Suppression of the neoclassical tearing modes in tokamaks under anomalous transverse transport conditions when the magnetic well effect predominates over the bootstrap drive

A study is made of the suppression of neoclassical tearing modes in tokamaks under anomalous transverse transport conditions when the magnetic well effect predominates over the bootstrap drive. It is stressed that the corresponding effect, which is called the compound suppression effect, depends strongly on the profiles of the electron and ion temperature perturbations. Account is taken of the fact that the temperature profile can be established as a result of the competition between anomalous transverse heat transport, on the one hand, and longitudinal collisional heat transport, longitudinal heat convection, longitudinal inertial transport, and transport due to the rotation of magnetic islands, on the other hand. The role of geodesic effects is discussed. The cases of competition just mentioned are described by the model sets of reduced transport equations, which are called, respectively, collisional, convective, inertial, and rotational plasmophysical models. The magnetic well is calculated with allowance for geodesic effects. It is shown that, for strong anomalous heat transport conditions, the contribution of the magnetic well to the generalized Rutherford equation for the island width W is independent of W not only in the collisional model (which has been investigated earlier) but also in the convective and inertial models and depends very weakly (logarithmically) on W in the rotational model. It is this weak dependence that gives rise to the compound effect, which is the subject of the present study. A criterion for the stabilization of neoclassical tearing modes by the compound effect at an arbitrary level of the transverse heat transport by electrons and ions is derived and is analyzed for two cases: when the electron heat transport and ion heat transport are both strong, and when the electron heat transport is strong and the ion heat transport is weak.     

Nonstationary kinetic theory of ion transport in plasma with small perturbations

A theory of charged particle transport for small potential perturbations in a fully ionized plasma is developed on the basis of solving a linearized kinetic equation with the Landau collision integral. This theory is free of any constraints on the characteristic time and spatial scales of perturbations. Ion fluxes appropriate for an arbitrary ion-ion collision frequency that can ensure nonlocal space-time transport in the plasma are calculated. The obtained ion transport coefficients are used to calculate the partial contribution of ions to the longitudinal permittivity of collisional plasma. The resulting expression for the plasma permittivity is applicable in the entire range of frequencies and wavenumbers.     

An analytic approach to developing transport threshold models of neoclassical tearing modes in tokamaks

Transport threshold models of neoclassical tearing modes in tokamaks are investigated analytically. An analysis is made of the competition between strong transverse heat transport, on the one hand, and longitudinal heat transport, longitudinal heat convection, longitudinal inertial transport, and rotational transport, on the other hand, which leads to the establishment of the perturbed temperature profile in magnetic islands. It is shown that, in all these cases, the temperature profile can be found analytically by using rigorous solutions to the heat conduction equation in the near and far regions of a chain of magnetic islands and then by matching these solutions. Analytic expressions for the temperature profile are used to calculate the contribution of the bootstrap current to the generalized Rutherford equation for the island width evolution with the aim of constructing particular transport threshold models of neoclassical tearing modes. Four transport threshold models, differing in the underlying competing mechanisms, are analyzed: collisional, convective, inertial, and rotational models. The collisional model constructed analytically is shown to coincide exactly with that calculated numerically; the reason is that the analytical temperature profile turns out to be the same as the numerical profile. The results obtained can be useful in developing the next generation of general threshold models. The first steps toward such models have already been made.     

Nonlinear dynamics of drift structures in a magnetized dissipative plasma

A study is made of the nonlinear dynamics of solitary vortex structures in an inhomogeneous magnetized dissipative plasma. A nonlinear transport equation for long-wavelength drift wave structures is derived with allowance for the nonuniformity of the plasma density and temperature equilibria, as well as the magnetic and collisional viscosity of the medium and its friction. The dynamic equation describes two types of nonlinearity: scalar (due to the temperature inhomogeneity) and vector (due to the convectively polarized motion of the particles of the medium). The equation is fourth order in the spatial derivatives, in contrast to the second-order Hasegawa-Mima equations. An analytic steady solution to the nonlinear equation is obtained that describes a new type of solitary dipole vortex. The nonlinear dynamic equation is integrated numerically. A new algorithm and a new finite difference scheme for solving the equation are proposed, and it is proved that the solution so obtained is unique. The equation is used to investigate how the initially steady dipole vortex constructed here behaves unsteadily under the action of the factors just mentioned. Numerical simulations revealed that the role of the vector nonlinearity is twofold: it helps the dispersion or the scalar nonlinearity (depending on their magnitude) to ensure the mutual equilibrium and, thereby, promote self-organization of the vortical structures. It is shown that dispersion breaks the initial dipole vortex into a set of tightly packed, smaller scale, less intense monopole vortices-alternating cyclones and anticyclones. When the dispersion of the evolving initial dipole vortex is weak, the scalar nonlinearity symmetrically breaks a cyclone-anticyclone pair into a cyclone and an anticyclone, which are independent of one another and have essentially the same intensity, shape, and size. The stronger the dispersion, the more anisotropic the process whereby the structures break: the anticyclone is more intense and localized, while the cyclone is less intense and has a larger size. In the course of further evolution, the cyclone persists for a relatively longer time, while the anticyclone breaks into small-scale vortices and dissipation hastens this process. It is found that the relaxation of the vortex by viscous dissipation differs in character from that by the frictional force. The time scale on which the vortex is damped depends strongly on its typical size: larger scale vortices are longer lived structures. It is shown that, as the instability develops, the initial vortex is amplified and the lifetime of the dipole pair components-cyclone and anticyclone-becomes longer. As time elapses, small-scale noise is generated in the system, and the spatial structure of the perturbation potential becomes irregular. The pattern of interaction of solitary vortex structures among themselves and with the medium shows that they can take part in strong drift turbulence and anomalous transport of heat and matter in an inhomogeneous magnetized plasma.     

Determination of the electron density in the tokamak edge plasma from the time evolution of a laser-induced fluorescence signal from atomic helium

The time evolution of a laser-induced fluorescence signal from neutral helium He I in the edge and divertor plasmas in modern magnetic confinement devices is considered. Computations are performed on the basis of a nonstationary collisional-radiative model involving ten singlet and nine triplet states of helium that affect the time evolution of the fluorescence signal. A new method is proposed for determining the electron density from measurements of the time derivative of the profile of the fluorescence spectral line.     

Turbulent-convective block for the ASTRA transport code

A physical model for the enhanced transport code is presented, which explicitly takes into account the contribution of turbulent convection to the processes of particle and heat transport in the hot core of the tokamak plasma. The model is based on the specially developed CONTRA-A turbulent block, while an adapted version of the existing ASTRA transport code is used as a transport envelope. The CONTRA-A turbulent block, based on the adiabatically reduced quasi-2D magnetohydrodynamic equations, calculates the generation and self-consistent evolution of low-frequency turbulence, including the spatiotemporal structure of turbulent fluctuations of the plasma velocity, density, and temperatures of electrons and ions. Using the obtained data on fluctuations, the CONTRA-A block calculates the turbulent-convective particle and heat fluxes and transfers them to the modified ASTRA code, which computes the evolution of quasi-equilibrium plasma parameters. To illustrate the capabilities of the enhanced transport model, the results of simulations of turbulent plasma evolution in two discharge scenarios with nonstationary auxiliary plasma heating in the T-10 and T-15MD tokamaks are presented.     

Numerical simulation of convective and diffusive transport effects on a high-pressure-induced inactivation process

High-pressure-induced conversions, such as the inactivation of enzymes or of microorganisms, are dependent on the applied pressure and the temperature of the process. The former can be considered to be a spatially homogeneous quantity, while the latter, being a transport quantity, varies over space and time. Here we question whether the uniformity of a high-pressure conversion can be disturbed by convective and conductive heat and mass transport conditions. Enzyme inactivation is taken as a model process for a high-pressure conversion. To cover a broad range of parameters and to consider scale-up effects, the investigation is based on mathematical modeling and numerical simulation for different sizes of the pressure chamber and different solvent viscosities. Apart from viscosity, the physical properties of the enzyme solutions are assumed to be identical in all cases. Therefore, matrix effects other than that of viscosity are excluded. Moreover, the authors postulate that viscosity solely acts on the continuum mechanical scale of momentum exchange but not on the molecular scale on the inactivation kinetics. It has been found that nonuniform thermal conditions can strongly influence the result of a high-pressure process. A variation of the activity retention between 28% and 48% can be observed after 20 minutes for a 0.8-L high-pressure chamber and a matrix fluid with a viscosity comparable to that of edible oils. The same process carried out in a 6.3-L device leads to an activity retention that varies between 16% and 40%. From the analysis of the time scales for the inactivation and for hydrodynamic and thermal compensation, it can be deduced that a nonuniform activity retention has to be expected if the inactivation time scale is larger than the hydrodynamic time scale and smaller than the thermal compensation time scale.     

Ionization of molecular nitrogen by radiation from a channel surface discharge

Ionization of atmospheric-pressure nitrogen by nearly blackbody radiation from a channel surface discharge is investigated. By analyzing the data from measurements of the current of an electrostatic electron detector, the ionization rate of nitrogen and the time evolution of the electron density are determined. It is shown that the electron density reaches its maximum ～5 μs after the irradiation pulse. The results obtained indicate that the most probable mechanism for the observed nitrogen ionization is the formation of an ensemble of nitrogen molecules in metastable states and their subsequent collisional ionization, rather than direct one-photon or multiphoton ionization.     

Cattaneo-Christov Heat Flux Model for MHD Three-Dimensional Flow of Maxwell Fluid over a Stretching Sheet

This letter investigates the MHD three-dimensional flow of upper-convected Maxwell (UCM) fluid over a bi-directional stretching surface by considering the Cattaneo-Christov heat flux model. This model has tendency to capture the characteristics of thermal relaxation time. The governing partial differential equations even after employing the boundary layer approximations are non linear. Accurate analytic solutions for velocity and temperature distributions are computed through well-known homotopy analysis method (HAM). It is noticed that velocity decreases and temperature rises when stronger magnetic field strength is accounted. Penetration depth of temperature is a decreasing function of thermal relaxation time. The analysis for classical Fourier heat conduction law can be obtained as a special case of the present work. To our knowledge, the Cattaneo-Christov heat flux model law for three-dimensional viscoelastic flow problem is just introduced here.     

Effect of Elevated Temperatures on the Activity of Alternative Pathways of Photosynthetic Electron Transport in Intact Barley and Maize Leaves

The light-induced rise in chlorophyll fluorescence and the subsequent decay of fluorescence in darkness were measured in barley and maize leaves exposed to heat treatment. The redox conversions of the photosystem I primary donor P700, induced by far-red light, were also monitored from the absorbance changes at 830 nm. After heating of leaves at temperatures above 40°C, the ratio of variable and maximum fluorescence decreased for leaves of both plant species, indicating the inhibition of photosystem II (PSII) activity. A twofold reduction of this ratio in barley and maize leaves was observed after heating at 45.3 and 48.1°C, respectively, which suggests the higher functional resistance of PSII in maize. The amplitude of the slow phase in the dark relaxation of variable fluorescence did not change after the treatment of barley and maize leaves at temperatures up to 48°C. In leaves treated at 42 and 46°C, the slow phase of dark relaxation deviated from an exponential curve. The relaxation kinetics included a temporary increase in fluorescence to a peak about 1 s after turning off the actinic light. Unlike the slow component, the fast and intermediate phases in the dark relaxation of variable fluorescence disappeared fully or partly after the treatment of leaves at 46°C. The photooxidation of P700 in heat-treated leaves was saturated at much higher irradiances of far-red light than in untreated leaves. At the same time, the dark reduction of P700⁺ was substantially accelerated after heat treatment. The data provide evidence that the heating of leaves stimulated the alternative pathways of electron transport, i.e., cyclic transport around photosystem I and/or the donation of electrons to the plastoquinone pool from the reduced compounds located in the chloroplast stroma. The rate of alternative electron transport after the heat treatment was higher in maize leaves than in barley leaves. It is supposed that the stimulation of alternative electron transport, associated with proton pumping into the thylakoid, represents a protective mechanism that prevents the photoinhibition of PSII in leaves upon a strong suppression of linear electron transport in chloroplasts exposed to heat treatment.     

Nonlocal transport in hot plasma. Part I

The problem of describing charged particle transport in hot plasma under the conditions in which the ratio of the electron mean free path to the gradient length is not too small is one of the key problems of plasma physics. However, up to now, there was a deficit of the systematic interpretation of the current state of this problem, which, in most studies, is formulated as the problem of nonlocal transport. In this review, we fill this gap by presenting a self-consistent linear theory of nonlocal transport for small plasma perturbations and an arbitrary collisionality from the classical highly collisional hydrodynamic regime to the collisionless regime. We describe a number of nonlinear transport models and demonstrate the application of the nonclassical transport theory to the solution of some problems of plasma physics, first of all for plasmas produced by nanosecond laser pulses with intensities of 10¹³–10¹⁶ W/cm².     

A new hypothesis for the evolution of biological electron transport

A new hypothesis for the evolution of biological electron transport is presented. According to this hypothesis biological electron transport originated close to the potential of the hydrogen electrode and evolved in various advantageous directions including, when molecular oxygen became available on the Earth, that of the oxygen electrode. This implies stepwise evolution along and across the potential scale. The hypothesis is based mainly on existing information obtained from studies of primary and tertiary structural relationships of proteins. It is hoped to provide a framework for closer understanding of both evolution and mechanisms of cellular oxidation-reduction as well as energy coupling reactions.     

Laser sideband spectroscopy: a macromolecular probe

We have previously developed a model which includes energy and phasechanging collisional relaxations in a system of chemically reacting molecules absorbing light from a monochromatic field while immersed in an inert thermal bath. Some aspects of the model are presented here which relate to scattered light measurements on macromolecular systems. We predict that in the presence of low-intensity laser light the elastic component of the scattered light will be broadened by the rate constant for the chemical reaction. In the presence of high-intensity laser light, the scattered field may contain, in addition to the Rayleigh scattered light, two sidebands symmetrically displaced to either side of the Rayleigh band; the magnitude of the displacement is a function of the laser intensity. The Rayleigh band width is a direct measure of the phase relaxation time, and the sideband widths are a measure of the energy and phase relaxation times. We discuss several experimental systems in which sideband scattering data might be used to provide information related to relaxation and reaction mechanisms in macromolecular systems of biological interest; bound enzyme-substrate and enzyme-dye systems can be investigated as can vibrational energy transfer on membrane-bound systems. Some numerical computations are included for the magnitude of the sideband displacement and scattered intensities.     

微生物胞外长距离电子传递网络研究进展

[目的] 解析一株从黄河三角洲湿地甲烷氧化富集物中分离获得的甲烷氧化菌伴生菌的生理学及电化学特性,并探究该菌株对甲烷氧化过程的影响。[方法] 使用高通量测序技术解析甲烷氧化富集物的菌群结构,采用稀释涂布法、平板划线法分离甲烷氧化菌的伴生菌,通过16S rRNA基因测序技术进行菌株初步鉴定。利用扫描电子显微镜观察菌株形态,并通过气相色谱（gas chromatography,GC）检测伴生菌利用甲烷情况及对甲烷氧化菌氧化甲烷效率的影响。采用双室微生物燃料电池（microbial fuel cells,MFCs）及差分脉冲伏安法（differential pulse voltammetry,DPV）检测菌株的电化学活性。[结果] 黄河三角洲湿地土壤甲烷氧化富集物主要的好氧甲烷氧化菌为甲基杆菌属Methylobacter,同时还发现一些伴生菌。分离得到一株甲醇利用菌P7,其16S rRNA基因序列与恶臭假单胞菌Pseudomonasputida的相似性达99.79%。扫描电镜结果显示该菌株为杆状,长约1.5-2.5μm,宽度约为0.5μm。GC检测结果显示,该菌株不能利用甲烷,但与甲烷氧化菌共培养时,可以促进甲烷氧化（P<0.05）。双室MFCs检测结果显示该菌株具有电活性,最大电流输出密度为28 mA/m²,DPV检测结果显示该菌株主要的氧化峰和还原峰分别位于-0.17 V和-0.25 V。[结论] 本研究从黄河三角洲湿地甲烷氧化富集物中获得一株具有电活性的甲烷氧化菌的伴生菌恶臭假单胞菌Pseudomonas putida P7,该菌株可以促进甲烷氧化。本研究加深了对甲烷氧化过程中伴生菌的生理学特性及功能的认识。     

矿物电子能量协同微生物胞外电子传递与生长代谢

微生物的电子传递过程在生命进化和生物地球化学循环中发挥着关键作用。近年来,随着微生物电子传递研究的深入开展,微生物纳米导线、导电生物被膜及种间电子传递等多种新型的微生物胞外电子传递机制不断被发现,微生物电子传递的距离也从纳米级拓展至厘米级。这些微生物的长距离电子传递过程环环相扣、相互协同,从而构成长距离电子传递网络,并在物质循环和能量转化中共同发挥作用。微生物长距离电子传递网络的结构功能及其调控机制已成为多个学科共同关注的焦点。本文以电子传递的距离为主线,对不同尺度的微生物长距离电子传递过程及网络研究的新进展进行综述,包括纳米尺度的电子传递网络（周质空间和外膜表层）、微米至毫米尺度的电子传递网络（纳米导线、细胞间电子和导电生物被膜）、厘米尺度的电子传递网络（电缆细菌）等,并分析了该研究现存的主要问题和下一步的发展方向,以期为进一步推进微生物长距离电子传递网络理论和应用研究提供科学参考。     

Perturbations both trigger and delay seizures due to generic properties of slow-fast relaxation oscillators

The mechanisms underlying the emergence of seizures are one of the most important unresolved issues in epilepsy research. In this paper, we study how perturbations, exogenous or endogenous, may promote or delay seizure emergence. To this aim, due to the increasingly adopted view of epileptic dynamics in terms of slow-fast systems, we perform a theoretical analysis of the phase response of a generic relaxation oscillator. As relaxation oscillators are effectively bistable systems at the fast time scale, it is intuitive that perturbations of the non-seizing state with a suitable direction and amplitude may cause an immediate transition to seizure. By contrast, and perhaps less intuitively, smaller amplitude perturbations have been found to delay the spontaneous seizure initiation. By studying the isochrons of relaxation oscillators, we show that this is a generic phenomenon, with the size of such delay depending on the slow flow component. Therefore, depending on perturbation amplitudes, frequency and timing, a train of perturbations causes an occurrence increase, decrease or complete suppression of seizures. This dependence lends itself to analysis and mechanistic understanding through methods outlined in this paper. We illustrate this methodology by computing the isochrons, phase response curves and the response to perturbations in several epileptic models possessing different slow vector fields. While our theoretical results are applicable to any planar relaxation oscillator, in the motivating context of epilepsy they elucidate mechanisms of triggering and abating seizures, thus suggesting stimulation strategies with effects ranging from mere delaying to full suppression of seizures.     

Numerical Study of Cattaneo-Christov Heat Flux Model for Viscoelastic Flow Due to an Exponentially Stretching Surface

This work deals with the flow and heat transfer in upper-convected Maxwell fluid above an exponentially stretching surface. Cattaneo-Christov heat flux model is employed for the formulation of the energy equation. This model can predict the effects of thermal relaxation time on the boundary layer. Similarity approach is utilized to normalize the governing boundary layer equations. Local similarity solutions are achieved by shooting approach together with fourth-fifth-order Runge-Kutta integration technique and Newton’s method. Our computations reveal that fluid temperature has inverse relationship with the thermal relaxation time. Further the fluid velocity is a decreasing function of the fluid relaxation time. A comparison of Fourier’s law and the Cattaneo-Christov’s law is also presented. Present attempt even in the case of Newtonian fluid is not yet available in the literature.     

A nonlinear single-mode structure in a plasma with anisotropic temperature

An exact solution is derived to the equations of vortex electron anisotropic hydrodynamics for a plasma that is unstable against the Weibel instability driven by the electron temperature anisotropy. This solution describes saturation of the Weibel instability in the single-mode regime with an arbitrary wavelength and corresponds to a standing helical wave of magnetic perturbations in which the amplitude of the generated magnetic field varies periodically over time. The longitudinal and transverse (with respect to the rotating anisotropy axis) plasma temperatures are subject to the same periodic variations. In this case, the maximum magnetic field energy can be on the order of the plasma thermal energy.

     

Hydration and packing along the folding pathway of SH3 domains by pressure-dependent NMR

The volumetric properties associated with protein folding transitions reflect changes in protein packing and hydration of the states that participate in the folding reaction. Here, NMR spin relaxation techniques are employed to probe the folding-unfolding kinetics of two SH3 domains as a function of pressure so that the changes in partial molar volumes along the folding pathway can be measured. The two domains fold with rates that differ by approximately 3 orders of magnitude, so their folding dynamics must be probed using different NMR relaxation experiments. In the case of the drkN SH3 domain that folds via a two-state mechanism on a time scale of seconds, nitrogen magnetization exchange spectroscopy is employed, while for the G48M mutant of the Fyn SH3 domain where the folding occurs on the millisecond time scale (three-step reaction), relaxation dispersion experiments are utilized. The NMR methodology is extremely sensitive to even small changes in equilibrium and rate constants, so reliable estimates of partial molar volumes can be obtained using low pressures (1-120 bar), thus minimizing perturbations to any of the states along the folding reaction coordinate. The volumetric data that were obtained are consistent with a similar folding mechanism for both SH3 domains, involving early chain compaction to states that are at least partially hydrated. This work emphasizes the role of NMR spin relaxation in studying dynamic processes over a wide range of time scales.     

Valinomycin-mediated ion transport through neutral lipid membranes: Influence of hydrocarbon chain length and temperature

Summary Stationary electrical conductance experiments together with nonstationary relaxation experiments allow a quantitative determination of rate constants describing carrier-mediated ion transport. Valinomycin-induced ion transport across neutral lipid membranes was studied. The dependence of the transport parameters on the chain length of the lipid molecules, on the kind of alkali ion, and on the temperature was determined. The relaxation time the current following a voltage jump shows a marked increase with decreasing temperature or with increasing chain length of the lipid molecules. This variation of is interpreted on the basis of a varying membrane fluidity. It is shown that under favorable circumstances the equilibrium constant of complex formation in the aqueous phase may be obtained from membrane experiments. Furthermore, the kinetics of exchange of valinomycin between membrane and water was studied. We found a marked influence of the totus surrounding the black film on the kinetics as well as on the total amount of valinomycin molecules in the membrane. The problem of location of the free carrier molecules inside the membrane is discussed.