Model reduction for nonlinear aerodynamics and aeroelasticity using a Discrete Empirical Interpolation Method

A novel surrogate model is proposed in lieu of Computational Fluid Dynamics (CFD) solvers, for fast nonlinear aerodynamic and aeroelastic modeling. A nonlinear function is identified on selected interpolation points by
a discrete empirical interpolation method (DEIM). The flow field is then reconstructed using a least square approximation of the flow modes extracted
by proper orthogonal decomposition (POD). The aeroelastic reduce order
model (ROM) is completed by introducing a nonlinear mapping function
between displacements and the DEIM points. The proposed model is investigated to predict the aerodynamic forces due to forced motions using
a N ACA 0012 airfoil undergoing a prescribed pitching oscillation. To investigate aeroelastic problems at transonic conditions, a pitch/plunge airfoil
and a cropped delta wing aeroelastic models are built using linear structural models. The presence of shock-waves triggers the appearance of limit
cycle oscillations (LCO), which the model is able to predict. For all cases
tested, the new ROM shows the ability to replicate the nonlinear aerodynamic forces, structural displacements and reconstruct the complete flow
field with sufficient accuracy at a fraction of the cost of full order CFD
model.

Monitoring and model updating of an FRP pedestrian truss bridge

This paper presents the results of a real bridge field experiment, carried out on a fiber reinforced polymer (FRP) pedestrian truss bridge of which nodes are reinforced with stainless steel plates. The aim of this paper is to identify the dynamic parameters of this bridge by using both conventional techniques and a model updating algorithm. In the field experiment, the bridge was instrumented with accelerometers at a number of locations on the bridge deck, recording both vertical and transverse vibrations. It was excited via jump tests at particular locations along its span and the resulting acceleration signals are used to identify dynamic parameters, such as the bridge mode shape, natural frequency and damping constant. Pedestrianinduced vibrations are also measured and utilized to identify dynamic parameters of the bridge. For a complete analysis of the bridge, a numerical model of the FRP bridge is created whose properties are calibrated utilizing a model updating algorithm. Comparable frequencies and mode shapes to those from the experiment were obtained by the FE models considering the reinforcement by increasing elastic modulus at every node of the bridge by stainless steel plate. Moreover, considering boundary conditions at both ends as fixed in the model resulted in modal properties comparable/similar to those from the experiment. This study also demonstrated that the effect of reinforcement and boundary conditions must be properly considered in an FE model to analyze real behavior of the FRP bridge.

The FIREDASS (Fire Detection and Suppression Simulation) Model

The FIREDASS (FIRE Detection And Suppression Simulation) project is concerned with the development of fine water mist systems as a possible replacement for the halon fire suppression system currently used in aircraft cargo holds. The project is funded by the European Commission, under the BRITE EURAM programme. The FIREDASS consortium is made up of a combination of Industrial, Academic, Research and Regulatory partners. As part of this programme of work, a computational model has been developed to help engineers optimise the design of the water mist suppression system. This computational model is based on Computational Fluid Dynamics (CFD) and is composed of the following components: fire model; mist model; two-phase radiation model; suppression model and detector/activation model. The fire model - developed by the University of Greenwich - uses prescribed release rates for heat and gaseous combustion products to represent the fire load. Typical release rates have been determined through experimentation conducted by SINTEF. The mist model - developed by the University of Greenwich - is a Lagrangian particle tracking procedure that is fully coupled to both the gas phase and the radiation field. The radiation model - developed by the National Technical University of Athens - is described using a six-flux radiation model. The suppression model - developed by SINTEF and the University of Greenwich - is based on an extinguishment crietrion that relies on oxygen concentration and temperature. The detector/ activation model - developed by Cerberus - allows the configuration of many different detector and mist configurations to be tested within the computational model. These sub-models have been integrated by the University of Greenwich into the FIREDASS software package. The model has been validated using data from the SINTEF/GEC test campaigns and it has been found that the computational model gives good agreement with these experimental results. The best agreement is obtained at the ceiling which is where the detectors and misting nozzles would be located in a real system. In this paper the model is briefly described and some results from the validation of the fire and mist model are presented.

Investigating disease persistence in host vector systems: dengue as a case study

The investigation of pathogen persistence in vector-borne diseases is important in different ecological and epidemiological contexts. In this thesis, I have developed deterministic and stochastic models to help investigating the pathogen persistence in host-vector systems by using efficient modelling paradigms. A general introduction with aims and objectives of the studies conducted in the thesis are provided in Chapter 1. The mathematical treatment of models used in the thesis is provided in Chapter 2 where the models are found locally asymptotically stable. The models used in the rest of the thesis are based on either the same or similar mathematical structure studied in this chapter. After that, there are three different experiments that are conducted in this thesis to study the pathogen persistence. In Chapter 3, I characterize pathogen persistence in terms of the Critical Community Size (CCS) and find its relationship with the model parameters. In this study, the stochastic versions of two epidemiologically different host-vector models are used for estimating CCS. I note that the model parameters and their algebraic combination, in addition to the seroprevalence level of the host population, can be used to quantify CCS. The study undertaken in Chapter 4 is used to estimate pathogen persistence using both deterministic and stochastic versions of a model with seasonal birth rate of the vectors. Through stochastic simulations we investigate the pattern of epidemics after the introduction of an infectious individual at different times of the year. The results show that the disease dynamics are altered by the seasonal variation. The higher levels of pre-existing seroprevalence reduces the probability of invasion of dengue. In Chapter 5, I considered two alternate ways to represent the dynamics of a host-vector model. Both of the approximate models are investigated for the parameter regions where the approximation fails to hold. Moreover, three metrics are used to compare them with the Full model. In addition to the computational benefits, these approximations are used to investigate to what degree the inclusion of the vector population in the dynamics of the system is important. Finally, in Chapter 6, I present the summary of studies undertaken and possible extensions for the future work.

Bumps and rings in a two-dimensional neural field: splitting and rotational instabilities

In this paper we consider instabilities of localised solutions in planar neural field firing rate models of Wilson-Cowan or Amari type. Importantly we show that angular perturbations can destabilise spatially localised solutions. For a scalar model with Heaviside firing rate function we calculate symmetric one-bump and ring solutions explicitly and use an Evans function approach to predict the point of instability and the shapes of the dominant growing modes. Our predictions are shown to be in excellent agreement with direct numerical simulations. Moreover, beyond the instability our simulations demonstrate the emergence of multi-bump and labyrinthine patterns. With the addition of spike-frequency adaptation, numerical simulations of the resulting vector model show that it is possible for structures without rotational symmetry, and in particular multi-bumps, to undergo an instability to a rotating wave. We use a general argument, valid for smooth firing rate functions, to establish the conditions necessary to generate such a rotational instability. Numerical continuation of the rotating wave is used to quantify the emergent angular velocity as a bifurcation parameter is varied. Wave stability is found via the numerical evaluation of an associated eigenvalue problem.

A SCR Model based on Reactor and Engine Experimental Studies for a Cu-zeolite Catalyst

A NOx reduction efficiency higher than 95% with NH3 slip less than 30 ppm is desirable for heavy-duty diesel (HDD) engines using selective catalytic reduction (SCR) systems to meet the US EPA 2010 NOx standard and the 2014-2018 fuel consumption regulation. The SCR performance needs to be improved through experimental and modeling studies. In this research, a high fidelity global kinetic 1-dimensional 2-site SCR model with mass transfer, heat transfer and global reaction mechanisms was developed for a Cu-zeolite catalyst. The model simulates the SCR performance for the engine exhaust conditions with NH3 maldistribution and aging effects, and the details are presented. SCR experimental data were collected for the model development, calibration and validation from a reactor at Oak Ridge National Laboratory (ORNL) and an engine experimental setup at Michigan Technological University (MTU) with a Cummins 2010 ISB engine. The model was calibrated separately to the reactor and engine data. The experimental setup, test procedures including a surrogate HD-FTP cycle developed for transient studies and the model calibration process are described. Differences in the model parameters were determined between the calibrations developed from the reactor and the engine data. It was determined that the SCR inlet NH3 maldistribution is one of the reasons causing the differences. The model calibrated to the engine data served as a basis for developing a reduced order SCR estimator model. The effect of the SCR inlet NO2/NOx ratio on the SCR performance was studied through simulations using the surrogate HD-FTP cycle. The cumulative outlet NOx and the overall NOx conversion efficiency of the cycle are highest with a NO2/NOx ratio of 0.5. The outlet NH3 is lowest for the NO2/NOx ratio greater than 0.6. A combined engine experimental and simulation study was performed to quantify the NH3 maldistribution at the SCR inlet and its effects on the SCR performance and kinetics. The uniformity index (UI) of the SCR inlet NH3 and NH3/NOx ratio (ANR) was determined to be below 0.8 for the production system. The UI was improved to 0.9 after installation of a swirl mixer into the SCR inlet cone. A multi-channel model was developed to simulate the maldistribution effects. The results showed that reducing the UI of the inlet ANR from 1.0 to 0.7 caused a 5-10% decrease in NOx reduction efficiency and 10-20 ppm increase in the NH3 slip. The simulations of the steady-state engine data with the multi-channel model showed that the NH3 maldistribution is a factor causing the differences in the calibrations developed from the engine and the reactor data. The Reactor experiments were performed at ORNL using a Spaci-IR technique to study the thermal aging effects. The test results showed that the thermal aging (at 800°C for 16 hours) caused a 30% reduction in the NH3 stored on the catalyst under NH3 saturation conditions and different axial concentration profiles under SCR reaction conditions. The kinetics analysis showed that the thermal aging caused a reduction in total NH3 storage capacity (94.6 compared to 138 gmol/m3), different NH3 adsorption/desorption properties and a decrease in activation energy and the pre-exponential factor for NH3 oxidation, standard and fast SCR reactions. Both reduction in the storage capability and the change in kinetics of the major reactions contributed to the change in the axial storage and concentration profiles observed from the experiments.

DYNAMIC MODEL BASED STATE ESTIMATION IN A HEAVY DUTY DIESEL AFTERTREATMENT SYSTEM FOR ONBOARD DIAGNOSTICS AND CONTROLS

Estimating un-measurable states is an important component for onboard diagnostics (OBD) and control strategy development in diesel exhaust aftertreatment systems. This research focuses on the development of an Extended Kalman Filter (EKF) based state estimator for two of the main components in a diesel engine aftertreatment system: the Diesel Oxidation Catalyst (DOC) and the Selective Catalytic Reduction (SCR) catalyst. One of the key areas of interest is the performance of these estimators when the catalyzed particulate filter (CPF) is being actively regenerated. In this study, model reduction techniques were developed and used to develop reduced order models from the 1D models used to simulate the DOC and SCR. As a result of order reduction, the number of states in the estimator is reduced from 12 to 1 per element for the DOC and 12 to 2 per element for the SCR. The reduced order models were simulated on the experimental data and compared to the high fidelity model and the experimental data. The results show that the effect of eliminating the heat transfer and mass transfer coefficients are not significant on the performance of the reduced order models. This is shown by an insignificant change in the kinetic parameters between the reduced order and 1D model for simulating the experimental data. An EKF based estimator to estimate the internal states of the DOC and SCR was developed. The DOC and SCR estimators were simulated on the experimental data to show that the estimator provides improved estimation of states compared to a reduced order model. The results showed that using the temperature measurement at the DOC outlet improved the estimates of the CO , NO , NO2 and HC concentrations from the DOC. The SCR estimator was used to evaluate the effect of NH3 and NOX sensors on state estimation quality. Three sensor combinations of NOX sensor only, NH3 sensor only and both NOX and NH3 sensors were evaluated. The NOX only configuration had the worst performance, the NH3 sensor only configuration was in the middle and both the NOX and NH3 sensor combination provided the best performance.

Vector self-pulsing in erbium-doped fiber lasers

Insight into instabilities of fiber laser regimes leading to complex self-pulsing operations is an opportunity to unlock the high power and dynamic operation tunability of lasers. Though many models have been suggested, there is no complete covering of self-pulsing complexity observed experimentally. Here, I further generalized our previous vector model of erbium-doped fiber laser and, for the first time, to the best of my knowledge, map tunability of complex vector self-pulsing on Poincare sphere (limit cycles and double scroll polarization attractors) for laser parameters, e.g., power, ellipticity of the pump wave, and in-cavity birefringence. Analysis validated by extensive numerical simulations demonstrates good correspondence to the experimental results on complex self-pulsing regimes obtained by many authors during the last 20 years.

Toxicity of polychlorinated biphenyls and N-phenyl-1-naphthylamine in the juvenile turtle, Chelydra serpentina

Polychlorinated biphenyls (PCBs) and substituted phenylamine antioxidants (SPAs) are two chemical groups that have been used in multiple Canadian industrial processes. Despite the production ban of PCBs in North America in 1977, they are still ubiquitous in the environment and in wildlife tissues. Previous studies of fish, amphibians, birds, and mammals have shown that PCBs are toxic and act as endocrine disruptors. In contrast, SPAs, specifically N-phenyl-1-naphthylamine (PANA), have received very little attention despite their current use in Canada and their expected environmental releases. The effects of PCB and PANA exposures in reptiles remain unknown thus, juvenile Chelydra serpentina were used in this thesis as a model vertebrate to fill in missing toxicity research gaps due to their importance as an environmental indicator. First, food pellets were spiked at an environmentally relevant concentration of the PCB mixture Aroclor 1254 (A1254) to model hepatic bioaccumulation (0.45 μg/g A1254 for 31 days) and depuration (clean food for 50 days) of PCBs in turtles. No significant differences in PCB concentrations were observed between the control and treated animals, suggesting that juvenile turtles exposed to environmentally relevant concentrations of PCBs can likely detoxify low concentrations of PCBs. Additionally, two dose-response experiments were performed using A1254 or PANA spiked food (0-12.7 μg/g and 0-3,446 μg/g, respectively) to determine hepatic toxicity and bioaccumulation in juvenile C. serpentina. An increase in hepatic cyp1a was observed when exposed to the highest dose of both chemicals: 1) for A1254, induction correlated to the significant increase in hepatic PCB congeners that are known to be metabolized by CYP1A; and 2) for PANA, induction suggested that CYP1A has a potential role in its detoxification. PCBs are known endocrine disruptors, but no significant changes were observed for both thyroid receptors (alpha and beta) or by estrogen and androgen receptors. This lack of response, also noted in the PANA exposure, suggests that C. serpentina is less sensitive to endocrine disruption than other vertebrates. Furthermore, the expression of genes involved in cellular stress was not altered in PCB and PANA exposed animals, supporting the resilience of turtles to oxidative stress. This is the first study to demonstrate the toxicity of PCBs and PANA in C. serpentina, demonstrating the turtle’s high tolerance to contamination.

Percutaneous vertebroplasty: a new animal model.

Background Context Percutaneous vertebroplasty (PVP) is a minimally invasive surgical procedure and is frequently performed in humans who need surgical treatment of vertebral fractures. PVP involves cement injection into the vertebral body, thereby providing rapid and significant pain relief. Purpose The testing of novel biomaterials depends on suitable animal models. The aim of this study was to develop a reproducible and safe model of PVP in sheep. Study Design This study used ex vivo and in vivo large animal model study (Merino sheep). Methods Ex vivo vertebroplasty was performed through a bilateral modified parapedicular access in 24 ovine lumbar hemivertebrae, divided into four groups (n=6). Cerament (Bone Support, Lund, Sweden) was the control material. In the experimental group, a novel composite was tested—Spine-Ghost—which consisted of an alpha-calcium sulfate matrix enriched with micrometric particles of mesoporous bioactive glass. All vertebrae were assessed by micro-computed tomography (micro-CT) and underwent mechanical testing. For the in vivo study, 16 sheep were randomly allocated into control and experimental groups (n=8), and underwent PVP using the same bone cements. All vertebrae were assessed postmortem by micro-CT, histology, and reverse transcription-polymerase chain reaction (rt-PCR). This work has been supported by the European Commission under the 7th Framework Programme for collaborative projects (600,000–650,000 USD). Results In the ex vivo model, the average defect volume was 1,275.46±219.29 mm3. Adequate defect filling with cement was observed. No mechanical failure was observed under loads which were higher than physiological. In the in vivo study, cardiorespiratory distress was observed in two animals, and one sheep presented mild neurologic deficits in the hind limbs before recovering. Conclusions The model of PVP is considered suitable for preclinical in vivo studies, mimicking clinical application. All sheep recovered and completed a 6-month implantation period. There was no evidence of cement leakage into the vertebral foramen in the postmortem examination.

Covariant Spectator Theory of heavy–light and heavy mesons and the predictive power of covariant interaction kernels

The Covariant Spectator Theory (CST) is used to calculate the mass spectrum and vertex functions of heavy–light and heavy mesons in Minkowski space. The covariant kernel contains Lorentz scalar, pseudoscalar, and vector contributions. The numerical calculations are performed in momentum space, where special care is taken to treat the strong singularities present in the confining kernel. The observed meson spectrum is very well reproduced after fitting a small number of model parameters. Remarkably, a fit to a few pseudoscalar meson states only, which are insensitive to spin–orbit and tensor forces and do not allow to separate the spin–spin from the central interaction, leads to essentially the same model parameters as a more general fit. This demonstrates that the covariance of the chosen interaction kernel is responsible for the very accurate prediction of the spin-dependent quark–antiquark interactions.

Longitudinal Micro CT-driven biomarkers as a tool to evaluate lung fibrosis progression and antifibrotic efficacy in a refined Bleomycin mouse model

Idiopathic pulmonary fibrosis (IPF) is a chronic progressive disease with no curative pharmacological treatment. Animal models play an essential role in revealing molecular mechanisms involved in the pathogenesis of the disease. Bleomycin (BLM)-induced lung fibrosis is the most widely used and characterized model for anti-fibrotic drugs screening. However, several issues have been reported, such as the identification of an optimal BLM dose and administration scheme as well as gender-specificity. Moreover, the balance between disease resolution, an appropriate time window for therapeutic intervention and animal welfare remains critical aspects yet to be fully elucidated. In this thesis, Micro CT imaging has been used as a tool to identify the ideal BLM dose regimen to induce sustained lung fibrosis in mice as well as to assess the anti-fibrotic effect of Nintedanib (NINT) treatment upon this BLM administration regimen. In order to select the optimal BLM dose scheme, C57bl/6 male mice were treated with BLM via oropharyngeal aspiration (OA), following either double or triple BLM administration. The triple BLM administration resulted in the most promising scheme, able to balance disease resolution, appropriate time-window for therapeutic intervention and animal welfare. The fibrosis progression was longitudinally assessed by micro-CT every 7 days for 5 weeks after BLM administration and 5 animals were sacrificed at each timepoint for the BALF and histological evaluation. The antifibrotic effect of NINT was assessed following different treatment regimens in this model. Herein, we have developed an optimized mouse model of pulmonary fibrosis, enabling three weeks of the therapeutic window to screen putative anti-fibrotic drugs. micro-CT scanning, allowed us to monitor the progression of lung fibrosis and the therapeutical response longitudinally in the same subject, drastically reducing the number of animals involved in the experiment.

Chagas Cardiomyopathy Manifestations and Trypanosoma cruzi Genotypes Circulating in Chronic Chagasic Patients

Chagas disease caused by Trypanosoma cruzi is a complex disease that is endemic and an important problem in public health in Latin America. The T. cruzi parasite is classified into six discrete taxonomic units (DTUs) based on the recently proposed nomenclature (TcI, TcII, TcIII, TcIV, TcV and TcVI). The discovery of genetic variability within TcI showed the presence of five genotypes (Ia, Ib, Ic, Id and Ie) related to the transmission cycle of Chagas disease. In Colombia, TcI is more prevalent but TcII has also been reported, as has mixed infection by both TcI and TcII in the same Chagasic patient. The objectives of this study were to determine the T. cruzi DTUs that are circulating in Colombian chronic Chagasic patients and to obtain more information about the molecular epidemiology of Chagas disease in Colombia. We also assessed the presence of electrocardiographic, radiologic and echocardiographic abnormalities with the purpose of correlating T. cruzi genetic variability and cardiac disease. Molecular characterization was performed in Colombian adult chronic Chagasic patients based on the intergenic region of the mini-exon gene, the 24S alpha and 18S regions of rDNA and the variable region of satellite DNA, whereby the presence of T. cruzi I, II, III and IV was detected. In our population, mixed infections also occurred, with TcI-TcII, TcI-TcIII and TcI-TcIV, as well as the existence of the TcI genotypes showing the presence of genotypes Ia and Id. Patients infected with TcI demonstrated a higher prevalence of cardiac alterations than those infected with TcII. These results corroborate the predominance of TcI in Colombia and show the first report of TcIII and TcIV in Colombian Chagasic patients. Findings also indicate that Chagas cardiomyopathy manifestations are more correlated with TcI than with TcII in Colombia.

Vaccination of Mice with Salmonella Expressing VapA: Mucosal and Systemic Th1 Responses Provide Protection against Rhodococcus equi Infection

Conventional vaccines to prevent the pneumonia caused by Rhodococcus equi have not been successful. We have recently demonstrated that immunization with Salmonella enterica Typhimurium expressing the VapA antigen protects mice against R. equi infection. We now report that oral vaccination of mice with this recombinant strain results in high and persistent fecal levels of antigen-specific IgA, and specific proliferation of the spleen cells of immunized mice in response to the in vitro stimulation with R. equi antigen. After in vitro stimulation, spleen cells of immunized mice produce high levels of Th1 cytokines and show a prominent mRNA expression of the Th1 transcription factor T-bet, in detriment of the Th2 transcription factor GATA-3. Following R. equi challenge, a high H(2)O(2), NO, IL-12, and IFN-gamma content is detected in the organs of immunized mice. On the other hand, TNF-alpha and IL-4 levels are markedly lower in the organs of vaccinated mice, compared with the non-vaccinated ones. The IL-10 content and the mRNA transcription level of TGF-beta are also higher in the organs of immunized mice. A greater incidence of CD4(+) and CD8(+) T cells and B lymphocytes is verified in vaccinated mice. However, there is no difference between vaccinated and non-vaccinated mice in terms of the frequency of CD4(+)CD25(+)Foxp3(+) T cells. Finally, we show that the vaccination confers a long-term protection against R. equi infection. Altogether, these data indicate that the oral vaccination of mice with S. enterica Typhimurium expressing VapA induces specific and long-lasting humoral and cellular responses against the pathogen, which are appropriately regulated and allow tissue integrity after challenge.

Melatonin reduces LH, 17 beta-estradiol and induces differential regulation of sex steroid receptors in reproductive tissues during rat ovulation

Background: Melatonin is associated with direct or indirect actions upon female reproductive function. However, its effects on sex hormones and steroid receptors during ovulation are not clearly defined. This study aimed to verify whether exposure to long-term melatonin is able to cause reproductive hormonal disturbances as well as their role on sex steroid receptors in the rat ovary, oviduct and uterus during ovulation. Methods: Twenty-four adult Wistar rats, 60 days old (+/-250 g) were randomly divided into two groups. Control group (Co): received 0.9% NaCl 0.3 mL + 95% ethanol 0.04 mL as vehicle; Melatonin-treated group (MEL): received vehicle + melatonin [ 100 mu g/100 g BW/day] both intraperitoneally during 60 days. All animals were euthanized by decapitation during the morning estrus at 4 a. m. Results: Melatonin significantly reduced the plasma levels of LH and 17 beta-estradiol, while urinary 6-sulfatoximelatonin (STM) was increased at the morning estrus. In addition, melatonin promoted differential regulation of the estrogen receptor (ER), progesterone receptor (PR), androgen receptor (AR) and melatonin receptor (MTR) along the reproductive tissues. In ovary, melatonin induced a down-regulation of ER-alpha and PRB levels. Conversely, it was observed that PRA and MT1R were up-regulated. In oviduct, AR and ER-alpha levels were down-regulated, in contrast to high expression of both PRA and PRB. Finally, the ER-beta and PRB levels were down-regulated in uterus tissue and only MT1R was up-regulated. Conclusions: We suggest that melatonin partially suppress the hypothalamus-pituitary-ovarian axis, in addition, it induces differential regulation of sex steroid receptors in the ovary, oviduct and uterus during ovulation.