URANS calculations for smooth circular cylinder flow in a wide range of Reynolds Numbers: solution verification and validation

The flow around circular smooth fixed cylinder in a large range of Reynolds numbers is considered in this paper. In order to investigate this canonical case, we perform CFD calculations and apply verification & validation (V&V) procedures to draw conclusions regarding numerical error and, afterwards, assess the modeling errors and capabilities of this (U)RANS method to solve the problem. Eight Reynolds numbers between Re = 10 and Re 5 x 10(5) will be presented with, at least, four geometrically similar grids and five discretization in time for each case (when unsteady), together with strict control of iterative and round-off errors, allowing a consistent verification analysis with uncertainty estimation. Two-dimensional RANS, steady or unsteady, laminar or turbulent calculations are performed. The original 1994 k - omega SST turbulence model by Menter is used to model turbulence. The validation procedure is performed by comparing the numerical results with an extensive set of experimental results compiled from the literature. [DOI: 10.1115/1.4007571]

Modeling of continuous thermal processing of a non-Newtonian liquid food under diffusive laminar flow in a tubular system

The classic conservative approach for thermal process design can lead to over-processing, especially for laminar flow, when a significant distribution of temperature and of residence time occurs. In order to optimize quality retention, a more comprehensive model is required. A model comprising differential equations for mass and heat transfer is proposed for the simulation of the continuous thermal processing of a non-Newtonian food in a tubular system. The model takes into account the contribution from heating and cooling sections, the heat exchange with the ambient air and effective diffusion associated with non-ideal laminar flow. The study case of soursop juice processing was used to test the model. Various simulations were performed to evaluate the effect of the model assumptions. An expressive difference in the predicted lethality was observed between the classic approach and the proposed model. The main advantage of the model is its flexibility to represent different aspects with a small computational time, making it suitable for process evaluation and design. (C) 2012 Elsevier Ltd. All rights reserved.

Flow Boiling Characteristics for R1234ze(E) in 1.0 and 2.2 mm Circular Channels

Experimental flow boiling heat transfer results are presented for horizontal 1.0 and 2.2 mm I. D. (internal diameter) stainless steel tubes for tests with R1234ze(E), a new refrigerant developed as a substitute for R134a with a much lower global warming potential (GWP). The experiments were performed for these two tube diameters in order to investigate a possible transition between macro and microscale flow boiling behavior. The experimental campaign includes mass velocities ranging from 50 to 1500 kg/m(2) s, heat fluxes from 10 to 300 kW/m(2), exit saturation temperatures of 25, 31 and 35 degrees C, vapor qualities from 0.05 to 0.99 and heated lengths of 180 mm and 361 mm. Flow pattern characterization was performed using high speed videos. Heat transfer coefficient, critical heat flux and flow pattern data were obtained. R1234ze(E) demonstrated similar thermal performance to R134a data when running at similar conditions. [DOI: 10.1115/1.4004933]

Inclusive charged hadron elliptic flow in Au+Au collisions at root s(NN)=7.7-39 GeV

A systematic study is presented for centrality, transverse momentum (p(T)), and pseudorapidity (eta) dependence of the inclusive charged hadron elliptic flow (v(2)) at midrapidity (vertical bar eta vertical bar < 1.0) in Au + Au collisions at root s(NN) = 7.7, 11.5, 19.6, 27, and 39 GeV. The results obtained with different methods, including correlations with the event plane reconstructed in a region separated by a large pseudorapidity gap and four-particle cumulants (v(2){4}), are presented to investigate nonflow correlations and v(2) fluctuations. We observe that the difference between v(2){2} and v(2){4} is smaller at the lower collision energies. Values of v(2), scaled by the initial coordinate space eccentricity, v(2)/epsilon, as a function of p(T) are larger in more central collisions, suggesting stronger collective flow develops in more central collisions, similar to the results at higher collision energies. These results are compared to measurements at higher energies at the Relativistic Heavy Ion Collider (root s(NN) = 62.4 and 200 GeV) and at the Large Hadron Collider (Pb + Pb collisions at root s(NN) = 2.76 TeV). The v(2)(pT) values for fixed pT rise with increasing collision energy within the pT range studied (<2 GeV/c). A comparison to viscous hydrodynamic simulations is made to potentially help understand the energy dependence of v(2)(pT). We also compare the v(2) results to UrQMD and AMPT transport model calculations, and physics implications on the dominance of partonic versus hadronic phases in the system created at beam energy scan energies are discussed.

Application of magnetically induced hyperthermia in the model protozoan Crithidia fasciculata as a potential therapy against parasitic infections

Background: Magnetic hyperthermia is currently a clinical therapy approved in the European Union for treatment of tumor cells, and uses magnetic nanoparticles (MNPs) under time-varying magnetic fields (TVMFs). The same basic principle seems promising against trypanosomatids causing Chagas disease and sleeping sickness, given that the therapeutic drugs available have severe side effects and that there are drug-resistant strains. However, no applications of this strategy against protozoan-induced diseases have been reported so far. In the present study, Crithidia fasciculata, a widely used model for therapeutic strategies against pathogenic trypanosomatids, was targeted with Fe3O4 MNPs in order to provoke cell death remotely using TVMFs. Methods: Iron oxide MNPs with average diameters of approximately 30 nm were synthesized by precipitation of FeSO4 in basic medium. The MNPs were added to C. fasciculata choanomastigotes in the exponential phase and incubated overnight, removing excess MNPs using a DEAE-cellulose resin column. The amount of MNPs uploaded per cell was determined by magnetic measurement. The cells bearing MNPs were submitted to TVMFs using a homemade AC field applicator (f = 249 kHz, H = 13 kA/m), and the temperature variation during the experiments was measured. Scanning electron microscopy was used to assess morphological changes after the TVMF experiments. Cell viability was analyzed using an MTT colorimetric assay and flow cytometry. Results: MNPs were incorporated into the cells, with no noticeable cytotoxicity. When a TVMF was applied to cells bearing MNPs, massive cell death was induced via a nonapoptotic mechanism. No effects were observed by applying TVMF to control cells not loaded with MNPs. No macroscopic rise in temperature was observed in the extracellular medium during the experiments. Conclusion: As a proof of principle, these data indicate that intracellular hyperthermia is a suitable technology to induce death of protozoan parasites bearing MNPs. These findings expand the possibilities for new therapeutic strategies combating parasitic infection.

Directed Flow of Identified Particles in Au plus Au Collisions at root S-NN=200 GeV at RHIC

STAR's measurements of directed flow (v(1)) around midrapidity for pi(+/-), K-+/-, K-S(0), p, and (p) over bar in Au + Au collisions at root s(NN) = 200 GeV are presented. A negative v(1) (y) slope is observed for most of produced particles (pi(+/-), K-+/-, K-S(0), p, and (p) over bar). In 5%-30% central collisions, a sizable difference is present between the v(1)(y) slope of protons and antiprotons, with the former being consistent with zero within errors. The v(1) excitation function is presented. Comparisons to model calculations (RQMD, UrQMD, AMPT, QGSM with parton recombination, and a hydrodynamics model with a tilted source) are made. For those models which have calculations of v(1) for both pions and protons, none of them can describe v(1()y) forpions and protons simultaneously. The hydrodynamics model with a tilted source as currently implemented cannot explain the centrality dependence of the difference between the v(1)(y) slopes of protons and antiprotons.

Anisotropic Flow in Event-by-Event Ideal Hydrodynamic Simulations of root s(NN) 200 GeV Au+Au Collisions

We simulate top-energy Au + Au collisions using ideal hydrodynamics in order to make the first comparison to the complete set of midrapidity flow measurements made by the PHENIX Collaboration. A simultaneous calculation of nu(2), nu(3), nu(4), and the first event-by-event calculation of quadrangular flow defined with respect to the nu(2) event plane (nu(4){Psi(2)}) gives good agreement with measured values, including the dependence on both transverse momentum and centrality. This provides confirmation that the collision system is indeed well described as a quark-gluon plasma with an extremely small viscosity and that correlations are dominantly generated from collective effects. In addition, we present a prediction for nu(5).

Modeling gene expression regulatory networks with the sparse vector autoregressive model

Abstract Background To understand the molecular mechanisms underlying important biological processes, a detailed description of the gene products networks involved is required. In order to define and understand such molecular networks, some statistical methods are proposed in the literature to estimate gene regulatory networks from time-series microarray data. However, several problems still need to be overcome. Firstly, information flow need to be inferred, in addition to the correlation between genes. Secondly, we usually try to identify large networks from a large number of genes (parameters) originating from a smaller number of microarray experiments (samples). Due to this situation, which is rather frequent in Bioinformatics, it is difficult to perform statistical tests using methods that model large gene-gene networks. In addition, most of the models are based on dimension reduction using clustering techniques, therefore, the resulting network is not a gene-gene network but a module-module network. Here, we present the Sparse Vector Autoregressive model as a solution to these problems. Results We have applied the Sparse Vector Autoregressive model to estimate gene regulatory networks based on gene expression profiles obtained from time-series microarray experiments. Through extensive simulations, by applying the SVAR method to artificial regulatory networks, we show that SVAR can infer true positive edges even under conditions in which the number of samples is smaller than the number of genes. Moreover, it is possible to control for false positives, a significant advantage when compared to other methods described in the literature, which are based on ranks or score functions. By applying SVAR to actual HeLa cell cycle gene expression data, we were able to identify well known transcription factor targets. Conclusion The proposed SVAR method is able to model gene regulatory networks in frequent situations in which the number of samples is lower than the number of genes, making it possible to naturally infer partial Granger causalities without any a priori information. In addition, we present a statistical test to control the false discovery rate, which was not previously possible using other gene regulatory network models.

Parallel implementation of a robust optical flow technique

[EN] The accuracy and performance of current variational optical ow methods have considerably increased during the last years. The complexity of these techniques is high and enough care has to be taken for the implementation. The aim of this work is to present a comprehensible implementation of recent variational optical flow methods. We start with an energy model that relies on brightness and gradient constancy terms and a ow-based smoothness term. We minimize this energy model and derive an e cient implicit numerical scheme. In the experimental results, we evaluate the accuracy and performance of this implementation with the Middlebury benchmark database. We show that it is a competitive solution with respect to current methods in the literature. In order to increase the performance, we use a simple strategy to parallelize the execution on multi-core processors.

3D reconstruction from a vascular tree model

[EN] In this paper, we present a vascular tree model made with synthetic materials and which allows us to obtain images to make a 3D reconstruction.We have used PVC tubes of several diameters and lengths that will let us evaluate the accuracy of our 3D reconstruction. In order to calibrate the camera we have used a corner detector. Also we have used Optical Flow techniques to follow the points through the images going and going back. We describe two general techniques to extract a sequence of corresponding points from multiple views of an object. The resulting sequence of points will be used later to reconstruct a set of 3D points representing the object surfaces on the scene. We have made the 3D reconstruction choosing by chance a couple of images and we have calculated the projection error. After several repetitions, we have found the best 3D location for the point.

Model of vessels for the 3D reconstruction

[EN] In this paper, we present a vascular tree model made with synthetic materials and which allows us to obtain images to make a 3D reconstruction. In order to create this model, we have used PVC tubes of several diameters and lengths that will let us evaluate the accuracy of our 3D reconstruction. We have made the 3D reconstruction from a series of images that we have from our model and after we have calibrated the camera. In order to calibrate it we have used a corner detector. Also we have used Optical Flow techniques to follow the points through the images going and going back. Once we have the set of images where we have located a point, we have made the 3D reconstruction choosing by chance a couple of images and we have calculated the projection error. After several repetitions, we have found the best 3D location for the point.

A PDE model for computing the optical flow

[EN] In this paper we present a new model for optical flow calculation using a variational formulation which preserves discontinuities of the flow much better than classical methods. We study the Euler-Lagrange equations asociated to the variational problem. In the case of quadratic energy, we show the existence and uniqueness of the corresponding evolution problem. Since our method avoid linearization in the optical flow constraint, it can recover large displacement in the scene. We avoid convergence to irrelevant local minima by embedding our method into a linear scale-space framework and using a focusing strategy from coarse to fine scales.

Reduced-order modelling, circuit-level design and SOI fabrication of microelectromechanical resonators

This thesis deals with two important research aspects concerning radio frequency (RF) microresonators and switches. First, a new approach for compact modeling and simulation of these devices is presented. Then, a combined process flow for their simultaneous fabrication on a SOI substrate is proposed. Compact models for microresonators and switches are extracted by applying mathematical model order reduction (MOR) to the devices finite element (FE) description in ANSYS c° . The behaviour of these devices includes forms of nonlinearities. However, an approximation in the creation of the FE model is introduced, which enables the use of linear model order reduction. Microresonators are modeled with the introduction of transducer elements, which allow for direct coupling of the electrical and mechanical domain. The coupled system element matrices are linearized around an operating point and reduced. The resulting macromodel is valid for small signal analysis around the bias point, such as harmonic pre-stressed analysis. This is extremely useful for characterizing the frequency response of resonators. Compact modelling of switches preserves the nonlinearity of the device behaviour. Nonlinear reduced order models are obtained by reducing the number of nonlinearities in the system and handling them as input to the system. In this way, the system can be reduced using linear MOR techniques and nonlinearities are introduced directly in the reduced order model. The reduction of the number of system nonlinearities implies the approximation of all distributed forces in the model with lumped forces. Both for microresonators and switches, a procedure for matrices extraction has been developed so that reduced order models include the effects of electrical and mechanical pre-stress. The extraction process is fast and can be done automatically from ANSYS binary files. The method has been applied for the simulation of several devices both at devices and circuit level. Simulation results have been compared with full model simulations, and, when available, experimental data. Reduced order models have proven to conserve the accuracy of finite element method and to give a good description of the overall device behaviour, despite the introduced approximations. In addition, simulation is very fast, both at device and circuit level. A combined process-flow for the integrated fabrication of microresonators and switches has been defined. For this purpose, two processes that are optimized for the independent fabrication of these devices are merged. The major advantage of this process is the possibility to create on-chip circuit blocks that include both microresonators and switches. An application is, for example, aswitched filter bank for wireless transceiver. The process for microresonators fabrication is characterized by the use of silicon on insulator (SOI) wafers and on a deep reactive ion etching (DRIE) step for the creation of the vibrating structures in single-crystal silicon and the use of a sacrificial oxide layer for the definition of resonator to electrode distance. The fabrication of switches is characterized by the use of two different conductive layers for the definition of the actuation electrodes and by the use of a photoresist as a sacrificial layer for the creation of the suspended structure. Both processes have a gold electroplating step, for the creation of the resonators electrodes, transmission lines and suspended structures. The combined process flow is designed such that it conserves the basic properties of the original processes. Neither the performance of the resonators nor the performance of the switches results affected by the simultaneous fabrication. Moreover, common fabrication steps are shared, which allows for cheaper and faster fabrication.

Study of apoptotic deletion mediated by Bifidobacterium longum with construction of recombinant strains for Serpin encoding gene and phenotypes comparison in a pig cell model

The first part of the research project of the Co-Advisorship Ph.D Thesis was aimed to select the best Bifidobacterium longum strains suitable to set the basis of our study. We were looking for strains with the abilities to colonize the intestinal mucosa and with good adhesion capacities, so that we can test these strains to investigate their ability to induce apoptosis in “damaged” intestinal cells. Adhesion and apoptosis are the two process that we want to study to better understand the role of an adhesion protein that we have previously identified and that have top scores homologies with the recent serpin encoding gene identified in B. longum by Nestlè researchers. Bifidobacterium longum is a probiotic, known for its beneficial effects to the human gut and even for its immunomodulatory and antitumor activities. Recently, many studies have stressed out the intimate relation between probiotic bacteria and the GIT mucosa and their influence on human cellular homeostasis. We focused on the apoptotic deletion of cancer cells induced by B. longum. This has been valued in vitro, performing the incubation of three B.longum strains with enterocyte-like Caco- 2 cells, to evidence DNA fragmentation, a cornerstone of apoptosis. The three strains tested were defined for their adhesion properties using adhesion and autoaggregation assays. These features are considered necessary to select a probiotic strain. The three strains named B12, B18 and B2990 resulted respectively: “strong adherent”, “adherent” and “non adherent”. Then, bacteria were incubated with Caco-2 cells to investigate apoptotic deletion. Cocultures of Caco-2 cells with B. longum resulted positive in DNA fragmentation test, only when adherent strains were used (B12 and B18). These results indicate that the interaction with adherent B. longum can induce apoptotic deletion of Caco-2 cells, suggesting a role in cellular homeostasis of the gastrointestinal tract and in restoring the ecology of damaged colon tissues. These results were used to keep on researching and the strains tested were used as recipient of recombinant techniques aimed to originate new B.longum strains with enhanced capacity of apoptotic induction in “damaged” intestinal cells. To achieve this new goal it was decided to clone the serpin encoding gene of B. longum, so that we can understand its role in adhesion and apoptosis induction. Bifidobacterium longum has immunostimulant activity that in vitro can lead to apoptotic response of Caco-2 cell line. It secretes a hypothetical eukaryotic type serpin protein, which could be involved in this kind of deletion of damaged cells. We had previously characterised a protein that has homologies with the hypothetical serpin of B. longum (DD087853). In order to create Bifidobacterium serpin transformants, a B. longum cosmid library was screened with a PCR protocol using specific primers for serpin gene. After fragment extraction, the insert named S1 was sub-cloned into pRM2, an Escherichia coli - Bifidobacterium shuttle vector, to construct pRM3. Several protocols for B. longum transformation were performed and the best efficiency was obtained using MRS medium and raffinose. Finally bacterial cell supernatants were tested in a dotblot assay to detect antigens presence against anti-antitrypsin polyclonal antibody. The best signal was produced by one starin that has been renamed B. longum BLKS 7. Our research study was aimed to generate transformants able to over express serpin encoding gene, so that we can have the tools for a further study on bacterial apoptotic induction of Caco-2 cell line. After that we have originated new trasformants the next step to do was to test transformants abilities when exposed to an intestinal cell model. In fact, this part of the project was achieved in the Department of Biochemistry of the Medical Faculty of the University of Maribor, guest of the abroad supervisor of the Co-Advisorship Doctoral Thesis: Prof. Avrelija Cencic. In this study we examined the probiotic ability of some bacterial strains using intestinal cells from a 6 years old pig. The use of intestinal mammalian cells is essential to study this symbiosis and a functional cell model mimics a polarised epithelium in which enterocytes are separated by tight junctions. In this list of strains we have included the Bifidobacterium longum BKS7 transformant strain that we have previously originated; in order to compare its abilities. B. longum B12 wild type and B. longum BKS7 transformant and eight Lactobacillus strains of different sources were co-cultured with porcine small intestine epithelial cells (PSI C1) and porcine blood monocytes (PoM2) in Transwell filter inserts. The strains, including Lb. gasseri, Lb. fermentum, Lb. reuterii, Lb. plantarum and unidentified Lactobacillus from kenyan maasai milk and tanzanian coffee, were assayed for activation of cell lines, measuring nitric oxide by Griess reaction, H202 by tetramethylbenzidine reaction and O2 - by cytochrome C reduction. Cytotoxic effect by crystal violet staining and induction on metabolic activity by MTT cell proliferation assay were tested too. Transepithelial electrical resistance (TER) of polarised PSI C1 was measured during 48 hours co-culture. TER, used to observe epithelium permeability, decrease during pathogenesis and tissue becomes permeable to ion passive flow lowering epithelial barrier function. Probiotics can prevent or restore increased permeability. Lastly, dot-blot was achieved against Interleukin-6 of treated cells supernatants. The metabolic activity of PoM2 and PSI C1 increased slightly after co-culture not affecting mitochondrial functions. No strain was cytotoxic over PSI C1 and PoM2 and no cell activation was observed, as measured by the release of NO2, H202 and O2 - by PoM2 and PSI C1. During coculture TER of polarised PSI C1 was two-fold higher comparing with constant TER (~3000 ) of untreated cells. TER raise generated by bacteria maintains a low permeability of the epithelium. During treatment Interleukin-6 was detected in cell supernatants at several time points, confirming immunostimulant activity. All results were obtained using Lactobacillus paracasei Shirota e Carnobacterium divergens as controls. In conclusion we can state that both the list of putative probiotic bacteria and our new transformant strain of B. longum are not harmful when exposed to intestinal cells and could be selected as probiotics, because can strengthen epithelial barrier function and stimulate nonspecific immunity of intestinal cells on a pig cell model. Indeed, we have found out that none of the strains tested that have good adhesion abilities presents citotoxicity to the intestinal cells and that non of the strains tested can induce cell lines to produce high level of ROS, neither NO2. Moreover we have assayed even the capacity of producing certain citokynes that are correlated with immune response. The detection of Interleukin-6 was assayed in all our samples, including B.longum transformant BKS 7 strain, this result indicates that these bacteria can induce a non specific immune response in the intestinal cells. In fact, when we assayed the presence of Interferon-gamma in cells supernatant after bacterial exposure, we have no positive signals, that means that there is no activation of a specific immune response, thus confirming that these bacteria are not recognize as pathogen by the intestinal cells and are certainly not harmful for intestinal cells. The most important result is the measure of Trans Epithelial Electric Resistance that have shown how the intestinal barrier function get strengthen when cells are exposed to bacteria, due to a reduction of the epithelium permeability. We have now a new strain of B. longum that will be used for further studies above the mechanism of apoptotic induction to “damaged cells” and above the process of “restoring ecology”. This strain will be the basis to originate new transformant strains for Serpin encoding gene that must have better performance and shall be used one day even in clinical cases as in “gene therapy” for cancer treatment and prevention.

Two fluid numerical model for coastal applications

Wave breaking is an important coastal process, influencing hydro-morphodynamic processes such as turbulence generation and wave energy dissipation, run-up on the beach and overtopping of coastal defence structures. During breaking, waves are complex mixtures of air and water (“white water”) whose properties affect velocity and pressure fields in the vicinity of the free surface and, depending on the breaker characteristics, different mechanisms for air entrainment are usually observed. Several laboratory experiments have been performed to investigate the role of air bubbles in the wave breaking process (Chanson & Cummings, 1994, among others) and in wave loading on vertical wall (Oumeraci et al., 2001; Peregrine et al., 2006, among others), showing that the air phase is not negligible since the turbulent energy dissipation involves air-water mixture. The recent advancement of numerical models has given valuable insights in the knowledge of wave transformation and interaction with coastal structures. Among these models, some solve the RANS equations coupled with a free-surface tracking algorithm and describe velocity, pressure, turbulence and vorticity fields (Lara et al. 2006 a-b, Clementi et al., 2007). The single-phase numerical model, in which the constitutive equations are solved only for the liquid phase, neglects effects induced by air movement and trapped air bubbles in water. Numerical approximations at the free surface may induce errors in predicting breaking point and wave height and moreover, entrapped air bubbles and water splash in air are not properly represented. The aim of the present thesis is to develop a new two-phase model called COBRAS2 (stands for Cornell Breaking waves And Structures 2 phases), that is the enhancement of the single-phase code COBRAS0, originally developed at Cornell University (Lin & Liu, 1998). In the first part of the work, both fluids are considered as incompressible, while the second part will treat air compressibility modelling. The mathematical formulation and the numerical resolution of the governing equations of COBRAS2 are derived and some model-experiment comparisons are shown. In particular, validation tests are performed in order to prove model stability and accuracy. The simulation of the rising of a large air bubble in an otherwise quiescent water pool reveals the model capability to reproduce the process physics in a realistic way. Analytical solutions for stationary and internal waves are compared with corresponding numerical results, in order to test processes involving wide range of density difference. Waves induced by dam-break in different scenarios (on dry and wet beds, as well as on a ramp) are studied, focusing on the role of air as the medium in which the water wave propagates and on the numerical representation of bubble dynamics. Simulations of solitary and regular waves, characterized by both spilling and plunging breakers, are analyzed with comparisons with experimental data and other numerical model in order to investigate air influence on wave breaking mechanisms and underline model capability and accuracy. Finally, modelling of air compressibility is included in the new developed model and is validated, revealing an accurate reproduction of processes. Some preliminary tests on wave impact on vertical walls are performed: since air flow modelling allows to have a more realistic reproduction of breaking wave propagation, the dependence of wave breaker shapes and aeration characteristics on impact pressure values is studied and, on the basis of a qualitative comparison with experimental observations, the numerical simulations achieve good results.