Conditional moment closure for chemical reactions in laminar chaotic flows

We implement conditional moment closure (CMC) for simulation of chemical reactions in laminar chaotic flows. The CMC approach predicts the expected concentration of reactive species, conditional upon the concentration of a corresponding nonreactive scalar. Closure is obtained by neglecting the difference between the local concentration of the reactive scalar and its conditional average. We first use a Monte Carlo method to calculate the evolution of the moments of a conserved scalar; we then reconstruct the corresponding probability density function and dissipation rate. Finally, the concentrations of the reactive scalars are determined. The results are compared (and show excellent agreement) with full numerical simulations of the reaction processes in a chaotic laminar flow. This is a preprint of an article published in AlChE Journal copyright (2007) American Institute of Chemical Engineers: http://www3.interscience.wiley.com/

Factors influencing temporal changes in chemical composition of biogenic deposits in the middle Tążyna River Valley (Kuyavian Lakeland, central Poland)

The present paper discusses the influence of geochemical properties on biogenic deposits in the Wilkostowo mire near Toruń, central Poland. The analysed core has allowed the documentation of environmental changes between the older part of the Atlantic Period and the present day (probably interrupted at the turn of the Meso- and Neoholocene). In order to reconstruct the main stages in the sedimentation of biogenic deposits, we have used stratigraphic variability of selected litho-geochemical elements (organic matter, calcium carbonate, biogenic and terrigenous silica, macro- and micro-elements: Na, K, Mg, Ca, Fe, Mn, Cu, Zn, Pb, Cr and Ni). The main litho-geochemical component is CaCO 3 ; its content ranges from 4.1 per cent to 92 per cent. The variability of CaCO 3 content reflects mainly changes in hydrolog- ical and geomorphological conditions within the catchment area. The effects of prehistoric anthropogenic activities in the catchment of the River Tążyna, e.g., the use of saline water for economic purposes, are recorded in a change from calcareous gyttja into detritus-calcareous gyttja sedimentation and an increased content of lithophilous elements (Na, K, Mg and Ni) in the sediments. Principal component analysis (PCA) has enabled the distinction the most important factors that affected the chemical composition of sediments at the Wilkostowo site, i.e., mechanical and chemical den- udation processes in the catchment, changes in redox conditions, bioaccumulation of selected elements and human activity. Sediments of the Wilkostowo mire are located in the direct vicinity of an archaeological site, where traces of intensive settlement dating back to the Neolithic have been documented. The settlement phase is recorded both in li- thology and geochemical properties of biogenic deposits which fill the reservoir formed at the bottom of the Parchania Canal Valley.

Adaptive coatings based on polyaniline for direct 2D observation of diffusion processes in microfluidic systems

[EN] Therefore the understanding and proper evaluation of the flow and mixing behaviour at microscale becomes a very important issue. In this study, the diffusion behaviour of two reacting solutions of HCI and NaOH were directly observed in a glass/polydimethylsiloxane microfluidic device using adaptive coatings based on the conductive polymer polyaniline that are covalently attached to the microchannel walls. The two liquid streams were combined at the junction of a Y-shaped microchannel, and allowed to diffuse into each other and react. The results showed excellent correlation between optical observation of the diffusion process and the numerical results. A numerical model which is based on finite volume method (FVM) discretisation of steady Navier-Stokes (fluid flow) equations and mass transport equations without reactions was used to calculate the flow variables at discrete points in the finite volume mesh element. The high correlation between theory and practical data indicates the potential of such coatings to monitor diffusion processes and mixing behaviour inside microfluidic channels in a dye free environment.

Reduced models of chemical reaction in chaotic flows

We describe and evaluate two reduced models for nonlinear chemical reactions in a chaotic laminar flow. Each model involves two separate steps to compute the chemical composition at a given location and time. The “manifold tracking model” first tracks backwards in time a segment of the stable manifold of the requisite point. This then provides a sample of the initial conditions appropriate for the second step, which requires solving one-dimensional problems for the reaction in Lagrangian coordinates. By contrast, the first step of the “branching trajectories model” simulates both the advection and diffusion of fluid particles that terminate at the appropriate point; the chemical reaction equations are then solved along each of the branched trajectories in a second step. Results from each model are compared with full numerical simulations of the reaction processes in a chaotic laminar flow.

Biological and chemical strategies for the recovery of precious and rare metals as nanoparticles

Tese de Doutoramento, Ciências do Mar da Terra e do Ambiente, Ramo: Ciências e Tecnologias do Ambiente, Especialidade em Biotecnologia, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2016

Chemical Reaction Dynamics of the Liquid/Vapor Interface Studied by Mass Spectrometry

This thesis presents investigations of chemical reactions occurring at the liquid/vapor interface studied using novel sampling methodologies coupled with detection by mass spectrometry. Chapters 2 and 3 utilize the recently developed technique of field-induced droplet ionization mass spectrometry (FIDI-MS), in which the application of a strong electric field to a pendant microliter droplet results in the ejection of highly charged progeny droplets from the liquid surface. In Chapter 2, this method is employed to study the base-catalyzed dissociation of a surfactant molecule at the liquid/vapor interface upon uptake of ammonia from the gas phase. This process is observed to occur without significant modulation of the bulk solution pH, suggesting a transient increase in surface pH following the uptake of gaseous ammonia. Chapter 3 presents real-time studies of the oxidation of the model tropospheric organic compound glycolaldehyde by photodissociation of iron (III) oxalate complexes. The oxidation products of glycolaldehyde formed in this process are identified, and experiments in a deoxygenated environment identify the role of oxygen in the oxidation pathway and in the regeneration of iron (III) following photo-initiated reduction. Chapter 4 explores alternative methods for the study of heterogeneous reaction processes by mass spectrometric sampling from liquid surfaces. Bursting bubble ionization (BBI) and interfacial sampling with an acoustic transducer (ISAT) generate nanoliter droplets from a liquid surface that can be sampled via the atmospheric pressure interface of a mass spectrometer. Experiments on the oxidation of oleic acid by ozone using ISAT are also presented. Chapters 5 and 6 detail mechanistic studies and applications of free-radical-initiated peptide sequencing (FRIPS), a technique employing gas-phase free radical chemistry to the sequencing of peptides and proteins by mass spectrometry. Chapter 5 presents experimental and theoretical studies on the anomalous mechanism of dissociation observed in the presence of serine and threonine residues in peptides. Chapter 6 demonstrates the combination of FRIPS with ion mobility-mass spectrometry (IM-MS) for the separation of isomeric peptides.

OC-OT-LIBS: A novel approach to the chemical characterization of single particles

Spectral identification of individual micro- and nano-sized particles by the sequential intervention of optical catapulting, optical trapping and laser-induced breakdown spectroscopy is presented [1]. The three techniques are used for different purposes. Optical catapulting (OC) serves to put the particulate material under inspection in aerosol form [2-4]. Optical trapping (OT) permits the isolation and manipulation of individual particles from the aerosol, which are subsequently analyzed by laser-induced breakdown spectroscopy (LIBS). Once catapulted, the dynamics of particle trapping depends on the laser beam characteristics (power and intensity gradient) and on the particle properties (size, mass and shape). Particles are stably trapped in air at atmospheric pressure and can be conveniently manipulated for a precise positioning for LIBS analysis. The spectra acquired from the individually trapped particles permit a straightforward identification of the inspected material. The current work focuses on the development of a procedure for simultaneously acquiring dual information about the particle under study via LIBS and time-resolved plasma images by taking advantage of the aforementioned features of the OC-OT-LIBS instrument to align the multiple lines in a simple yet highly accurate way. The plasma imaging does not only further reinforce the spectral data, but also allows a better comprehension of the chemical and physical processes involved during laser-particle interaction. Also, a thorough determination of the optimal excitation conditions generating the most information out of each laser event was run along the determination of parameters such as the width of the optical trap, its stability as a function of the laser power and the laser wavelength. The extreme sensibility of the presented OC-OT-LIBS technology allows a detection power of attograms for single/individual particle analysis.

SELECTED CHEMOAUTOTROPHIC PROCESSES IN WASTEWATER TREATMENT: LOW TEMPERATURE NITRIFICATION INHIBITION BY AN AZO DYE AND BIOFILTRATION FOR ODOR CONTROL OF HYDROGEN SULFIDE

Biochemical processes by chemoautotrophs such as nitrifiers and sulfide and iron oxidizers are used extensively in wastewater treatment. The research described in this dissertation involved the study of two selected biological processes utilized in wastewater treatment mediated by chemoautotrophic bacteria: nitrification (biological removal of ammonia and nitrogen) and hydrogen sulfide (H2S) removal from odorous air using biofiltration. A municipal wastewater treatment plant (WWTP) receiving industrial dyeing discharge containing the azo dye, acid black 1 (AB1) failed to meet discharge limits, especially during the winter. Dyeing discharge mixed with domestic sewage was fed to sequencing batch reactors at 22oC and 7oC. Complete nitrification failure occurred at 7oC with more rapid nitrification failure as the dye concentration increased; slight nitrification inhibition occurred at 22oC. Dye-bearing wastewater reduced chemical oxygen demand (COD) removal at 7oC and 22oC, increased i effluent total suspended solids (TSS) at 7oC, and reduced activated sludge quality at 7oC. Decreasing AB1 loading resulted in partial nitrification recovery. Eliminating the dye-bearing discharge to the full-scale WWTP led to improved performance bringing the WWTP into regulatory compliance. BiofilterTM, a dynamic model describing the biofiltration processes for hydrogen sulfide removal from odorous air emissions, was calibrated and validated using pilot- and full-scale biofilter data. In addition, the model predicted the trend of the measured data under field conditions of changing input concentration and low effluent concentrations. The model demonstrated that increasing gas residence time and temperature and decreasing influent concentration decreases effluent concentration. Model simulations also showed that longer residence times are required to treat loading spikes. BiofilterTM was also used in the preliminary design of a full-scale biofilter for the removal of H2S from odorous air. Model simulations illustrated that plots of effluent concentration as a function of residence time or bed area were useful to characterize and design biofilters. Also, decreasing temperature significantly increased the effluent concentration. Model simulations showed that at a given temperature, a biofilter cannot reduce H2S emissions below a minimum value, no matter how large the biofilter.

Determining magmatic processes from analysis of phenocrysts and gabbroic xenoliths contained in Calbuco andesites

Calbuco Volcano, in Southern Chile, has eruptive products of predominantly andesitic hornblende-bearing lava. A purpose of this work is to understand magmatic processes and how Calbuco magma chemistry is related to the explosive volcanic character. Calbuco lava has a mineral assemblage of plagioclase, hornblende, orthopyroxene, clinopyroxene, olivine, and magnetite and entrained gabbroic xenoliths with the same mineral assemblage. The presence of hornblende is evidence for dissolved water in the magma. Detailed petrographic/textural analysis has been done using petrographic microscopy and back-scattered electron imaging (BSE); geochemical analysis by electron microprobe (EPMA). Major findings include 1) that hornblende and hornblende-bearing gabbroic cumulates crystallize from Calbuco magma, 2) that plagioclase grains are compositionally zoned, recording evidence of temperature, chemical, and water content fluctuations in the magma, and 3) that hornblende is unstable under upper magma chamber conditions at Calbuco, and is breaking down into plagioclase, olivine, orthopyroxene, clinopyroxene, and magnetite in the magma.

Challenges in imaging and predictive modeling of rhizosphere processes

Background Plant-soil interaction is central to human food production and ecosystem function. Thus, it is essential to not only understand, but also to develop predictive mathematical models which can be used to assess how climate and soil management practices will affect these interactions. Scope In this paper we review the current developments in structural and chemical imaging of rhizosphere processes within the context of multiscale mathematical image based modeling. We outline areas that need more research and areas which would benefit from more detailed understanding. Conclusions We conclude that the combination of structural and chemical imaging with modeling is an incredibly powerful tool which is fundamental for understanding how plant roots interact with soil. We emphasize the need for more researchers to be attracted to this area that is so fertile for future discoveries. Finally, model building must go hand in hand with experiments. In particular, there is a real need to integrate rhizosphere structural and chemical imaging with modeling for better understanding of the rhizosphere processes leading to models which explicitly account for pore scale processes.

Morphological and chemical characterization of tintypes and ambrotypes

The present work was done on two ambrotypes and two tintypes. It aimed evaluate their chemical and physical characteristics, especially their degradation patterns. Moreover, to understand the materials used for their production and cross-check analytical and historical information about the production processes. To do so multi-analytical, non-destructive methods were applied. Technical photography highlighted the surface morphology of the objects and showed the distribution of the protective coatings on their surfaces through UV radiation, which were very different between the four pieces. OM allowed for a detailed observation of the surfaces along with the selection of areas of interest to be analysed with SEM-EDS. SEM-EDS was the technique used most extensively and the one that provided the most insightful results: it allowed to observe the morphology of the image forming particles and the differences between highlights, dark areas and the interfaces between them. Also, elemental point analysis and elemental maps were used to identify the image forming particles as silver and to detect the presence of compounds related to the production, particularly gold used to highlight jewellery, iron as the red pigment and traces of the compounds used in the photographic process containing Ag, I, Na and S . Also, some degradation compounds were analysed containing Ag, Cu, S and Cl. With μ-FT-IR the presence of collodion was confirmed and the source of the protective varnishes was identified, particularly mastic and shellac, in either mixtures of the two or only one. μ-Raman detected the presence of metallic silver and silver chloride on the objects and identified one of the red pigments as Mars red. Finally, μ-XRD showed the presence of metallic silver and silver iodide on both ambrotypes and tintypes and hematite, magnetite and wuestite on the tintypes; RESUMO: O presente estudo foi desenvolvido sobre dois ambrótipos e dois ferrótipos. O propósito consiste em estudar as suas características químicas e físicas, dando particular ênfase aos padrões de degradação. Também é pretendido compreender os materiais usados na sua produção e relacionar esta informação analítca com dados históricos de manuais técnicos contemporâneos à produção dos objectos. Para tal foram utilizadas técnicas multi-analíticas e não destrutivas. O uso da fotografia técnica permitiu uma observação da morfologia das superficies dos objectos e da distribuição das camadas de verniz através da radiação UV, muito diferente entre os quatro. A microscopia óptica proporcionou uma observação detalhada das superfícies assim como a selecção de pontos de interesse para serem analisados com SEM-EDS. SEM-EDS foi a técnica usada mais extensivamente e a que proporcionou os resultados mais detalhados: observação da morofologia das partículas formadoras da imagem e as diferenças entre zonas de altas luzes, baixas luzes e as interfaces entre elas. A análise elemental e os mapas elementares foram usados para detectar prata nas partículas formadoras da imagem e a presença de compostos relacionados com a produção, em particular ouro utilizado para realçar joalharia, ferro no pigmento vermelho e vestígios de compostos utilizados no processo fotográfico incluindo Ag, I, Na e S. Do mesmo modo, alguns compostos de degradação foram analisados contendo Ag, Cu, S e Cl. Com μ-FT-IR a presença de colódio foi confirmada e identificada a origem dos vernizes, mástique e goma-laca, tanto em misturas dos dois como apenas um. Com μ-Raman foi detectada a presença de prata metálica e de cloreto de prata e identificado um dos pigmentos vermelhos como Mars red. Finalmente, μ-DRX revelou a presença de prata metálica e iodeto de prata tanto nos ambrótipos como nos ferrótipos e hematite, magnetite e wuestite nos ferrótipos.

Sexual selection in a tropical fruit fly : role of a plant derived chemical in mate choice

The specific mechanisms by which selective pressures affect individuals are often difficult to resolve. In tephritid fruit flies, males respond strongly and positively to certain plant derived chemicals. Sexual selection by female choice has been hypothesized as the mechanism driving this behaviour in certain species, as females preferentially mate with males that have fed on these chemicals. This hypothesis is, to date, based on studies of only very few species and its generality is largely untested. We tested the hypothesis on different spatial scales (small cage and seminatural field-cage) using the monophagous fruit fly, Bactrocera cacuminata. This species is known to respond to methyl eugenol (ME), a chemical found in many plant species and one upon which previous studies have focused. Contrary to expectation, no obvious female choice was apparent in selecting ME-fed males over unfed males as measured by the number of matings achieved over time, copulation duration, or time of copulation initiation. However, the number of matings achieved by ME-fed males was significantly greater than unfed males 16 and 32 days after exposure to ME in small cages (but not in a field-cage). This delayed advantage suggests that ME may not influence the pheromone system of B. cacuminata but may have other consequences, acting on some other fitness consequence (e.g., enhancement of physiology or survival) of male exposure to these chemicals. We discuss the ecological and evolutionary implications of our findings to explore alternate hypotheses to explain the patterns of response of dacine fruit flies to specific plant-derived chemicals.