Lattice Boltzmann simulation of flow around bluff-bodies

In this work, results from a 2-D Lattice Boltzmann (LB) solver are presented simulating flow past rectangular square cylinders at low Reynolds numbers (\u3c 250). The LBGK equation is a hyperbolic equation that approximates the Navier Stokes equations in the nearly incompressible limit. It is a system of 9 one dimensional partial differential Hamiltonian-Jacobian equations, consisting of an advection and diffusive portion. The LB method is an alternative computational fluid dynamics (CFD) method used to numerically predict incompressible viscous flow. The current LB method uses a statistical mechanics formulation to solve the Boltzmann equation. The LB model captures the nonlinear Navier Stokes advection terms using linear streaming operators. In this thesis, the LB model is classified as an explicit, Lagrangian, finite-hyperbolicity and weakly compressible approximation of the Navier Stokes equations. The momentum flux tensor is captured locally as opposed to a pressure field eliminating the need to solve the Poisson equation. This allows the fluid structure interactions (FSI) behavior to be calculated elegantly at the interface through the mesoscopic momentum transfer between the fluid and structure. At this level, the forces are simultaneously calculated. The LB equations are discretized both in time and phase space using a standard D2Q9 lattice model. Validation tests for flow around single square cylinders at different aspect ratio at low Reynolds numbers are presented. Good agreement with other investigators is achieved. Flow past multiple bluff bodies (representing building in a city) is also presented. The vortex shedding simulations presented provide preliminary indications in terms of St that the LB method can be used to simulate high Re flow

Lattice Boltzmann modeling for shallow water equations using high performance computing

The aim of this dissertation project is to extend the standard Lattice Boltzmann method (LBM) for shallow water flows in order to deal with three dimensional flow fields. The shallow water and mass transport equations have wide applications in ocean, coastal, and hydraulic engineering, which can benefit from the advantages of the LBM. The LBM has recently become an attractive numerical method to solve various fluid dynamics phenomena; however, it has not been extensively applied to modeling shallow water flow and mass transport. Only a few works can be found on improving the LBM for mass transport in shallow water flows and even fewer on extending it to model three dimensional shallow water flow fields. The application of the LBM to modeling the shallow water and mass transport equations has been limited because it is not clearly understood how the LBM solves the shallow water and mass transport equations. The project first focuses on studying the importance of choosing enhanced collision operators such as the multiple-relaxation-time (MRT) and two-relaxation-time (TRT) over the standard single-relaxation-time (SRT) in LBM. A (MRT) collision operator is chosen for the shallow water equations, while a (TRT) method is used for the advection-dispersion equation. Furthermore, two speed-of-sound techniques are introduced to account for heterogeneous and anisotropic dispersion coefficients. By selecting appropriate equilibrium distribution functions, the standard LBM is extended to solve three-dimensional wind-driven and density-driven circulation by introducing a multi-layer LB model. A MRT-LBM model is used to solve for each layer coupled by the vertical viscosity forcing term. To increase solution stability, an implicit step is suggested to obtain stratified flow velocities. Numerical examples are presented to verify the multi-layer LB model against analytical solutions. The model’s capability of calculating lateral and vertical distributions of the horizontal velocities is demonstrated for wind- and density- driven circulation over non-uniform bathymetry. The parallel performance of the LBM on central processing unit (CPU) based and graphics processing unit (GPU) based high performance computing (HPC) architectures is investigated showing attractive performance in relation to speedup and scalability

Inflammasomes Coordinate Pyroptosis and Natural Killer Cell Cytotoxicity to Clear Infection by a Ubiquitous Environmental Bacterium

Defective neutrophils in patients with chronic granulomatous disease (CGD) cause susceptibility to extracellular and intracellular infections. Microbes must first be ejected from intracellular niches to expose them to neutrophil attack, so we hypothesized that inflammasomes detect certain CGD pathogens upstream of neutrophil killing. Here, we identified one such ubiquitous environmental bacterium, Chromobacterium violaceum, whose extreme virulence was fully counteracted by the NLRC4 inflammasome. Caspase-1 protected via two parallel pathways that eliminated intracellular replication niches. Pyroptosis was the primary bacterial clearance mechanism in the spleen, but both pyroptosis and interleukin-18 (IL-18)-driven natural killer (NK) cell responses were required for liver defense. NK cells cleared hepatocyte replication niches via perforin-dependent cytotoxicity, whereas interferon-γ was not required. These insights suggested a therapeutic approach: exogenous IL-18 restored perforin-dependent cytotoxicity during infection by the inflammasome-evasive bacterium Listeria monocytogenes. Therefore, inflammasomes can trigger complementary programmed cell death mechanisms, directing sterilizing immunity against intracellular bacterial pathogens

Galaxy Zoo: dust and molecular gas in early-type galaxies with prominent dust lanes

We study dust and associated molecular gas in 352 nearby early-type galaxies (ETGs) with prominent dust lanes. 65% of these `dusty ETGs' (D-ETGs) are morphologically disturbed, suggesting a merger origin. This is consistent with the D-ETGs residing in lower density environments compared to the controls drawn from the general ETG population. 80% of D-ETGs inhabit the field (compared to 60% of the controls) and <2% inhabit clusters (compared to 10% of the controls). Compared to the controls, D-ETGs exhibit bluer UV-optical colours (indicating enhanced star formation) and an AGN fraction that is more than an order of magnitude greater (indicating higher incidence of nuclear activity). The clumpy dust mass residing in large-scale features is estimated, using the SDSS r-band images, to be 10^{4.5}-10^{6.5} MSun. A comparison to the total (clumpy + diffuse) dust masses- calculated using the far-IR fluxes of 15% of the D-ETGs that are detected by the IRAS- indicates that only ~20% of the dust resides in these large-scale features. The dust masses are several times larger than the maximum value expected from stellar mass loss, ruling out an internal origin. The dust content shows no correlation with the blue luminosity, indicating that it is not related to a galactic scale cooling flow. No correlation is found with the age of the recent starburst, suggesting that the dust is accreted directly in the merger rather than being produced in situ by the triggered star formation. Using molecular gas-to-dust ratios of ETGs in the literature we estimate that the median current and initial molecular gas fraction are ~1.3% and ~4%, respectively. Recent work suggests that the merger activity in nearby ETGs largely involves minor mergers (mass ratios between 1:10 and 1:4). If the IRAS-detected D-ETGs form via this channel, then the original gas fractions of the accreted satellites are 20%-44%. [Abridged]Comment: 11 pages, 18 figures, 1 table, MNRAS (Accepted for publication- 2012 March 19

Autologous Transplantation as Consolidation for Aggressive Non-Hodgkin's Lymphoma

The efficacy of autologous stem-cell transplantation during the first remission in patients with diffuse, aggressive non-Hodgkin's lymphoma classified as high-intermediate risk or high risk on the International Prognostic Index remains controversial and is untested in the rituximab era

Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution.

Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists

MRT-Lattice Boltzmann Model for Multilayer Shallow Water Flow

The objectives of this study are to introduce a multiple-relaxation-time (MRT) lattice Boltzmann model (LBM) to simulate multilayer shallow water flows and to introduce graphics processing unit (GPU) computing to accelerate the lattice Boltzmann model. Using multiple relaxation times in the lattice Boltzmann model has an advantage of handling very low kinematic viscosity without causing a stability problem in the shallow water equations. This study develops a multilayer MRT-LBM to solve the multilayer Saint-Venant equations to obtain horizontal flow velocities in various depths. In the multilayer MRT-LBM, vertical kinematic viscosity forcing is the key term to couple adjacent layers. We implemented the multilayer MRT-LBM to a GPU-based high-performance computing (HPC) architecture. The multilayer MRT-LBM was verified by analytical solutions for cases of wind-driven, density-driven, and combined circulations with non-uniform bathymetry. The results show good speedup and scalability for large problems. Numerical solutions compared well to the analytical solutions. The multilayer MRT-LBM is promising for simulating lateral and vertical distributions of the horizontal velocities in shallow water flow

The Accessory Nerve: A Comprehensive Review of its Anatomy, Development, Variations, Landmarks and Clinical Considerations.

INTRODUCTION: The eleventh cranial nerve, the accessory nerve, has a complex and unique anatomy and has been the subject of much debate. Herein, we review the morphology, embryology, surgical anatomy, and clinical manifestations of the accessory nerve. Included in this review, we mention variant anatomy, molecular development, histology, and imaging of the accessory nerve. CONCLUSIONS: The accessory nerve continues to be a topic of much discussion regarding its exact function and in particular to its cranial roots. Recently, various surgical procedures have been devised that repurpose the accessory nerve (e.g., lengthening procedures, contralateral neurotization procedures). Currently, we continue to learn and have much to learn about this lower cranial nerve. Anat Rec, 302:620-629, 2019. © 2018 Wiley Periodicals, Inc

Anatomical study of the mastoid foramina and mastoid emissary veins: classification and application to localizing the sigmoid sinus

: The mastoid foramen (MF) is located on the mastoid process of the temporal bone, adjacent to the occipitomastoid suture or the parietomastoid suture, and contains the mastoid emissary vein (MEV). In retrosigmoid craniotomy, the MEV has been used to localize the position of the sigmoid sinus and, thus, the placement of the initial burr hole. Therefore, this study aimed to examine the exact location and variants of the MF and MEV to determine if their use in localizing the sigmoid sinus is reasonable. The sample in this study comprised 22 adult dried skulls (44 sides). MF were identified and classified into five types based on location, prevalence, whether they communicated with the sigmoid sinus and exact entrance into the groove of the sigmoid sinus. The diameters and relative locations of the MF in the skull were measured and recorded. Finally, the skulls were drilled to investigate the course of the MEV. Additionally, ten latex-injected sides from human cadavers were also dissected to follow the MEV, especially in cases with more than one vein. We found that type I MFs (single foramen) were the most prevalent (50%). These MFs were mainly located on the occipitomastoid suture; only one case on the right side was adjacent to the parietomastoid suture. Type II (paired foramina) was the second most prevalent (22.73%), followed by type III (13.64%), type 0 (9.09%), and type IV (4.55%). The diameter of the external opening in a connecting MF (2.43 ± 0.79) was twice that of a non-connecting MF (1.14 ± 0.56). Interestingly, on one side, two MFs on the external surface shared a single internal opening; the MEV bifurcated. MFs followed three different courses: ascending, almost horizontal, and descending. Regardless of how many external openings there were for the MF, these all ended at a single opening in the groove for the sigmoid sinus. For cadaveric specimens with multiple MEVs, all terminated in the sigmoid sinus as a single vein, with the more medial veins terminating more medially into the sinus. Based on our study, the MF/MEV can guide the surgeon and help localize the deeper-lying sigmoid sinus. Knowledge of this anatomical relationship could be an adjunct to neuronavigational technologies