Two-dimensional turbulence in magnetised plasmas

In an inhomogeneous magnetised plasma the transport of energy and particles perpendicular to the magnetic field is in general mainly caused by quasi two-dimensional turbulent fluid mixing. The physics of turbulence and structure formation is of ubiquitous importance to every magnetically confined laboratory plasma for experimental or industrial application. Specifically, high temperature plasmas for fusion energy research are also dominated by the properties of this turbulent transport. Self-organisation of turbulent vortices to mesoscopic structures like zonal flows is related to the formation of transport barriers that can significantly enhance the confinement of a fusion plasma. This subject of great importance in research is rarely touched on in introductory plasma physics or continuum dynamics courses. Here a brief tutorial on 2D fluid and plasma turbulence is presented as an introduction to the field, appropriate for inclusion in undergraduate and graduate courses.Comment: This is an author-created, un-copyedited version of an article published in European Journal of Physics. IOP Publishing Ltd is not responsible for any errors or omissions in this version of the manuscript or any version derived from it. The definitive publisher authenticated version is available online at doi: 10.1088/0143-0807/29/5/00

ELM triggering conditions for the integrated modeling of H-mode plasmas

Recent advances in the integrated modeling of ELMy H-mode plasmas are presented. A model for the H-mode pedestal and for the triggering of ELMs predicts the height, width, and shape of the H-mode pedestal and the frequency and width of ELMs. Formation of the pedestal and the L-H transition is the direct result of ExB flow shear suppression of anomalous transport. The periodic ELM crashes are triggered by either the ballooning or peeling MHD instabilities. The BALOO, DCON, and ELITE ideal MHD stability codes are used to derive a new parametric expression for the peeling-ballooning threshold. The new dependence for the peeling-ballooning threshold is implemented in the ASTRA transport code. Results of integrated modeling of DIII-D like discharges are presented and compared with experimental observations. The results from the ideal MHD stability codes are compared with results from the resistive MHD stability code NIMROD.Comment: 12th International Congress on Plasma Physics, 25-29 October 2004, Nice (France

Composite Skyrme Model with Vector Mesons

We study the composite Skyrme model, proposed by Cheung and G\"{u}rsey, introducing vector mesons in a chiral Lagrangian. We calculate the static properties of baryons and compare with results obtained from models without vector mesons.Comment: LaTeX, 9 pages, 3 figures, to be published in Phys. Rev.

Gyrokinetic Simulation of Global Turbulent Transport Properties in Tokamak Experiments

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

Pathophysiology of acute experimental pancreatitis: Lessons from genetically engineered animal models and new molecular approaches

The incidence of acute pancreatitis is growing and worldwide population-based studies report a doubling or tripling since the 1970s. 25% of acute pancreatitis are severe and associated with histological changes of necrotizing pancreatitis. There is still no specific medical treatment for acute pancreatitis. The average mortality resides around 10%. In order to develop new specific medical treatment strategies for acute pancreatitis, a better understanding of the pathophysiology during the onset of acute pancreatitis is necessary. Since it is difficult to study the early acinar events in human pancreatitis, several animal models of acute pancreatitis have been developed. By this, it is hoped that clues into human pathophysiology become possible. In the last decade, while employing molecular biology techniques, a major progress has been made. The genome of the mouse was recently sequenced. Various strategies are possible to prove a causal effect of a single gene or protein, using either gain-of-function (i.e., overexpression of the protein of interest) or loss-of-function studies (i.e., genetic deletion of the gene of interest). The availability of transgenic mouse models and gene deletion studies has clearly increased our knowledge about the pathophysiology of acute pancreatitis and enables us to study and confirm in vitro findings in animal models. In addition, transgenic models with specific genetic deletion or overexpression of genes help in understanding the role of one specific protein in a cascade of inflammatory processes such as pancreatitis where different proteins interact and co-react. This review summarizes the recent progress in this field. Copyright (c) 2005 S. Karger AG, Basel

Depression and the vision-related quality of life in patients with retinitis pigmentosa

AIMS: To assess the relationship between depression and the vision-related quality of life in patients with retinitis pigmentosa (RP). METHODS: The study included 144 patients diagnosed as having RP. The mean age of the patients was 38.5 (SD 13.3) years, and 42% of the subjects were women. They answered the National Eye Institute Visual Function Questionnaire (NEI-VFQ) to assess the vision-related quality of life and the Beck Depression Inventory (BDI) to assess depressive symptoms. Patients were classified into groups with and without depression according to the BDI score. The NEI-VFQ composite and subscale scores were compared between groups. The correlations between the BDI and the NEI-VFQ, weighted visual acuity (WVA) and functional vision score (FVS) were investigated. RESULTS: The depressed group had significantly less subjective visual function compared with the non-depressed group. A negative correlation was observed between the BDI and the NEI-VFQ scores, while no correlation was found between the BDI score and WVA or FVS. CONCLUSION: The RP patients with depression had poorer vision-related functions compared with those patients without depression, which cannot be explained by the visual acuity. Interventions to diagnose and treat depression are necessary to enhance the overall quality of life in RP patients

Inclusion of bedrock vadose zone in dynamic global vegetation models is key for simulating vegetation structure and function

Across many upland environments, soils are thin and plant roots extend into fractured and weathered bedrock where moisture and nutrients can be obtained. Root water extraction from unsaturated weathered bedrock is widespread and, in many environments, can explain gradients in vegetation community composition, transpiration, and plant sensitivity to climate. Despite increasing recognition of its importance, the “rock moisture” reservoir is rarely incorporated into vegetation and Earth system models. Here, we address this weakness in a widely used dynamic global vegetation model (DGVM; LPJ-GUESS). First, we use a water flux-tracking deficit approach to more accurately parameterize plant-accessible water storage capacity across the contiguous United States, which critically includes the water in bedrock below depths typically prescribed by soil databases. Secondly, we exploit field-based knowledge of contrasting plant-available water storage capacity in weathered bedrock across two bedrock types in the Northern California Coast Ranges as a detailed case study. For the case study in Northern California, climate and soil water storage capacity are similar at the two study areas, but the site with thick weathered bedrock and ample rock moisture supports a temperate mixed broadleaf–needleleaf evergreen forest, whereas the site with thin weathered bedrock and limited rock moisture supports an oak savanna. The distinct biomes, seasonality and magnitude of transpiration and primary productivity, and baseflow magnitudes only emerge from the DGVM when a new and simple subsurface storage structure and hydrology scheme is parameterized with storage capacities extending beyond the soil into the bedrock. Across the contiguous United States, the updated hydrology and subsurface storage improve annual evapotranspiration estimates as compared to satellite-derived products, particularly in seasonally dry regions. Specifically, the updated hydrology and subsurface storage allow for enhanced evapotranspiration through the dry season that better matches actual evapotranspiration patterns. While we made changes to both the subsurface water storage capacity and the hydrology, the most important impacts on model performance derive from changes to the subsurface water storage capacity. Our findings highlight the importance of rock moisture in explaining and predicting vegetation structure and function, particularly in seasonally dry climates. These findings motivate efforts to better incorporate the rock moisture reservoir into vegetation, climate, and landscape evolution models.</p

Finite-Element Modelling of Biotransistors

Current research efforts in biosensor design attempt to integrate biochemical assays with semiconductor substrates and microfluidic assemblies to realize fully integrated lab-on-chip devices. The DNA biotransistor (BioFET) is an example of such a device. The process of chemical modification of the FET and attachment of linker and probe molecules is a statistical process that can result in variations in the sensed signal between different BioFET cells in an array. In order to quantify these and other variations and assess their importance in the design, complete physical simulation of the device is necessary. Here, we perform a mean-field finite-element modelling of a short channel, two-dimensional BioFET device. We compare the results of this model with one-dimensional calculation results to show important differences, illustrating the importance of the molecular structure, placement and conformation of DNA in determining the output signal

Size Scaling of Turbulent Transport in Magnetically Confined Plasmas

Transport scaling with respect to device size in magnetically confined plasmas is critically examined for electrostatic ion temperature gradient turbulence using global gyrokinetic particle simulations. It is found, by varying device size normalized by ion gyroradius while keeping other dimensionless plasma parameters fixed, that fluctuation scale length is microscopic in the presence of zonal flows. The local transport coefficient exhibits a gradual transition from a Bohm-like scaling for device sizes corresponding to present-day experiments to a gyro-Bohm scaling for future larger devices

DNA-decorated carbon nanotubes for chemical sensing

We demonstrate a new, versatile class of nanoscale chemical sensors based on single-stranded DNA (ss-DNA) as the chemical sensors recognition site and single-walled carbon nanotube field effect transistors (swCN-FET) as the electronic read-out component. swCN-FETs with a nanoscale coating of ss-DNA respond to gas odors that do not cause a detectable conductivity change in bare devices. Responses of ss-DNA/swCN-FETs differ in sign and magnitude for different gases, and can be tuned by choosing the base sequence of the ss-DNA. ss-DNA/swCN-FET sensors detect a variety of odors, with rapid response and recovery times on the scale of seconds. The sensor surface is self-regenerating: samples maintain a constant response with no need for sensor refreshing through at least 50 gas exposure cycles. This very remarkable set of attributes makes sensors based on ss-DNA decorated nanotubes very promising for "electronic nose" and "electronic tongue" applications ranging from homeland security to disease diagnosis.Comment: 9 pages, 5 figures, Nano Letters web release: 23-Aug-200