Dispersion of ion gyrocenters in models of anisotropic plasma turbulence

Turbulent dispersion of ion gyrocenters in a magnetized plasma is studied in the context of a stochastic Hamiltonian transport model and nonlinear, self-consistent gyrokinetic simulations. The Hamiltonian model consists of a superposition of drift waves derived from the linearized Hasegawa-Mima equation and a zonal shear flow perpendicular to the density gradient. Finite Larmor radius (FLR) effects are included. Because there is no particle transport in the direction of the density gradient, the focus is on transport parallel to the shear flow. The prescribed flow produces strongly asymmetric non-Gaussian probability distribution functions (PDFs) of particle displacements, as was previously known. For kρ=0, where k is the characteristic wavelength of the flow and ρ is the thermal Larmor radius, a transition is observed in the scaling of the second moment of particle displacements. The transition separates nearly ballistic superdiffusive dispersion from weaker superdiffusion at later times. FLR effects eliminate this transition. Important features of the PDFs of displacements are reproduced accurately with a fractional diffusion model. The gyroaveraged ExB drift dispersion of a sample of tracer ions is also examined in a two-dimensional, nonlinear, self-consistent gyrokinetic particle-in-cell (PIC) simulation. Turbulence in the simulation is driven by a density gradient and magnetic curvature, resulting in the unstable ρ scale kinetic entropy mode. The dependence of dispersion in both the axial and radial directions is characterized by displacement and velocity increment distributions. The strength of the density gradient is varied, using the local approximation, in three separate trials. A filtering procedure is used to separate trajectories according to whether they were caught in an eddy during a set observation time. Axial displacements are compared to results from the Hasegawa-Mima model. Superdiffusion and ballistic transport are found, depending on filtering and strength of the gradient. The radial dispersion of particles, as measured by the variance of tracer displacements, is diffusive. The dependence of the running diffusion coefficient on ρ for each value of the density gradient is considered

Fractional diffusion emulates a human mobility network during a simulated disease outbreak

From footpaths to flight routes, human mobility networks facilitate the spread of communicable diseases. Control and elimination efforts depend on characterizing these networks in terms of connections and flux rates of individuals between contact nodes. In some cases, transport can be parameterized with gravity-type models or approximated by a diffusive random walk. As a alternative, we have isolated intranational commercial air traffic as a case study for the utility of non-diffusive, heavy-tailed transport models. We implemented new stochastic simulations of a prototypical influenza-like infection, focusing on the dense, highly-connected United States air travel network. We show that mobility on this network can be described mainly by a power law, in agreement with previous studies. Remarkably, we find that the global evolution of an outbreak on this network is accurately reproduced by a two-parameter space-fractional diffusion equation, such that those parameters are determined by the air travel network.Comment: 26 pages, 4 figure

Environmental (Natural and Anthropogenic) Effects on Host-parasite (Snail-trematode) Interactions

This dissertation explored environmental effects on host�parasite interactions. Chapter 2 was published in Ecotoxicology and assessed the effects of the herbicide atrazine on freshwater snails. The results indicated that snails are affected by atrazine at the subcellular and cellular levels. However, effects at those levels were not transitive to effects on individual snail fitness or on snail populations. Chapter 3 was published in Journal of Parasitology and explored the dose�response effects of trematodes on snails. The results indicated that as the trematode egg dose increased, the probability of snail reproduction and survival decreased; however, the probability of establishing an infection increased. Chapter 4 was published in Parasitology Research and addressed the effects of atrazine on trematode transmission and host�parasite interactions. The results showed that atrazine reduced infected snail survival at higher atrazine concentrations, resulting in fewer cercariae being produced. On top of that, atrazine reduced the infectivity of worms to the final host. Combined, these effects reduced the transmission of an amphibian trematode. Chapter 5 was published in Evolutionary Ecology Research and was a common garden experiment assessing the effects of environment on snail shell morphology. The shell shape of offspring from stream and wetland snails converged within a single generation whereas shell size took 2 generations to converge, suggesting the two ecomorphs are a single species. Sequence data confirmed they were the same species. Chapter 6 was published in Journal of Morphology and assessed the interactive effects of the environment and parasitism on snail shell morphology. The results showed that the environment was the major driver of snail shell morphology. Parasitism played a secondary role and only affected shell crush resistance in stream snails. Trematode communities were significantly different between wetland and stream snails but the effect on shell crush resistance was not driven by differences in trematode communities.Zoolog

Color and pigment polymorphisms of northern leopard frogs on a prairie landscape

Variation allows populations to adapt to changing conditions. As human activities continue to alter environments and evolutionary processes, it becomes increasingly important to conserve standing genetic variation. Despite technical advances in population genetics, it is still useful to have inexpensive methods of detecting and monitoring genetic variation, particularly in traits that potentially influence fitness. In the Northern Leopard Frog, Lithobates pipiens (= Rana pipiens), genetically determined color (green [dominant: G] or brown [recessive: g]) and two pigment pattern polymorphisms (Burnsi/spotless [B] or spotted [b]; Kandiyohi/mottled [K] or non-mottled[k]) are hypothesized to have adaptive benefits. We assessed spatiotemporal patterns of these polymorphisms during two time periods in one of the largest remaining grasslands in North America. The frequency of the dominant green phenotype remained consistent from the early-to-late 2000s; however, we observed Kandiyohi phenotypes more frequently during 2001–2002 compared to 2009–2010. By contrast, we observed dominant Burnsi phenotypes more frequently in the latter time period. Although not statistically significant, we observed green phenotypes more frequently in areas with less water on the landscape and in locations closer to tree cover. Burnsi phenotypes were more common in wetlands that did not dry out and Kandiyohi phenotypes were more common in wetlands with aquatic vegetation, although not significantly. No pigment polymorphism was associated with body size. We found no indication of spatial structure, suggesting ample gene flow. The correlations were generally weak, but some were consistent with hypotheses of adaptive benefits. This genetically determined phenotypic variation could be important under changing climactic conditions or if land uses change

Dispersion of fast ions in models of anisotropic plasma turbulence

oral conference presentatio

An inorganic capping strategy for the seeded growth of versatile bimetallic nanostructures

Metal nanostructures have attracted great attention in various fields due to their tunable properties through precisely tailored sizes, compositions and structures. Using mesoporous silica (mSiO2) as the inorganic capping agent and encapsulated Pt nanoparticles as the seeds, we developed a robust seeded growth method to prepare uniform bimetallic nanoparticles encapsulated in mesoporous silica shells (PtM@mSiO2, M = Pd, Rh, Ni and Cu). Unexpectedly, we found that the inorganic silica shell is able to accommodate an eight-fold volume increase in the metallic core by reducing its thickness. The bimetallic nanoparticles encapsulated in mesoporous silica shells showed enhanced catalytic properties and thermal stabilities compared with those prepared with organic capping agents. This inorganic capping strategy could find a broad application in the synthesis of versatile bimetallic nanostructures with exceptional structural control and enhanced catalytic properties

Investigation of fast ion transport in TORPEX

Basic aspects of fast ion transport in ideal interchange-mode unstable plasmas are investigated in the simple toroidal plasma device TORPEX. Fast ions are generated by a miniaturized lithium 6+ ion source with energies up to 1 keV, and are detected using a double-gridded energy analyser mounted on a two-dimensional movable system in the poloidal cross-section. The signal-to-noise ratio is enhanced by applying a modulated biasing voltage to the fast ion source and using a synchronous detection scheme. An analogue lock-in amplifier has been developed, which allows removing the capacitive noise associated with the voltage modulation. We characterize vertical and radial transport of the fast ions, which is associated with the plasma turbulence. Initial experimental results show good agreement with numerical simulations of the fast ion transport in a global fluid simulation of the TORPEX plasma

Suprathermal ion transport theory and experiments in the SMT

Recent advances in the suprathermal ion diagnostic in the basic plasma experiment TORPEX have inspired our comprehensive theoretical study of suprathermal ion transport. TORPEX, an example of a simple magnetized toroidal plasma (SMT), is equipped with a flexible fast ion source and detector capable of exploring fast ion dynamics in a wide range of positions and energies. We simulate an ensemble of ion tracer trajectories as specified by ideal interchange-mode turbulence imported from a validated numerical simulation based on the drift-reduced Braginskii model. Using the variance of displacements, $\sigma^2(t) \sim t^{\gamma}$, we find that $\gamma$ depends strongly on suprathermal ion injection energy and the magnitude of turbulent fluctuations. When the beam interacts with the turbulence, we find the remarkable presence of three regimes of dispersion: superdiffusive, diffusive, and subdiffusive, depending on the energy of the suprathermal ions and the amplitude of the turbulent fluctuations. Results from the source on TORPEX are consistent with the theoretical predictions