Center for Gyrokinetic/MHD Hybrid Simulation of Energetic Particle Physics in Toroidal Plasmas (CSEPP). Final report

International Nuclear Information System (INIS)

Chen, Yang

2012-01-01

At Colorado University-Boulder the primary task is to extend our gyrokinetic Particle-in-Cell simulation of tokamak micro-turbulence and transport to the area of energetic particle physics. We have implemented a gyrokinetic ion/massless fluid electron hybrid model in the global δf-PIC code GEM, and benchmarked the code with analytic results on the thermal ion radiative damping rate of Toroidal Alfven Eigenmodes (TAE) and with mode frequency and spatial structure from eigenmode analysis. We also performed nonlinear simulations of both a single-n mode (n is the toroidal mode number) and multiple-n modes, and in the case of single-n, benchmarked the code on the saturation amplitude vs. particle collision rate with analytical theory. Most simulations use the f method for both ions species, but we have explored the full-f method for energetic particles in cases where the burst amplitude of the excited instabilities is large as to cause significant re-distribution or loss of the energetic particles. We used the hybrid model to study the stability of high-n TAEs in ITER. Our simulations show that the most unstable modes in ITER lie in the rage of 10 α (0) = 0.7% for the fully shaped ITER equilibrium. We also carried nonlinear simulations of the most unstable n = 15 mode and found that the saturation amplitude for the nominal ITER discharge is too low to cause large redistribution or loss of alpha particles. To include kinetic electron effects in the hybrid model we have studied a kinetic electron closure scheme for the fluid electron model. The most important element of the closure scheme is a complete Ohm's law for the parallel electric field E || , derived by combining the quasi-neutrality condition, the Ampere's equation and the v || moment of the gyrokinetic equations. A discretization method for the closure scheme is studied in detail for a three-dimensional shear-less slab plasma. It is found that for long-wavelength shear Alfven waves the kinetic closure scheme

Detailed study of spontaneous rotation generation in diverted H-mode plasma using the full-f gyrokinetic code XGC1

Science.gov (United States)

Seo, Janghoon; Chang, C. S.; Ku, S.; Kwon, J. M.; Yoon, E. S.

2013-10-01

The Full-f gyrokinetic code XGC1 is used to study the details of toroidal momentum generation in H-mode plasma. Diverted DIII-D geometry is used, with Monte Carlo neutral particles that are recycled at the limiter wall. Nonlinear Coulomb collisions conserve particle, momentum, and energy. Gyrokinetic ions and adiabatic electrons are used in the present simulation to include the effects from ion gyrokinetic turbulence and neoclassical physics, under self-consistent radial electric field generation. Ion orbit loss physics is automatically included. Simulations show a strong co-Ip flow in the H-mode layer at outside midplane, similarly to the experimental observation from DIII-D and ASDEX-U. The co-Ip flow in the edge propagates inward into core. It is found that the strong co-Ip flow generation is mostly from neoclassical physics. On the other hand, the inward momentum transport is from turbulence physics, consistently with the theory of residual stress from symmetry breaking. Therefore, interaction between the neoclassical and turbulence physics is a key factor in the spontaneous momentum generation.

Gyrokinetic simulation of particle and heat transport in the presence of Wide orbits and strong profile variations in the Edge plasma

International Nuclear Information System (INIS)

Heikkinen, J.A.; Henriksson, S.; Janhunen, S.; Kiviniemi, T.P.; Ogando, F.

2006-01-01

A full f nonlinear 5D gyrokinetic electrostatic particle-in-cell code ELMFIRE using an implicit direct solution method for ion polarization drift and electron parallel velocity response to electric field and its validation are described. The developed code is applied for transport analysis in a tokamak plasma at steep pressure gradient. The role of turbulence and neoclassical equilibrium in determining the flux surface averaged radial electric field component are investigated, as well as the role of the latter in affecting the saturation level of the turbulence. (copyright 2006 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

Visual interrogation of gyrokinetic particle simulations

International Nuclear Information System (INIS)

Jones, Chad; Ma, K-L; Sanderson, Allen; Myers, Lee Roy Jr

2007-01-01

Gyrokinetic particle simulations are critical to the study of anomalous energy transport associated with plasma microturbulence in magnetic confinement fusion experiments. The simulations are conducted on massively parallel computers and produce large quantities of particles, variables, and time steps, thus presenting a formidable challenge to data analysis tasks. We present two new visualization techniques for scientists to improve their understanding of the time-varying, multivariate particle data. One technique allows scientists to examine correlations in multivariate particle data with tightly coupled views of the data in both physical space and variable space, and to visually identify and track features of interest. The second technique, built into SCIRun, allows scientists to perform range-based queries over a series of time slices and visualize the resulting particles using glyphs. The ability to navigate the multiple dimensions of the particle data, as well as query individual or a collection of particles, enables scientists to not only validate their simulations but also discover new phenomena in their data

Memory-efficient optimization of Gyrokinetic particle-to-grid interpolation for multicore processors

Energy Technology Data Exchange (ETDEWEB)

Madduri, Kamesh [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Williams, Samuel [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Ethier, Stephane [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Oliker, Leonid [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Shalf, John [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Strohmaier, Erich [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Yelicky, Katherine [Univ. of California, Berkeley, CA (United States)

2009-01-01

We present multicore parallelization strategies for the particle-to-grid interpolation step in the Gyrokinetic Toroidal Code (GTC), a 3D particle-in-cell (PIC) application to study turbulent transport in magnetic-confinement fusion devices. Particle-grid interpolation is a known performance bottleneck in several PIC applications. In GTC, this step involves particles depositing charges to a 3D toroidal mesh, and multiple particles may contribute to the charge at a grid point. We design new parallel algorithms for the GTC charge deposition kernel, and analyze their performance on three leading multicore platforms. We implement thirteen different variants for this kernel and identify the best-performing ones given typical PIC parameters such as the grid size, number of particles per cell, and the GTC-specific particle Larmor radius variation. We find that our best strategies can be 2x faster than the reference optimized MPI implementation, and our analysis provides insight into desirable architectural features for high-performance PIC simulation codes.

Recent advances in gyrokinetic full-f particle simulation of medium sized Tokamaks with ELMFIRE

International Nuclear Information System (INIS)

Janhunen, S.J.; Kiviniemi, T.P.; Korpio, T.; Leerink, S.; Nora, M.; Heikkinen, J.A.; Ogando, F.

2010-01-01

Large-scale kinetic simulations of toroidal plasmas based on first principles are called for in studies of transition from low to high confinement mode and internal transport barrier formation in the core plasma. Such processes are best observed and diagnosed in detached plasma conditions in mid-sized tokamaks, so gyrokinetic simulations for these conditions are warranted. A first principles test-particle based kinetic model ELMFIRE[1] has been developed and used in interpretation[1,2] of FT-2 and DIII-D experiments. In this work we summarize progress in Cyclone (DIII-D core) and ASDEX Upgrade pedestal region simulations, and show that in simulations the choice of adiabatic electrons results in quenching of turbulence (copyright 2010 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

Recent advances in gyrokinetic full-f particle simulation of medium sized Tokamaks with ELMFIRE

Energy Technology Data Exchange (ETDEWEB)

Janhunen, S.J.; Kiviniemi, T.P.; Korpio, T.; Leerink, S.; Nora, M. [Helsinki University of Technology, Euratom-Tekes Association, Espoo (Finland); Heikkinen, J.A. [VTT, Euratom-Tekes Association, Espoo (Finland); Ogando, F. [Helsinki University of Technology, Euratom-Tekes Association, Espoo (Finland); Universidad Nacional de Educacion a Distancia, Madrid (Spain)

2010-05-15

Large-scale kinetic simulations of toroidal plasmas based on first principles are called for in studies of transition from low to high confinement mode and internal transport barrier formation in the core plasma. Such processes are best observed and diagnosed in detached plasma conditions in mid-sized tokamaks, so gyrokinetic simulations for these conditions are warranted. A first principles test-particle based kinetic model ELMFIRE[1] has been developed and used in interpretation[1,2] of FT-2 and DIII-D experiments. In this work we summarize progress in Cyclone (DIII-D core) and ASDEX Upgrade pedestal region simulations, and show that in simulations the choice of adiabatic electrons results in quenching of turbulence (copyright 2010 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

Thermostatted delta f

International Nuclear Information System (INIS)

Krommes, J.A.

2000-01-01

The delta f simulation method is revisited. Statistical coarse-graining is used to rigorously derive the equation for the fluctuation delta f in the particle distribution. It is argued that completely collisionless simulation is incompatible with the achievement of true statistically steady states with nonzero turbulent fluxes because the variance of the particle weights w grows with time. To ensure such steady states, it is shown that for dynamically collisionless situations a generalized thermostat or W-stat may be used in lieu of a full collision operator to absorb the flow of entropy to unresolved fine scales in velocity space. The simplest W-stat can be implemented as a self-consistently determined, time-dependent damping applied to w. A precise kinematic analogy to thermostatted nonequilibrium molecular dynamics (NEMD) is pointed out, and the justification of W-stats for simulations of turbulence is discussed. An extrapolation procedure is proposed such that the long-time, steady-state, collisionless flux can be deduced from several short W-statted runs with large effective collisionality, and a numerical demonstration is given

Partially linearized algorithms in gyrokinetic particle simulation

Energy Technology Data Exchange (ETDEWEB)

Dimits, A.M.; Lee, W.W.

1990-10-01

In this paper, particle simulation algorithms with time-varying weights for the gyrokinetic Vlasov-Poisson system have been developed. The primary purpose is to use them for the removal of the selected nonlinearities in the simulation of gradient-driven microturbulence so that the relative importance of the various nonlinear effects can be assessed. It is hoped that the use of these procedures will result in a better understanding of the transport mechanisms and scaling in tokamaks. Another application of these algorithms is for the improvement of the numerical properties of the simulation plasma. For instance, implementations of such algorithms (1) enable us to suppress the intrinsic numerical noise in the simulation, and (2) also make it possible to regulate the weights of the fast-moving particles and, in turn, to eliminate the associated high frequency oscillations. Examples of their application to drift-type instabilities in slab geometry are given. We note that the work reported here represents the first successful use of the weighted algorithms in particle codes for the nonlinear simulation of plasmas.

Partially linearized algorithms in gyrokinetic particle simulation

International Nuclear Information System (INIS)

Dimits, A.M.; Lee, W.W.

1990-10-01

In this paper, particle simulation algorithms with time-varying weights for the gyrokinetic Vlasov-Poisson system have been developed. The primary purpose is to use them for the removal of the selected nonlinearities in the simulation of gradient-driven microturbulence so that the relative importance of the various nonlinear effects can be assessed. It is hoped that the use of these procedures will result in a better understanding of the transport mechanisms and scaling in tokamaks. Another application of these algorithms is for the improvement of the numerical properties of the simulation plasma. For instance, implementations of such algorithms (1) enable us to suppress the intrinsic numerical noise in the simulation, and (2) also make it possible to regulate the weights of the fast-moving particles and, in turn, to eliminate the associated high frequency oscillations. Examples of their application to drift-type instabilities in slab geometry are given. We note that the work reported here represents the first successful use of the weighted algorithms in particle codes for the nonlinear simulation of plasmas

Towards the optimization of a gyrokinetic Particle-In-Cell (PIC) code on large-scale hybrid architectures

International Nuclear Information System (INIS)

Ohana, N; Lanti, E; Tran, T M; Brunner, S; Hariri, F; Villard, L; Jocksch, A; Gheller, C

2016-01-01

With the aim of enabling state-of-the-art gyrokinetic PIC codes to benefit from the performance of recent multithreaded devices, we developed an application from a platform called the “PIC-engine” [1, 2, 3] embedding simplified basic features of the PIC method. The application solves the gyrokinetic equations in a sheared plasma slab using B-spline finite elements up to fourth order to represent the self-consistent electrostatic field. Preliminary studies of the so-called Particle-In-Fourier (PIF) approach, which uses Fourier modes as basis functions in the periodic dimensions of the system instead of the real-space grid, show that this method can be faster than PIC for simulations with a small number of Fourier modes. Similarly to the PIC-engine, multiple levels of parallelism have been implemented using MPI+OpenMP [2] and MPI+OpenACC [1], the latter exploiting the computational power of GPUs without requiring complete code rewriting. It is shown that sorting particles [3] can lead to performance improvement by increasing data locality and vectorizing grid memory access. Weak scalability tests have been successfully run on the GPU-equipped Cray XC30 Piz Daint (at CSCS) up to 4,096 nodes. The reduced time-to-solution will enable more realistic and thus more computationally intensive simulations of turbulent transport in magnetic fusion devices. (paper)

Three dimensional [delta]f simulations of beams in the SSC

Energy Technology Data Exchange (ETDEWEB)

Koga, J.; Tajima, T. (Texas Univ., Austin, TX (United States). Inst. for Fusion Studies); Machida, S. (Superconducting Super Collider Lab., Dallas, TX (United States))

1993-02-01

A three dimensional [delta]f strong-strong algorithm has been developed to apply to the study of such effects as space charge and beam-beam interaction phenomena in the Superconducting Super Collider (SSC). The algorithm is obtained from the merging of the particle tracking code Simpsons used for 3-dimensional space charge effects and a [delta]f code. The [delta]f method is used to follow the evolution of the non-gaussian part of the beam distribution. The advantages of this method are twofold. First, the Simpsons code utilizes a realistic accelerator model including synchrotron oscillations and energy ramping in 6-dimensional phase space with electromagnetic fields of the beams calculated using a realistic 3-dimensional field solver. Second, the beams are evolving in the fully self-consistent strong-strong sense where finite particle fluctuation noise is greatly reduced as opposed to the weak-strong models where one beam is fixed.

Three dimensional {delta}f simulations of beams in the SSC

Energy Technology Data Exchange (ETDEWEB)

Koga, J.; Tajima, T. [Texas Univ., Austin, TX (United States). Inst. for Fusion Studies; Machida, S. [Superconducting Super Collider Lab., Dallas, TX (United States)

1993-02-01

A three dimensional {delta}f strong-strong algorithm has been developed to apply to the study of such effects as space charge and beam-beam interaction phenomena in the Superconducting Super Collider (SSC). The algorithm is obtained from the merging of the particle tracking code Simpsons used for 3-dimensional space charge effects and a {delta}f code. The {delta}f method is used to follow the evolution of the non-gaussian part of the beam distribution. The advantages of this method are twofold. First, the Simpsons code utilizes a realistic accelerator model including synchrotron oscillations and energy ramping in 6-dimensional phase space with electromagnetic fields of the beams calculated using a realistic 3-dimensional field solver. Second, the beams are evolving in the fully self-consistent strong-strong sense where finite particle fluctuation noise is greatly reduced as opposed to the weak-strong models where one beam is fixed.

Fully Electromagnetic Nonlinear Gyrokinetic Equations for Tokamak Edge Turbulence

International Nuclear Information System (INIS)

Hahm, T.S.; Wang, Lu; Madsen, J.

2008-01-01

An energy conserving set of the fully electromagnetic nonlinear gyrokinetic Vlasov equation and Maxwell's equations, which is applicable to both L-mode turbulence with large amplitude and H-mode turbulence in the presence of high E x B shear has been derived. The phase-space action variational Lie perturbation method ensures the preservation of the conservation laws of the underlying Vlasov-Maxwell system. Our generalized ordering takes ρ i θi ∼ L E ∼ L p i is the thermal ion Larmor radius and ρ θi = B/B θ ρ i ), as typically observed in the tokamak H-mode edge, with L E and L p being the radial electric field and pressure gradient lengths. We take k # perpendicular# ρ i ∼ 1 for generality, and keep the relative fluctuation amplitudes e(delta)φ/T i ∼ (delta)B/B up to the second order. Extending the electrostatic theory in the presence of high E x B shear [Hahm, Phys. Plasmas 3, 4658 (1996)], contributions of electromagnetic fluctuations to the particle charge density and current are explicitly evaluated via pull-back transformation from the gyrocenter distribution function in the gyrokinetic Maxwell's equation

Alfven Waves in Gyrokinetic Plasmas

International Nuclear Information System (INIS)

Lee, W.W.; Qin, H.

2003-01-01

A brief comparison of the properties of Alfven waves that are based on the gyrokinetic description with those derived from the MHD equations is presented. The critical differences between these two approaches are the treatment of the ion polarization effects. As such, the compressional Alfven waves in a gyrokinetic plasma can be eliminated through frequency ordering, whereas geometric simplifications are needed to decouple the shear Alfven waves from the compressional Alfven waves within the context of MHD. Theoretical and numerical procedures of using gyrokinetic particle simulation for studying microturbulence and kinetic-MHD physics including finite Larmor radius effects are also presented

A Generalized Weight-Based Particle-In-Cell Simulation Scheme

International Nuclear Information System (INIS)

Lee, W.W.; Jenkins, T.G.; Ethier, S.

2010-01-01

A generalized weight-based particle simulation scheme suitable for simulating magnetized plasmas, where the zeroth-order inhomogeneity is important, is presented. The scheme is an extension of the perturbative simulation schemes developed earlier for particle-in-cell (PIC) simulations. The new scheme is designed to simulate both the perturbed distribution ((delta)f) and the full distribution (full-F) within the same code. The development is based on the concept of multiscale expansion, which separates the scale lengths of the background inhomogeneity from those associated with the perturbed distributions. The potential advantage for such an arrangement is to minimize the particle noise by using (delta)f in the linear stage stage of the simulation, while retaining the flexibility of a full-F capability in the fully nonlinear stage of the development when signals associated with plasma turbulence are at a much higher level than those from the intrinsic particle noise.

Fully non-linear multi-species Fokker-Planck-Landau collisions for gyrokinetic particle-in-cell simulations of fusion plasma

Science.gov (United States)

Hager, Robert; Yoon, E. S.; Ku, S.; D'Azevedo, E. F.; Worley, P. H.; Chang, C. S.

2015-11-01

We describe the implementation, and application of a time-dependent, fully nonlinear multi-species Fokker-Planck-Landau collision operator based on the single-species work of Yoon and Chang [Phys. Plasmas 21, 032503 (2014)] in the full-function gyrokinetic particle-in-cell codes XGC1 [Ku et al., Nucl. Fusion 49, 115021 (2009)] and XGCa. XGC simulations include the pedestal and scrape-off layer, where significant deviations of the particle distribution function from a Maxwellian can occur. Thus, in order to describe collisional effects on neoclassical and turbulence physics accurately, the use of a non-linear collision operator is a necessity. Our collision operator is based on a finite volume method using the velocity-space distribution functions sampled from the marker particles. Since the same fine configuration space mesh is used for collisions and the Poisson solver, the workload due to collisions can be comparable to or larger than the workload due to particle motion. We demonstrate that computing time spent on collisions can be kept affordable by applying advanced parallelization strategies while conserving mass, momentum, and energy to reasonable accuracy. We also show results of production scale XGCa simulations in the H-mode pedestal and compare to conventional theory. Work supported by US DOE OFES and OASCR.

Verification of gyrokinetic particle simulation of current-driven instability in fusion plasmas. II. Resistive tearing mode

International Nuclear Information System (INIS)

Liu, Dongjian; Zhang, Wenlu; McClenaghan, Joseph; Wang, Jiaqi; Lin, Zhihong

2014-01-01

Global gyrokinetic particle simulation of resistive tearing modes has been developed and verified in the gyrokinetic toroidal code (GTC). GTC linear simulations in the fluid limit of the kink-tearing and resistive tearing modes in the cylindrical geometry agree well with the resistive magnetohydrodynamic eigenvalue and initial value codes. Ion kinetic effects are found to reduce the radial width of the tearing modes. GTC simulations of the resistive tearing modes in the toroidal geometry find that the toroidicity reduces the growth rates

A new hybrid-Lagrangian numerical scheme for gyrokinetic simulation of tokamak edge plasma

Energy Technology Data Exchange (ETDEWEB)

Ku, S., E-mail: sku@pppl.gov [Princeton Plasma Physics Laboratory, Princeton University, Princeton, NJ 08543 (United States); Hager, R.; Chang, C.S. [Princeton Plasma Physics Laboratory, Princeton University, Princeton, NJ 08543 (United States); Kwon, J.M. [National Fusion Research Institute (Korea, Republic of); Parker, S.E. [University of Colorado Boulder (United States)

2016-06-15

In order to enable kinetic simulation of non-thermal edge plasmas at a reduced computational cost, a new hybrid-Lagrangian δf scheme has been developed that utilizes the phase space grid in addition to the usual marker particles, taking advantage of the computational strengths from both sides. The new scheme splits the particle distribution function of a kinetic equation into two parts. Marker particles contain the fast space-time varying, δf, part of the distribution function and the coarse-grained phase-space grid contains the slow space-time varying part. The coarse-grained phase-space grid reduces the memory-requirement and the computing cost, while the marker particles provide scalable computing ability for the fine-grained physics. Weights of the marker particles are determined by a direct weight evolution equation instead of the differential form weight evolution equations that the conventional delta-f schemes use. The particle weight can be slowly transferred to the phase space grid, thereby reducing the growth of the particle weights. The non-Lagrangian part of the kinetic equation – e.g., collision operation, ionization, charge exchange, heat-source, radiative cooling, and others – can be operated directly on the phase space grid. Deviation of the particle distribution function on the velocity grid from a Maxwellian distribution function – driven by ionization, charge exchange and wall loss – is allowed to be arbitrarily large. The numerical scheme is implemented in the gyrokinetic particle code XGC1, which specializes in simulating the tokamak edge plasma that crosses the magnetic separatrix and is in contact with the material wall.

Three dimensional [delta][ital f] simulations of beams in the SSC

Energy Technology Data Exchange (ETDEWEB)

Koga, J.; Tajima, T. (Institute for Fusion Studies, The University of Texas at Austin, Austin, Texas 78712-1060 (United States)); Machida, S. (SSC Laboratory, 2550 Beckleymeade Avenue, Dallas, Texas 75237 (United States))

1993-12-25

A three dimensional [delta][ital f] strong-strong algorithm has been developed to apply to the study of such effects as space charge and beam-beam interaction phenomena in the Superconducting Super Collider (SSC). The algorithm is obtained from the merging of the particle tracking code Simpsons used for 3 dimensional space charge effects and a [delta][ital f] code. The [delta][ital f] method is used to follow the evolution of the non-gaussian part of the beam distribution. The advantages of this method are twofold. First, the Simpsons code utilizes a realistic accelerator model including synchrotron oscillations and energy ramping in 6 dimensional phase space with electromagnetic fields of the beams calculated using a realistic 3 dimensional field solver. Second, the beams are evolving in the fully self-consistent strong-strong sense with finite particle fluctuation noise is greatly reduced as opposed to the weak-strong models where one beam is fixed.

Gyrokinetic modelling of the quasilinear particle flux for plasmas with neutral-beam fuelling

Science.gov (United States)

Narita, E.; Honda, M.; Nakata, M.; Yoshida, M.; Takenaga, H.; Hayashi, N.

2018-02-01

A quasilinear particle flux is modelled based on gyrokinetic calculations. The particle flux is estimated by determining factors, namely, coefficients of off-diagonal terms and a particle diffusivity. In this paper, the methodology to estimate the factors is presented using a subset of JT-60U plasmas. First, the coefficients of off-diagonal terms are estimated by linear gyrokinetic calculations. Next, to obtain the particle diffusivity, a semi-empirical approach is taken. Most experimental analyses for particle transport have assumed that turbulent particle fluxes are zero in the core region. On the other hand, even in the stationary state, the plasmas in question have a finite turbulent particle flux due to neutral-beam fuelling. By combining estimates of the experimental turbulent particle flux and the coefficients of off-diagonal terms calculated earlier, the particle diffusivity is obtained. The particle diffusivity should reflect a saturation amplitude of instabilities. The particle diffusivity is investigated in terms of the effects of the linear instability and linear zonal flow response, and it is found that a formula including these effects roughly reproduces the particle diffusivity. The developed framework for prediction of the particle flux is flexible to add terms neglected in the current model. The methodology to estimate the quasilinear particle flux requires so low computational cost that a database consisting of the resultant coefficients of off-diagonal terms and particle diffusivity can be constructed to train a neural network. The development of the methodology is the first step towards a neural-network-based particle transport model for fast prediction of the particle flux.

Gyrokinetic simulation of finite-β plasmas on parallel architectures

International Nuclear Information System (INIS)

Reynders, J.V.W.

1993-01-01

Much research exists on the linear and non-linear properties of plasma microinstabilities induced by density and temperature gradients. There has been an interest in the electromagnetic or finite-β effects on these microinstabilities. This thesis focuses on the finite-β modification of an ion temperature gradient (ITG) driven microinstability in a two-dimensional shearless and sheared-slab geometries. A gyrokinetic model is employed in the numerical and analytic studies of this instability. Chapter 1 introduces the electromagnetic gyrokinetic model employed in the numerical and analytic studies of the ITG instability. Some discussion of the Klimontovich particle representation of the gyrokinetic Vlasov equation and a multiple scale model of the background plasma gradient is presented. Chapter 2 details the computational issues facing an electromagnetic gyrokinetic particle simulation of the ITG mode. An electromagnetic extension of the partially linearized algorithm is presented with a comparison of quiet particle initialization routines. Chapter 3 presents and compares algorithms for the gyrokinetic particle simulation technique on SIMD and MIMD computing platforms. Chapter 4 discusses electromagnetic gyrokinetic fluctuation theory and provides a comparison of analytic and numerical results. Chapter 5 contains a linear and a non-linear three-wave coupling analysis of the finite-β modified ITG mode in a shearless slab geometry. Comparisons are made with linear and partially linearized gyrokinetic simulation results. Chapter 6 presents results from a finite-β modified ITG mode in a sheared slab geometry. The linear dispersion relation is derived and results from an integral eigenvalue code are presented. Comparisons are made with the gyrokinetic particle code in a variety of limits with both adiabatic and non-adiabatic electrons. Evidence of ITG driven microtearing is presented

Gyrokinetic linearized Landau collision operator

DEFF Research Database (Denmark)

Madsen, Jens

2013-01-01

, which is important in multiple ion-species plasmas. Second, the equilibrium operator describes drag and diffusion of the magnetic field aligned component of the vorticity associated with the E×B drift. Therefore, a correct description of collisional effects in turbulent plasmas requires the equilibrium......The full gyrokinetic electrostatic linearized Landau collision operator is calculated including the equilibrium operator, which represents the effect of collisions between gyrokinetic Maxwellian particles. First, the equilibrium operator describes energy exchange between different plasma species...... operator, even for like-particle collisions....

Gyrokinetic simulation of internal kink modes

International Nuclear Information System (INIS)

Naitou, Hiroshi; Tsuda, Kenji; Lee, W.W.; Sydora, R.D.

1995-05-01

Internal disruption in a tokamak has been simulated using a three-dimensional magneto-inductive gyrokinetic particle code. The code operates in both the standard gyrokinetic mode (total-f code) and the fully nonlinear characteristic mode (δf code). The latter, a recent addition, is a quiet low noise algorithm. The computational model represents a straight tokamak with periodic boundary conditions in the toroidal direction. The plasma is initially uniformly distributed in a square cross section with perfectly conducting walls. The linear mode structure of an unstable m = 1 (poloidal) and n = 1 (toroidal) kinetic internal kink mode is clearly observed, especially in the δf code. The width of the current layer around the x-point, where magnetic reconnection occurs, is found to be close to the collisionless electron skin depth. This is consistent with the theory in which electron inertia has a dominant role. The nonlinear behavior of the mode is found to be quite similar for both codes. Full reconnection in the Alfven time scale is observed along with the electrostatic potential structures created during the full reconnection phase. The E x B drift due to this electrostatic potential dominates the nonlinear phase of the development after the full reconnection

Discrete particle noise in particle-in-cell simulations of plasma microturbulence

International Nuclear Information System (INIS)

Nevins, W.M.; Hammett, G.W.; Dimits, A.M.; Dorland, W.; Shumaker, D.E.

2005-01-01

Recent gyrokinetic simulations of electron temperature gradient (ETG) turbulence with the global particle-in-cell (PIC) code GTC [Z. Lin et al., Proceedings of the 20th Fusion Energy Conference, Vilamoura, Portugal, 2004 (IAEA, Vienna, 2005)] yielded different results from earlier flux-tube continuum code simulations [F. Jenko and W. Dorland, Phys. Rev. Lett. 89, 225001 (2002)] despite similar plasma parameters. Differences between the simulation results were attributed to insufficient phase-space resolution and novel physics associated with global simulation models. The results of the global PIC code are reproduced here using the flux-tube PIC code PG3EQ [A. M. Dimits et al., Phys. Rev. Lett. 77, 71 (1996)], thereby eliminating global effects as the cause of the discrepancy. The late-time decay of the ETG turbulence and the steady-state heat transport observed in these PIC simulations are shown to result from discrete particle noise. Discrete particle noise is a numerical artifact, so both these PG3EQ simulations and, by inference, the GTC simulations that they reproduced have little to say about steady-state ETG turbulence and the associated anomalous heat transport. In the course of this work several diagnostics are developed to retrospectively test whether a particular PIC simulation is dominated by discrete particle noise

Nonlinear gyrokinetic Maxwell-Vlasov equations using magnetic coordinates

International Nuclear Information System (INIS)

Brizard, A.

1988-09-01

A gyrokinetic formalism using magnetic coordinates is used to derive self-consistent, nonlinear Maxwell-Vlasov equations that are suitable for particle simulation studies of finite-β tokamak microturbulence and its associated anomalous transport. The use of magnetic coordinates is an important feature of this work as it introduces the toroidal geometry naturally into our gyrokinetic formalism. The gyrokinetic formalism itself is based on the use of the Action-variational Lie perturbation method of Cary and Littlejohn, and preserves the Hamiltonian structure of the original Maxwell-Vlasov system. Previous nonlinear gyrokinetic sets of equations suitable for particle simulation analysis have considered either electrostatic and shear-Alfven perturbations in slab geometry, or electrostatic perturbations in toroidal geometry. In this present work, fully electromagnetic perturbations in toroidal geometry are considered. 26 refs

Gyrokinetic full f analysis of electric field dynamics and poloidal velocity in the FT2-tokamak configuration

International Nuclear Information System (INIS)

Leerink, S.; Heikkinen, J. A.; Janhunen, S. J.; Kiviniemi, T. P.; Nora, M.; Ogando, F.

2008-01-01

The ELMFIRE gyrokinetic simulation code has been used to perform full f simulations of the FT-2 tokamak. The dynamics of the radial electric field and the creation of poloidal velocity in the presence of turbulence are presented.

Three-dimensional gyrokinetic particle-in-cell simulation of plasmas on a massively parallel computer: Final report on LDRD Core Competency Project, FY 1991--FY 1993

International Nuclear Information System (INIS)

Byers, J.A.; Williams, T.J.; Cohen, B.I.; Dimits, A.M.

1994-01-01

One of the programs of the Magnetic fusion Energy (MFE) Theory and computations Program is studying the anomalous transport of thermal energy across the field lines in the core of a tokamak. We use the method of gyrokinetic particle-in-cell simulation in this study. For this LDRD project we employed massively parallel processing, new algorithms, and new algorithms, and new formal techniques to improve this research. Specifically, we sought to take steps toward: researching experimentally-relevant parameters in our simulations, learning parallel computing to have as a resource for our group, and achieving a 100 x speedup over our starting-point Cray2 simulation code's performance

Fluid and gyrokinetic modelling of particle transport in plasmas with hollow density profiles

International Nuclear Information System (INIS)

Tegnered, D; Oberparleiter, M; Nordman, H; Strand, P

2016-01-01

Hollow density profiles occur in connection with pellet fuelling and L to H transitions. A positive density gradient could potentially stabilize the turbulence or change the relation between convective and diffusive fluxes, thereby reducing the turbulent transport of particles towards the center, making the fuelling scheme inefficient. In the present work, the particle transport driven by ITG/TE mode turbulence in regions of hollow density profiles is studied by fluid as well as gyrokinetic simulations. The fluid model used, an extended version of the Weiland transport model, Extended Drift Wave Model (EDWM), incorporates an arbitrary number of ion species in a multi-fluid description, and an extended wavelength spectrum. The fluid model, which is fast and hence suitable for use in predictive simulations, is compared to gyrokinetic simulations using the code GENE. Typical tokamak parameters are used based on the Cyclone Base Case. Parameter scans in key plasma parameters like plasma β, R/L T , and magnetic shear are investigated. It is found that β in particular has a stabilizing effect in the negative R/L n region, both nonlinear GENE and EDWM show a decrease in inward flux for negative R/L n and a change of direction from inward to outward for positive R/L n . This might have serious consequences for pellet fuelling of high β plasmas. (paper)

Pullback Transformations in Gyrokinetic Theory

International Nuclear Information System (INIS)

Qin, H.; Tang, W.M.

2003-01-01

The Pullback transformation of the distribution function is a key component of the gyrokinetic theory. In this paper, a systematic treatment of this subject is presented, and results from applications of the uniform framework developed are reviewed. The focus is on providing a clear exposition of the basic formalism which arises from the existence of three distinct coordinate systems in gyrokinetic theory. The familiar gyrocenter coordinate system, where the gyromotion is decoupled from the rest of particle's dynamics, is non-canonical and non-fabric. On the other hand, Maxwell's equations, which are needed to complete a kinetic system, are initially only defined in the fabric laboratory phase space coordinate system. The pullback transformations provide a rigorous connection between the distribution functions in gyrocenter coordinates and Maxwell's equations in laboratory phase space coordinates. This involves the generalization of the usual moment integrals originally defined on the cotangent fiber of the phase space to the moment integrals on a general 6D symplectic manifold, is shown to be an important step in the proper formulation of gyrokinetic theory. The resultant systematic treatment of the moment integrals enabled by the pullback transformation. Without this vital element, a number of prominent physics features, such as the presence of the compressional Alfven wave and a proper description of the gyrokinetic equilibrium, cannot be readily recovered

Neoclassical simulation of tokamak plasmas using the continuum gyrokinetic code TEMPEST.

Science.gov (United States)

Xu, X Q

2008-07-01

We present gyrokinetic neoclassical simulations of tokamak plasmas with a self-consistent electric field using a fully nonlinear (full- f ) continuum code TEMPEST in a circular geometry. A set of gyrokinetic equations are discretized on a five-dimensional computational grid in phase space. The present implementation is a method of lines approach where the phase-space derivatives are discretized with finite differences, and implicit backward differencing formulas are used to advance the system in time. The fully nonlinear Boltzmann model is used for electrons. The neoclassical electric field is obtained by solving the gyrokinetic Poisson equation with self-consistent poloidal variation. With a four-dimensional (psi,theta,micro) version of the TEMPEST code, we compute the radial particle and heat fluxes, the geodesic-acoustic mode, and the development of the neoclassical electric field, which we compare with neoclassical theory using a Lorentz collision model. The present work provides a numerical scheme for self-consistently studying important dynamical aspects of neoclassical transport and electric field in toroidal magnetic fusion devices.

Effects of collisions on conservation laws in gyrokinetic field theory

Energy Technology Data Exchange (ETDEWEB)

Sugama, H.; Nunami, M. [National Institute for Fusion Science, Toki 509-5292 (Japan); Department of Fusion Science, SOKENDAI (The Graduate University for Advanced Studies), Toki 509-5292 (Japan); Watanabe, T.-H. [Department of Physics, Nagoya University, Nagoya 464-8602 (Japan)

2015-08-15

Effects of collisions on conservation laws for toroidal plasmas are investigated based on the gyrokinetic field theory. Associating the collisional system with a corresponding collisionless system at a given time such that the two systems have the same distribution functions and electromagnetic fields instantaneously, it is shown how the collisionless conservation laws derived from Noether's theorem are modified by the collision term. Effects of the external source term added into the gyrokinetic equation can be formulated similarly with the collisional effects. Particle, energy, and toroidal momentum balance equations including collisional and turbulent transport fluxes are systematically derived using a novel gyrokinetic collision operator, by which the collisional change rates of energy and canonical toroidal angular momentum per unit volume in the gyrocenter space can be given in the conservative forms. The ensemble-averaged transport equations of particles, energy, and toroidal momentum given in the present work are shown to include classical, neoclassical, and turbulent transport fluxes which agree with those derived from conventional recursive formulations.

Turbulent transport of toroidal angular momentum in low flow gyrokinetics

International Nuclear Information System (INIS)

Parra, Felix I; Catto, Peter J

2010-01-01

We derive a self-consistent equation for the turbulent transport of toroidal angular momentum in tokamaks in the low flow ordering that only requires solving gyrokinetic Fokker-Planck and quasineutrality equations correct to second order in an expansion on the gyroradius over scale length. We also show that according to our orderings the long wavelength toroidal rotation and the long wavelength radial electric field satisfy the neoclassical relation that gives the toroidal rotation as a function of the radial electric field and the radial gradients of pressure and temperature. Thus, the radial electric field can be solved for once the toroidal rotation is calculated from the transport of toroidal angular momentum. Unfortunately, even though this methodology only requires a gyrokinetic model correct to second order in gyroradius over scale length, current gyrokinetic simulations are only valid to first order. To overcome this difficulty, we exploit the smallish ratio B p /B, where B is the total magnetic field and B p is its poloidal component. When B p /B is small, the usual first order gyrokinetic equation provides solutions that are accurate enough to employ for our expression for the transport of toroidal angular momentum. We show that current δf and full f simulations only need small corrections to achieve this accuracy. Full f simulations, however, are still unable to determine the long wavelength, radial electric field from the quasineutrality equation.

Full-f XGC1 gyrokinetic study of improved ion energy confinement from impurity stabilization of ITG turbulence

Science.gov (United States)

Kim, Kyuho; Kwon, Jae-Min; Chang, C. S.; Seo, Janghoon; Ku, S.; Choe, W.

2017-06-01

Flux-driven full-f gyrokinetic simulations are performed to study carbon impurity effects on the ion temperature gradient (ITG) turbulence and ion thermal transport in a toroidal geometry. Employing the full-f gyrokinetic code XGC1, both main ions and impurities are evolved self-consistently including turbulence and neoclassical physics. It is found that the carbon impurity profile self-organizes to form an inwardly peaked density profile, which weakens the ITG instabilities and reduces the overall fluctuations and ion thermal transport. A stronger reduction appears in the low frequency components of the fluctuations. The global structure of E × B flow also changes, resulting in the reduction of global avalanche like transport events in the impure plasma. Detailed properties of impurity transport are also studied, and it is revealed that both the inward neoclassical pinch and the outward turbulent transport are equally important in the formation of the steady state impurity profile.

Improvements on nonlinear gyrokinetic particle simulations based on δf-discretization scheme

International Nuclear Information System (INIS)

Zorat, R.; Tessarotto, M.

1998-01-01

In this work various issues regarding the definition of improved theoretical models appropriate to describe the dynamics of confined magnetoplasmas by particle simulation methods are proposed. These concern in particular an improved non linear δf discretization scheme and the treatment of binary, i.e. Coulomb, and collective interactions. (orig.)

Gyrokinetic simulations of ETG Turbulence*

Science.gov (United States)

Nevins, William

2005-10-01

Recent gyrokinetic simulations of electron temperature gradient (ETG) turbulence [1,2] produced different results despite similar plasma parameters. Ref.[1] differs from Ref.[2] in that [1] eliminates magnetically trapped particles ( r/R=0 ), while [2] retains magnetically trapped particles ( r/R 0.18 ). Differences between [1] and [2] have been attributed to insufficient phase-space resolution and novel physics associated with toroidicity and/or global simulations[2]. We have reproduced the results reported in [2] using a flux-tube, particle-in-cell (PIC) code, PG3EQ[3], thereby eliminating global effects as the cause of the discrepancy. We observe late-time decay of ETG turbulence and the steady-state heat transport in agreement with [2], and show this results from discrete particle noise. Discrete particle noise is a numerical artifact, so both the PG3EQ simulations reported here and those reported in Ref.[2] have little to say about steady-state ETG turbulence and the associated anomalous electron heat transport. Our attempts to benchmark PIC and continuum[4] codes at the plasma parameters used in Ref.[2] produced very large, intermittent transport. We will present an alternate benchmark point for ETG turbulence, where several codes reproduce the same transport levels. Parameter scans about this new benchmark point will be used to investigate the parameter dependence of ETG transport and to elucidate saturation mechanisms proposed in Refs.[1,2] and elsewhere[5-7].*In collaboration with A. Dimits (LLNL), J. Candy, C. Estrada-Mila (GA), W. Dorland (U of MD), F. Jenko, T. Dannert (Max-Planck Institut), and G. Hammett (PPPL). Work at LLNL performed for US DOE under Contract W7405-ENG-48.[1] F. Jenko and W. Dorland, PRL 89, 225001 (2002).[2] Z. Lin et al, 2004 Sherwood Mtg.; 2004 TTF Mtg.; Fusion Energy 2004 (IAEA, Vienna, 2005); Bull. Am. Phys. Soc. (November, 2004); 2005 TTF Mtg.; 2005 Sherwood Mtg.; Z. Lin, et al, Phys. Plasmas 12, 056125 (2005). [3] A.M. Dimits

Global gyrokinetic and fluid hybrid simulations of tokamaks and stellarators

Energy Technology Data Exchange (ETDEWEB)

Cole, Michael David John

2016-07-15

Achieving commercial production of electricity by magnetic confinement fusion requires improvements in energy and particle confinement. In order to better understand and optimise confinement, numerical simulations of plasma phenomena are useful. One particularly challenging regime is that in which long wavelength MHD phenomena interact with kinetic phenomena. In such a regime, global electromagnetic gyrokinetic simulations are necessary. In this regime, computational requirements have been excessive for Eulerian methods, while Particle-in-Cell (PIC) methods have been particularly badly affected by the 'cancellation problem', a numerical problem resulting from the structure of the electromagnetic gyrokinetic equations. A number of researchers have been working on mitigating this problem with some significant successes. Another alternative to mitigating the problem is to move to a hybrid system of fluid and gyrokinetic equations. At the expense of reducing the physical content of the numerical model, particularly electron kinetic physics, it is possible in this way to perform global electromagnetic PIC simulations retaining ion gyrokinetic effects but eliminating the cancellation problem. The focus of this work has been the implementation of two such hybrid models into the gyrokinetic code EUTERPE. The two models treat electrons and the entire bulk plasma respectively as a fluid. Both models are additionally capable of considering the self-consistent interaction of an energetic ion species, described gyrokinetically, with the perturbed fields. These two models have been successfully benchmarked in linear growth rate and frequency against other codes for a Toroidal Alfven Eigenmode (TAE) case in both the linear and non-linear regimes. The m=1 internal kink mode, which is particularly challenging in terms of the fully gyrokinetic cancellation problem, has also been successfully benchmarked using the hybrid models with the MHD eigenvalue code CKA. Non

Global gyrokinetic and fluid hybrid simulations of tokamaks and stellarators

International Nuclear Information System (INIS)

Cole, Michael David John

2016-01-01

Achieving commercial production of electricity by magnetic confinement fusion requires improvements in energy and particle confinement. In order to better understand and optimise confinement, numerical simulations of plasma phenomena are useful. One particularly challenging regime is that in which long wavelength MHD phenomena interact with kinetic phenomena. In such a regime, global electromagnetic gyrokinetic simulations are necessary. In this regime, computational requirements have been excessive for Eulerian methods, while Particle-in-Cell (PIC) methods have been particularly badly affected by the 'cancellation problem', a numerical problem resulting from the structure of the electromagnetic gyrokinetic equations. A number of researchers have been working on mitigating this problem with some significant successes. Another alternative to mitigating the problem is to move to a hybrid system of fluid and gyrokinetic equations. At the expense of reducing the physical content of the numerical model, particularly electron kinetic physics, it is possible in this way to perform global electromagnetic PIC simulations retaining ion gyrokinetic effects but eliminating the cancellation problem. The focus of this work has been the implementation of two such hybrid models into the gyrokinetic code EUTERPE. The two models treat electrons and the entire bulk plasma respectively as a fluid. Both models are additionally capable of considering the self-consistent interaction of an energetic ion species, described gyrokinetically, with the perturbed fields. These two models have been successfully benchmarked in linear growth rate and frequency against other codes for a Toroidal Alfven Eigenmode (TAE) case in both the linear and non-linear regimes. The m=1 internal kink mode, which is particularly challenging in terms of the fully gyrokinetic cancellation problem, has also been successfully benchmarked using the hybrid models with the MHD eigenvalue code CKA. Non-linear simulations

SciDAC GSEP: Gyrokinetic Simulation of Energetic Particle Turbulence and Transport

Energy Technology Data Exchange (ETDEWEB)

Lin, Zhihong [Univ. of California, Irvine, CA (United States)

2017-12-30

Energetic particle (EP) confinement is a key physics issue for burning plasma experiment ITER, the crucial next step in the quest for clean and abundant energy, since ignition relies on self-heating by energetic fusion products (α-particles). Due to the strong coupling of EP with burning thermal plasmas, plasma confinement property in the ignition regime is one of the most uncertain factors when extrapolating from existing fusion devices to the ITER tokamak. EP population in current tokamaks are mostly produced by auxiliary heating such as neutral beam injection (NBI) and radio frequency (RF) heating. Remarkable progress in developing comprehensive EP simulation codes and understanding basic EP physics has been made by two concurrent SciDAC EP projects GSEP funded by the Department of Energy (DOE) Office of Fusion Energy Science (OFES), which have successfully established gyrokinetic turbulence simulation as a necessary paradigm shift for studying the EP confinement in burning plasmas. Verification and validation have rapidly advanced through close collaborations between simulation, theory, and experiment. Furthermore, productive collaborations with computational scientists have enabled EP simulation codes to effectively utilize current petascale computers and emerging exascale computers. We review here key physics progress in the GSEP projects regarding verification and validation of gyrokinetic simulations, nonlinear EP physics, EP coupling with thermal plasmas, and reduced EP transport models. Advances in high performance computing through collaborations with computational scientists that enable these large scale electromagnetic simulations are also highlighted. These results have been widely disseminated in numerous peer-reviewed publications including many Phys. Rev. Lett. papers and many invited presentations at prominent fusion conferences such as the biennial International Atomic Energy Agency (IAEA) Fusion Energy Conference and the annual meeting of the

On push-forward representations in the standard gyrokinetic model

International Nuclear Information System (INIS)

Miyato, N.; Yagi, M.; Scott, B. D.

2015-01-01

Two representations of fluid moments in terms of a gyro-center distribution function and gyro-center coordinates, which are called push-forward representations, are compared in the standard electrostatic gyrokinetic model. In the representation conventionally used to derive the gyrokinetic Poisson equation, the pull-back transformation of the gyro-center distribution function contains effects of the gyro-center transformation and therefore electrostatic potential fluctuations, which is described by the Poisson brackets between the distribution function and scalar functions generating the gyro-center transformation. Usually, only the lowest order solution of the generating function at first order is considered to explicitly derive the gyrokinetic Poisson equation. This is true in explicitly deriving representations of scalar fluid moments with polarization terms. One also recovers the particle diamagnetic flux at this order because it is associated with the guiding-center transformation. However, higher-order solutions are needed to derive finite Larmor radius terms of particle flux including the polarization drift flux from the conventional representation. On the other hand, the lowest order solution is sufficient for the other representation, in which the gyro-center transformation part is combined with the guiding-center one and the pull-back transformation of the distribution function does not appear

On push-forward representations in the standard gyrokinetic model

Energy Technology Data Exchange (ETDEWEB)

Miyato, N., E-mail: miyato.naoaki@jaea.go.jp; Yagi, M. [Japan Atomic Energy Agency, 2-116 Omotedate, Obuchi, Rokkasho, Aomori 039-3212 (Japan); Scott, B. D. [Max-Planck-Institut für Plasmaphysik, D-85748 Garching (Germany)

2015-01-15

Two representations of fluid moments in terms of a gyro-center distribution function and gyro-center coordinates, which are called push-forward representations, are compared in the standard electrostatic gyrokinetic model. In the representation conventionally used to derive the gyrokinetic Poisson equation, the pull-back transformation of the gyro-center distribution function contains effects of the gyro-center transformation and therefore electrostatic potential fluctuations, which is described by the Poisson brackets between the distribution function and scalar functions generating the gyro-center transformation. Usually, only the lowest order solution of the generating function at first order is considered to explicitly derive the gyrokinetic Poisson equation. This is true in explicitly deriving representations of scalar fluid moments with polarization terms. One also recovers the particle diamagnetic flux at this order because it is associated with the guiding-center transformation. However, higher-order solutions are needed to derive finite Larmor radius terms of particle flux including the polarization drift flux from the conventional representation. On the other hand, the lowest order solution is sufficient for the other representation, in which the gyro-center transformation part is combined with the guiding-center one and the pull-back transformation of the distribution function does not appear.

Beyond scale separation in gyrokinetic turbulence

International Nuclear Information System (INIS)

Garbet, X.; Sarazin, Y.; Grandgirard, V.; Dif-Pradalier, G.; Darmet, G.; Ghendrih, Ph.; Angelino, P.; Bertrand, P.; Besse, N.; Gravier, E.; Morel, P.; Sonnendruecker, E.; Crouseilles, N.; Dischler, J.-M.; Latu, G.; Violard, E.; Brunetti, M.; Brunner, S.; Lapillonne, X.; Tran, T.-M.; Villard, L.; Boulet, M.

2007-01-01

This paper presents the results obtained with a set of gyrokinetic codes based on a semi-Lagrangian scheme. Several physics issues are addressed, namely, the comparison between fluid and kinetic descriptions, the intermittent behaviour of flux driven turbulence and the role of large scale flows in toroidal ITG turbulence. The question of the initialization of full-F simulations is also discussed

Global gyrokinetic simulations of TEM microturbulence

Science.gov (United States)

Vernay, T.; Brunner, S.; Villard, L.; McMillan, B. F.; Jolliet, S.; Bottino, A.; Görler, T.; Jenko, F.

2013-07-01

Global gyrokinetic simulations of electrostatic temperature-gradient-driven trapped-electron-mode (TEM) turbulence using the δf particle-in-cell code ORB5 are presented. The electron response is either fully kinetic or hybrid, i.e. considering kinetic trapped and adiabatic passing electrons. A linear benchmark in the TEM regime against the Eulerian-based code GENE is presented. Two different methods for controlling the numerical noise, based, respectively, on a Krook operator and a so-called coarse-graining approach, are discussed and successfully compared. Both linear and non-linear studies are carried out for addressing the issue of finite-ρ*-effects and finite electron collisionality on TEM turbulence. Electron collisions are found to damp TEMs through the detrapping process, while finite-ρ*-effects turn out to be important in the non-linear regime but very small in the linear regime. Finally, the effects of zonal flows on TEM turbulence are briefly considered as well and shown to be unimportant in the temperature-gradient-driven TEM regime. Consistently, basically no difference is found between linear and non-linear critical electron temperature gradients in the TEM regime.

Benchmark test of drift-kinetic and gyrokinetic codes through neoclassical transport simulations

International Nuclear Information System (INIS)

Satake, S.; Sugama, H.; Watanabe, T.-H.; Idomura, Yasuhiro

2009-09-01

Two simulation codes that solve the drift-kinetic or gyrokinetic equation in toroidal plasmas are benchmarked by comparing the simulation results of neoclassical transport. The two codes are the drift-kinetic δf Monte Carlo code (FORTEC-3D) and the gyrokinetic full- f Vlasov code (GT5D), both of which solve radially-global, five-dimensional kinetic equation with including the linear Fokker-Planck collision operator. In a tokamak configuration, neoclassical radial heat flux and the force balance relation, which relates the parallel mean flow with radial electric field and temperature gradient, are compared between these two codes, and their results are also compared with the local neoclassical transport theory. It is found that the simulation results of the two codes coincide very well in a wide rage of plasma collisionality parameter ν * = 0.01 - 10 and also agree with the theoretical estimations. The time evolution of radial electric field and particle flux, and the radial profile of the geodesic acoustic mode frequency also coincide very well. These facts guarantee the capability of GT5D to simulate plasma turbulence transport with including proper neoclassical effects of collisional diffusion and equilibrium radial electric field. (author)

The low-temperature structures of Hgsub(3-delta)SbF6 and Hgsub(3-delta)TaF6

International Nuclear Information System (INIS)

Tun, Z.; Brown, I.D.

1986-01-01

The Hg chains in both Hgsub(3-delta)SbF 6 and Hgsub(3-delta)TaF 6 order below room temperature. Down to about 190 K the ordering results from the interaction between parallel chains. It is short range and is different for the two compounds. Below 190 K both compounds transform to an isostructural long-range-ordered phase which is driven by the interaction between perpendicular chains. The structure of this phase in both compounds has been determined. Hgsub(3-delta)SbF 6 at 173 K, delta=0.134(1), Msub(r)=810.6(2). It is monoclinic but pseudotetragonal with I4 1 /amd, a=7.655(1), c=12.558(1) A, V=735.9(2) A 3 , Z=4, Dsub(x)=7.314(3) Mg m -3 , graphite-monochromated Mo Kα radiation, lambda=0.71069 A, μ=64.8 mm -1 , F(000)=1337.1(3). Hgsub(3-delta)TaF 6 at 150 K is isostructural but has delta=0.142(1), Msub(r)=868.2(2), a=7.634(1), c=12.610(2) A, V=734.9(2) A, Dsub(x)=7.844(3) Mg m -3 , μ=76.4 mm -1 , F(000)=1422.6(3). Comparison of the low-temperature structures with those at room temperature shows that the thermal contraction results from the shortening of interatomic distances associated with the weak bonds, with the result that the MF 6 (M=Sb, Ta) host lattice shrinks more than the Hg chains. Variation of the atomic displacement parameters with temperature indicates that the large librational displacements of the MF 6 ion result from thermal motion rather than static disorder. (orig.)

Gyrokinetic equivalence

International Nuclear Information System (INIS)

Parra, Felix I; Catto, Peter J

2009-01-01

We compare two different derivations of the gyrokinetic equation: the Hamiltonian approach in Dubin D H E et al (1983 Phys. Fluids 26 3524) and the recursive methodology in Parra F I and Catto P J (2008 Plasma Phys. Control. Fusion 50 065014). We prove that both approaches yield the same result at least to second order in a Larmor radius over macroscopic length expansion. There are subtle differences in the definitions of some of the functions that need to be taken into account to prove the equivalence.

Hamiltonian reductions in plasma physics about intrinsic gyrokinetic

International Nuclear Information System (INIS)

Guillebon de Resnes, L. de

2013-01-01

Gyrokinetic is a key model for plasma micro-turbulence, commonly used for fusion plasmas or small-scale astrophysical turbulence, for instance. The model still suffers from several issues, which could imply to reconsider the equations. This thesis dissertation clarifies three of them. First, one of the coordinates caused questions, both from a physical and from a mathematical point of view; a suitable constrained coordinate is introduced, which removes the issues from the theory and explains the intrinsic structures underlying the questions. Second, the perturbative coordinate transformation for gyrokinetic was computed only at lowest orders; explicit induction relations are obtained to go arbitrary order in the expansion. Third, the introduction of the coupling between the plasma and the electromagnetic field was not completely satisfactory; using the Hamiltonian structure of the dynamics, it is implemented in a more appropriate way, with strong consequences on the gyrokinetic equations, especially about their Hamiltonian structure. In order to address these three main points, several other results are obtained, for instance about the origin of the guiding-center adiabatic invariant, about a very efficient minimal guiding center transformation, or about an intermediate Hamiltonian model between Vlasov-Maxwell and gyrokinetic, where the characteristics include both the slow guiding-center dynamics and the fast gyro-angle dynamics. In addition, various reduction methods are used, introduced or developed, e.g. a Lie-transform of the equations of motion, a lifting method to transfer particle reductions to the corresponding Hamiltonian field dynamics, or a truncation method related both to Dirac's theory of constraints and to a projection onto a Lie-subalgebra. Besides gyrokinetic, this is useful to clarify other Hamiltonian reductions in plasma physics, for instance for incompressible or electrostatic dynamics, for magnetohydrodynamics, or for fluid closures including

Center for Gyrokinetic Particle Simulation of Turbulent Transport in Burning Plasma

International Nuclear Information System (INIS)

Decyk, Viktor K.

2008-01-01

The UCLA work on this grant was to design and help implement an object-oriented version of the GTC code, which is written in Fortran90. The GTC code is the main global gyrokinetic code used in this project, and over the years multiple, incompatible versions have evolved. The reason for this effort is to allow multiple authors to work together on GTC and to simplify future enhancements to GTC. The effort was designed to proceed incrementally. Initially, an upper layer of classes (derived types and methods) was implemented which called the original GTC code 'under the hood.' The derived types pointed to data in the original GTC code, and the methods called the original GTC subroutines. The original GTC code was modified only very slightly. This allowed one to define (and refine) a set of classes which described the important features of the GTC code in a new, more abstract way, with a minimum of implementation. Furthermore, classes could be added one at a time, and at the end of the each day, the code continued to work correctly. This work was done in close collaboration with Y. Nishimura from UC Irvine and Stefan Ethier from PPPL. Ten classes were ultimately defined and implemented: gyrokinetic and drift kinetic particles, scalar and vector fields, a mesh, jacobian, FLR, equilibrium, interpolation, and particles species descriptors. In the second state of this development, some of the scaffolding was removed. The constructors in the class objects now allocated the data and the array data in the original GTC code was removed. This isolated the components and now allowed multiple instantiations of the objects to be created, in particular, multiple ion species. Again, the work was done incrementally, one class at a time, so that the code was always working properly. This work was done in close collaboration with Y. Nishimura and W. Zhang from UC Irvine and Stefan Ethier from PPPL. The third stage of this work was to integrate the capabilities of the various versions of

Gauge-free gyrokinetic theory

Science.gov (United States)

Burby, Joshua; Brizard, Alain

2017-10-01

Test-particle gyrocenter equations of motion play an essential role in the diagnosis of turbulent strongly-magnetized plasmas, and are playing an increasingly-important role in the formulation of kinetic-gyrokinetic hybrid models. Previous gyrocenter models required the knowledge of the perturbed electromagnetic potentials, which are not directly observable quantities (since they are gauge-dependent). A new gauge-free formulation of gyrocenter motion is presented, which enables gyrocenter trajectories to be determined using only measured values of the directly-observable electromagnetic field. Our gauge-free gyrokinetic theory is general enough to allow for gyroradius-scale fluctuations in both the electric and magnetic field. In addition, we provide gauge-free expressions for the charge and current densities produced by a distribution of gyrocenters, which explicitly include guiding-center and gyrocenter polarization and magnetization effects. This research was supported by the U.S. DOE Contract Nos. DE-SC0014032 (AB) and DE-AC05-06OR23100 (JB).

Investigating Particle Transport and Fate in the Sacramento–San Joaquin Delta Using a Particle-Tracking Model

Directory of Open Access Journals (Sweden)

Wim J. Kimmerer

2008-02-01

Full Text Available Movements of pelagic organisms in the tidal freshwater regions of estuaries are sensitive to the movements of water. In the Sacramento-San Joaquin Delta—the tidal freshwater reach of the San Francisco Estuary—such movements are key to losses of fish and other organisms to entrainment in large water-export facilities. We used the Delta Simulation Model-2 hydrodynamic model and its particle tracking model to examine the principal determinants of entrainment losses to the export facilities and how movement of fish through the Delta may be influenced by flow. We modeled 936 scenarios for 74 different conditions of flow, diversions, tides, and removable barriers to address seven questions regarding hydrodynamics and entrainment risk in the Delta. Tide had relatively small effects on fate and residence time of particles. Release location and hydrology interacted to control particle fate and residence time. The ratio of flow into the export facilities to freshwater flow into the Delta (export:inflow or EI ratio was a useful predictor of entrainment probability if the model were allowed to run long enough to resolve particles’ ultimate fate. Agricultural diversions within the Delta increased total entrainment losses and altered local movement patterns. Removable barriers in channels of the southern Delta and gates in the Delta Cross Channel in the northern Delta had minor effects on particles released in the rivers above these channels. A simulation of losses of larval delta smelt showed substantial cumulative losses depending on both inflow and export flow. A simulation mimicking mark–recapture experiments on Chinook salmon smolts suggested that both inflow and export flow may be important factors determining survival of salmon in the upper estuary. To the extent that fish behave passively, this model is probably suitable for describing Delta-wide movement, but it is less suitable for smaller scales or alternative configurations of the Delta.

Diminished self-chaperoning activity of the DeltaF508 mutant of CFTR results in protein misfolding.

Directory of Open Access Journals (Sweden)

Adrian W R Serohijos

2008-02-01

Full Text Available The absence of a functional ATP Binding Cassette (ABC protein called the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR from apical membranes of epithelial cells is responsible for cystic fibrosis (CF. Over 90% of CF patients carry at least one mutant allele with deletion of phenylalanine at position 508 located in the N-terminal nucleotide binding domain (NBD1. Biochemical and cell biological studies show that the DeltaF508 mutant exhibits inefficient biosynthetic maturation and susceptibility to degradation probably due to misfolding of NBD1 and the resultant misassembly of other domains. However, little is known about the direct effect of the Phe508 deletion on the NBD1 folding, which is essential for rational design strategies of cystic fibrosis treatment. Here we show that the deletion of Phe508 alters the folding dynamics and kinetics of NBD1, thus possibly affecting the assembly of the complete CFTR. Using molecular dynamics simulations, we find that meta-stable intermediate states appearing on wild type and mutant folding pathways are populated differently and that their kinetic accessibilities are distinct. The structural basis of the increased misfolding propensity of the DeltaF508 NBD1 mutant is the perturbation of interactions in residue pairs Q493/P574 and F575/F578 found in loop S7-H6. As a proof-of-principle that the S7-H6 loop conformation can modulate the folding kinetics of NBD1, we virtually design rescue mutations in the identified critical interactions to force the S7-H6 loop into the wild type conformation. Two redesigned NBD1-DeltaF508 variants exhibited significantly higher folding probabilities than the original NBD1-DeltaF508, thereby partially rescuing folding ability of the NBD1-DeltaF508 mutant. We propose that these observed defects in folding kinetics of mutant NBD1 may also be modulated by structures separate from the 508 site. The identified structural determinants of increased misfolding propensity of

Metriplectic Gyrokinetics and Discretization Methods for the Landau Collision Integral

Science.gov (United States)

Hirvijoki, Eero; Burby, Joshua W.; Kraus, Michael

2017-10-01

We present two important results for the kinetic theory and numerical simulation of warm plasmas: 1) We provide a metriplectic formulation of collisional electrostatic gyrokinetics that is fully consistent with the First and Second Laws of Thermodynamics. 2) We provide a metriplectic temporal and velocity-space discretization for the particle phase-space Landau collision integral that satisfies the conservation of energy, momentum, and particle densities to machine precision, as well as guarantees the existence of numerical H-theorem. The properties are demonstrated algebraically. These two result have important implications: 1) Numerical methods addressing the Vlasov-Maxwell-Landau system of equations, or its reduced gyrokinetic versions, should start from a metriplectic formulation to preserve the fundamental physical principles also at the discrete level. 2) The plasma physics community should search for a metriplectic reduction theory that would serve a similar purpose as the existing Lagrangian and Hamiltonian reduction theories do in gyrokinetics. The discovery of metriplectic formulation of collisional electrostatic gyrokinetics is strong evidence in favor of such theory and, if uncovered, the theory would be invaluable in constructing reduced plasma models. Supported by U.S. DOE Contract Nos. DE-AC02-09-CH11466 (EH) and DE-AC05-06OR23100 (JWB) and by European Union's Horizon 2020 research and innovation Grant No. 708124 (MK).

Full-f gyrokinetic simulation over a confinement time

Energy Technology Data Exchange (ETDEWEB)

Idomura, Yasuhiro, E-mail: idomura.yasuhiro@jaea.go.jp [Japan Atomic Energy Agency, Kashiwanoha 5-1-5, Kashiwa, Chiba 277-8587 (Japan)

2014-02-15

A long time ion temperature gradient driven turbulence simulation over a confinement time is performed using the full-f gyrokinetic Eulerian code GT5D. The convergence of steady temperature and rotation profiles is examined, and it is shown that the profile relaxation can be significantly accelerated when the simulation is initialized with linearly unstable temperature profiles. In the steady state, the temperature profile and the ion heat diffusivity are self-consistently determined by the power balance condition, while the intrinsic rotation profile is sustained by complicated momentum transport processes without momentum input. The steady turbulent momentum transport is characterized by bursty non-diffusive fluxes, and the resulting turbulent residual stress is consistent with the profile shear stress theory [Y. Camenen et al., “Consequences of profile shearing on toroidal momentum transport,” Nucl. Fusion 51, 073039 (2011)] in which the residual stress depends not only on the profile shear and the radial electric field shear but also on the radial electric field itself. Based on the toroidal angular momentum conservation, it is found that in the steady null momentum transport state, the turbulent residual stress is cancelled by the neoclassical counterpart, which is greatly enhanced in the presence of turbulent fluctuations.

Analysis and optimization of gyrokinetic toroidal simulations on homogenous and heterogenous platforms

International Nuclear Information System (INIS)

Ibrahim, Khaled Z.; Madduri, Kamesh; Williams, Samuel; Wang, Bei; Oliker, Leonid

2013-01-01

The Gyrokinetic Toroidal Code (GTC) uses the particle-in-cell method to efficiently simulate plasma microturbulence. This paper presents novel analysis and optimization techniques to enhance the performance of GTC on large-scale machines. We introduce cell access analysis to better manage locality vs. synchronization tradeoffs on CPU and GPU-based architectures. Finally, our optimized hybrid parallel implementation of GTC uses MPI, OpenMP, and NVIDIA CUDA, achieves up to a 2× speedup over the reference Fortran version on multiple parallel systems, and scales efficiently to tens of thousands of cores.

Gyrokinetic magnetohydrodynamics and the associated equilibria

Science.gov (United States)

Lee, W. W.; Hudson, S. R.; Ma, C. H.

2017-12-01

The gyrokinetic magnetohydrodynamic (MHD) equations, related to the recent paper by W. W. Lee ["Magnetohydrodynamics for collisionless plasmas from the gyrokinetic perspective," Phys. Plasmas 23, 070705 (2016)], and their associated equilibria properties are discussed. This set of equations consists of the time-dependent gyrokinetic vorticity equation, the gyrokinetic parallel Ohm's law, and the gyrokinetic Ampere's law as well as the equations of state, which are expressed in terms of the electrostatic potential, ϕ, and the vector potential, A , and support both spatially varying perpendicular and parallel pressure gradients and the associated currents. The corresponding gyrokinetic MHD equilibria can be reached when ϕ→0 and A becomes constant in time, which, in turn, gives ∇.(J∥+J⊥)=0 and the associated magnetic islands, if they exist. Examples of simple cylindrical geometry are given. These gyrokinetic MHD equations look quite different from the conventional MHD equations, and their comparisons will be an interesting topic in the future.

Including collisions in gyrokinetic tokamak and stellarator simulations

Energy Technology Data Exchange (ETDEWEB)

Kauffmann, Karla

2012-04-10

Particle and heat transport in fusion devices often exceed the neoclassical prediction. This anomalous transport is thought to be produced by turbulence caused by microinstabilities such as ion and electron-temperature-gradient (ITG/ETG) and trapped-electron-mode (TEM) instabilities, the latter ones known for being strongly influenced by collisions. Additionally, in stellarators, the neoclassical transport can be important in the core, and therefore investigation of the effects of collisions is an important field of study. Prior to this thesis, however, no gyrokinetic simulations retaining collisions had been performed in stellarator geometry. In this work, collisional effects were added to EUTERPE, a previously collisionless gyrokinetic code which utilizes the {delta}f method. To simulate the collisions, a pitch-angle scattering operator was employed, and its implementation was carried out following the methods proposed in [Takizuka and Abe 1977, Vernay Master's thesis 2008]. To test this implementation, the evolution of the distribution function in a homogeneous plasma was first simulated, where Legendre polynomials constitute eigenfunctions of the collision operator. Also, the solution of the Spitzer problem was reproduced for a cylinder and a tokamak. Both these tests showed that collisions were correctly implemented and that the code is suited for more complex simulations. As a next step, the code was used to calculate the neoclassical radial particle flux by neglecting any turbulent fluctuations in the distribution function and the electric field. Particle fluxes in the neoclassical analytical regimes were simulated for tokamak and stellarator (LHD) configurations. In addition to the comparison with analytical fluxes, a successful benchmark with the DKES code was presented for the tokamak case, which further validates the code for neoclassical simulations. In the final part of the work, the effects of collisions were investigated for slab and toroidal

3-D electromagnetic plasma particle simulations on the Intel Delta parallel computer

International Nuclear Information System (INIS)

Wang, J.; Liewer, P.C.

1994-01-01

A three-dimensional electromagnetic PIC code has been developed on the 512 node Intel Touchstone Delta MIMD parallel computer. This code is based on the General Concurrent PIC algorithm which uses a domain decomposition to divide the computation among the processors. The 3D simulation domain can be partitioned into 1-, 2-, or 3-dimensional sub-domains. Particles must be exchanged between processors as they move among the subdomains. The Intel Delta allows one to use this code for very-large-scale simulations (i.e. over 10 8 particles and 10 6 grid cells). The parallel efficiency of this code is measured, and the overall code performance on the Delta is compared with that on Cray supercomputers. It is shown that their code runs with a high parallel efficiency of ≥ 95% for large size problems. The particle push time achieved is 115 nsecs/particle/time step for 162 million particles on 512 nodes. Comparing with the performance on a single processor Cray C90, this represents a factor of 58 speedup. The code uses a finite-difference leap frog method for field solve which is significantly more efficient than fast fourier transforms on parallel computers. The performance of this code on the 128 node Cray T3D will also be discussed

Effect of delta wing on the particle flow in a novel gas supersonic separator

DEFF Research Database (Denmark)

Wen, Chuang; Yang, Yan; Walther, Jens Honore

2016-01-01

The present work presents numerical simulations of the complex particle motion in a supersonic separator with a delta wing located in the supersonic flow. The effect of the delta wing on the strong swirling flow is analysed using the Discrete Particle Method. The results show that the delta wings...

SciDAC Center for Gyrokinetic Particle Simulation of Turbulent Transport in Burning Plasmas

Energy Technology Data Exchange (ETDEWEB)

Lin, Zhihong [Univ. of California, Irvine, CA (United States)

2013-12-18

During the first year of the SciDAC gyrokinetic particle simulation (GPS) project, the GPS team (Zhihong Lin, Liu Chen, Yasutaro Nishimura, and Igor Holod) at the University of California, Irvine (UCI) studied the tokamak electron transport driven by electron temperature gradient (ETG) turbulence, and by trapped electron mode (TEM) turbulence and ion temperature gradient (ITG) turbulence with kinetic electron effects, extended our studies of ITG turbulence spreading to core-edge coupling. We have developed and optimized an elliptic solver using finite element method (FEM), which enables the implementation of advanced kinetic electron models (split-weight scheme and hybrid model) in the SciDAC GPS production code GTC. The GTC code has been ported and optimized on both scalar and vector parallel computer architectures, and is being transformed into objected-oriented style to facilitate collaborative code development. During this period, the UCI team members presented 11 invited talks at major national and international conferences, published 22 papers in peer-reviewed journals and 10 papers in conference proceedings. The UCI hosted the annual SciDAC Workshop on Plasma Turbulence sponsored by the GPS Center, 2005-2007. The workshop was attended by about fifties US and foreign researchers and financially sponsored several gradual students from MIT, Princeton University, Germany, Switzerland, and Finland. A new SciDAC postdoc, Igor Holod, has arrived at UCI to initiate global particle simulation of magnetohydrodynamics turbulence driven by energetic particle modes. The PI, Z. Lin, has been promoted to the Associate Professor with tenure at UCI.

Verification of gyrokinetic particle simulation of current-driven instability in fusion plasmas. I. Internal kink mode

Energy Technology Data Exchange (ETDEWEB)

McClenaghan, J.; Lin, Z.; Holod, I.; Deng, W.; Wang, Z. [University of California, Irvine, California 92697 (United States)

2014-12-15

The gyrokinetic toroidal code (GTC) capability has been extended for simulating internal kink instability with kinetic effects in toroidal geometry. The global simulation domain covers the magnetic axis, which is necessary for simulating current-driven instabilities. GTC simulation in the fluid limit of the kink modes in cylindrical geometry is verified by benchmarking with a magnetohydrodynamic eigenvalue code. Gyrokinetic simulations of the kink modes in the toroidal geometry find that ion kinetic effects significantly reduce the growth rate even when the banana orbit width is much smaller than the radial width of the perturbed current layer at the mode rational surface.

Gyrokinetic energy conservation and Poisson-bracket formulation

International Nuclear Information System (INIS)

Brizard, A.

1989-01-01

An integral expression for the gyrokinetic total energy of a magnetized plasma, with general magnetic field configuration perturbed by fully electromagnetic fields, was recently derived through the use of a gyrocenter Lie transformation. It is shown that the gyrokinetic energy is conserved by the gyrokinetic Hamiltonian flow to all orders in perturbed fields. An explicit demonstration that a gyrokinetic Hamiltonian containing quadratic nonlinearities preserves the gyrokinetic energy up to third order is given. The Poisson-bracket formulation greatly facilitates this demonstration with the help of the Jacobi identity and other properties of the Poisson brackets

A fast low-to-high confinement mode bifurcation dynamics in the boundary-plasma gyrokinetic code XGC1

Science.gov (United States)

Ku, S.; Chang, C. S.; Hager, R.; Churchill, R. M.; Tynan, G. R.; Cziegler, I.; Greenwald, M.; Hughes, J.; Parker, S. E.; Adams, M. F.; D'Azevedo, E.; Worley, P.

2018-05-01

A fast edge turbulence suppression event has been simulated in the electrostatic version of the gyrokinetic particle-in-cell code XGC1 in a realistic diverted tokamak edge geometry under neutral particle recycling. The results show that the sequence of turbulent Reynolds stress followed by neoclassical ion orbit-loss driven together conspire to form the sustaining radial electric field shear and to quench turbulent transport just inside the last closed magnetic flux surface. The main suppression action is located in a thin radial layer around ψN≃0.96 -0.98 , where ψN is the normalized poloidal flux, with the time scale ˜0.1 ms.

A minimal collision operator for implementing neoclassical transport in gyrokinetic simulations

International Nuclear Information System (INIS)

Garbet, X.; Dif-Pradalier, G.; Nguyen, C.; Angelino, P.; Sarazin, Y.; Grandgirard, V.; Ghendrih, P.; Samain, A.

2008-01-01

This paper presents a class of collision operators, which reproduce neoclassical transport and comply with the constraints of a full-f global gyrokinetic code. The assessment of these operators is based on a variational entropy method, which allows a fast calculation of the neoclassical diffusivity and poloidal velocity.

GYSELA, a full-f global gyrokinetic Semi-Lagrangian code for ITG turbulence simulations

International Nuclear Information System (INIS)

Grandgirard, V.; Sarazin, Y.; Garbet, X.; Dif-Pradalier, G.; Ghendrih, Ph.; Crouseilles, N.; Latu, G.; Sonnendruecker, E.; Besse, N.; Bertrand, P.

2006-01-01

This work addresses non-linear global gyrokinetic simulations of ion temperature gradient (ITG) driven turbulence with the GYSELA code. The particularity of GYSELA code is to use a fixed grid with a Semi-Lagrangian (SL) scheme and this for the entire distribution function. The 4D non-linear drift-kinetic version of the code already showns the interest of such a SL method which exhibits good properties of energy conservation in non-linear regime as well as an accurate description of fine spatial scales. The code has been upgrated to run 5D simulations of toroidal ITG turbulence. Linear benchmarks and non-linear first results prove that semi-lagrangian codes can be a credible alternative for gyrokinetic simulations

A Numerical Instability in an ADI Algorithm for Gyrokinetics

International Nuclear Information System (INIS)

Belli, E.A.; Hammett, G.W.

2004-01-01

We explore the implementation of an Alternating Direction Implicit (ADI) algorithm for a gyrokinetic plasma problem and its resulting numerical stability properties. This algorithm, which uses a standard ADI scheme to divide the field solve from the particle distribution function advance, has previously been found to work well for certain plasma kinetic problems involving one spatial and two velocity dimensions, including collisions and an electric field. However, for the gyrokinetic problem we find a severe stability restriction on the time step. Furthermore, we find that this numerical instability limitation also affects some other algorithms, such as a partially implicit Adams-Bashforth algorithm, where the parallel motion operator v parallel ∂/∂z is treated implicitly and the field terms are treated with an Adams-Bashforth explicit scheme. Fully explicit algorithms applied to all terms can be better at long wavelengths than these ADI or partially implicit algorithms

Inclusive photoproduction of delta(980) and B(1235) at high xsub(F)

International Nuclear Information System (INIS)

Lassalle, J.C.; Patrick, G.N.; Storr, K.M.; Atkinson, M.; Axon, T.J.; Barberis, D.; Brodbeck, T.J.; Brookes, G.R.; Bunn, J.J.; Bussey, P.J.; Clegg, A.B.; Dainton, J.B.; Davenport, M.; Dickinson, B.; Diekmann, B.; Donnachie, A.; Ellison, R.J.; Flower, P.; Flynn, P.J.; Galbraith, W.; Heinloth, K.; Henderson, R.C.W.; Hughes-Jones, R.E.; Hutton, J.S.; Ibbotson, M.; Jakob, H.P.; Jung, M.; Kumar, B.R.; Laberrigue, J.; Lafferty, G.D.; Lane, J.B.; Levy, J.M.; Liebenau, V.; McClatchey, R.; Mercer, D.; Morris, J.A.G.; Morris, J.V.; Newton, D.; Paterson, C.; Paul, E.; Raine, C.; Reidenbach, M.; Rotscheidt, H.; Schloesser, A.; Sharp, P.H.; Skillicorn, I.O.; Smith, K.M.; Thompson, R.J.; Vaissiere, C. de la; Waite, A.P.; Worsell, M.F.; Yiou, T.P.

1984-01-01

Inclusive photoproduction of deltasup(+-)(980) and Bsup(+-0) (1235) at high xsub(F) is reported. Production of B 0 is largely due to double diffractive dissociation. The charged states are produced as leading particles, their production being described by the quark recombination picture. The relatively strong production of the delta(980) by this process is evidence that it is a anti qanti q state rather than a qqanti qanti q state. (orig.)

Proinflammatory effect of sodium 4-phenylbutyrate in deltaF508-cystic fibrosis transmembrane conductance regulator lung epithelial cells: involvement of extracellular signal-regulated protein kinase 1/2 and c-Jun-NH2-terminal kinase signaling.

Science.gov (United States)

Roque, Telma; Boncoeur, Emilie; Saint-Criq, Vinciane; Bonvin, Elise; Clement, Annick; Tabary, Olivier; Jacquot, Jacky

2008-09-01

Sodium 4-phenylbutyrate (4-PBA) has attracted a great deal of attention in cystic fibrosis (CF) pathology due to its capacity to traffic DeltaF508-cystic fibrosis transmembrane conductance regulator (CFTR) to the cell membrane and restore CFTR chloride function at the plasma membrane of CF lung cells in vitro and in vivo. Using two different DeltaF508-CFTR lung epithelial cell lines (CFBE41o- and IB3-1 cells, characterized with DeltaF508-homozygous and heterozygous genotype, respectively) in vitro, 4-PBA induced an increase of proinflammatory cytokine interleukin (IL)-8 production in a concentration-dependent manner. This 4-PBA-induced IL-8 production was associated with a strong reduction of proteasome and nuclear factor-kappaB transcriptional activities in the two DeltaF508-CFTR lung cells either in a resting state or after tumor necrosis factor-alpha stimulation. In contrast, a strong increase of activator protein-1 transcriptional activity was observed. The inhibition of extracellular signal-regulated protein kinase 1/2 (ERK1/2) by 1,4-diamino-2,3-dicyano-1,4-bis[2-aminophenylthio] butadiene (U0126) and 2-(2-amino-3-methoxyphenyl)-4H-1-benzopyran-4-one (PD98059) and c-Jun-NH(2)-terminal kinase (JNK) mitogen-activated protein kinase (MAPK) by anthra[1,9-cd] pyrazol-6 (2H)-one (SP600125), respectively, was associated with a reduction (2-3.5-fold) of IL-8 production in both DeltaF508-CFTR lung cell lines treated with 4-PBA. No significant change of IL-8 production was observed after an inhibition of p38 MAPK with 4-[4-(4-fluorophenyl)-5-(4-pyridinyl)-1H-imidazol-2-yl] phenol (SB202190). Therefore, we suggest that inhibition of both ERK1/2 and JNK signaling may be a means to strongly reduce 4-PBA-induced IL-8 production in combination with 4-PBA treatment to restore CFTR Cl(-) channel function in lung epithelial cells of patients with CF.

DeltaF508 heterozygosity in cystic fibrosis and susceptibility to asthma

DEFF Research Database (Denmark)

Dahl, Morten; Tybjaerg-Hansen, A; Lange, P

1998-01-01

Cystic fibrosis is a recessive disorder mainly characterised by lung disease. We tested the hypothesis that individuals heterozygous for the common cystic fibrosis deltaF508 mutation are at risk of obstructive pulmonary disease.......Cystic fibrosis is a recessive disorder mainly characterised by lung disease. We tested the hypothesis that individuals heterozygous for the common cystic fibrosis deltaF508 mutation are at risk of obstructive pulmonary disease....

Comparisons of 'Identical' Simulations by the Eulerian Gyrokinetic Codes GS2 and GYRO

Science.gov (United States)

Bravenec, R. V.; Ross, D. W.; Candy, J.; Dorland, W.; McKee, G. R.

2003-10-01

A major goal of the fusion program is to be able to predict tokamak transport from first-principles theory. To this end, the Eulerian gyrokinetic code GS2 was developed years ago and continues to be improved [1]. Recently, the Eulerian code GYRO was developed [2]. These codes are not subject to the statistical noise inherent to particle-in-cell (PIC) codes, and have been very successful in treating electromagnetic fluctuations. GS2 is fully spectral in the radial coordinate while GYRO uses finite-differences and ``banded" spectral schemes. To gain confidence in nonlinear simulations of experiment with these codes, ``apples-to-apples" comparisons (identical profile inputs, flux-tube geometry, two species, etc.) are first performed. We report on a series of linear and nonlinear comparisons (with overall agreement) including kinetic electrons, collisions, and shaped flux surfaces. We also compare nonlinear simulations of a DIII-D discharge to measurements of not only the fluxes but also the turbulence parameters. [1] F. Jenko, et al., Phys. Plasmas 7, 1904 (2000) and refs. therein. [2] J. Candy, J. Comput. Phys. 186, 545 (2003).

Low-noise electromagnetic δf particle-in-cell simulation of electron Bernstein waves

International Nuclear Information System (INIS)

Xiang Nong; Cary, John R.; Barnes, Daniel C.; Carlsson, John

2006-01-01

The conversion of the extraordinary (X) mode to an electron Bernstein wave (EBW) is one way to get rf energy into an overdense plasma. Analysis of this is complex, as the EBW is a fully kinetic wave, and so its linear propagation is described by an intractable integro-differential equation. Nonlinear effects cannot be calculated within this rubric at all. Full particle-in-cell (PIC) simulations cannot be used for these analyses, as the noise levels for reasonable simulation parameters are much greater than the typical rf amplitudes. It is shown that the delta-f computations are effective for this analysis. In particular, the accuracy of those computations has been verified by comparison with full PIC, cold plasma theory, and small gyroradius theory. This computational method is then used to analyze mode conversion in different frequency regimes. In particular, reasonable agreement with the theoretical predictions of Ram and Schultz [Phys. Plasmas 7, 4084 (2000)] in the linear regime is found, where 100% X-B mode conversion has been obtained when the driving frequency is less than twice the electron gyrofrequency. The results show that cold-plasma theory well predicts the mode conversion efficiency, as is consistent with the phase-space picture of mode conversion. From this it can be shown that nearly 100% X-B mode conversion cannot be obtained when the frequency is higher than the electron second harmonic cyclotron frequency

Neoclassical equilibrium in gyrokinetic simulations

International Nuclear Information System (INIS)

Garbet, X.; Dif-Pradalier, G.; Nguyen, C.; Sarazin, Y.; Grandgirard, V.; Ghendrih, Ph.

2009-01-01

This paper presents a set of model collision operators, which reproduce the neoclassical equilibrium and comply with the constraints of a full-f global gyrokinetic code. The assessment of these operators is based on an entropy variational principle, which allows one to perform a fast calculation of the neoclassical diffusivity and poloidal velocity. It is shown that the force balance equation is recovered at lowest order in the expansion parameter, the normalized gyroradius, hence allowing one to calculate correctly the radial electric field. Also, the conventional neoclassical transport and the poloidal velocity are reproduced in the plateau and banana regimes. The advantages and drawbacks of the various model operators are discussed in view of the requirements for neoclassical and turbulent transport.

Gyrokinetic global analysis of ion temperature gradient driven mode in reversed shear tokamaks

International Nuclear Information System (INIS)

Idomura, Y.; Tokuda, S.; Kishimoto, Y.

2003-01-01

A new toroidal gyrokinetic particle code has been developed to study the ion temperature gradient driven (ITG) turbulence in reactor relevant tokamak parameters. We use a new method based on a canonical Maxwellian distribution F CM (P φ , ε, μ), which is defined by three constants of motion in the axisymmetric toroidal system, the canonical angular momentum P φ , the energy ε, and the magnetic moment μ. A quasi-ballooning representation enables linear and nonlinear high-m,n global calculations with a good numerical convergence. Conservation properties are improved by using the optimized loading method. From comprehensive linear global analyses over a wide range of an unstable toroidal mode number spectrum (n=0∼100) in large tokamak parameters (a/ρ ti =320∼460), properties of the ITG modes in reversed shear tokamaks are discussed. In the nonlinear simulation, it is found that a new method based on F CM can simulate a zonal flow damping correctly, and spurious zonal flow oscillations, which are observed in a conventional method based on a local Maxwellian distribution F LM (ψ, ε, μ), do not appear in the nonlinear regime. (author)

Gamma Delta T-Cells Regulate Inflammatory Cell Infiltration of the Lung after Trauma-Hemorrhage

Science.gov (United States)

2015-06-01

suggesting a role for this T- cell subset in both innate and acquired immunity (7, 8). Studies have shown that +% T cells are required for both controlled...increased infiltration of both lymphoid and myeloid cells in WT mice after TH-induced ALI. In parallel to +% T cells , myeloid cells (i.e., monocytes...GAMMA DELTA T CELLS REGULATE INFLAMMATORY CELL INFILTRATION OF THE LUNG AFTER TRAUMA-HEMORRHAGE Meenakshi Rani,* Qiong Zhang,* Richard F. Oppeltz

Epithelial cell specific properties and genetic complementation in a delta F508 cystic fibrosis nasal polyp cell line.

Science.gov (United States)

Kunzelmann, K; Lei, D C; Eng, K; Escobar, L C; Koslowsky, T; Gruenert, D C

1995-09-01

Analysis of vectorial ion transport and protein trafficking in transformed cystic fibrosis (CF) epithelial cells has been limited because the cells tend to lose their tight junctions with multiple subcultures. To elucidate ion transport and protein trafficking in CF epithelial cells, a polar cell line with apical and basolateral compartments will facilitate analysis of the efficacy of different gene therapy strategies in a "tight epithelium" in vitro. This study investigates the genotypic and phenotypic properties of a CF nasal polyp epithelial, delta F508 homozygote, cell line that has tight junctions pre-crisis. The cells (sigma CFNPE14o-) were transformed with an origin-of-replication defective SV40 plasmid. They develop transepithelial resistance in Ussing chambers and are defective in cAMP-dependent Cl- transport as measured by efflux of radioactive Cl-, short circuit current (Isc), or whole-cell patch clamp. Stimulation of the cells by bradykinin, histamine, or ATP seems to activate both K(+)- and Ca(+2)-dependent Cl- transport. Measurement of 36Cl- efflux following stimulation with A23187 and ionomycin indicate a Ca(+2)-dependent Cl- transport. Volume regulatory capacity of the cells is indicated by cell swelling conductance. Expression of the CF transmembrane conductance regulator mRNA was indicated by RT-PCR amplification. When cells are grown at 26 degrees C for 48 h there is no indication of cAMP-dependent Cl- as has been previously indicated in heterologous expression systems. Antibodies specific for secretory cell antigens indicate the presence of antigens found in goblet, serous, and mucous cells; in goblet and serous cells; or in goblet and mucous cells; but not antigens found exclusively in mucous or serous cells.(ABSTRACT TRUNCATED AT 250 WORDS)

Cystic fibrosis Delta F508 heterozygotes, smoking, and reproduction

DEFF Research Database (Denmark)

Dahl, Morten; Tybjaerg-Hansen, A; Wittrup, H H

1998-01-01

Cystic fibrosis is the most common fatal autosomal recessive disease affecting Caucasian populations. It remains a puzzle how this disease is maintained at such a remarkably high incidence, however, it could be due to a reproductive advantage in cystic fibrosis heterozygotes. We tested this hypot......Cystic fibrosis is the most common fatal autosomal recessive disease affecting Caucasian populations. It remains a puzzle how this disease is maintained at such a remarkably high incidence, however, it could be due to a reproductive advantage in cystic fibrosis heterozygotes. We tested.......001). In conclusion, overall these results do not support a reproductive advantage for cystic fibrosis DeltaF508 heterozygotes. However, the data cannot totally exclude the possibility that nonsmoking DeltaF508 heterozygotes experience a reproductive advantage while smoking DeltaF508 heterozygotes experience...... the opposite, a reproductive disadvantage. Accordingly, the data suggest a previously undocumented role of smoking on fecundity among cystic fibrosis heterozygotes....

Non-physical momentum sources in slab geometry gyrokinetics

International Nuclear Information System (INIS)

Parra, Felix I; Catto, Peter J

2010-01-01

We investigate momentum transport in the Hamiltonian electrostatic gyrokinetic formulation of Dubin et al (1983 Phys. Fluids 26 3524). We prove that the long wavelength electric field obtained from the gyrokinetic quasineutrality introduces a non-physical momentum source in the low flow ordering.

Nonlinear electromagnetic gyrokinetic equations for rotating axisymmetric plasmas

International Nuclear Information System (INIS)

Artun, M.; Tang, W.M.

1994-03-01

The influence of sheared equilibrium flows on the confinement properties of tokamak plasmas is a topic of much current interest. A proper theoretical foundation for the systematic kinetic analysis of this important problem has been provided here by presented the derivation of a set of nonlinear electromagnetic gyrokinetic equations applicable to low frequency microinstabilities in a rotating axisymmetric plasma. The subsonic rotation velocity considered is in the direction of symmetry with the angular rotation frequency being a function of the equilibrium magnetic flux surface. In accordance with experimental observations, the rotation profile is chosen to scale with the ion temperature. The results obtained represent the shear flow generalization of the earlier analysis by Frieman and Chen where such flows were not taken into account. In order to make it readily applicable to gyrokinetic particle simulations, this set of equations is cast in a phase-space-conserving continuity equation form

Efficient Eulerian gyrokinetic simulations with block-structured grids

International Nuclear Information System (INIS)

Jarema, Denis

2017-01-01

Gaining a deep understanding of plasma microturbulence is of paramount importance for the development of future nuclear fusion reactors, because it causes a strong outward transport of heat and particles. Gyrokinetics has proven itself as a valid mathematical model to simulate such plasma microturbulence effects. In spite of the advantages of this model, nonlinear radially extended (or global) gyrokinetic simulations are still extremely computationally expensive, involving a very large number of computational grid points. Hence, methods that reduce the number of grid points without a significant loss of accuracy are a prerequisite to be able to run high-fidelity simulations. At the level of the mathematical model, the gyrokinetic approach achieves a reduction from six to five coordinates in comparison to the fully kinetic models. This reduction leads to an important decrease in the total number of computational grid points. However, the velocity space mixed with the radial direction still requires a very fine resolution in grid based codes, due to the disparities in the thermal speed, which are caused by a strong temperature variation along the radial direction. An attempt to address this problem by modifying the underlying gyrokinetic set of equations leads to additional nonlinear terms, which are the most expensive parts to simulate. Furthermore, because of these modifications, well-established and computationally efficient implementations developed for the original set of equations can no longer be used. To tackle such issues, in this thesis we introduce an alternative approach of blockstructured grids. This approach reduces the number of grid points significantly, but without changing the underlying mathematical model. Furthermore, our technique is minimally invasive and allows the reuse of a large amount of already existing code using rectilinear grids, modifications being necessary only on the block boundaries. Moreover, the block-structured grid can be

Efficient Eulerian gyrokinetic simulations with block-structured grids

Energy Technology Data Exchange (ETDEWEB)

Jarema, Denis

2017-01-20

Gaining a deep understanding of plasma microturbulence is of paramount importance for the development of future nuclear fusion reactors, because it causes a strong outward transport of heat and particles. Gyrokinetics has proven itself as a valid mathematical model to simulate such plasma microturbulence effects. In spite of the advantages of this model, nonlinear radially extended (or global) gyrokinetic simulations are still extremely computationally expensive, involving a very large number of computational grid points. Hence, methods that reduce the number of grid points without a significant loss of accuracy are a prerequisite to be able to run high-fidelity simulations. At the level of the mathematical model, the gyrokinetic approach achieves a reduction from six to five coordinates in comparison to the fully kinetic models. This reduction leads to an important decrease in the total number of computational grid points. However, the velocity space mixed with the radial direction still requires a very fine resolution in grid based codes, due to the disparities in the thermal speed, which are caused by a strong temperature variation along the radial direction. An attempt to address this problem by modifying the underlying gyrokinetic set of equations leads to additional nonlinear terms, which are the most expensive parts to simulate. Furthermore, because of these modifications, well-established and computationally efficient implementations developed for the original set of equations can no longer be used. To tackle such issues, in this thesis we introduce an alternative approach of blockstructured grids. This approach reduces the number of grid points significantly, but without changing the underlying mathematical model. Furthermore, our technique is minimally invasive and allows the reuse of a large amount of already existing code using rectilinear grids, modifications being necessary only on the block boundaries. Moreover, the block-structured grid can be

Comment on 'On higher order corrections to gyrokinetic Vlasov-Poisson equations in the long wavelength limit' [Phys. Plasmas 16, 044506 (2009)

International Nuclear Information System (INIS)

Parra, Felix I.; Catto, Peter J.

2009-01-01

A recent publication [F. I. Parra and P. J. Catto, Plasma Phys. Controlled Fusion 50, 065014 (2008)] warned against the use of the lower order gyrokinetic Poisson equation at long wavelengths because the long wavelength, radial electric field must remain undetermined to the order the equation is obtained. Another reference [W. W. Lee and R. A. Kolesnikov, Phys. Plasmas 16, 044506 (2009)] criticizes these results by arguing that the higher order terms neglected in the most common gyrokinetic Poisson equation are formally smaller than the terms that are retained. This argument is flawed and ignores that the lower order terms, although formally larger, must cancel without determining the long wavelength, radial electric field. The reason for this cancellation is discussed. In addition, the origin of a nonlinear term present in the gyrokinetic Poisson equation [F. I. Parra and P. J. Catto, Plasma Phys. Controlled Fusion 50, 065014 (2008)] is explained.

Limitations, insights and improvements to gyrokinetics

International Nuclear Information System (INIS)

Catto, Peter J.; Parra, Felix I.; Kagan, Grigory; Simakov, Andrei N.

2009-01-01

We first consider gyrokinetic quasineutrality limitations when evaluating the axisymmetric radial electric field in a non-turbulent tokamak by an improved examination of intrinsic ambipolarity. We next prove that the background ions in a pedestal of poloidal ion gyroradius scale must be Maxwellian and nearly isothermal in Pfirsch-Schlueter and banana regime tokamak plasmas, and then consider zonal flow behaviour in a pedestal. Finally, we focus on a simplifying procedure for our transport time scale hybrid gyrokinetic-fluid treatment that removes the limitations of gyrokinetic quasineutrality and remains valid in the pedestal.

T-cell receptor gamma delta bearing cells in normal human skin

NARCIS (Netherlands)

Bos, J. D.; Teunissen, M. B.; Cairo, I.; Krieg, S. R.; Kapsenberg, M. L.; Das, P. K.; Borst, J.

1990-01-01

T-cell antigen receptors (TCR) are divided into common alpha beta and less common gamma delta types. In the murine skin, TCR gamma delta+ cells have been reported to form the great majority of epidermal T lymphocytes. We have examined the relative contribution of TCR alpha beta+ and TCR gamma delta+

Intrinsic rotation with gyrokinetic models

International Nuclear Information System (INIS)

Parra, Felix I.; Barnes, Michael; Catto, Peter J.; Calvo, Iván

2012-01-01

The generation of intrinsic rotation by turbulence and neoclassical effects in tokamaks is considered. To obtain the complex dependences observed in experiments, it is necessary to have a model of the radial flux of momentum that redistributes the momentum within the tokamak in the absence of a preexisting velocity. When the lowest order gyrokinetic formulation is used, a symmetry of the model precludes this possibility, making small effects in the gyroradius over scale length expansion necessary. These effects that are usually small become important for momentum transport because the symmetry of the lowest order gyrokinetic formulation leads to the cancellation of the lowest order momentum flux. The accuracy to which the gyrokinetic equation needs to be obtained to retain all the physically relevant effects is discussed.

Grid-based Parallel Data Streaming Implemented for the Gyrokinetic Toroidal Code

International Nuclear Information System (INIS)

Klasky, S.; Ethier, S.; Lin, Z.; Martins, K.; McCune, D.; Samtaney, R.

2003-01-01

We have developed a threaded parallel data streaming approach using Globus to transfer multi-terabyte simulation data from a remote supercomputer to the scientist's home analysis/visualization cluster, as the simulation executes, with negligible overhead. Data transfer experiments show that this concurrent data transfer approach is more favorable compared with writing to local disk and then transferring this data to be post-processed. The present approach is conducive to using the grid to pipeline the simulation with post-processing and visualization. We have applied this method to the Gyrokinetic Toroidal Code (GTC), a 3-dimensional particle-in-cell code used to study microturbulence in magnetic confinement fusion from first principles plasma theory

Cell-to-cell communication and cellular environment alter the somatostatin status of delta cells

Energy Technology Data Exchange (ETDEWEB)

Kelly, Catriona, E-mail: catriona.kelly@qub.ac.uk [SAAD Centre for Pharmacy and Diabetes, School of Biomedical Sciences, University of Ulster, Coleraine (United Kingdom); Flatt, Peter R.; McClenaghan, Neville H. [SAAD Centre for Pharmacy and Diabetes, School of Biomedical Sciences, University of Ulster, Coleraine (United Kingdom)

2010-08-20

Research highlights: {yields} TGP52 cells display enhanced functionality in pseudoislet form. {yields} Somatostatin content was reduced, but secretion increased in high glucose conditions. {yields} Cellular interactions and environment alter the somatostatin status of TGP52 cells. -- Abstract: Introduction: Somatostatin, released from pancreatic delta cells, is a potent paracrine inhibitor of insulin and glucagon secretion. Islet cellular interactions and glucose homeostasis are essential to maintain normal patterns of insulin secretion. However, the importance of cell-to-cell communication and cellular environment in the regulation of somatostatin release remains unclear. Methods: This study employed the somatostatin-secreting TGP52 cell line maintained in DMEM:F12 (17.5 mM glucose) or DMEM (25 mM glucose) culture media. The effect of pseudoislet formation and culture medium on somatostatin content and release in response to a variety of stimuli was measured by somatostatin EIA. In addition, the effect of pseudoislet formation on cellular viability (MTT and LDH assays) and proliferation (BrdU ELISA) was determined. Results: TGP52 cells readily formed pseudoislets and showed enhanced functionality in three-dimensional form with increased E-cadherin expression irrespective of the culture environment used. However, culture in DMEM decreased cellular somatostatin content (P < 0.01) and increased somatostatin secretion in response to a variety of stimuli including arginine, calcium and PMA (P < 0.001) when compared with cells grown in DMEM:F12. Configuration of TGP52 cells as pseudoislets reduced the proliferative rate and increased cellular cytotoxicity irrespective of culture medium used. Conclusions: Somatostatin secretion is greatly facilitated by cell-to-cell interactions and E-cadherin expression. Cellular environment and extracellular glucose also significantly influence the function of delta cells.

Cell-to-cell communication and cellular environment alter the somatostatin status of delta cells

International Nuclear Information System (INIS)

Kelly, Catriona; Flatt, Peter R.; McClenaghan, Neville H.

2010-01-01

Research highlights: → TGP52 cells display enhanced functionality in pseudoislet form. → Somatostatin content was reduced, but secretion increased in high glucose conditions. → Cellular interactions and environment alter the somatostatin status of TGP52 cells. -- Abstract: Introduction: Somatostatin, released from pancreatic delta cells, is a potent paracrine inhibitor of insulin and glucagon secretion. Islet cellular interactions and glucose homeostasis are essential to maintain normal patterns of insulin secretion. However, the importance of cell-to-cell communication and cellular environment in the regulation of somatostatin release remains unclear. Methods: This study employed the somatostatin-secreting TGP52 cell line maintained in DMEM:F12 (17.5 mM glucose) or DMEM (25 mM glucose) culture media. The effect of pseudoislet formation and culture medium on somatostatin content and release in response to a variety of stimuli was measured by somatostatin EIA. In addition, the effect of pseudoislet formation on cellular viability (MTT and LDH assays) and proliferation (BrdU ELISA) was determined. Results: TGP52 cells readily formed pseudoislets and showed enhanced functionality in three-dimensional form with increased E-cadherin expression irrespective of the culture environment used. However, culture in DMEM decreased cellular somatostatin content (P < 0.01) and increased somatostatin secretion in response to a variety of stimuli including arginine, calcium and PMA (P < 0.001) when compared with cells grown in DMEM:F12. Configuration of TGP52 cells as pseudoislets reduced the proliferative rate and increased cellular cytotoxicity irrespective of culture medium used. Conclusions: Somatostatin secretion is greatly facilitated by cell-to-cell interactions and E-cadherin expression. Cellular environment and extracellular glucose also significantly influence the function of delta cells.

Final Report for grant ER54958, 'Gyrokinetic Particle Simulation of Turbulent Transport in Burning Plasmas'

International Nuclear Information System (INIS)

Decyk, Viktor K.

2011-01-01

The UCLA contribution to this collaborative proposal is in two general areas. One area is to enhance the performance of GTC to perform optimally on the DOE leadership class computers, the other part is to contribute to the overall object-based design for GTC as it evolves. Most of the effort during this grant period has been in the former area. High performance computing is undergoing a revolution of greatly increasing parallelism, which is expected to lead to an exaflop computer by the end of the decade. However, the path there is uncertain. A number of hardware architectures have been proposed as well as new parallel languages. It is a disruptive time. In addition to this grant, this work is also funded by a gift from Northrop Grumman and UCLA's Institute for Digital Research and Education. In spite of the variety of proposed hardware, we feel that there is a hardware abstraction that describes the most likely features of the next generation high performance computers. This abstraction consists of a hierarchy of computational layers. At the lowest layer, we have a SIMD (vector) processor whose computational elements work together in lockstep and have fast synchronization and shared memory. At the next higher layer, we have a collection of such processors which communicate through a slower shared memory. At the highest layer, we have a cluster of such collections, which communicate via message-passing. The bottom two layers of this abstraction has been implemented in a language called OpenCL. Although different hardware implements different features of this abstraction, such as the SIMD or vector length, such an abstraction allows one to design parameterizable algorithms that can adapt to different hardware. We believe the hardware which most closely resembles a future exaflop computer is a collection of Graphical Processing Units (GPUs), and we have focused our attention on developing Particle-in-Cell (PIC) algorithms for this hardware initially. PIC codes are

Transcriptomic profiling of pancreatic alpha, beta and delta cell populations identifies delta cells as a principal target for ghrelin in mouse islets

DEFF Research Database (Denmark)

Adriaenssens, Alice E; Svendsen, Berit; Lam, Brian Y H

2016-01-01

cytometry and analysed by RNA sequencing. The role of the ghrelin receptor was validated by imaging delta cell calcium concentrations using islets with delta cell restricted expression of the calcium reporter GCaMP3, and in perfused mouse pancreases. RESULTS: A database was constructed of all genes...... expressed in alpha, beta and delta cells. The gene encoding the ghrelin receptor, Ghsr, was highlighted as being highly expressed and enriched in delta cells. Activation of the ghrelin receptor raised cytosolic calcium levels in primary pancreatic delta cells and enhanced somatostatin secretion in perfused...... pancreases, correlating with a decrease in insulin and glucagon release. The inhibition of insulin secretion by ghrelin was prevented by somatostatin receptor antagonism. CONCLUSIONS/INTERPRETATION: Our transcriptomic database of genes expressed in the principal islet cell populations will facilitate...

Gyrokinetic neoclassical study of the bootstrap current in the tokamak edge pedestal with fully non-linear Coulomb collisions

Energy Technology Data Exchange (ETDEWEB)

Hager, Robert, E-mail: rhager@pppl.gov; Chang, C. S., E-mail: cschang@pppl.gov [Princeton Plasma Physics Laboratory, P.O. Box 451, Princeton, New Jersey 08543 (United States)

2016-04-15

As a follow-up on the drift-kinetic study of the non-local bootstrap current in the steep edge pedestal of tokamak plasma by Koh et al. [Phys. Plasmas 19, 072505 (2012)], a gyrokinetic neoclassical study is performed with gyrokinetic ions and drift-kinetic electrons. Besides the gyrokinetic improvement of ion physics from the drift-kinetic treatment, a fully non-linear Fokker-Planck collision operator—that conserves mass, momentum, and energy—is used instead of Koh et al.'s linearized collision operator in consideration of the possibility that the ion distribution function is non-Maxwellian in the steep pedestal. An inaccuracy in Koh et al.'s result is found in the steep edge pedestal that originated from a small error in the collisional momentum conservation. The present study concludes that (1) the bootstrap current in the steep edge pedestal is generally smaller than what has been predicted from the small banana-width (local) approximation [e.g., Sauter et al., Phys. Plasmas 6, 2834 (1999) and Belli et al., Plasma Phys. Controlled Fusion 50, 095010 (2008)], (2) the plasma flow evaluated from the local approximation can significantly deviate from the non-local results, and (3) the bootstrap current in the edge pedestal, where the passing particle region is small, can be dominantly carried by the trapped particles in a broad trapped boundary layer. A new analytic formula based on numerous gyrokinetic simulations using various magnetic equilibria and plasma profiles with self-consistent Grad-Shafranov solutions is constructed.

Full-F gyrofluid model

DEFF Research Database (Denmark)

Madsen, Jens

2013-01-01

variables. The fluid moment hierarchy is closed by approximating the gyrokinetic distribution function as a finite order Hermite-Laguerre polynomial and by determining closure approximations for terms involving the gyrokinetic gyro-averaging operator. The model exactly conserves the gyrokinetic full......A global electromagnetic gyrofluid model based on the full-F gyrokinetic model is derived. The gyrofluid moment variables are not split into fluctuating and equilibrium parts. Profiles are evolved freely, and gyro-averaging operators are not parametrized, but are functions of the gyrofluid moment...

A hybrid gyrokinetic ion and isothermal electron fluid code for astrophysical plasma

Science.gov (United States)

Kawazura, Y.; Barnes, M.

2018-05-01

This paper describes a new code for simulating astrophysical plasmas that solves a hybrid model composed of gyrokinetic ions (GKI) and an isothermal electron fluid (ITEF) Schekochihin et al. (2009) [9]. This model captures ion kinetic effects that are important near the ion gyro-radius scale while electron kinetic effects are ordered out by an electron-ion mass ratio expansion. The code is developed by incorporating the ITEF approximation into AstroGK, an Eulerian δf gyrokinetics code specialized to a slab geometry Numata et al. (2010) [41]. The new code treats the linear terms in the ITEF equations implicitly while the nonlinear terms are treated explicitly. We show linear and nonlinear benchmark tests to prove the validity and applicability of the simulation code. Since the fast electron timescale is eliminated by the mass ratio expansion, the Courant-Friedrichs-Lewy condition is much less restrictive than in full gyrokinetic codes; the present hybrid code runs ∼ 2√{mi /me } ∼ 100 times faster than AstroGK with a single ion species and kinetic electrons where mi /me is the ion-electron mass ratio. The improvement of the computational time makes it feasible to execute ion scale gyrokinetic simulations with a high velocity space resolution and to run multiple simulations to determine the dependence of turbulent dynamics on parameters such as electron-ion temperature ratio and plasma beta.

HPC parallel programming model for gyrokinetic MHD simulation

International Nuclear Information System (INIS)

Naitou, Hiroshi; Yamada, Yusuke; Tokuda, Shinji; Ishii, Yasutomo; Yagi, Masatoshi

2011-01-01

The 3-dimensional gyrokinetic PIC (particle-in-cell) code for MHD simulation, Gpic-MHD, was installed on SR16000 (“Plasma Simulator”), which is a scalar cluster system consisting of 8,192 logical cores. The Gpic-MHD code advances particle and field quantities in time. In order to distribute calculations over large number of logical cores, the total simulation domain in cylindrical geometry was broken up into N DD-r × N DD-z (number of radial decomposition times number of axial decomposition) small domains including approximately the same number of particles. The axial direction was uniformly decomposed, while the radial direction was non-uniformly decomposed. N RP replicas (copies) of each decomposed domain were used (“particle decomposition”). The hybrid parallelization model of multi-threads and multi-processes was employed: threads were parallelized by the auto-parallelization and N DD-r × N DD-z × N RP processes were parallelized by MPI (message-passing interface). The parallelization performance of Gpic-MHD was investigated for the medium size system of N r × N θ × N z = 1025 × 128 × 128 mesh with 4.196 or 8.192 billion particles. The highest speed for the fixed number of logical cores was obtained for two threads, the maximum number of N DD-z , and optimum combination of N DD-r and N RP . The observed optimum speeds demonstrated good scaling up to 8,192 logical cores. (author)

Managing locality in grand challenge applications: a case study of the gyrokinetic toroidal code

Energy Technology Data Exchange (ETDEWEB)

Marin, G; Jin, G; Mellor-Crummey, J [Department of Computer Science, Rice University, Houston, TX 77005 (United States)

2008-07-15

Achieving high performance with grand challenge applications on today's large-scale parallel systems requires tailoring applications for the characteristics of the modern microprocessor architectures. As part of the US Department of Energy's Scientific Discovery through Advanced Computing (SciDAC) program, we studied and tuned the Gyrokinetic Toroidal Code (GTC), a particle-in-cell code for simulating turbulent transport of particles and energy in burning plasma, developed at Princeton Plasma Physics Laboratory. In this paper, we present a performance study of the application that revealed several opportunities for improving performance by enhancing its data locality. We tuned GTC by performing three kinds of transformations: static data structure reorganization to improve spatial locality, loop nest restructuring for better temporal locality, and dynamic data reordering at run-time to enhance both spatial and temporal reuse. Experimental results show that these changes improve execution time by more than 20% on large parallel systems, including a Cray XT4.

Managing locality in grand challenge applications: a case study of the gyrokinetic toroidal code

International Nuclear Information System (INIS)

Marin, G; Jin, G; Mellor-Crummey, J

2008-01-01

Achieving high performance with grand challenge applications on today's large-scale parallel systems requires tailoring applications for the characteristics of the modern microprocessor architectures. As part of the US Department of Energy's Scientific Discovery through Advanced Computing (SciDAC) program, we studied and tuned the Gyrokinetic Toroidal Code (GTC), a particle-in-cell code for simulating turbulent transport of particles and energy in burning plasma, developed at Princeton Plasma Physics Laboratory. In this paper, we present a performance study of the application that revealed several opportunities for improving performance by enhancing its data locality. We tuned GTC by performing three kinds of transformations: static data structure reorganization to improve spatial locality, loop nest restructuring for better temporal locality, and dynamic data reordering at run-time to enhance both spatial and temporal reuse. Experimental results show that these changes improve execution time by more than 20% on large parallel systems, including a Cray XT4

Gyrokinetic Studies of Turbulence in Steep Gradient Region: Role of Turbulence Spreading and E x B Shear

Energy Technology Data Exchange (ETDEWEB)

T.S. Hahm; Z. Lin; P.H. Diamond; G. Rewoldt; W.X. Wang; S. Ethier; O. Gurcan; W.W. Lee; W.M. Tang

2004-12-21

An integrated program of gyrokinetic particle simulation and theory has been developed to investigate several outstanding issues in both turbulence and neoclassical physics. Gyrokinetic particle simulations of toroidal ion temperature gradient (ITG) turbulence spreading using the GTC code and its related dynamical model have been extended to the case with radially increasing ion temperature gradient, to study the inward spreading of edge turbulence toward the core. Due to turbulence spreading from the edge, the turbulence intensity in the core region is significantly enhanced over the value obtained from simulations of the core region only. Even when the core gradient is within the Dimits shift regime (i.e., self-generated zonal flows reduce the transport to a negligible value), a significant level of turbulence and transport is observed in the core due to spreading from the edge. The scaling of the turbulent front propagation speed is closer to the prediction from our nonlinear diffusion model than one based on linear toroidal coupling. A calculation of ion poloidal rotation in the presence of sharp density and toroidal angular rotation frequency gradients from the GTC-Neo particle simulation code shows that the results are significantly different from the conventional neoclassical theory predictions. An energy conserving set of a fully electromagnetic nonlinear gyrokinetic Vlasov equation and Maxwell's equations, which is applicable to edge turbulence, is being derived via the phase-space action variational Lie perturbation method. Our generalized ordering takes the ion poloidal gyroradius to be on the order of the radial electric field gradient length.

Gyrokinetic studies of turbulence in steep gradient region: Role of turbulence spreading and E x B shear

International Nuclear Information System (INIS)

Hahm, T.S.; Lin, Z.; Diamond, P.H.; Gurcan, O.; Rewoldt, G.; Wang, W.X.; Ethier, S.; Lee, W.W.; Lewandowski, J.L.V.; Tang, W.M.

2005-01-01

An integrated program of gyrokinetic particle simulation and theory has been developed to investigate several outstanding issues in both turbulence and neoclassical physics. Gyrokinetic particle simulations of toroidal ion temperature gradient (ITG) turbulence spreading using the GTC code and its related dynamical model have been extended to the case with radially increasing ion temperature gradient, to study the inward spreading of edge turbulence toward the core. Due to turbulence spreading from the edge, the turbulence intensity in the core region is significantly enhanced over the value obtained from simulations of the core region only. Even when the core gradient is within the Dimits shift regime (i.e., self-generated zonal flows reduce the transport to a negligible value), a significant level of turbulence and transport is observed in the core due to spreading from the edge. The scaling of the turbulent front propagation speed is closer to the prediction from our nonlinear diffusion model than one based on linear toroidal coupling. A calculation of ion poloidal rotation in the presence of sharp density and toroidal angular rotation frequency gradients from the GTC-Neo particle simulation code shows that the results are significantly different from the conventional neoclassical theory predictions. An energy conserving set of a fully electromagnetic nonlinear gyrokinetic Vlasov equation and Maxwell's equations, which is applicable to edge turbulence, is being derived via the phase-space action variational Lie perturbation method. Our generalized ordering takes the ion poloidal gyroradius to be on the order of the radial electric field gradient length. (author)

A quasi-linear gyrokinetic transport model for tokamak plasmas

International Nuclear Information System (INIS)

Casati, A.

2009-10-01

After a presentation of some basics around nuclear fusion, this research thesis introduces the framework of the tokamak strategy to deal with confinement, hence the main plasma instabilities which are responsible for turbulent transport of energy and matter in such a system. The author also briefly introduces the two principal plasma representations, the fluid and the kinetic ones. He explains why the gyro-kinetic approach has been preferred. A tokamak relevant case is presented in order to highlight the relevance of a correct accounting of the kinetic wave-particle resonance. He discusses the issue of the quasi-linear response. Firstly, the derivation of the model, called QuaLiKiz, and its underlying hypotheses to get the energy and the particle turbulent flux are presented. Secondly, the validity of the quasi-linear response is verified against the nonlinear gyro-kinetic simulations. The saturation model that is assumed in QuaLiKiz, is presented and discussed. Then, the author qualifies the global outcomes of QuaLiKiz. Both the quasi-linear energy and the particle flux are compared to the expectations from the nonlinear simulations, across a wide scan of tokamak relevant parameters. Therefore, the coupling of QuaLiKiz within the integrated transport solver CRONOS is presented: this procedure allows the time-dependent transport problem to be solved, hence the direct application of the model to the experiment. The first preliminary results regarding the experimental analysis are finally discussed

Stringent tests of constrained Minimal Flavor Violation through {Delta}F=2 transitions

Energy Technology Data Exchange (ETDEWEB)

Buras, Andrzej J. [TUM-IAS, Garching (Germany); Girrbach, Jennifer [TUM, Physik Department, Garching (Germany)

2013-09-15

New Physics contributions to {Delta}F=2 transitions in the simplest extensions of the Standard Model (SM), the models with constrained Minimal Flavor Violation (CMFV), are parametrized by a single variable S(v), the value of the real box diagram function that in CMFV is bounded from below by its SM value S{sub 0}(x{sub t}). With already very precise experimental values of {epsilon}{sub K}, {Delta}M{sub d}, {Delta}M{sub s} and precise values of the CP-asymmetry S{sub {psi}K{sub S}} and of B{sub K} entering the evaluation of {epsilon}{sub K}, the future of CMFV in the {Delta}F = 2 sector depends crucially on the values of vertical stroke V{sub cb} vertical stroke, vertical stroke V{sub ub} vertical stroke, {gamma}, F{sub B{sub s}} {radical}(B{sub B{sub s}}) and F{sub B{sub d}} {radical}(B{sub B{sub d}}). The ratio {xi} of the latter two non-perturbative parameters, already rather precisely determined from lattice calculations, allows then together with {Delta}M{sub s} / {Delta}M{sub d} and S{sub {psi}K{sub S}} to determine the range of the angle {gamma} in the unitarity triangle independently of the value of S(v). Imposing in addition the constraints from vertical stroke {epsilon}{sub K} vertical stroke and {Delta}M{sub d} allows to determine the favorite CMFV values of vertical stroke V{sub cb} vertical stroke, vertical stroke V{sub ub} vertical stroke, F{sub B{sub s}} {radical}(B{sub B{sub s}}) and F{sub B{sub d}} {radical}(B{sub B{sub d}}) as functions of S(v) and {gamma}. The vertical stroke V{sub cb} vertical stroke {sup 4} dependence of {epsilon}{sub K} allows to determine vertical stroke V{sub cb} vertical stroke for a given S(v) and {gamma} with a higher precision than it is presently possible using tree-level decays. The same applies to vertical stroke V{sub ub} vertical stroke, vertical stroke V{sub td} vertical stroke and vertical stroke V{sub ts} vertical stroke that are automatically determined as functions of S(v) and {gamma}. We derive correlations

Nonlinear gyrokinetic simulations of the I-mode high confinement regime and comparisons with experiment

Energy Technology Data Exchange (ETDEWEB)

White, A. E., E-mail: whitea@mit.edu; Howard, N. T.; Creely, A. J.; Chilenski, M. A.; Greenwald, M.; Hubbard, A. E.; Hughes, J. W.; Marmar, E.; Rice, J. E.; Sierchio, J. M.; Sung, C.; Walk, J. R.; Whyte, D. G. [MIT Plasma Science and Fusion Center, Cambridge, Massachusetts 02139 (United States); Mikkelsen, D. R.; Edlund, E. M.; Kung, C. [Princeton Plasma Physics Laboratory, Princeton, New Jersey 08540 (United States); Holland, C. [University of California, San Diego (UCSD) San Diego, California 92093 (United States); Candy, J.; Petty, C. C. [General Atomics, P.O. Box 85608, San Diego, California 92186 (United States); Reinke, M. L. [York University, Heslington, York YO10 5DD (United Kingdom); and others

2015-05-15

For the first time, nonlinear gyrokinetic simulations of I-mode plasmas are performed and compared with experiment. I-mode is a high confinement regime, featuring energy confinement similar to H-mode, but without enhanced particle and impurity particle confinement [D. G. Whyte et al., Nucl. Fusion 50, 105005 (2010)]. As a consequence of the separation between heat and particle transport, I-mode exhibits several favorable characteristics compared to H-mode. The nonlinear gyrokinetic code GYRO [J. Candy and R. E. Waltz, J Comput. Phys. 186, 545 (2003)] is used to explore the effects of E × B shear and profile stiffness in I-mode and compare with L-mode. The nonlinear GYRO simulations show that I-mode core ion temperature and electron temperature profiles are more stiff than L-mode core plasmas. Scans of the input E × B shear in GYRO simulations show that E × B shearing of turbulence is a stronger effect in the core of I-mode than L-mode. The nonlinear simulations match the observed reductions in long wavelength density fluctuation levels across the L-I transition but underestimate the reduction of long wavelength electron temperature fluctuation levels. The comparisons between experiment and gyrokinetic simulations for I-mode suggest that increased E × B shearing of turbulence combined with increased profile stiffness are responsible for the reductions in core turbulence observed in the experiment, and that I-mode resembles H-mode plasmas more than L-mode plasmas with regards to marginal stability and temperature profile stiffness.

Gyrokinetic Magnetohydrodynamics and the Associated Equilibrium

Science.gov (United States)

Lee, W. W.; Hudson, S. R.; Ma, C. H.

2017-10-01

A proposed scheme for the calculations of gyrokinetic MHD and its associated equilibrium is discussed related a recent paper on the subject. The scheme is based on the time-dependent gyrokinetic vorticity equation and parallel Ohm's law, as well as the associated gyrokinetic Ampere's law. This set of equations, in terms of the electrostatic potential, ϕ, and the vector potential, ϕ , supports both spatially varying perpendicular and parallel pressure gradients and their associated currents. The MHD equilibrium can be reached when ϕ -> 0 and A becomes constant in time, which, in turn, gives ∇ . (J|| +J⊥) = 0 and the associated magnetic islands. Examples in simple cylindrical geometry will be given. The present work is partially supported by US DoE Grant DE-AC02-09CH11466.

Electromagnetic nonlinear gyrokinetics with polarization drift

International Nuclear Information System (INIS)

Duthoit, F.-X.; Hahm, T. S.; Wang, Lu

2014-01-01

A set of new nonlinear electromagnetic gyrokinetic Vlasov equation with polarization drift and gyrokinetic Maxwell equations is systematically derived by using the Lie-transform perturbation method in toroidal geometry. For the first time, we recover the drift-kinetic expression for parallel acceleration [R. M. Kulsrud, in Basic Plasma Physics, edited by A. A. Galeev and R. N. Sudan (North-Holland, Amsterdam, 1983)] from the nonlinear gyrokinetic equations, thereby bridging a gap between the two formulations. This formalism should be useful in addressing nonlinear ion Compton scattering of intermediate-mode-number toroidal Alfvén eigenmodes for which the polarization current nonlinearity [T. S. Hahm and L. Chen, Phys. Rev. Lett. 74, 266 (1995)] and the usual finite Larmor radius effects should compete

Plasma simulation studies using multilevel physics models

International Nuclear Information System (INIS)

Park, W.; Belova, E.V.; Fu, G.Y.

2000-01-01

The question of how to proceed toward ever more realistic plasma simulation studies using ever increasing computing power is addressed. The answer presented here is the M3D (Multilevel 3D) project, which has developed a code package with a hierarchy of physics levels that resolve increasingly complete subsets of phase-spaces and are thus increasingly more realistic. The rationale for the multilevel physics models is given. Each physics level is described and examples of its application are given. The existing physics levels are fluid models (3D configuration space), namely magnetohydrodynamic (MHD) and two-fluids; and hybrid models, namely gyrokinetic-energetic-particle/MHD (5D energetic particle phase-space), gyrokinetic-particle-ion/fluid-electron (5D ion phase-space), and full-kinetic-particle-ion/fluid-electron level (6D ion phase-space). Resolving electron phase-space (5D or 6D) remains a future project. Phase-space-fluid models are not used in favor of delta f particle models. A practical and accurate nonlinear fluid closure for noncollisional plasmas seems not likely in the near future

Equilibrium fluctuation energy of gyrokinetic plasma

International Nuclear Information System (INIS)

Krommes, J.A.; Lee, W.W.; Oberman, C.

1985-11-01

The thermal equilibrium electric field fluctuation energy of the gyrokinetic model of magnetized plasma is computed, and found to be smaller than the well-known result (k)/8π = 1/2T/[1 + (klambda/sub D/) 2 ] valid for arbitrarily magnetized plasmas. It is shown that, in a certain sense, the equilibrium electric field energy is minimum in the gyrokinetic regime. 13 refs., 2 figs

Gyroaveraging operations using adaptive matrix operators

Science.gov (United States)

Dominski, Julien; Ku, Seung-Hoe; Chang, Choong-Seock

2018-05-01

A new adaptive scheme to be used in particle-in-cell codes for carrying out gyroaveraging operations with matrices is presented. This new scheme uses an intermediate velocity grid whose resolution is adapted to the local thermal Larmor radius. The charge density is computed by projecting marker weights in a field-line following manner while preserving the adiabatic magnetic moment μ. These choices permit to improve the accuracy of the gyroaveraging operations performed with matrices even when strong spatial variation of temperature and magnetic field is present. Accuracy of the scheme in different geometries from simple 2D slab geometry to realistic 3D toroidal equilibrium has been studied. A successful implementation in the gyrokinetic code XGC is presented in the delta-f limit.

Cross-code gyrokinetic verification and benchmark on the linear collisionless dynamics of the geodesic acoustic mode

Science.gov (United States)

Biancalani, A.; Bottino, A.; Ehrlacher, C.; Grandgirard, V.; Merlo, G.; Novikau, I.; Qiu, Z.; Sonnendrücker, E.; Garbet, X.; Görler, T.; Leerink, S.; Palermo, F.; Zarzoso, D.

2017-06-01

The linear properties of the geodesic acoustic modes (GAMs) in tokamaks are investigated by means of the comparison of analytical theory and gyrokinetic numerical simulations. The dependence on the value of the safety factor, finite-orbit-width of the ions in relation to the radial mode width, magnetic-flux-surface shaping, and electron/ion mass ratio are considered. Nonuniformities in the plasma profiles (such as density, temperature, and safety factor), electro-magnetic effects, collisions, and the presence of minority species are neglected. Also, only linear simulations are considered, focusing on the local dynamics. We use three different gyrokinetic codes: the Lagrangian (particle-in-cell) code ORB5, the Eulerian code GENE, and semi-Lagrangian code GYSELA. One of the main aims of this paper is to provide a detailed comparison of the numerical results and analytical theory, in the regimes where this is possible. This helps understanding better the behavior of the linear GAM dynamics in these different regimes, the behavior of the codes, which is crucial in the view of a future work where more physics is present, and the regimes of validity of each specific analytical dispersion relation.

A conservative scheme of drift kinetic electrons for gyrokinetic simulation of kinetic-MHD processes in toroidal plasmas

Science.gov (United States)

Bao, J.; Liu, D.; Lin, Z.

2017-10-01

A conservative scheme of drift kinetic electrons for gyrokinetic simulations of kinetic-magnetohydrodynamic processes in toroidal plasmas has been formulated and verified. Both vector potential and electron perturbed distribution function are decomposed into adiabatic part with analytic solution and non-adiabatic part solved numerically. The adiabatic parallel electric field is solved directly from the electron adiabatic response, resulting in a high degree of accuracy. The consistency between electrostatic potential and parallel vector potential is enforced by using the electron continuity equation. Since particles are only used to calculate the non-adiabatic response, which is used to calculate the non-adiabatic vector potential through Ohm's law, the conservative scheme minimizes the electron particle noise and mitigates the cancellation problem. Linear dispersion relations of the kinetic Alfvén wave and the collisionless tearing mode in cylindrical geometry have been verified in gyrokinetic toroidal code simulations, which show that the perpendicular grid size can be larger than the electron collisionless skin depth when the mode wavelength is longer than the electron skin depth.

Implementation of a 3D plasma particle-in-cell code on a MIMD parallel computer

International Nuclear Information System (INIS)

Liewer, P.C.; Lyster, P.; Wang, J.

1993-01-01

A three-dimensional plasma particle-in-cell (PIC) code has been implemented on the Intel Delta MIMD parallel supercomputer using the General Concurrent PIC algorithm. The GCPIC algorithm uses a domain decomposition to divide the computation among the processors: A processor is assigned a subdomain and all the particles in it. Particles must be exchanged between processors as they move. Results are presented comparing the efficiency for 1-, 2- and 3-dimensional partitions of the three dimensional domain. This algorithm has been found to be very efficient even when a large fraction (e.g. 30%) of the particles must be exchanged at every time step. On the 512-node Intel Delta, up to 125 million particles have been pushed with an electrostatic push time of under 500 nsec/particle/time step

Parallel magnetic field perturbations in gyrokinetic simulations

International Nuclear Information System (INIS)

Joiner, N.; Hirose, A.; Dorland, W.

2010-01-01

At low β it is common to neglect parallel magnetic field perturbations on the basis that they are of order β 2 . This is only true if effects of order β are canceled by a term in the ∇B drift also of order β[H. L. Berk and R. R. Dominguez, J. Plasma Phys. 18, 31 (1977)]. To our knowledge this has not been rigorously tested with modern gyrokinetic codes. In this work we use the gyrokinetic code GS2[Kotschenreuther et al., Comput. Phys. Commun. 88, 128 (1995)] to investigate whether the compressional magnetic field perturbation B || is required for accurate gyrokinetic simulations at low β for microinstabilities commonly found in tokamaks. The kinetic ballooning mode (KBM) demonstrates the principle described by Berk and Dominguez strongly, as does the trapped electron mode, in a less dramatic way. The ion and electron temperature gradient (ETG) driven modes do not typically exhibit this behavior; the effects of B || are found to depend on the pressure gradients. The terms which are seen to cancel at long wavelength in KBM calculations can be cumulative in the ion temperature gradient case and increase with η e . The effect of B || on the ETG instability is shown to depend on the normalized pressure gradient β ' at constant β.

Introduction to Gyrokinetic Theory with Applications in Magnetic Confinement Research in Plasma Physics

International Nuclear Information System (INIS)

Tang, W.M.

2005-01-01

The present lecture provides an introduction to the subject of gyrokinetic theory with applications in the area of magnetic confinement research in plasma physics--the research arena from which this formalism was originally developed. It was presented as a component of the ''Short Course in Kinetic Theory within the Thematic Program in Partial Differential Equations'' held at the Fields Institute for Research in Mathematical Science (24 March 2004). This lecture also discusses the connection between the gyrokinetic formalism and powerful modern numerical simulations. Indeed, simulation, which provides a natural bridge between theory and experiment, is an essential modern tool for understanding complex plasma behavior. Progress has been stimulated in particular by the exponential growth of computer speed along with significant improvements in computer technology. The advances in both particle and fluid simulations of fine-scale turbulence and large-scale dynamics have produced increasingly good agreement between experimental observations and computational modeling. This was enabled by two key factors: (i) innovative advances in analytic and computational methods for developing reduced descriptions of physics phenomena spanning widely disparate temporal and spatial scales and (ii) access to powerful new computational resources

Gyrokinetic Electron and Fully Kinetic Ion Particle Simulation of Collisionless Plasma Dynamics

Energy Technology Data Exchange (ETDEWEB)

Yu Lin; Xueyi Wang; Liu Chen; Zhihong Lin

2009-08-11

Fully kinetic-particle simulations and hybrid simulations have been utilized for decades to investigate various fundamental plasma processes, such as magnetic reconnection, fast compressional waves, and wave-particle interaction. Nevertheless, due to disparate temporal and spatial scales between electrons and ions, existing fully kinetic-particle codes have to employ either unrealistically high electron-to-ion mass ratio, me/mi, or simulation domain limited to a few or a few ten's of the ion Larmor radii, or/and time much less than the global Alfven time scale in order to accommodate available computing resources. On the other hand, in the hybrid simulation, the ions are treated as fully kinetic particles but the electrons are treated as a massless fluid. The electron kinetic effects, e.g., wave-particle resonances and finite electron Larmor radius effects, are completely missing. Important physics, such as the electron transit time damping of fast compressional waves or the triggering mechanism of magnetic reconnection in collisionless plasmas is absent in the hybrid codes. Motivated by these considerations and noting that dynamics of interest to us has frequencies lower than the electron gyrofrequency, we planned to develop an innovative particle simulation model, gyrokinetic (GK) electrons and fully kinetic (FK) ions. In the GK-electron and FK-ion (GKe/FKi) particle simulation model, the rapid electron cyclotron motion is removed, while keeping finite electron Larmor radii, realistic me/mi ratio, wave-particle interactions, and off-diagonal components of electron pressure tensor. The computation power can thus be significantly improved over that of the full-particle codes. As planned in the project DE-FG02-05ER54826, we have finished the development of the new GK-electron and FK-ion scheme, finished its benchmark for a uniform plasma in 1-D, 2-D, and 3-D systems against linear waves obtained from analytical theories, and carried out a further convergence

Gyrokinetic Electron and Fully Kinetic Ion Particle Simulation of Collisionless Plasma Dynamics

International Nuclear Information System (INIS)

Lin, Yu; Wang, Xueyi; Chen, Liu; Lin, Zhihong

2009-01-01

Fully kinetic-particle simulations and hybrid simulations have been utilized for decades to investigate various fundamental plasma processes, such as magnetic reconnection, fast compressional waves, and wave-particle interaction. Nevertheless, due to disparate temporal and spatial scales between electrons and ions, existing fully kinetic-particle codes have to employ either unrealistically high electron-to-ion mass ratio, me/mi, or simulation domain limited to a few or a few ten's of the ion Larmor radii, or/and time much less than the global Alfven time scale in order to accommodate available computing resources. On the other hand, in the hybrid simulation, the ions are treated as fully kinetic particles but the electrons are treated as a massless fluid. The electron kinetic effects, e.g., wave-particle resonances and finite electron Larmor radius effects, are completely missing. Important physics, such as the electron transit time damping of fast compressional waves or the triggering mechanism of magnetic reconnection in collisionless plasmas is absent in the hybrid codes. Motivated by these considerations and noting that dynamics of interest to us has frequencies lower than the electron gyrofrequency, we planned to develop an innovative particle simulation model, gyrokinetic (GK) electrons and fully kinetic (FK) ions. In the GK-electron and FK-ion (GKe/FKi) particle simulation model, the rapid electron cyclotron motion is removed, while keeping finite electron Larmor radii, realistic me/mi ratio, wave-particle interactions, and off-diagonal components of electron pressure tensor. The computation power can thus be significantly improved over that of the full-particle codes. As planned in the project DE-FG02-05ER54826, we have finished the development of the new GK-electron and FK-ion scheme, finished its benchmark for a uniform plasma in 1-D, 2-D, and 3-D systems against linear waves obtained from analytical theories, and carried out a further convergence test

Study of 4f hybridization in CeNiX with X=Sn{sub d}eltaGe{sub 1-d}elta, 0<=delta<=1

Energy Technology Data Exchange (ETDEWEB)

Fuente, C. de la, E-mail: cesar@unizar.e [Depto. Fisica de la Materia Condensada, Laboratorio de Magnetismo, Universidad de Zaragoza and ICMA-CSIC (Spain); Moral, A. del [Depto. Fisica de la Materia Condensada, Laboratorio de Magnetismo, Universidad de Zaragoza and ICMA-CSIC (Spain); Adroja, D.T. [ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 0QX (United Kingdom); Fraile, A. [Depto. Fisica de la Materia Condensada, Laboratorio de Magnetismo, Universidad de Zaragoza and ICMA-CSIC (Spain); Arnaudas, J.I. [Instituto de Nanociencia de Aragon, Universidad de Zaragoza (Spain)

2010-05-15

We report inelastic neutron scattering and core-level X-ray photoemission spectroscopy experiments for studying the Kondo problem in the CeNiX, X=Sn{sub d}eltaGe{sub 1-d}elta 0<=delta<=1 series. The neutron results confirm that they behave like a Kondo lattice for delta>=0.85, showing broad maxima at around 30 meV, typical of a crystal field magnetic scattering. So, the Ge doping could produce the suppression of the cerium magnetism observed for delta<=0.25. To open a more deep sight on this point, we have analyzed the 3d core-level XPS spectra by using the well-known Gunnarsson-Schoenhammer model. From this analysis, we have obtained the 'on-site' Coulomb bare repulsion for f states, U, and hybridization parameter, DELTA, related with the hopping from the f states to the conduction ones. These U values are very similar for all compounds, about 7 eV, but the hybridization parameter slightly changes from 0.2 to 0.16 eV on increasing the Sn concentration. In Sn-rich compounds, the 4f occupation is close to spin limit fluctuation, which allows us to obtain an estimation of the Kondo temperatures, approx1200 K, and the static 0 K susceptibility, approx1.1x10{sup -3} emu/mol. Finally, we have done 'ab-initio' calculations based on the LDA+U+SO which confirm the existence of a small electronic gap opening in the DOS of Ge-rich compounds for U values lower than 7 eV.

Impact of the [delta]F508 Mutation in First Nucleotide-binding Domain of Human Cystic Fibrosis Transmembrane Conductance Regulator on Domain Folding and Structure

Energy Technology Data Exchange (ETDEWEB)

Lewis, Hal A.; Zhao, Xun; Wang, Chi; Sauder, J. Michael; Rooney, Isabelle; Noland, Brian W.; Lorimer, Don; Kearins, Margaret C.; Conners, Kris; Condon, Brad; Maloney, Peter C.; Guggino, William B.; Hunt, John F.; Emtage, Spencer (SG); (Columbia); (JHU)

2010-07-19

Cystic fibrosis is caused by defects in the cystic fibrosis transmembrane conductance regulator (CFTR), commonly the deletion of residue Phe-508 (DeltaF508) in the first nucleotide-binding domain (NBD1), which results in a severe reduction in the population of functional channels at the epithelial cell surface. Previous studies employing incomplete NBD1 domains have attributed this to aberrant folding of DeltaF508 NBD1. We report structural and biophysical studies on complete human NBD1 domains, which fail to demonstrate significant changes of in vitro stability or folding kinetics in the presence or absence of the DeltaF508 mutation. Crystal structures show minimal changes in protein conformation but substantial changes in local surface topography at the site of the mutation, which is located in the region of NBD1 believed to interact with the first membrane spanning domain of CFTR. These results raise the possibility that the primary effect of DeltaF508 is a disruption of proper interdomain interactions at this site in CFTR rather than interference with the folding of NBD1. Interestingly, increases in the stability of NBD1 constructs are observed upon introduction of second-site mutations that suppress the trafficking defect caused by the DeltaF508 mutation, suggesting that these suppressors might function indirectly by improving the folding efficiency of NBD1 in the context of the full-length protein. The human NBD1 structures also solidify the understanding of CFTR regulation by showing that its two protein segments that can be phosphorylated both adopt multiple conformations that modulate access to the ATPase active site and functional interdomain interfaces.

Plant delta 15N correlates with the transpiration efficiency of nitrogen acquisition in tropical trees.

Science.gov (United States)

Cernusak, Lucas A; Winter, Klaus; Turner, Benjamin L

2009-11-01

Based upon considerations of a theoretical model of (15)N/(14)N fractionation during steady-state nitrate uptake from soil, we hypothesized that, for plants grown in a common soil environment, whole-plant delta(15)N (deltaP) should vary as a function of the transpiration efficiency of nitrogen acquisition (F(N)/v) and the difference between deltaP and root delta(15)N (deltaP - deltaR). We tested these hypotheses with measurements of several tropical tree and liana species. Consistent with theoretical expectations, both F(N)/v and deltaP - deltaR were significant sources of variation in deltaP, and the relationship between deltaP and F(N)/v differed between non-N(2)-fixing and N(2)-fixing species. We interpret the correlation between deltaP and F(N)/v as resulting from variation in mineral nitrogen efflux-to-influx ratios across plasma membranes of root cells. These results provide a simple explanation of variation in delta(15)N of terrestrial plants and have implications for understanding nitrogen cycling in ecosystems.

Fractional variational problems and particle in cell gyrokinetic simulations with fuzzy logic approach for tokamaks

Directory of Open Access Journals (Sweden)

Rastović Danilo

2009-01-01

Full Text Available In earlier Rastovic's papers [1] and [2], the effort was given to analyze the stochastic control of tokamaks. In this paper, the deterministic control of tokamak turbulence is investigated via fractional variational calculus, particle in cell simulations, and fuzzy logic methods. Fractional integrals can be considered as approximations of integrals on fractals. The turbulent media could be of the fractal structure and the corresponding equations should be changed to include the fractal features of the media.

Deformation characteristics of {delta} phase in the delta-processed Inconel 718 alloy

Energy Technology Data Exchange (ETDEWEB)

Zhang, H.Y., E-mail: haiyanzhang@imr.ac.cn [Institute of Metal Research, Chinese Academy of Sciences, Shenyang 110016 (China); Zhang, S.H., E-mail: shzhang@imr.ac.cn [Institute of Metal Research, Chinese Academy of Sciences, Shenyang 110016 (China); Cheng, M. [Institute of Metal Research, Chinese Academy of Sciences, Shenyang 110016 (China); Li, Z.X. [Beijing Institute of Aeronautica1 Materials, Beijing 100095 (China)

2010-01-15

The hot working characteristics of {delta} phase in the delta-processed Inconel 718 alloy during isothermal compression deformation at temperature of 950 deg. C and strain rate of 0.005 s{sup -1}, were studied by using optical microscope, scanning electron microscope and quantitative X-ray diffraction technique. The results showed that the dissolution of plate-like {delta} phase and the precipitation of spherical {delta} phase particles coexisted during the deformation, and the content of {delta} phase decreased from 7.05 wt.% to 5.14 wt.%. As a result of deformation breakage and dissolution breakage, the plate-like {delta} phase was spheroidized and transferred to spherical {delta} phase particles. In the center with largest strain, the plate-like {delta} phase disappeared and spherical {delta} phase appeared in the interior of grains and grain boundaries.

Theoretical and Numerical Properties of a Gyrokinetic Plasma: Issues Related to Transport Time Scale Simulation

International Nuclear Information System (INIS)

Lee, W.W.

2003-01-01

Particle simulation has played an important role for the recent investigations on turbulence in magnetically confined plasmas. In this paper, theoretical and numerical properties of a gyrokinetic plasma as well as its relationship with magnetohydrodynamics (MHD) are discussed with the ultimate aim of simulating microturbulence in transport time scale using massively parallel computers

Modelling the turbulent transport of angular momentum in tokamak plasmas - A quasi-linear gyrokinetic approach

International Nuclear Information System (INIS)

Cottier, Pierre

2013-01-01

The magnetic confinement in tokamaks is for now the most advanced way towards energy production by nuclear fusion. Both theoretical and experimental studies showed that rotation generation can increase its performance by reducing the turbulent transport in tokamak plasmas. The rotation influence on the heat and particle fluxes is studied along with the angular momentum transport with the quasi-linear gyro-kinetic eigenvalue code QuaLiKiz. For this purpose, the QuaLiKiz code is modified in order to take the plasma rotation into account and compute the angular momentum flux. It is shown that QuaLiKiz framework is able to correctly predict the angular momentum flux including the E*B shear induced residual stress as well as the influence of rotation on the heat and particle fluxes. The major approximations of QuaLiKiz formalisms are reviewed, in particular the ballooning representation at its lowest order and the eigenfunctions calculated in the hydrodynamic limit. The construction of the quasi-linear fluxes is also reviewed in details and the quasi-linear angular momentum flux is derived. The different contributions to the turbulent momentum flux are studied and successfully compared both against non-linear gyro-kinetic simulations and experimental data. (author) [fr

Local gyrokinetic study of electrostatic microinstabilities in dipole plasmas

Science.gov (United States)

Xie, Hua-sheng; Zhang, Yi; Huang, Zi-cong; Ou, Wei-ke; Li, Bo

2017-12-01

A linear gyrokinetic particle-in-cell scheme, which is valid for an arbitrary perpendicular wavelength k⊥ρi and includes the parallel dynamic along the field line, is developed to study the local electrostatic drift modes in point and ring dipole plasmas. We find that the most unstable mode in this system can be either the electron mode or the ion mode. The properties and relations of these modes are studied in detail as a function of k⊥ρi , the density gradient κn, the temperature gradient κT, electron to ion temperature ratio τ=Te/Ti , and mass ratio mi/me . For conventional weak gradient parameters, the mode is on the ground state (with eigenstate number l = 0) and especially k∥˜0 for small k⊥ρi . Thus, the bounce averaged dispersion relation is also derived for comparison. For strong gradient and large k⊥ρi , most interestingly, higher order eigenstate modes with even (e.g., l = 2, 4) or odd (e.g., l = 1) parity can be most unstable, which is not expected in the previous studies. High order eigenstate can also easily be most unstable at weak gradient when τ>10 . This work can be particularly important to understand the turbulent transport in laboratory and space magnetosphere.

Mechanisms for ITB formation and control in Alcator C-Mod identified through gyrokinetic simulations of TEM turbulence

International Nuclear Information System (INIS)

Ernst, D.R.; Basse, N.; Bonoli, P.T.; Catto, P.J.; Fiore, C.L.; Greenwald, M.; Hubbard, A.E.; Marmar, E.S.; Porkolab, M.; Rice, J.E.; Zeller, K.; Zhurovich, K.; Dorland, W.

2005-01-01

Internal particle and thermal energy transport barriers are produced in Alcator C-Mod with off-axis ICRF heating, with core densities exceeding 10 21 m -3 , without core fueling, and with little change in the temperature profile. Applying on-axis ICRF heating controls the core density gradient and rate of rise. The present study employs linear and nonlinear gyrokinetic simulations of trapped electron mode (TEM) turbulence to explore mechanisms for ITB formation and control in Alcator C-Mod ITB experiments. Anomalous pinches are found to be negligible in our simulations; further, the collisional Ware pinch is sufficient to account for the slow density rise, lasting many energy confinement times. The simulations have revealed new nonlinear physics of TEM turbulence. The critical density gradient for onset of TEM turbulent transport is nonlinearly up-shifted by zonal flows. As the density profile peaks, during ITB formation, this nonlinear critical gradient is eventually exceeded, and the turbulent particle diffusivity from GS2 gyrokinetic simulations matches the particle diffusivity from transport analysis, within experimental errors. A stable equilibrium is then established when the TEM turbulent diffusion balances the Ware pinch in the ITB. This equilibrium is sensitive to temperature through gyroBohm scaling of the TEM turbulent transport, and the collisionality dependence of the neoclassical pinch, providing for control of the density rate of rise with on-axis RF heating. With no core particle fueling, and ∼1 mm between density spatial channels, the C-Mod experiments provide a nearly ideal test bed for particle transport studies. The pure TEM is the only unstable drift mode in the ITB, producing particle transport driven by the density gradient. (author)

Global gyrokinetic simulation of tokamak transport

International Nuclear Information System (INIS)

Furnish, G.; Horton, W.; Kishimoto, Y.; LeBrun, M.J.; Tajima, T.

1998-10-01

A kinetic simulation code based on the gyrokinetic ion dynamics in global general metric (including a tokamak with circular or noncircular cross-section) has been developed. This gyrokinetic simulation is capable of examining the global and semi-global driftwave structures and their associated transport in a tokamak plasma. The authors investigate the property of the ion temperature gradient (ITG) or η i (η i ≡ ∂ ell nT i /∂ ell n n i ) driven drift waves in a tokamak plasma. The emergent semi-global drift wave modes give rise to thermal transport characterized by the Bohm scaling

Gyrokinetic simulations in general geometry and applications to collisional damping of zonal flows

International Nuclear Information System (INIS)

Lin, Z.; Hahm, T.S.; Lee, W.W.; Tang, W.M.; White, R.B.

2000-01-01

A fully three-dimensional gyrokinetic particle code using magnetic coordinates for general geometry has been developed and applied to the investigation of zonal flows dynamics in toroidal ion-temperature-gradient turbulence. Full torus simulation results support the important conclusion that turbulence-driven zonal flows significantly reduce the turbulent transport. Linear collisionless simulations for damping of an initial poloidal flow perturbation exhibit an asymptotic residual flow. The collisional damping of this residual causes the dependence of ion thermal transport on the ion-ion collision frequency even in regimes where the instabilities are collisionless

Including collisions in gyrokinetic tokamak and stellarator simulations

International Nuclear Information System (INIS)

Kauffmann, Karla

2012-01-01

Particle and heat transport in fusion devices often exceed the neoclassical prediction. This anomalous transport is thought to be produced by turbulence caused by microinstabilities such as ion and electron-temperature-gradient (ITG/ETG) and trapped-electron-mode (TEM) instabilities, the latter ones known for being strongly influenced by collisions. Additionally, in stellarators, the neoclassical transport can be important in the core, and therefore investigation of the effects of collisions is an important field of study. Prior to this thesis, however, no gyrokinetic simulations retaining collisions had been performed in stellarator geometry. In this work, collisional effects were added to EUTERPE, a previously collisionless gyrokinetic code which utilizes the δf method. To simulate the collisions, a pitch-angle scattering operator was employed, and its implementation was carried out following the methods proposed in [Takizuka and Abe 1977, Vernay Master's thesis 2008]. To test this implementation, the evolution of the distribution function in a homogeneous plasma was first simulated, where Legendre polynomials constitute eigenfunctions of the collision operator. Also, the solution of the Spitzer problem was reproduced for a cylinder and a tokamak. Both these tests showed that collisions were correctly implemented and that the code is suited for more complex simulations. As a next step, the code was used to calculate the neoclassical radial particle flux by neglecting any turbulent fluctuations in the distribution function and the electric field. Particle fluxes in the neoclassical analytical regimes were simulated for tokamak and stellarator (LHD) configurations. In addition to the comparison with analytical fluxes, a successful benchmark with the DKES code was presented for the tokamak case, which further validates the code for neoclassical simulations. In the final part of the work, the effects of collisions were investigated for slab and toroidal ITGs and

[Alterations in expression of F-actin and DNA of fluid shear stress treated-mesenchymal stem cells affected by titanium particles loading].

Science.gov (United States)

Wu, Jiang; Chen, Huiqing; Cao, Hui; Zhou, Jiang; Zhang, Li; Sung, K L

2004-02-01

Particulate wear debris within the bone-prosthesis microenvironment generated by normal wear and corrosion of orthopaedic implants is considered to be one of the main factors responsible for chronic aseptic inflammation and development of osteolysis in the long-term instability and failure of total joint arthroplasty. While the decrease in bone volume caused by wear debris-induced osteolysis could have been compensated by enough new bone matrix secreted by osteoblasts. Actually, the normal osteoblastic population depend on the regular differentiation and proliferation of their progenitor cells--bone marrow mesenchymal stem cells (MSCs). This study aims to investigate the potential mechanism for the rat MSCs cytotoxicity upon exposure to Titanium (Ti) particles. Rat mesenchymal stem cells (rMSCs) isolated from 3-month-old male Sprague-Dawley rats by Percoll intensity gradient method were cultured in DMEM medium (low glucose) supplemented with 10% fetal bovine serum, 100 U/ml penicillin, and 100 micrograms/ml streptomycin in a humidified incubator with 5% CO2 at 37 degrees C. In order to gain the homogenous cell population, rMSCs were passaged to 3-4th subpassage which were used in all the experiment groups. Then rMSCs were seeded in the 6 well culture plates and exposed to three different circle diameters (mean size, TD1: 0.9 micron, TD2: 2.7 microns, TD3: 6.9 microns) with three different concentrations (0.1 wt%, 0.05 wt%, 0.01 wt%, W/V) at different durations (8 h, 16 h, 24 h,), respectively. Unexposed rMSCs were used as control. In the given periods of Ti loading, fluid shear stress (FSS) was applied to each group cells. The expression of F-actin and DNA of the rMSCs at the indicated time were determined with laser confocal scanning microscopy and image analysis software. The results showed that there was up-regulation expression of F-actin in the rMSCs without Ti particles loading but in the presence of FSS. Ti particles loading can suppress the expression of F

Alpha-, gamma- and delta-tocopherols reduce inflammatory angiogenesis in human microvascular endothelial cells.

Science.gov (United States)

Wells, Shannon R; Jennings, Merilyn H; Rome, Courtney; Hadjivassiliou, Vicky; Papas, Konstantinos A; Alexander, Jonathon S

2010-07-01

Vitamin E, a micronutrient (comprising alpha-, beta-, gamma- and delta-tocopherols, alpha-, beta-, gamma- and delta-tocotrienols), has documented antioxidant and non-antioxidant effects, some of which inhibit inflammation and angiogenesis. We compared the abilities of alpha-, gamma- and delta-tocopherols to regulate human blood cytotoxicity (BEC) and lymphatic endothelial cytotoxicity (LEC), proliferation, invasiveness, permeability, capillary formation and suppression of TNF-alpha-induced VCAM-1 as in vitro models of inflammatory angiogenesis. alpha-, gamma- and delta-tocopherols were not toxic to either cell type up to 40 microM. In BEC, confluent cell density was decreased by all concentrations of delta- and gamma-tocopherol (10-40 microM) but not by alpha-tocopherol. LEC showed no change in cell density in response to tocopherols. delta-Tocopherol (40 microM), but not other isomers, decreased BEC invasiveness. In LEC, all doses of gamma-tocopherol, as well as the highest dose of alpha-tocopherol (40 microM), decreased cell invasiveness. delta-Tocopherol had no effect on LEC invasiveness at any molarity. delta-Tocopherol dose dependently increased cell permeability at 48 h in BEC and LEC; alpha- and gamma-tocopherols showed slight effects. Capillary tube formation was decreased by high dose (40 microM) concentrations of alpha-, gamma- and delta-tocopherol, but showed no effects with smaller doses (10-20 microM) in BEC. gamma-Tocopherol (10-20 microM) and alpha-tocopherol (10 microM), but not delta-tocopherol, increased LEC capillary tube formation. Lastly, in BEC, alpha-, gamma- and delta-tocopherol each dose-dependently reduced TNF-alpha-induced expression of VCAM-1. In LEC, there was no significant change to TNF-alpha-induced VCAM-1 expression with any concentration of alpha-, gamma- or delta-tocopherol. These data demonstrate that physiological levels (0-40 microM) of alpha-, gamma- and delta-tocopherols are nontoxic and dietary tocopherols, especially delta

Gyrokinetic Statistical Absolute Equilibrium and Turbulence

International Nuclear Information System (INIS)

Zhu, Jian-Zhou; Hammett, Gregory W.

2011-01-01

A paradigm based on the absolute equilibrium of Galerkin-truncated inviscid systems to aid in understanding turbulence (T.-D. Lee, 'On some statistical properties of hydrodynamical and magnetohydrodynamical fields,' Q. Appl. Math. 10, 69 (1952)) is taken to study gyrokinetic plasma turbulence: A finite set of Fourier modes of the collisionless gyrokinetic equations are kept and the statistical equilibria are calculated; possible implications for plasma turbulence in various situations are discussed. For the case of two spatial and one velocity dimension, in the calculation with discretization also of velocity v with N grid points (where N + 1 quantities are conserved, corresponding to an energy invariant and N entropy-related invariants), the negative temperature states, corresponding to the condensation of the generalized energy into the lowest modes, are found. This indicates a generic feature of inverse energy cascade. Comparisons are made with some classical results, such as those of Charney-Hasegawa-Mima in the cold-ion limit. There is a universal shape for statistical equilibrium of gyrokinetics in three spatial and two velocity dimensions with just one conserved quantity. Possible physical relevance to turbulence, such as ITG zonal flows, and to a critical balance hypothesis are also discussed.

Gyrokinetic statistical absolute equilibrium and turbulence

International Nuclear Information System (INIS)

Zhu Jianzhou; Hammett, Gregory W.

2010-01-01

A paradigm based on the absolute equilibrium of Galerkin-truncated inviscid systems to aid in understanding turbulence [T.-D. Lee, Q. Appl. Math. 10, 69 (1952)] is taken to study gyrokinetic plasma turbulence: a finite set of Fourier modes of the collisionless gyrokinetic equations are kept and the statistical equilibria are calculated; possible implications for plasma turbulence in various situations are discussed. For the case of two spatial and one velocity dimension, in the calculation with discretization also of velocity v with N grid points (where N+1 quantities are conserved, corresponding to an energy invariant and N entropy-related invariants), the negative temperature states, corresponding to the condensation of the generalized energy into the lowest modes, are found. This indicates a generic feature of inverse energy cascade. Comparisons are made with some classical results, such as those of Charney-Hasegawa-Mima in the cold-ion limit. There is a universal shape for statistical equilibrium of gyrokinetics in three spatial and two velocity dimensions with just one conserved quantity. Possible physical relevance to turbulence, such as ITG zonal flows, and to a critical balance hypothesis are also discussed.

Expansion of mycobacterium-reactive gamma delta T cells by a subset of memory helper T cells.

Science.gov (United States)

Vila, L M; Haftel, H M; Park, H S; Lin, M S; Romzek, N C; Hanash, S M; Holoshitz, J

1995-04-01

Human gamma delta T cells expressing the V gamma 9/V delta 2 T-cell receptor have been previously found to proliferate in response to certain microorganisms and to expand throughout life, presumably because of extrathymic activation by foreign antigens. In vitro expansion of V gamma 9/V delta 2 cells by mycobacteria has been previously shown to be dependent on accessory cells. In order to gain an insight into the mechanisms involved in the expansion of these cells, we have undertaken to identify the peripheral blood subset of cells on which proliferation of V gamma 9/V delta 2 cells in response to mycobacteria is dependent. Contrary to their role in antigen presentation to alpha beta T cells, professional antigen-presenting cells, such as monocytes, B cells, and dendritic cells, were unable to provide the cellular support for the expansion of V gamma 9/V delta 2 cells. Selective depletion of T-cell subsets, as well as the use of highly purified T-cell populations, indicated that the only subset of peripheral blood cells that could expand V gamma 9/V delta 2 cells were CD4+ CD45RO+ CD7- alpha beta T cells. These cells underwent distinct intracellular signaling events after stimulation with the mycobacterial antigen. Expansion of V gamma 9/V delta 2 cells by alpha beta T cells was dependent on cell-cell contact. This is the first evidence that a small subset of the memory helper T-cell population is exclusively responsible for the peripheral expansion of V gamma 9/V delta 2 cells. These data illustrate a unique aspect of antigen recognition by gamma delta T cells and provide new means to study their immune defense role.

Plasticity of gamma delta T cells: impact on the anti-tumor response

Directory of Open Access Journals (Sweden)

Virginie eLafont

2014-12-01

Full Text Available The tumor immune microenvironment contributes to tumor initiation, progression and response to therapy. Among the immune cell subsets that play a role in the tumor microenvironment, innate-like T cells that express T cell receptors composed of gamma and delta chains (gamma delta T cells are of particular interest. gamma delta T cells can contribute to the immune response against many tumor types (lymphoma, myeloma, melanoma, breast, colon, lung, ovary and prostate cancer directly through their cytotoxic activity and indirectly by stimulating or regulating the biological functions of other cell types required for the initiation and establishment of the anti-tumor immune response, such as dendritic cells and cytotoxic CD8+ T cells. However, the notion that tumor-infiltrating gamma delta T cells are a good prognostic marker in cancer was recently challenged by studies showing that the presence of these cells in the tumor microenvironment was associated with poor prognosis in both breast and colon cancer. These findings suggest that gamma delta T cells may also display pro-tumor activities. Indeed, breast tumor-infiltrating gamma deltaT cells could exert an immunosuppressive activity by negatively regulating DC maturation. Furthermore, recent studies demonstrated that signals from the microenvironment, particularly cytokines, can confer some plasticity to gamma delta T cells and promote their differentiation into gamma delta T cells with regulatory functions. This review focuses on the current knowledge on the functional plasticity of gamma delta T cells and its effect on their anti-tumor activities. It also discusses the putative mechanisms underlying gamma delta T cell expansion, differentiation and recruitment in the tumor microenvironment.

Gyrokinetic Simulation of Global Turbulent Transport Properties in Tokamak Experiments

Energy Technology Data Exchange (ETDEWEB)

Wang, W.X.; Lin, Z.; Tang, W.M.; Lee, W.W.; Ethier, S.; Lewandowski, J.L.V.; Rewoldt, G.; Hahm, T.S.; Manickam, J.

2006-01-01

A general geometry gyro-kinetic model for particle simulation of plasma turbulence in tokamak experiments is described. It incorporates the comprehensive influence of noncircular cross section, realistic plasma profiles, plasma rotation, neoclassical (equilibrium) electric fields, and Coulomb collisions. An interesting result of global turbulence development in a shaped tokamak plasma is presented with regard to nonlinear turbulence spreading into the linearly stable region. The mutual interaction between turbulence and zonal flows in collisionless plasmas is studied with a focus on identifying possible nonlinear saturation mechanisms for zonal flows. A bursting temporal behavior with a period longer than the geodesic acoustic oscillation period is observed even in a collisionless system. Our simulation results suggest that the zonal flows can drive turbulence. However, this process is too weak to be an effective zonal flow saturation mechanism.

Clinical applications of gamma delta T cells with multivalent immunity

Directory of Open Access Journals (Sweden)

Drew C Deniger

2014-12-01

Full Text Available Gamma delta T cells hold promise for adoptive immunotherapy because of their reactivity to bacteria, viruses, and tumors. However, these cells represent a small fraction (1-5% of the peripheral T-cell pool and require activation and propagation to achieve clinical benefit. Aminobisphosphonates specifically expand the Vgamma9Vdelta2 subset of gamma delta T cells and have been used in clinical trials of cancer where objective responses were detected. The Vgamma9Vdelta2 TCR heterodimer binds multiple ligands and results in a multivalent attack by a monoclonal T cell population. Alternatively, populations of gamma delta T cells with oligoclonal or polyclonal TCR repertoire could be infused for broad-range specificity. However, this goal has been restricted by a lack of applicable expansion protocols for non-Vgamma9Vdelta2 cells. Recent advances using immobilized antigens, agonistic monoclonal antibodies (mAbs, tumor-derived artificial antigen presenting cells (aAPC, or combinations of activating mAbs and aAPC have been successful in expanding gamma delta T cells with oligoclonal or polyclonal TCR repertoires. Immobilized MHC Class-I chain-related A was a stimulus for gamma delta T cells expressing TCRdelta1 isotypes, and plate-bound activating antibodies have expanded Vdelta1 and Vdelta2 cells ex vivo. Clinically-sufficient quantities of TCRdelta1, TCRdelta2, and TCRdelta1negTCRdelta2neg have been produced following co-culture on aAPC, and these subsets displayed differences in memory phenotype and reactivity to tumors in vitro and in vivo. Gamma delta T cells are also amenable to genetic modification as evidenced by introduction of alpha beta TCRs, chimeric antigen receptors (CARs, and drug-resistance genes. This represents a promising future for the clinical application of oligoclonal or polyclonal gamma delta T cells in autologous and allogeneic settings that builds on current trials testing the safety and efficacy of Vgamma9Vdelta2 T cells.

Visualizing Gyrokinetic Turbulence in a Tokamak

Science.gov (United States)

Stantchev, George

2005-10-01

Multi-dimensional data output from gyrokinetic microturbulence codes are often difficult to visualize, in part due to the non-trivial geometry of the underlying grids, in part due to high irregularity of the relevant scalar field structures in turbulent regions. For instance, traditional isosurface extraction methods are likely to fail for the electrostatic potential field whose level sets may exhibit various geometric pathologies. To address these issues we develop an advanced interactive 3D gyrokinetic turbulence visualization framework which we apply in the study of microtearing instabilities calculated with GS2 in the MAST and NSTX geometries. In these simulations GS2 uses field-line-following coordinates such that the computational domain maps in physical space to a long, twisting flux tube with strong cross-sectional shear. Using statistical wavelet analysis we create a sparse multiple-scale volumetric representation of the relevant scalar fields, which we visualize via a variation of the so called splatting technique. To handle the problem of highly anisotropic flux tube configurations we adapt a geometry-driven surface illumination algorithm that places local light sources for effective feature-enhanced visualization.

Introducing a distributed unstructured mesh into gyrokinetic particle-in-cell code, XGC

Science.gov (United States)

Yoon, Eisung; Shephard, Mark; Seol, E. Seegyoung; Kalyanaraman, Kaushik

2017-10-01

XGC has shown good scalability for large leadership supercomputers. The current production version uses a copy of the entire unstructured finite element mesh on every MPI rank. Although an obvious scalability issue if the mesh sizes are to be dramatically increased, the current approach is also not optimal with respect to data locality of particles and mesh information. To address these issues we have initiated the development of a distributed mesh PIC method. This approach directly addresses the base scalability issue with respect to mesh size and, through the use of a mesh entity centric view of the particle mesh relationship, provides opportunities to address data locality needs of many core and GPU supported heterogeneous systems. The parallel mesh PIC capabilities are being built on the Parallel Unstructured Mesh Infrastructure (PUMI). The presentation will first overview the form of mesh distribution used and indicate the structures and functions used to support the mesh, the particles and their interaction. Attention will then focus on the node-level optimizations being carried out to ensure performant operation of all PIC operations on the distributed mesh. Partnership for Edge Physics Simulation (EPSI) Grant No. DE-SC0008449 and Center for Extended Magnetohydrodynamic Modeling (CEMM) Grant No. DE-SC0006618.

Advax™, a novel microcrystalline polysaccharide particle engineered from delta inulin, provides robust adjuvant potency together with tolerability and safety.

Science.gov (United States)

Petrovsky, Nikolai; Cooper, Peter D

2015-11-04

There is an ongoing need for new adjuvants to facilitate development of vaccines against HIV, tuberculosis, malaria and cancer, amongst many others. Unfortunately, the most potent adjuvants are often associated with toxicity and safety issues. Inulin, a plant-derived polysaccharide, has no immunological activity in its native soluble form but when crystallized into a stable microcrystalline particulate from (delta inulin) acquires potent adjuvant activity. Delta inulin has been shown to enhance humoral and cellular immune responses against a broad range of co-administered viral, bacterial, parasitic and toxin antigens. Inulin normally crystallizes as large heterogeneous particles with a broad size distribution and variable solubility temperatures. To ensure reproducible delta inulin particles with a consistent size distribution and temperature of solubility, a current Good Manufacturing Practice (cGMP) process was designed to produce Advax™ adjuvant. In its cCMP form, Advax™ adjuvant has proved successful in human trials of vaccines against seasonal and pandemic influenza, hepatitis B and insect sting anaphylaxis, enhancing antibody and T-cell responses while being safe and well tolerated. Advax™ adjuvant represents a novel human adjuvant that enhances both humoral and cellular immunity. This review describes the discovery and development of Advax™ adjuvant and research into its unique mechanism of action. Copyright © 2015 Elsevier Ltd. All rights reserved.

Particles on surfaces of laser ablated Y{sub 1}Ba{sub 2}Cu{sub 3}O{sub 7-{delta}} films

Energy Technology Data Exchange (ETDEWEB)

Zheng, X.Y.; Zhu, S. [Tennessee Univ., Knoxville, TN (United States); Lowndes, D.H.; Warmack, R.J. [Oak Ridge National Lab., TN (United States)

1993-09-01

Pulsed laser deposition of Y{sub 1}Ba{sub 2}Cu{sub 3}O{sub 7-{delta}} films grown at heater temperature of 720 and 800 C on SrTiO{sub 3} and MgO substrates with thickness ranging from a nominal 5 unit cells to 200 nm were studied by STM and SEM. Size and density of particles present in the films were found to depend on film thickness, growth temperature and substrate. STM images indicate a correlation between film growth mode and particle density: the onset of big particles comes after the growth mode changes from layer-like to island growth.

Variational principle for nonlinear gyrokinetic Vlasov--Maxwell equations

International Nuclear Information System (INIS)

Brizard, Alain J.

2000-01-01

A new variational principle for the nonlinear gyrokinetic Vlasov--Maxwell equations is presented. This Eulerian variational principle uses constrained variations for the gyrocenter Vlasov distribution in eight-dimensional extended phase space and turns out to be simpler than the Lagrangian variational principle recently presented by H. Sugama [Phys. Plasmas 7, 466 (2000)]. A local energy conservation law is then derived explicitly by the Noether method. In future work, this new variational principle will be used to derive self-consistent, nonlinear, low-frequency Vlasov--Maxwell bounce-gyrokinetic equations, in which the fast gyromotion and bounce-motion time scales have been eliminated

Gyrokinetic particle simulation of neoclassical transport in the pedestal/scrape-off region of a tokamak plasma

Energy Technology Data Exchange (ETDEWEB)

Ku, S [Courant Institute of Mathematical Sciences, New York University (United States); Chang, C-S [Courant Institute of Mathematical Sciences, New York University (United States); Adams, M [Columbia University (United States); Cummings, J [California Institute of Technology (United States); Hinton, F [Hinton Associates (United States); Keyes, D [Columbia University (United States); Klasky, S [Oak Ridge National Laboratory (United States); Lee, W [Princeton Plasma Physics Laboratory (United States); Lin, Z [University of California at Irvine (United States); Parker, S [University of Colorado at Boulder (United States)

2006-09-15

A gyrokinetic neoclassical solution for a diverted tokamak edge plasma has been obtained for the first time using the massively parallel Jaguar XT3 computer at Oak Ridge National Laboratory. The solutions show similar characteristics to the experimental observations: electric potential is positive in the scrape-off layer and negative in the H-mode layer, and the parallel rotation is positive in the scrape-off layer and at the inside boundary of the H-mode layer. However, the solution also makes a new physical discovery that there is a strong ExB convective flow in the scrape-off plasma. A general introduction to the edge simulation problem is also presented.

Nonlinear gyrokinetics: a powerful tool for the description of microturbulence in magnetized plasmas

International Nuclear Information System (INIS)

Krommes, John A

2010-01-01

Gyrokinetics is the description of low-frequency dynamics in magnetized plasmas. In magnetic-confinement fusion, it provides the most fundamental basis for numerical simulations of microturbulence; there are astrophysical applications as well. In this tutorial, a sketch of the derivation of the novel dynamical system comprising the nonlinear gyrokinetic (GK) equation (GKE) and the coupled electrostatic GK Poisson equation will be given by using modern Lagrangian and Lie perturbation methods. No background in plasma physics is required in order to appreciate the logical development. The GKE describes the evolution of an ensemble of gyrocenters moving in a weakly inhomogeneous background magnetic field and in the presence of electromagnetic perturbations with wavelength of the order of the ion gyroradius. Gyrocenters move with effective drifts, which may be obtained by an averaging procedure that systematically, order by order, removes gyrophase dependence. To that end, the use of the Lagrangian differential one-form as well as the content and advantages of Lie perturbation theory will be explained. The electromagnetic fields follow via Maxwell's equations from the charge and current density of the particles. Particle and gyrocenter densities differ by an important polarization effect. That is calculated formally by a 'pull-back' (a concept from differential geometry) of the gyrocenter distribution to the laboratory coordinate system. A natural truncation then leads to the closed GK dynamical system. Important properties such as GK energy conservation and fluctuation noise will be mentioned briefly, as will the possibility (and difficulties) of deriving nonlinear gyrofluid equations suitable for rapid numerical solution-although it is probably best to directly simulate the GKE. By the end of the tutorial, students should appreciate the GKE as an extremely powerful tool and will be prepared for later lectures describing its applications to physical problems.

Nonlinear Gyrokinetics: A Powerful Tool for the Description of Microturbulence in Magnetized Plasmas

International Nuclear Information System (INIS)

Krommes, John E.

2010-01-01

Gyrokinetics is the description of low-frequency dynamics in magnetized plasmas. In magnetic-confinement fusion, it provides the most fundamental basis for numerical simulations of microturbulence; there are astrophysical applications as well. In this tutorial, a sketch of the derivation of the novel dynamical system comprising the nonlinear gyrokinetic (GK) equation (GKE) and the coupled electrostatic GK Poisson equation will be given by using modern Lagrangian and Lie perturbation methods. No background in plasma physics is required in order to appreciate the logical development. The GKE describes the evolution of an ensemble of gyrocenters moving in a weakly inhomogeneous background magnetic field and in the presence of electromagnetic perturbations with wavelength of the order of the ion gyroradius. Gyrocenters move with effective drifts, which may be obtained by an averaging procedure that systematically, order by order, removes gyrophase dependence. To that end, the use of the Lagrangian differential one-form as well as the content and advantages of Lie perturbation theory will be explained. The electromagnetic fields follow via Maxwell's equations from the charge and current density of the particles. Particle and gyrocenter densities differ by an important polarization effect. That is calculated formally by a 'pull-back' (a concept from differential geometry) of the gyrocenter distribution to the laboratory coordinate system. A natural truncation then leads to the closed GK dynamical system. Important properties such as GK energy conservation and fluctuation noise will be mentioned briefly, as will the possibility (and diffculties) of deriving nonlinear gyro fluid equations suitable for rapid numerical solution - although it is probably best to directly simulate the GKE. By the end of the tutorial, students should appreciate the GKE as an extremely powerful tool and will be prepared for later lectures describing its applications to physical problems.

Conservation Laws for Gyrokinetic Equations for Large Perturbations and Flows

Science.gov (United States)

Dimits, Andris

2017-10-01

Gyrokinetic theory has proved to be very useful for the understanding of magnetized plasmas, both to simplify analytical treatments and as a basis for efficient numerical simulations. Gyrokinetic theories were previously developed in two extended orderings that are applicable to large fluctuations and flows as may arise in the tokamak edge and scrapeoff layer. In the present work, we cast the resulting equations in a field-theoretical variational form, and derive, up to second order in the respective orderings, the associated global and local energy and (linear and toroidal) momentum conservation relations that result from Noether's theorem. The consequences of these for the various possible choices of numerical discretization used in gyrokinetic simulations are considered. Prepared for US DOE by LLNL under Contract DE-AC52-07NA27344 and supported by the U.S. DOE, OFES.

Characterization of T cell receptor assembly and expression in a Ti gamma delta-positive cell line

DEFF Research Database (Denmark)

Kuhlmann, J; Caspar-Bauguil, S; Geisler, C

1993-01-01

- variants of the T cell Lyon were induced and found to produce all of the Ti/CD3 components, with the exception of Ti-delta. Biochemical analysis indicated that: (1) Ti-gamma/CD3 gamma, delta, epsilon complexes were formed in the endoplasmic reticulum in the absence of Ti-delta; (2) the CD3-zeta chain did...

Femosecond dynamics of quasi-particles in YBa sub 2 Cu sub 3 O sub 7 minus. delta. superconductor films

Energy Technology Data Exchange (ETDEWEB)

Han, S.G.; Vardeny, Z.V.; Symko, O.G. (Utah Univ., Salt Lake City, UT (United States). Dept. of Physics); Koren, G. (Technion-Israel Inst. of Tech., Haifa (Israel). Dept. of Physics)

1991-03-01

This paper reports on the transient electronic response of YBa{sub 2}Cu{sub 3}O{sub 7{minus}{delta}} epitaxially grown HT{sub c} superconductor thin films in the femtosecond time domain, using transient photoinduced reflectivity ({Delta}R) with 60 fsec time resolution. For temperatures T {gt} T{sub c} only a bolometric signal was observed with {Delta}R {gt} O. For T {lt} T{sub c} {Delta}R {lt} O with a temperature dependent rise time of order 300 fsec followed by a relaxation (of order 3 psec) into a state with {Delta} are explained in terms of quasi-particle (QP) electronic response giving {Delta}R {lt} O. Thus the femtosecond rise time is interpreted as avalanche multiplication of QP across the gap 2{Delta} and the subsequent picosecond relaxation as QP recombination. The QP optical response is explained within the two fluid model.

Development of a global toroidal gyrokinetic Vlasov code with new real space field solver

International Nuclear Information System (INIS)

Obrejan, Kevin; Imadera, Kenji; Li, Ji-Quan; Kishimoto, Yasuaki

2015-01-01

This work introduces a new full-f toroidal gyrokinetic (GK) Vlasov simulation code that uses a real space field solver. This solver enables us to compute the gyro-averaging operators in real space to allow proper treatment of finite Larmor radius (FLR) effects without requiring any particular hypothesis and in any magnetic field configuration (X-point, D-shaped etc). The code was well verified through benchmark tests such as toroidal Ion Temperature Gradient (ITG) instability and collisionless damping of zonal flow. (author)

Anisotropy-Driven Instability in Intense Charged Particle Beams

CERN Document Server

Startsev, Edward; Qin, Hong

2005-01-01

In electrically neutral plasmas with strongly anisotropic distribution functions, free energy is available to drive different collective instabilities such as the electrostatic Harris instability and the transverse electromagnetic Weibel instability. Such anisotropies develop naturally in particle accelerators and may lead to a detoriation of beam quality. We have generalized the analysis of the classical Harris and Weibel instabilities to the case of a one-component intense charged particle beam with anisotropic temperature including the important effects of finite transverse geometry and beam space-charge. For a long costing beam, the delta-f particle-in-cell code BEST and the eighenmode code bEASt have been used to determine detailed 3D stability properties over a wide range of temperature anisotropy and beam intensity. A theoretical model is developed which describes the essential features of the linear stage of these instabilities. Both, the simulations and analytical theory, clearly show that moderately...

Local and global eulerian gyrokinetic simulations of microturbulence in realistic geometry with applications to the TCV Tokamak

International Nuclear Information System (INIS)

Lapillonne, X.

2010-04-01

In magnetically confined fusion devices, the energy and particle transport is significantly larger than expected from purely collisional processes. This degraded confinement mostly results from small-scale turbulence and prevents from reaching self-sustained burning plasma conditions in present day experiments. A better understanding of these nonlinear phenomena is therefore of key importance on the way towards controlled fusion. The small-scale microinstabilities and associated turbulence are investigated for Tokamak plasmas by means of numerical simulations in the frame of the gyrokinetic theory. This model describes the evolution of the particle distribution functions in phase space together with self-consistent electromagnetic fields, while neglecting the fast motion associated with the Larmor orbit of particles around the magnetic field lines. In the course of this thesis work, substantial modifications to the existing Eulerian gyrokinetic code GENE have been carried out in collaboration with the Max-Planck- Institute f¨ur Plasmaphysik in Garching, Germany. The code has been extended from a local approximation, which only considers a reduced volume of a fusion plasma, to a global version which fully includes radial temperature and density profiles as well as radial magnetic equilibrium variations. To this end, the gyrokinetic equations have been formulated for general magnetic geometry, keeping radial variations of equilibrium quantities, and considering field aligned coordinates, suitable for their numerical implementation. The numerical treatment of the radial direction has been modified from a Fourier representation in the local approach to real space in the global code. This has in particular required to adapt the radial derivatives, the field solver, and to implement a real space dealiasing scheme for the treatment of the nonlinearity. A heat source was in addition introduced to allow for steady state global nonlinear simulations. An important part of

Considering fluctuation energy as a measure of gyrokinetic turbulence

International Nuclear Information System (INIS)

Plunk, G G; Tatsuno, T; Dorland, W

2012-01-01

In gyrokinetic theory, there are two quadratic measures of fluctuation energy, left invariant under nonlinear interactions, that constrain turbulence. In a recent work (Plunk and Tatsuno 2011 Phys. Rev. Lett. 106 165003) we reported on the novel consequences that this constraint has for the direction and locality of spectral energy transfer. This paper builds on that previous work. We provide a detailed analysis in support of the results of Plunk and Tatsuno (2011 Phys. Rev. Lett. 106 165003), but significantly broaden the scope and use additional methods to address the problem of energy transfer. The perspective taken here is that the fluctuation energies are not merely formal invariants of an idealized model (two-dimensional gyrokinetics (Plunk et al 2010 J. Fluid Mech. 664 407–35)) but also general measures of gyrokinetic turbulence, i.e. quantities that can be used to predict the behavior of turbulence. Although many questions remain open, this paper collects evidence in favor of this perspective by demonstrating in several contexts that constrained spectral energy transfer governs the dynamics. (paper)

Verification of gyrokinetic microstability codes with an LHD configuration

Energy Technology Data Exchange (ETDEWEB)

Mikkelsen, D. R. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Nunami, M. [National Inst. for Fusion Science (Japan); Watanabe, T. -H. [Nagoya Univ. (Japan); Sugama, H. [National Inst. for Fusion Science (Japan); Tanaka, K. [National Inst. for Fusion Science (Japan)

2014-11-01

We extend previous benchmarks of the GS2 and GKV-X codes to verify their algorithms for solving the gyrokinetic Vlasov-Poisson equations for plasma microturbulence. Code benchmarks are the most complete way of verifying the correctness of implementations for the solution of mathematical models for complex physical processes such as those studied here. The linear stability calculations reported here are based on the plasma conditions of an ion-ITB plasma in the LHD configuration. The plasma parameters and the magnetic geometry differ from previous benchmarks involving these codes. We find excellent agreement between the independently written pre-processors that calculate the geometrical coefficients used in the gyrokinetic equations. Grid convergence tests are used to establish the resolution and domain size needed to obtain converged linear stability results. The agreement of the frequencies, growth rates and eigenfunctions in the benchmarks reported here provides additional verification that the algorithms used by the GS2 and GKV-X codes are correctly finding the linear eigenvalues and eigenfunctions of the gyrokinetic Vlasov-Poisson equations.

CCL20, (gamma)(delta) T cells, and IL-22 in corneal epithelial healing

Science.gov (United States)

After corneal epithelial abrasion, leukocytes and platelets rapidly enter the corneal stroma, and CCR6 (+) IL-17(+) gamma delta T cells migrate into the epithelium. Gamma delta T-cell-deficient (TCRd(-/-)) mice have significantly reduced inflammation and epithelial wound healing. Epithelial CCL20 mR...

Testing Gyrokinetics on C-Mod and NSTX

International Nuclear Information System (INIS)

Redi, M.H.; Dorland, W.; Fiore, C.L.; Stutman, D.; Baumgaertel, J.A.; Davis, B.; Kaye, S.M.; McCune, D.C.; Menard, J.; Rewoldt, G.

2005-01-01

Quantitative benchmarks of computational physics codes against experiment are essential for the credible application of such codes. Fluctuation measurements can provide necessary critical tests of nonlinear gyrokinetic simulations, but such require extraordinary computational resources. Linear micro-stability calculations with the GS2 [1] gyrokinetic code have been carried out for tokamak and ST experiments which exhibit internal transport barriers (ITB) and good plasma confinement. Qualitative correlation is found for improved confinement before and during ITB plasmas on Alcator C-Mod [2] and NSTX [3], with weaker long wavelength micro-instabilities in the plasma core regions. Mixing length transport models are discussed. The NSTX L-mode is found to be near marginal stability for kinetic ballooning modes. Fully electromagnetic, linear, gyrokinetic calculations of the Alcator C-Mod ITB during off-axis rf heating, following four plasma species and including the complete electron response show ITG/TEM microturbulence is suppressed in the plasma core and in the barrier region before barrier formation, without recourse to the usual requirements of velocity shear or reversed magnetic shear [4-5]. No strongly growing long or short wavelength drift modes are found in the plasma core but strong ITG/TEM and ETG drift wave turbulence is found outside the barrier region. Linear microstability analysis is qualitatively consistent with the experimental transport analysis, showing low transport inside and high transport outside the ITB region before barrier formation, without consideration of ExB shear stabilization

The implementation of a toroidal limiter model into the gyrokinetic code ELMFIRE

Energy Technology Data Exchange (ETDEWEB)

Leerink, S.; Janhunen, S.J.; Kiviniemi, T.P.; Nora, M. [Euratom-Tekes Association, Helsinki University of Technology (Finland); Heikkinen, J.A. [Euratom-Tekes Association, VTT, P.O. Box 1000, FI-02044 VTT (Finland); Ogando, F. [Universidad Nacional de Educacion a Distancia, Madrid (Spain)

2008-03-15

The ELMFIRE full nonlinear gyrokinetic simulation code has been developed for calculations of plasma evolution and dynamics of turbulence in tokamak geometry. The code is applicable for calculations of strong perturbations in particle distribution function, rapid transients and steep gradients in plasma. Benchmarking against experimental reflectometry data from the FT2 tokamak is being discussed and in this paper a model for comparison and studying poloidal velocity is presented. To make the ELMFIRE code suitable for scrape-off layer simulations a simplified toroidal limiter model has been implemented. The model is be discussed and first results are presented. (copyright 2008 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

Tractable flux-driven temperature, density, and rotation profile evolution with the quasilinear gyrokinetic transport model QuaLiKiz

Science.gov (United States)

Citrin, J.; Bourdelle, C.; Casson, F. J.; Angioni, C.; Bonanomi, N.; Camenen, Y.; Garbet, X.; Garzotti, L.; Görler, T.; Gürcan, O.; Koechl, F.; Imbeaux, F.; Linder, O.; van de Plassche, K.; Strand, P.; Szepesi, G.; Contributors, JET

2017-12-01

Quasilinear turbulent transport models are a successful tool for prediction of core tokamak plasma profiles in many regimes. Their success hinges on the reproduction of local nonlinear gyrokinetic fluxes. We focus on significant progress in the quasilinear gyrokinetic transport model QuaLiKiz (Bourdelle et al 2016 Plasma Phys. Control. Fusion 58 014036), which employs an approximated solution of the mode structures to significantly speed up computation time compared to full linear gyrokinetic solvers. Optimisation of the dispersion relation solution algorithm within integrated modelling applications leads to flux calculations × {10}6-7 faster than local nonlinear simulations. This allows tractable simulation of flux-driven dynamic profile evolution including all transport channels: ion and electron heat, main particles, impurities, and momentum. Furthermore, QuaLiKiz now includes the impact of rotation and temperature anisotropy induced poloidal asymmetry on heavy impurity transport, important for W-transport applications. Application within the JETTO integrated modelling code results in 1 s of JET plasma simulation within 10 h using 10 CPUs. Simultaneous predictions of core density, temperature, and toroidal rotation profiles for both JET hybrid and baseline experiments are presented, covering both ion and electron turbulence scales. The simulations are successfully compared to measured profiles, with agreement mostly in the 5%-25% range according to standard figures of merit. QuaLiKiz is now open source and available at www.qualikiz.com.

Gyrokinetic simulations of turbulent transport: size scaling and chaotic behaviour

International Nuclear Information System (INIS)

Villard, L; Brunner, S; Casati, A; Aghdam, S Khosh; Lapillonne, X; McMillan, B F; Bottino, A; Dannert, T; Goerler, T; Hatzky, R; Jenko, F; Merz, F; Chowdhury, J; Ganesh, R; Garbet, X; Grandgirard, V; Latu, G; Sarazin, Y; Idomura, Y; Jolliet, S

2010-01-01

Important steps towards the understanding of turbulent transport have been made with the development of the gyrokinetic framework for describing turbulence and with the emergence of numerical codes able to solve the set of gyrokinetic equations. This paper presents some of the main recent advances in gyrokinetic theory and computing of turbulence. Solving 5D gyrokinetic equations for each species requires state-of-the-art high performance computing techniques involving massively parallel computers and parallel scalable algorithms. The various numerical schemes that have been explored until now, Lagrangian, Eulerian and semi-Lagrangian, each have their advantages and drawbacks. A past controversy regarding the finite size effect (finite ρ * ) in ITG turbulence has now been resolved. It has triggered an intensive benchmarking effort and careful examination of the convergence properties of the different numerical approaches. Now, both Eulerian and Lagrangian global codes are shown to agree and to converge to the flux-tube result in the ρ * → 0 limit. It is found, however, that an appropriate treatment of geometrical terms is necessary: inconsistent approximations that are sometimes used can lead to important discrepancies. Turbulent processes are characterized by a chaotic behaviour, often accompanied by bursts and avalanches. Performing ensemble averages of statistically independent simulations, starting from different initial conditions, is presented as a way to assess the intrinsic variability of turbulent fluxes and obtain reliable estimates of the standard deviation. Further developments concerning non-adiabatic electron dynamics around mode-rational surfaces and electromagnetic effects are discussed.

Subcellular topological effect of particle monolayers on cell shapes and functions.

Science.gov (United States)

Miura, Manabu; Fujimoto, Keiji

2006-12-01

We studied topological effects of subcellular roughness displayed by a closely packed particle monolayer on adhesion and growth of endothelial cells. Poly(styrene-co-acrylamide) (SA) particles were prepared by soap-free emulsion copolymerization. Particle monolayers were prepared by Langmuir-Blodgett deposition using particles, which were 527 (SA053) and 1270 nm (SA127) in diameter. After 24-h incubation, cells tightly adhered on a tissue culture polystyrene dish and randomly spread. On the other hand, cells attached on particle monolayers were stretched into a narrow stalk-like shape. Lamellipodia spread from the leading edge of cells attached on SA053 monolayer to the top of the particles and gradually gathered to form clusters. This shows that cell-cell adhesion became stronger than cell-substrate interaction. Cells attached to SA127 monolayer extended to the reverse side of a particle monolayer and engulfed particles. They remained immobile without migration 24h after incubation. This shows that the inhibition of extensions on SA127 monolayer could inhibit cell migration and cell proliferation. Cell growth on the particle monolayers was suppressed compared with a flat TCPS dish. The number of cells on SA053 gradually increased, whereas that on SA127 decreased with time. When the cell seeding density was increased to 200,000 cells cm(-2), some adherent cells gradually became into contact with adjacent cells. F-actin condensations were formed at the frame of adherent cells and the thin filaments grew from the edges to connect each other with time. For the cell culture on SA053 monolayer, elongated cells showed a little alignment. Cells showed not arrangement of actin stress fibers but F-actin condensation at the contact regions with neighboring cells. Interestingly, the formed cell monolayer could be readily peeled from the particle monolayer. These results indicate that endothelial cells could recognize the surface roughness displayed by particle monolayers and

COMPREHENSIVE GYROKINETIC SIMULATION OF TOKAMAK TURBULENCE AT FINITE RELATIVE GYRORADIUS

International Nuclear Information System (INIS)

WALTZ, R.E.; CANDY, J.; ROSENBLUTH, M.N.

2002-01-01

OAK B202 COMPREHENSIVE GYROKINETIC SIMULATION OF TOKAMAK TURBULENCE AT FINITE RELATIVE GYRORADIUS. A continuum global gyrokinetic code GYRO has been developed to comprehensively simulate turbulent transport in actual experimental profiles and allow direct quantitative comparisons to the experimental transport flows. GYRO not only treats the now standard ion temperature gradient (ITG) mode turbulence, but also treats trapped and passing electrons with collisions and finite beta, and all in real tokamak geometry. Most importantly the code operates at finite relative gyroradius (ρ*) so as to treat the profile shear stabilization effects which break gyroBohm scaling. The code operates in a cyclic flux tube limit which allows only gyroBohm scaling and a noncyclic radial annulus with physical profile variation. The later requires an adaptive source to maintain equilibrium profiles. Simple ITG simulations demonstrate the broken gyroBohm scaling depends on the actual rotational velocity shear rates competing with mode growth rates, direct comprehensive simulations of the DIII-D ρ*-scaled L-mode experiments are presented as a quantitative test of gyrokinetics and the paradigm

Measurement of delta-rays in ATLAS silicon sensors

CERN Document Server

The ATLAS collaboration

2013-01-01

In the inner detector of the ATLAS experiment at the LHC, $\\delta$-rays originating from particle interactions in the silicon sensors may cause additional hit channels. A method for identifying silicon hit clusters that are enlarged due to the emission of a $\\delta$-ray is presented. Using pp collision data the expectation is confirmed that the $\\delta$-ray production rate depends linearly on the path length of the particle in silicon, independently of layer radius and detector technology. The range of the $\\delta$-rays, which is a property of the material and should not depend on anything else, is indeed found to be constant as a function of detector layer, path length in silicon and momentum of the particle traversing the silicon. As a by-product of this analysis a method is proposed that could correct for the effect of these $\\delta$-rays, and this could be used to improve track reconstruction.

C-terminal cleavage of DeltaNp63alpha is associated with TSA-induced apoptosis in immortalized corneal epithelial cells.

Science.gov (United States)

Robertson, Danielle M; Ho, Su-Inn; Cavanagh, H Dwight

2010-08-01

In the central human corneal epithelium, loss of DeltaNp63 occurs in all surface epithelial cells preparing to undergo desquamation, suggesting a potential role for DeltaNp63 isoforms in mediating surface cell apoptotic shedding. In this study, the authors investigated a role for DeltaNp63 isoforms in caspase-mediated apoptosis in a telomerase-immortalized corneal epithelial cell line. For in vitro studies, hTCEpi cells were cultured in KGM-2 serum-free culture media containing 0.15 mM calcium. To assess dynamic protein interactions among individual DeltaNp63 isoforms, DeltaNp63-EGFP expression plasmids were transiently expressed in hTCEpi cells and evaluated by FRAP. Trichostatin-A (TSA; 3.31 muM) was used to induce cell death as measured by caspase activity. Cleavage and loss of endogenous DeltaNp63alpha, DeltaNp63-EGFP expression plasmids, and p53 were assessed after treatment with TSA and siRNA. Transient expression of DeltaNp63-EGFP alpha and beta isoforms resulted in the formation of a smaller isoform similar in size to DeltaNp63gamma-EGFP. FRAP demonstrated that DeltaNp63alpha-EGFP has greater immobile fraction than beta or gamma. TSA induced caspase-mediated apoptotic pathways; caspase induction was accompanied by a decrease in endogenous DeltaNp63alpha and p53. TSA upregulated DeltaNp63-EGFP plasmid expression; this was accompanied by a selective increase in cleavage of DeltaNp63alpha-EGFP. siRNA knockdown of DeltaNp63alpha correlated with a reduction in p53 independently of TSA. DeltaNp63alpha is the dominant active isoform in corneal epithelial cell nuclei. Loss of DeltaNp63alpha occurs during apoptotic signaling by cleavage at the C terminus. The corresponding loss of p53 suggests that a significant relationship appears to exist between these two regulatory proteins.

Controlling fluctuations in an ITB and comparison with gyrokinetic simulations

Science.gov (United States)

Ernst, D. R.; Fiore, C. L.; Dominguez, A.; Podpaly, Y.; Reinke, M. L.; Terry, J. L.; Tsujii, N.; Bespamyatnov, I.; Churchill, M.; Greenwald, M.; Hubbard, A.; Hughes, J. W.; Lee, J.; Ma, Y.; Wolfe, S.; Wukitch, S.

2011-10-01

We have modulated on-axis ICRF minority heating to trigger fluctuations and core electron transport in Alcator C-Mod Internal Transport Barriers (ITB's). Temperature swings of 50% produced strong bursts of density fluctuations, measured by phase contrast imaging (PCI), while edge fluctuations from reflectometry, Mirnov coils, and gas puff imaging (GPI) simultaneously diminished. The PCI fluctuations are in phase with sawteeth, further evidence that they originate within the ITB foot. Linear gyrokinetic analysis with GS2 shows TEMs are driven unstable in the ITB by the on-axis heating, as in Refs.,. Nonlinear gyrokinetic simulations of turbulence in the ITB are compared with fluctuation data using a synthetic diagnostic. Strong ITB's were produced with high quality ion and electron profile data. Supported by U.S. DoE awards DE-FC02-99ER54512, DE-FG02-91ER54109, DE-FC02-08ER54966.

Full radius linear and nonlinear gyrokinetic simulations for tokamaks and stellarators: Zonal flows, applied E x B flows, trapped electrons and finite beta

International Nuclear Information System (INIS)

Villard, L.; Allfrey, S.J.; Bottino, A.

2003-01-01

The aim of this paper is to report on recent advances made on global gyrokinetic simulations of Ion Temperature Gradient modes (ITG) and other microinstabilities. The nonlinear development and saturation of ITG modes and the role of E x B zonal flows are studied with a global nonlinear δ f formulation that retains parallel nonlinearity and thus allows for a check of the energy conservation property as a means to verify the quality of the numerical simulation. Due to an optimised loading technique the conservation property is satisfied with an unprecedented quality well into the nonlinear stage. The zonal component of the perturbation establishes a quasi-steady state with regions of ITG suppression, strongly reduced radial energy flux and steepened effective temperature profile alternating with regions of higher ITG mode amplitudes, larger radial energy flux and flattened effective temperature profile. A semi-Lagrangian approach free of statistical noise is proposed as an alternative to the nonlinear δf formulation. An ASDEX-Upgrade experiment with an Internal Transport Barrier (ITB) is analysed with a global gyrokinetic code that includes trapped electron dynamics. The weakly destabilizing effect of trapped electron dynamics on ITG modes in an axisymmetric bumpy configuration modelling W7-X is shown in global linear simulations that retain the full electron dynamics. Finite β effects on microinstabilities are investigated with a linear global spectral electromagnetic gyrokinetic formulation. The radial global structure of electromagnetic modes shows a resonant behaviour with rational q values. (author)

Possible applications of the sigma delta digitizer in particle physics

International Nuclear Information System (INIS)

Hallgren, B.

1991-01-01

The sigma delta (ΣΔ) principle is an analog-to-digital conversion technique based on high-frequency sampling and low-pass filtering of the quantization noise. Resolution in time is exchanged for that in amplitude so as to avoid the difficulty of implementing complex precision analog circuits, in favour of digital circuits. The approach is attractive because it will make it possible to integrate complete channels of high resolution analog-to-digital converters and time digitizers in submicron digital VLSI technologies. Advantage is taken of the fact that the state-of-the-art VLSI is better suited for providing fast digital circuits than for providing precise analog circuits. This article describes the principle and the performance of the ideal ΣΔ digitizer. The design and measurements of a new 10 MHz prototype circuit of a second-order ΣΔ is presented to show the high speed operation of such a circuit. The expected performance of a CMOS test design using the same principles is discussed. Digital filters, useful for particle physics, are introduced. A comparison to other digitizing techniques is made and the potential applications of the ΣΔ digitizer in particle physics are outlined. (orig.)

Global approach to the spectral problem of microinstabilities in tokamak plasmas using a gyrokinetic model

International Nuclear Information System (INIS)

Brunner, S.

1997-08-01

Ion temperature gradient (ITG)-related instabilities are studied in tokamak-like plasmas with the help of a new global eigenvalue code. Ions are modelled in the frame of gyrokinetic theory so that finite Larmor radius effects of these particles are retained to all orders. Non-adiabatic trapped electron dynamics is taken into account through the bounce-averaged drift kinetic equation. Assuming electrostatic perturbations, the system is closed with the quasineutrality relation. Practical methods are presented which make this global approach feasible. These include a non-standard wave decomposition compatible with the curved geometry as well as adapting an efficient root finding algorithm for computing the unstable spectrum. These techniques are applied to a low pressure configuration given by a large aspect ratio torus with circular, concentric magnetic surfaces. Simulations from a linear, time evolution, particle in cell code provide a useful benchmark. Comparisons with local ballooning calculations for different parameter scans enable further validation while illustrating the limits of that representation at low toroidal wave numbers or for non-interchange-like instabilities. The stabilizing effect of negative magnetic shear is also considered, in which case the global results show not only an attenuation of the growth rate but also a reduction of the radial extent induced by a transition from the toroidal- to the slab-ITG mode. Contributions of trapped electrons to the ITG instability as well as the possible coupling to the trapped electron mode are clearly brought to the fore. (author) figs., tabs., 69 refs

A generalized gyrokinetic Poisson solver

International Nuclear Information System (INIS)

Lin, Z.; Lee, W.W.

1995-03-01

A generalized gyrokinetic Poisson solver has been developed, which employs local operations in the configuration space to compute the polarization density response. The new technique is based on the actual physical process of gyrophase-averaging. It is useful for nonlocal simulations using general geometry equilibrium. Since it utilizes local operations rather than the global ones such as FFT, the new method is most amenable to massively parallel algorithms

Non-linear gyrokinetic simulations of microturbulence in TCV electron internal transport barriers

Science.gov (United States)

Lapillonne, X.; Brunner, S.; Sauter, O.; Villard, L.; Fable, E.; Görler, T.; Jenko, F.; Merz, F.

2011-05-01

Using the local (flux-tube) version of the Eulerian code GENE (Jenko et al 2000 Phys. Plasmas 7 1904), gyrokinetic simulations of microturbulence were carried out considering parameters relevant to electron-internal transport barriers (e-ITBs) in the TCV tokamak (Sauter et al 2005 Phys. Rev. Lett. 94 105002), generated under conditions of low or negative shear. For typical density and temperature gradients measured in such barriers, the corresponding simulated fluctuation spectra appears to simultaneously contain longer wavelength trapped electron modes (TEMs, for typically k⊥ρi 0.5). The contributions to the electron particle flux from these two types of modes are, respectively, outward/inward and may cancel each other for experimentally realistic gradients. This mechanism may partly explain the feasibility of e-ITBs. The non-linear simulation results confirm the predictions of a previously developed quasi-linear model (Fable et al 2010 Plasma Phys. Control. Fusion 52 015007), namely that the stationary condition of zero particle flux is obtained through the competitive contributions of ITG and TEM. A quantitative comparison of the electron heat flux with experimental estimates is presented as well.

Ternary particle yields in 249Cf(nth,f)

Science.gov (United States)

Tsekhanovich, I.; Büyükmumcu, Z.; Davi, M.; Denschlag, H. O.; Gönnenwein, F.; Boulyga, S. F.

2003-03-01

An experiment measuring ternary particle yields in 249Cf(nth,f) was carried out at the high flux reactor of the Institut Laue-Langevin using the Lohengrin recoil mass separator. Parameters of energy distributions were determined for 27 ternary particles up to 30Mg and their yields were calculated. The yields of 17 further ternary particles were estimated on the basis of the systematics developed. The heaviest particles observed in the experiment are 37Si and 37S; their possible origin is discussed.

Over-production, renaturation and reconstitution of delta and epsilon subunits from chloroplast and cyanobacterial F1

NARCIS (Netherlands)

Steinemann, D.; Lill, H; Junge, Wolfgang; Engelbrecht, Siegfried

1994-01-01

We studied the functioning of chimeric F0F1-ATPases by replacing subunits delta and epsilon of spinach CF1 with their counterparts from Synechocystis sp. PCC 6803. The sequence identities between these subunits are 26 and 41%, respectively. For a systematic approach to such studies and later

Ternary particle yields in 249Cf(nth,f)

International Nuclear Information System (INIS)

Tsekhanovich, I.; Bueyuekmumcu, Z.; Davi, M.; Denschlag, H.O.; Goennenwein, F.; Boulyga, S.F.

2003-01-01

An experiment measuring ternary particle yields in 249 Cf(n th ,f) was carried out at the high flux reactor of the Institut Laue-Langevin using the Lohengrin recoil mass separator. Parameters of energy distributions were determined for 27 ternary particles up to 30 Mg and their yields were calculated. The yields of 17 further ternary particles were estimated on the basis of the systematics developed. The heaviest particles observed in the experiment are 37 Si and 37 S; their possible origin is discussed

DeltaFosB induces osteosclerosis and decreases adipogenesis by two independent cell-autonomous mechanisms

DEFF Research Database (Denmark)

Kveiborg, Marie; Sabatakos, George; Chiusaroli, Riccardo

2004-01-01

establishes that the skeletal phenotype is cell autonomous to the osteoblast lineage and independent of adipocyte formation. It also strongly suggests that the decreased fat phenotype of NSE-DeltaFosB mice is independent of the changes in the osteoblast lineage. In vitro, overexpression of Delta......Osteoblasts and adipocytes may develop from common bone marrow mesenchymal precursors. Transgenic mice overexpressing DeltaFosB, an AP-1 transcription factor, under the control of the neuron-specific enolase (NSE) promoter show both markedly increased bone formation and decreased adipogenesis...... of DeltaFosB on adipocyte differentiation appears to occur at early stages of stem cell commitment, affecting C/EBPbeta functions. It is concluded that the changes in osteoblast and adipocyte differentiation in DeltaFosB transgenic mice result from independent cell-autonomous mechanisms....

Effects of alpha-particles on survival and chromosomal aberrations in human mammary epithelial cells

Science.gov (United States)

Durante, M.; Grossi, G. F.; Gialanella, G.; Pugliese, M.; Nappo, M.; Yang, T. C.

1995-01-01

We have studied the radiation responses of a human mammary epithelial cell line, H184B5 F5-1 M/10. This cell line was derived from primary mammary cells after treatment with chemicals and heavy ions. The F5-1 M/10 cells are immortal, density-inhibited in growth, and non-tumorigenic in athymic nude mice and represent an in vitro model of the human epithelium for radiation studies. Because epithelial cells are the target of alpha-particles emitted from radon daughters, we concentrated our studies on the efficiency of alpha-particles. Confluent cultures of M/10 cells were exposed to accelerated alpha-particles [beam energy incident at the cell monolayer = 3.85 MeV, incident linear energy transfer (LET) in cell = 109 keV/microns] and, for comparison, to 80 kVp x-rays. The following endpoints were studied: (1) survival, (2) chromosome aberrations at the first postirradiation mitosis, and (3) chromosome alterations at later passages following irradiation. The survival curve was exponential for alpha-particles (D0 = 0.73 +/- 0.04 Gy), while a shoulder was observed for x-rays (alpha/beta = 2.9 Gy; D0 = 2.5 Gy, extrapolation number 1.6). The relative biological effectiveness (RBE) of high-LET alpha-particles for human epithelial cell killing was 3.3 at 37% survival. Dose-response curves for the induction of chromosome aberrations were linear for alpha-particles and linearquadratic for x-rays. The RBE for the induction of chromosome aberrations varied with the type of aberration scored and was high (about 5) for chromosome breaks and low (about 2) for chromosome exchanges.(ABSTRACT TRUNCATED AT 250 WORDS).

Linear relativistic gyrokinetic equation in general magnetically confined plasmas

International Nuclear Information System (INIS)

Tsai, S.T.; Van Dam, J.W.; Chen, L.

1983-08-01

The gyrokinetic formalism for linear electromagnetic waves of arbitrary frequency in general magnetic-field configurations is extended to include full relativistic effects. The derivation employs the small adiabaticity parameter rho/L 0 where rho is the Larmor radius and L 0 the equilibrium scale length. The effects of the plasma and magnetic field inhomogeneities and finite Larmor-radii effects are also contained

Novel primary thymic defect with T lymphocytes expressing gamma delta T cell receptor

DEFF Research Database (Denmark)

Geisler, C; Pallesen, G; Platz, P

1989-01-01

Flow cytometric analysis of the peripheral blood mononuclear cells in a six year old girl with a primary cellular immune deficiency showed a normal fraction of CD3 positive T cells. Most (70%) of the CD3 positive cells, however, expressed the gamma delta and not the alpha beta T cell receptor....... Immunoprecipitation and sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) showed that most of the gamma delta T cell receptors existed as disulphide-linked heterodimers. Proliferative responses to mitogens were severely reduced, but specific antibody responses after vaccination could be detected...... deficiency associated with a high proportion of T cells expressing the gamma delta T cell receptor has been described in nude mice, and it is suggested that the immune deficiency of this patient may represent a human analogue....

Gyrokinetic simulations with external resonant magnetic perturbations: Island torque and nonambipolar transport with plasma rotation

Science.gov (United States)

Waltz, R. E.; Waelbroeck, F. L.

2012-03-01

Static external resonant magnetic field perturbations (RMPs) have been added to the gyrokinetic code GYRO [J. Candy and R. E. Waltz, J. Comp. Phys. 186, 545 (2003)]. This allows nonlinear gyrokinetic simulations of the nonambipolar radial current flow jr, and the corresponding j→×B→ plasma torque (density) R[jrBp/c], induced by magnetic islands that break the toroidal symmetry of a tokamak. This extends the previous GYRO formulation for the transport of toroidal angular momentum (TAM) [R. E. Waltz, G. M. Staebler, J. Candy, and F. L. Hinton, Phys. Plasmas 14, 122507 (2007); errata 16, 079902 (2009)]. The focus is on electrostatic full torus radial slice simulations of externally induced q =m/n=6/3 islands with widths 5% of the minor radius or about 20 ion gyroradii. Up to moderately strong E ×B rotation, the island torque scales with the radial electric field at the resonant surface Er, the island width w, and the intensity I of the high-n micro-turbulence, as Erw√I . The radial current inside the island is carried (entirely in the n =3 component) and almost entirely by the ion E ×B flux, since the electron E ×B and magnetic flutter particle fluxes are cancelled. The net island torque is null at zero Er rather than at zero toroidal rotation. This means that while the expected magnetic braking of the toroidal plasma rotation occurs at strong co- and counter-current rotation, at null toroidal rotation, there is a small co-directed magnetic acceleration up to the small diamagnetic (ion pressure gradient driven) co-rotation corresponding to the zero Er and null torque. This could be called the residual stress from an externally induced island. At zero Er, the only effect is the expected partial flattening of the electron temperature gradient within the island. Finite-beta GYRO simulations demonstrate almost complete RMP field screening and n =3 mode unlocking at strong Er.

Gyrokinetic continuum simulations of turbulence in the Texas Helimak

Science.gov (United States)

Bernard, T. N.; Shi, E. L.; Hammett, G. W.; Hakim, A.; Taylor, E. I.

2017-10-01

We have used the Gkeyll code to perform 3x-2v full-f gyrokinetic continuum simulations of electrostatic plasma turbulence in the Texas Helimak. The Helimak is an open field-line experiment with magnetic curvature and shear. It is useful for validating numerical codes due to its extensive diagnostics and simple, helical geometry, which is similar to the scrape-off layer region of tokamaks. Interchange and drift-wave modes are the main turbulence mechanisms in the device, and potential biasing is applied to study the effect of velocity shear on turbulence reduction. With Gkeyll, we varied field-line pitch angle and simulated biased and unbiased cases to study different turbulent regimes and turbulence reduction. These are the first kinetic simulations of the Helimak and resulting plasma profiles agree fairly well with experimental data. This research demonstrates Gkeyll's progress towards 5D simulations of the SOL region of fusion devices. Supported by the U.S. DOE SCGSR program under contract DE-SC0014664, the Max-Planck/Princeton Center for Plasma Physics, the SciDAC Center for the Study of Plasma Microturbulence, and DOE contract DE-AC02-09CH11466.

The role of zonal flows in the saturation of multi-scale gyrokinetic turbulence

Energy Technology Data Exchange (ETDEWEB)

Staebler, G. M.; Candy, J. [General Atomics, San Diego, California 92186 (United States); Howard, N. T. [Oak Ridge Institute for Science Education (ORISE), Oak Ridge, Tennessee 37831 (United States); Holland, C. [University of California San Diego, San Diego, California 92093 (United States)

2016-06-15

The 2D spectrum of the saturated electric potential from gyrokinetic turbulence simulations that include both ion and electron scales (multi-scale) in axisymmetric tokamak geometry is analyzed. The paradigm that the turbulence is saturated when the zonal (axisymmetic) ExB flow shearing rate competes with linear growth is shown to not apply to the electron scale turbulence. Instead, it is the mixing rate by the zonal ExB velocity spectrum with the turbulent distribution function that competes with linear growth. A model of this mechanism is shown to be able to capture the suppression of electron-scale turbulence by ion-scale turbulence and the threshold for the increase in electron scale turbulence when the ion-scale turbulence is reduced. The model computes the strength of the zonal flow velocity and the saturated potential spectrum from the linear growth rate spectrum. The model for the saturated electric potential spectrum is applied to a quasilinear transport model and shown to accurately reproduce the electron and ion energy fluxes of the non-linear gyrokinetic multi-scale simulations. The zonal flow mixing saturation model is also shown to reproduce the non-linear upshift in the critical temperature gradient caused by zonal flows in ion-scale gyrokinetic simulations.

Regulation of Mammary Stem Cell Quiescence via Post-Translational Modification of DeltaNp63alpha

Science.gov (United States)

2012-12-01

This document is the Annual Summary Report on the training grant awarded to Andrew DeCastro entitled Regulation of Mammary Stem Cell Quiescence via...screen) mediated phosphorylation of deltaNPdelta3 on stem cell behavior and mitotic activity. Task 1 aims to determine the effects of wild-type, phospho...ablative and phospho-mimetic alleles of deltaNP63delta phosphorylation on stem cell behavior in vitro. Thus far, we demonstrate that stem cell enriched

Measuring bovine gamma delta T cell function at the site of Mycobacterium bovis infection

Science.gov (United States)

Bovine gamma delta T cells are amongst the first cells to accumulate at the site of Mycobacterium bovis infection; however, their role in the developing lesion remains unclear. We utilized transcriptomics analysis, in situ hybridization, and a macrophage/gamma delta T cell co-culture system to eluc...

Independence of protein kinase C-delta activity from activation loop phosphorylation: structural basis and altered functions in cells.

Science.gov (United States)

Liu, Yin; Belkina, Natalya V; Graham, Caroline; Shaw, Stephen

2006-04-28

Activation loop phosphorylation plays critical regulatory roles for many kinases. Unlike other protein kinase Cs (PKC), PKC-delta does not require phosphorylation of its activation loop (Thr-507) for in vitro activity. We investigated the structural basis for this unusual capacity and its relevance to PKC-delta function in intact cells. Mutational analysis demonstrated that activity without Thr-507 phosphorylation depends on 20 residues N-terminal to the kinase domain and a pair of phenylalanines (Phe-500/Phe-527) unique to PKC-delta in/near the activation loop. Molecular modeling demonstrated that these elements stabilize the activation loop by forming a hydrophobic chain of interactions from the C-lobe to activation loop to N-terminal (helical) extension. In cells PKC-delta mediates both apoptosis and transcription regulation. We found that the T507A mutant of the PKC-delta kinase domain resembled the corresponding wild type in mediating apoptosis in transfected HEK293T cells. But the T507A mutant was completely defective in AP-1 and NF-kappaB reporter assays. A novel assay in which the kinase domain of PKC-delta and its substrate (a fusion protein of PKC substrate peptide with green fluorescent protein) were co-targeted to lipid rafts revealed a major substrate-selective defect of the T507A mutant in phosphorylating the substrate in cells. In vitro analysis showed strong product inhibition on the T507A mutant with particular substrates whose characteristics suggest it contributes to the substrate selective defect of the PKC-delta T507A mutant in cells. Thus, activation loop phosphorylation of PKC-delta may regulate its function in cells in a novel way.

Structures in the K-shell delta electron spectrum near threshold for ionization by fast charged particles

International Nuclear Information System (INIS)

Amundsen, P.A.; Aashamar, K.

Results of calculations of the delta electron spectrum for K-shell ionization of atoms by fast charged particles for target charges in the range 6 2 <=40 are presented. Appreciable structure is found in the spectrum near the ionization threshold, in particular for fast projectiles and heavy target elements. The structure can be quite sensitive to the details of the effective atomic potentials. (Auth.)

Parallel pic plasma simulation through particle decomposition techniques

International Nuclear Information System (INIS)

Briguglio, S.; Vlad, G.; Di Martino, B.; Naples, Univ. 'Federico II'

1998-02-01

Particle-in-cell (PIC) codes are among the major candidates to yield a satisfactory description of the detail of kinetic effects, such as the resonant wave-particle interaction, relevant in determining the transport mechanism in magnetically confined plasmas. A significant improvement of the simulation performance of such codes con be expected from parallelization, e.g., by distributing the particle population among several parallel processors. Parallelization of a hybrid magnetohydrodynamic-gyrokinetic code has been accomplished within the High Performance Fortran (HPF) framework, and tested on the IBM SP2 parallel system, using a 'particle decomposition' technique. The adopted technique requires a moderate effort in porting the code in parallel form and results in intrinsic load balancing and modest inter processor communication. The performance tests obtained confirm the hypothesis of high effectiveness of the strategy, if targeted towards moderately parallel architectures. Optimal use of resources is also discussed with reference to a specific physics problem [it

Gyrokinetic Simulations with External Resonant Magnetic Perturbations: Island Torque and Nonambipolar Transport with Rotation

Science.gov (United States)

Waltz, R. E.; Waelbroeck, F. L.

2012-03-01

Static external resonant magnetic perturbations (RMPs) have been added to the δf gyrokinetic code GYRO. This allows nonlinear gyrokinetic simulations of the nonambipolar radial current flow jr and the corresponding plasma torque (density) R[jrBθ/c], induced by islands that break the toroidal symmetry of a tokamak. This extends previous GYRO simulations for the transport of toroidal angular momentum (TAM) [1,2]. The focus is on full torus radial slice electrostatic simulations of induced q=m/n=6/3 islands with widths 5% of the minor radius. The island torque scales with the radial electric field Er the island width w, and the intensity I of the high-n micro-turbulence, as wErI^1/2. The net island torque is null at zero Er rather than at zero toroidal rotation. This means that there is a small co-directed magnetic acceleration to the small diamagnetic co-rotation corresponding to the zero Er which can be called the residual stress [2] from an externally induced island. Finite-beta GYRO simulations of a core radial slice demonstrate island unlocking and the RMP screening. 6pt[1] R.E. Waltz, et al., Phys. Plasmas 14, 122507 (2007). [2] R.E. Waltz, et al., Phys. Plasmas 18, 042504 (2011).

Bringing global gyrokinetic turbulence simulations to the transport timescale using a multiscale approach

Science.gov (United States)

Parker, Jeffrey B.; LoDestro, Lynda L.; Told, Daniel; Merlo, Gabriele; Ricketson, Lee F.; Campos, Alejandro; Jenko, Frank; Hittinger, Jeffrey A. F.

2018-05-01

The vast separation dividing the characteristic times of energy confinement and turbulence in the core of toroidal plasmas makes first-principles prediction on long timescales extremely challenging. Here we report the demonstration of a multiple-timescale method that enables coupling global gyrokinetic simulations with a transport solver to calculate the evolution of the self-consistent temperature profile. This method, which exhibits resiliency to the intrinsic fluctuations arising in turbulence simulations, holds potential for integrating nonlocal gyrokinetic turbulence simulations into predictive, whole-device models.

Performance of particle in cell methods on highly concurrent computational architectures

International Nuclear Information System (INIS)

Adams, M.F.; Ethier, S.; Wichmann, N.

2009-01-01

Particle in cell (PIC) methods are effective in computing Vlasov-Poisson system of equations used in simulations of magnetic fusion plasmas. PIC methods use grid based computations, for solving Poisson's equation or more generally Maxwell's equations, as well as Monte-Carlo type methods to sample the Vlasov equation. The presence of two types of discretizations, deterministic field solves and Monte-Carlo methods for the Vlasov equation, pose challenges in understanding and optimizing performance on today large scale computers which require high levels of concurrency. These challenges arises from the need to optimize two very different types of processes and the interactions between them. Modern cache based high-end computers have very deep memory hierarchies and high degrees of concurrency which must be utilized effectively to achieve good performance. The effective use of these machines requires maximizing concurrency by eliminating serial or redundant work and minimizing global communication. A related issue is minimizing the memory traffic between levels of the memory hierarchy because performance is often limited by the bandwidths and latencies of the memory system. This paper discusses some of the performance issues, particularly in regard to parallelism, of PIC methods. The gyrokinetic toroidal code (GTC) is used for these studies and a new radial grid decomposition is presented and evaluated. Scaling of the code is demonstrated on ITER sized plasmas with up to 16K Cray XT3/4 cores.

Performance of particle in cell methods on highly concurrent computational architectures

International Nuclear Information System (INIS)

Adams, M F; Ethier, S; Wichmann, N

2007-01-01

Particle in cell (PIC) methods are effective in computing Vlasov-Poisson system of equations used in simulations of magnetic fusion plasmas. PIC methods use grid based computations, for solving Poisson's equation or more generally Maxwell's equations, as well as Monte-Carlo type methods to sample the Vlasov equation. The presence of two types of discretizations, deterministic field solves and Monte-Carlo methods for the Vlasov equation, pose challenges in understanding and optimizing performance on today large scale computers which require high levels of concurrency. These challenges arises from the need to optimize two very different types of processes and the interactions between them. Modern cache based high-end computers have very deep memory hierarchies and high degrees of concurrency which must be utilized effectively to achieve good performance. The effective use of these machines requires maximizing concurrency by eliminating serial or redundant work and minimizing global communication. A related issue is minimizing the memory traffic between levels of the memory hierarchy because performance is often limited by the bandwidths and latencies of the memory system. This paper discusses some of the performance issues, particularly in regard to parallelism, of PIC methods. The gyrokinetic toroidal code (GTC) is used for these studies and a new radial grid decomposition is presented and evaluated. Scaling of the code is demonstrated on ITER sized plasmas with up to 16K Cray XT3/4 cores

The roles of MCP-1 and protein kinase C delta activation in human eosinophilic leukemia EoL-1 cells.

Science.gov (United States)

Lee, Ji-Sook; Yang, Eun Ju; Kim, In Sik

2009-12-01

Idiopathic hypereosinophilc syndrome is a disorder associated with clonally eosinophilic proliferation. The importance of FIP1-like-1-platelet-derived growth factor receptor-alpha (FIP1L1-PDGFRA) in the pathogenesis and classification of HES has been recently reported. In this study, we investigated the contribution of monocyte chemoattractant protein-1 (MCP-1)/CCL2 to chemotactic activity and protein kinase C delta (PKC delta in the human eosinophilic leukemia cell line EoL-1. These cells express CCR2 protein among the CC chemokine receptors (CCR1-5). MCP-1 induces strong migration of EoL-1 cells and the chemotaxis signal in response to MCP-1 involves a G(i)/G(o) protein, phospholipase C (PLC), PKC delta, p38 MAPK and NF-kappaB. MCP-1 activates p38 MAPK via G(i)/G(o) protein, PLC and PKC delta cascade. MCP-1 also induces NF-kappaB translocation and the activation is inhibited by PKC delta activation. The increase in the basal expression and activity of PKC delta in EoL-1 cells, compared to normal eosinophils, inhibits apoptosis in EoL-1 cells. Anti-apoptotic mechanism of PKC delta is related to inhibition of caspase 3 and caspase 9, but not to FIP1L1-PDGFRA. PKC delta functions as an anti-apoptotic molecule, and is involved in EoL-1 cell movement stimulated by MCP-1. This study contributes to an understanding of MCP-1 in eosinophil biology and pathogenic mechanism of eosinophilic disorders.

Direct identification of predator-prey dynamics in gyrokinetic simulations

Energy Technology Data Exchange (ETDEWEB)

Kobayashi, Sumire, E-mail: sumire.kobayashi@lpp.polytechnique.fr; Gürcan, Özgür D [Laboratoire de Physique des Plasmas, CNRS, Paris-Sud, Ecole Polytechnique, UMR7648, F-91128 Palaiseau (France); Diamond, Patrick H. [University of California, San Diego, La Jolla, California 92093-0319 (United States)

2015-09-15

The interaction between spontaneously formed zonal flows and small-scale turbulence in nonlinear gyrokinetic simulations is explored in a shearless closed field line geometry. It is found that when clear limit cycle oscillations prevail, the observed turbulent dynamics can be quantitatively captured by a simple Lotka-Volterra type predator-prey model. Fitting the time traces of full gyrokinetic simulations by such a reduced model allows extraction of the model coefficients. Scanning physical plasma parameters, such as collisionality and density gradient, it was observed that the effective growth rates of turbulence (i.e., the prey) remain roughly constant, in spite of the higher and varying level of primary mode linear growth rates. The effective growth rate that was extracted corresponds roughly to the zonal-flow-modified primary mode growth rate. It was also observed that the effective damping of zonal flows (i.e., the predator) in the parameter range, where clear predator-prey dynamics is observed, (i.e., near marginal stability) agrees with the collisional damping expected in these simulations. This implies that the Kelvin-Helmholtz-like instability may be negligible in this range. The results imply that when the tertiary instability plays a role, the dynamics becomes more complex than a simple Lotka-Volterra predator prey.

Gyrokinetic analysis of linear microinstabilities for the stellarator Wendelstein 7-X

Science.gov (United States)

Xanthopoulos, P.; Jenko, F.

2007-04-01

A linear collisionless gyrokinetic investigation of ion temperature gradient (ITG) modes—considering both adiabatic and full electron dynamics—and trapped electron modes (TEMs) is presented for the stellarator Wendelstein 7-X (W7-X) [G. Grieger et al., Plasma Physics and Controlled Nuclear Fusion Research 1990 (International Atomic Energy Agency, Vienna, 1991), Vol. 3, p. 525]. The study of ITG modes reveals that in W7-X, microinstabilities of distinct character coexist. The effect of changes in the density gradient and temperature ratio is discussed. Substantial differences with respect to the axisymmetric geometry appear in W7-X, concerning the relative separation of regions with a large fraction of helically trapped particles and those of pronounced bad curvature. For both ITG modes and TEMs, the dependence of their linear growth rates on the background gradients is studied along with their parallel mode structure.

Flux tube gyrokinetic simulations of the edge pedestal

Science.gov (United States)

Parker, Scott; Wan, Weigang; Chen, Yang

2011-10-01

The linear instabilities of DIII-D H-mode pedestal are studied with gyrokinetic micro-turbulence simulations. The simulation code GEM is an electromagnetic δf code with global tokamak geometry in the form of Miller equilibrium. Local flux tube simulations are carried out for multiple positions of two DIII-D profiles: shot #98889 and shot #131997. Near the top of the pedestal, the instability is clearly ITG. The dominant instability of the pedestal appears at the steep gradient region, and it is identified as a low frequency mode mostly driven by electron temperature gradient. The mode propagates along the electron diamagnetic direction for low n and may propagate along the ion direction for high n. At some positions near the steep gradient region, an ion instability is found which shows some characteristics of kinetic ballooning mode (KBM). These results will be compared to the results of E. Wang et al. and D. Fulton et al. in the same session. We thank R. Groebner and P. Snyder for providing experimental profiles and helpful discussions.

Progress in gyrokinetic simulations of toroidal ITG turbulence

International Nuclear Information System (INIS)

Nevins, W.M.; Dimits, A.M.; Cohen, B.I.; Shumaker, D.E.

2001-01-01

The 3-D nonlinear toroidal gyrokinetic simulation code PG3EQ is used to study toroidal ion temperature gradient (ITG) driven turbulence - a key cause of the anomalous transport that limits tokamak plasma performance. Systematic studies of the dependence of ion thermal transport on various parameters and effects are presented, including dependence on E-vectorxB-vector and toroidal velocity shear, sensitivity to the force balance in simulations with radial temperature gradient variation, and the dependences on magnetic shear and ion temperature gradient. (author)

Neoclassical and gyrokinetic analysis of time-dependent helium transport experiments on MAST

Science.gov (United States)

Henderson, S. S.; Garzotti, L.; Casson, F. J.; Dickinson, D.; Fox, M. F. J.; O'Mullane, M.; Patel, A.; Roach, C. M.; Summers, H. P.; Valovič, M.; The MAST Team

2014-09-01

Time-dependent helium gas puff experiments have been performed on the Mega Ampère Spherical Tokamak (MAST) during a two point plasma current scan in L-mode and a confinement scan at 900 kA. An evaluation of the He II (n = 4 → 3) spectrum line induced by charge exchange suggests anomalous rates of diffusion and inward convection in the outer regions of both L-mode plasmas. Similar rates of diffusion are found in the H-mode plasma, however these rates are consistent with neoclassical predictions. The anomalous inward pinch found in the core of L-mode plasmas is also not apparent in the H-mode core. Linear gyrokinetic simulations of one flux surface in L-mode using the GS2 and GKW codes find that equilibrium flow shear is sufficient to stabilize ITG modes, consistent with beam emission spectroscopy (BES) observations, and suggest that collisionless TEMs may dominate the anomalous helium particle transport. A quasilinear estimate of the dimensionless peaking factor associated with TEMs is in good agreement with experiment. Collisionless TEMs are more stable in H-mode because the electron density gradient is flatter. The steepness of this gradient is therefore pivotal in determining the inward neoclassical particle pinch and the particle flux associated with TEM turbulence.

Astrophysical gyrokinetics: turbulence in pressure-anisotropic plasmas at ion scales and beyond

Science.gov (United States)

Kunz, M. W.; Abel, I. G.; Klein, K. G.

2018-04-01

We present a theoretical framework for describing electromagnetic kinetic turbulence in a multi-species, magnetized, pressure-anisotropic plasma. The turbulent fluctuations are assumed to be small compared to the mean field, to be spatially anisotropic with respect to it and to have frequencies small compared to the ion cyclotron frequency. At scales above the ion-Larmor radius, the theory reduces to the pressure-anisotropic generalization of kinetic reduced magnetohydrodynamics (KRMHD) formulated by Kunz et al. (J. Plasma Phys., vol. 81, 2015, 325810501). At scales at and below the ion-Larmor radius, three main objectives are achieved. First, we analyse the linear response of the pressure-anisotropic gyrokinetic system, and show it to be a generalization of previously explored limits. The effects of pressure anisotropy on the stability and collisionless damping of Alfvénic and compressive fluctuations are highlighted, with attention paid to the spectral location and width of the frequency jump that occurs as Alfvén waves transition into kinetic Alfvén waves. Secondly, we derive and discuss a very general gyrokinetic free-energy conservation law, which captures both the KRMHD free-energy conservation at long wavelengths and dual cascades of kinetic Alfvén waves and ion entropy at sub-ion-Larmor scales. We show that non-Maxwellian features in the distribution function change the amount of phase mixing and the efficiency of magnetic stresses, and thus influence the partitioning of free energy amongst the cascade channels. Thirdly, a simple model is used to show that pressure anisotropy, even within the bounds imposed on it by firehose and mirror instabilities, can cause order-of-magnitude variations in the ion-to-electron heating ratio due to the dissipation of Alfvénic turbulence. Our theory provides a foundation for determining how pressure anisotropy affects turbulent fluctuation spectra, the differential heating of particle species and the ratio of parallel

Non-linear gyrokinetic simulations of microturbulence in TCV electron internal transport barriers

Energy Technology Data Exchange (ETDEWEB)

Lapillonne, X; Brunner, S; Sauter, O; Villard, L [Centre de Recherches en Physique des Plasmas, Association EURATOM-Confederation Suisse, Ecole Polytechnique Federale de Lausanne, CH-1015 Lausanne (Switzerland); Fable, E; Goerler, T; Jenko, F; Merz, F, E-mail: stephan.brunner@epfl.ch [Max-Planck-Institut fuer Plasmaphysik, EURATOM Association, Boltzmannstrasse 2, D-85748 Garching (Germany)

2011-05-15

Using the local (flux-tube) version of the Eulerian code GENE (Jenko et al 2000 Phys. Plasmas 7 1904), gyrokinetic simulations of microturbulence were carried out considering parameters relevant to electron-internal transport barriers (e-ITBs) in the TCV tokamak (Sauter et al 2005 Phys. Rev. Lett. 94 105002), generated under conditions of low or negative shear. For typical density and temperature gradients measured in such barriers, the corresponding simulated fluctuation spectra appears to simultaneously contain longer wavelength trapped electron modes (TEMs, for typically k{sub p}erpendicular{rho}{sub i} < 0.5, k{sub p}erpendicular being the characteristic perpendicular wavenumber and {rho}{sub i} the ion Larmor radius) and shorter wavelength ion temperature gradient modes (ITG, k{sub p}erpendicular{rho}{sub i} > 0.5). The contributions to the electron particle flux from these two types of modes are, respectively, outward/inward and may cancel each other for experimentally realistic gradients. This mechanism may partly explain the feasibility of e-ITBs. The non-linear simulation results confirm the predictions of a previously developed quasi-linear model (Fable et al 2010 Plasma Phys. Control. Fusion 52 015007), namely that the stationary condition of zero particle flux is obtained through the competitive contributions of ITG and TEM. A quantitative comparison of the electron heat flux with experimental estimates is presented as well.

Roles of POLD4, smallest subunit of DNA polymerase {delta}, in nuclear structures and genomic stability of human cells

Energy Technology Data Exchange (ETDEWEB)

Huang, Qin Miao [Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya (Japan); Akashi, Tomohiro [Division of Molecular Mycology and Medicine, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya (Japan); Masuda, Yuji; Kamiya, Kenji [Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8553 (Japan); Takahashi, Takashi [Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya (Japan); Suzuki, Motoshi, E-mail: msuzuki@med.nagoya-u.ac.jp [Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya (Japan)

2010-01-01

Mammalian DNA polymerase {delta} (pol {delta}) is essential for DNA replication, though the functions of this smallest subunit of POLD4 have been elusive. We investigated pol {delta} activities in vitro and found that it was less active in the absence of POLD4, irrespective of the presence of the accessory protein PCNA. shRNA-mediated reduction of POLD4 resulted in a marked decrease in colony formation activity by Calu6, ACC-LC-319, and PC-10 cells. We also found that POLD4 reduction was associated with an increased population of karyomere-like cells, which may be an indication of DNA replication stress and/or DNA damage. The karyomere-like cells retained an ability to progress through the cell cycle, suggesting that POLD4 reduction induces modest genomic instability, while allowing cells to grow until DNA damage reaches an intolerant level. Our results indicate that POLD4 is required for the in vitro pol {delta} activity, and that it functions in cell proliferation and maintenance of genomic stability of human cells.

Asymptotic and spectral analysis of the gyrokinetic-waterbag integro-differential operator in toroidal geometry

Energy Technology Data Exchange (ETDEWEB)

Besse, Nicolas, E-mail: Nicolas.Besse@oca.eu [Laboratoire J.-L. Lagrange, UMR CNRS/OCA/UCA 7293, Université Côte d’Azur, Observatoire de la Côte d’Azur, Bd de l’Observatoire CS 34229, 06304 Nice Cedex 4 (France); Institut Jean Lamour, UMR CNRS/UL 7198, Université de Lorraine, BP 70239 54506 Vandoeuvre-lès-Nancy Cedex (France); Coulette, David, E-mail: David.Coulette@ipcms.unistra.fr [Institut Jean Lamour, UMR CNRS/UL 7198, Université de Lorraine, BP 70239 54506 Vandoeuvre-lès-Nancy Cedex (France); Institut de Physique et Chimie des Matériaux de Strasbourg, UMR CNRS/US 7504, Université de Strasbourg, 23 Rue du Loess, 67034 Strasbourg (France)

2016-08-15

Achieving plasmas with good stability and confinement properties is a key research goal for magnetic fusion devices. The underlying equations are the Vlasov–Poisson and Vlasov–Maxwell (VPM) equations in three space variables, three velocity variables, and one time variable. Even in those somewhat academic cases where global equilibrium solutions are known, studying their stability requires the analysis of the spectral properties of the linearized operator, a daunting task. We have identified a model, for which not only equilibrium solutions can be constructed, but many of their stability properties are amenable to rigorous analysis. It uses a class of solution to the VPM equations (or to their gyrokinetic approximations) known as waterbag solutions which, in particular, are piecewise constant in phase-space. It also uses, not only the gyrokinetic approximation of fast cyclotronic motion around magnetic field lines, but also an asymptotic approximation regarding the magnetic-field-induced anisotropy: the spatial variation along the field lines is taken much slower than across them. Together, these assumptions result in a drastic reduction in the dimensionality of the linearized problem, which becomes a set of two nested one-dimensional problems: an integral equation in the poloidal variable, followed by a one-dimensional complex Schrödinger equation in the radial variable. We show here that the operator associated to the poloidal variable is meromorphic in the eigenparameter, the pulsation frequency. We also prove that, for all but a countable set of real pulsation frequencies, the operator is compact and thus behaves mostly as a finite-dimensional one. The numerical algorithms based on such ideas have been implemented in a companion paper [D. Coulette and N. Besse, “Numerical resolution of the global eigenvalue problem for gyrokinetic-waterbag model in toroidal geometry” (submitted)] and were found to be surprisingly close to those for the original

US SciDAC Program on Integrated Simulation of Edge Transport in Fusion Plasmas, and its Progress

International Nuclear Information System (INIS)

Chang, C.S.

2007-01-01

The multi-institutional collaborative center for plasma edge simulation (CPES) has been launched in the USA under the SciDAC (Scientific Discovery through Advanced Computing) Fusion Simulation Program. This is a multi-disciplinary effort among physicists, applied mathematicians, and computer scientists from 15 national laboratories and universities. Its goal is to perform first principles simulations on plasma transport in the edge region from the top of the pedestal to the scrape off/divertor regions bounded by a material wall, and to predict L-H transition, pedestal buildup, ELM crashes, scrape-off transport and divertor heat load. As a major part of the effort, a PIC gyrokinetic edge code XGC is constructed. The gyrokinetic edge code XGC is coupled to a nonlinear edge MHD/2fluid code (M3D and NIMROD) to predict the cycle of pedestal buildup and ELM crash. The magnetic geometry includes the realistic separatrix, X-point, open field lines and material wall. In the first phase of this effort, the electrostatic version of the PIC gyrokinetic code XGC-1 has been built, to be extended into an electromagnetic version soon in the next phase. XGC-1 includes the gyrokinetic ions, electrons, and Monte Carlo neutrals with wall recycling. Since the ions have non-Maxwellian distribution function in the edge, as demonstrated in XGC, a full-f ion technique is used. Electrons are, though, handled with a mixed-f technique: the full-f technique for neoclassical and adiabatic or delta-f split-weight techniques for turbulence physics. The mixed-f electron approach used in XGC is new, successfully integrating the neoclassical and turbulence physics. Recent progress and results on neoclassical and electrostatic turbulence transports will be reported, which includes the pedestal buildup by neutral ionization, density pedestal width scaling, electrostatic potential and plasma flow distributions in the pedestal and scrape-off, and other important physical effects in the pedestal

The in vivo therapeutic efficacy of the oncolytic adenovirus Delta24-RGD is mediated by tumor-specific immunity.

Directory of Open Access Journals (Sweden)

Anne Kleijn

Full Text Available The oncolytic adenovirus Delta24-RGD represents a new promising therapeutic agent for patients with a malignant glioma and is currently under investigation in clinical phase I/II trials. Earlier preclinical studies showed that Delta24-RGD is able to effectively lyse tumor cells, yielding promising results in various immune-deficient glioma models. However, the role of the immune response in oncolytic adenovirus therapy for glioma has never been explored. To this end, we assessed Delta24-RGD treatment in an immune-competent orthotopic mouse model for glioma and evaluated immune responses against tumor and virus. Delta24-RGD treatment led to long-term survival in 50% of mice and this effect was completely lost upon administration of the immunosuppressive agent dexamethasone. Delta24-RGD enhanced intra-tumoral infiltration of F4/80+ macrophages, CD4+ and CD8+ T-cells, and increased the local production of pro-inflammatory cytokines and chemokines. In treated mice, T cell responses were directed to the virus as well as to the tumor cells, which was reflected in the presence of protective immunological memory in mice that underwent tumor rechallenge. Together, these data provide evidence that the immune system plays a vital role in the therapeutic efficacy of oncolytic adenovirus therapy of glioma, and may provide angles to future improvements on Delta24-RGD therapy.

Porting the 3D Gyrokinetic Particle-in-cell Code GTC to the CRAY/NEC SX-6 Vector Architecture: Perspectives and Challenges

International Nuclear Information System (INIS)

Ethier, S.; Lin, Z.

2003-01-01

Several years of optimization on the super-scalar architecture has made it more difficult to port the current version of the 3D particle-in-cell code GTC to the CRAY/NEC SX-6 vector architecture. This paper explains the initial work that has been done to port this code to the SX-6 computer and to optimize the most time consuming parts. Early performance results are shown and compared to the same test done on the IBM SP Power 3 and Power 4 machines

Electromagnetic ''particle-in-cell'' plasma simulation

International Nuclear Information System (INIS)

Langdon, A.B.

1985-01-01

''PIC'' simulation tracks particles through electromagnetic fields calculated self-consistently from the charge and current densities of the particles themselves, external sources, and boundaries. Already used extensively in plasma physics, such simulations have become useful in the design of accelerators and their r.f. sources. 5 refs

On the Universality of CP Violation in Delta F = 1 Processes

CERN Document Server

Gedalia, Oram; Ligeti, Zoltan; Perez, Gilad

2012-01-01

We show that new physics that breaks the left-handed SU(3)_Q quark flavor symmetry induces contributions to CP violation in Delta F = 1 processes which are approximately universal, in that they are not affected by flavor rotations between the up and the down mass bases. Therefore, such flavor violation cannot be aligned, and is constrained by the strongest bound from either the up or the down sectors. We use this result to show that the bound from eps'/eps prohibits an SU(3)_Q breaking explanation of the recent LHCb evidence for CP violation in D meson decays. Another consequence of this universality is that supersymmetric alignment models with a moderate mediation scale are consistent with the data, and are harder to probe via CP violating observables. With current constraints, therefore, squarks need not be degenerate. However, future improvements in the measurement of CP violation in D-Dbar mixing will start to probe alignment models.

Neoclassical and gyrokinetic analysis of time-dependent helium transport experiments on MAST

International Nuclear Information System (INIS)

Henderson, S.S.; O'Mullane, M.; Summers, H.P.; Garzotti, L.; Casson, F.J.; Dickinson, D.; Fox, M.F.J.; Patel, A.; Roach, C.M.; Valovič, M.

2014-01-01

Time-dependent helium gas puff experiments have been performed on the Mega Ampère Spherical Tokamak (MAST) during a two point plasma current scan in L-mode and a confinement scan at 900 kA. An evaluation of the He II (n = 4 → 3) spectrum line induced by charge exchange suggests anomalous rates of diffusion and inward convection in the outer regions of both L-mode plasmas. Similar rates of diffusion are found in the H-mode plasma, however these rates are consistent with neoclassical predictions. The anomalous inward pinch found in the core of L-mode plasmas is also not apparent in the H-mode core. Linear gyrokinetic simulations of one flux surface in L-mode using the GS2 and GKW codes find that equilibrium flow shear is sufficient to stabilize ITG modes, consistent with beam emission spectroscopy (BES) observations, and suggest that collisionless TEMs may dominate the anomalous helium particle transport. A quasilinear estimate of the dimensionless peaking factor associated with TEMs is in good agreement with experiment. Collisionless TEMs are more stable in H-mode because the electron density gradient is flatter. The steepness of this gradient is therefore pivotal in determining the inward neoclassical particle pinch and the particle flux associated with TEM turbulence. (paper)

Inclusive production of. delta. /sup + +/(1232) in pn interactions at 19 GeV/c

Energy Technology Data Exchange (ETDEWEB)

Bakken, V.; Breivik, F.O.; Jacobsen, T.; Rudjord, A.L. (Oslo Univ. (Norway) Fysisk Inst.)

1982-12-21

We present a study of ..delta../sup + +/ production in pn interactions at 19 GeV/c, where the ..delta../sup + +/ is emitted in the protonlike (..delta..sub(F)/sup + +/) and neutron-like (..delta..sub(B)/sup + +/) c.m. hemispheres. The cross-section sigma(pn->..delta..sub(F)/sup + +/+X)=(3.09+-0.43) mb is about three times larger than sigma(pn->..delta..sub(B)/sup + +/+X)=(0.94+-0.34) mb. About 2/3 of ..delta..sub(F)/sup + +/ is peripherally produced with vertical stroketsub(p,..delta..)vertical stroke<1 (GeV/c)/sup 2/, while the cross-section for ..delta..sub(B)/sup + +/ production is nearly zero for vertical stroketsub(n,..delta..)vertical stroke<1 (GeV/c)/sup 2/. We have made a detailed study of the energy dependence of the reaction ap->..delta../sup + +/+X (a=p, anti p, n, ..pi..sup(+-), Ksup(+-)) for vertical stroketsub(p,..delta..)vertical stroke<1 (GeV/c)/sup 2/, by applying the same fitting procedure to extract the ..delta../sup + +/ cross-section to all available mass spectra. All the normalized cross-sections R=sigma(..delta../sup + +/)/sigmasub(inel) can be well described by R=R/sub 0/+R/sub 1/sup(a)psup(-..cap alpha..)sub(lab), where R/sub 0/ and ..cap alpha.. are the same for all reactions, while R/sub 1/sup(a) varies with the beam type a. The value of ..cap alpha.. is slightly below unity. The differential cross section of pn->..delta..sub(F)/sup + +/+X has been determined as a function of the variables t, t', x, y, psub(T)/sup 2/ and Msub(X)/sup 2/ both in the whole kinematical region and for vertical stroketsub(p,..delta..)vertical stroke<1 (GeV/c)/sup 2/. We show that the peripherally produced ..delta..sub(F)/sup + +/ is consistent with the dominance of the one-pion exchange mechanism. This follows from a study of the density matrix elements, the comparison of some properties of the system X with real ..pi../sup +/p data and from the results of a triple-Regge analysis.

Effects of Plasma Shaping on Nonlinear Gyrokinetic Turbulence

Energy Technology Data Exchange (ETDEWEB)

Belli, E. A. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Hammett, G. W. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Dorland, W. [Univ. of Maryland, College Park, MD (United States)

2008-08-01

The effects of flux surface shape on the gyrokinetic stability and transport of tokamak plasmas are studied using the GS2 code [M. Kotschenreuther, G. Rewoldt, and W.M. Tang, Comput. Phys. Commun. 88, 128 (1995); W. Dorland, F. Jenko, M. Kotschenreuther, and B.N. Rogers, Phys. Rev. Lett. 85, 5579 (2000)]. Studies of the scaling of nonlinear turbulence with shaping parameters are performed using analytic equilibria based on interpolations of representative shapes of the Joint European Torus (JET) [P.H. Rebut and B.E. Keen, Fusion Technol. 11, 13 (1987)]. High shaping is found to be a stabilizing influence on both the linear ion-temperature-gradient (ITG) instability and the nonlinear ITG turbulence. For the parameter regime studied here, a scaling of the heat flux with elongation of χ ~ κ^-1.5 or κ^-2.0, depending on the triangularity, is observed at fixed average temperature gradient. While this is not as strong as empirical elongation scalings, it is also found that high shaping results in a larger Dimits upshift of the nonlinear critical temperature gradient due to an enhancement of the Rosenbluth-Hinton residual zonal flows.

Effects of Plasma Shaping on Nonlinear Gyrokinetic Turbulence

International Nuclear Information System (INIS)

E.A. Belli, G.W. Hammett and W. Dorland

2008-01-01

The effects of flux surface shape on the gyrokinetic stability and transport of tokamak plasmas are studied using the GS2 code [M. Kotschenreuther, G. Rewoldt, and W.M. Tang, Comput. Phys. Commun. 88, 128 (1995); W. Dorland, F. Jenko, M. Kotschenreuther, and B.N. Rogers, Phys. Rev. Lett. 85, 5579 (2000)]. Studies of the scaling of nonlinear turbulence with shaping parameters are performed using analytic equilibria based on interpolations of representative shapes of the Joint European Torus (JET) [P.H. Rebut and B.E. Keen, Fusion Technol. 11, 13 (1987)]. High shaping is found to be a stabilizing influence on both the linear ion-temperature-gradient (ITG) instability and the nonlinear ITG turbulence. For the parameter regime studied here, a scaling of the heat flux with elongation of χ ∼ κ -1.5 or κ -2.0 , depending on the triangularity, is observed at fixed average temperature gradient. While this is not as strong as empirical elongation scalings, it is also found that high shaping results in a larger Dimits upshift of the nonlinear critical temperature gradient due to an enhancement of the Rosenbluth-Hinton residual zonal flows

Enhanced stopping of macro-particles in particle-in-cell simulations

International Nuclear Information System (INIS)

May, J.; Tonge, J.; Ellis, I.; Mori, W. B.; Fiuza, F.; Fonseca, R. A.; Silva, L. O.; Ren, C.

2014-01-01

We derive an equation for energy transfer from relativistic charged particles to a cold background plasma appropriate for finite-size particles that are used in particle-in-cell simulation codes. Expressions for one-, two-, and three-dimensional particles are presented, with special attention given to the two-dimensional case. This energy transfer is due to the electric field of the wake set up in the background plasma by the relativistic particle. The enhanced stopping is dependent on the q 2 /m, where q is the charge and m is the mass of the relativistic particle, and therefore simulation macro-particles with large charge but identical q/m will stop more rapidly. The stopping power also depends on the effective particle shape of the macro-particle. These conclusions are verified in particle-in-cell simulations. We present 2D simulations of test particles, relaxation of high-energy tails, and integrated fast ignition simulations showing that the enhanced drag on macro-particles may adversely affect the results of these simulations in a wide range of high-energy density plasma scenarios. We also describe a particle splitting algorithm which can potentially overcome this problem and show its effect in controlling the stopping of macro-particles

Aerodynamic improvement of a delta wing in combination with leading edge flaps

Directory of Open Access Journals (Sweden)

Tadateru Ishide

2017-11-01

Full Text Available Recently, various studies of micro air vehicle (MAV and unmanned air vehicle (UAV have been reported from wide range points of view. The aim of this study is to research the aerodynamic improvement of delta wing in low Reynold’s number region to develop an applicative these air vehicle. As an attractive tool in delta wing, leading edge flap (LEF is employed to directly modify the strength and structure of vortices originating from the separation point along the leading edge. Various configurations of LEF such as drooping apex flap and upward deflected flap are used in combination to enhance the aerodynamic characteristics in the delta wing. The fluid force measurement by six component load cell and particle image velocimetry (PIV analysis are performed as the experimental method. The relations between the aerodynamic superiority and the vortex behavior around the models are demonstrated.

A gyrokinetic calculation of transmission and reflection of the fast wave in the ion cyclotron range of frequencies

International Nuclear Information System (INIS)

Lashmore-Davies, C.N.; Fuchs, V.; Dendy, R.O.

1993-01-01

A full-wave equation has been obtained from the gyrokinetic theory for the fast wave traversing a minority cyclotron resonance [Phys. Fluids B 4, 493 (1992)] with the aid of the fast wave approximation [Phys. Fluids 31, 1614 (1988)]. This theory describes the transmission, reflection, and absorption of the fast wave for arbitrary values of the parallel wave number. For oblique propagation the absorption is due to both ion cyclotron damping by minority ions and mode conversion to the ion Bernstein wave. The results for a 3 He minority in a D plasma indicate that for perpendicular propagation and minority temperatures of a few keV the power lost by the fast wave is all mode converted whereas for minority temperatures ∼100 keV∼30% of the incident power is dissipated by the minority ions due to the gyrokinetic correction. The gyrokinetic correction also results in a significant reduction in the reflection coefficient for low field side incidence when k zLB approx-lt 1 and the minority and hybrid resonances overlap

Investigation of the biodistribution, breakdown and excretion of delta inulin adjuvant.

Science.gov (United States)

Wang, Lixin; Barclay, Thomas; Song, Yunmei; Joyce, Paul; Sakala, Isaac G; Petrovsky, Nikolai; Garg, Sanjay

2017-08-03

Insoluble, nanostructured delta inulin particles enhance the immunogenicity of co-administered protein antigens and consequently are used as a vaccine adjuvant (Advax™). To better understand their immunomodulatory properties, the in vitro hydrolysis and in vivo distribution of delta inulin particles were investigated. Delta inulin particle hydrolysis under bio-relevant acidic conditions resulted in no observable change to the bulk morphology using SEM, and HPLC results showed that only 6.1% of the inulin was hydrolysed over 21days. However, 65% of the terminal glucose groups were released, showing that acid hydrolysis relatively rapidly releases surface bound chemistries. This was used to explain in vivo biodistribution results in which delta inulin particles surface-labelled with fluorescein-5-thiosemicabizide were administered to mice using intramuscular (I.M.) or subcutaneous (S.C.) routes. Comparison analysis of the fluorescence of soluble inulin in the supernatants of homogenised tissues maintained at room temperature or heated to 100°C to solubilise particulate inulin was used to distinguish between fluorescent probe on soluble inulin and probe bound to inulin within particles. Following both I.M. and S.C. injection delta inulin exhibited a depot behaviour with local injection site residence for several weeks. Over this time, as injection site inulin reduced, there was measurable transport of intact delta inulin particles by macrophages to secondary lymphoid organs and the liver. Ultimately, the injected delta inulin became solubilised resulting in its detection in the plasma and in the urine. Thus injected delta inulin particles are initially taken up by macrophages at the site of injection, trafficked to secondary lymphoid tissue and the liver, and hydrolysed resulting in their becoming soluble and diffusing into the blood stream, from whence they are glomerularly filtered and excreted into the urine. These results provide important insights into the

Perturbation and proinflammatory type activation of Vd1+ gamma delta T cells in African children with Plasmodium falciparum malaria

DEFF Research Database (Denmark)

Hviid, L; Kurtzhals, J A; Adabayeri, V

2001-01-01

of Plasmodium falciparum malaria in Ghanaian children and they can constitute 30 to 50% of all T cells shortly after initiation of antimalarial chemotherapy. The bulk of the gamma delta T cells involved in this perturbation expressed V delta 1 and had a highly activated phenotype. Analysis of the T...

Asymptotic description of plasma turbulence: Krylov-Bogoliubov methods and quasi-particles

International Nuclear Information System (INIS)

Sosenko, P.P.; Bertrand, P.; Decyk, V.K.

2001-01-01

The asymptotic theory of charged particle motion in electromagnetic fields is developed for the general case of finite Larmor-radius effects by means of Krylov-Bogoliubov averaging method. The correspondence between the general asymptotic methods, elaborated by M. Krylov and M.Bogoliubov, the quasi-particle description and gyrokinetics is established. Such a comparison is used to shed more light on the physical sense of the reduced Poisson equation, introduced in gyrokinetics, and the particle polarization drift. It is shown that the modification of the Poisson equation in the asymptotic theory is due to the non-conservation of the magnetic moment and gyrophase trembling. it is shown that the second-order modification of the adiabatic invariant can determine the conditions of global plasma stability and introduces new nonlinear terms into the reduced Poisson equation. Such a modification is important for several plasma orderings, e.g. NHD type ordering. The feasibility of numerical simulation schemes in which the polarization drift is included into the quasi-particle equations of motion, and the Poisson equation remains unchanged is analyzed. A consistent asymptotic model is proposed in which the polarization drift is included into the quasi-particle equations of motion and the particle and quasi-particle velocities are equal. It is shown that in such models there are additional modifications of the reduced Poisson equation. The latter becomes even more complicated in contrast to earlier suggestions

Nonlinear Gyrokinetic Theory With Polarization Drift

International Nuclear Information System (INIS)

Wang, L.; Hahm, T.S.

2010-01-01

A set of the electrostatic toroidal gyrokinetic Vlasov equation and the Poisson equation, which explicitly includes the polarization drift, is derived systematically by using Lie-transform method. The polarization drift is introduced in the gyrocenter equations of motion, and the corresponding polarization density is derived. Contrary to the wide-spread expectation, the inclusion of the polarization drift in the gyrocenter equations of motion does not affect the expression for the polarization density significantly. This is due to modification of the gyrocenter phase-space volume caused by the electrostatic potential [T. S. Hahm, Phys. Plasmas 3, 4658 (1996)].

Gyrokinetic Calculations of Microinstabilities and Transport During RF H-Modes on Alcator C-Mod

International Nuclear Information System (INIS)

Redi, M.H.; Fiore, C.; Bonoli, P.; Bourdelle, C.; Budny, R.; Dorland, W.D.; Ernst, D.; Hammett, G.; Mikkelsen, D.; Rice, J.; Wukitch, S.

2002-01-01

Physics understanding for the experimental improvement of particle and energy confinement is being advanced through massively parallel calculations of microturbulence for simulated plasma conditions. The ultimate goal, an experimentally validated, global, non-local, fully nonlinear calculation of plasma microturbulence is still not within reach, but extraordinary progress has been achieved in understanding microturbulence, driving forces and the plasma response in recent years. In this paper we discuss gyrokinetic simulations of plasma turbulence being carried out to examine a reproducible, H-mode, RF heated experiment on the Alcator CMOD tokamak3, which exhibits an internal transport barrier (ITB). This off axis RF case represents the early phase of a very interesting dual frequency RF experiment, which shows density control with central RF heating later in the discharge. The ITB exhibits steep, spontaneous density peaking: a reduction in particle transport occurring without a central particle source. Since the central temperature is maintained while the central density is increasing, this also suggests a thermal transport barrier exists. TRANSP analysis shows that ceff drops inside the ITB. Sawtooth heat pulse analysis also shows a localized thermal transport barrier. For this ICRF EDA H-mode, the minority resonance is at r/a * 0.5 on the high field side. There is a normal shear profile, with q monotonic

[mRNA expression of notch ligand-delta-like-1 and jagged-1 in mesenchymal stem cells of MDS patients].

Science.gov (United States)

Fei, Cheng-Ming; Gu, Shu-Cheng; Zhao, You-Shan; Guo, Juan; Li, Xiao; Chang, Chun-Kang

2014-12-01

This study was aimed to investigated the mRNA expression levels of Notch ligands- Delta-like-1 and Jagged-1 in bone marrow mesenchymal stem cells of patients with myelodysplastic syndrome (MDS), and to explore their relation with onset of MDS. Bone marrow mesenchymal stem cells of 38 patients with MDS and 16 normal subjects as control were collected to detect mRNA expression of Delta-like-1 and Jagged-1 by using real-time quantitative polymerase chain reaction. The results showed that the expression levels of Delta-like-1 and Jagged-1 in mesenchymal stem cells of MDS patients were significantly higher than that in normal controls (P MDS patients (r = 0.502, P MDS patients with abnormal karyotypes were significantly higher than those in MDS patients with normal karyotypes (P 0.05). It is concluded that the changes of Delta-like-1 and Jagged-1 expression level in MSC may play a role in the pathogenesis of myelodysplastic syndrome.

Transport modelling and gyrokinetic analysis of advanced high performance discharges

International Nuclear Information System (INIS)

Kinsey, J.E.; Imbeaux, F.; Staebler, G.M.; Budny, R.; Bourdelle, C.; Fukuyama, A.; Garbet, X.; Tala, T.; Parail, V.

2005-01-01

Predictive transport modelling and gyrokinetic stability analyses of demonstration hybrid (HYBRID) and advanced tokamak (AT) discharges from the International Tokamak Physics Activity (ITPA) profile database are presented. Both regimes have exhibited enhanced core confinement (above the conventional ITER reference H-mode scenario) but differ in their current density profiles. Recent contributions to the ITPA database have facilitated an effort to study the underlying physics governing confinement in these advanced scenarios. In this paper, we assess the level of commonality of the turbulent transport physics and the relative roles of the transport suppression mechanisms (i.e. E x B shear and Shafranov shift (α) stabilization) using data for select HYBRID and AT discharges from the DIII-D, JET and AUG tokamaks. GLF23 transport modelling and gyrokinetic stability analysis indicate that E x B shear and Shafranov shift stabilization play essential roles in producing the improved core confinement in both HYBRID and AT discharges. Shafranov shift stabilization is found to be more important in AT discharges than in HYBRID discharges. We have also examined the competition between the stabilizing effects of E x B shear and Shafranov shift stabilization and the destabilizing effects of higher safety factors and parallel velocity shear. Linear and nonlinear gyrokinetic simulations of idealized low and high safety factor cases reveal some interesting consequences. A low safety factor (i.e. HYBRID relevant) is directly beneficial in reducing the transport, and E x B shear stabilization can dominate parallel velocity shear destabilization allowing the turbulence to be quenched. However, at low-q/high current, Shafranov shift stabilization plays less of a role. Higher safety factors (as found in AT discharges), on the other hand, have larger amounts of Shafranov shift stabilization, but parallel velocity shear destabilization can prevent E x B shear quenching of the turbulent

Transport modeling and gyrokinetic analysis of advanced high performance discharges

International Nuclear Information System (INIS)

Kinsey, J.; Imbeaux, F.; Bourdelle, C.; Garbet, X.; Staebler, G.; Budny, R.; Fukuyama, A.; Tala, T.; Parail, V.

2005-01-01

Predictive transport modeling and gyrokinetic stability analyses of demonstration hybrid (HYBRID) and Advanced Tokamak (AT) discharges from the International Tokamak Physics Activity (ITPA) profile database are presented. Both regimes have exhibited enhanced core confinement (above the conventional ITER reference H-mode scenario) but differ in their current density profiles. Recent contributions to the ITPA database have facilitated an effort to study the underlying physics governing confinement in these advanced scenarios. In this paper, we assess the level of commonality of the turbulent transport physics and the relative roles of the transport suppression mechanisms (i.e. ExB shear and Shafranov shift (α) stabilization) using data for select HYBRID and AT discharges from the DIII-D, JET, and AUG tokamaks. GLF23 transport modeling and gyrokinetic stability analysis indicates that ExB shear and Shafranov shift stabilization play essential roles in producing the improved core confinement in both HYBRID and AT discharges. Shafranov shift stabilization is found to be more important in AT discharges than in HYBRID discharges. We have also examined the competition between the stabilizing effects of ExB shear and Shafranov shift stabilization and the destabilizing effects of higher safety factors and parallel velocity shear. Linear and nonlinear gyrokinetic simulations of idealized low and high safety factor cases reveals some interesting consequences. A low safety factor (i.e. HYBRID relevant) is directly beneficial in reducing the transport, and ExB shear stabilization can win out over parallel velocity shear destabilization allowing the turbulence to be quenched. However, at low-q/high current, Shafranov shift stabilization plays less of a role. Higher safety factors (as found in AT discharges), on the other hand, have larger amounts of Shafranov shift stabilization, but parallel velocity shear destabilization can prevent ExB shear quenching of the turbulent

Advances in continuum kinetic and gyrokinetic simulations of turbulence on open-field line geometries

Science.gov (United States)

Hakim, Ammar; Shi, Eric; Juno, James; Bernard, Tess; Hammett, Greg

2017-10-01

For weakly collisional (or collisionless) plasmas, kinetic effects are required to capture the physics of micro-turbulence. We have implemented solvers for kinetic and gyrokinetic equations in the computational plasma physics framework, Gkeyll. We use a version of discontinuous Galerkin scheme that conserves energy exactly. Plasma sheaths are modeled with novel boundary conditions. Positivity of distribution functions is maintained via a reconstruction method, allowing robust simulations that continue to conserve energy even with positivity limiters. We have performed a large number of benchmarks, verifying the accuracy and robustness of our code. We demonstrate the application of our algorithm to two classes of problems (a) Vlasov-Maxwell simulations of turbulence in a magnetized plasma, applicable to space plasmas; (b) Gyrokinetic simulations of turbulence in open-field-line geometries, applicable to laboratory plasmas. Supported by the Max-Planck/Princeton Center for Plasma Physics, the SciDAC Center for the Study of Plasma Microturbulence, and DOE Contract DE-AC02-09CH11466.

Quenching of scintillation in BaF2 for light charged particles

International Nuclear Information System (INIS)

Matulewicz, T.

1992-01-01

Detectors made of a barium fluoride (BaF 2 ) crystal have recently become popular in the spectroscopy of photons and light charged particles at intermediate energies. The quenching of the scintillation light of BaF 2 crystals is described in the framework of Birks law for light charged particles in the energy range of 20-100 A MeV. Based on the recently published data, the analysis yields a value of Birks constant equal to 1.8±0.3 mg MeV -1 cm -2 and a scintillation efficiency equal to 0.79±0.05 MeV ee MeV -1 . (R.P.) 10 refs.; 2 figs

Comprehensive gyrokinetic simulation of tokamak turbulence at finite relative gyroradius

International Nuclear Information System (INIS)

Waltz, R.E.; Candy, J.; Rosenbluth, M.N.

2003-01-01

A continuum global gyrokinetic code GYRO has been developed to comprehensively simulate turbulent transport in actual experimental profiles and allow direct quantitative comparisons to the experimental transport flows. GYRO not only treats the now standard ion temperature gradient (ITG) mode turbulence, but also treats trapped and passing electrons with collisions and finite beta, and all in real tokamak geometry. Most importantly the code operates at finite relative gyroradius (ρ*) so as to treat the profile shear stabilization effects which break gyro Bohm scaling. The code operates in a cyclic flux tube limit which allows only gyro Bohm scaling and a noncylic radial annulus with physical profile variation. The later requires an adaptive source to maintain equilibrium profiles. Simple ITG simulations demonstrate the broken gyro Bohm scaling paradigm of Garbet and Waltz [Phys. Plasmas 3, 1898 (1996)]. Since broken gyro Bohm scaling depends on the actual rotational velocity shear rates competing with mode growth rates, direct comprehensive simulations of the DIII-D ρ*-scaled L-mode experiments are presented as a quantitative test of gyrokinetics and the paradigm. (author)

Activation of PPAR{delta} up-regulates fatty acid oxidation and energy uncoupling genes of mitochondria and reduces palmitate-induced apoptosis in pancreatic {beta}-cells

Energy Technology Data Exchange (ETDEWEB)

Wan, Jun; Jiang, Li; Lue, Qingguo; Ke, Linqiu [Department of Endocrinology, West China Hospital of Sichuan University, 37 Guoxue Lane, Chengdu, Sichuan 610041 (China); Li, Xiaoyu [State Key Laboratory of Oral Diseases, Sichuan University, No. 14, 3rd Section, Renmin South Road, Chengdu, Sichuan 610041 (China); Tong, Nanwei, E-mail: buddyjun@hotmail.com [Department of Endocrinology, West China Hospital of Sichuan University, 37 Guoxue Lane, Chengdu, Sichuan 610041 (China)

2010-01-15

Recent evidence indicates that decreased oxidative capacity, lipotoxicity, and mitochondrial aberrations contribute to the development of insulin resistance and type 2 diabetes. The goal of this study was to investigate the effects of peroxisome proliferator-activated receptor {delta} (PPAR{delta}) activation on lipid oxidation, mitochondrial function, and insulin secretion in pancreatic {beta}-cells. After HIT-T15 cells (a {beta}-cell line) were exposed to high concentrations of palmitate and GW501516 (GW; a selective agonist of PPAR{delta}), we found that administration of GW increased the expression of PPAR{delta} mRNA. GW-induced activation of PPAR{delta} up-regulated carnitine palmitoyltransferase 1 (CPT1), long-chain acyl-CoA dehydrogenase (LCAD), pyruvate dehydrogenase kinase 4 (PDK4), and uncoupling protein 2 (UCP2); alleviated mitochondrial swelling; attenuated apoptosis; and reduced basal insulin secretion induced by increased palmitate in HIT cells. These results suggest that activation of PPAR{delta} plays an important role in protecting pancreatic {beta}-cells against aberrations caused by lipotoxicity in metabolic syndrome and diabetes.

Mixing state of oxalic acid containing particles in the rural area of Pearl River Delta, China: implication for seasonal formation mechanism of Secondary Organic Aerosol (SOA)

OpenAIRE

Cheng, Chunlei; Li, Mei; Chan, Chak K.; Tong, Haijie; Chen, Changhong; Chen, Duohong; Wu, Dui; Li, Lei; Cheng, Peng; Gao, Wei; Huang, Zhengxu; Li, Xue; Fu, Zhong; Bi, Yanru; Zhou, Zhen

2016-01-01

The formation of oxalic acid and its mixing state in atmospheric particulate matter (PM) were studied using a single particle aerosol mass spectrometer (SPAMS) in the summer and winter of 2014 in Heshan, a supersite in the rural area of the Pearl River Delta (PRD) region in China. Oxalic acid-containing particles accounted for 2.5 % and 2.7 % in total detected ambient particles in summer and winter, respectively. Oxalic acid was measured in particles classified as elemental carb...

Changes in thymocytes due to local irradiation of a portion of the maxilla in mice. A study of NKT cells and {gamma}{delta}T cells

Energy Technology Data Exchange (ETDEWEB)

Satho, Taigo; Tamasawa, Ken; Yosue, Takashi [Nippon Dental Univ., Tokyo (Japan); Arai, Thiaki

2000-07-01

We have been investigating the changes of lymphocyte subsets in immune organs after head and neck irradiation. The aim of the present study was to determine the influence of local irradiation (10 Gy) of a portion of the maxilla on the thymocyte subsets, specifically NKT cells and {gamma}{delta}T cells in mice. The thymocyte subsets were analyzed following irradiation using a fluorometer (anti-CD4, CD8, TCR{alpha}{beta}, TCR{gamma}{delta} and NK1.1 monoclonal antibodies) and the outcome compared with that obtained from no-irradiation groups. The following results were obtained: The total number of thymocytes showed a significant decrease one day and three days after irradiation. The absolute number of DN (double negative; CD4{sup -} CD8{sup -}), CD4{sup +} SP (CD4{sup +} single positive; CD4{sup +} CD8{sup -}) and CD8{sup +} SP (CD8{sup +} single positive; CD4{sup -} CD8{sup +}) thymocytes showed a significant decrease one day after irradiation. The absolute number of DP (double positive; CD4{sup +} CD8{sup +}) thymocytes showed a significant decrease one day and three days after irradiation. The absolute number of NKT and {gamma}{delta}T cells showed a significant decrease one day after irradiation. In conclusion, the results suggest that NKT cells and {gamma}{delta}T cells exhibit behavior which is the same as main stream thymocytes, except DP thymocytes. (author)

Dopaminergic neurotoxicant 6-OHDA induces oxidative damage through proteolytic activation of PKC{delta} in cell culture and animal models of Parkinson's disease

Energy Technology Data Exchange (ETDEWEB)

Latchoumycandane, Calivarathan; Anantharam, Vellareddy; Jin, Huajun; Kanthasamy, Anumantha; Kanthasamy, Arthi, E-mail: arthik@iastate.edu

2011-11-15

The neurotoxicant 6-hydroxydopamine (6-OHDA) is used to investigate the cellular and molecular mechanisms underlying selective degeneration of dopaminergic neurons in Parkinson's disease (PD). Oxidative stress and caspase activation contribute to the 6-OHDA-induced apoptotic cell death of dopaminergic neurons. In the present study, we sought to systematically characterize the key downstream signaling molecule involved in 6-OHDA-induced dopaminergic degeneration in cell culture and animal models of PD. Treatment of mesencephalic dopaminergic neuronal N27 cells with 6-OHDA (100 {mu}M) for 24 h significantly reduced mitochondrial activity and increased cytosolic cytochrome c, followed by sequential activation of caspase-9 and caspase-3. Co-treatment with the free radical scavenger MnTBAP (10 {mu}M) significantly attenuated 6-OHDA-induced caspase activities. Interestingly, 6-OHDA induced proteolytic cleavage and activation of protein kinase C delta (PKC{delta}) was completely suppressed by treatment with a caspase-3-specific inhibitor, Z-DEVD-FMK (50 {mu}M). Furthermore, expression of caspase-3 cleavage site-resistant mutant PKC{delta}{sup D327A} and kinase dead PKC{delta}{sup K376R} or siRNA-mediated knockdown of PKC{delta} protected against 6-OHDA-induced neuronal cell death, suggesting that caspase-3-dependent PKC{delta} promotes oxidative stress-induced dopaminergic degeneration. Suppression of PKC{delta} expression by siRNA also effectively protected N27 cells from 6-OHDA-induced apoptotic cell death. PKC{delta} cleavage was also observed in the substantia nigra of 6-OHDA-injected C57 black mice but not in control animals. Viral-mediated delivery of PKC{delta}{sup D327A} protein protected against 6-OHDA-induced PKC{delta} activation in mouse substantia nigra. Collectively, these results strongly suggest that proteolytic activation of PKC{delta} is a key downstream event in dopaminergic degeneration, and these results may have important translational value for

Circulating gamma delta T cells are activated and depleted during progression of high-grade gliomas: Implications for gamma delta T cell therapy of GBM

Science.gov (United States)

Glioblastoma multiforme (GBM) remains frustratingly impervious to any existing therapy. We have previously shown that GBM is sensitive to recognition and lysis by ex vivo activated gamma delta T cells, a minor subset of lymphocytes that innately recognize autologous stress-associated target antigens...

Investigation of energetic particle induced geodesic acoustic mode

Science.gov (United States)

Schneller, Mirjam; Fu, Guoyong; Chavdarovski, Ilija; Wang, Weixing; Lauber, Philipp; Lu, Zhixin

2017-10-01

Energetic particles are ubiquitous in present and future tokamaks due to heating systems and fusion reactions. Anisotropy in the distribution function of the energetic particle population is able to excite oscillations from the continuous spectrum of geodesic acoustic modes (GAMs), which cannot be driven by plasma pressure gradients due to their toroidally and nearly poloidally symmetric structures. These oscillations are known as energetic particle-induced geodesic acoustic modes (EGAMs) [G.Y. Fu'08] and have been observed in recent experiments [R. Nazikian'08]. EGAMs are particularly attractive in the framework of turbulence regulation, since they lead to an oscillatory radial electric shear which can potentially saturate the turbulence. For the presented work, the nonlinear gyrokinetic, electrostatic, particle-in-cell code GTS [W.X. Wang'06] has been extended to include an energetic particle population following either bump-on-tail Maxwellian or slowing-down [Stix'76] distribution function. With this new tool, we study growth rate, frequency and mode structure of the EGAM in an ASDEX Upgrade-like scenario. A detailed understanding of EGAM excitation reveals essential for future studies of EGAM interaction with micro-turbulence. Funded by the Max Planck Princeton Research Center. Computational resources of MPCDF and NERSC are greatefully acknowledged.

Advantages of CaF2 over ZnS in an α-particle scintillation detector

International Nuclear Information System (INIS)

Sabol, B.; Schery, S.D.

1981-01-01

Results are reported for using a europium-activated calcium fluoride (CaF 2 ) scintillation crystal as a α-particle detector in a two-filter monitor of atmospheric radon. CaF 2 detectors are cheaper and can cover a larger surface area than the higher-resolution solid-state detectors. Compared to ZnS scintillators, the energy resolution for CaF 2 is improved from 3.0 MeV to 1.1 MeV for 4.7 MeV α-particles; however the light output from CaF 2 is considerably lower. It is concluded that a thin CaF 2 crystal is a cost-effective method of improving energy and time resolutions for the two-filter monitor. (U.K.)

Measurements of double differential charged particle emission cross sections and development of a wide range charged particles spectrometer for ten`s MeV neutrons

Energy Technology Data Exchange (ETDEWEB)

Nauchi, Yasushi; Baba, Mamoru; Kiyosumi, Takehide [Tohoku Univ., Sendai (Japan). Faculty of Engineering] [and others

1997-03-01

We measured (n,xp), (n,xd) cross sections of C and Al for En=64.3 MeV neutrons at the {sup 7}Li(p,n) neutron sources facility at TIARA (Takasaki Establishment, JAERI) by using a conventional SSD-NaI telescope placed in the air. They show characteristic energy and angular dependence in high energy regions. In order to extend the measurements to low energy protons and {alpha} particles, a new spectrometer consisting of low pressure gas counters and BaF{sub 2} scintillators is now under development. A low threshold for low energy {alpha} particles will be achieved by using the gas counters. The particle identification over a wide energy range will be achieved by combining the {Delta}E-E method for low energy particles with the pulse shape discrimination (PSD) method of BaF{sub 2} for high energy particles. (author)

Gyrokinetic simulation of microtearing turbulence

International Nuclear Information System (INIS)

Doerk, Hauke

2013-01-01

In modern fusion experiments, plasma turbulence is responsible for the radial heat transport and thus determines the plasma confinement within the magnetic field of tokamak devices. Deeper theoretical understanding is needed to explain today's and future fusion experiments. The goal of fusion research is to establish nuclear fusion as a safe and sustainable energy source. In future fusion power plants, and also in large fusion experiments like the presently constructed ITER, plasma heating predominantly affects the electron species. The reason is of fundamental nature: the collisional cross section of fast ions that are produced by the heating systems is larger for thermal electrons than for thermal ions. It is thus essential to correctly predict electron thermal transport, but the overall picture still continues to evolve. Besides microinstabilities on the electron gyroradius scales, also a stochastized magnetic field can contribute to enhanced electron transport. Already since the 1970's, the so-called microtearing instability is discussed as a source of stochastic fields. This microinstability deserves its name for breaking up the magnetic field structure by forming small-scale magnetic islands. The linear microtearing instability and its nonlinear, turbulent behavior is investigated in this thesis by means of numerical simulations with the gyrokinetic turbulence code Gene. The underlying gyrokinetic equations are not only appropriate to predict turbulent transport, but also describe neoclassical transport that is drift-kinetic in nature. Besides revealing interesting physics on long time scales, solving the neoclassical equation serves as an excellent test for the numerical implementation of the collision operator in Gene. Focusing on the local limit, it is found that a modification of this implementation that considers certain symmetries is necessary to obtain a satisfactory agreement with the well-established drift-kinetic neoclassical code Neo. Also the

Spatially Localized Particle Energization by Landau Damping in Current Sheets

Science.gov (United States)

Howes, G. G.; Klein, K. G.; McCubbin, A. J.

2017-12-01

Understanding the mechanisms of particle energization through the removal of energy from turbulent fluctuations in heliospheric plasmas is a grand challenge problem in heliophysics. Under the weakly collisional conditions typical of heliospheric plasma, kinetic mechanisms must be responsible for this energization, but the nature of those mechanisms remains elusive. In recent years, the spatial localization of plasma heating near current sheets in the solar wind and numerical simulations has gained much attention. Here we show, using the innovative and new field-particle correlation technique, that the spatially localized particle energization occurring in a nonlinear gyrokinetic simulation has the velocity space signature of Landau damping, suggesting that this well-known collisionless damping mechanism indeed actively leads to spatially localized heating in the vicinity of current sheets.

Complex rearrangements within the human J delta-C delta/J alpha-C alpha locus and aberrant recombination between J alpha segments

NARCIS (Netherlands)

Baer, R.; Boehm, T.; Yssel, H.; Spits, H.; Rabbitts, T. H.

1988-01-01

We have examined DNA rearrangements within a 120 kb cloned region of the human T cell receptor J delta-C delta/J alpha-C alpha locus. Three types of pattern emerge from an analysis of T cell lines and clones. Firstly, cells with two rearrangements within J delta-C delta; secondly, cells with one

Backward production of mesons associated with. Delta. sup ++ (1232) in. pi. sup + p interactions at 20 GeV/c

Energy Technology Data Exchange (ETDEWEB)

Perepelitsa, V.F.; Mikhailichenko, V.I.; Nikitin, S.Ya.; Zhokin, A.S. (Institut Teoreticheskoj i Ehksperimental' noj Fiziki, Moscow (USSR)); Akopov, N.Z.; Grigoryan, A.A.; Karapetyan, V.V. (Erevanskij Fizicheskij Inst., Erevan (USSR)); Dorsaz, L.; Sonderegger, P. (European Organization for Nuclear Research, Geneva (Switzerland)); Ferrer, A. (Centro Mixto Valencia Univ./CSIC, Valencia (Spain). Inst. de Fisica Corpuscular)

1991-05-01

We have analyzed backward meson production in {pi}{sup +}p reactions at 20 GeV/c, which were measured in the CERN {Omega} spectrometer triggered by a fast proton (p{sub f}), in experiment WA 56. Production via baryon exchange of quasi-two-body final states {Delta}{sup ++}(1232) rho{sup 0}(770), {Delta}{sup ++}(1232) f{sub 2}(1270) and {Delta}{sup ++}(1232) rho{sub 3}{sup 0}(1690) is clearly identified. The density matrix elements of meson resonances and of {Delta}{sup ++}(1232) are analyzed. We have observed also the reactions {pi}{sup +}p->{Delta}{sup ++}(1232){pi}{sup 0} and {pi}{sup +}p->{Delta}{sup ++}(1232){omega} in the p{sub f}{pi}{sup +}{pi}{sup 0} and p{sub f}{pi}{sup +}{pi}{sup +}{pi}{sup -}{pi}{sup 0} final states. (orig.).

Momentum transport in gyrokinetic turbulence

Energy Technology Data Exchange (ETDEWEB)

Buchholz, Rico

2016-07-01

In this thesis, the gyrokinetic-Vlasov code GKW is used to study turbulent transport, with a focus on radial transport of toroidal momentum. To support the studies on turbulent transport an eigenvalue solver has been implemented into GKW. This allows to find, not only the most unstable mode, but also subdominant modes. Furthermore it is possible to follow the modes in parameter scans. Furthermore, two fundamental mechanisms that can generate an intrinsic rotation have been investigated: profile shearing and the velocity nonlinearity. The study of toroidal momentum transport in a tokamak due to profile shearing reveals that the momentum flux can not be accurately described by the gradient in the turbulent intensity. Consequently, a description using the profile variation is used. A linear model has been developed that is able to reproduce the variations in the momentum flux as the profiles of density and temperature vary, reasonably well. It uses, not only the gradient length of density and temperature profile, but also their derivative, i.e. the second derivative of the logarithm of the temperature and the density profile. It is shown that both first as well as second derivatives contribute to the generation of a momentum flux. A difference between the linear and nonlinear simulations has been found with respect to the behaviour of the momentum flux. In linear simulations the momentum flux is independent of the normalized Larmor radius ρ{sub *}, whereas it is linear in ρ{sub *} for nonlinear simulations, provided ρ{sub *} is small enough (≤4.10{sup -3}). Nonlinear simulations reveal that the profile shearing can generate an intrinsic rotation comparable to that of current experiments. Under reactor conditions, however, the intrinsic rotation from the profile shearing is expected to be small due to the small normalized Larmor radius ρ{sub *}in GKW has been tested

Haematological and genetic features of delta beta-thalassaemia in Pakistan

International Nuclear Information System (INIS)

Ahmad, S.; Anwar, M.

2006-01-01

Objective: To describe the hematological and genetic features of delta beta-thalassaemia in Pakistani patients. Design: Descriptive case series. Place and Duration of Study: Department of Pathology, PNS Shifa, Karachi and Department of Hematology, Armed Forces Institute of Pathology, Rawalpindi, from January 1994 to April 2004. Patients and Methods: Thirteen individuals from six unrelated Pakistani families with a hematological diagnosis of delta beta-thalassaemia were studied. A brief clinical history, and the results of blood counts, absolute values, Hb-F, Hb-A/sub 2/, and hemoglobin electrophoresis were recorded. The DNA from each subject was first screened for the delta beta-thalassaemia mutations found in the Pakistani population. The samples were then screened for the Invl Del sup G/gamma(sup A/gamma delta beta). Results: The subjects included six heterozygote, six homozygotes and one compound heterozygote of delta beta and delta beta-thalassaemia. All heterozygote and 4/6 homozygotes were asymptomatic. One homo zygote had thalassaemia intermedia while another had transfusion dependent anemia. The mean Hb, TRBC, MCV, MCH, Hb-F and Hb-A/sub 2/ in delta beta-thalassaemia heterozygote were 11.6 g/dl, 5.37 x 1012/L, 70.9 fl, and 21.7 pg, 14% and 2.6% respectively. The same values in the four un transfused homo zygote were 10.6 g/dl, 5.34x1012/L, 69.211, and 20.8pg, 100% and 0% respectively. The mutation analysis revealed that all 13 individuals had the same Invl Del sup G/gamma(sup A/gamma delta beta). Conclusion: delta beta-thalassaemia is a rare disorder in Pakistan. Although the clinical picture is very mild its combination with delta beta-thalassaemia trait can produce a sever transfusion dependent thalassaemia. The DNA based diagnosis is possible in the prenatal as well as the postnatal period. (author)

Delta Cell Hyperplasia in Adult Goto-Kakizaki (GK/MolTac) Diabetic Rats

Czech Academy of Sciences Publication Activity Database

Alán, Lukáš; Olejár, Tomáš; Cahová, M.; Zelenka, Jaroslav; Berková, Z.; Smětáková, M.; Saudek, F.; Matěj, R.; Ježek, Petr

2015-01-01

Roč. 2015, č. 2015 (2015), s. 385395 ISSN 2314-6745 R&D Projects: GA ČR(CZ) GA13-06666S Institutional support: RVO:67985823 Keywords : Goto Kakizaki rats * diabetes * delta cell hyperplasia * somatostatin * pancreatic polypeptide deficiency Subject RIV: FB - Endocrinology, Diabetology, Metabolism, Nutrition Impact factor: 2.431, year: 2015

Detection of Staphylococcus aureus delta-toxin production by whole-cell MALDI-TOF mass spectrometry.

Directory of Open Access Journals (Sweden)

Julie Gagnaire

Full Text Available The aim of the present study was to detect the Staphylococcus aureus delta-toxin using Whole-Cell (WC Matrix Assisted Laser Desorption Ionization-Time-of-Flight (MALDI-TOF mass spectrometry (MS, correlate delta-toxin expression with accessory gene regulator (agr status, and assess the prevalence of agr deficiency in clinical isolates with and without resistance to methicillin and glycopeptides. The position of the delta-toxin peak in the mass spectrum was identified using purified delta-toxin and isogenic wild type and mutant strains for agr-rnaIII, which encodes delta-toxin. Correlation between delta-toxin production and agr RNAIII expression was assessed by northern blotting. A series of 168 consecutive clinical isolates and 23 unrelated glycopeptide-intermediate S. aureus strains (GISA/heterogeneous GISA were then tested by WC-MALDI-TOF MS. The delta-toxin peak was detected at 3005±5 Thomson, as expected for the naturally formylated delta toxin, or at 3035±5 Thomson for its G10S variant. Multivariate analysis showed that chronicity of S. aureus infection and glycopeptide resistance were significantly associated with delta-toxin deficiency (p = 0.048; CI 95%: 1.01-10.24; p = 0.023; CI 95%: 1.20-12.76, respectively. In conclusion, the S. aureus delta-toxin was identified in the WC-MALDI-TOF MS spectrum generated during routine identification procedures. Consequently, agr status can potentially predict infectious complications and rationalise application of novel virulence factor-based therapies.

Global gyrokinetic simulation of Tokamak edge pedestal instabilities.

Science.gov (United States)

Wan, Weigang; Parker, Scott E; Chen, Yang; Yan, Zheng; Groebner, Richard J; Snyder, Philip B

2012-11-02

Global electromagnetic gyrokinetic simulations show the existence of near threshold conditions for both a high-n kinetic ballooning mode (KBM) and an intermediate-n kinetic version of peeling-ballooning mode (KPBM) in the edge pedestal of two DIII-D H-mode discharges. When the magnetic shear is reduced in a narrow region of steep pressure gradient, the KPBM is significantly stabilized, while the KBM is weakly destabilized and hence becomes the most-unstable mode. Collisions decrease the KBM's critical β and increase the growth rate.

Full-f gyrokinetic simulation of edge pedestal in Textor

Energy Technology Data Exchange (ETDEWEB)

Kiviniemi, Timo [Aalto Univ. (Finland)

2016-11-01

In ongoing simulations we have noticed that change phase angle between electric field and density oscillation may be important for changes in particle transport for different isotopes which could explain part of the so-called isotope-effect. Even the present database from the PRACE simulation (about 20 cases and some 4 TB of data) can still be further explored for this as the 3D data for both electric field and density exists. After finishing the PRACE project the code has been updated to include scrape-off-layer (SOL) which has opened several possibilities for future research.

Nature of turbulent transport across sheared zonal flows: insights from gyrokinetic simulations

International Nuclear Information System (INIS)

Sanchez, R; Newman, D E; Leboeuf, J-N; Decyk, V K

2011-01-01

The traditional view regarding the reduction of turbulence-induced transport across a stable sheared flow invokes a reduction of the characteristic length scale in the direction perpendicular to the flow as a result of the shearing and stretching of eddies caused by the differential pull exerted in the direction of the flow. A reduced effective transport coefficient then suffices to capture the reduction, that can then be readily incorporated into a transport model. However, recent evidence from gyrokinetic simulations of the toroidal ion-temperature-gradient mode suggests that the dynamics of turbulent transport across sheared flows changes in a more fundamental manner, and that the use of reduced effective transport coefficients fails to capture the full dynamics that may exhibit both subdiffusion and non-Gaussian statistics. In this contribution, after briefly reviewing these results, we propose some candidates for the physical mechanisms responsible for endowing transport with such non-diffusive characteristics, backing these proposals with new numerical gyrokinetic data.

Quantum 1/f noise in non-degerate semiconductors and emission statistics of alpha particles

International Nuclear Information System (INIS)

Kousik, G.S.

1985-01-01

Charged particle scattering is accompanied by the emission of soft photons. Handel's theory of 1/f noise, based on the infrared divergent coupling of the system to the electromagnetic field or other elementary excitations, states that the current associated with a beam of scattered particles will exhibit 1/f noise. The fraction of the particles scattered with an energy loss epsilon to soft photon emission is proportional to 1/epsilon and herein lies the origin of the quantum theory of 1/f noise. The 1/f noise caused by mobility fluctuations in semiconductors is related to the scattering cross section fluctuation given by Handel's theory, through the relaxation time. Chapters Two through Five of this dissertation presents the results of the detailed calculation of mobility fluctuation 1/f noise and Hooge parameter in nondegenerate semiconductors. Numerical results are given for silicon and gallium arsenide. Data obtained from extensive measurements on counting techniques for alpha-particles radioactive decay from a source containing 94 Pu 239 , 95 Am 241 and 96 Cm 244 are presented in Chapters Six and Seven of this dissertation. These data show that the statistics are non-Poissonian for large counting times (of the order of 1000 minutes) contrary to the popular belief that alpha-decay is an example of Poissonian statistics. Measurements of the Allan variance indicated the presence of a slow Lorentzian flicker noise and 1/f noise and the magnitude of the noise for large counting times is considerably larger than that predicted by Poissonian statistics

Kinetic simulations of neoclassical and anomalous transport processes in helical systems

International Nuclear Information System (INIS)

Sugama, Hideo; Watanabe, Tomohiko; Nunami, Masanori; Satake, Shinsuke; Matsuoka, Seikichi; Tanaka, Kenji

2012-01-01

Drift kinetic and gyrokinetic theories and simulations are powerful means for quantitative predictions of neoclassical and anomalous transport fluxes in helical systems such as the Large Helical Device (LHD). The δf Monte Carlo particle simulation code, FORTEC-3D, is used to predict radial profiles of the neoclassical particle and heat transport fluxes and the radial electric field in helical systems. The radial electric field profiles in the LHD plasmas are calculated from the ambipolarity condition for the neoclassical particle fluxes obtained by the global simulations using the FORTEC-3D code, in which effects of ion or electron finite orbit widths are included. Gyrokinetic Vlasov simulations using the GKV code verify the theoretical prediction that the neoclassical optimization of helical magnetic configuration enhances the zonal flow generation which leads to the reduction of the turbulent heat diffusivity χ i due to the ion temperature gradient (ITG) turbulence. Comparisons between results for the high ion temperature LHD experiment and the gyrokinetic simulations using the GKV-X code show that the χ i profile and the poloidal wave number spectrum of the density fluctuation obtained from the simulations are in reasonable agreements with the experimental results. It is predicted theoretically and confirmed by the linear GKV simulations that the E × B rotation due to the background radial electric field E r can enhance the zonal-flow response to a given source. Thus, in helical systems, the turbulent transport is linked to the neoclassical transport through E r which is determined from the ambipolar condition for neoclassical particle fluxes and influences the zonal flow generation leading to reduction of the turbulent transport. In order to investigate the E r effect on the regulation of the turbulent transport by the zonal flow generation, the flux-tube bundle model is proposed as a new method for multiscale gyrokinetic simulations. (author)

Visualization of particle in cell simulation

International Nuclear Information System (INIS)

Chen Ming; Cheng Yinhui

2003-01-01

This paper is trying to provide a new technique of the visualization for the Particle In Cell simulation, which takes effect by using the MATLAB external interface, so the real-time obsevation of particles came easier and more efficient. With this method, state of the particles, considered as 'particle cloud' can be found in the image produced automatically and their movement can be predicted. (authors)

Steady-State Gyrokinetics Transport Code (SSGKT), A Scientific Application Partnership with the Framework Application for Core-Edge Transport Simulations, Final Report

Energy Technology Data Exchange (ETDEWEB)

Fahey, Mark R. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Candy, Jeff [General Atomics, San Diego, CA (United States)

2013-11-07

This project initiated the development of TGYRO - a steady-state Gyrokinetic transport code (SSGKT) that integrates micro-scale GYRO turbulence simulations into a framework for practical multi-scale simulation of conventional tokamaks as well as future reactors. Using a lightweight master transport code, multiple independent (each massively parallel) gyrokinetic simulations are coordinated. The capability to evolve profiles using the TGLF model was also added to TGYRO and represents a more typical use-case for TGYRO. The goal of the project was to develop a steady-state Gyrokinetic transport code (SSGKT) that integrates micro-scale gyrokinetic turbulence simulations into a framework for practical multi-scale simulation of a burning plasma core ? the International Thermonuclear Experimental Reactor (ITER) in particular. This multi-scale simulation capability will be used to predict the performance (the fusion energy gain, Q) given the H-mode pedestal temperature and density. At present, projections of this type rely on transport models like GLF23, which are based on rather approximate fits to the results of linear and nonlinear simulations. Our goal is to make these performance projections with precise nonlinear gyrokinetic simulations. The method of approach is to use a lightweight master transport code to coordinate multiple independent (each massively parallel) gyrokinetic simulations using the GYRO code. This project targets the practical multi-scale simulation of a reactor core plasma in order to predict the core temperature and density profiles given the H-mode pedestal temperature and density. A master transport code will provide feedback to O(16) independent gyrokinetic simulations (each massively parallel). A successful feedback scheme offers a novel approach to predictive modeling of an important national and international problem. Success in this area of fusion simulations will allow US scientists to direct the research path of ITER over the next two

Feasibility study of electrophoresis deposition of DyF3 on Nd-Fe-B particles for coercivity enhancement

Science.gov (United States)

Kim, K. M.; Kang, M. S.; Kwon, H. W.; Lee, J. G.; Yu, J. H.

2018-05-01

Feasibility of the electrophoresis deposition (EPD) technique for homogeneous and adhesive deposition of DyF3 particles on the Nd-Fe-B-type particles was studied, and coercivity enhancement in the diffusion-treated Nd-Fe-B-type particles deposited with DyF3 by EPD was investigated. HDDR-treated Nd12.5Fe80.6B6.4Ga0.3Nb0.2 particles were deposited with DyF3 particles by EPD. More homogeneous and adhesive deposition of DyF3 particles on the surface of Nd-Fe-B particles was made by the EPD with respect to conventional dip-coating, and this led to more active and homogeneous diffusion of Dy. More profound coercivity enhancement was achieved in the diffusion-treated Nd-Fe-B-type particles deposited with DyF3 by EPD compared to dip-coated particles.

Gyrokinetic simulations of neoclassical transport using a minimal collision operator

International Nuclear Information System (INIS)

Dif-Pradalier, G.; Grandgirard, V.; Sarazin, Y.; Garbet, X.; Ghendrih, Ph.; Angelino, P.

2008-01-01

Conventional neoclassical predictions are successfully recovered within a gyrokinetic framework using a minimal Fokker-Planck collision operator. This operator is shown to accurately describe some essential features of neoclassical theory, namely the neoclassical transport, the poloidal rotation and the linear damping of axisymmetric flows while interestingly preserving a high numerical efficiency. Its form makes it especially adapted to Eulerian or Semi-Lagrangian schemes.

Lava delta deformation as a proxy for submarine slope instability

Science.gov (United States)

Di Traglia, Federico; Nolesini, Teresa; Solari, Lorenzo; Ciampalini, Andrea; Frodella, William; Steri, Damiano; Allotta, Benedetto; Rindi, Andrea; Marini, Lorenzo; Monni, Niccolò; Galardi, Emanuele; Casagli, Nicola

2018-04-01

The instability of lava deltas is a recurrent phenomenon affecting volcanic islands, which can potentially cause secondary events such as littoral explosions (due to interactions between hot lava and seawater) and tsunamis. It has been shown that Interferometric Synthetic Aperture Radar (InSAR) is a powerful technique to forecast the collapse of newly emplaced lava deltas. This work goes further, demonstrating that the monitoring of lava deltas is a successful strategy by which to observe the long-term deformation of subaerial-submarine landslide systems on unstable volcanic flanks. In this paper, displacement measurements derived from Synthetic Aperture Radar (SAR) imagery were used to detect lava delta instability at Stromboli volcano (Italy). Recent flank eruptions (2002-2003, 2007 and 2014) affected the Sciara del Fuoco (SdF) depression, created a "stacked" lava delta, which overlies a pre-existing scar produced by a submarine-subaerial tsunamigenic landslide that occurred on 30 December 2002. Space-borne X-band COSMO-SkyMED (CSK) and C-band SENTINEL-1A (SNT) SAR data collected between February 2010 and October 2016 were processed using the SqueeSAR algorithm. The obtained ground displacement maps revealed the differential ground motion of the lava delta in both CSK and SNT datasets, identifying a stable area (characterized by less than 2 mm/y in both datasets) within the northern sector of the SdF and an unstable area (characterized by velocity fields on the order of 30 mm/y and 160 mm/y in the CSK and SNT datasets, respectively) in the central sector of the SdF. The slope stability of the offshore part of the SdF, as reconstructed based on a recently performed multibeam bathymetric survey, was evaluated using a 3D Limit Equilibrium Method (LEM). In all the simulations, Factor of Safety (F) values between 0.9 and 1.1 always characterized the submarine slope between the coastline and -250 m a.s.l. The critical surfaces for all the search volumes corresponded to

Comparison of [18F]FLT and [18F]FDG in in vitro cancer cell uptake and glucose effect

International Nuclear Information System (INIS)

Soo Jung Lim; Jin-Sook Ryu; Heuiran Lee; Seok Young Kim; Seung Jun Oh; Dae Hyuk Moon

2004-01-01

[18F]FLT is a new radiopharmaceutical for cell proliferation. We compared [18F]FLT and [18F]FDG in in vitro cancer cell uptake and glucose effect. Method: In vitro cancer cell uptake of [18F]FLT was evaluated using SCC7(mouse squamous cell carcinoma). At 24 hours after seeding 1 x 106 cells/well in 6 well plates with RPMI 1640 medium, culture media were changed to medium with glucose free or glucose concentration of 100 mg/dl. Then, [18F]FLT 5 μCi/50 ml was added to each well. After incubation for 30, 60, 90, 120 minutes, cells were washed twice by PBS, and harvested using 0.25% trypsin-EDTA. After centrifugation and counting at gamma counter, cell uptake was calculated by % activity of cellular uptake to total activity of cell and supernatant. For comparison, same tumor cell uptake experiment was performed with [18F]FDG. Results: After incubation with SCC7 cell line for 30, 60, 90, 120 minutes, [18F]FLT showed 1.95%, 2.17%, 2.10% and 2.80% of cell uptake in glucose free media, respectively. The results [18F]FLT uptake in glucose 100 mg/dl media were 1.82%, 1.87%, 1.97%, and 2.94%, respectively. The results of [18F]FDG in glucose free media were 2.50%, 3.47%, 5.04%, and 10.4%, whereas those in glucose 100 mg/dl media were 1.60%, 1.79%, 1.53%, and 1.82%, respectively. Conclusion: In contrast to [18F]FDG, [18F]FLT uptake in cancer cell was not affected by glucose concentration. In physiologic glucose concentration, [18F]FLT uptake in SCC7 cell line was significantly higher than [18F]FDG uptake after 120 minutes incubation. In [18F]FLT PET imaging may not need fasting for preparation before imaging study. (authors)

Redistribution of energetic particles by background turbulence

International Nuclear Information System (INIS)

Hauff, T.; Jenko, F.

2007-01-01

The quest to understand the turbulent transport of particles, momentum and energy in magnetized plasmas remains a key challenge in fusion research. A basic issue being .still relatively poorly understood is the turbulent ExB advection of charged test particles with large gyroradii. Especially the interaction of alpha particles or impurities with the background turbulence is of great interest. In order to understand the dependence of the particle diffusivity on the interaction mechanisms between FLR effects and the special structure of a certain type of turbulence, direct numerical simulations are done in artificially created two dimensional turbulent electrostatic fields, assuming a constant magnetic field. Finite gyroradius effects are introduced using the gyrokinetic approximation which means that the gyrating particle is simply replaced by a charged ring. Starting from an idealized isotropic potential with Gaussian autocorrelation function, numerous test particle simulations are done varying both the gyroradius and the Kubo number of the potential. It is found that for Kubo numbers larger than about unity, the particle diffusivity is almost independent of the gyroradius as long as the latter does not exceed the correlation length of the electrostatic potential, whereas for small Kubo numbers the diffusivity is monotonically reduced. The underlying physical mechanisms of this behavior are identified and an analytic approach is developed which favorably agrees with the simulation results. The investigations are extended by introducing anisotropic structures like streamers and zonal flows into the artificial potential, leading to quantitative modulations of the gyroradius dependence of the diffusion coefficient. Analytic models are used to explain these various effects. After having developed a general overview on the behavior in simplified artificial potentials, test particle simulations in realistic turbulence created by the gyrokinetic turbulence code GENE are

Continuum Gyrokinetic Simulations of Turbulence in a Helical Model SOL with NSTX-type parameters

Science.gov (United States)

Hammett, G. W.; Shi, E. L.; Hakim, A.; Stoltzfus-Dueck, T.

2017-10-01

We have developed the Gkeyll code to carry out 3D2V full- F gyrokinetic simulations of electrostatic plasma turbulence in open-field-line geometries, using special versions of discontinuous-Galerkin algorithms to help with the computational challenges of the edge region. (Higher-order algorithms can also be helpful for exascale computing as they reduce the ratio of communications to computations.) Our first simulations with straight field lines were done for LAPD-type cases. Here we extend this to a helical model of an SOL plasma and show results for NSTX-type parameters. These simulations include the basic elements of a scrape-off layer: bad-curvature/interchange drive of instabilities, narrow sources to model plasma leaking from the core, and parallel losses with model sheath boundary conditions (our model allows currents to flow in and out of the walls). The formation of blobs is observed. By reducing the strength of the poloidal magnetic field, the heat flux at the divertor plate is observed to broaden. Supported by the Max-Planck/Princeton Center for Plasma Physics, the SciDAC Center for the Study of Plasma Microturbulence, and DOE Contract DE-AC02-09CH11466.

Gyrokinetics Simulation of Energetic Particle Turbulence and Transport

Energy Technology Data Exchange (ETDEWEB)

Diamond, Patrick H.

2011-09-21

Progress in research during this year elucidated the physics of precession resonance and its interaction with radial scattering to form phase space density granulations. Momentum theorems for drift wave-zonal flow systems involving precession resonance were derived. These are directly generalizable to energetic particle modes. A novel nonlinear, subcritical growth mechanism was identified, which has now been verified by simulation. These results strengthen the foundation of our understanding of transport in burning plasmas

Gyrokinetics Simulation of Energetic Particle Turbulence and Transport

International Nuclear Information System (INIS)

Diamond, Patrick H.

2011-01-01

Progress in research during this year elucidated the physics of precession resonance and its interaction with radial scattering to form phase space density granulations. Momentum theorems for drift wave-zonal flow systems involving precession resonance were derived. These are directly generalizable to energetic particle modes. A novel nonlinear, subcritical growth mechanism was identified, which has now been verified by simulation. These results strengthen the foundation of our understanding of transport in burning plasmas

Feasibility study of electrophoresis deposition of DyF3 on Nd-Fe-B particles for coercivity enhancement

Directory of Open Access Journals (Sweden)

K. M. Kim

2018-05-01

Full Text Available Feasibility of the electrophoresis deposition (EPD technique for homogeneous and adhesive deposition of DyF3 particles on the Nd-Fe-B-type particles was studied, and coercivity enhancement in the diffusion-treated Nd-Fe-B-type particles deposited with DyF3 by EPD was investigated. HDDR-treated Nd12.5Fe80.6B6.4Ga0.3Nb0.2 particles were deposited with DyF3 particles by EPD. More homogeneous and adhesive deposition of DyF3 particles on the surface of Nd-Fe-B particles was made by the EPD with respect to conventional dip-coating, and this led to more active and homogeneous diffusion of Dy. More profound coercivity enhancement was achieved in the diffusion-treated Nd-Fe-B-type particles deposited with DyF3 by EPD compared to dip-coated particles.

MMTV-Wnt1 and -DeltaN89beta-catenin induce canonical signaling in distinct progenitors and differentially activate Hedgehog signaling within mammary tumors.

Directory of Open Access Journals (Sweden)

Brigitte Teissedre

Full Text Available Canonical Wnt/beta-catenin signaling regulates stem/progenitor cells and, when perturbed, induces many human cancers. A significant proportion of human breast cancer is associated with loss of secreted Wnt antagonists and mice expressing MMTV-Wnt1 and MMTV-DeltaN89beta-catenin develop mammary adenocarcinomas. Many studies have assumed these mouse models of breast cancer to be equivalent. Here we show that MMTV-Wnt1 and MMTV-DeltaN89beta-catenin transgenes induce tumors with different phenotypes. Using axin2/conductin reporter genes we show that MMTV-Wnt1 and MMTV-DeltaN89beta-catenin activate canonical Wnt signaling within distinct cell-types. DeltaN89beta-catenin activated signaling within a luminal subpopulation scattered along ducts that exhibited a K18(+ER(-PR(-CD24(highCD49f(low profile and progenitor properties. In contrast, MMTV-Wnt1 induced canonical signaling in K14(+ basal cells with CD24/CD49f profiles characteristic of two distinct stem/progenitor cell-types. MMTV-Wnt1 produced additional profound effects on multiple cell-types that correlated with focal activation of the Hedgehog pathway. We document that large melanocytic nevi are a hitherto unreported hallmark of early hyperplastic Wnt1 glands. These nevi formed along the primary mammary ducts and were associated with Hedgehog pathway activity within a subset of melanocytes and surrounding stroma. Hh pathway activity also occurred within tumor-associated stromal and K14(+/p63(+ subpopulations in a manner correlated with Wnt1 tumor onset. These data show MMTV-Wnt1 and MMTV-DeltaN89beta-catenin induce canonical signaling in distinct progenitors and that Hedgehog pathway activation is linked to melanocytic nevi and mammary tumor onset arising from excess Wnt1 ligand. They further suggest that Hedgehog pathway activation maybe a critical component and useful indicator of breast tumors arising from unopposed Wnt1 ligand.

Destabilizing effect of alpha particles in a Maxwellian plasma

International Nuclear Information System (INIS)

Wang, M.Y.

1976-01-01

Various plasma waves which are possibly excited by MeV alphas have been investigated. For a delta birth distribution it is found that: a) The right-circularly polarized Alfven wave can be excited. Its growth rate is linearly proportional to the α-particle density. b) The drift Alfven wave is stable against α-particles. c) For a uniform temperature, the plasma wave spectrum changes from three branches with n/sub α/ = 0 to four branches for n/sub α/ not equal to 0 case. d) α-particles can destabilize the ion drift acoustic wave even with uniform temperature. However, the ion acoustic wave appears to be stable against fusion products in a fusion grade plasma. e) If their effect on the background plasma spectrum is neglected, α-particles can excite the electromagnetic cyclotron wave in a range of harmonics (band structure). The growth rate is proportional to the square root of α-particle density. f) If the effect of α-particle on the plasma spectrum is included, we find that electromagnetic cyclotron wave is stable

Investigating the radial structure of axisymmetric fluctuations in the TCV tokamak with local and global gyrokinetic GENE simulations

Science.gov (United States)

Merlo, G.; Brunner, S.; Huang, Z.; Coda, S.; Görler, T.; Villard, L.; Bañón Navarro, A.; Dominski, J.; Fontana, M.; Jenko, F.; Porte, L.; Told, D.

2018-03-01

Axisymmetric (n = 0) density fluctuations measured in the TCV tokamak are observed to possess a frequency f 0 which is either varying (radially dispersive oscillations) or a constant over a large fraction of the plasma minor radius (radially global oscillations) as reported in a companion paper (Z Huang et al, this issue). Given that f 0 scales with the sound speed and given the poloidal structure of density fluctuations, these oscillations were interpreted as Geodesic Acoustic Modes, even though f 0 is in fact smaller than the local linear GAM frequency {f}{GAM}. In this work we employ the Eulerian gyrokinetic code GENE to simulate TCV relevant conditions and investigate the nature and properties of these oscillations, in particular their relation to the safety factor profile. Local and global simulations are carried out and a good qualitative agreement is observed between experiments and simulations. By varying also the plasma temperature and density profiles, we conclude that a variation of the edge safety factor alone is not sufficient to induce a transition from global to radially inhomogeneous oscillations, as was initially suggested by experimental results. This transition appears instead to be the combined result of variations in the different plasma profiles, collisionality and finite machine size effects. Simulations also show that radially global GAM-like oscillations can be observed in all fluxes and fluctuation fields, suggesting that they are the result of a complex nonlinear process involving also finite toroidal mode numbers and not just linear global GAM eigenmodes.

Effects of recharge and discharge on delta2H and delta18O composition and chloride concentration of high arsenic/fluoride groundwater from the Datong Basin, northern China.

Science.gov (United States)

Xie, Xianjun; Wang, Yanxin; Su, Chunli; Duan, Mengyu

2013-02-01

To better understand the effects of recharge and discharge on the hydrogeochemistry of high levels of arsenic (As) and fluoride (F) in groundwater, environmental isotopic composition (delta2H and delta18O) and chloride (Cl) concentrations were analyzed in 29 groundwater samples collected from the Datong Basin. High arsenic groundwater samples (As > 50 micog/L) were found to be enriched in lighter isotopic composition that ranged from -92 to -78 per thousand for deuterium (delta2H) and from -12.5 to -9.9 per thousand for oxygen-18 (delta18O). High F-containing groundwater (F > 1 mg/L) was relatively enriched in heavier isotopic composition and varied from -90 to -57 per thousand and from -12.2 to -6.7 per thousand for delta2H and delta18O, respectively. High chloride concentrations and delta18O values were primarily measured in groundwater samples from the northern and southwestern portions of the study area, indicating the effect of evaporation on groundwater. The observation of relatively homogenized and low delta18O values and chloride concentrations in groundwater samples from central part of the Datong Basin might be a result of fast recharge by irrigation returns, which suggests that irrigation using arsenic-contaminated groundwater affected the occurrence of high arsenic-containing groundwater in the basin.

A novel mouse PKC{delta} splice variant, PKC{delta}IX, inhibits etoposide-induced apoptosis

Energy Technology Data Exchange (ETDEWEB)

Kim, Jung D. [School of Biological Sciences, University of Ulsan, Ulsan (Korea, Republic of); Seo, Kwang W. [Department of Internal Medicines, Ulsan University Hospital and School of Medicine, University of Ulsan, Ulsan (Korea, Republic of); Lee, Eun A.; Quang, Nguyen N. [School of Biological Sciences, University of Ulsan, Ulsan (Korea, Republic of); Cho, Hong R. [Department of Surgery, Ulsan University Hospital and School of Medicine, University of Ulsan, Ulsan (Korea, Republic of); Biomedical Research Center, Ulsan University Hospital and School of Medicine, University of Ulsan, Ulsan (Korea, Republic of); Kwon, Byungsuk, E-mail: bskwon@mail.ulsan.as.kr [School of Biological Sciences, University of Ulsan, Ulsan (Korea, Republic of); Biomedical Research Center, Ulsan University Hospital and School of Medicine, University of Ulsan, Ulsan (Korea, Republic of)

2011-07-01

Highlights: {yields} A novel PKC{delta} isoform, named PKC{delta}IX, that lacks the C1 domain and the ATP-binding site is ubiquitously expressed. {yields} PKC{delta}IX inhibits etoposide-induced apoptosis. {yields} PKC{delta}IX may function as an endogenous dominant negative isoform for PKC{delta}. -- Abstract: Protein kinase C (PKC) {delta} plays an important role in cellular proliferation and apoptosis. The catalytic fragment of PKC{delta} generated by caspase-dependent cleavage is essential for the initiation of etoposide-induced apoptosis. In this study, we identified a novel mouse PKC{delta} isoform named PKC{delta}IX (Genebank Accession No. (HQ840432)). PKC{delta}IX is generated by alternative splicing and is ubiquitously expressed, as seen in its full-length PKC{delta}. PKC{delta}IX lacks the C1 domain, the caspase 3 cleavage site, and the ATP binding site but preserves an almost intact c-terminal catalytic domain and a nuclear localization signal (NLS). The structural characteristics of PKC{delta}IX provided a possibility that this PKC{delta} isozyme functions as a novel dominant-negative form for PKC{delta} due to its lack of the ATP-binding domain that is required for the kinase activity of PKC{delta}. Indeed, overexpression of PKC{delta}IX significantly inhibited etoposide-induced apoptosis in NIH3T3 cells. In addition, an in vitro kinase assay showed that recombinant PKC{delta}IX protein could competitively inhibit the kinase activity of PKC{delta}. We conclude that PKC{delta}IX can function as a natural dominant-negative inhibitor of PKC{delta}in vivo.

Self-consistent gyrokinetic modeling of neoclassical and turbulent impurity transport

OpenAIRE

Estève , D. ,; Sarazin , Y.; Garbet , X.; Grandgirard , V.; Breton , S. ,; Donnel , P. ,; Asahi , Y. ,; Bourdelle , C.; Dif-Pradalier , G; Ehrlacher , C.; Emeriau , C.; Ghendrih , Ph; Gillot , C.; Latu , G.; Passeron , C.

2018-01-01

International audience; Trace impurity transport is studied with the flux-driven gyrokinetic GYSELA code [V. Grandgirard et al., Comp. Phys. Commun. 207, 35 (2016)]. A reduced and linearized multi-species collision operator has been recently implemented, so that both neoclassical and turbulent transport channels can be treated self-consistently on an equal footing. In the Pfirsch-Schlüter regime likely relevant for tungsten, the standard expression of the neoclassical impurity flux is shown t...

First-principle description of collisional gyrokinetic turbulence in tokamak plasmas

Energy Technology Data Exchange (ETDEWEB)

Dif-Pradalier, G

2008-10-15

This dissertation starts in chapter 1 with a comprehensive introduction to nuclear fusion, its basic physics, goals and means. It especially defines the concept of a fusion plasma and some of its essential physical properties. The following chapter 2 discusses some fundamental concepts of statistical physics. It introduces the kinetic and the fluid frameworks, compares them and highlights their respective strengths and limitations. The end of the chapter is dedicated to the fluid theory. It presents two new sets of closure relations for fluid equations which retain important pieces of physics, relevant in the weakly collisional tokamak regimes: collective resonances which lead to Landau damping and entropy production. Nonetheless, since the evolution of the turbulence is intrinsically nonlinear and deeply influenced by velocity space effects, a kinetic collisional description is most relevant. First focusing on the kinetic aspect, chapter 3 introduces the so-called gyrokinetic framework along with the numerical solver - the GYSELA code - which will be used throughout this dissertation. Very generically, code solving is an initial value problem. The impact on turbulent nonlinear evolution of out of equilibrium initial conditions is discussed while studying transient flows, self-organizing dynamics and memory effects due to initial conditions. This dissertation introduces an operational definition, now of routine use in the GYSELA code, for the initial state and concludes on the special importance of the accurate calculation of the radial electric field. The GYSELA framework is further extended in chapter 4 to describe Coulomb collisions. The implementation of a collision operator acting on the full distribution function is presented. Its successful confrontation to collisional theory (neoclassical theory) is also shown. GYSELA is now part of the few gyrokinetic codes which can self-consistently address the interplay between turbulence and collisions. While

First-principle description of collisional gyrokinetic turbulence in tokamak plasmas

International Nuclear Information System (INIS)

Dif-Pradalier, G.

2008-10-01

This dissertation starts in chapter 1 with a comprehensive introduction to nuclear fusion, its basic physics, goals and means. It especially defines the concept of a fusion plasma and some of its essential physical properties. The following chapter 2 discusses some fundamental concepts of statistical physics. It introduces the kinetic and the fluid frameworks, compares them and highlights their respective strengths and limitations. The end of the chapter is dedicated to the fluid theory. It presents two new sets of closure relations for fluid equations which retain important pieces of physics, relevant in the weakly collisional tokamak regimes: collective resonances which lead to Landau damping and entropy production. Nonetheless, since the evolution of the turbulence is intrinsically nonlinear and deeply influenced by velocity space effects, a kinetic collisional description is most relevant. First focusing on the kinetic aspect, chapter 3 introduces the so-called gyrokinetic framework along with the numerical solver - the GYSELA code - which will be used throughout this dissertation. Very generically, code solving is an initial value problem. The impact on turbulent nonlinear evolution of out of equilibrium initial conditions is discussed while studying transient flows, self-organizing dynamics and memory effects due to initial conditions. This dissertation introduces an operational definition, now of routine use in the GYSELA code, for the initial state and concludes on the special importance of the accurate calculation of the radial electric field. The GYSELA framework is further extended in chapter 4 to describe Coulomb collisions. The implementation of a collision operator acting on the full distribution function is presented. Its successful confrontation to collisional theory (neoclassical theory) is also shown. GYSELA is now part of the few gyrokinetic codes which can self-consistently address the interplay between turbulence and collisions. While

Performance evaluations of advanced massively parallel platforms based on gyrokinetic toroidal five-dimensional Eulerian code GT5D

International Nuclear Information System (INIS)

Idomura, Yasuhiro; Jolliet, Sebastien

2010-01-01

A gyrokinetic toroidal five dimensional Eulerian code GT5D is ported on six advanced massively parallel platforms and comprehensive benchmark tests are performed. A parallelisation technique based on physical properties of the gyrokinetic equation is presented. By extending the parallelisation technique with a hybrid parallel model, the scalability of the code is improved on platforms with multi-core processors. In the benchmark tests, a good salability is confirmed up to several thousands cores on every platforms, and the maximum sustained performance of ∼18.6 Tflops is achieved using 16384 cores of BX900. (author)

Role of Natural Killer and Gamma-Delta T cells in West Nile Virus Infection

Directory of Open Access Journals (Sweden)

Thomas Welte

2013-09-01

Full Text Available Natural Killer (NK cells and Gamma-delta T cells are both innate lymphocytes that respond rapidly and non-specifically to viral infection and other pathogens. They are also known to form a unique link between innate and adaptive immunity. Although they have similar immune features and effector functions, accumulating evidence in mice and humans suggest these two cell types have distinct roles in the control of infection by West Nile virus (WNV, a re-emerging pathogen that has caused fatal encephalitis in North America over the past decade. This review will discuss recent studies on these two cell types in protective immunity and viral pathogenesis during WNV infection.

Profile stiffness measurements in the Helically Symmetric experiment and comparison to nonlinear gyrokinetic calculations

Energy Technology Data Exchange (ETDEWEB)

Weir, G. M.; Faber, B. J.; Likin, K. M.; Talmadge, J. N.; Anderson, D. T.; Anderson, F. S. B. [HSX Plasma Laboratory, University of Wisconsin–Madison, Madison, Wisconsin 53706 (United States)

2015-05-15

Stiffness measurements are presented in the quasi-helically symmetric experiment (HSX), in which the neoclassical transport is comparable to that in a tokamak and turbulent transport dominates throughout the plasma. Electron cyclotron emission is used to measure the local electron temperature response to modulated electron cyclotron resonant heating. The amplitude and phase of the heat wave through the steep electron temperature gradient (ETG) region of the plasma are used to determine a transient electron thermal diffusivity that is close to the steady-state diffusivity. The low stiffness in the region between 0.2 ≤ r/a ≤ 0.4 agrees with the scaling of the steady-state heat flux with temperature gradient in this region. These experimental results are compared to gyrokinetic calculations in a flux-tube geometry using the gyrokinetic electromagnetic numerical experiment code with two kinetic species. Linear simulations show that the ETG mode may be experimentally relevant within r/a ≤ 0.2, while the Trapped Electron Mode (TEM) is the dominant long-wavelength microturbulence instability across most of the plasma. The TEM is primarily driven by the density gradient. Non-linear calculations of the saturated heat flux driven by the TEM and ETG bracket the experimental heat flux.

Self-consistent gyrokinetic modeling of neoclassical and turbulent impurity transport

Science.gov (United States)

Estève, D.; Sarazin, Y.; Garbet, X.; Grandgirard, V.; Breton, S.; Donnel, P.; Asahi, Y.; Bourdelle, C.; Dif-Pradalier, G.; Ehrlacher, C.; Emeriau, C.; Ghendrih, Ph.; Gillot, C.; Latu, G.; Passeron, C.

2018-03-01

Trace impurity transport is studied with the flux-driven gyrokinetic GYSELA code (Grandgirard et al 2016 Comput. Phys. Commun. 207 35). A reduced and linearized multi-species collision operator has been recently implemented, so that both neoclassical and turbulent transport channels can be treated self-consistently on an equal footing. In the Pfirsch-Schlüter regime that is probably relevant for tungsten, the standard expression for the neoclassical impurity flux is shown to be recovered from gyrokinetics with the employed collision operator. Purely neoclassical simulations of deuterium plasma with trace impurities of helium, carbon and tungsten lead to impurity diffusion coefficients, inward pinch velocities due to density peaking, and thermo-diffusion terms which quantitatively agree with neoclassical predictions and NEO simulations (Belli et al 2012 Plasma Phys. Control. Fusion 54 015015). The thermal screening factor appears to be less than predicted analytically in the Pfirsch-Schlüter regime, which can be detrimental to fusion performance. Finally, self-consistent nonlinear simulations have revealed that the tungsten impurity flux is not the sum of turbulent and neoclassical fluxes computed separately, as is usually assumed. The synergy partly results from the turbulence-driven in-out poloidal asymmetry of tungsten density. This result suggests the need for self-consistent simulations of impurity transport, i.e. including both turbulence and neoclassical physics, in view of quantitative predictions for ITER.

Interleukin-1 beta induced synthesis of protein kinase C-delta and protein kinase C-epsilon in EL4 thymoma cells: possible involvement of phosphatidylinositol 3-kinase.

Science.gov (United States)

Varley, C L; Royds, J A; Brown, B L; Dobson, P R

2001-01-01

We present evidence here that the proinflammatory cytokine, interleukin-1 beta (IL-1 beta) stimulates a significant increase in protein kinase C (PKC)-epsilon and PKC-delta protein levels and increases PKC-epsilon, but not PKC-delta, transcripts in EL4 thymoma cells. Incubation of EL4 cells with IL-1 beta induced protein synthesis of PKC-epsilon (6-fold increase) by 7 h and had a biphasic effect on PKC-delta levels with peaks at 4 h (2-fold increase) and 24 h (4-fold increase). At the level of mRNA, PKC-epsilon, but not PKC-delta levels, were induced after incubation of EL4 cells with IL-1 beta. The signalling mechanisms utilized by IL-1 beta to induce the synthesis of these PKC isoforms were investigated. Two phosphatidylinositol (PI) 3-kinase-specific inhibitors, wortmannin and LY294002, inhibited IL-1 beta-induced synthesis of PKC-epsilon. However, the PI 3-kinase inhibitors had little effect on the IL-1 beta-induced synthesis of PKC-delta in these cells. Our results indicate that IL-1 beta induced both PKC-delta and PKC-epsilon expression over different time periods. Furthermore, our evidence suggests that IL-1 beta induction of PKC-epsilon, but not PKC-delta, may occur via the PI 3-kinase pathway. Copyright 2001 S. Karger AG, Basel

18F-FET and 18F-FCH uptake in human glioblastoma T98G cell lines

International Nuclear Information System (INIS)

Persico, Marco Giovanni; Buroni, Federica Eleonora; Pasi, Francesca; Lodola, Lorenzo; Aprile, Carlo; Nano, Rosanna; Hodolic, Marina

2016-01-01

Despite complex treatment of surgery, radiotherapy and chemotherapy, high grade gliomas often recur. Differentiation between post-treatment changes and recurrence is difficult. 18 F-methyl-choline ( 18 F-FCH) is frequently used in staging and detection of recurrent prostate cancer disease as well as some brain tumours; however accumulation in inflammatory tissue limits its specificity. The 18 F-ethyl-tyrosine ( 18 F-FET) shows a specific uptake in malignant cells, resulting from increased expression of amino acid transporters or diffusing through the disrupted blood-brain barrier. 18 F-FET exhibits lower uptake in machrophages and other inflammatory cells. Aim of this study was to evaluate 18 F-FCH and 18 F-FET uptake by human glioblastoma T98G cells. Human glioblastoma T98G or human dermal fibroblasts cells, seeded at a density to obtain 2 × 10 5 cells per flask when radioactive tracers were administered, grew adherent to the plastic surface at 37°C in 5% CO 2 in complete medium. Equimolar amounts of radiopharmaceuticals were added to cells for different incubation times (20 to 120 minutes) for 18 F-FCH and 18 F-FET respectively. The cellular radiotracer uptake was determined with a gamma counter. All experiments were carried out in duplicate and repeated three times. The uptake measurements are expressed as the percentage of the administered dose of tracer per 2 × 10 5 cells. Data (expressed as mean values of % uptake of radiopharmaceuticals) were compared using parametric or non-parametric tests as appropriate. Differences were regarded as statistically significant when p<0.05. A significant uptake of 18 F-FCH was seen in T98G cells at 60, 90 and 120 minutes. The percentage uptake of 18 F-FET in comparison to 18 F-FCH was lower by a factor of more than 3, with different kinetic curves. 18 F-FET showed a more rapid initial uptake up to 40 minutes and 18 F-FCH showed a progressive rise reaching a maximum after 90 minutes. 18 F-FCH and 18 F-FET are candidates

COMMD1 regulates the delta epithelial sodium channel ({delta}ENaC) through trafficking and ubiquitination

Energy Technology Data Exchange (ETDEWEB)

Chang, Tina; Ke, Ying; Ly, Kevin [Department of Physiology, University of Otago, P.O. Box 913, Dunedin 9054 (New Zealand); McDonald, Fiona J., E-mail: fiona.mcdonald@otago.ac.nz [Department of Physiology, University of Otago, P.O. Box 913, Dunedin 9054 (New Zealand)

2011-08-05

Highlights: {yields} The COMM domain of COMMD1 mediates binding to {delta}ENaC. {yields} COMMD1 reduces the cell surface population of {delta}ENaC. {yields} COMMD1 increases the population of {delta}ENaC-ubiquitin. {yields} Both endogenous and transfected {delta}ENaC localize with COMMD1 and transferrin suggesting they are located in early/recycling endosomes. -- Abstract: The delta subunit of the epithelial sodium channel ({delta}ENaC) is a member of the ENaC/degenerin family of ion channels. {delta}ENaC is distinct from the related {alpha}-, {beta}- and {gamma}ENaC subunits, known for their role in sodium homeostasis and blood pressure control, as {delta}ENaC is expressed in brain neurons and activated by external protons. COMMD1 (copper metabolism Murr1 domain 1) was previously found to associate with and downregulate {delta}ENaC activity. Here, we show that COMMD1 interacts with {delta}ENaC through its COMM domain. Co-expression of {delta}ENaC with COMMD1 significantly reduced {delta}ENaC surface expression, and led to an increase in {delta}ENaC ubiquitination. Immunocytochemical and confocal microscopy studies show that COMMD1 promoted localization of {delta}ENaC to the early/recycling endosomal pool where the two proteins were localized together. These results suggest that COMMD1 downregulates {delta}ENaC activity by reducing {delta}ENaC surface expression through promoting internalization of surface {delta}ENaC to an intracellular recycling pool, possibly via enhanced ubiquitination.

A set of particle locating algorithms not requiring face belonging to cell connectivity data

Science.gov (United States)

Sani, M.; Saidi, M. S.

2009-10-01

Existing efficient directed particle locating (host determination) algorithms rely on the face belonging to cell relationship (F2C) to find the next cell on the search path and the cell in which the target is located. Recently, finite volume methods have been devised which do not need F2C. Therefore, existing search algorithms are not directly applicable (unless F2C is included). F2C is a major memory burden in grid description. If the memory benefit from these finite volume methods are desirable new search algorithms should be devised. In this work two new algorithms (line of sight and closest cell) are proposed which do not need F2C. They are based on the structure of the sparse coefficient matrix involved (stored for example in the compressed row storage, CRS, format) to determine the next cell. Since F2C is not available, testing a cell for the presence of the target is not possible. Therefore, the proposed methods may wrongly mark a nearby cell as the host in some rare cases. The issue of importance of finding the correct host cell (not wrongly hitting its neighbor) is addressed. Quantitative measures are introduced to assess the efficiency of the methods and comparison is made for typical grid types used in computational fluid dynamics. In comparison, the closest cell method, having a lower computational cost than the family of line of sight and the existing efficient maximum dot product methods, gives a very good performance with tolerable and harmless wrong hits. If more accuracy is needed, the method of approximate line of sight then closest cell (LS-A-CC) is recommended.

Cell-cell transmission of VSV-G pseudotyped lentivector particles.

Directory of Open Access Journals (Sweden)

Amy M Skinner

Full Text Available Many replicating viruses, including HIV-1 and HTLV-1, are efficiently transmitted from the cell surface of actively infected cells upon contact with bystander cells. In a previous study, we reported the prolonged cell surface retention of VSV-G replication-deficient pseudotyped lentivector prior to endocytic entry. However, the competing kinetics of cell surface versus dissociation, neutralization or direct transfer to other cells have received comparatively little attention. Here we demonstrate that the relative efficiency of cell-cell surface transmission can outpace "cell-free" transduction at limiting vector input. This coincides with the prolonged half-life of cell bound vector but occurs, unlike HTLV-1, without evidence for particle aggregation. These studies suggest that cell-surface attachment stabilizes particles and alters neutralization kinetics. Our experiments provide novel insight into the underexplored cell-cell transmission of pseudotyped particles.

Advances in comprehensive gyrokinetic simulations of transport in tokamaks

International Nuclear Information System (INIS)

Waltz, R.E.; Candy, J.; Hinton, F.L.; Estrada-Mila, C.; Kinsey, J.E.

2005-01-01

A continuum global gyrokinetic code GYRO has been developed to comprehensively simulate core turbulent transport in actual experimental profiles and enable direct quantitative comparisons to the experimental transport flows. GYRO not only treats the now standard ion temperature gradient (ITG) mode turbulence, but also treats trapped and passing electrons with collisions and finite β, equilibrium ExB shear stabilization, and all in real tokamak geometry. Most importantly the code operates at finite relative gyroradius (ρ*) so as to treat the profile shear stabilization and nonlocal effects which can break gyroBohm scaling. The code operates in either a cyclic flux-tube limit (which allows only gyroBohm scaling) or globally with physical profile variation. Bohm scaling of DIII-D L-mode has been simulated with power flows matching experiment within error bars on the ion temperature gradient. Mechanisms for broken gyroBohm scaling, neoclassical ion flows embedded in turbulence, turbulent dynamos and profile corrugations, are illustrated. (author)

ADVANCES IN COMPREHENSIVE GYROKINETIC SIMULATIONS OF TRANSPORT IN TOKAMAKS

International Nuclear Information System (INIS)

WALTZ, R. E; CANDY, J; HINTON, F. L; ESTRADA-MILA, C; KINSEY, J.E

2004-01-01

A continuum global gyrokinetic code GYRO has been developed to comprehensively simulate core turbulent transport in actual experimental profiles and enable direct quantitative comparisons to the experimental transport flows. GYRO not only treats the now standard ion temperature gradient (ITG) mode turbulence, but also treats trapped and passing electrons with collisions and finite β, equilibrium ExB shear stabilization, and all in real tokamak geometry. Most importantly the code operates at finite relative gyroradius (ρ * ) so as to treat the profile shear stabilization and nonlocal effects which can break gyroBohm scaling. The code operates in either a cyclic flux-tube limit (which allows only gyroBohm scaling) or globally with physical profile variation. Bohm scaling of DIII-D L-mode has been simulated with power flows matching experiment within error bars on the ion temperature gradient. Mechanisms for broken gyroBohm scaling, neoclassical ion flows embedded in turbulence, turbulent dynamos and profile corrugations, are illustrated

Measurement of $\\Delta^{++}$(1232) production in hadronic Z decays

CERN Document Server

Abreu, P; Adye, T; Agasi, E; Ajinenko, I; Aleksan, Roy; Alekseev, G D; Allport, P P; Almehed, S; Alvsvaag, S J; Amaldi, Ugo; Amato, S; Andreazza, A; Andrieux, M L; Antilogus, P; Anykeyev, V B; Apel, W D; Arnoud, Y; Åsman, B; Augustin, J E; Augustinus, A; Baillon, Paul; Bambade, P; Barão, F; Barate, R; Bardin, Dimitri Yuri; Barker, G J; Baroncelli, A; Bärring, O; Barrio, J A; Bartl, Walter; Bates, M J; Battaglia, Marco; Baubillier, M; Baudot, J; Becks, K H; Begalli, M; Beillière, P; Belokopytov, Yu A; Benvenuti, Alberto C; Berggren, M; Bertrand, D; Bianchi, F; Bigi, M; Bilenky, S M; Billoir, P; Bloch, D; Blume, M; Blyth, S; Bocci, V; Bolognese, T; Bonesini, M; Bonivento, W; Booth, P S L; Borisov, G; Bosio, C; Bosworth, S; Botner, O; Bouquet, B; Bourdarios, C; Bowcock, T J V; Bozzo, M; Branchini, P; Brand, K D; Brenke, T; Brenner, R A; Bricman, C; Brillault, L; Brown, R C A; Brückman, P; Brunet, J M; Bugge, L; Buran, T; Burgsmüller, T; Buschmann, P; Buys, A; Caccia, M; Calvi, M; Camacho-Rozas, A J; Camporesi, T; Canale, V; Canepa, M; Cankocak, K; Cao, F; Carena, F; Carrilho, P; Carroll, L; Caso, Carlo; Castillo-Gimenez, M V; Cattai, A; Cavallo, F R; Cerrito, L; Chabaud, V; Charpentier, P; Chaussard, L; Chauveau, J; Checchia, P; Chelkov, G A; Chierici, R; Chliapnikov, P V; Chochula, P; Chorowicz, V; Cindro, V; Collins, P; Contreras, J L; Contri, R; Cortina, E; Cosme, G; Cossutti, F; Crawley, H B; Crennell, D J; Crosetti, G; Cuevas-Maestro, J; Czellar, S; Dahl-Jensen, Erik; Dahm, J; D'Almagne, B; Dam, M; Damgaard, G; Daum, A; Dauncey, P D; Davenport, Martyn; Da Silva, W; Defoix, C; Della Ricca, G; Delpierre, P A; Demaria, N; De Angelis, A; De Boeck, H; de Boer, Wim; De Brabandere, S; De Clercq, C; La Vaissière, C de; De Lotto, B; De Min, A; De Paula, L S; De Saint-Jean, C; Dijkstra, H; Di Ciaccio, Lucia; Djama, F; Dolbeau, J; Dönszelmann, M; Doroba, K; Dracos, M; Drees, J; Drees, K A; Dris, M; Dufour, Y; Dupont, F; Edsall, D M; Ehret, R; Eigen, G; Ekelöf, T J C; Ekspong, Gösta; Elsing, M; Engel, J P; Ershaidat, N; Erzen, B; Espirito-Santo, M C; Falk, E; Fassouliotis, D; Feindt, Michael; Ferrer, A; Filippas-Tassos, A; Firestone, A; Fischer, P A; Föth, H; Fokitis, E; Fontanelli, F; Formenti, F; Franek, B J; Frenkiel, P; Fries, D E C; Frodesen, A G; Frühwirth, R; Fulda-Quenzer, F; Fuster, J A; Galloni, A; Gamba, D; Gandelman, M; García, C; García, J; Gaspar, C; Gasparini, U; Gavillet, P; Gazis, E N; Gelé, D; Gerber, J P; Gibbs, M; Gokieli, R; Golob, B; Gopal, Gian P; Gorn, L; Górski, M; Guz, Yu; Gracco, Valerio; Graziani, E; Grosdidier, G; Gunnarsson, P; Günther, M; Guy, J; Haedinger, U; Hahn, F; Hahn, M; Hahn, S; Hajduk, Z; Hallgren, A; Hamacher, K; Hao, W; Harris, F J; Hedberg, V; Henriques, R P; Hernández, J J; Herquet, P; Herr, H; Hessing, T L; Higón, E; Hilke, Hans Jürgen; Hill, T S; Holmgren, S O; Holt, P J; Holthuizen, D J; Houlden, M A; Hrubec, Josef; Huet, K; Hultqvist, K; Ioannou, P; Jackson, J N; Jacobsson, R; Jalocha, P; Janik, R; Jarlskog, G; Jarry, P; Jean-Marie, B; Johansson, E K; Jönsson, L B; Jönsson, P E; Joram, Christian; Juillot, P; Kaiser, M; Kapusta, F; Karlsson, M; Karvelas, E; Katsanevas, S; Katsoufis, E C; Keränen, R; Khomenko, B A; Khovanskii, N N; King, B J; Kjaer, N J; Klein, H; Klovning, A; Kluit, P M; Köhne, J H; Köne, B; Kokkinias, P; Koratzinos, M; Kostyukhin, V; Kourkoumelis, C; Kuznetsov, O; Kramer, P H; Krammer, Manfred; Kreuter, C; Królikowski, J; Kronkvist, I J; Krumshtein, Z; Krupinski, W; Kubinec, P; Kucewicz, W; Kurvinen, K L; Lacasta, C; Laktineh, I; Lamblot, S; Lamsa, J; Lanceri, L; Lane, D W; Langefeld, P; Lapin, V; Last, I; Laugier, J P; Lauhakangas, R; Leder, Gerhard; Ledroit, F; Lefébure, V; Legan, C K; Leitner, R; Lemoigne, Y; Lemonne, J; Lenzen, Georg; Lepeltier, V; Lesiak, T; Liko, D; Lindner, R; Lipniacka, A; Lippi, I; Lörstad, B; Lokajícek, M; Loken, J G; López, J M; López-Fernandez, A; López-Aguera, M A; Loukas, D; Lutz, P; Lyons, L; Maehlum, G; Maio, A; Malychev, V; Mandl, F; Marco, J; Maréchal, B; Margoni, M; Marin, J C; Mariotti, C; Markou, A; Maron, T; Martínez-Rivero, C; Martínez-Vidal, F; Martí i García, S; Matorras, F; Matteuzzi, C; Matthiae, Giorgio; Mazzucato, M; McCubbin, M L; McKay, R; McNulty, R; Medbo, J; Meroni, C; Meyer, W T; Michelotto, M; Migliore, E; Mirabito, L; Mitaroff, Winfried A; Mjörnmark, U; Moa, T; Møller, R; Mönig, K; Monge, M R; Morettini, P; Müller, H; Mundim, L M; Murray, W J; Muryn, B; Myatt, Gerald; Naraghi, F; Navarria, Francesco Luigi; Navas, S; Negri, P; Némécek, S; Neumann, W; Neumeister, N; Nicolaidou, R; Nielsen, B S; Nieuwenhuizen, M; Nikolaenko, V; Niss, P; Nomerotski, A; Normand, Ainsley; Oberschulte-Beckmann, W; Obraztsov, V F; Olshevskii, A G; Onofre, A; Orava, Risto; Österberg, K; Ouraou, A; Paganini, P; Paganoni, M; Pagès, P; Palka, H; Papadopoulou, T D; Pape, L; Parkes, C; Parodi, F; Passeri, A; Pegoraro, M; Pernegger, H; Pernicka, Manfred; Perrotta, A; Petridou, C; Petrolini, A; Phillips, H T; Piana, G; Pierre, F; Pimenta, M; Pindo, M; Plaszczynski, S; Podobrin, O; Pol, M E; Polok, G; Poropat, P; Pozdnyakov, V; Prest, M; Privitera, P; Pukhaeva, N; Pullia, Antonio; Radojicic, D; Ragazzi, S; Rahmani, H; Rames, J; Ratoff, P N; Read, A L; Reale, M; Rebecchi, P; Redaelli, N G; Regler, Meinhard; Reid, D; Renton, P B; Resvanis, L K; Richard, F; Richardson, J; Rídky, J; Rinaudo, G; Ripp, I; Romero, A; Roncagliolo, I; Ronchese, P; Roos, L; Rosenberg, E I; Rosso, E; Roudeau, Patrick; Rovelli, T; Rückstuhl, W; Ruhlmann-Kleider, V; Ruiz, A; Rybicki, K; Rybin, A; Saarikko, H; Sacquin, Yu; Sadovskii, A; Sajot, G; Salt, J; Sánchez, J; Sannino, M; Schneider, H; Schyns, M A E; Sciolla, G; Scuri, F; Seager, P; Sedykh, Yu; Segar, A M; Seitz, A; Sekulin, R L; Shellard, R C; Siccama, I; Siegrist, P; Simonetti, S; Simonetto, F; Sissakian, A N; Sitár, B; Skaali, T B; Smadja, G; Smirnova, O G; Smith, G R; Sosnowski, R; Souza-Santos, D; Spassoff, Tz; Spiriti, E; Sponholz, P; Squarcia, S; Stanescu, C; Stapnes, Steinar; Stavitski, I; Stepaniak, K; Stichelbaut, F; Stocchi, A; Strauss, J; Strub, R; Stugu, B; Szczekowski, M; Szeptycka, M; Tabarelli de Fatis, T; Tavernet, J P; Chikilev, O G; Tilquin, A; Timmermans, J; Tkatchev, L G; Todorov, T; Toet, D Z; Tomaradze, A G; Tomé, B; Tortora, L; Tranströmer, G; Treille, D; Trischuk, W; Tristram, G; Trombini, A; Troncon, C; Tsirou, A L; Turluer, M L; Tyapkin, I A; Tyndel, M; Tzamarias, S; Überschär, B; Ullaland, O; Uvarov, V; Valenti, G; Vallazza, E; Van der Velde, C; van Apeldoorn, G W; van Dam, P; Van Doninck, W K; Van Eldik, J; Vassilopoulos, N; Vegni, G; Ventura, L; Venus, W A; Verbeure, F; Verlato, M; Vertogradov, L S; Vilanova, D; Vincent, P; Vitale, L; Vlasov, E; Vodopyanov, A S; Vrba, V; Wahlen, H; Walck, C; Waldner, F; Weierstall, M; Weilhammer, Peter; Wetherell, Alan M; Wicke, D; Wickens, J H; Wielers, M; Wilkinson, G R; Williams, W S C; Winter, M; Witek, M; Woschnagg, K; Yip, K; Yushchenko, O P; Zach, F; Zacharatou-Jarlskog, C; Zaitsev, A; Zalewska-Bak, A; Zalewski, Piotr; Zavrtanik, D; Zevgolatakos, E; Zhigunov, V P; Zimin, N I; Zito, M; Zontar, D; Zuberi, R; Zucchelli, G C; Zumerle, G

1995-01-01

A measurement of the \\Delta^{++}(1232) inclusive production in hadronic decays of the Z at LEP is presented, based on 1.3 million hadronic events collected~ by the DELPHI~ detector in the 1994 LEP running~ period. The DELPHI ring imaging Cherenkov counters are used for identifying hadrons. The average \\Delta^{++}(1232) multiplicity per hadronic event is 0.079 \\pm 0.015 which is more than a factor of two below the JETSET, HERWIG and UCLA model predictions. It agrees with a recently proposed universal mass dependence of particle production rates in e^{+}e^- annihilations.

Internalisation of engineered nanoparticles into mammalian cells in vitro: influence of cell type and particle properties

International Nuclear Information System (INIS)

Busch, Wibke; Bastian, Susanne; Trahorsch, Ulrike; Iwe, Maria; Kühnel, Dana; Meißner, Tobias; Springer, Armin; Gelinsky, Michael; Richter, Volkmar; Ikonomidou, Chrysanthy; Potthoff, Annegret; Lehmann, Irina; Schirmer, Kristin

2011-01-01

Cellular internalisation of industrial engineered nanoparticles is undesired and a reason for concern. Here we investigated and compared the ability of seven different mammalian cell cultures in vitro to incorporate six kinds of engineered nanoparticles, focussing on the role of cell type and particle properties in particle uptake. Uptake was examined using light and electron microscopy coupled with energy dispersive X-ray spectroscopy (EDX) for particle element identification. Flow cytometry was applied for semi-quantitative analyses of particle uptake and for exploring the influence on uptake by the phagocytosis inhibitor Cytochalasin D (CytoD). All particles studied were found to enter each kind of cultured cells. Yet, particles were never found within cell nuclei. The presence of the respective particles within the cells was confirmed by EDX. Live-cell imaging revealed the time-dependent process of internalisation of technical nanoparticles, which was exemplified by tungsten carbide particle uptake into the human skin cells, HaCaT. Particles were found to co-localise with lysosomal structures within the cells. The incorporated nanoparticles changed the cellular granularity, as measured by flow cytometry, already after 3 h of exposure in a particle specific manner. By correlating particle properties with flow cytometry data, only the primary particle size was found to be a weakly influential property for particle uptake. CytoD, an inhibitor of actin filaments and therewith of phagocytosis, significantly inhibited the internalisation of particle uptake in only two of the seven investigated cell cultures. Our study, therefore, supports the notion that nanoparticles can enter mammalian cells quickly and easily, irrespective of the phagocytic ability of the cells.

On the Composition and Neutrix Composition of the Delta Function and the Function cosh^{-1}(|x|^{1/r}+1

Directory of Open Access Journals (Sweden)

Brian Fisher

2017-03-01

Full Text Available Let $F$ be a distribution in $\\mathcal{D'}$ and let $f$ be a locally summable function. The composition $F(f(x$ of $F$ and $f$ is said to exist and be equal to the distribution $h(x$ if the limit of the sequence $\\{ F_{n}(f(x\\}$ is equal to $h(x$, where $F_n(x =F(x*\\delta _n(x$ for $n=1,2, \\ldots$ and $\\{\\delta_n(x\\}$ is a certain regular sequence converging to the Dirac delta function. It is proved that the neutrix composition $ \\delta^{(s}[\\cosh^{-1} (x_+^{1/r}+1] $ exists and \\beqa \\delta^{(s}[\\cosh^{-1} (x_+^{1/r}+1] = - \\sum _{k=0} ^{M-1} \\sum_{i=0}^{kr+r} {k \\choose i}{(-1^{i+k}rc_{r,s,k} \\over (kr+rk!}\\delta ^{(k}(x, for $s =M-1,M, M+1,\\ldots$ and $r=1,2,\\ldots,$ where $$c_{r,s,k}=\\sum _{j=0}^{i} {i \\choose j}{ (-1^{kr+r-i}(2j-i^{s+1}\\over 2^{s+i+1} },$$ $M$ is the smallest integer for which $s-2r+1 < 2Mr$ and $r\\le s/(2M+2.$ Further results are also proved.

Cell inactivation by heavy charged particles

Energy Technology Data Exchange (ETDEWEB)

Blakely, E A [Lawrence Berkeley Lab., CA (United States). Cell and Molecular Biology Div.

1992-06-01

The inactivation of cells resulting in lethal or aberrant effects by charged particles is of growing interest. Charged particles at extremely high LET are capable of completely eliminating cell-type and cell-line differences in repair capacity. It is still not clear however whether the repair systems are inactivated, or merely that heavy-ion lesions are less repairable. Studies correlating the particle inactivation dose of radioresistant cells with intact DNA analyzed with pulse field gel electrophoresis and other techniques may be useful, but more experiments are also needed to assess the fidelity of repair. For particle irradiations between 40-100 keV/{mu}m there is however evidence for particle-induced activation of specific genes in mammalian cells, and certain repair processes in bacteria. New data are available on the inactivation of developmental processes in several systems including seeds, and cells of the nematode C. elegans. Future experimental and theoretical modeling research emphasis should focus on exploring particle-induced inactivation of endpoints assessing functionality and not just lethality, and on analyzing molecular damage and genetic effects arising in damage but non-inactivated survivors. The discrete nature of selective types of particle damage as a function of radiation quality indicates the value of accelerated ions as probes of normal and aberrant biological processes. Information obtained from molecular analyses of damage and repair must however be integrated into the context of cellular and tissue functions of the organism. (orig.).

The HDAC Inhibitors Scriptaid and LBH589 Combined with the Oncolytic Virus Delta24-RGD Exert Enhanced Anti-Tumor Efficacy in Patient-Derived Glioblastoma Cells.

Directory of Open Access Journals (Sweden)

Lotte M E Berghauser Pont

Full Text Available A phase I/II trial for glioblastoma with the oncolytic adenovirus Delta24-RGD was recently completed. Delta24-RGD conditionally replicates in cells with a disrupted retinoblastoma-pathway and enters cells via αvβ3/5 integrins. Glioblastomas are differentially sensitive to Delta24-RGD. HDAC inhibitors (HDACi affect integrins and share common cell death pathways with Delta24-RGD. We studied the combination treatment effects of HDACi and Delta24-RGD in patient-derived glioblastoma stem-like cells (GSC, and we determined the most effective HDACi.SAHA, Valproic Acid, Scriptaid, MS275 and LBH589 were combined with Delta24-RGD in fourteen distinct GSCs. Synergy was determined by Chou Talalay method. Viral infection and replication were assessed using luciferase and GFP encoding vectors and hexon-titration assays. Coxsackie adenovirus receptor and αvβ3 integrin levels were determined by flow cytometry. Oncolysis and mechanisms of cell death were studied by viability, caspase-3/7, LDH and LC3B/p62, phospho-p70S6K. Toxicity was studied on normal human astrocytes. MGMT promotor methylation status, TCGA classification, Rb-pathway and integrin gene expression levels were assessed as markers of responsiveness.Scriptaid and LBH589 acted synergistically with Delta24-RGD in approximately 50% of the GSCs. Both drugs moderately increased αvβ3 integrin levels and viral infection in responding but not in non-responding GSCs. LBH589 moderately increased late viral gene expression, however, virus titration revealed diminished viral progeny production by both HDACi, Scriptaid augmented caspase-3/7 activity, LC3B conversion, p62 and phospho-p70S6K consumption, as well as LDH levels. LBH589 increased LDH and phospho-p70S6K consumption. Responsiveness correlated with expression of various Rb-pathway genes and integrins. Combination treatments induced limited toxicity to human astrocytes.LBH589 and Scriptaid combined with Delta24-RGD revealed synergistic anti

Radiation-induced apoptosis in F9 teratocarcinoma cells

International Nuclear Information System (INIS)

Langley, R.E.; Palayoor, S.T.; Coleman, C.N.; Bump, E.A.

1994-01-01

We have found that F9 murine teratocarcinoma cells undergo morphological changes and internucleosomal DNA fragmentation characteristic of apoptosis after exposure to ionizing radiation. We studied the time course, radiation dose-response, and the effects of protein and RNA synthesis inhibitors on this process. The response is dose dependent in the range 2-12 Gy. Internucleosomal DNA fragmentation can be detected as early as 6 h postirradiation and is maximal by 48 h. Cycloheximide, a protein synthesis inhibitor, and 5,6-dichloro-1-β-D-ribofuranosylbenzimidazole, an RNA synthesis inhibitor, both induced internucleosomal DNA fragmentation in the unirradiated cells and enhanced radiation-induced DNA fragmentation. F9 cells can be induced to differentiate into cells resembling endoderm with retinoic acid. After irradiation, differentiated F9 cells exhibit less DNA fragmentation than stem cells. This indicates that ionizing radiation can induce apoptosis in non-lymphoid tumours. We suggest that embryonic tumour cells may be particularly susceptible to agents that induce apoptosis. (Author)

Radiation-induced apoptosis in F9 teratocarcinoma cells

Energy Technology Data Exchange (ETDEWEB)

Langley, R E; Palayoor, S T; Coleman, C N; Bump, E A [Joint Center for Radiation Therapy and Dana Farber Cancer Inst., Boston (United States)

1994-05-01

We have found that F9 murine teratocarcinoma cells undergo morphological changes and internucleosomal DNA fragmentation characteristic of apoptosis after exposure to ionizing radiation. We studied the time course, radiation dose-response, and the effects of protein and RNA synthesis inhibitors on this process. The response is dose dependent in the range 2-12 Gy. Internucleosomal DNA fragmentation can be detected as early as 6 h postirradiation and is maximal by 48 h. Cycloheximide, a protein synthesis inhibitor, and 5,6-dichloro-1-[beta]-D-ribofuranosylbenzimidazole, an RNA synthesis inhibitor, both induced internucleosomal DNA fragmentation in the unirradiated cells and enhanced radiation-induced DNA fragmentation. F9 cells can be induced to differentiate into cells resembling endoderm with retinoic acid. After irradiation, differentiated F9 cells exhibit less DNA fragmentation than stem cells. This indicates that ionizing radiation can induce apoptosis in non-lymphoid tumours. We suggest that embryonic tumour cells may be particularly susceptible to agents that induce apoptosis. (Author).

Aerosol number size distribution and new particle formation at a rural/coastal site in Pearl River Delta (PRD) of China

Science.gov (United States)

Liu, Shang; Hu, Min; Wu, Zhijun; Wehner, Birgit; Wiedensohler, Alfred; Cheng, Yafang

Continuous measurements of aerosol number size distribution in the range of 3 nm-10 μm were performed in Pearl River Delta (PRD), China. These measurements were made during the period of 3 October to 5 November in 2004 at rural/coastal site, Xinken (22°37'N, 113°35'E, 6 m above sea level), in the south suburb of Guangzhou City (22°37'N, 113°35'E, 6 m above sea level), using a Twin Differential Mobility Particle Sizer (TDMPS) combined with an Aerodynamic Particle Sizer (APS). The aerosol particles at Xinken were divided into four groups according to the observation results: nucleation mode particles (3-30 nm), Aitken mode particles (30-130 nm), accumulation mode particles (130-1000 nm) and coarse mode particles (1-10 μm). Concentrations of nucleation mode, Aitken mode and accumulation mode particles were observed in the same order of magnitude (about 10,000 cm -3), among which the concentration of Aitken mode particle was the highest. The Aitken mode particles usually had two peaks: the morning peak may be caused by the land-sea circulation, which is proven to be important for transporting aged aerosols back to the sampling site, while the noon peak was ascribed to the condensational growth of new particles. New particle formation events were found on 7 days of 27 days, the new particle growth rates ranged from 2.2 to 19.8 nm h -1 and the formation rates ranged from 0.5 to 5.2 cm -3 s -1, both of them were in the range of typical observed formation rates (0.01-10 cm -3 s -1) and typical particle growth rates (1-20 nm h -1). The sustained growth of the new particles for several hours under steady northeast wind indicated that the new particle formation events may occur in a large homogeneous air mass.

Fluid and gyrokinetic simulations of impurity transport at JET

DEFF Research Database (Denmark)

Nordman, H; Skyman, A; Strand, P

2011-01-01

Impurity transport coefficients due to ion-temperature-gradient (ITG) mode and trapped-electron mode turbulence are calculated using profile data from dedicated impurity injection experiments at JET. Results obtained with a multi-fluid model are compared with quasi-linear and nonlinear gyrokinetic...... simulation results obtained with the code GENE. The sign of the impurity convective velocity (pinch) and its various contributions are discussed. The dependence of the impurity transport coefficients and impurity peaking factor −∇nZ/nZ on plasma parameters such as impurity charge number Z, ion logarithmic...

A deformable particle-in-cell method for advective transport in geodynamic modeling

Science.gov (United States)

Samuel, Henri

2018-06-01

This paper presents an improvement of the particle-in-cell method commonly used in geodynamic modeling for solving pure advection of sharply varying fields. Standard particle-in-cell approaches use particle kernels to transfer the information carried by the Lagrangian particles to/from the Eulerian grid. These kernels are generally one-dimensional and non-evolutive, which leads to the development of under- and over-sampling of the spatial domain by the particles. This reduces the accuracy of the solution, and may require the use of a prohibitive amount of particles in order to maintain the solution accuracy to an acceptable level. The new proposed approach relies on the use of deformable kernels that account for the strain history in the vicinity of particles. It results in a significant improvement of the spatial sampling by the particles, leading to a much higher accuracy of the numerical solution, for a reasonable computational extra cost. Various 2D tests were conducted to compare the performances of the deformable particle-in-cell method with the particle-in-cell approach. These consistently show that at comparable accuracy, the deformable particle-in-cell method was found to be four to six times more efficient than standard particle-in-cell approaches. The method could be adapted to 3D space and generalized to cases including motionless transport.

NiF2/NaF:CaF2/Ca Solid-State High-Temperature Battery Cells

Science.gov (United States)

West, William; Whitacre, Jay; DelCastillo, Linda

2009-01-01

Experiments and theoretical study have demonstrated the promise of all-solid-state, high-temperature electrochemical battery cells based on NiF2 as the active cathode material, CaF2 doped with NaF as the electrolyte material, and Ca as the active anode material. These and other all-solid-state cells have been investigated in a continuing effort to develop batteries for instruments that must operate in environments much hotter than can be withstood by ordinary commercially available batteries. Batteries of this type are needed for exploration of Venus (where the mean surface temperature is about 450 C), and could be used on Earth for such applications as measuring physical and chemical conditions in geothermal wells and oil wells. All-solid-state high-temperature power cells are sought as alternatives to other high-temperature power cells based, variously, on molten anodes and cathodes or molten eutectic salt electrolytes. Among the all-solid-state predecessors of the present NiF2/NaF:CaF2/Ca cells are those described in "Solid-State High-Temperature Power Cells" (NPO-44396), NASA Tech Briefs, Vol. 32, No. 5 (May 2008), page 40. In those cells, the active cathode material is FeS2, the electrolyte material is a crystalline solid solution of equimolar amounts of Li3PO4 and LiSiO4, and the active anode material is Li contained within an alloy that remains solid in the intended high operational temperature range.

Validation of gyrokinetic simulations with measurements of electron temperature fluctuations and density-temperature phase angles on ASDEX Upgrade

Science.gov (United States)

Freethy, S. J.; Görler, T.; Creely, A. J.; Conway, G. D.; Denk, S. S.; Happel, T.; Koenen, C.; Hennequin, P.; White, A. E.; ASDEX Upgrade Team

2018-05-01

Measurements of turbulent electron temperature fluctuation amplitudes, δTe ⊥/Te , frequency spectra, and radial correlation lengths, Lr(Te ⊥) , have been performed at ASDEX Upgrade using a newly upgraded Correlation ECE diagnostic in the range of scales k⊥scale non-linear gyrokinetic turbulence simulations of the outer core (ρtor = 0.75) of a low density, electron heated L-mode plasma, performed using the gyrokinetic simulation code, GENE. The ion and electron temperature gradients were scanned within uncertainties. It is found that gyrokinetic simulations are able to match simultaneously the electron and ion heat flux at this radius within the experimental uncertainties. The simulations were performed based on a reference discharge for which δTe ⊥/Te measurements were available, and Lr(Te ⊥) and αnT were then predicted using synthetic diagnostics prior to measurements in a repeat discharge. While temperature fluctuation amplitudes are overestimated by >50% for all simulations within the sensitivity scans performed, good quantitative agreement is found for Lr(Te ⊥) and αnT. A validation metric is used to quantify the level of agreement of individual simulations with experimental measurements, and the best agreement is found close to the experimental gradient values.

Renormalized perturbation theory: Vlasov-Poisson System, weak turbulence limit and gyrokinetics

International Nuclear Information System (INIS)

Zhang, Y.Z.; Mahajan, S.M.

1987-10-01

The Self-consistency of the renormalized perturbation theory is demonstrated by applying it to the Vlasov-Poisson System and showing that the theory has the correct weak turbulence limit. Energy conservation is proved to arbitrary high order for the electrostatic drift waves. The theory is applied to derive renormalized equations for a low-β gyrokinetic system. Comparison of our theory with other current theories is presented. 22 refs

Autonomous patterning of cells on microstructured fine particles

International Nuclear Information System (INIS)

Takeda, Iwori; Kawanabe, Masato; Kaneko, Arata

2015-01-01

Regularly patterned cells can clarify cellular function and are required in some biochip applications. This study examines cell patterning along microstructures and the effect of microstructural geometry on selective cellular adhesion. Particles can be autonomously assembled on a soda-lime glass substrate that is chemically patterned by immersion in a suspension of fine particles. By adopting various sizes of fine particles, we can control the geometry of the microstructure. Cells adhere more readily to microstructured fine particles than to flat glass substrate. Silica particles hexagonally packed in 5–40 μm line and space microstructures provide an effective cell scaffold on the glass substrate. Cultured cells tend to attach and proliferate along the microstructured region while avoiding the flat region. The difference in cell adhesion is attributed to their geometries, as both of the silica particles and soda-lime glass are hydrophilic related with cell adhesiveness. After cell seeding, cells adhered to the flat region migrated toward the microstructured region. For most of the cells to assemble on the scaffold, the scaffolding microstructures must be spaced by at most 65 μm. - Highlights: • PS and SiO 2 particles provide effective scaffolds for cells. • Cells that adhere to microstructured particles successfully proliferate and differentiate. • Selective adhesion and growth along the scaffold can be achieved by patterning the fine particle microstructure. • Cells adhered to flat regions migrate toward microstructured regions. • Selective adhesion by cells depends on the microstructural geometry; specifically, on the inter-line spacing

TEM heat transport and fluctuations in the HSX stellarator: experiments and comparison with gyrokinetic simulation

Science.gov (United States)

Smoniewski, J.; Faber, B. J.; Sánchez, E.; Calvo, I.; Pueschel, M. J.; Likin, K. M.; Deng, C. B.; Talmadge, J. N.

2017-10-01

The Helically Symmetric eXperiment (HSX) has demonstrated reduced neoclassical transport in the plasma core with quasi-symmetry [Lore Thesis 2010], while outside this region the electron thermal diffusivity is well above the neoclassical level, likely due to the Trapped Electron Mode (TEM) [Weir PoP 2015, Faber PoP 2015]. We compare gyrokinetic simulations of the TEM to experimental heat flux and density fluctuation measurements for two configurations: Quasi-Helical Symmetry (QHS) and broken symmetry (Mirror). Both experiment and simulation show that the heat flux for Mirror is larger than for QHS by about a factor of two. Initial interferometer measurements provide evidence that density-gradient-driven TEMs are driving turbulence. Calculations of the collisionless damping of zonal flows provide another perspective into the difference between geometries. Similar to other stellarators [Monreal PPCF 2016], the zonal flow residual goes to zero at long wavelengths in both configurations. Additionally, the very short time decay of the zonal flow due to neoclassical polarization is constant between configurations. However, the collisionless damping time is longer and the zonal flow oscillation frequency is smaller in QHS than Mirror, consistent with reduced radial particle drifts. Work supported by the US DOE under Grant DE-FG02-93ER54222.

Gyro-Landau fluid model of tokamak core fluctuations

International Nuclear Information System (INIS)

Leboeuf, J.N.; Carreras, B.A.; Dominguez, N.; Hedrick, C.L.; Sidikman, K.L.; Lynch, V.E.; Drake, J.B.; Walker, D.W.

1992-01-01

Dissipative trapped electron modes (DTEM) may be one of the causes of deterioration of confinement in tokamak and stellatator plasmas. We have implemented a fluid model to study DTEM turbulence in slab geometry. The electron dynamics include in addition to the adiabatic part, a non-adiabatic piece modeled with an i-delta-type response. The ion dynamics include Landau damping and FLR corrections through Landau fluid approximate techniques and Pade approximants for Γ 0 (b)=I 0 (b)e -b . The model follows from the gyrokinetic equation. Evolution equations, which closely resemble those used in standard reduced MHD, are presented since these are better suited to non-linear calculations. The numerical results of radially resolved calculations will be discussed. A recently developed hybrid model, which consists of a gyrokinetic implementation for the ions using particles and the same description for the electron dynamics as in the fluid model, will also be presented

Supralinearity and particle discrimination in nuclear emulsion

International Nuclear Information System (INIS)

Katz, R.; Larsson, L.; Pinkerton, F.E.; Benton, E.V.

1977-01-01

Nuclear emulsions may be desensitized in manufacture and/or may be so processed as to discriminate against small latent image sites; to yield supralinear sensitometric response after x-irradiation; and to discriminate against lightly ionizing radiations in favor of heavily ionizing particles. In a circumstance where one electron passing through an emulsion grain is unlikely to generate a latent image sufficiently large to yield a visible grain after development, some larger number of electrons is required, resulting in 'many-hit' statistics, supralinearity, and particle discrimination: for lightly ionizing particles are not likely to generate more than one delta-ray (secondary electron) in their passage through or near a grain. Since these properties are analogous to the response of many biological cells to ionizing radiations, such emulsion-developer combinations have the potential to mimic the response of biological systems to particulate radiations of different charge and speed. (author)

Detecting molecules and cells labeled with magnetic particles using an atomic magnetometer

International Nuclear Information System (INIS)

Yu Dindi; Ruangchaithaweesuk, Songtham; Yao Li; Xu Shoujun

2012-01-01

The detection of magnetically labeled molecules and cells involves three essential parameters: sensitivity, spatial resolution, and molecular specificity. We report on the use of atomic magnetometry and its derivative techniques to achieve high performance in terms of all these parameters. With a sensitivity of 80 fT/√Hz for dc magnetic fields, we show that 7,000 streptavidin-conjugated magnetic microparticles magnetized by a permanent magnet produce a magnetic field of 650 pT; this result predicts that a single such particle can be detected during one second of signal averaging. Spatial information is obtained using a scanning magnetic imaging scheme. The spatial resolution is 20 μm with a detection distance of more than 1 cm; this distance is much longer than that in previous reports. The molecular specificity is achieved using force-induced remnant magnetization spectroscopy, which currently uses an atomic magnetometer for detection. As an example, we perform measurement of magnetically labeled human CD4+ T cells, whose count in the blood is the diagnostic criterion for human immunodeficiency virus infection. Magnetic particles that are specifically bound to the cells are resolved from nonspecifically bound particles and quantitatively correlate with the number of cells. The magnetic particles have an overall size of 2.8 μm, with a magnetic core in nanometer regime. The combination of our techniques is predicted to be useful in molecular and cellular imaging.

Detecting molecules and cells labeled with magnetic particles using an atomic magnetometer

Energy Technology Data Exchange (ETDEWEB)

Yu Dindi; Ruangchaithaweesuk, Songtham; Yao Li; Xu Shoujun, E-mail: sxu7@uh.edu [University of Houston, Department of Chemistry (United States)

2012-09-15

The detection of magnetically labeled molecules and cells involves three essential parameters: sensitivity, spatial resolution, and molecular specificity. We report on the use of atomic magnetometry and its derivative techniques to achieve high performance in terms of all these parameters. With a sensitivity of 80 fT/{radical}Hz for dc magnetic fields, we show that 7,000 streptavidin-conjugated magnetic microparticles magnetized by a permanent magnet produce a magnetic field of 650 pT; this result predicts that a single such particle can be detected during one second of signal averaging. Spatial information is obtained using a scanning magnetic imaging scheme. The spatial resolution is 20 {mu}m with a detection distance of more than 1 cm; this distance is much longer than that in previous reports. The molecular specificity is achieved using force-induced remnant magnetization spectroscopy, which currently uses an atomic magnetometer for detection. As an example, we perform measurement of magnetically labeled human CD4+ T cells, whose count in the blood is the diagnostic criterion for human immunodeficiency virus infection. Magnetic particles that are specifically bound to the cells are resolved from nonspecifically bound particles and quantitatively correlate with the number of cells. The magnetic particles have an overall size of 2.8 {mu}m, with a magnetic core in nanometer regime. The combination of our techniques is predicted to be useful in molecular and cellular imaging.

Multifield stochastic particle production: beyond a maximum entropy ansatz

Energy Technology Data Exchange (ETDEWEB)

Amin, Mustafa A.; Garcia, Marcos A.G.; Xie, Hong-Yi; Wen, Osmond, E-mail: mustafa.a.amin@gmail.com, E-mail: marcos.garcia@rice.edu, E-mail: hxie39@wisc.edu, E-mail: ow4@rice.edu [Physics and Astronomy Department, Rice University, 6100 Main Street, Houston, TX 77005 (United States)

2017-09-01

We explore non-adiabatic particle production for N {sub f} coupled scalar fields in a time-dependent background with stochastically varying effective masses, cross-couplings and intervals between interactions. Under the assumption of weak scattering per interaction, we provide a framework for calculating the typical particle production rates after a large number of interactions. After setting up the framework, for analytic tractability, we consider interactions (effective masses and cross couplings) characterized by series of Dirac-delta functions in time with amplitudes and locations drawn from different distributions. Without assuming that the fields are statistically equivalent, we present closed form results (up to quadratures) for the asymptotic particle production rates for the N {sub f}=1 and N {sub f}=2 cases. We also present results for the general N {sub f} >2 case, but with more restrictive assumptions. We find agreement between our analytic results and direct numerical calculations of the total occupation number of the produced particles, with departures that can be explained in terms of violation of our assumptions. We elucidate the precise connection between the maximum entropy ansatz (MEA) used in Amin and Baumann (2015) and the underlying statistical distribution of the self and cross couplings. We provide and justify a simple to use (MEA-inspired) expression for the particle production rate, which agrees with our more detailed treatment when the parameters characterizing the effective mass and cross-couplings between fields are all comparable to each other. However, deviations are seen when some parameters differ significantly from others. We show that such deviations become negligible for a broad range of parameters when N {sub f}>> 1.

Strength decoupling from the giant dipole resonance upon diagonalizing a Gaussian force and a delta-force on a particle-hole basis

International Nuclear Information System (INIS)

Csernai, L.P.; Zimanyi, J.; Gyarmati, B.; Lovas, R.G.

1978-01-01

The finite-range Gaussian force and delta-force have been diagonalized in a basis of 27 particle-hole states with Jsup(π)=1 - in 116 Sn. Depending on the range of the force, 3.9-7.1% of the total transition rate has been found in the 6-9 MeV excitation energy region, which comprises the unperturbed energies of the basis states containing neutron threshold states. (Auth.)

ADVANCES IN COMPREHENSIVE GYROKINETIC SIMULATIONS OF TRANSPORT IN TOKAMAKS

International Nuclear Information System (INIS)

WALTZ, RE; CANDY, J; HINTON, FL; ESTRADA-MILA, C; KINSEY, JE.

2004-01-01

A continuum global gyrokinetic code GYRO has been developed to comprehensively simulate core turbulent transport in actual experimental profiles and enable direct quantitative comparisons to the experimental transport flows. GYRO not only treats the now standard ion temperature gradient (ITG) mode turbulence, but also treats trapped and passing electrons with collisions and finite β, equilibrium ExB shear stabilization, and all in real tokamak geometry. Most importantly the code operates at finite relative gyroradius (ρ * ) so as to treat the profile shear stabilization and nonlocal effects which can break gyroBohm scaling. The code operates in either a cyclic flux-tube limit (which allows only gyroBohm scaling) or a globally with physical profile variation. Rohm scaling of DIII-D L-mode has been simulated with power flows matching experiment within error bars on the ion temperature gradient. Mechanisms for broken gyroBohm scaling, neoclassical ion flows embedded in turbulence, turbulent dynamos and profile corrugations, plasma pinches and impurity flow, and simulations at fixed flow rather than fixed gradient are illustrated and discussed

Two-particle correlations in pp collisions at 13 TeV measured with CMS

CERN Document Server

AUTHOR|(CDS)2079326

2016-01-01

Results on two-particle angular correlations for charged particles emitted in $pp$ collisions at a center-of-mass energy of 13 TeV are presented as a function of charged-particle multiplicity and transverse momentum $(p_{T})$. In high$-$multiplicity events, a long-range $(\\mid \\eta \\mid> 2.0)$, near-side $(\\Delta \\phi = 0)$ structure emerges in the two-particle $\\Delta\\eta - \\Delta\\phi $ correlation functions. The overall correlation strength is similar to that found in earlier $pp$ data at 7 TeV, but is measured up to much higher multiplicity values. A detailed study in $pp$ collisions at 7 TeV of the second-order $(v_{2})$ % and third-order $(v_{3})$ azimuthal anisotropy harmonics of charged particles, $K_{S}^{0}$ and $\\Lambda/\\bar{\\Lambda}$ particles are extracted from long-range two-particle correlations as a function of particle multiplicity and transverse momentum and are also compared with values obtained in pPb and PbPb collisions at similar multiplicities.

The spectral problem of global microinstabilities in tokamak-like plasmas using a gyrokinetic model

International Nuclear Information System (INIS)

Brunner, S.; Vaclavik, J.; Fivaz, M.; Appert, K.

1996-01-01

Tokamak-like plasmas are modeled by a periodic cylindrical system with magnetic shear and realistic density and temperature profiles. Linear electrostatic microinstabilities in such plasmas are studied by solving the eigenvalue problem starting from gyrokinetic theory. The actual eigenvalue equation is then of integral type. With this approach, finite Larmor radius (FLR) effects to all orders are taken into account. FLR effects provide for the only radial coupling in a cylinder and to lowest order correspond to polarization drift. This effectively one-dimensional problem helped us to gain useful knowledge for solving gyrokinetic equations in a curved system. When searching for the eigenfrequencies of the global modes, two different methods have been tested and compared. Either the true eigenvalue problem is solved by finding the zeros of the characteristic equation, or one considers a system driven by an antenna and looks for resonances in the power response of the plasma. In addition, mode structures were computed as well in direct as in Fourier space. The advantages and disadvantages of these various approaches are discussed. Ion temperature gradient (ITG) instabilities are studied over a wide range of parameters and for wavelengths perpendicular to the magnetic field down to the scale of ion Larmor radii. Flute instabilities driven by magnetic curvature drifts are also considered. Some of these results are compared with a time evolution PIC code. Such comparisons are valuable as the convergence of PIC results is often questioned. Work considering true toroidal geometry is in progress

Affinity crosslinking of /sup 125/I-human beta-endorphin to cell lines possessing either mu or delta type opioid binding sites

Energy Technology Data Exchange (ETDEWEB)

Keren, O.; Gioannini, T.L.; Hiller, J.M.; Simon, E.J.

1986-01-01

Affinity crosslinking of human /sup 125/I-beta-Endorphin to cell lines possessing either mu or delta binding sites was carried out. Autoradiography of SDS-PAGE gels from these crosslinked cell lines revealed that these two sites contain major peptide subunits that differ in molecular size. This confirms our earlier finding in mammalian brain which demonstrated separate and distinct subunits for mu and delta opioid receptors.

Formation of conjugated delta8,delta10-double bonds by delta12-oleic-acid desaturase-related enzymes: biosynthetic origin of calendic acid.

Science.gov (United States)

Cahoon, E B; Ripp, K G; Hall, S E; Kinney, A J

2001-01-26

Divergent forms of the plant Delta(12)-oleic-acid desaturase (FAD2) have previously been shown to catalyze the formation of acetylenic bonds, epoxy groups, and conjugated Delta(11),Delta(13)-double bonds by modification of an existing Delta(12)-double bond in C(18) fatty acids. Here, we report a class of FAD2-related enzymes that modifies a Delta(9)-double bond to produce the conjugated trans-Delta(8),trans-Delta(10)-double bonds found in calendic acid (18:3Delta(8trans,10trans,12cis)), the major component of the seed oil of Calendula officinalis. Using an expressed sequence tag approach, cDNAs for two closely related FAD2-like enzymes, designated CoFADX-1 and CoFADX-2, were identified from a C. officinalis developing seed cDNA library. The deduced amino acid sequences of these polypeptides share 40-50% identity with those of other FAD2 and FAD2-related enzymes. Expression of either CoFADX-1 or CoFADX-2 in somatic soybean embryos resulted in the production of calendic acid. In embryos expressing CoFADX-2, calendic acid accumulated to as high as 22% (w/w) of the total fatty acids. In addition, expression of CoFADX-1 and CoFADX-2 in Saccharomyces cerevisiae was accompanied by calendic acid accumulation when induced cells were supplied exogenous linoleic acid (18:2Delta(9cis,12cis)). These results are thus consistent with a route of calendic acid synthesis involving modification of the Delta(9)-double bond of linoleic acid. Regiospecificity for Delta(9)-double bonds is unprecedented among FAD2-related enzymes and further expands the functional diversity found in this family of enzymes.

TAF6delta controls apoptosis and gene expression in the absence of p53.

Directory of Open Access Journals (Sweden)

Emmanuelle Wilhelm

Full Text Available BACKGROUND: Life and death decisions of metazoan cells hinge on the balance between the expression of pro- versus anti-apoptotic gene products. The general RNA polymerase II transcription factor, TFIID, plays a central role in the regulation of gene expression through its core promoter recognition and co-activator functions. The core TFIID subunit TAF6 acts in vitro as an essential co-activator of transcription for the p53 tumor suppressor protein. We previously identified a splice variant of TAF6, termed TAF6delta that can be induced during apoptosis. METHODOLOGY/PRINCIPAL FINDINGS: To elucidate the impact of TAF6delta on cell death and gene expression, we have employed modified antisense oligonucleotides to enforce expression of endogenous TAF6delta. The induction of endogenous TAF6delta triggered apoptosis in tumor cell lines, including cells devoid of p53. Microarray experiments revealed that TAF6delta activates gene expression independently of cellular p53 status. CONCLUSIONS: Our data define TAF6delta as a pivotal node in a signaling pathway that controls gene expression programs and apoptosis in the absence of p53.

Response to Comment on 'On Higher-Order Corrections to Gyrokinetic Vlasov-Poisson Equations in the Long Wavelength Limit [Phys. Plasmas 16,044506 (2009)]'

International Nuclear Information System (INIS)

Lee, W.W.; Kolesnikov, R.A.

2009-01-01

We show in this Response that the nonlinear Poisson's equation in our original paper derived from the drift kinetic approach can be verified by using the nonlinear gyrokinetic Poisson's equation of Dubin et al. (Phys. Fluids 26, 3524 (1983)). This nonlinear contribution in φ 2 is indeed of the order of k # perpendicular# 4 in the long wavelength limit and remains finite for zero ion temperature, in contrast to the nonlinear term by Parra and Catto (Plasma Phys. Control. Fusion 50, 065014 (2008)), which is of the order of k # perpendicular# 2 and diverges for T i → 0. For comparison, the leading term for the gyrokinetic Poisson's equation in this limit is of the order of k # perpendicular# 2 φ.

Subway particles are more genotoxic than street particles and induce oxidative stress in cultured human lung cells.

Science.gov (United States)

Karlsson, Hanna L; Nilsson, Lennart; Möller, Lennart

2005-01-01

Epidemiological studies have shown an association between airborne particles and a wide range of adverse health effects. The mechanisms behind these effects include oxidative stress and inflammation. Even though traffic gives rise to high levels of particles in the urban air, people are exposed to even higher levels in the subway. However, there is a lack of knowledge regarding how particles from different urban subenvironments differ in toxicity. The main aim of the present study was to compare the ability of particles from a subway station and a nearby very busy urban street, respectively, to damage DNA and to induce oxidative stress. Cultured human lung cells (A549) were exposed to particles, DNA damage was analyzed using single cell gel electrophoresis (the comet assay), and the ability to induce oxidative stress was measured as 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) formation in lung cell DNA. We found that the subway particles were approximately eight times more genotoxic and four times more likely to cause oxidative stress in the lung cells. When the particles, water extracts from the particles, or particles treated with the metal chelator deferoxamine mesylate were incubated with 2'-deoxyguanosine (dG) and 8-oxodG was analyzed, we found that the oxidative capacity of the subway particles was due to redox active solid metals. Furthermore, analysis of the atomic composition showed that the subway particles to a dominating degree (atomic %) consisted of iron, mainly in the form of magnetite (Fe3O4). By using electron microscopy, the interaction between the particles and the lung cells was shown. The in vitro reactivity of the subway particles in combination with the high particle levels in subway systems give cause of concern due to the high number of people that are exposed to subway particles on a daily basis. To what extent the subway particles cause health effects in humans needs to be further evaluated.

Nanoscale imaging of alteration layers of corroded international simple glass particles using ToF-SIMS

Energy Technology Data Exchange (ETDEWEB)

Zhang, Jiandong; Neeway, James J.; Zhang, Yanyan; Ryan, Joseph V.; Yuan, Wei; Wang, Tieshan; Zhu, Zihua

2017-08-01

Glass particles with dimensions typically ranging from tens to hundreds of microns are often used in glass corrosion research in order to accelerate testing. Two-dimensional and three-dimensional nanoscale imaging techniques are badly needed to characterize the alteration layers at the surfaces of these corroded glass particles. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) can provide a lateral resolution as low as ~100 nm, and, compared to other imaging techniques, is sensitive to elements lighter than carbon. In this work, we used ToF-SIMS to characterize the alteration layers of corroded international simple glass (ISG) particles. At most particle surfaces, inhomogeneous or no alteration layers were observed, indicating that the thickness of the alterations layers may be too thin to be observable by ToF-SIMS imaging. Relatively thick (e.g., 1-10 microns) alteration layers were inhomogeneously distributed at a small portion of surfaces. More interestingly, some large-size (tens of microns) glass particles were fully altered. Above observations suggest that weak attachment and the defects on ISG particle surfaces play an important role in ISG glass corrosion.

A modified suspension spray combined with particle gradation method for preparation of protonic ceramic membrane fuel cells

Energy Technology Data Exchange (ETDEWEB)

Xie, Kui; Wang, Songlin; Chen, Xiaorui; Jiang, Tao; Lin, Bin; Wei, Ming; Liu, Xingqin; Meng, Guangyao [Department of Materials Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026 (China); Yan, Ruiqiang [Department of Materials Engineering, Taizhou University, Linhai, Zhejiang 317000 (China); Dong, Dehua [Department of Chemical Engineering, Monash University, Clayton, VIC 3800 (Australia)

2008-05-01

In order to prepare a dense proton-conductive Ba(Zr{sub 0.1}Ce{sub 0.7})Y{sub 0.2}O{sub 3-{delta}} (BZCY7) electrolyte membrane, a proper anode composition with 65% Ni{sub 2}O{sub 3} in weight ratio was determined after investigating the effects of anode compositions on anode shrinkages for co-sintering. The thermal expansion margins between sintered anodes and electrolytes, which were less than 1% below 750 C, also showed good thermal expansion compatibility. A suspension spray combined with particle gradation method had been introduced to prepare dense electrolyte membrane on porous anode support. After a heat treatment at 1400 C for 5 h, a cell with La{sub 0.5}Sr{sub 0.5}CoO{sub 3-{delta}} (LSCO) cathode was assembled and tested with hydrogen and ammonia as fuels. The outputs reached as high as 330 mW cm{sup -2} in hydrogen and 300 mW cm{sup -2} in ammonia at 700 C, respectively. Comparing with the interface of another cell prepared by dry-pressing method, this one also showed a good interface contact between electrodes and electrolyte. To sum up, this combined technique can be considered as commercial fabrication technology candidate. (author)

Gamma delta T cells promote inflammation and insulin resistance during high fat diet-induced obesity in mice

Science.gov (United States)

Gamma delta T cells are resident in adipose tissue and increase during diet-induced obesity. Their possible contribution to the inflammatory response that accompanies diet-induced obesity was investigated in mice after a 5-10 week high milk fat diet. The high milk fat diet resulted in significant in...

Nonlinear gyrokinetic equations for low-frequency electromagnetic waves in general plasma equilibria

International Nuclear Information System (INIS)

Frieman, E.A.; Chen, L.

1981-10-01

A nonlinear gyrokinetic formalism for low-frequency (less than the cyclotron frequency) microscopic electromagnetic perturbations in general magnetic field configurations is developed. The nonlinear equations thus derived are valid in the strong-turbulence regime and contain effects due to finite Larmor radius, plasma inhomogeneities, and magentic field geometries. The specific case of axisymmetric tokamaks is then considered, and a model nonlinear equation is derived for electrostatic drift waves. Also, applying the formalism to the shear Alfven wave heating sceme, it is found that nonlinear ion Landau damping of kinetic shear-Alfven waves is modified, both qualitatively and quantitatively, by the diamagnetic drift effects. In particular, wave energy is found to cascade in wavenumber instead of frequency

Binding of 18F by cell membranes and cell walls of Streptococcus mutans

International Nuclear Information System (INIS)

Yotis, W.W.; Zeb, M.; McNulty, J.; Kirchner, F.; Reilly, C.; Glendenin, L.

1983-01-01

The binding of 18 F to isolated cell membranes and cell walls of Streptococcus mutans GS-5 or other bacteria was assayed. The attachment of 18 F to these cell envelopes proceeded slowly and reached equilibrium within 60 min. 18 F binding was stimulated by Ca 2+ (1 mM). The binding of 18 F to cellular components was dependent upon the pH, as well as the amount of 18 F and dose of the binder employed. The binding of 18 F by cell walls prepared from fluoride-sensitive and fluoride-resistant cells of S. salivarius and S. mutans did not differ significantly. The pretreatment of cell walls or cell membranes for 60 min at 30 degrees C with 1 mg of RNase, DNase, or trypsin per ml did not influence the binding of 18 F by the walls and membranes of S. mutans GS-5. However, prior exposure of cell membranes to sodium dodecyl sulfate caused a significant reduction in the number of 18 F atoms bound by the membranes. In saturated assay systems, cell membranes of S. mutans GS-5 bound 10(15) to 10(16) atoms of 18 F per mg (dry weight), whereas cell walls from S. mutans GS-5, FA-1, and HS-6 or Actinomyces viscosus T14V and T14AV bound 10(12) to 10(13) atoms of 18 F per mg (dry weight). 18 F in this quantity (10(12) to 10(13) atoms) cannot be detected with the fluoride electrode. The data provide, for the first time, a demonstration of 18 F binding by cell membranes and walls of oral flora

Epoetin Delta Reduces Oxidative Stress in Primary Human Renal Tubular Cells

Directory of Open Access Journals (Sweden)

Annelies De Beuf

2010-01-01

Full Text Available Erythropoietin (EPO exerts (renal tissue protective effects. Since it is unclear whether this is a direct effect of EPO on the kidney or not, we investigated whether EPO is able to protect human renal tubular epithelial cells (hTECs from oxidative stress and if so which pathways are involved. EPO (epoetin delta could protect hTECs against oxidative stress by a dose-dependent inhibition of reactive oxygen species formation. This protective effect is possibly related to the membranous expression of the EPO receptor (EPOR since our data point to the membranous EPOR expression as a prerequisite for this protective effect. Oxidative stress reduction went along with the upregulation of renoprotective genes. Whilst three of these, heme oxygenase-1 (HO-1, aquaporin-1 (AQP-1, and B-cell CLL/lymphoma 2 (Bcl-2 have already been associated with EPO-induced renoprotection, this study for the first time suggests carboxypeptidase M (CPM, dipeptidyl peptidase IV (DPPIV, and cytoglobin (Cygb to play a role in this process.

DNA repair synthesis in human fibroblasts requires DNA polymerase delta

International Nuclear Information System (INIS)

Nishida, C.; Reinhard, P.; Linn, S.

1988-01-01

When UV-irradiated cultured diploid human fibroblasts were permeabilized with Brij-58 then separated from soluble material by centrifugation, conservative DNA repair synthesis could be restored by a soluble factor obtained from the supernatant of similarly treated HeLa cells. Extensive purification of this factor yielded a 10.2 S, 220,000-dalton polypeptide with the DNA polymerase and 3'- to 5'-exonuclease activities reported for DNA polymerase delta II. Monoclonal antibody to KB cell DNA polymerase alpha, while binding to HeLa DNA polymerase alpha, did not bind to the HeLa DNA polymerase delta. Moreover, at micromolar concentrations N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate (BuPdGTP) and 2-(p-n-butylanilino)-2'-deoxyadenosine 5'-triphosphate (BuAdATP) were potent inhibitors of DNA polymerase alpha, but did not inhibit the DNA polymerase delta. Neither purified DNA polymerase alpha nor beta could promote repair DNA synthesis in the permeabilized cells. Furthermore, under conditions which inhibited purified DNA polymerase alpha by greater than 90%, neither monoclonal antibodies to DNA polymerase alpha, BuPdGTP, nor BuAdATP was able to inhibit significantly the DNA repair synthesis mediated by the DNA polymerase delta. Thus, it appears that a major portion of DNA repair synthesis induced by UV irradiation might be catalyzed by DNA polymerase delta. When xeroderma pigmentosum human diploid fibroblasts were utilized, DNA repair synthesis dependent upon ultraviolet light could be restored by addition of both T4 endonuclease V and DNA polymerase delta, but not by addition of either one alone

Protein Kinase C-{delta} mediates down-regulation of heterogeneous nuclear ribonucleoprotein K protein: involvement in apoptosis induction

Energy Technology Data Exchange (ETDEWEB)

Gao, Feng-Hou [NO.3 People' s Hospital affiliated to Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 201900 (China); The Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200025 (China); Wu, Ying-Li [The Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200025 (China); Zhao, Meng [Institute of Health Science, SJTU-SM/Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai (China); Liu, Chuan-Xu; Wang, Li-Shun [The Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200025 (China); Chen, Guo-Qiang, E-mail: chengq@shsmu.edu.cn [The Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200025 (China); Institute of Health Science, SJTU-SM/Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai (China)

2009-11-15

We reported previously that NSC606985, a camptothecin analogue, induces apoptosis of acute myeloid leukemia (AML) cells through proteolytic activation of protein kinase C delta ({Delta}PKC-{delta}). By subcellular proteome analysis, heterogeneous nuclear ribonucleoprotein K (hnRNP K) was identified as being significantly down-regulated in NSC606985-treated leukemic NB4 cells. HnRNP K, a docking protein for DNA, RNA, and transcriptional or translational molecules, is implicated in a host of processes involving the regulation of gene expression. However, the molecular mechanisms of hnRNP K reduction and its roles during apoptosis are still not understood. In the present study, we found that, following the appearance of the {Delta}PKC-{delta}, hnRNP K protein was significantly down-regulated in NSC606985, doxorubicin, arsenic trioxide and ultraviolet-induced apoptosis. We further provided evidence that {Delta}PKC-{delta} mediated the down-regulation of hnRNP K protein during apoptosis: PKC-{delta} inhibitor could rescue the reduction of hnRNP K; hnRNP K failed to be decreased in PKC-{delta}-deficient apoptotic KG1a cells; conditional induction of {Delta}PKC-{delta} in U937T cells directly down-regulated hnRNP K protein. Moreover, the proteasome inhibitor also inhibited the down-regulation of hnRNP K protein by apoptosis inducer and the conditional expression of {Delta}PKC-{delta}. More intriguingly, the suppression of hnRNP K with siRNA transfection significantly induced apoptosis. To our knowledge, this is the first demonstration that proteolytically activated PKC-{delta} down-regulates hnRNP K protein in a proteasome-dependent manner, which plays an important role in apoptosis induction.

Particle-in-Cell Laser-Plasma Simulation on Xeon Phi Coprocessors

OpenAIRE

Surmin, I. A.; Bastrakov, S. I.; Efimenko, E. S.; Gonoskov, A. A.; Korzhimanov, A. V.; Meyerov, I. B.

2015-01-01

This paper concerns development of a high-performance implementation of the Particle-in-Cell method for plasma simulation on Intel Xeon Phi coprocessors. We discuss suitability of the method for Xeon Phi architecture and present our experience of porting and optimization of the existing parallel Particle-in-Cell code PICADOR. Direct porting with no code modification gives performance on Xeon Phi close to 8-core CPU on a benchmark problem with 50 particles per cell. We demonstrate step-by-step...

A comprehensive gyrokinetic description of global electrostatic microinstabilities in a tokamak

Science.gov (United States)

Chowdhury, J.; Ganesh, R.; Brunner, S.; Vaclavik, J.; Villard, L.; Angelino, P.

2009-05-01

It is believed that low frequency microinstabilities such as ion temperature gradient (ITG) driven modes and trapped electron modes (TEMs) are largely responsible for the experimentally observed anomalous transport via the ion and electron channels in a tokamak. In the present work, a comprehensive global linear gyrokinetic model incorporating fully kinetic (trapped and passing) electrons and ions, actual ion to electron mass ratio, radial coupling, and profile variation is used to investigate the ITG driven modes and pure TEMs. These modes are found to exhibit multiscale structures in the presence of nonadiabatic passing electrons. The multiscale structure is related to the large nonadiabaticity of electrons in the vicinity of mode rational magnetic surfaces and leads to reduced mixing length estimates of transport compared to those obtained from adiabatic electron models.

Delta opioid receptor on equine sperm cells: subcellular localization and involvement in sperm motility analyzed by computer assisted sperm analyzer (CASA

Directory of Open Access Journals (Sweden)

Lacalandra Giovanni M

2010-06-01

Full Text Available Abstract Background Opioid receptors and endogenous opioid peptides act not only in the control of nociceptive pathways, indeed several reports demonstrate the effects of opiates on sperm cell motility and morphology suggesting the importance of these receptors in the modulation of reproduction in mammals. In this study we investigated the expression of delta opioid receptors on equine spermatozoa by western blot/indirect immunofluorescence and its relationship with sperm cell physiology. Methods We analyzed viability, motility, capacitation, acrosome reaction and mitochondrial activity in the presence of naltrindole and DPDPE by means of a computer assisted sperm analyzer and a fluorescent confocal microscope. The evaluation of viability, capacitation and acrosome reaction was carried out by the double CTC/Hoechst staining, whereas mitochondrial activity was assessed by means of MitoTracker Orange dye. Results We showed that in equine sperm cells, delta opioid receptor is expressed as a doublet of 65 and 50 kDa molecular mass and is localized in the mid piece of tail; we also demonstrated that naltrindole, a delta opioid receptor antagonist, could be utilized in modulating several physiological parameters of the equine spermatozoon in a dose-dependent way. We also found that low concentrations of the antagonist increase sperm motility whereas high concentrations show the opposite effect. Moreover low concentrations hamper capacitation, acrosome reaction and viability even if the percentage of cells with active mitochondria seems to be increased; the opposite effect is exerted at high concentrations. We have also observed that the delta opioid receptor agonist DPDPE is scarcely involved in affecting the same parameters at the employed concentrations. Conclusions The results described in this paper add new important details in the comprehension of the mammalian sperm physiology and suggest new insights for improving reproduction and for

Gyrokinetic Stability Studies of the Microtearing Mode in the National Spherical Torus Experiment H-mode

International Nuclear Information System (INIS)

Baumgaertel J.A., Redi M.H., Budny R.V., Rewoldt G., Dorland W.

2005-01-01

Insight into plasma microturbulence and transport is being sought using linear simulations of drift waves on the National Spherical Torus Experiment (NSTX), following a study of drift wave modes on the Alcator C-Mod Tokamak. Microturbulence is likely generated by instabilities of drift waves, which cause transport of heat and particles. Understanding this transport is important because the containment of heat and particles is required for the achievement of practical nuclear fusion. Microtearing modes may cause high heat transport through high electron thermal conductivity. It is hoped that microtearing will be stable along with good electron transport in the proposed low collisionality International Thermonuclear Experimental Reactor (ITER). Stability of the microtearing mode is investigated for conditions at mid-radius in a high density NSTX high performance (H-mode) plasma, which is compared to the proposed ITER plasmas. The microtearing mode is driven by the electron temperature gradient, and believed to be mediated by ion collisions and magnetic shear. Calculations are based on input files produced by TRXPL following TRANSP (a time-dependent transport analysis code) analysis. The variability of unstable mode growth rates is examined as a function of ion and electron collisionalities using the parallel gyrokinetic computational code GS2. Results show the microtearing mode stability dependence for a range of plasma collisionalities. Computation verifies analytic predictions that higher collisionalities than in the NSTX experiment increase microtearing instability growth rates, but that the modes are stabilized at the highest values. There is a transition of the dominant mode in the collisionality scan to ion temperature gradient character at both high and low collisionalities. The calculations suggest that plasma electron thermal confinement may be greatly improved in the low-collisionality ITER

Interaction of plasma vortices with resonant particles

DEFF Research Database (Denmark)

Jovanovic, D.; Pécseli, Hans; Juul Rasmussen, J.

1990-01-01

Kinetic effects associated with the electron motion along magnetic field lines in low‐beta plasmas are studied. Using the gyrokinetic description of electrons, a kinetic analog of the reduced magnetohydrodynamic equations is derived, and it is shown that in the strongly nonlinear regime...... particles. The evolution equations indicate the possibility of excitation of plasma vortices by electron beams....... they possess localized solutions in the form of dipolar vortices, which can efficiently interact with resonant electrons. In the adiabatic limit, evolution equations are derived for the vortex parameters, describing exchange of the energy, enstrophy, and of the Poynting vector between the vortex and resonant...

Recent Advances in Understanding Flow Dynamics and Transport of Water-Quality Constituents in the Sacramento–San Joaquin River Delta

Directory of Open Access Journals (Sweden)

David H. Schoellhamer

2016-12-01

Full Text Available doi: https://doi.org/10.15447/sfews.2016v14iss4art1This paper, part of the collection of research comprising the State of Bay–Delta Science 2016, describes advances during the past decade in understanding flow dynamics and how water-quality constituents move within California’s Sacramento–San Joaquin River Delta (Delta. Water-quality constituents include salinity, heat, oxygen, nutrients, contaminants, organic particles, and inorganic particles. These constituents are affected by water diversions and other human manipulations of flow, and they greatly affect the quantity and quality of benthic, pelagic, and intertidal habitat in the Delta. The Pacific Ocean, the Central Valley watershed, human intervention, the atmosphere, and internal biogeochemical processes are all drivers of flow and transport in the Delta. These drivers provide a conceptual framework for presenting recent findings. The tremendous expansion of acoustic and optical instruments deployed in the Delta over the past decade has greatly improved our understanding of how tidal variability affects flow and transport. Sediment is increasingly viewed as a diminishing resource needed to sustain pelagic habitat and tidal marsh, especially as sea level rises. Connections among the watershed, Delta, and San Francisco Bay that have been quantified recently highlight that a landscape view of this system is needed, rather than consideration of each region in isolation. We discuss interactions of multiple drivers and information gaps.

Growth laws for sub-delta crevasses in the Mississippi River Delta

Science.gov (United States)

Yocum, T. A.; Georgiou, I. Y.; Straub, K. M.

2017-12-01

River deltas are threatened by environmental change, including subsidence, global sea level rise, reduced sediment inputs and other local factors. In the Mississippi River Delta (MRD) these impacts are exemplified, and have led to proposed solutions to build land that include sediment diversions to reinitiate the delta cycle. Deltas were studied extensively using numerical models, theoretical and conceptual frameworks, empirical scaling relationships, laboratory models and field observations. But predicting the future of deltas relies on field observations where for most deltas data are still lacking. Moreover, empirical and theoretical scaling laws may be influenced by the data used to develop them, while laboratory deltas may be influenced by scaling issues. Anthropogenic crevasses in the MRD are large enough to overcome limitations of laboratory deltas, and small enough to allow for rapid channel and wetland development, providing an ideal setting to investigate delta development mechanics. Here we assessed growth laws of sub-delta crevasses (SDC) in the MRD, in two experimental laboratory deltas (LD - weakly and strongly cohesive) and compared them to river dominated deltas worldwide. Channel and delta geometry metrics for each system were obtained using geospatial tools, bathymetric datasets, sediment size, and hydrodynamic observations. Results show that SDC follow growth laws similar to large river dominated deltas, with the exception of some that exhibit anomalous behavior with respect to the frequency and distance to a bifurcation and the fraction of wetted delta shoreline (allometry metrics). Most SDC exhibit a systematic decrease of non-dimensional channel geometries with increased bifurcation order, indicating that channels are adjusting to decreased flow after bifurcations occur, and exhibit linear trends for land allometry and width-depth ratio, although geometries decrease more rapidly per bifurcation order. Measured distance to bifurcations in SDC

Particle acceleration in modified shocks

Energy Technology Data Exchange (ETDEWEB)

Drury, L.O' C. (Max-Planck-Institut fuer Kernphysik, Heidelberg (Germany, F.R.)); Axford, W.I. (Max-Planck-Institut fuer Aeronomie, Katlenburg-Lindau (Germany, F.R.)); Summers, D. (Memorial Univ. of Newfoundland, St. John' s (Canada))

1982-03-01

Efficient particle acceleration in shocks must modify the shock structure with consequent changes in the particle acceleration. This effect is studied and analytic solutions are found describing the diffusive acceleration of particles with momentum independent diffusion coefficients in hyperbolic tangent type velocity transitions. If the input particle spectrum is a delta function, the shock smoothing replaces the truncated power-law downstream particle spectrum by a more complicated form, but one which has a power-law tail at high momenta. For a cold plasma this solution can be made completely self-consistent. Some problems associated with momentum dependent diffusion coefficients are discussed.

Particle acceleration in modified shocks

International Nuclear Information System (INIS)

Drury, L.O'C.; Axford, W.I.; Summers, D.

1982-01-01

Efficient particle acceleration in shocks must modify the shock structure with consequent changes in the particle acceleration. This effect is studied and analytic solutions are found describing the diffusive acceleration of particles with momentum independent diffusion coefficients in hyperbolic tangent type velocity transitions. If the input particle spectrum is a delta function, the shock smoothing replaces the truncated power-law downstream particle spectrum by a more complicated form, but one which has a power-law tail at high momenta. For a cold plasma this solution can be made completely self-consistent. Some problems associated with momentum dependent diffusion coefficients are discussed. (author)

Tracks, spurs, blobs and delta-rays

International Nuclear Information System (INIS)

Magee, J.L.; Chatterjee, A.

1983-01-01

The track of a high-energy particle is the collection of all transient species created by the particle in the total degradation of its energy. Visible electron tracks are called delta rays. A microscopic description of the track with all its knocked-out electrons leads to spurs, blobs, and short tracks. Energy deposition criteria for these three track entities are 6 to 100 eV, 100 to 500 eV, and 500 eV to 5 keV, respectively

Sparse grid techniques for particle-in-cell schemes

Science.gov (United States)

Ricketson, L. F.; Cerfon, A. J.

2017-02-01

We propose the use of sparse grids to accelerate particle-in-cell (PIC) schemes. By using the so-called ‘combination technique’ from the sparse grids literature, we are able to dramatically increase the size of the spatial cells in multi-dimensional PIC schemes while paying only a slight penalty in grid-based error. The resulting increase in cell size allows us to reduce the statistical noise in the simulation without increasing total particle number. We present initial proof-of-principle results from test cases in two and three dimensions that demonstrate the new scheme’s efficiency, both in terms of computation time and memory usage.

photon-plasma: A modern high-order particle-in-cell code

International Nuclear Information System (INIS)

Haugbølle, Troels; Frederiksen, Jacob Trier; Nordlund, Åke

2013-01-01

We present the photon-plasma code, a modern high order charge conserving particle-in-cell code for simulating relativistic plasmas. The code is using a high order implicit field solver and a novel high order charge conserving interpolation scheme for particle-to-cell interpolation and charge deposition. It includes powerful diagnostics tools with on-the-fly particle tracking, synthetic spectra integration, 2D volume slicing, and a new method to correctly account for radiative cooling in the simulations. A robust technique for imposing (time-dependent) particle and field fluxes on the boundaries is also presented. Using a hybrid OpenMP and MPI approach, the code scales efficiently from 8 to more than 250.000 cores with almost linear weak scaling on a range of architectures. The code is tested with the classical benchmarks particle heating, cold beam instability, and two-stream instability. We also present particle-in-cell simulations of the Kelvin-Helmholtz instability, and new results on radiative collisionless shocks

Microfluidic-Based Synthesis of Hydrogel Particles for Cell Microencapsulation and Cell-Based Drug Delivery

Directory of Open Access Journals (Sweden)

Jiandi Wan

2012-04-01

Full Text Available Encapsulation of cells in hydrogel particles has been demonstrated as an effective approach to deliver therapeutic agents. The properties of hydrogel particles, such as the chemical composition, size, porosity, and number of cells per particle, affect cellular functions and consequently play important roles for the cell-based drug delivery. Microfluidics has shown unparalleled advantages for the synthesis of polymer particles and been utilized to produce hydrogel particles with a well-defined size, shape and morphology. Most importantly, during the encapsulation process, microfluidics can control the number of cells per particle and the overall encapsulation efficiency. Therefore, microfluidics is becoming the powerful approach for cell microencapsulation and construction of cell-based drug delivery systems. In this article, I summarize and discuss microfluidic approaches that have been developed recently for the synthesis of hydrogel particles and encapsulation of cells. I will start by classifying different types of hydrogel material, including natural biopolymers and synthetic polymers that are used for cell encapsulation, and then focus on the current status and challenges of microfluidic-based approaches. Finally, applications of cell-containing hydrogel particles for cell-based drug delivery, particularly for cancer therapy, are discussed.

Carbon fuel particles used in direct carbon conversion fuel cells

Science.gov (United States)

Cooper, John F.; Cherepy, Nerine

2012-10-09

A system for preparing particulate carbon fuel and using the particulate carbon fuel in a fuel cell. Carbon particles are finely divided. The finely dividing carbon particles are introduced into the fuel cell. A gas containing oxygen is introduced into the fuel cell. The finely divided carbon particles are exposed to carbonate salts, or to molten NaOH or KOH or LiOH or mixtures of NaOH or KOH or LiOH, or to mixed hydroxides, or to alkali and alkaline earth nitrates.

Carbon Fuel Particles Used in Direct Carbon Conversion Fuel Cells

Science.gov (United States)

Cooper, John F.; Cherepy, Nerine

2008-10-21

A system for preparing particulate carbon fuel and using the particulate carbon fuel in a fuel cell. Carbon particles are finely divided. The finely dividing carbon particles are introduced into the fuel cell. A gas containing oxygen is introduced into the fuel cell. The finely divided carbon particles are exposed to carbonate salts, or to molten NaOH or KOH or LiOH or mixtures of NaOH or KOH or LiOH, or to mixed hydroxides, or to alkali and alkaline earth nitrates.

Motion of the relativistic charged particle in an axisymmetric toroidal system

Energy Technology Data Exchange (ETDEWEB)

Chiyoda, K; Sugimoto, H [Electrotechnical Labs., Sakura, Ibaraki (Japan)

1980-01-01

The relativistic theory of motion of one particle by Morozov and Solov'ev is summarized for convenience of the present study. Then, a drift equation is given and four constants of motion, E/sub 0/, J perpendicular, J and J parallel, are obtained. These constants of motion are used in analyzing the particle motion in an axisymmetric toroidal system. The displacement of the particle from the magnetic surface, ..delta..r, and the period of the banana motion, tau, are obtained. The relativistic expressions of the displacement, ..delta..r, and the period, tau, are obtained by multiplying the corresponding nonrelativistic expressions by (1 - v parallel/sup 2//c/sup 2/) - 1/2, where the relativistic expression of ..delta..r includes the relativistic mass in terms of Larmor radius r/sub L/.

Alpha particle effects on MHD ballooning

International Nuclear Information System (INIS)

1991-01-01

During the period, as the first step towards the goal of detail understanding of the effects of alpha particle on MHD Ballooning Modes, a new numerical approach to investigate the stability of low-frequency fluctuations in high temperature tokamaks was developed by solving the gyrokinetic equations for the ion and electron directly as an initial value problem. The advantage of this approach is the inclusion of many important kinetic features of the problem without approximations and computationally more economical than particle-pushing simulation. The ion-temperature-gradient-mode was investigated to benchmark this new simulation technique. Previous results in literature were recovered. Both the adiabatic electron model and the full drift-kinetic electron model are studied. Numerical result shows that the full drift-kinetic electron model is more unstable. The development of subcycling technique to handle the fast electron bounce time is particularly significant to apply this new approach to the alpha particle problem since alpha particle bounce frequency is also significantly higher than the mode frequency. This new numerical technique will be the basis of future study of the microstability in high temperature tokamaks with alpha particles (or any energetic species). 15 refs., 13 figs

Gyrokinetic theory of slab universal modes and the non-existence of the gradient drift coupling (GDC) instability

Science.gov (United States)

Rogers, Barrett N.; Zhu, Ben; Francisquez, Manaure

2018-05-01

A gyrokinetic linear stability analysis of a collisionless slab geometry in the local approximation is presented. We focus on k∥=0 universal (or entropy) modes driven by plasma gradients at small and large plasma β. These are small scale non-MHD instabilities with growth rates that typically peak near k⊥ρi˜1 and vanish in the long wavelength k⊥→0 limit. This work also discusses a mode known as the Gradient Drift Coupling (GDC) instability previously reported in the gyrokinetic literature, which has a finite growth rate γ=√{β/[2 (1 +β)] }Cs/|Lp| with Cs2=p0/ρ0 for k⊥→0 and is universally unstable for 1 /Lp≠0 . We show that the GDC instability is a spurious, unphysical artifact that erroneously arises due to the failure to respect the total equilibrium pressure balance p0+B02/(8 π)=constant , which renders the assumption B0'=0 inconsistent if p0'≠0 .