Global particle simulations of the lower hybrid (LH) waves have been carried out using fully kinetic ions and drift kinetic electrons with a realistic electron-to-ion mass ratio. The LH wave frequency, mode structure, and electron Landau damping from the electrostatic simulations agree very well with the analytic theory. Linear simulation of the propagation of a LH wave-packet in the toroidal geometry shows that the wave propagates faster in the high field side than the low field side, in agreement with a ray tracing calculation. This poloidal asymmetry arises from the non-conservation of the poloidal mode number due to the non-uniform magnetic field. In contrast, the poloidal mode number is conserved in the cylindrical geometry with the uniform magnetic field. © 2014 IOP Publishing Ltd.

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.

Magnetic islands have been implemented in the gyrokinetic toroidal code to study the effects of the islands on microturbulence. The pressure profile flattening is verified in the simulation with the islands. Simulations of ion temperature gradient instability find that different toroidal modes are linearly coupled together and that toroidal spectra become broader when the island width increases. The real frequencies and growth rates of different toroidal modes approach each other with the averaged value independent of the island width. The linear mode structures are enhanced at the island separatrices and weakened at the island centers, consistent with the flattening of the pressure profile inside the islands.

Aerobic respiration of intracellular polyglucose reserves is postulated to playa central role in oxygen adaptive response in obligatory anaerobes like Desulfovibrios, but it has been difficult to probe this event at chemical scale in vivo. Here we present a non-invasive synchrotron infrared (SIR) spectromicroscopy approach to reveal timedependentcomposition and structure changes at a lateral scale of several individual Desulfovirbio vulgaris. The advantage of infrared spectroscopy is that it is non-invasive, and it uses vibration movements of atoms and chemical bonds within functional groups of biomolecules as an intrinsic contrasting mechanism; thus it allows one to immediately detect composition and structure changes within living cells. The advantage of using a synchrotron light source is that its high brightness allows us to detect signals -1000 times weaker then the conventional infrared spectroscopy allows us to. Comparative analysis of SIR spectra of the same individual D. vulgaris exposed to air-level oxygen at different time points reveals chronological information regarding the level of oxidative stress and the extent of cellular injury and repair. These results, together with microscopy images, mark a critical step toward the use of SIR spectromicroscopy as an uninterrupted microprobe at a chemical scale level of physiological events in microbiology applications.

A dynamical theory of turbulence spreading and nonlocal interaction phenomena is presented. The basic model is derived using Fokker-Planck theory, and supported by wave-kinetic and K-ε type closures. In the absence of local growth, the model predicts subdiffusive spreading of turbulence. With local growth and saturation via nonlinear damping, ballistic propagation of turbulence intensity fronts is possible. The time asymptotic front speed is set by the geometric mean of local growth and turbulent diffusion. The leading edge of the front progresses as the turbulence comes to local saturation. Studies indicate that turbulence can jump gaps in the local growth rate profile and can penetrate locally marginal or stable regions. In particular, significant fluctuation energy from a turbulent edge can easily spread into the marginally stable core, thus creating an intermediate zone of strong turbulence. This suggests that the traditional distinction between core and edge should be reconsidered. © 2005 American Institute of Physics.

The concurrent or sequential usage of multiple substances during adolescence is a serious public health problem. Given the importance of understanding interdependence in substance use during adolescence, the purpose of this study is to examine the co-evolution of cigarette smoking, alcohol, and marijuana use within the ever-changing landscape of adolescent friendship networks, which are a primary socialization context for adolescent substance use. Utilizing Stochastic Actor-Based models, we examine how multiple simultaneous social processes co-evolve with adolescent smoking, drinking, and marijuana use within adolescent friendship networks using two school samples from early waves of the National Longitudinal Study of Adolescent to Adult Health (Add Health). We also estimate two separate models examining the effects from using one substance to the initiation and cessation of other substances for each sample. Based on the initial model results, we simulate the model forward in time by turning off one key effect in the estimated model at a time, and observe how the distribution of use of each substance changes. We find evidence of a unilateral causal relationship from marijuana use to subsequent smoking and drinking behaviors, resulting in the initiation of drinking behavior. Marijuana use is also associated with smoking initiation in a school with a low substance use level, and smoking cessation in a school with a high substance use level. In addition, in a simulation model excluding the effect from marijuana use to smoking and drinking behavior, the number of smokers and drinkers decreases precipitously. Overall, our findings indicate some evidence of sequential drug use, as marijuana use increased subsequent smoking and drinking behavior and indicate that an adolescent's level of marijuana use affects the initiation and continuation of smoking and drinking.

The gyrokinetic toroidal code has been upgraded for global simulations by coupling the core and scrape-off layer regions across the separatrix with field-aligned particle-grid interpolations. A fully kinetic particle pusher for high frequency waves (ion cyclotron frequency and beyond) and a guiding center pusher for low frequency waves have been implemented using cylindrical coordinates in a global toroidal geometry. The two integrators correctly capture the particle orbits and agree well with each other, conserving energy and canonical angular momentum. As a verification and application of this new capability, ion guiding center simulations have been carried out to study ion orbit losses at the edge of the DIII-D tokamak for single null magnetic separatrix discharges. The ion loss conditions are examined as a function of the pitch angle for cases without and with a radial electric field. The simulations show good agreement with past theoretical results and with the experimentally observed feature in which high energy ions flow out along the ion drift orbits and then hit the divertor plates. A measure of the ion direct orbit loss fraction shows that the loss fraction increases with the ion energy for DIII-D in the initial velocity space. Finally, as a further verification of the capability of the new code, self-consistent simulations of zonal flows in the core region of the DIII-D tokamak were carried out. All DIII-D simulations were performed in the absence of turbulence.

We study the simplest problem of turbulence spreading corresponding to the spatio-temporal propagation of a patch of turbulence from a region where it is locally excited to a region of weaker excitation or even local damping. A single model equation for the local turbulence intensity, I(x, t), includes the effects of local linear growth and damping, spatially local nonlinear coupling to dissipation and spatial scattering of turbulence energy induced by nonlinear coupling. In the absence of dissipation, front propagation into the linearly stable zone occurs with the property of rapid progression at small t, followed by slower sub-diffusive progression at late times. The turbulence radial spreading into the linearly stable zone reduces the turbulent intensity in the linearly unstable zone and introduces an additional dependence on the ρ* ≡ ρi/a to the turbulent intensity and the transport scaling. These are in broad, semi-quantitative agreement with a number of global gyrokinetic simulation results with zonal flows and without zonal flows. Front propagation stops when the radial flux of fluctuation energy from the linearly unstable region is balanced by local dissipation in the linearly stable region.

One of the nagging, unresolved questions in fusion theory is concerned with the extent of the edge. Gyrokinetic particle simulations of toroidal ion temperature gradient turbulence spreading using the gyrokinetic toroidal code [Z. Lin, T. S. Hahm, W. W. Lee, W. M. Tang, and R. B. White, Science 281, 1835 (1998)] and its related dynamical model have been extended to a system with radially varying ion temperature gradient, in order to study the inward spreading of edge turbulence toward the core plasma. Due to such spreading, the turbulence intensity in the core region is significantly enhanced over the value obtained from the simulations of the core region only, and the precise boundary of the edge region is blurred. Even when the core gradient is within the Dimits shift regime (i.e., dominated by self-generated zonal flows which reduce the transport to a negligible value), a significant level of turbulence can penetrate to the core due to spreading from the edge. The scaling of the turbulent front propagation speed is closer to the prediction from a nonlinear diffusion model than from the one based on linear toroidal coupling. © 2005 American Institute of Physics.