Investigation of the interaction between competing types of nondiffusive transport in drift wave turbulence

Radial transport in turbulence dominated tokamak plasmas has been observed to deviate from classical diffusion in certain regimes relevant for magnetic confinement fusion. These situations at least include near-marginal turbulence, where radial transport becomes superdiffusive and mediated by elongated radial structures (or avalanches) and transport across radially sheared poloidal flows, where radial subdiffusion often ensues. In this paper, the interaction between very different physical ingredients responsible for these two types of nondiffusive dynamics (namely, turbulent profile relaxation close to a local threshold and the interaction with radially sheared zonal flows) is studied in detail in the context of a simple two-dimensional electrostatic plasma fluid turbulence model based on the dissipative trapped electron mode. It is shown that, depending on the relative relevance of each of these ingredients, which can be tuned in various ways, a variety of nondiffusive radial transport behaviors can be found in the system. The results also illustrate the fact that the classical diffusion paradigm is often insufficient to describe turbulent transport in systems with self-generated flows and turbulent profile relaxations. Published by AIP Publishing.This work was supported by U.S. DOE under Contract No. DE-FG02-04ER54741 with the University of Alaska Fairbanks and in part by a grant of HPC resources from the Arctic Region Supercomputing Center at the University of Alaska Fairbanks. This research was also sponsored in part by DGICT (Direccion General de Investigaciones Cientıficas y Tecnologicas) of Spain under Project No. ENE2015-68265

Transport dynamics of self-consistent, near-marginal drift-wave turbulence. II. Characterization of transport by means of passive scalars

From theoretical and modeling points of view, following Lagrangian trajectories is the most straightforward way to characterize the transport dynamics. In real plasmas, following Lagrangian trajectories is difficult or impossible. Using a blob of passive scalar (a tracer blob) allows a quasi-Lagrangian view of the dynamics. Using a simple two-dimensional electrostatic plasma turbulence model, this work demonstrates that the evolution of the tracers and the passive scalar field is equivalent between these two fluid transport viewpoints. When both the tracers and the passive scalar evolve in tandem and closely resemble stable distributions, namely, Gaussian distributions, the underlying turbulent transport character can be recovered from the temporal scaling of the second moments of both. This local transport approach corroborates the use of passive scalar as a turbulent transport measurement. The correspondence between the local transport character and the underlying transport is quantified for different transport regimes ranging from subdiffusive to superdiffusive. This correspondence is limited to the initial time periods of the spread of both the tracers and the passive scalar in the given transport regimes.This work was supported by U.S. DOE Contract No. DE-FG02-04ER54741 with the University of Alaska Fairbanks and in part by a grant of HPC resources from the Arctic Region Supercomputing Center at the University of Alaska Fairbanks. This research was also sponsored in part by DGICYT (Dirección General de Investigaciones Científicas y Tecnológicas) of Spain under Project No. ENE2015-68265

Tracer particle transport dynamics in the diffusive sandpile cellular automaton

The confinement properties of the diffusive running sandpile are characterized by tracking the motion of a population of marked grains of sand. It is found that, as the relative strength of the avalanching to the diffusive transport channel is varied, a point is reached at which the particle global confinement time and the probability density functions of the jump-sizes and waiting-times of the tracked grains experience a sudden change, thus revealing a dynamical transition, that is consistent with previous studies (Newman DE et al., Phys Rev Lett 2002;88(20):204304). Across this transition, the sandpile moves from a regime characterized by self-similarity and memory, where avalanches of all possible sizes dominate transport across the system, to another regime where transport is taken over by near system-size, quasi-periodic avalanches. Values for the fractional transport exponents that quantify effective transport across the sandpile prior to the transition are also obtained.This research has been sponsored in part by Ministerio de Economía y Competitividad of Spain under Projects No. ENE2015- 68265-P and No. ENE2015-66444-R. Research also supported in part by DOE-OFES Grant No. DE-FG02-04ER5741 at University of Alaska. Sandpile simulations have been run in Uranus, a supercomputer cluster at Universidad Carlos III de Madrid (Spain) that has been funded by the Spanish Government via the national projects UNC313-4E-2361, ENE2009-12213-C03-03, ENE2012-33219 and ENE2012-31753

Comparison of Lures Loaded with Codlemone and Pear Ester for Capturing Codling Moths, Cydia pomonella, in Apple and Pear Orchards using Mating Disruption

Studies were conducted in apple, Malus domestica Borkhausen and pear, Pyrus communis L. (Rosales: Rosaceae), orchards to evaluate the attractiveness of grey halobutyl septa loaded with 1 (L2) and 10 (Mega) mg of codlemone, 8E, 10E-dodecadien-1-ol, 3 mg of pear ester, ethyl (E,Z)-2,4-decadienoate (DA2313), and 3 mg of pear ester plus 3 mg of codlemone (Combo) to adult codling moth, Cydia pomonella (L.) (Lepidoptera: Tortricidae). All studies were conducted in orchards treated with pheromone mating disruption. All four lures were tested on diamond-shaped sticky traps placed in 60 plots of apple and 40 plots of pears in 2003/04, and in 62 plots of apples and 30 of pears in 2004–05. Combo lures attracted significantly more moths (males + females) than all the others in both years. Comparisons among flights showed significant differences mainly for flight 1 and 2, but not always for flight 3. Mega lures provided no significant improvement compared with L2 lures during both seasons regarding the total number of moths. Combo and DA2313 lures attracted fewer females than males during the whole season. For most sample dates, more virgin than mated females were attracted to Combo lures, except during the third flight, and the overall ratio was 60:40, although the difference was not statistically significant. We conclude that the Combo lures are better indicators of codling moth activity in pheromone treated orchards, regardless of pest population level, when compared with similar lures containing codlemone or pear ester alone

Implementation of 2D Domain Decomposition in the UCAN Gyrokinetic Particle-in-Cell Code and Resulting Performance of UCAN2

The massively parallel, nonlinear, three-dimensional (3D), toroidal, electrostatic, gyrokinetic, particle-in-cell (PIC), Cartesian geometry UCAN code, with particle ions and adiabatic electrons, has been successfully exercised to identify non-diffusive transport characteristics in present day tokamak discharges. The limitation in applying UCAN to larger scale discharges is the 1D domain decomposition in the toroidal (or z-) direction for massively parallel implementation using MPI which has restricted the calculations to a few hundred ion Larmor radii or gyroradii per plasma minor radius. To exceed these sizes, we have implemented 2D domain decomposition in UCAN with the addition of the y-direction to the processor mix. This has been facilitated by use of relevant components in the P2LIB library of field and particle management routines developed for UCLA's UPIC Framework of conventional PIC codes. The gyro-averaging specific to gyrokinetic codes is simplified by the use of replicated arrays for efficient charge accumulation and force deposition. The 2D domain-decomposed UCAN2 code reproduces the original 1D domain nonlinear results within round-off. Benchmarks of UCAN2 on the Cray XC30 Edison at NERSC demonstrate ideal scaling when problem size is increased along with processor number up to the largest power of 2 available, namely 131,072 processors. These particle weak scaling benchmarks also indicate that the 1 nanosecond per particle per time step and 1 TFlops barriers are easily broken by UCAN2 with 1 billion particles or more and 2000 or more processors.This work was supported in part in the USA by Grant No. DE-FG02-04ER54741 to the University of Alaska, Fairbanks, AK, from the Office of Fusion Energy Sciences, Office of Science, United States Department of Energy. It was also supported in part at Universidad Carlos III, Madrid, Spain, by Spanish National Project No. ENE2009-12213-C03-03. This research used resources of the National Energy Research Scientific Computing Center (NERSC), which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. It also took advantage of resources at the Barcelona Supercomputing Center (BSC), Centro Nacional de Supercomputación, Barcelona, Spain. One of us (Leboeuf) would particularly like to thank David Vicente from BSC and Zhengji Zhao from NERSC for their help in the porting, debugging, and optimization of UCAN2 on the mainframes at their respective centers

Low-pH cement mortar-bentonite perturbations in a small-scale pilot laboratory experiment

This article has been published in a revised form in Clay Minerals [http://doi.org/10.1180/clm.2018.16]. This version is free to view and download for private research and study only. Not for re-distribution, re-sale or use in derivative worksA novel method to perform small-scale laboratory experiments that reproduce concrete–bentonite and concrete–groundwater interactions has been developed. Such interfaces will prevail in engineered barrier systems used for isolation of nuclear waste. With the goal of optimizing the experimental method, this work has analysed the geochemical interaction of distilled water, low-pH cement mortar and FEBEX-bentonite for 75 days. Limited but evident reactivity between the materials was observed, mainly decalcification in cement mortar, carbonation at the interface with bentonite and Mg enrichment in bentonite. These results are consistent with the state-of-the-art literature and were used to validate this small-scale pilot laboratory experiment to establish the basis for further studies comparing the behaviour of different buffer and cement materialsThe research leading to these results has received funding from the European Union's Horizon 2020 Research and Training 305 Programme of the EURATOM (H2020-NFRP-2014/2015) under grant agreement n° 662147 (CEBAMA

The behavior of kinetic parameters in production of pectinase and xylanase by solid-state fermentation

AbstractSolid-state fermentation (SSF) is defined as the growth of microbes without a free-flowing aqueous phase. The feasibility of using a citrus peel for producing pectinase and xylanase via the SSF process by Aspergillus niger F3 was evaluated in a 2kg bioreactor. Different aeration conditions were tested to optimize the pectinase and xylanase production. The best air flow intensity was 1VkgM (volumetric air flow per kilogram of medium), which allowed a sufficient amount of O2 for the microorganism growth producing 265U/g and 65U/g pectinases and xylanases, respectively. A mathematical model was applied to determine the different kinetic parameters related to SSF. The specific growth rate and biomass oxygen yield decreased during fermentation, whereas an increase in the maintenance coefficient for the different employed carbon sources was concurrently observed

Fourier signature of filamentary vorticity structures in two-dimensional turbulence

It is shown that coherent regions of isotropic two-dimensional (2D) turbulence can be clearly identified in the phase part of the Fourier spectrum. Certain spectral phase events are particularly prominent, and are much stronger in the range of wave numbers corresponding to the dissipation range. It is shown that these events are associated with spatially localized filamentary structures in the 2D vorticity field that historically have been related to the intermittency of dissipation. The identified phase signature provides a particularly transparent diagnostic of the temporal evolution of the coherent coupling of disparate scales in anisostropic intermittent dissipative events. These results open the possibility of using the phase of the Fourier transform as a new turbulence diagnostic that identifies and quantitatively characterizes details pertaining to dissipative events.Research supported in part by the Spanish national projects No. ENE2009-12213-C03-03, ENE2012-33219, UNC313-4E-2361 and ENE2012-31753 and the US DOE Office of Science Grants No. DE-FG02-04ER54741 and DE-FG02-89ER53291. Simulations run at the Uranus supercomputer cluster at Universidad Carlos III de Madrid

Role of ¿1-pyrroline-5-carboxylate dehydrogenase supports mitochondrial metabolism and host-cell invasion of Trypanosoma cruzi

Proline is crucial for energizing critical events throughout the life cycle of Trypanosoma cruzi, the etiological agent of Chagas disease. The proline breakdown pathway consists of two oxidation steps, both of which produce reducing equivalents as follows: the conversion of proline to ¿1-pyrroline-5-carboxylate (P5C), and the subsequent conversion of P5C to glutamate. We have identified and characterized the ¿1-pyrroline-5-carboxy- late dehydrogenase from T. cruzi (TcP5CDH) and report here on how this enzyme contributes to a central metabolic pathway in this parasite. Size-exclusion chromatography, two-dimen- sional gel electrophoresis, and small angle x-ray scattering analysis of TcP5CDH revealed an oligomeric state composed of two subunits of six protomers. TcP5CDH was found to complement a yeast strain deficient in PUT2 activity, confirming the enzyme’s functional role; and the biochemical parameters (Km, kcat, and kcat/Km) of the recombinant TcP5CDH were determined, exhibiting values comparable with those from T. cruzi lysates. In addition, TcP5CDH exhibited mitochondrial staining during the main stages of the T. cruzi life cycle. mRNA and enzymatic activity levels indicated the up-regulation (6-fold change) of TcP5CDH during the infective stages of the parasite. The participation of P5C as an energy source was also demonstrated. Overall, we propose that this enzymatic step is crucial for the viability of both replicative and infective forms of T. cruzi

Rearranging Edgeworth-Cornish-Fisher Expansions

This paper applies a regularization procedure called increasing rearrangement to monotonize Edgeworth and Cornish-Fisher expansions and any other related approximations of distribution and quantile functions of sample statistics. Besides satisfying the logical monotonicity, required of distribution and quantile functions, the procedure often delivers strikingly better approximations to the distribution and quantile functions of the sample mean than the original Edgeworth-Cornish-Fisher expansions.Comment: 17 pages, 3 figure