, whereas the inactive state is compact. Here we show the first three-dimensional structure of the myoV inactive state. Each myoV molecule consists of two heads that contain an amino-terminal motor domain followed by a lever arm that binds six calmodulins. The heads are followed by a coiled-coil dimerization domain (S2) and a carboxy-terminal globular cargo-binding domain. In the inactive structure, bending of myoV at the head-S2 junction places the cargo-binding domain near the motor domain's ATP-binding pocket, indicating that ATPase inhibition might occur through decreased rates of nucleotide exchange. The actin-binding interfaces are unobstructed, and the lever arm is oriented in a position typical of strong actin-binding states. This structure indicates that motor recycling after cargo delivery might occur through transport on actively treadmilling actin filaments rather than by diffusion.

Spectrum of Plasma Oscillations in Slot Diode with Two-Dimensional Electron Channel

We strictly calculate the spectrum of plasma oscillations in a slot diode containing a two-dimensional electron channel with strip-like highly conducting contacts. The spectrum of plasma oscillations in a gated two-dimensional electron channel (without contacts) is calculated as well. We use the hydrodynamic electron transport model involving a two-dimensional Poisson equation. It is shown that the features of the structure geometry affect the oscillation spectrum.

Mammalian Class I Myosin, Myo1b, Is Monomeric and Cross-Links Actin Filaments as Determined by Hydrodynamic Studies and Electron Microscopy

The class I myosin, Myo1b, is a calmodulin- and actin-associated molecular motor widely expressed in mammalian tissues. Analytical ultracentrifugation studies indicate that Myo1b purified from rat liver has a Stokes radius of 6.7 nm and a sedimentation coefficient, s 20,w, of 7.0 S with a predicted molar mass of 213 kg/mol. These results indicate that Myo1b is monomeric and consists primarily of a splice variant having five associated calmodulins. Molecular modeling based on the analytical ultracentrifugation studies are supported by electron microscopy studies that depict Myo1b as a single-headed, tadpole-shaped molecule with outer dimensions of 27.9 × 4.0 nm. Above a certain Myo1b/actin ratio, Myo1b bundles actin filaments presumably by virtue of a second actin-binding site. These studies provide new information regarding the oligomeric state and morphology of Myo1b and support a model in which Myo1b cross-links actin through a cryptic actin-binding site.

Plasma oscillations in a slot diode structure with a two-dimensional electron channel

We calculate the spectrum of plasma oscillations in a diode structure with a two-dimensional electron channel in a slot between strip-like short circuited contacts. Hydrodynamic electron transport equations coupled with a two-dimensional Poissons equation for the self-consistent electric potential area used. The obtained results can be useful in designing of devices operating at terahertz frequencies based on two-dimensional electron systems and device optimization.

Myosin V: regulation by calcium, calmodulin, and the tail domain.

Calcium activates the ATPase activity of tissue-purified myosin V, but not that of shorter expressed constructs. Here, we resolve this discrepancy by comparing an expressed full-length myosin V (dFull) to three shorter constructs. Only dFull has low ATPase activity in EGTA, and significantly higher activity in calcium. Based on hydrodynamic data and electron microscopic images, the inhibited state is due to a compact conformation that is possible only with the whole molecule. The paradoxical finding that dFull moved actin in EGTA suggests that binding of the molecule to the substratum turns it on, perhaps mimicking cargo activation. Calcium slows, but does not stop the rate of actin movement if excess calmodulin (CaM) is present. Without excess CaM, calcium binding to the high affinity sites dissociates CaM and stops motility. We propose that a folded-to-extended conformational change that is controlled by calcium and CaM, and probably by cargo binding itself, regulates myosin V's ability to transport cargo in the cell.

Type III Protein Translocase: HrcN IS A PERIPHERAL MEMBRANE ATPASE THAT IS ACTIVATED BY OLIGOMERIZATION

Type III protein secretion (TTS) is catalyzed by translocases that span both membranes of Gram-negative bacteria. A hydrophilic TTS component homologous to F1/V1-ATPases is ubiquitous and essential for secretion. We show that hrcN encodes the putative TTS ATPase of Pseudomonas syringae pathovar phaseolicola and that HrcN is a peripheral protein that assembles in clusters at the membrane. A decahistidinyl HrcN derivative was overexpressed in Escherichia coli and purified to homogeneity in a folded state. Hydrodynamic analysis, cross-linking, and electron microscopy revealed four distinct HrcN forms: I, 48 kDa (monomer); II, approximately 300 kDa (putative hexamer); III, 575 kDa (dodecamer); and IV, approximately 3.5 MDa. Form III is the predominant form of HrcN at the membrane, and its ATPase activity is dramatically stimulated (>700-fold) over the basal activity of Form I. We propose that TTS ATPases catalyze protein translocation as activated homo-oligomers at the plasma membrane.

Admittance of a slot diode with a two-dimensional electron channel

We calculate the frequency-dependent admittance of a diode with a two-dimensional electron channel in a slot between strip-like contacts. Hydrodynamic electron transport equations coupled with a two-dimensional Poisson equation for the self-consistent electric potential are used. Using the calculated expression for the admittance, we analyze the effect of the planar contacts and external capacitance on the plasma oscillations in the system under consideration. The obtained results are useful for the interpretation of experimental observation of plasma effects in high-electron mobility transistors and optimization of terahertz devices based on these transistors.

Modeling of saturation and refraction in x-ray lasers

We model an experiment in which an iron slab target is irradiated by superimposing the six beams of the LULI facility onto a $22\mathrm{mm}\ifmmode\times\else\texttimes\fi{}100\ensuremath{\mu}\mathrm{m}$ focal line. The driving laser is composed of two Gaussian pulses of 130-ps duration (full width at half maximum), preceded by a prepulse. A strong enhancement of the $3p\ensuremath{-}3s$ 0-1 x-ray line at 25.5 nm in neonlike iron was observed. Saturation is attained for plasma lengths near 1 cm. A ray-trace code working as a postprocessor to a hydroatomic code is used to model the x-ray laser beam refraction due to the variation of the electron density versus the distance to the target surface. Knowing the hydrodynamic conditions, i.e., electron density, and electron and ion temperatures, along the ray paths, the radiative transfer equation, and the population equations are solved self-consistently by using a Maxwell-Bloch approach. A more tractable approach, requiring also the intensity of saturation as a function of time and space, is also presented. In this case, calculation time is much less than in the Maxwell-Bloch approach.

Calculation of van der Waals coefficients in hydrodynamic approach to time-dependent density functional theory

In this paper we employ hydrodynamic formulation of time-dependent density-functional theory to obtain coefficient C6 of the long-range part of the van der Waals interaction between alkali-metal clusters of large sizes. Such a calculation becomes computationally very demanding in the orbital-based Kohn–Sham formalism, but is quite simple in the hydrodynamic approach. This is because in hydrodynamic formulation, electron density and current density, rather than the orbitals, are employed as basic variables. We show that for intercations between the clusters of same sizes, C6 scales as the sixth power of the cluster radius and approaches the classically predicted value for large size clusters.

Variational approaches to the problems of plasma stability and of nonlinear plasma dynamics

A variational method is developed in order to investigate the nonlinear dynamics and stability of plasma using hydrodynamic plasma models, namely, the one-fluid, Hall, and electron MHD models. The key idea of the method is to adequately take into account variational symmetries and the associated conservation laws inherent in these hydrodynamic models. This approach is applied to derive variational criteria for the stability of a steadily moving plasma and to propose a variational method of the adiabatic separation of fast and slow motions, which makes it possible to simplify (reduce) the basic hydrodynamic models.

2D Simulation of Perpendicular Collisionless Shock Wave

Perpendicular collisionless shock waves (CSW) in a plasma with initial zero electron and small ion β are studied accounting for anomalous resistance in 2D formulation. A hybrid model with ion kinetics and hydrodynamic electron description is used. CSW are generated using a piston with a small 2D perturbation. The relative contribution of electron and ion heating as well as ion distribution downstream the wave front are presented. For Alfvén-Mach numbers MA > 2, similar to 1D computations, the main contribution to the ion component heating is made by ions which have experienced reflection at the wave front and whose velocities downstream the front are very high. In the formulation studied the 2D effects are not very considerable for low Alfvén-Mach numbers (MA ≤ 5): the magnetic field direction has little deviations from the ambient field, ions take on low velocities along the field, and quantitative plasma characteristics downstream the shock are close to 1D ones. For higher Alfvén-Mach numbers the 2D effects become more pronounced and the ion distribution function anisotropy is relaxed.

Nonlinear dynamics of electromagnetic turbulence in a nonuniform magnetized plasma

By using the hydrodynamic electron response with fixed (kinetic) ions along with Poisson’s equation as well as Ampère’s law, a system of nonlinear equations for low-frequency (in comparison with the electron gyrofrequency) long-(short-) wavelength electromagnetic waves in a nonuniform resistive magnetoplasma has been derived. The plasma contains equilibrium density gradient and sheared equilibrium plasma flows. In the linear limit, local dispersion relations are obtained and analyzed. It is found that sheared equilibrium flows can cause instability of Alfvén-like electromagnetic waves even in the absence of a density gradient. Furthermore, it is shown that possible stationary solutions of the nonlinear equations without dissipation can be represented in the form of various types of vortices. On the other hand, the temporal behavior of our nonlinear dissipative systems without the equilibrium density inhomogeneity can be described by the generalized Lorenz equations which admit chaotic trajectories. The density inhomogeneity may lead to even qualitative changes in the chaotic dynamics. The results of our investigation should be useful in understanding the linear and nonlinear properties of nonthermal electromagnetic waves in space and laboratory plasmas.

Bending of DNA by the mitomycin C-induced, GpG intrastrand cross-link.

Mitomycin C (MC) forms interstrand and intrastrand cross-link adducts and monoalkylation products (monoadducts) with DNA. Each of the three types of adducts was incorporated site-specifically into both a 15-mer and a 21-mer oligodeoxyribonucleotide duplex. The adduct-containing duplexes were 32P-phosphorylated and ligated to form multimers, which were then analyzed for anomalous electrophoretic mobility by nondenaturing polyacrylamide gel electrophoresis, using the method of Koo and Crothers [(1988) Proc. Natl. Acad. Sci. U.S.A. 85, 1763-1767] in order to detect DNA curvature caused by the adducts. The intrastrand cross-link adduct was found to induce a 14.6 +/- 2.0 degrees DNA bend per lesion (minimum value) while no DNA bending was detected for either the interstrand cross-link or the monoadduct. Molecular mechanics modeling indicated that the possible origin of the bend lies in a considerable deviation from parallel of the normals to the best planes of the intrastrand cross-linked guanines, due to a shorter than normal distance between their N2 atoms forced upon them by the cross-link. The observed bending by the MC intrastrand lesion may be the cause of the increased flexibility of MC-modified DNA, localized to distinct regions, as observed in earlier work by hydrodynamic methods and electron microscopy. The MC adduct-caused DNA bend may serve as a recognition site for certain DNA-binding proteins.

Hydrodynamic electron flow in high-mobility wires.

Hydrodynamic electron flow is experimentally observed in the differential resistance of electrostatically defined wires in the two-dimensional electron gas in (Al,Ga)As heterostructures. In these experiments current heating is used to induce a controlled increase in the number of electron-electron collisions in the wire. The interplay between the partly diffusive wire-boundary scattering and the electron-electron scattering leads first to an increase and then to a decrease of the resistance of the wire with increasing current. These effects are the electronic analog of Knudsen and Poiseuille flow in gas transport, respectively. The electron flow is studied theoretically through a Boltzmann transport equation, which includes impurity, electron-electron, and boundary scattering. A solution is obtained for arbitrary scattering parameters. By calculation of flow profiles inside the wire it is demonstrated how normal flow evolves into Poiseuille flow. The boundary-scattering parameters for the gate-defined wires can be deduced from the magnitude of the Knudsen effect. Good agreement between experiment and theory is obtained.

Monte Carlo simulation of electron swarms at low reduced electric fields.

A Monte Carlo method, based on the classical null collision technique, is developed and applied for electron swarm simulation in weakly ionized gases at low E/N values (E being the electric field and N the background gas density). The dominant low energy collisional processes (elastic, inelastic, and superelastic collisions) are properly considered. The influence of the thermal motion of background gas (target not assumed at rest) on electron kinetics, which can play an important role at very low E/N, is also taken into account. At zero field and low E/N conditions, the influence of low energy collision processes on space and time evolution of electron swarm parameters is emphasized in atomic (He) and molecular (${\mathrm{H}}_{2}$O) gases. Then, the present Monte Carlo method is adapted to the low E/N cases in strongly electronegative gases such as ${\mathrm{SF}}_{6}$ to overcome the problem of the vanishing of seed electrons by attachment processes which can stop the simulation. In that case, an additional fictitious ionization process with constant collision frequency is considered to obtain hydrodynamic electron swarm parameters in ${\mathrm{SF}}_{6}$ at low E/N.