Chaotic mixing of a competitive-consecutive reaction

The evolution of a competitive-consecutive chemical reaction is computed numerically in a two-dimensional chaotic fluid flow with initially segregated reactants. Results from numerical simulations are used to evaluate a variety of reduced models commonly adopted to model the full advection-reaction-diffusion problem. Particular emphasis is placed upon fast reactions, where the yield varies most significantly with Peclet number (the ratio of diffusive to advective time scales). When effects of the fluid mechanical mixing are strongest, we find that the yield of the reaction is underestimated by a one-dimensional lamellar model that ignores the effects of fluid mixing, but overestimated by two other lamellar models that include fluid mixing.

Analysis of the four wave mixing effect (FWM) in a dispersion decreasing fiber (DDF) for a WDM system

We did a numerical investigation of the propagation of short light pulses in the region of 1.55 mu m and the conversion efficiency (CE) for the four wave mixing generation (FWM) of ordinary and dispersion decreasing fibers for use in wavelength division multiplexing (WDM) systems, Our simulations studies three different profiles, linear, hyperbolic. and constant, One conclude that for all the profiles there is decrease of the conversion efficiency with the increase in the channel separation. The hyperbolic profile present a higher efficiency of around 1000 above in magnitude compared with the others profiles at 0.2 nm of channel separation. We calculate the conversion efficiency versus the fiber length for the three profiles. The conversion efficiency for the hyperbolic profile is higher when compared to the constant and linear profiles. The other interesting point of the hyperbolic profile is that the increase of the CE in the beginning of the fiber does not show my oscillation in the CE value (log eta), which was observed for the constant and linear profiles. For all the profiles there is an increase of the conversion efficiency with the increase of the pump power. The compression factor C-i for the generated FWM signal at omega(3) was measured along the DDF's and the constant profile fibers. One can conclude that with the use of decreasing dispersion profile (DDF) fibers one can have a control of the (CE) conversion efficiency and the compression factor of the four wave mixing (FWM) generation in WDM systems. (c) 2005 Elsevier B.V. All rights reserved.

RELATIONSHIP BETWEEN COLUMN DENSITY AND SURFACE MIXING RATIO FOR O3 AND NO2: IMPLICATIONS FOR SATELLITE OBSERVATIONS AND THE IMPACTS OF VERTICAL MIXING

Satellites have great potential for diagnosis of surface air quality conditions, though reduced sensitivity of satellite instrumentation to the lower troposphere currently impedes their applicability. One objective of the NASA DISCOVER-AQ project is to provide information relevant to improving our ability to relate satellite-observed columns to surface conditions for key trace gases and aerosols. In support of DISCOVER-AQ, this dissertation investigates the degree of correlation between O3 and NO2 column abundance and surface mixing ratio during the four DISCOVER-AQ deployments; characterize the variability of the aircraft in situ and model-simulated O3 and NO2 profiles; and use the WRF-Chem model to further investigate the role of boundary layer mixing in the column-surface connection for the Maryland 2011 deployment, and determine which of the available boundary layer schemes best captures the observations. Simple linear regression analyses suggest that O3 partial column observations from future satellite instruments with sufficient sensitivity to the lower troposphere may be most meaningful for surface air quality under the conditions associated with the Maryland 2011 campaign, which included generally deep, convective boundary layers, the least wind shear of all four deployments, and few geographical influences on local meteorology, with exception of bay breezes. Hierarchical clustering analysis of the in situ O3 and NO2 profiles indicate that the degree of vertical mixing (defined by temperature lapse rate) associated with each cluster exerted an important influence on the shapes of the median cluster profiles for O3, as well as impacted the column vs. surface correlations for many clusters for both O3 and NO2. However, comparisons to the CMAQ model suggest that, among other errors, vertical mixing is overestimated, causing too great a column-surface connection within the model. Finally, the WRF-Chem model, a meteorology model with coupled chemistry, is used to further investigate the impact of vertical mixing on the O3 and NO2 column-surface connection, for an ozone pollution event that occurred on July 26-29, 2011. Five PBL schemes were tested, with no one scheme producing a clear, consistent “best” comparison with the observations for PBLH and pollutant profiles; however, despite improvements, the ACM2 scheme continues to overestimate vertical mixing.

Changes in phytoplankton composition in response to tides, wind-induced mixing conditions, and freshwater outflows in an urbanised estuarine complex

Estudos recentes na baía de Santos (sudeste do Brasil), localizada em um sistema estuarino altamente urbanizado, mostraram o aumento de espécies fitoplanctônicas potencialmente nocivas. Apesar da importância da previsão das florações algais nocivas, é difícil determinar a estrutura da comunidade fitoplanctônica em ambientes extremamente dinâmicos. O presente estudo analisa florações dominadas pelo microfitoplâncton e sua relação com variáveis físicas e meteorológicas, a fim de determinar padrões associados às marés e às estações do ano. Foram comparadas oito situações e obtidos cinco cenários de dominância relacionados aos ventos, marés e pluviosidade: i) Surfers, diatomáceas associadas à zona de surfe, de alta energia; ii) Sinkers, diatomáceas de tamanho grande que ocorrem nas marés de sizígia, depois de períodos de alta pluviosidade; iii) Opportunistic mixers, diatomáceas pequenas ou alongadas, formadoras de cadeia, que ocorrem durante períodos de quadratura; iv) Local mixers, diatomáceas e dinoflagelados microplanctônicos que foram abundantes em todas as 298 estações amostradas, e v) Mixotrophic dinoflagellates, que ocorrem após intensas descargas estuarinas. Os resultados sugerem uma alteração no padrão temporal de algumas espécies formadoras de florações, enquanto outras apresentaram abundâncias superiores aos valores seguros para a saúde publica. Esta abordagem ilustra também os possíveis impactos de variações na descarga de água doce em estuários altamente eutrofizados.

Bahadur representation of linear kernel quantile estimator of VaR under mixing assumptions

Bahadur representation and its applications have attracted a large number of publications and presentations on a wide variety of problems. Mixing dependency is weak enough to describe the dependent structure of random variables, including observations in time series and longitudinal studies. This note proves the Bahadur representation of sample quantiles for strongly mixing random variables (including ½-mixing and Á-mixing) under very weak mixing coe±cients. As application, the asymptotic normality is derived. These results greatly improves those recently reported in literature.

Mixing, Chemical Reactions, and Combustion in Supersonic Flows

Experiments were conducted at the GALCIT supersonic shear-layer facility to investigate aspects of reacting transverse jets in supersonic crossflow using chemiluminescence and schlieren image-correlation velocimetry. In particular, experiments were designed to examine mixing-delay length dependencies on jet-fluid molar mass, jet diameter, and jet inclination.

The experimental results show that mixing-delay length depends on jet Reynolds number, when appropriately normalized, up to a jet Reynolds number of 500,000. Jet inclination increases the mixing-delay length, but causes less disturbance to the crossflow when compared to normal jet injection. This can be explained, in part, in terms of a control-volume analysis that relates jet inclination to flow conditions downstream of injection.

In the second part of this thesis, a combustion-modeling framework is proposed and developed that is tailored to large-eddy simulations of turbulent combustion in high-speed flows. Scaling arguments place supersonic hydrocarbon combustion in a regime of autoignition-dominated distributed reaction zones (DRZ). The proposed evolution-variable manifold (EVM) framework incorporates an ignition-delay data-driven induction model with a post-ignition manifold that uses a Lagrangian convected 'balloon' reactor model for chemistry tabulation. A large-eddy simulation incorporating the EVM framework captures several important reacting-flow features of a transverse hydrogen jet in heated-air crossflow experiment.

Geminivirus Rep Protein Interferes with the Plant DNA Methylation Machinery and Modifies the Host Epigenome

The apparent simplicity of viruses hides the complexity of their interactions with their hosts. Viruses are masters at circumventing host defenses and manipulating the cellular environment for their own benefit. The replication of the largest known family of single-stranded DNA viruses, Geminiviridae, is impaired by DNA methylation and Arabidopsis mutants affected in cytosine methylation are hypersusceptible to geminivirus infection. This implies that plants might use methylation as a defense against geminiviruses and that the viral genome is a target for plant DNA methyltransferases. We have found a novel counter-defense strategy used by geminiviruses, that reduces the expression of the plant maintenance DNA methyltransferases, MET1 and CMT3, in both, locally and systemically infected tissues. Furthermore, we demonstrated that the virus-mediated repression of these two maintenance DNA methyltransferases is widely spread among different geminivirus species. Additionally, we identified Rep as the geminiviral protein responsible for the repression of MET1 and CMT3, and another viral protein, C4, as an ancillary player in MET1 downregulation. The presence of Rep, suppresses TGS of an Arabidopsis transgene and of host loci whose expression is strongly controlled by CG methylation. Bisulfite sequencing analyses showed that the expression of Rep caused a substantial reduction in the levels of DNA methylation at CG sites. Our findings suggest that Rep, the only viral protein essential for geminiviral replication, displays TGS suppressor activity through a mechanism distinct from the one thus far described for geminiviruses.

Investigations of Cloud Microphysical Response to Mixing Using Digital Holography

Cloud edge mixing plays an important role in the life cycle and development of clouds. Entrainment of subsaturated air affects the cloud at the microscale, altering the number density and size distribution of its droplets. The resulting effect is determined by two timescales: the time required for the mixing event to complete, and the time required for the droplets to adjust to their new environment. If mixing is rapid, evaporation of droplets is uniform and said to be homogeneous in nature. In contrast, slow mixing (compared to the adjustment timescale) results in the droplets adjusting to the transient state of the mixture, producing an inhomogeneous result. Studying this process in real clouds involves the use of airborne optical instruments capable of measuring clouds at the `single particle' level. Single particle resolution allows for direct measurement of the droplet size distribution. This is in contrast to other `bulk' methods (i.e. hot-wire probes, lidar, radar) which measure a higher order moment of the distribution and require assumptions about the distribution shape to compute a size distribution. The sampling strategy of current optical instruments requires them to integrate over a path tens to hundreds of meters to form a single size distribution. This is much larger than typical mixing scales (which can extend down to the order of centimeters), resulting in difficulties resolving mixing signatures. The Holodec is an optical particle instrument that uses digital holography to record discrete, local volumes of droplets. This method allows for statistically significant size distributions to be calculated for centimeter scale volumes, allowing for full resolution at the scales important to the mixing process. The hologram also records the three dimensional position of all particles within the volume, allowing for the spatial structure of the cloud volume to be studied. Both of these features represent a new and unique view into the mixing problem. In this dissertation, holographic data recorded during two different field projects is analyzed to study the mixing structure of cumulus clouds. Using Holodec data, it is shown that mixing at cloud top can produce regions of clear but humid air that can subside down along the edge of the cloud as a narrow shell, or advect down shear as a `humid halo'. This air is then entrained into the cloud at lower levels, producing mixing that appears to be very inhomogeneous. This inhomogeneous-like mixing is shown to be well correlated with regions containing elevated concentrations of large droplets. This is used to argue in favor of the hypothesis that dilution can lead to enhanced droplet growth rates. I also make observations on the microscale spatial structure of observed cloud volumes recorded by the Holodec.

The average mixing matrix signature

Laplacian-based descriptors, such as the Heat Kernel Signature and the Wave Kernel Signature, allow one to embed the vertices of a graph onto a vectorial space, and have been successfully used to find the optimal matching between a pair of input graphs. While the HKS uses a heat di↵usion process to probe the local structure of a graph, the WKS attempts to do the same through wave propagation. In this paper, we propose an alternative structural descriptor that is based on continuoustime quantum walks. More specifically, we characterise the structure of a graph using its average mixing matrix. The average mixing matrix is a doubly-stochastic matrix that encodes the time-averaged behaviour of a continuous-time quantum walk on the graph. We propose to use the rows of the average mixing matrix for increasing stopping times to develop a novel signature, the Average Mixing Matrix Signature (AMMS). We perform an extensive range of experiments and we show that the proposed signature is robust under structural perturbations of the original graphs and it outperforms both the HKS and WKS when used as a node descriptor in a graph matching task.

Mixing theory for culture and harvest in bioreactors of human mesenchymal stem cells on microcarriers

The use of human mesenchymal stem cells (hMSCs) in regenerative medicine is a potential major advance for the treatment of many medical conditions, especially with the use of allogeneic therapies where the cells from a single donor can be used to treat ailments in many patients. Such cells must be grown attached to surfaces and for large scale production, it is shown that stirred bioreactors containing ~200 μm particles (microcarriers) can provide such a surface. It is also shown that the just suspended condition, agitator speed NJS, provides a satisfactory condition for cell growth by minimizing the specific energy dissipation rate, εT, in the bioreactor whilst still meeting the oxygen demand of the cells. For the cells to be used for therapeutic purposes, they must be detached from the microcarriers before being cryopreserved. A strategy based on a short period (~7 min) of very high εT, based on theories of secondary nucleation, is effective at removing >99% cells. Once removed, the cells are smaller than the Kolmogorov scale of turbulence and hence not damaged. This approach is shown to be successful for culture and detachment in 4 types of stirred bioreactors from 15 mL to 5 L.

The periplasmic domain of the barrel assembly machinery protein A (BamA) from Escherichia coli assists folding of outer membrane protein A

The assembly of outer membranes of the cell wall of Gram-negative bacteria and of various organelles of eukaryotic cells requires the evolutionarily conserved β-barrel-assembly machinery (BAM) complex. This thesis describes the biochemical and biophysical properties of the periplasmic domain of the β-barrel assembly machinery protein A (PD-BamA) of the E. coli BAM complex, its effect on insertion and folding of the Outer membrane protein A (OmpA) into lipid bilayers and the identification of regions of PD-BamA that may be involved in protein-protein interactions. The secondary structure of PD-BamA in mixed lipid bilayers, analyzed by Circular dichroism (CD) spectroscopy, contained less β-sheet at an increased content of phosphatidylglycerol (PG) in the lipid membrane. This result showed membrane binding, albeit only in the presence of negatively charged lipids. Fluorescence spectroscopy demonstrated that PD-BamA only binds to lipid bilayers containing the negatively charged DOPG, confirming the results of CD spectroscopy. PD-BamA did not bind to zwitterionic but overall neutral lipid bilayers. PD-BamA bound to OmpA at a stoichiometry of 1:1. PD-BamA strongly facilitated insertion and folding of OmpA into lipid membranes. Kinetics of PD-BamA mediated folding of OmpA was well described by two parallel folding processes, a fast folding process and a slow folding process, differing by 2-3 orders of magnitude in their rate constants. The folding yields of OmpA depended on the concentration of lipid membranes and also on the lipid head groups. The presence of PD-BamA resulted in increased folding yields of OmpA in negatively charged DOPG, but PD-BamA did not affect the folding kinetics of OmpA into bilayers of zwitterionic but overall neutral lipids. The efficiency of folding and insertion of OmpA into lipid bilayers strongly depended on the ratio PD-BamA/OmpA and was optimal at equimolar concentrations of PD-BamA and OmpA. To examine complexes of unfolded OmpA with PD-BamA in more detail, site-directed spectroscopy was used to explore contact regions in both, PD-BamA and OmpA. Similarly, contact regions were also investigated for another protein complex formed by PD-BamA and the lipoprotein BamD. The obtained data suggest, that the site of interaction on PD-BamA for OmpA might be oriented towards the exterior environment away from the preceding POTRA domains, but that PD-BamA is oriented with its short α-helix α1 of POTRA domain 5 towards the C-terminal end of BamD.

A spatial data warehouse to predict lithic sources of tombs from South of Portugal: mixing geochemistry, petrology, cartography and archaeology in spatial analysis

MEGAGEO - Moving megaliths in the Neolithic is a project that intends to find the provenience of lithic materials in the construction of tombs. A multidisciplinary approach is carried out, with researchers from several of the knowledge fields involved. This work presents a spatial data warehouse specially developed for this project that comprises information from national archaeological databases, geographic and geological information and new geochemical and petrographic data obtained during the project. The use of the spatial data warehouse proved to be essential in the data analysis phase of the project. The Redondo Area is presented as a case study for the application of the spatial data warehouse to analyze the relations between geochemistry, geology and the tombs in this area.