Simulations of tokamak discharges with fast L-H transitions

Results are presented from the simulations of discharges with fast L-H transitions in the JET tokamak. During a transition, electron temperature perturbations propagate into the plasma core over a time much shorter than the transport time characteristic of this device. It is shown that the experimentally observed variations in the electron temperature may be caused by the change in the particle source intensity in the plasma when the atomic flux decreases, which is detected from the drop in the intensity of the D_α hydrogen spectral line. Hence, the experiments under consideration can be explained without the assumption about the nonlocal character of transport processes in tokamaks, which was made in some papers devoted to JET experiments. The plasma component responsible for the apparent nonlocal character of transport processes is the neutral component, whose propagation time across the plasma column is sufficiently short (t<100 μs). __________ Translated from Fizika Plazmy, Vol. 28, No. 1, 2002, pp. 3–8. Original Russian Text Copyright ? 2002 by Leonov.     

Study of plasma fluctuations in the TUMAN-3M tokamak during various types of L-H transitions

The reflectometer method is used to comparatively study plasma fluctuations in the edge plasma of the TUMAN-3M tokamak during L—H transitions initiated by different methods. It is shown that the width of the spectrum of backscattered microwave radiation is the most representative parameter when comparing the results obtained in different confinement regimes. The following methods for affecting the edge plasma were applied: gas puffing, a fast current ramp-up, a rapid increase in the toroidal magnetic field, and ion cyclotron heating. The studies were performed at different positions of the cutoff of O-and X-mode probing waves. A similar behavior of the spectral width was observed during transitions triggered by the fast current ramp-up and the rapid increase in the toroidal field. This provides evidence that the mechanism for transition to the H-mode is the same in both cases in spite of the different character of the evolution of the current density profiles. The fastest and strongest narrowing of the spectra was observed during the transition triggered by ion cyclotron heating. Possible reasons for similarities and differences in the behavior of the spectra during the transitions to the improved confinement regime are discussed.     

Radial electric field and rotation of the ensemble of plasma particles in tokamak

The velocity of macroscopic rotation of an ensemble of charged particles in a tokamak in the presence of an electric field has been calculated in a collisionless approximation. It is shown that the velocity of toroidal rotation does not reduce to a local velocity of electric drift and has opposite directions on the inner and outer sides of the torus. This result is supplemented by an analysis of the trajectories of motion of individual particles in the ensemble, which shows that the passing and trapped particles of the ensemble acquire in the electric field, on the average, different toroidal velocities. For the trapped particles, this velocity is equal to that of electric drift in the poloidal magnetic field, while the velocity of passing particles is significantly different. It is shown that, although the electric-field-induced shift of the boundaries between trapped and passing particles in the phase space depends on the particle mass and charge and is, in the general case, asymmetric, this does not lead to current generation.     

Numerical modeling of L-H transitions in the presence of a radial current at the edge of a tokamak plasma

Hydrodynamic equations describing wall plasma turbulence are analyzed numerically using a two-dimensional four-field model. Turbulent transport coefficients are calculated with consideration of the radial current. Numerical analysis revealed a possible scenario for L-H transitions that is associated with the radial current driven by nonambipolar processes. It is shown that the transition of a plasma to an improved confinement mode can also be triggered by other mechanisms.     

Peripheral fluctuations and particle transport during an L-H transition in the FT-2 tokamak

Experimental data on the processes in edge plasma that accompany the transition to an improved confinement regime during lower hybrid heating in the FT-2 tokamak are presented. The poloidal and radial distributions of the plasma parameters and drift particle fluxes were measured with the use of mobile mulitielectrode Langmuir probes and were found to be substantially nonuniform in the poloidal direction. The evolution of the plasma parameters in the course of heating and during an L-H transition is investigated. It is shown that, in FT-2 experiments, the drift of plasma particles in a slowly varying (quasi-steady) electric field and the fluctuation-induced particle fluxes make comparable contributions to the radial particle transport, whereas the contribution of fluctuations to poloidal plasma fluxes is negligibly small. The effective coefficient of radial diffusion is determined. The measurement results show that the L-H transition is accompanied by a substantial decrease in this coefficient.     

Investigation of statistical properties of peripheral fluctuations during an L-H transition in the FT-2 tokamak

The statistical properties of fluctuations of the plasma density and radial drift particle flux in the peripheral region of the FT-2 tokamak are analyzed using data from probe measurements. It is found that the probability distribution functions of the quantities under study vary over the radius and poloidal angle and change significantly after a transition to an improved confinement mode during auxiliary lower hybrid heating. Using experimental data and existing theoretical models, an analytic expression for the probability distribution function of the plasma density fluctuations is derived in a strongly nonlinear approximation. The expression is shown to agree well with experimental observations.     

Calculation of the energy confinement time and power threshold for L-H transitions in a tokamak with allowance for the parameters of the transport barrier

The ASTRA-ETL code is used to simulate L-H transition scenarios and calculate the energy confinement time and the threshold power of the L-H transition as functions of the averaged electron density 〈n〉, the averaged magnetic field B, the neutral density n _n , and the neutral temperature T _n , as well as the values of T _Se , T _Si , and n _S at the separatrix. It is shown that the linear dependence of the threshold power of the L-H transition on the averaged electron density, Q _L-H∝〈n〉, is associated with an increase in the viscosity of a poloidally rotating plasma due to charge exchange and is governed exclusively by an increase in the neutral density n _n . When the averaged electron density 〈n〉 is low, the threshold power rises because T _Si and T _Se increase. The accuracy of predictions for the power threshold of the L-H transition can be improved if the scaling of Q _L-H versus 〈n〉 and B is derived by processing experimental data from discharges with close parameter values at the separatrix. The hysteresis effect during an L-H-L transition triggered by varying the input power is modeled. The global energy confinement time τ_E is shown to increase linearly with 〈n〉 in the range 〈n〉<3.6×10¹⁹ m^?3 and to saturate at higher electron densities; this behavior is found to be characteristic of the Ohmic, L-, and H-modes. The saturation is associated with the fact that losses via the ion channel (when the transport coefficients are density-independent) dominate over losses via the electron channel. The dependence of τ _E on the input power is determined from the calculated database and is found to be τ _E =0.12Q _L-H ^?0.46 at a fixed averaged electron density 〈n〉. In the simulations of the L-H transition, the energy confinement time τ _E increases by a factor of 2 only if the thermal diffusivity inside the transport barrier is lower than that in the central plasma by a factor of more than 6.     

Determination of the resonant harmonics of the error field from dynamic magnetic measurements in a tokamak

The possibility is discussed of determining the amplitude and phase of a static resonant error field in a tokamak by means of dynamic magnetic measurements. The method proposed assumes measuring the plasma response to a varying external helical magnetic field with a small (a few gauss) amplitude. The case is considered in which the plasma is probed by square pulses with a duration much longer than the time of the transition process. The plasma response is assumed to be linear, with a proportionality coefficient being dependent on the plasma state. The analysis is carried out in a standard cylindrical approximation. The model is based on Maxwell’s equations and Ohm’s law and is thus capable of accounting for the interaction of large-scale modes with the conducting wall of the vacuum chamber. The method can be applied to existing tokamaks.     

Effect of the radial electric field on lower hybrid plasma heating in the FT-2 tokamak

Conditions for efficient ion heating in the interaction of lower hybrid waves with plasma are experimentally determined. Experiments show that efficient lower hybrid heating stimulates a transition to the improved confinement mode. The formation of internal and external transport barriers is associated with strong central ion heating, which results in a change of the radial electric field E _r and an increase in the shear of the poloidal plasma velocity. The improved confinement mode in the central region of the discharge is attained under the combined action of lower hybrid heating and an additional rapid increase in the plasma current. A new mechanism for the generation of an additional field E _r is proposed to explain the formation of a transport barrier.     

Tracing dynamic biological processes during phase transition

Background

Phase transition widely exists in the biological world, such as transformation of cell cycle phases, cell differentiation stages, disease development, and so on. Such a nonlinear phenomenon is considered as the conversion of a biological system from one phenotype/state to another. Studies on the molecular mechanisms of biological phase transition have attracted much attention, in particular, on different genotypes (or expression variations) in a specific phase, but with less of focus on cascade changes of genes' functions (or system state) during the phase shift or transition process. However, it is a fundamental but important mission to trace the temporal characteristics of a biological system during a specific phase transition process, which can offer clues for understanding dynamic behaviors of living organisms.

Results

By overcoming the hurdles of traditional time segmentation and temporal biclustering methods, a causal process model (CPM) in the present work is proposed to study the biological phase transition in a systematic manner, i.e. first, we make gene-specific segmentation on time-course expression data by developing a new boundary gene estimation scheme, and then infer functional cascade dynamics by constructing a temporal block network. After the computational validation on synthetic data, CPM was used to analyze the well-known Yeast cell cycle data. It was found that the dynamics of the boundary genes are periodic and consistent with the phases of the cell cycle, and the temporal block network indeed demonstrates a meaningful cascade structure of the enriched biological functions. In addition, we further studied protein modules based on the temporal block network, which reflect temporal features in different cycles.

Conclusions

All of these results demonstrate that CPM is effective and efficient comparing to traditional methods, and is able to elucidate essential regulatory mechanism of a biological system even with complicated nonlinear phase transitions.

     

Edge-mediated effects on stand dynamic processes in forest interiors: a coupled field and simulation approach

Researchers studying forest edge effects in fragmented landscapes have begun to move beyond merely documenting changes along the edge itself to examining the dynamic influences that edges may have on processes in adjacent areas. One such "edge-mediated effect" is the influence that edges may have on canopy gap replacement processes within the forest interior by acting as seed sources for shade-intolerant plant species. In this paper, we coupled analyses of woody species composition in gap and non-gap areas within the interior of an Ohio hardwood forest with a simple cellular automata model of forest dynamics. Non-gap composition was primarily correlated with disturbance history and site conditions (topographic position and slope) while a comparable analysis using a 24-year time series of composition in gaps showed that gap composition was related most strongly to the proximity of edge communities for the first 10–15 years. However, after 15–20 years of gap succession, composition was correlated with essentially the same variables and to the same degree as non-gap vegetation, suggesting that the influence of edge proximity on interior stand dynamic processes was transient. These results were used to develop a simple mathematical model of stand dynamics that showed that losses of interior forest area may be much greater than typically predicted by core-area models, which do not consider dynamic, edge-mediated effects. Further, our findings suggest the importance of considering disturbance interval in mediating edge-interior relationships, particularly as it may interact with forest size and shape.     

Septin stability and recycling during dynamic structural transitions in cell division and development

Septins are conserved proteins found in hetero-oligomeric complexes that are incorporated into distinct structures during cell division and differentiation; yeast septins Cdc3, Cdc10, Cdc11, and Cdc12 form hetero-octamers and polymerize into filaments, which form a "collar" at the mother-bud neck [1]. Posttranslational modifications, nucleotide binding, and protein-protein and protein-lipid interactions influence assembly and disassembly of septin structures [2], but whether individual septins are used repeatedly to build higher-order assemblies was not known. We used fluorescence-based pulse-chase methods to visualize the fate of pre-existing (old) and newly synthesized (new) molecules of two septins, Cdc10 and Cdc12. They were recycled through multiple mitotic divisions, and old and new molecules were incorporated indistinguishably into the collar. Likewise, old and new subunits intermixed within hetero-octamers, indicating that exchange occurs at this organizational level. Remarkably, in meiosis, Cdc10 made during vegetative growth was reutilized to build sporulation-specific structures and reused again during spore germination for budding and during subsequent mitotic divisions. Although Cdc12 also persisted during sporulation, it was excluded from septin structures and replaced by another subunit, Spr3; only new Cdc12 populated the collar of germinating spores. Thus, mechanisms governing septin incorporation are specific to each subunit and to the developmental state of the cell.     

Effect of anomalous ion inertia and oblique ion viscosity on the radial electric field in FT-2 tokamak experiments

Results are presented from numerical simulations that show that, in a plasma with well-developed turbulence, the radial electric field can be positive in the region where the gradients of the plasma parameters are steep. In a plasma in which the turbulence is suppressed (as is the case with auxiliary lower hybrid heating), the radial electric field is found to exhibit a nearly neoclassical behavior during the formation of a transport barrier and transition to the H-mode.     

On the displacement of cooperative transitions of linear biopolymers by an electric field

A basic theory for equilibrium properties of cooperative transitions (particularly helix–coil transformations) of sufficiently long linear biopolymers under the influence of an electric field is developed. General relations for the calculation of the distribution of uninterrupted sequences of elementary subunit states (e.g., helical fragments) as well as the overall degree of transition θ are given. Strong cooperativity is found to permit simplifications. It is shown that only in this case can a practically significant field effect be expected. Numerical results are presented for a special example of experimental interest.     

Numerical analysis of the near field of ICRH antennas in a tokamak

Results are presented from numerical calculations of the near fields of ICRH antennas in the quasisteady current approximation in two-dimensional geometry. The distributions of the vacuum electric and magnetic fields as well as of the surface current density in the antenna elements and inside the tokamak chamber are obtained. The electrotechnical characteristics of the antennas are analyzed numerically as functions of their geometric parameters.     

The cardiac electric field in psychrophilic and thermophilic fish during atrial depolarization

In psychrophilic and thermophilic fish, significant differences were revealed under an optimal body temperature in the heart rate, initial atrial activity duration and descending slope of the P _II wave. Differences were also detected in atrial electric activity during the initial and final periods of depolarization, reflecting different localization of the initial excitation area and the movement of the depolarization front toward the atrioventricular border.     

Microbiological processes in a high-temperature oil field

Thermophilic sulfate-reducing bacteria (SRB) oxidizing lactate, butyrate, and C12-C16 n-alkanes of oil at a temperature of 90 degrees C were isolated from samples of water and oil originating from oil reservoirs of the White Tiger high-temperature oil field (Vietnam). At the same time, no thermophiles were detected in the injected seawater, which contained mesophilic microorganisms and was the site of low-temperature processes of sulfate reduction and methanogenesis. Thermophilic SRB were also found in samples of liquid taken from various engineering reservoirs used for oil storage, treatment, and transportation. These samples also contained mesophilic SRB, methanogens, aerobic oil-oxidizing bacteria, and heterotrophs. Rates of bacterial production of hydrogen sulfide varied from 0.11-2069.63 at 30 degrees C and from 1.18-173.86 at 70 degrees C micrograms S/(1 day); and those of methane production, varied from 58.4-100 629.8 nl CH4/(1 day) (at 30 degrees C). The sulfur isotopic compositions of sulfates contained in reservoir waters and of hydrogen sulfide of the accompanying gas indicate that bacterial sulfate reduction might be effective in the depth of the oil field.     

Unsteady processes during stimulated emission from a relativistic electron beam in a quasi-longitudinal electrostatic pump field

The problem of stimulated emission from a relativistic electron beam in an external electrostatic pump field is studied. A set of nonlinear time-dependent equations for the spatiotemporal dynamics of the undulator radiation amplitude and the amplitude of the beam space charge field is derived. The beam electrons are described by a modified version of the macroparticle method. The regimes of the single-particle and collective Cherenkov effects during convective and absolute instabilities are considered. The nonlinear dynamics of radiation pulses emitted during the instabilities of the beam in its interaction with the forward and backward electromagnetic waves is investigated.     

Disentangling invasion processes in a dynamic shipping-boating network

The relative importance of multiple vectors to the initial establishment, spread and population dynamics of invasive species remains poorly understood. This study used molecular methods to clarify the roles of commercial shipping and recreational boating in the invasion by the cosmopolitan tunicate, Botryllus schlosseri. We evaluated (i) single vs. multiple introduction scenarios, (ii) the relative importance of shipping and boating to primary introductions, (iii) the interaction between these vectors for spread (i.e. the presence of a shipping-boating network) and (iv) the role of boating in determining population similarity. Tunicates were sampled from 26 populations along the Nova Scotia, Canada, coast that were exposed to either shipping (i.e. ports) or boating (i.e. marinas) activities. A total of 874 individuals (c. 30 per population) from five ports and 21 marinas was collected and analysed using both mitochondrial cytochrome c oxidase subunit I gene (COI) and 10 nuclear microsatellite markers. The geographical location of multiple hotspot populations indicates that multiple invasions have occurred in Nova Scotia. A loss of genetic diversity from port to marina populations suggests a stronger influence of ships than recreational boats on primary coastal introductions. Population genetic similarity analysis reveals a dependence of marina populations on those that had been previously established in ports. Empirical data on marina connectivity because of boating better explains patterns in population similarities than does natural spread. We conclude that frequent primary introductions arise by ships and that secondary spread occurs gradually thereafter around individual ports, facilitated by recreational boating.