Assessment of a high-order MUSCL method for rotor flows

This work presents the implementation of a high-order, finite-volume scheme suitable for rotor flows. The formulation is based on the variable extrapolation MUSCL-scheme, where high-order spatial accuracy (up to 4th-order) is achieved using correction terms obtained through successive differentiation. A variety of results are presented, including two-and three-dimensional test cases. Results with the proposed scheme, showed better wake and higher resolution of vortical structures compared with the standard MUSCL, even when coarse meshes were employed. The method was also demonstrated for three-dimensional unsteady flows using overset and moving grids for the UH-60A rotor in forward flight and the ERICA tiltrotor in aeroplane mode. For medium grids, the present method adds reasonable CPU and memory overheads and offers good accuracy on relatively coarse grids

Impact of fully coupled hydrology-atmosphere processes on atmosphere conditions: investigating the performance of the WRF-Hydro model in the Three River source region on the Tibetan Plateau, China

The newly developed WRF-Hydro model is a fully coupled atmospheric and hydrological processes model suitable for studying the intertwined atmospheric hydrological processes. This study utilizes the WRF-Hydro system on the Three-River source region. The Nash-Sutcliffe efficiency for the runoff simulation is 0.55 compared against the observed daily discharge amount of three stations. The coupled WRF-Hydro simulations are better than WRF in terms of six ground meteorological elements and turbulent heat flux, compared to the data from 14 meteorological stations located in the plateau residential area and two flux stations located around the lake. Although WRF-Hydro overestimates soil moisture, higher anomaly correlation coefficient scores (0.955 versus 0.941) were achieved. The time series of the basin average demonstrates that the hydrological module of WRF-hydro functions during the unfrozen period. The rainfall intensity and frequency simulated by WRF-Hydro are closer to global precipitation mission (GPM) data, attributed to higher convective available potential energy (CAPE) simulated by WRF-Hydro. The results emphasized the necessity of a fully coupled atmospheric-hydrological model when investigating land-atmosphere interactions on a complex topography and hydrology region

On the fourth-order accurate compact ADI scheme for solving the unsteady Nonlinear Coupled Burgers' Equations

The two-dimensional unsteady coupled Burgers' equations with moderate to severe gradients, are solved numerically using higher-order accurate finite difference schemes; namely the fourth-order accurate compact ADI scheme, and the fourth-order accurate Du Fort Frankel scheme. The question of numerical stability and convergence are presented. Comparisons are made between the present schemes in terms of accuracy and computational efficiency for solving problems with severe internal and boundary gradients. The present study shows that the fourth-order compact ADI scheme is stable and efficient

Investigation of low-dissipation monotonicity-preserving scheme for direct numerical simulation of compressible turbulent flows

© 2014 Elsevier Ltd. The influence of numerical dissipation on direct numerical simulation (DNS) of decaying isotropic turbulence and turbulent channel flow is investigated respectively by using the seventh-order low-dissipation monotonicity-preserving (MP7-LD) scheme with different levels of bandwidth dissipation. It is found that for both benchmark test cases, small-scale turbulence fluctuations can be largely suppressed by high level of scheme dissipation, while the appearance of numerical errors in terms of high-frequency oscillations could destabilize the computation if the dissipation is reduced to a very low level. Numerical studies show that reducing the bandwidth dissipation to 70% of the conventional seventh-order upwind scheme can maximize the efficiency of the MP7-LD scheme in resolving small-scale turbulence fluctuations and, in the meantime preventing the accumulation of non-physical numerical errors. By using the optimized MP7-LD scheme, DNS of an impinging oblique shock-wave interacting with a spatially-developing turbulent boundary layer is conducted at an incoming free-stream Mach number of 2.25 and the shock angle of 33.2°. Simulation results of mean velocity profiles, wall surface pressure, skin friction and Reynolds stresses are validated against available experimental data and other DNS predictions in both the undisturbed equilibrium boundary layer region and the interaction zone, and good agreements are achieved. The turbulence kinetic energy transport equation is also analyzed and the balance of the equation is well preserved in the interaction region. This study demonstrates the capability of the optimized MP7-LD scheme for DNS of complex flow problems of wall-bounded turbulent flow interacting with shock-waves

CABARET in the ocean gyres

Author Posting. © The Author(s), 2009. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Ocean Modelling 30 (2009): 155-168, doi:10.1016/j.ocemod.2009.06.009.A new high-resolution Eulerian numerical method is proposed for modelling quasigeostrophic ocean dynamics in eddying regimes. The method is based on a novel, second-order non-dissipative and lowdispersive conservative advection scheme called CABARET. The properties of the new method are compared with those of several high-resolution Eulerian methods for linear advection and gas dynamics. Then, the CABARET method is applied to the classical model of the double-gyre ocean circulation and its performance is contrasted against that of the common vorticity-preserving Arakawa method. In turbulent regimes, the new method permits credible numerical simulations on much coarser computational grids.Supports from the Royal Society of London and from the Mary Sears Visitor Grant are acknowledged by SK with gratitude. The work of VG was supported by the Russian Foundation for Basic Research (RFBR), grant 06-01-00819a. Funding for PB was provided by the NSF grant 0725796

An intelligent interface for integrating climate, hydrology, agriculture, and socioeconomic models

Understanding the interactions between natural processes and human activities poses major challenges as it requires the integration of models and data across disparate disciplines. It typically takes many months and even years to create valid end-to-end simulations as different models need to be configured in consistent ways and generate data that is usable by other models. MINT is a novel framework for model integration that captures extensive knowledge about models and data and aims to automatically compose them together. MINT guides a user to pose a well-formed modeling question, select and configure appropriate models, find and prepare appropriate datasets, compose data and models into end-to-end workflows, run the simulations, and visualize the results. MINT currently includes hydrology, agriculture, and socioeconomic models.Office of the VP for Researc

Essential genes for astroglial development and axon pathfinding during zebrafish embryogenesis

The formation of the central nervous system depends on the coordinated development of neural and glial cell types that arise from a common precursor. Using an existing group of zebrafish mutants generated by viral insertion, we performed a “shelf-screen” to identify genes necessary for astroglial development and axon scaffold formation. We screened 274 of 315 viral insertion lines using antibodies that label axons (anti-Acetylated Tubulin) and astroglia (anti-Gfap) and identified 25 mutants with defects in gliogenesis, glial patterning, neurogenesis, and axon guidance. We also identified a novel class of mutants affecting radial glial cell numbers. Defects in astroglial patterning were always associated with axon defects, supporting an important role for axon-glial interactions during axon scaffold development. The genes disrupted in these viral lines have all been identified, providing a powerful new resource for the study of axon guidance, glio- and neurogenesis, and neuron-glial interactions during development of the vertebrate CNS.National Institutes of Health (U.S.) (Grant T32MH020051)National Institutes of Health (U.S.) (Grant F32NS043872

Network-Based Integration of GWAS and Gene Expression Identifies a HOX-Centric Network Associated with Serous Ovarian Cancer Risk

BACKGROUND: Genome-wide association studies (GWAS) have so far reported 12 loci associated with serous epithelial ovarian cancer (EOC) risk. We hypothesized that some of these loci function through nearby transcription factor (TF) genes and that putative target genes of these TFs as identified by coexpression may also be enriched for additional EOC risk associations. METHODS: We selected TF genes within 1 Mb of the top signal at the 12 genome-wide significant risk loci. Mutual information, a form of correlation, was used to build networks of genes strongly coexpressed with each selected TF gene in the unified microarray dataset of 489 serous EOC tumors from The Cancer Genome Atlas. Genes represented in this dataset were subsequently ranked using a gene-level test based on results for germline SNPs from a serous EOC GWAS meta-analysis (2,196 cases/4,396 controls). RESULTS: Gene set enrichment analysis identified six networks centered on TF genes (HOXB2, HOXB5, HOXB6, HOXB7 at 17q21.32 and HOXD1, HOXD3 at 2q31) that were significantly enriched for genes from the risk-associated end of the ranked list (P < 0.05 and FDR < 0.05). These results were replicated (P < 0.05) using an independent association study (7,035 cases/21,693 controls). Genes underlying enrichment in the six networks were pooled into a combined network. CONCLUSION: We identified a HOX-centric network associated with serous EOC risk containing several genes with known or emerging roles in serous EOC development. IMPACT: Network analysis integrating large, context-specific datasets has the potential to offer mechanistic insights into cancer susceptibility and prioritize genes for experimental characterization

Assessment of variation in immunosuppressive pathway genes reveals TGFBR2 to be associated with risk of clear cell ovarian cancer

BACKGROUND: Regulatory T (Treg) cells, a subset of CD4+ T lymphocytes, are mediators of immunosuppression in cancer, and, thus, variants in genes encoding Treg cell immune molecules could be associated with ovarian cancer. METHODS: In a population of 15,596 epithelial ovarian cancer (EOC) cases and 23,236 controls, we measured genetic associations of 1,351 SNPs in Treg cell pathway genes with odds of ovarian cancer and tested pathway and gene-level associations, overall and by histotype, for the 25 genes, using the admixture likelihood (AML) method. The most significant single SNP associations were tested for correlation with expression levels in 44 ovarian cancer patients. RESULTS: The most significant global associations for all genes in the pathway were seen in endometrioid (p = 0.082) and clear cell (p = 0.083), with the most significant gene level association seen with TGFBR2 (p = 0.001) and clear cell EOC. Gene associations with histotypes at p < 0.05 included: IL12 (p = 0.005 and p = 0.008, serous and high-grade serous, respectively), IL8RA (p = 0.035, endometrioid and mucinous), LGALS1 (p = 0.03, mucinous), STAT5B (p = 0.022, clear cell), TGFBR1 (p = 0.021 endometrioid) and TGFBR2 (p = 0.017 and p = 0.025, endometrioid and mucinous, respectively). CONCLUSIONS: Common inherited gene variation in Treg cell pathways shows some evidence of germline genetic contribution to odds of EOC that varies by histologic subtype and may be associated with mRNA expression of immune-complex receptor in EOC patients