Shear-based model for electron transport in hybrid hall thruster simulations

Abstract-An electron cross-field transport model based on instantaneous simulated plasma properties is incorporated into a radial-axial hybrid simulation of a Hall plasma thruster. The model is used to capture the reduction of fluctuation-based anomalous transport that is seen experimentally in the region of high axial shear in the electron fluid. Similar transport barriers are observed by the magnetic confinement fusion community due to shear suppression of plasma turbulence through an increase in the decorrelation rate of plasma eddies. The model assumes that the effective Hall parameter can be computed as the sum of the classical term, a near-wall conductivity term, and a fluctuationbased term that includes the effect of shear. A comparison is made between shear-based, experimental, and Bohm-type models for cross-field transport. Although the shear-based model predicts a wider transport barrier than experimentally observed, overall, it better predicts measured plasma properties than the Bohm model, particularly in the case of electron temperature and electric potential. The shear-based transport model also better predicts the breathing-mode oscillations and time-averaged discharge current than both the Bohm and experimental mobility models. The plasma property that is most sensitive to adjustment of the fitting parameters used in the shear-based model is the plasma density. Applications of these fitting parameters in other operating conditions and thruster geometries are examined in order to determine the robustness and portability of the model. Without changing the fitting parameters, the simulation was able to reproduce macroscopic properties, such as thrust and efficiency, of an SPT-100-type thruster within 30% and match qualitative expectations for a bismuth-fueled Hall thruster

Universality classes in nonequilibrium lattice systems

This work is designed to overview our present knowledge about universality classes occurring in nonequilibrium systems defined on regular lattices. In the first section I summarize the most important critical exponents, relations and the field theoretical formalism used in the text. In the second section I briefly address the question of scaling behavior at first order phase transitions. In section three I review dynamical extensions of basic static classes, show the effect of mixing dynamics and the percolation behavior. The main body of this work is given in section four where genuine, dynamical universality classes specific to nonequilibrium systems are introduced. In section five I continue overviewing such nonequilibrium classes but in coupled, multi-component systems. Most of the known nonequilibrium transition classes are explored in low dimensions between active and absorbing states of reaction-diffusion type of systems. However by mapping they can be related to universal behavior of interface growth models, which I overview in section six. Finally in section seven I summarize families of absorbing state system classes, mean-field classes and give an outlook for further directions of research.Comment: Updated comprehensive review, 62 pages (two column), 29 figs included. Scheduled for publication in Reviews of Modern Physics in April 200

Short-term changes in polysaccharide utilization mechanisms of marine bacterioplankton during a spring phytoplankton bloom

Spring phytoplankton blooms in temperate environments contribute disproportionately to global marine productivity. Bloom-derived organic matter, much of it occurring as polysaccharides, fuels biogeochemical cycles driven by interacting autotrophic and heterotrophic communities. We tracked changes in the mode of polysaccharide utilization by heterotrophic bacteria during the course of a diatom-dominated bloom in the German Bight, North Sea. Polysaccharides can be taken up in a ‘selfish’ mode, where initial hydrolysis is coupled to transport into the periplasm, such that little to no low-molecular weight (LMW) products are externally released to the environment. Alternatively, polysaccharides hydrolyzed by cell-surface attached or free extracellular enzymes (external hydrolysis) yield LMW products available to the wider bacterioplankton community. In the early bloom phase, selfish activity was accompanied by low extracellular hydrolysis rates of a few polysaccharides. As the bloom progressed, selfish uptake increased markedly, and external hydrolysis rates increased, but only for a limited range of substrates. The late bloom phase was characterized by high external hydrolysis rates of a broad range of polysaccharides and reduced selfish uptake of polysaccharides, except for laminarin. Substrate utilization mode is related both to substrate structural complexity and to the bloom-stage dependent composition of the heterotrophic bacterial community

Stochastic processes with finite correlation time: modeling and application to the generalized Langevin equation

The kangaroo process (KP) is characterized by various forms of the covariance and can serve as a useful model of random noises. We discuss properties of that process for the exponential, stretched exponential and algebraic (power-law) covariances. Then we apply the KP as a model of noise in the generalized Langevin equation and simulate solutions by a Monte Carlo method. Some results appear to be incompatible with requirements of the fluctuation-dissipation theorem because probability distributions change when the process is inserted into the equation. We demonstrate how one can construct a model of noise free of that difficulty. This form of the KP is especially suitable for physical applications.Comment: 22 pages (RevTeX) and 4 figure

Mapping gene associations in human mitochondria using clinical disease phenotypes

Nuclear genes encode most mitochondrial proteins, and their mutations cause diverse and debilitating clinical disorders. To date, 1,200 of these mitochondrial genes have been recorded, while no standardized catalog exists of the associated clinical phenotypes. Such a catalog would be useful to develop methods to analyze human phenotypic data, to determine genotype-phenotype relations among many genes and diseases, and to support the clinical diagnosis of mitochondrial disorders. Here we establish a clinical phenotype catalog of 174 mitochondrial disease genes and study associations of diseases and genes. Phenotypic features such as clinical signs and symptoms were manually annotated from full-text medical articles and classified based on the hierarchical MeSH ontology. This classification of phenotypic features of each gene allowed for the comparison of diseases between different genes. In turn, we were then able to measure the phenotypic associations of disease genes for which we calculated a quantitative value that is based on their shared phenotypic features. The results showed that genes sharing more similar phenotypes have a stronger tendency for functional interactions, proving the usefulness of phenotype similarity values in disease gene network analysis. We then constructed a functional network of mitochondrial genes and discovered a higher connectivity for non-disease than for disease genes, and a tendency of disease genes to interact with each other. Utilizing these differences, we propose 168 candidate genes that resemble the characteristic interaction patterns of mitochondrial disease genes. Through their network associations, the candidates are further prioritized for the study of specific disorders such as optic neuropathies and Parkinson disease. Most mitochondrial disease phenotypes involve several clinical categories including neurologic, metabolic, and gastrointestinal disorders, which might indicate the effects of gene defects within the mitochondrial system. The accompanying knowledgebase (http://www.mitophenome.org/) supports the study of clinical diseases and associated genes

Integrative Analysis of the Mitochondrial Proteome in Yeast

In this study yeast mitochondria were used as a model system to apply, evaluate, and integrate different genomic approaches to define the proteins of an organelle. Liquid chromatography mass spectrometry applied to purified mitochondria identified 546 proteins. By expression analysis and comparison to other proteome studies, we demonstrate that the proteomic approach identifies primarily highly abundant proteins. By expanding our evaluation to other types of genomic approaches, including systematic deletion phenotype screening, expression profiling, subcellular localization studies, protein interaction analyses, and computational predictions, we show that an integration of approaches moves beyond the limitations of any single approach. We report the success of each approach by benchmarking it against a reference set of known mitochondrial proteins, and predict approximately 700 proteins associated with the mitochondrial organelle from the integration of 22 datasets. We show that a combination of complementary approaches like deletion phenotype screening and mass spectrometry can identify over 75% of the known mitochondrial proteome. These findings have implications for choosing optimal genome-wide approaches for the study of other cellular systems, including organelles and pathways in various species. Furthermore, our systematic identification of genes involved in mitochondrial function and biogenesis in yeast expands the candidate genes available for mapping Mendelian and complex mitochondrial disorders in humans

LINT, a Novel dL(3)mbt-Containing Complex, Represses Malignant Brain Tumour Signature Genes

Mutations in the l(3)mbt tumour suppressor result in overproliferation of Drosophila larval brains. Recently, the derepression of different gene classes in l(3)mbt mutants was shown to be causal for transformation. However, the molecular mechanisms of dL(3)mbt-mediated gene repression are not understood. Here, we identify LINT, the major dL(3)mbt complex of Drosophila. LINT has three core subunits—dL(3)mbt, dCoREST, and dLint-1—and is expressed in cell lines, embryos, and larval brain. Using genome-wide ChIP–Seq analysis, we show that dLint-1 binds close to the TSS of tumour-relevant target genes. Depletion of the LINT core subunits results in derepression of these genes. By contrast, histone deacetylase, histone methylase, and histone demethylase activities are not required to maintain repression. Our results support a direct role of LINT in the repression of brain tumour-relevant target genes by restricting promoter access

A functional insulator screen identifies NURF and dREAM components to be required for enhancer-blocking

Chromatin insulators of higher eukaryotes functionally divide the genome into active and inactive domains. Furthermore, insulators regulate enhancer/promoter communication, which is evident from the Drosophila bithorax locus in which a multitude of regulatory elements control segment specific gene activity. Centrosomal protein 190 (CP190) is targeted to insulators by CTCF or other insulator DNA-binding factors. Chromatin analyses revealed that insulators are characterized by open and nucleosome depleted regions. Here, we wanted to identify chromatin modification and remodelling factors required for an enhancer blocking function. We used the well-studied Fab-8 insulator of the bithorax locus to apply a genome-wide RNAi screen for factors that contribute to the enhancer blocking function of CTCF and CP190. Among 78 genes required for optimal Fab-8 mediated enhancer blocking, all four components of the NURF complex as well as several subunits of the dREAM complex were most evident. Mass spectrometric analyses of CTCF or CP190 bound proteins as well as immune precipitation confirmed NURF and dREAM binding. Both co-localise with most CP190 binding sites in the genome and chromatin immune precipitation showed that CP190 recruits NURF and dREAM. Nucleosome occupancy and histone H3 binding analyses revealed that CP190 mediated NURF binding results in nucleosomal depletion at CP190 binding sites. Thus, we conclude that CP190 binding to CTCF or to other DNA binding insulator factors mediates recruitment of NURF and dREAM. Furthermore, the enhancer blocking function of insulators is associated with nucleosomal depletion and requires NURF and dREAM

Ultra-broad near-infrared photoluminescence from crystalline (K-crypt)2Bi2 containing [Bi2]2- dimers

For the first time, we report that a single crystal of (K-crypt)2Bi2 containing [Bi2]2+ displays ultra-broad near-infrared photoluminescence (PL) peaking at around 1190 nm and having a full width at the half maximum of 212 nm, stemming from the inherent electronic transitions of [Bi2]2+.The results not only add to the number of charged Bi species with luminescence, but also deepen the understanding of Bi-related near-infrared emission behavior and lead to the reconsideration of the fundamentally important issue of Bi-related PL mechanisms in some material systems such as bulk glasses, fibers, and conventional optical crystals