Plasma kinetic theory

Kinetic theory studies the macroscopic properties of large numbers of particles, starting from their (classical) equations of motion while the thermodynamics describes the equilibrium behavior of macroscopic objects in terms of concepts such as work, heat, and entropy. The phenomenological laws of thermodynamics tell us how these quantities are constrained as a system approaches its equilibrium. At the microscopic level, we know that these systems are composed of particles (atoms, particles), whose interactions and dynamics are reasonably well understood in terms of more fundamental theories. If these microscopic descriptions are complete, we should be able to account for the macroscopic behavior, i.e. derive the laws governing the macroscopic state functions in equilibrium. Kinetic theory attempts to achieve this objective. In particular, we shall try to answer the following questions [1]: How can we define equilibrium for a system of moving particles? Do all systems naturally evolve towards an equilibrium state? What is the time evolution of a system that is not quite in equilibrium?

Global slowing of network oscillations in mouse neocortex by diazepam

SCHEFFZUK, C. , KUKUSHKA, V. , VYSSOTSKI, A. L. , DRAGUHN, A. , TORT, A. B. L. , BRANKACK, J. . Global slowing of network oscillations in mouse neocortex by diazepam. Neuropharmacology , v. 65, p. 123-133, 2013.

Theta-associated high-frequency oscillations (110–160 Hz) in the hippocampus and neocortex

TORT, A. B. L. ; SCHEFFER-TEIXEIRA, R ; Souza, B.C. ; DRAGUHN, A. ; BRANKACK, J. . Theta-associated high-frequency oscillations (110-160 Hz) in the hippocampus and neocortex. Progress in Neurobiology , v. 100, p. 1-14, 2013.

Selective Coupling between Theta Phase and Neocortical Fast Gamma Oscillations during REM-Sleep in Mice

TORT, A. B. L. ; SCHEFFER-TEIXEIRA, R ; Souza, B.C. ; DRAGUHN, A. ; BRANKACK, J. . Theta-associated high-frequency oscillations (110-160 Hz) in the hippocampus and neocortex. Progress in Neurobiology , v. 100, p. 1-14, 2013.

Kinetic study of solid phase demineralization by weak acids in one-step enzymatic bio-refinery of shrimp cuticles

We describe a one-step bio-refinery process for shrimp composites by-products. Its originality lies in a simple rapid (6 h) biotechnological cuticle fragmentation process that recovers all major compounds (chitins, peptides and minerals in particular calcium). The process consists of a controlled exogenous enzymatic proteolysis in a food-grade acidic medium allowing chitin purification (solid phase), and recovery of peptides and minerals (liquid phase). At a pH of between 3.5 and 4, protease activity is effective, and peptides are preserved. Solid phase demineralization kinetics were followed for phosphoric, hydrochloric, acetic, formic and citric acids with pKa ranging from 2.1 to 4.76. Formic acid met the initial aim of (i) 99 % of demineralization yield and (ii) 95 % deproteinization yield at a pH close to 3.5 and a molar ratio of 1.5. The proposed one-step process is proven to be efficient. To formalize the necessary elements for the future optimization of the process, two models to predict shell demineralization kinetics were studied, one based on simplified physical considerations and a second empirical one. The first model did not accurately describe the kinetics for times exceeding 30 minutes, the empirical one performed adequately.

Calcium oscillations

Changes in cellular calcium concentration control a wide range of physiological processes, from the subsecond release of synaptic neurotransmitters, to the regulation of gene expression over months or years. Calcium can also trigger cell death through both apoptosis and necrosis, and so the regulation of cellular calcium concentration must be tightly controlled through the concerted action of pumps, channels and buffers that transport calcium into and out of the cell cytoplasm. A hallmark of cellular calcium signalling is its spatiotemporal complexity: stimulation of cells by a hormone or neurotransmitter leads to oscillations in cytoplasmic calcium concentration that can vary markedly in time course, amplitude, frequency, and spatial range. In this chapter we review some of the biological roles of calcium, the experimental characterisation of complex dynamic changes in calcium concentration, and attempts to explain this complexity using computational models. We consider the "toolkit" of cellular proteins which influence calcium concentration, describe mechanistic models of key elements of the toolkit, and fit these into the framework of whole cell models of calcium oscillations and waves. Finally, we will touch on recent efforts to use stochastic modelling to elucidate elementary calcium signal events, and how these may evolve into global signals.

Increase in Hippocampal Theta Oscillations during Spatial Decision Making

The processing of spatial and mnemonic information is believed to depend on hippocampal theta oscillations (5–12 Hz). However, in rats both the power and the frequency of the theta rhythm are modulated by locomotor activity, which is a major confounding factor when estimating its cognitive correlates. Previous studies have suggested that hippocampal theta oscillations support decision-making processes. In this study, we investigated to what extent spatial decision making modulates hippocampal theta oscillations when controlling for variations in locomotion speed. We recorded local field potentials from the CA1 region of rats while animals had to choose one arm to enter for reward (goal) in a four-arm radial maze. We observed prominent theta oscillations during the decision-making period of the task, which occurred in the center of the maze before animals deliberately ran through an arm toward goal location. In speed-controlled analyses, theta power and frequency were higher during the decision period when compared to either an intertrial delay period (also at the maze center), or to the period of running toward goal location. In addition, theta activity was higher during decision periods preceding correct choices than during decision periods preceding incorrect choices. Altogether, our data support a cognitive function for the hippocampal theta rhythm in spatial decision making

Slow Oscillations in the Mouse Hippocampus Entrained by Nasal Respiration

Different types of network oscillations occur in different behavioral, cognitive, or vigilance states. The rodent hippocampus expresses prominentoscillations atfrequencies between 4 and 12Hz,which are superimposed by phase-coupledoscillations (30 –100Hz).These patterns entrain multineuronal activity over large distances and have been implicated in sensory information processing and memory formation. Here we report a new type of oscillation at near- frequencies (2– 4 Hz) in the hippocampus of urethane-anesthetized mice. The rhythm is highly coherent with nasal respiration and with rhythmic field potentials in the olfactory bulb: hence, we called it hippocampal respiration-induced oscillations. Despite the similarity in frequency range, several features distinguish this pattern from locally generatedoscillations: hippocampal respiration-induced oscillations have a unique laminar amplitude profile, are resistant to atropine, couple differentlytooscillations, and are abolished when nasal airflow is bypassed bytracheotomy. Hippocampal neurons are entrained by both the respiration-induced rhythm and concurrent oscillations, suggesting a direct interaction between endogenous activity in the hippocampus and nasal respiratory inputs. Our results demonstrate that nasal respiration strongly modulates hippocampal network activity in mice, providing a long-range synchronizing signal between olfactory and hippocampal networks.

Asymptotic preserving and time diminishing schemes for rarefied gas dynamic

In this work, we introduce a new class of numerical schemes for rarefied gas dynamic problems described by collisional kinetic equations. The idea consists in reformulating the problem using a micro-macro decomposition and successively in solving the microscopic part by using asymptotic preserving Monte Carlo methods. We consider two types of decompositions, the first leading to the Euler system of gas dynamics while the second to the Navier-Stokes equations for the macroscopic part. In addition, the particle method which solves the microscopic part is designed in such a way that the global scheme becomes computationally less expensive as the solution approaches the equilibrium state as opposite to standard methods for kinetic equations which computational cost increases with the number of interactions. At the same time, the statistical error due to the particle part of the solution decreases as the system approach the equilibrium state. This causes the method to degenerate to the sole solution of the macroscopic hydrodynamic equations (Euler or Navier-Stokes) in the limit of infinite number of collisions. In a last part, we will show the behaviors of this new approach in comparisons to standard Monte Carlo techniques for solving the kinetic equation by testing it on different problems which typically arise in rarefied gas dynamic simulations.

Three-dimensional kinetic simulations of active suspensions: effect of chemotaxis and steric interaction

In this work, the effects of chemotaxis and steric interactions in active suspensions are analyzed by extending the kinetic model proposed by Saintillan and Shelley [1, 2]. In this model, a conservation equation for the active particle configuration is coupled to the Stokes equation for the flow arising from the force dipole exerted by the particles on the fluid. The fluid flow equations are solved spectrally and the conservation equation is solved by second-order finite differencing in space and second-order Adams-Bashforth time marching. First, the dynamics in suspensions of oxytactic run-and-tumble bacteria confined in thin liquid films surrounded by air is investigated. These bacteria modify their tumbling behavior by making temporal comparisons of the oxygen concentration, and, on average, swim towards high concentrations of oxygen. The kinetic model proposed by Saintillan and Shelley [1, 2] is modified to include run-and-tumble effects and oxygentaxis. The spatio-temporal dynamics of the oxygen and bacterial concentration are analyzed. For small film thicknesses, there is a weak migration of bacteria to the boundaries, and the oxygen concentration is high inside the film as a result of diffusion; both bacterial and oxygen concentrations quickly reach steady states. Above a critical film thickness (approximately 200 micron), a transition to chaotic dynamics is observed and is characterized by turbulent-like 3D motion, the formation of bacterial plumes, enhanced oxygen mixing and transport into the film, and hydrodynamic velocities of magnitudes up to 7 times the single bacterial swimming speed. The simulations demonstrate that the combined effects of hydrodynamic interactions and oxygentaxis create collective three-dimensional instabilities which enhances oxygen availability for the bacteria. Our simulation results are consistent with the experimental findings of Sokolov et al. [3], who also observed a similar transition with increasing film thickness. Next, the dynamics in concentrated suspensions of active self-propelled particles in a 3D periodic domain are analyzed. We modify the kinetic model of Saintillan and Shelley [1, 2] by including an additional nematic alignment torque proportional to the local concentration in the equation for the rotational velocity of the particles, causing them to align locally with their neighbors (Doi and Edwards [4]). Large-scale three- dimensional simulations show that, in the presence of such a torque both pusher and puller suspensions are unstable to random fluctuations and are characterized by highly nematic structures. Detailed measures are defined to quantify the degree and direction of alignment, and the effects of steric interactions on pattern formation will be presented. Our analysis shows that steric interactions have a destabilizing effect in active suspensions.

A kinetic energy budget and internal instabilities in the Fine Resolution Antarctic Model

An energy analysis of the Fine Resolution Antarctic Model (FRAM) reveals the instability processes in the model. The main source of time-mean kinetic energy is the wind stress and the main sink is transfer to mean potential energy. The wind forcing thus helps maintain the density structure. Transient motions result from internal instabilities of the Bow rather than seasonal variations of the forcing. Baroclinic instability is found to be an important mechanism in FRAM. The highest values of available potential energy are found in the western boundary regions as well as in the Antarctic Circumpolar Current (ACC) region. All subregions with predominantly zonal flow are found to be baroclinically unstable. The observed deficit of eddy kinetic energy in FRAM occurs as a result of the high lateral friction, which decreases the growth rates of the most unstable waves. This high friction is required for the numerical stability of the model and can only be made smaller by using a finer horizontal resolution. A grid spacing of at least 10-15 km would be required to resolve the most unstable waves in the southern part of the domain. Barotropic instability is also found to be important for the total domain balance. The inverse transfer (that is, transfer from eddy to mean kinetic energy) does not occur anywhere, except in very localized tight jets in the ACC. The open boundary condition at the northern edge of the model domain does not represent a significant source or sink of eddy variability. However, a large exchange between internal and external mode energies is found to occur. It is still unclear how these boundary conditions affect the dynamics of adjacent regions.

Sequestering of Fe and Pb ions from Wastewater by Canarium schweinfurthii after carbonization and chemical treatment: Isothermal and Kinetic Modeling

In this paper agricultural waste; Canarium schweinfurthii was explored for the sequestering of Fe and Pb ions from wastewater solution after carbonization and chemical treatment at 400oC. Optimum time of 30 and 150 min with percentage removal of 95 and 98% at optimum pH of 2 and 6 was obtained for Fe and Pb ions. Kinetics model followed pseudofirst order as sum of absolute error (EABS) between Qe and Qc greater than that of pseudo second order. Parameters evaluated from isothermal equation (Freundlich and Langmuir) showed that KL and QO for Fe > Pb and R2 for Langmuir> Freundlich. The study reveals the suitability of the adsorbent for sequestering of Fe and Pb ions from industrial wastewater.

Sloshing and slamming oscillations in collapsible channel flow

We consider laminar high-Reynolds-number flow through a finite-length planar channel, where a portion of one wall is replaced by a thin massless elastic membrane that is held under longitudinal tension T and subject to an external pressure distribution. The flow is driven by a fixed pressure drop along the full length of the channel. We investigate the global stability of two-dimensional Poiseuille flow using a method of matched local eigenfunction expansions, which is compared to direct numerical simulations. We trace the neutral stability curve of the primary oscillatory instability of the system, illustrating a transition from high-frequency ‘sloshing’ oscillations at high T to vigorous ‘slamming’ motion at low T . Small-amplitude sloshing at high T can be captured using a low-order eigenmode truncation involving four surface-based modes in the compliant segment of the channel coupled to Womersley flow in the rigid segments. At lower tensions, we show that hydrodynamic modes contribute increasingly to the global instability and we demonstrate a change in the mechanism of energy transfer from the mean flow, with viscous effects being destabilising. Simulations of finite-amplitude oscillations at low T reveal a generic slamming motion, in which the the flexible membrane is drawn close to the opposite rigid wall before rapidly recovering. A simple model is used to demonstrate how fluid inertia in the downstream rigid channel segment, coupled to membrane curvature downstream of the moving constriction, together control slamming dynamics.

Kinetic Analysis of Gill (Na+,K+)-ATPase Activity in Selected Ontogenetic Stages of the Amazon River Shrimp, (Decapoda, Palaemonidae): Interactions at ATP- and Cation-Binding Sites

We investigated modulation by ATP, Mg2+, Na+, K+ and NH4 (+) and inhibition by ouabain of (Na+,K+)-ATPase activity in microsomal homogenates of whole zoeae I and decapodid III (formerly zoea IX) and whole-body and gill homogenates of juvenile and adult Amazon River shrimps, . (Na+,K+)-ATPase-specific activity was increased twofold in decapodid III compared to zoea I, juveniles and adults, suggesting an important role in this ontogenetic stage. The apparent affinity for ATP ( (M) = 0.09 +/- A 0.01 mmol L-1) of the decapodid III (Na+,K+)-ATPase, about twofold greater than the other stages, further highlights this relevance. Modulation of (Na+,K+)-ATPase activity by K+ also revealed a threefold greater affinity for K+ ( (0.5) = 0.91 +/- A 0.04 mmol L-1) in decapodid III than in other stages; NH4 (+) had no modulatory effect. The affinity for Na+ ( (0.5) = 13.2 +/- A 0.6 mmol L-1) of zoea I (Na+,K+)-ATPase was fourfold less than other stages. Modulation by Na+, Mg2+ and NH4 (+) obeyed cooperative kinetics, while K+ modulation exhibited Michaelis-Menten behavior. Rates of maximal Mg2+ stimulation of ouabain-insensitive ATPase activity differed in each ontogenetic stage, suggesting that Mg2+-stimulated ATPases other than (Na+,K+)-ATPase are present. Ouabain inhibition suggests that, among the various ATPase activities present in the different stages, Na+-ATPase may be involved in the ontogeny of osmoregulation in larval The NH4 (+)-stimulated, ouabain-insensitive ATPase activity seen in zoea I and decapodid III may reflect a stage-specific means of ammonia excretion since functional gills are absent in the early larval stages.