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Villain, Adrien. "Étude génomique des interactions diatomées-bactéries." Thesis, Aix-Marseille, 2018. http://www.theses.fr/2018AIXM0202/document.
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Les diatomées sont des algues microscopiques qui contribuent à hauteur de 25% environ à la production primaire planétaire. Les diatomées sont très souvent entourées d’une flore bactérienne, avec laquelle de nombreuses interactions ont été documentées. Les génomes de diatomées contiennent par ailleurs de nombreux gènes dont l’origine prédite est bactérienne.Nous avons étudié Asterionella formosa, une diatomée pennée présente dans de nombreux lacs et cours d’eau à l'aide de données omiques. L’utilisation de la métagénomique a permis de reconstruire 30 génomes bactériens, utilisés pour prédire d'éventuelles interactions avec la diatomée. Le séquençage de la sous-unité 16S de l’ARN ribosomique a montré que les différentes espèces bactériennes avaient une abondance variable au cours des phases de croissance de la diatomée, et que certaines étaient plus souvent au contact de la diatomée que libres dans le milieu. Le génome d'A. formosa a ensuite été séquencé à l'aide de la technologie Pacbio et comparé à ceux d'espèces proches. Enfin, l’impact des bactéries sur les diatomées a été abordé sous l’angle de l’évolution et des transferts horizontaux de gènes, qui ont été prédits à partir des données transcriptomiques d’une centaine de diatomées marines.Ce travail représente une première étape dans l'étude de la communauté bactérienne associée à A. formosa. Des expériences complémentaires incluant l’utilisation de transcriptomique ou métabolomique sont maintenant envisageables. Les données collectées et/ou analysées dans ce travail contribuent d'ores et déjà à l’effort global de caractérisation génomique des diatomées<br>Diatoms are ubiquitous microalgae that contribute approximately 25% to the primary production worldwide. Many interactions, either positive, neutral or negative, have been documented between diatoms and bacteria. Diatom genomes also harbor numerous genes of putative bacterial origin.We are studying Asterionella formosa, a freshwater pennate diatom. We characterized the community using a combination of omics and laboratory techniques. We reconstructed of the genome of the diatom as well as 30 individual genomes from co-cultured bacterial species and investigated metabolisms that could support diatom-bacteria interactions. 16S rRNA sequencing revealed that the abundance of some bacterial species was highly variable over the course of A. formosa growth. Some species seemed preferentially attached to the diatom while others were mainly free-living. Then, the reference sequence of the A. formosa genome was improved by additional long-read (Pacbio) sequencing. Last, relationships between diatoms and bacteria were investigated at a broader evolutionary scale, by looking at horizontal gene transfers using transcriptomic data of a hundred marine diatoms.This work is a first step in the study of the dynamic and complex bacterial community associated with the diatom A. formosa. The accurate identification and the reconstruction of the genome of these bacteria will enable further in silico predictions based on metabolic networks and new omics experiments using transcriptomic or metabolomic. This work already contributes to a global effort to study diatoms by the means of genomics
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Mason, Brian L. "An experimental investigation of charge transfer during ice contact interactions /." Thesis, Connect to this title online; UW restricted, 1998. http://hdl.handle.net/1773/9769.
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Khan, Anuja. "Solution structure and interactions of electron transfer proteins." Thesis, University of Nottingham, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.415724.
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Martin, Sarah Friede. "Fluorescence resonance energy transfer studies of protein interactions." Thesis, St Andrews, 2008. http://hdl.handle.net/10023/537.
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Nielsen, Jens Munk. "Species interactions and energy transfer in aquatic food webs." Doctoral thesis, Stockholms universitet, Institutionen för ekologi, miljö och botanik, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-123600.
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Food webs are structured by intricate nodes of species interactions which govern the flow of organic matter in natural systems. Despite being long recognized as a key component in ecology, estimation of food web functioning is still challenging due to the difficulty in accurately measuring species interactions within a food web. Novel tracing methods that estimate species diet uptake and trophic position are therefore needed for assessing food web dynamics. The focus of this thesis is the use of compound specific nitrogen and carbon stable isotopes and molecular techniques for assessing predator-prey interactions and energy flow in natural aquatic ecosystems, with a particular focus on the species links between phytoplankton and zooplankton. The use of δ15N amino acid values to predict organism trophic position are evaluated through a meta-analysis of available literature which included measurements from 359 marine species (article I). Through a controlled feeding study isotope incorporation in aquatic organisms, across both plant-animal and animal-animal species linkages is further assessed (article II). These studies showed that δ15N amino acid values are useful tools for categorizing animal trophic position. Organism feeding ecology influenced nitrogen trophic discrimination (difference in isotope ratio between consumer and diet), with higher discrimination in herbivores compared to omnivores and carnivores (article I). Nitrogen isotope trophic discrimination also varied among feeding treatments in the laboratory study (article II). The combined findings from articles I & II suggest that researchers should consider using group specific nitrogen trophic discrimination values to improve accuracy in species trophic position predictions. Another key finding in the controlled laboratory study (article II) was consistently low carbon isotope discrimination in essential amino acids across all species linkages, confirming that these compounds are reliable dietary tracers. The δ13C ratios of essential amino acids were applied to study seasonal dynamics in zooplankton resource use in the Baltic Sea (article III). Data from this study indicated that zooplankton assimilate variable resources throughout the growing season. Molecular diet analysis (article IV) showed that marine copepod and cladoceran species ingested both autotrophic and heterotrophic resources. Evidence from both articles III & IV also revealed that zooplankton feed on a relatively broad range of diet items but not opportunistically on all available food sources. Mesozooplankton feeding patterns suggested that energy and nutritional flows were channelled through an omnivorous zooplankton food web including microzooplankton prey items. Overall the results of this thesis highlight that stable isotope ratios in specific compounds and molecular techniques are useful tracing approaches that improve our understanding of food web functioning.<br><p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 4: Manuscript.</p><p> </p>
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Orange, Nicholas Brian. "Transfer Entropy Analysis of the Interactions of Flying Bats." Thesis, Virginia Tech, 2015. http://hdl.handle.net/10919/53955.
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In this document, a low-cost, portable, non-invasive method of collecting the 3D trajectories of flying bats is first presented. An array of commercially available camera and light components is used alongside a number of well-established calibration and triangulation techniques to resolve the motion of agents through a 3D volume. It is shown that this system is capable of accurately capturing the bats' flight paths in a field experiment. The use of non-visible illumination ensures that a natural cave environment is disturbed as little as possible for behavioral experiments.
Following is a transfer entropy analysis approach applied to the 3D paths of bats flying in pairs. The 3D trajectories are one-dimensionally characterized as inverse curvature time series to allow for entropy calculations. In addition to a traditional formulation of information flow between pair members, a path coupling hypothesis is pursued with time-delay modifications implemented in such a way as to not change the Markovianity of the process. With this modification, trends are found that suggest a leader-follower interaction between the front bat and the rear bat, although statistical significance is not reached due to the small number of pairs considered.<br>Master of Science
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Walker, Sarah Elizabeth. "Functional Studies of Transfer RNA Interactions in the Ribosome." The Ohio State University, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=osu1217605676.
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Moellman, Nicholas S. "ESSAYS ON TRANSFER-PROGRAM INTERACTIONS AMONG LOW-INCOME HOUSEHOLDS." UKnowledge, 2018. https://uknowledge.uky.edu/economics_etds/36.
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This dissertation consists of three essays examining the role of transfer-program interactions for families and households who participate in the social safety net. The safety net is comprised of many different programs, run by different agencies, governed by different rules, and often administered by disparate and secluded entities. However, many households participate in multiple programs, subjecting them to the milieu of administrative hurdles. In this dissertation, I try to untangle some of the intended and unintended effects of program participation that may be experienced by these households.
In Essay 1, I examine the effect of the Patient Protection and Affordable Care Act of 2010 (ACA) on food hardship in US households, utilizing food security information from the Food Security Supplement of the Current Population Survey. Because states adopted the Medicaid expansions provided under the ACA at different times beginning in 2014, the cross-state, over time variation allows me to separate the impact of the ACA on food hardship using triple difference specifications. The richness of questions in the Food Security Supplement allows me to examine the effect of the ACA across different measures of food hardship, and also examine differential response for households participating in the Supplemental Nutrition Assistance Program (SNAP). Examining the mechanisms through which the ACA could affect food insecurity, I find the ACA not only increased average weekly food expenditure, but also the probability a household participates in SNAP. I employ a two-stage, control function approach to address reverse causality between SNAP and food insecurity. I find that the ACA reduced the probability that a household participating in SNAP falls into the two lowest food security categories by 6.5 percentage points and reduced the probability of being food insecure by 14.2 percentage points. Across specifications, I find strong evidence for increasing returns to program participation, and evidence of a differential impact of the ACA across the distribution of food hardship.
In Essay 2, I examine how grant funding and fiscal structure affect program response over the business cycle. I compare child enrollment in Medicaid, a matching grant funding program, with enrollment the State Children's Health Insurance Program, a block grant funded program, utilizing the similarities in beneficiaries, program benefits, and administration to isolate the impact of fiscal structure. I utilize administrative enrollment records, along with individual level participation data, and find a one percentage point increase in the unemployment rate leads to a 7.6% decrease in the number of beneficiaries per person enrolled in block grant funded programs, and a 10% decrease in state expenditure per person decreases the probability of enrollment in a block grant program by 0.58 percentage points. I also find that enrollment is much more persistent among matching grant funded programs, and being enrolled in a block grant funded program the previous period increases the probability of enrolling in a matching grant program this period 75% more than remaining enrolled in the block grant funded program.
Finally, in Essay 3 I explore the effect of the minimum wage on the self-reported value of public assistance program benefits, and the joint effect of the minimum wage and public assistance programs on the income to poverty ratio using data from the 1995-2016 Current Population Survey Annual Social and Economic Supplement. In the first stage, I estimate a Tobit model controlling for the censoring of received benefits from below at zero, and examine the effect of changes in the minimum wage on the self-reported dollar value of benefits received for food stamps/the Supplemental Nutrition Assistance Program (SNAP), Aid to Families with Dependent Children (AFDC)/Temporary Assistance to Needy Families (TANF), Supplemental Security Income (SSI), and the Earned Income Tax Credit (EITC), as well as the total sum of benefits. I find that the minimum wage reduces the value of means-tested benefits, but that this effect is strongest for programs with strong work requirements. Utilizing the residuals from the first stage, I employ a control function approach to estimate the joint effect of the minimum wage and program benefits on the income to poverty ratio. I find the own-effect of the minimum wage provides a small increase in the income to poverty ratio, but that the total effect, accounting for changes in benefits, attenuates by approximately 30%.
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Mahmutovic, Anel. "Reaction-Diffusion kinetics of Protein DNA Interactions." Doctoral thesis, Uppsala universitet, Beräknings- och systembiologi, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-263527.
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Transcription factors need to rapidly find one specific binding site among millions of nonspecific sites on the chromosomal DNA. In this thesis I use various aspects of reaction-diffusion theory to investigate the interaction between proteins and DNA and to explain the searching, finding and binding to specific operator sites. Using molecular dynamics methods we calculate the free energy profile for the model protein LacI as it leaves a nonspecific stretch of DNA and as it slides along DNA. Based on the free energy profiles we estimate the microscopic dissociation rate constant, kdmicro ~1.45×104s-1, and the 1D diffusion coefficient, D1 ~ 0.05-0.29 μm2s-1 (2-40μs to slide 1 basepair (bp)). At a non-atomistic level of detail we estimate the number of microscopic rebindings before a macroscopic dissociation occurs which leads to the macroscopic residence time, τDmacro ~ 48±12ms resulting in a in vitro sliding length estimate of 135-345bp. When we fit the DNA interaction parameters for in vivo conditions to recent single molecule in vivo experiments we conclude that neither hopping nor intersegment transfer contribute to the target search for the LacI dimer, that it appears to bind the specific Osym operator site as soon as it slides into it, and that the sliding length is around 40bp in the cell. The estimated in vivo D1 ~ 0.025 μm2s-1 is higher than expected from estimates of D1 based on viscosity and the atomistic simulations. Surprisingly, we were also forced to conclude that the nonspecific association for the LacI dimer appeared reaction limited which is in conflict with the free energy profile. This inconsistency is resolved by allowing for steric effects. Using reaction-diffusion theory and simulations we show that an apparent reaction limited association can be diffusion limited if geometry and steric effects are taken into account. Furthermore, the simulations show that a protein binds ~2 times faster to a DNA molecule with a helical reactive patch than to a stripe patch running along the length of the DNA. This facilitated binding has a direct impact on the search time especially in the presence of other DNA binding proteins.
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Gardel, Emily Jeanette. "Microbe-electrode interactions: The chemico-physical environment and electron transfer." Thesis, Harvard University, 2013. http://dissertations.umi.com/gsas.harvard:11185.
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This thesis presents studies that examine microbial extracellular electron transfer that an emphasis characterizing how environmental conditions influence electron flux between microbes and a solid-phase electron donor or acceptor. I used bioelectrochemical systems (BESs), fluorescence and electron microscopy, chemical measurements, 16S rRNA analysis, and qRT-PCR to study these relationships among chemical, physical and biological parameters and processes.<br>Engineering and Applied Sciences
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Burch, Anita M. "Electrostatic interactions and the function of electron transfer haem proteins." Thesis, University of East Anglia, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.302998.
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Panitchob, Nuttanont. "Computational modelling of amino acid transfer interactions in the placenta." Thesis, University of Southampton, 2015. https://eprints.soton.ac.uk/384933/.
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Placental amino acid transport is essential for fetal development during pregnancy. Impaired transport has been associated with restricted fetal growth that can potentially lead to diseases in later life. However, quantitative understanding of placenta transport remains limited and therefore requires investigation. The aim of this study was to develop a computational framework that can represent the amino acid transport system in the placenta as a whole. The transfer of amino acid across the placenta is mediated by a broad array of specific membrane transporters. Mathematical models, based on carrier-mediated transport theory, were developed to mechanistically represent these transporters. These include accumulative transporters, which use secondary active transport driven by the sodium electrochemical potential; exchangers (antiporters), which swap one substrate for another on different sides of the membrane; and facilitative transporters, which transport substrate along its concentration gradient. The transporter models were thoroughly investigated and validated with experimental data with respect to their mechanistic characteristics and parameter sensitivity. Overall, the models were demonstrated to be adequate in representing the specific transporter behaviours. There are 20 amino acids, including 9 essential ones, and over 19 different transporters, all of which act on certain overlapping subsets of these amino acids. All transporters must work interdependently for successful transfer of the required amino acids from the maternal to the fetal side; however, this complex process is not fully understood. A compartmental model of placental amino acid transport incorporating kinetic transporter models was developed and revealed to be able to sufficiently capture the integrated transport system. Modelling results clearly demonstrated how modulating specific transporter activity can increase the transport of certain classes of amino acids, but that this comes at the price of decreasing the transport of others, which could have potential implications for developing new clinical treatment options. This integrated modelling approach along with kinetic models of transporters will help in gaining an improved quantitative understanding of epithelial transport in the placenta and other systems and it is ultimately hoped that this will contribute to the development of clinical applications to intervene or prevent impaired-transport related pathologies.
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Sun, Haili. "Ray-tracing internal wave/wave interactions and spectral energy transfer /." Thesis, Connect to this title online; UW restricted, 1997. http://hdl.handle.net/1773/10973.
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Hildebrandt, Nico, Loïc Charbonnière, Raymond F. Ziessel, and Hans-Gerd Löhmannsröben. "Quantum dots as resonance energy transfer acceptors for monitoring biological interactions." Universität Potsdam, 2006. http://opus.kobv.de/ubp/volltexte/2007/1221/.
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Quantum dots (QDs) are common as luminescing markers for imaging in biological applications because their optical properties seem to be inert against their surrounding solvent. This, together with broad and strong absorption bands and intense, sharp tuneable luminescence bands, makes them interesting candidates for methods utilizing Forster Resonance Energy Transfer (FRET), e. g. for sensitive homogeneous fluoroimmunoassays (FIA). In this work we demonstrate energy transfer from Eu3+-trisbipyridin (Eu-TBP) donors to CdSe-ZnS-QD acceptors in solutions with and without serum. The QDs are commercially available CdSe-ZnS core-shell particles emitting at 655 nm (QD655). The FRET system was achieved by the binding of the streptavidin conjugated donors with the biotin conjugated acceptors. After excitation of Eu-TBP and as result of the energy transfer, the luminescence of the QD655 acceptors also showed lengthened decay times like the donors. The energy transfer efficiency, as calculated from the decay times of the bound and the unbound components, amounted to 37%. The Forster-radius, estimated from the absorption and emission bands, was ca. 77Å. The effective binding ratio, which not only depends on the ratio of binding pairs but also on unspecific binding, was obtained from the donor emission dependent on the concentration. As serum promotes unspecific binding, the overall FRET efficiency of the assay was reduced. We conclude that QDs are good substitutes for acceptors in FRET if combined with slow decay donors like Europium. The investigation of the influence of the serum provides guidance towards improving binding properties of QD assays.
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Sawyer, Elizabeth Bryony. "Biophysical analysis of haem-protein interactions in bacterial haem transfer systems." Thesis, University of Cambridge, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.611709.
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Kim, Sung Jin. "Interfacial interactions in heat transfer and fluid flow through porous media /." The Ohio State University, 1989. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487675687171761.
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Barthram, Anita Marie. "Metal-metal interactions in polynuclear complexes of ruthenium and osmium." Thesis, University of Bristol, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.326683.
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McGrath, Caith Thomas. "An experimental study of electron transfer and emission during particle-surface interactions." Thesis, Queen's University Belfast, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.326351.
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Ponomariov, Branco Leonidov. "Student Centrality in University-Industry Interactions." Diss., Georgia Institute of Technology, 2006. http://hdl.handle.net/1853/11633.
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This thesis proposes and estimates a model of university scientists interactions with the private sector; in this model students are conceptualized as an important enabler of such interactions. The results of the study show that university scientists student-related behaviors such as grant support of students and research collaboration with students, and student-related attitudes such as mentoring orientation positively affect the probability that scientists will enter interactions with industry as well as the intensity of such interactions. Behaviors such as teaching and advising of students are not related to interactions with industry.
This study is motivated by the increased emphasis on closer relationships between universities and industry as a means to facilitate the commercial application of university research. Today, numerous policies and programs attempt to achieve such goals. As a result, university scientists are called on to perform many tasks which on the surface seem misaligned. There is substantial study of conflict between the teaching and research missions of universities, and a growing body of study on conflict related to university based commercial and technology transfer related activities. Fewer, there are studies suggesting that these activities are not so misaligned after all. This study falls into the latter category as it posits a complementary relationship between university scientists student related activities and their work related interactions with industry, research and otherwise.
Speculations regarding the importance of students in university industry relations and indirect evidence are scattered through the relevant literature, but little or no systematic empirical tests of their importance exist. This study uses data from a national survey of university researchers to discern the centrality of students to university-industry interactions. Theoretically, students are conceptualized as a dimension of university scientists respective research capacities that enable cross-sectoral processes of accumulative advantage and thereby help to enable their interactions with industry. As a component of scientists scientific and technical human capital, students help university scientists to identify and act upon on research opportunities originating in the private sector. Moreover, students increase the appeal of university scientists to industry agents seeking research partners in academe. Implications for theory and policy are discussed.
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Booker, Annette Casandra. "Optical Characterization and Evaluation of Dye-Nanoparticle Interactions." Thesis, Virginia Tech, 2006. http://hdl.handle.net/10919/36370.
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Surface plasmon resonance has become a widely investigated phenomenon in the past few years. Initially descriptive of light interactions with metallic films, research has branched out to encompass the nanoparticles as well. Generation of the maximum surface plasmon resonance for nanostructures is based on the resonance condition that the oscillatory behavior of the 'free' electrons on the surface of the particle become equivalent to the frequency of the excitation light; for films this required a specific geometry.
Metallic nanoparticles have also interested researchers because of their unique optical properties. Depending on the metal, observations of quenching as well as fluorescence enhancement have been reported. Based on the phenomenon of surface plasmon resonance as well as the properties of metallic nanoparticles, this research reports the interaction of gold and silver nanoparticles in an aqueous dye solution. Our research is the basis for developing an optical sensor used for water treatment centers as an alarm mechanism. Due to the inefficiency of the fluorophore used in similar optodes, sufficient fluorescence was not obtained. With the addition of the nanoparticles, we hoped to observe the transfer of energy from the nanoparticle to the fluorophore to increase the overall intensity, thereby creating a sufficient signal.
Using the excitation theories discovered by Raman, Mie, and Forster and Dexter as our foundation, we mixed a strongly fluorescent dye with gold nanoparticles and aagain with silver nanoparticles. After taken measurements via fluorescence spectroscopy, absorption spectroscopy, and photoluminescence excitation, we observed that the silver nanoparticles seemed to enhance the fluorescence of the dye while the gold nanoparticles quenched the fluorescence.<br>Master of Science
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Bashforth, Pauline S. "Mathematical modelling of interactions between a hot liquid and a cold horizontal substrate." Thesis, University of Bristol, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.294615.
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Teychené, Johanne. "Caractérisation multi-échelle des interactions sucre-électrolyte pour une meilleure compréhension du transfert en nanofiltration." Thesis, Toulouse 3, 2017. http://www.theses.fr/2017TOU30339/document.
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Différentes études ont mis en évidence que la présence d'électrolyte modifie les performances de la nanofiltration et que l'augmentation du transfert observée est majoritairement gouvernée par la modification des propriétés du soluté (interactions soluté / électrolyte). Cependant, de nombreux verrous scientifiques et techniques restent encore à lever pour promouvoir l'intégration de ces opérations à l'échelle industrielle. Dans ce contexte, le travail proposé vise à améliorer la compréhension des mécanismes de transfert en s'appuyant d'une part sur la caractérisation multi-échelle des interactions dans les systèmes soluté neutre / électrolyte et plus particulièrement l'hydratation des espèces, et d'autre part sur la recherche de corrélations entre ces propriétés et les grandeurs de transfert. Plus précisément, il s'agit de comprendre comment les ions agissent sur les propriétés d'hydratation des sucres et leur transfert à travers une membrane de nanofiltration. Dans un premier temps, les propriétés volumiques de sucres (xylose, glucose, saccharose), qui caractérisent l'hydratation des solutés à l'échelle macroscopique, déterminées pour différentes compositions ioniques (LiCl, NaCl, KCl, Na2SO4, K2SO4, CaCl2, MgCl2, MgSO4), montrent que la déshydratation des sucres est principalement gouvernée par les interactions sucre / ions, dépendantes des propriétés des ions (valence, taille). Dans un second temps, la mécanique quantique est utilisée pour décrire les propriétés d'hydratation des ions et des sucres, seuls, puis en mélange à l'échelle microscopique. Il est montré que les sucres et les ions se déshydratent et que les sucres sont d'autant plus déshydratés que le nombre d'interactions sucre / ions augmente, qui lui-même augmente avec le nombre de coordinations des ions dans l'eau. Enfin, des corrélations quantitatives sont obtenues entre les propriétés d'hydratation des espèces (nombre d'hydratation, nombre de coordinations, nombre d'interactions...) obtenues aux différentes échelles et les grandeurs caractérisant le transfert. Ainsi, à partir de ces résultats prometteurs, des travaux complémentaires devraient permettre d'améliorer la prédiction des performances de la nanofiltration pour le traitement de solutions contenant des solutés organiques en présence d'électrolyte<br>Different studies have shown that the presence of electrolyte modifies the nanofiltration performances and that the increase of the neutral solute transfer is mainly governed by the modification of the solute properties (neutral solute / electrolyte interactions). However, the development of such membrane processes is still limited since it is hardly possible to predict the process performances, In this context, the aim of this work is to study the neutral solute / electrolyte interactions using a fundamental multi scale approach in order to improve the knowledge of the transfer mechanisms taking place through nanofiltration membranes. More precisely, the objective is to understand how the ions act on the hydration properties of the saccharides and their transfer through a nanofiltration membrane. Firstly, the saccharide volumetric properties (xylose, glucose, sucrose), which characterize the solute hydration at the macroscopic scale, are determined in presence of various electrolytes (LiCl, NaCl, KCl, Na2SO4, K2SO4, CaCl2, MgCl2, MgSO4). The results show that the saccharide dehydration is due to the predominance of the saccharide / ions interactions depending on the ions' properties (valence, size). Secondly, quantum mechanics is used to describe the hydration properties of ions and saccharides, alone and then in a mixture at the microscopic scale. It is shown that both saccharide and ions are dehydrated and that the saccharides are more dehydrated for increasing saccharide / ions interactions number, which in turn increases with the ion's coordination number in water. It is also shown that the species hydration properties, obtained at different scales are consistent. Finally, quantitative correlations between the species hydration properties and the saccharide mass transfer parameters are obtained. Thus, from these promising results, further work will be devoted to improve the prediction of the performance of nanofiltration for the treatment of solutions containing organic solutes in the presence of electrolyte
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Eggleston, David. "An investigation into frictional surface interactions and their effect on brake judder." Thesis, Sheffield Hallam University, 2000. http://shura.shu.ac.uk/19601/.
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The chemical nature of the Transfer Film (T.F.) or Third-Body Layer (T.B.L.) formed at the friction interface of an automotive friction brake during off-brake motoring has been studied using Energy Dispersive X-ray (E.D.X.) analysis and Scanning Electron Microscopy (S.E.M.). Although these third-body layers are deposited on both mating surfaces of the friction couple, special attention has been paid to those formed on the disc brake rotor surface. Concurrently, detailed investigations have been undertaken examining the temperature-dependent, physico-chemical interactions of friction material constituents with each other, atmospheric oxygen and countermember materials using X-Ray Diffraction (X.R.D.).Evidence is presented relating the tribological performance of the friction pair to both the transfer film thermochemistry and the friction material composition. Among those characteristics describing the tribological performance of the friction couple, particular attention has been applied to the generation of Disc Thickness Variations (D.T.V.) induced by Off-Brake or Non-Braking Wear (O.B.W. or N.B.W.). The critical role of solid lubricants and abrasive friction modifiers and their effectiveness over a range of contact pressures / temperatures has received particular attention. Information obtained using various surface analytical techniques combined with detailed dimensional assessments of the affected triboelements has been used to show the considerable significance of abrasive particle size in determining the overall tribological behaviour of the friction pair, especially with respect to the wear regime and extent encountered at the surface of the countermember during O.B.W.Wear mechanisms are described for the generation of off-brake wear, these varying with friction material formulation. Dynamic and temperature-dependent influences on the level of in-service disc brake rotor runout are named as causes for particular forms of disc thickness variation generated by aggressive friction materials. Keywords: Third-body layer; Transfer film; Tribochemistry; Automotive Friction Braking; Cold Judder; Disc Thickness Variation; Disc Brake; Friction Material.
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Hoffert, Kara Anne. "Maternal-fetal interactions and angiogenesis in early bovine pregnancies derived from nuclear transfer /." For electronic version search Digital dissertations database. Restricted to UC campuses. Access is free to UC campus dissertations, 2005. http://uclibs.org/PID/11984.
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Kuo, Long-Sheng 1969. "Non-equilibrium energy transfer and phase change during intense picosecond laser-metal interactions." Thesis, Massachusetts Institute of Technology, 2001. http://hdl.handle.net/1721.1/34346.
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Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2001.<br>Includes bibliographical references (leaves 55-57).<br>Laser interactions with metals involve absorption of photon energy by electrons, energy coupling between electrons and the lattice, and energy transport by diffusion of electrons and lattice vibrations. During picosecond laser irradiation of metal films, electrons and the lattice are not in thermal equilibrium. On the other hand, rapid laser heating produces a large degree of superheating and undercooling during melting and solidification. First, this work investigates experimentally non-equilibrium heating processes during intense picosecond laser heating of metal films. Results show excellent agreement with predictions of the two-step radiation heating model. Second, this work develops a general model to characterize both non-equilibrium energy deposition and phase change processes. The predictions show that the non-equilibrium heating processes significantly increase the laser melting threshold, enlarge the thermal-affected region, reduce the lattice temperature rise, prolong the phase change duration, and reduce the solidification speed. These results are important for materials processing using ultrashort pulsed lasers.<br>by Long-Sheng Kuo.<br>S.M.
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Gangolf, Thomas. "Intense laser-plasma interactions with gaseous targets for energy transfer and particle acceleration." Thesis, Université Paris-Saclay (ComUE), 2017. http://www.theses.fr/2017SACLX110.
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Le plus fréquemment, l’interaction laser-matière est étudiée avec des lasers ayant des longueurs d’onde dans l’infrarouge proche (PIR), car ce sont les lasers qui peuvent générer les impulsions les plus intenses. Pour ces lasers, des cibles de densité allant de 0,05 à 2,5 fois la densité critique sont difficiles à créer mais elles offrent des perspectives intéressantes. Dans cette thèse, des jets d’hydrogène ayant de densité dans ce domaine sont utilisées dans le contexte de deux applications :Premièrement, des ions sont accélérées par choc non-collisionnel (collisionless shock acceleration, CSA). Lors de l’interaction d’une impulsion laser PIR avec une cible légè- rement sur-critique, un faisceau de protons est généré. Il est collimé, dirigé vers l’avant et quasiment monoénergetique. Des simulations indiquent que cela est lié à la formation d’un choc non-collisionnel et à l’accélération des protons par ce choc, en sus de leur accélération par le processus standard dit ”target normal sheath acceleration (TNSA)” qui est effectif en face arrière de la cible. Pour beaucoup d’applications, ces faisceaux de particules quasi-monoénergetiques sont plus appropriés que ceux à spectre large qui sont générés de façon routinière par TNSA.Deuxièmement, de l’énergie est transférée d’une impulsion laser (pump) vers une autre en contrepropagation (seed), par rétrodiffusion Brillouin stimulée, dans le régime de couplage fort (strong coupling-SBS), à des densités entre 0,05 et 0,2 fois la densité critique. Pour des impulsions à large bande (60 nanomètres), le rôle de la pré-ionisation sur la propagation et la rétrodiffusion Brillouin spontanée et stimulée est étudié, en incluant l’influence du chirp. Pour des lasers à bande plus étroite, il est démontré que l’impulsion seed peut être amplifiée par des dizaines de milliJoules, et des signatures d’amplification efficace et d’affaiblissement de l’impulsion laser pompe sont trouvées. Ce concept vise à l’amplification des impulsions laser à des puissances au-delà du seuil de dommage des amplificateurs laser basés sur des matériaux solides<br>Laser-matter interaction is studied mostly with near-infrared (NIR) lasers as they can generate the most intense pulses. For these lasers, targets between 0.05 to 2.5 times the critical density are challenging to create but offer interesting prospects. In this thesis, novel high-density Hydrogen gas jet targets with densities in this range are used in view of two applications:First, ions are accelerated by collisionless shock acceleration (CSA). Upon interaction of a NIR laser with a slightly overcritical gas jet target, a collimated, quasi-monoenergetic proton beam is generated in forward direction. Simulations indicate the formation of a collisionless shock and acceleration of protons both by the shock and target normal sheath acceleration (TNSA) on the target rear surface under these conditions. These directed, monoenergetic particle bunches are more suitable for many applications than the broadband particle beams already generated routinely.Second, at densities between 0.05 and 0.2 times the critical density, energy is transferred from one laser pulse (pump) to a counterpropagating pulse (seed), via Stimulated Brillouin Backscattering in the strongly-coupled regime (sc-SBS). For the case of broad- band (60 nanometers) pulses, the role of the preionization for pulse propagation and both spontaneous and stimulated Brillouin backscattering are studied, including the influence of the chirp. It is shown that for narrower bandwidths, the seed pulse is ampli- fied by tens of millijoules, and signatures of efficient amplification and pump depletion are found. This concept aims at amplifying laser pulses to powers above the damage thresholds of solid state amplifiers
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Conant, William Christopher. "Interactions between aerosol, water vapor, and solar radiation /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2000. http://wwwlib.umi.com/cr/ucsd/fullcit?p3025938.
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Tyson, Shelly. "Magma-cryosphere interactions on Mars : the influence of heat-transfer mechanisms on surface morphology." Thesis, Lancaster University, 2016. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.727389.
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Mars is thought to have a planet-wide cryosphere of several kilometres depth consisting of a mixture of rock and permanently frozen ice. The physical processes occurring during magma-cryosphere interaction (MCI) appear to have played a large part in the morphological development of many regions of Mars. The aim of this thesis was to investigate the physical and thermal processes that may take place X during non-explosive MCI. A mass-balance heat-flow model was developed to determine if MCIs could have independently resulted in the formation of features seen on Mars. Laboratory analogue experiments were used to investigate the effects resulting from the heating of a cryosphere analogue over a range of conditions. Two phase (solid particles and liquid water or air) and three phase (solid particles of sand or ice, liquid water and steam) systems were investigated. This enabled the identification of several heat transfer mechanisms; the dominance of these mechanisms varied with the conditions in each experiment. The influence of different heat transfer mechanisms on the development of surface features was also studied. This research has highlighted the complexity of the heat transfer mechanisms and physical interactions that take place during non-explosive magma-cryosphere processes on Mars. We have determined that heat transfer mechanisms can have a significant directional component that results in specific experimental surface morphologies. Similarity to Martian landforms provides insight into their formation mechanisms. This research provides constraints to assist identification and classification of newly discovered landforms within Mars’ landscape.
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Harpe, Anke von. "Polyethylenimine derivatives for gene transfer : Polymer synthesis, coupling of ligands and interactions with DNA /." Marburg : Görich & Weiershäuser, 2000. http://www.gbv.de/dms/bs/toc/319704181.pdf.
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Hodson, Andrew. "Climate, hydrology and sediment transfer process interactions in a sub-polar glacier basin, Svalbard." Thesis, University of Southampton, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.241002.
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Monaco, Serena. "Novel saturation transfer difference (STD) NMR approaches to understand biologically relevant protein-carbohydrate interactions." Thesis, University of East Anglia, 2018. https://ueaeprints.uea.ac.uk/68419/.
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Saturation transfer difference (STD) NMR spectroscopy is a powerful NMR technique extensively used to obtain epitope maps of ligands binding to biologically relevant protein receptors. This allows to reveal semi-quantitative structural details of the interaction, which is key to direct lead optimization efforts in drug discovery. However, it does not give information about the nature of the amino acids surrounding the ligand in the binding pocket. In this thesis, the main effort has been put to develop two novel implementations of STD NMR, aimed at elucidating the surroundings of the ligand (i.e., the amino acids lining the binding pocket, or an adjacent bound ligand) in biologically relevant complexes. First, we report the development of the novel “DiffErential EPitope mapping STD NMR” (DEEP‐STD NMR), a method producing differential epitope maps through i) differential frequency and/or ii) differential solvent (D2O/H2O) STD NMR experiments. These two approaches provide complementary information on the architecture of the binding pocket. The second novel method we propose is “Inter-ligand STD NMR” (IL-STD NMR), which relies on on-ligand differential frequency STD NMR to detect contacts between ligands bound to adjacent sites of a receptor. These novel STD NMR methodologies, in combination with traditional STD NMR and computational tools, have been applied to the study of two systems: the interactions of Cholera Toxin subunit B (CTB) with a set of promising inhibitors; and the interactions of an intramolecular trans-sialidase from Ruminococcus gnavus, a gut microbiota symbiont, with a set of mucin-related sialylated ligands. In the first study, we discovered the existence of a hitherto unknown binding subsite in the GM1 binding site of CTB. In the second study, we provided the first 3D molecular model of a Michaelis complex for an IT-sialidase. In both cases, we demonstrate that our newly developed approaches increase the level of resolution of STD NMR, widening its potential to impact the field of ligand design for biologically relevant receptors.
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Shaffer, Irena Marie. "Effects of Echolocation Calls on the Interactions of Bat Pairs using Transfer Entropy Analysis." Thesis, Virginia Tech, 2020. http://hdl.handle.net/10919/98672.
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Many animal species, including many species of bats, exhibit collective behavior where groups of individuals coordinate their motion. Most bats are unique among these animals in that they use the active sensing mechanism of echolocation as their primary means of navigation. Due to their use of echolocation in large groups, bats run the risk of signal interference from sonar jamming. However, several species of bats have developed various strategies to prevent interference which may lead to different behavior when flying with conspecifics than when flying alone. This thesis seeks to explore the role of this sensing on the behavior of bat pairs flying together. Field data from a maternity colony of gray bats (Myotis grisescens) were collected using an array of cameras and microphones. These data were analyzed using the information theoretic measure of transfer entropy in order to quantify the interaction between pairs of bats and to determine the effect echolocation calls have on this interaction. Results show that there is evidence of information transfer in both the speed of the bats and their turning behavior, and that such evidence is absent when we consider their heading directions. Unidirectional information transfer was found in some subsets of the data which could be evidence of a leader-follower interaction.<br>Master of Science<br>Manyanimalspeciesexhibitcollectivebehaviorwheregroupsofanimalscoordinatetheir motion, as in flocking or schooling. Many species of bats also demonstrate this behavior. Bats are unique among these animals in that they use echolocation as their primary means of navigation. Bats produce ultrasonic pulses or calls and listen to the returning echo to "visualize" their environment. Bats using echolocation in large groups run the risk of other bat calls interfering with their ability to hear their own calls. They have developed various waystopreventinterferencewhichmayleadtodifferentbehaviorwhenflyingwithotherbats thanwhenflyingalone. Fielddatafromamaternitycolonyofgraybatswerecollectedusing a system of cameras and microphones. These data were analyzed to quantify the interaction between pairs of bats and to determine the effect echolocation calls have on this interaction. Results show that there is evidence of information transfer about both the speed of the bats and their turning behavior. There was also evidence of a possible leader-follower interaction in some subsets of the data.
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Allcock, Philip. "A microscopic quantum electrodynamical theory of novel nonlinear optical processes." Thesis, University of East Anglia, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.338097.
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Bellows, Benjamin Davis. "Characterization of nonlinear heat release-acoustic interactions in gas turbine combustors." Diss., Available online, Georgia Institute of Technology, 2006, 2006. http://etd.gatech.edu/theses/available/etd-03262006-205604/.
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Thesis (Ph. D.)--Aerospace Engineering, Georgia Institute of Technology, 2006.<br>Dr. Jeffrey Cohen, Committee Member ; Dr. Jerry Seitzman, Committee Member ; Dr. Jeff Jagoda, Committee Member ; Dr. Ben Zinn, Committee Member ; Dr. Tim Lieuwen, Committee Chair.
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Öcalan, Özel Sila. "University-industry interactions : understanding university licensing strategies and beyond." Thesis, Strasbourg, 2018. http://www.theses.fr/2018STRAB009/document.
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Cette thèse porte principalement sur les stratégies de licence des universités. Afin de comprendre l’impact social des stratégies de licences universitaires, nous examinons le lien entre le degré d’exclusivité des licences et les diverses caractéristiques des inventions sous licence. Les résultats théoriques et empiriques de nos recherches suggèrent que les pratiques des OTTs ne sont peut-être pas toujours optimales, ce qui laisse à penser que des améliorations pourraient encore être apportées. Lorsque les innovations sont séquentielles, les universités pourraient introduire des stratégies alternatives de licences open source. Nous élargissons notre étude en examinant les interactions dynamiques entre divers canaux formels et informels de transfert de connaissances. Notre analyse qualitative longitudinale suggère que l’interaction dynamique crée un effet cumulatif important vis-à-vis de l’activité de valorisation de la recherche, et renforce la dimension collective de la valorisation<br>This thesis primarily focuses on university licensing. To understand the social impact of the university licensing strategies, we examine the link between the degree of exclusivity of licenses and the various characteristics of the licensed inventions. The theoretical and empirical findings of our research suggest that the practices of university technology transfer offices (TTOs) may not always be optimal, underlying the fact that there may still be room for the improvement. We also suggest that, when the innovations are sequential, universities might introduce alternative open source licensing (OSL) strategies. Furthermore, we expand our study by examining the dynamic interactions between various formal and informal channels of transfer. Our longitudinal qualitative methodology suggests that, dynamic interaction creates a strong cumulative effect with respect to the research valorization activity and reinforces the collective dimension of valorization
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El-Jaby, Samy. "[An]Illustrated Re-visitation of Energy Transfer and Energy Absorption in Photon Interactions with Matter." Thesis, McGill University, 2009. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=95609.
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This thesis revisits the processes of energy transfer and energy absorption in photon interactions with matter with particular focus paid towards the calculation of the mass energy transfer coefficient and the mass energy absorption coefficient. The concepts behind these two coefficients have been well enunciated, however, available references do not lend themselves to serve as a visual aid to promote better understanding of the dosimetric quantities related to energy transfer and energy absorption, as well as their relationship to the photon energy and absorber atomic number. An illustrative approach is utilized in explaining the functional relationships between the relevant quantities inherent to these coefficients. In addition, a Photon Energy Transfer and Absorption Coefficients (PETAC) software has been developed to allow for a graphical, dynamic, and interactive format upon which the student of medical physics may observe and intuitively grasp the processes behind energy transfer and energy absorption in photon interactions with matter .<br>Cette thèse révise les procédés de transfer et d'absorbtion d'énergie causés par l'interaction des photons avec la matière en accordant une attention toute particulière aux calculs du coefficient de transfert d'énergie massique et du coefficient d'absorbtion d'énergeie massique. Les concepts définissant ces coefficients son déjà bien établis, mais ils ne proposent pas une excellente comprehension des quantités dosimétriques reliées au transfert et à l'absorbtion d'énergie de même qu'à la relation existant entre l'énergie photonique et le numéro atomique absorbé. Une approche nouvelle et visuellement coherente est proposée afin de metre en lumière une relation fonctionnelle entre ces quantités et ces coefficients. De plus un application informatique, graphique, dynamique et interactive appelée PETAC (Photon Energy Transfer and Absorbtion Coefficients) à été devellopee pour aider les étudiants en physique médicale a visualiser et déduire intuitivement les lien entre les processus de transfert d'énergie, et d'absorbtion d'énergie dû à l'interaction des photons avec la matière .
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Sena, A. M. P. "Density functional theory studies of surface interactions and electron transfer in porphyrins and other molecules." Thesis, University College London (University of London), 2010. http://discovery.ucl.ac.uk/147572/.
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This thesis contains a series of density functional studies on porphyrins, surfaces and other molecules, that are of relevance to surface science and electron transfer. In chapter 1 the main concepts of the thesis and how they fit together, are outlined. Chapter 2 describes density functional theory (DFT), the principle theoretical technique used throughout. The thesis then considers two main aspects. Chapters 3, 4 and 5 look at how systems interact with surfaces and compare and contrast situations of differing interaction strengths. Chapter 3 investigates the weak interaction of a haem molecule with the Si(111):H surface and studies how this interaction can be tuned by desorbing hydrogen atoms from the surface. In chapter 4, the structure of experimentally observed Mn nanolines on the Si(001) surface is studied. How these lines self assemble and interact strongly with the surface is discussed. Elements of these two studies are then combined in chapter 5 with a study of manganese porphyrin on the Si(001) surface displaying some features common to both previous systems. In chapter 6, 7 and 8 the focus switches to electron transfer. The basics of electron transfer theory are outlined in chapter 6. Then, the difficulties faced by DFT when studying electron transfer in large systems, such as the self-interaction error and cubic scaling, are described. Chapter 7 describes the constrained DFT formalism and its implementation into the linear scaling DFT code CONQUEST. In chapter 8, this implementation is used to perform some electron transfer calculations on small organic molecules, with systems demonstrating both charge localization and charge separation investigated. Chapter 9 concludes the thesis indicating how, following this thesis, large scale electron transfer calculations of organic molecules on surfaces can be performed with some confidence and giving suggestions for future calculations.
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Ray, Matthew Preston. "The dynamics of energy and charge transfer in low and hyperthermal energy ion-solid interactions." Connect to this title online, 2009. http://etd.lib.clemson.edu/documents/1252424536/.
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Riachy, Lina. "Nouvelle technique de nanoscopie de fluorescence par excitation non radiative pour l’étude des interactions membrane/substrat." Thesis, Troyes, 2017. http://www.theses.fr/2017TROY0017/document.
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L’objectif de mon travail de thèse a été de mettre au point une nouvelle technique de nanoscopie de fluorescence par excitation non radiative pour l’étude des interactions membrane/substrat. Cette technique repose sur la modification d’une lamelle de verre par une monocouche de boîtes quantiques (QDs). Les QDs joueront alors le rôle de donneurs lors du transfert d’énergie non radiatif. Afin d’obtenir un transfert d’énergie entre cette surface et une membrane (vésicule géante unilamellaire ou cellule vivante), cette dernière est marquée par un fluorophore amphiphile jouant le rôle d’accepteur. Notre étude s’est principalement portée sur l’étude de l’adhésion des vésicules (système modèle de cellule) sur une surface de QDs recouverte de poly-L-lysine. Une attraction électrostatique forte est alors induite, conduisant à l’adhésion des vésicules sur la surface En ajoutant un sel en solution, nous avons pu contrôler finement la force de l’interaction et donc modifier la distance d’équilibre entre la surface et la membrane. A partir de mesure quantitative du quenching des QDs et de la fluorescence émise par le transfert non radiatif, nous avons pu calculer les distances d’équilibre et obtenir une cartographie de ces distances avec une résolution optique nanométrique. Nous avons également utilisé cette technique pour étudier l’adhésion membranaire des cellules U87MG sur différentes surfaces afin d’observer leur points focaux<br>The objective of my thesis work was to develop a new technique of Non-radiative Excitation Fluorescence Microscopy to study the interactions membrane/substrate.This technique is achieved by coating the substrate with donor species, such as quantum dots (QDs). Thus the dyes are not excited directly by the laser source, as in common fluorescence microscopy, but through a non-radiative energy transfer.To prevent dewetting of the donor film, we have implemented a silanization process to covalently bond the QDs on the substrate. A monolayer of QDs was then deposited on only one side of the coverslips. We highlight the potential of our method through the study of Giant Unilamellar Vesicles (GUVs) labeled with DiD as acceptor, in interaction with surface functionalized with poly-L-lysine. In the presence of GUVs, we observed together a quenching of QDs emission and emission of DiD located in the membrane, which clearly indicated that non-radiative energy transfer from QDs to DiD occurs. By changing salt concentration in the solution, we have been able to finely control the force of the interaction and thus modify the equilibrium distance between the surface and the membrane. From quantitative measurements of quenching of QDs and fluorescence emitted by non-radiative transfer, we calculate the equilibrium distances and obtain a mapping of these distances with a nanometric optical resolution. Based on this study, our functionalization technique is also used to observe the adhesion of living cells, U87MG on different surfaces in order to observe their focal points
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Deutsch, Christopher Wayne. "Discovery and Characterization of the Proteins Involved in the Synthesis of N⁶-Threonylcarbamoyl Adenosine, a Nucleoside Modification of tRNA." PDXScholar, 2016. http://pdxscholar.library.pdx.edu/open_access_etds/3080.
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N6-threonylcarbamoyl adenosine (t6A) is a universally conserved tRNA modification found at position 37 of tRNAs which decode ANN codons. Structural studies have implicated its presence as a requirement for the disruption of a U-turn motif in certain tRNAs, leading to the formation of properly structured anticodon stem loop. This structure is proposed to enhance the base pairing between U36 of tRNA and A1 of the codon which aids in translational frame maintenance.
Despite significant effort since its discovery in the 1970s the enzymes involved in its biosynthesis remained undiscovered. Bioinformatic analysis identified two proteins as likely candidates for t6A synthesis, YrdC and YgjD. Subsequent gene knockout experiments in yeast were consistent with their involvement in t6A biosynthesis in vivo. Furthermore, clustering between the bacterial genes ygjD, yeaZ and yjeE as well as the identification of a protein interaction network between YgjD, YeaZ, and YjeE suggested that YeaZ and YjeE might be involved in t6A biosynthesis.
The genes encoding ygjD, yeaZ, yrdC and yjeE were cloned from E. coli and the recombinant protein was purified. Experiments analyzing the incorporation of [U-14C]-L-threonine and [14C]-bicarbonate (substrates previously indicated in its biosynthesis) into tRNA in the presence of these four proteins demonstrated the first reconstitution of the t6A pathway in vitro. LC-MS analysis verified the formation of t6A, and these proteins were renamed TsaD (YgjD), TsaB (YeaZ), TsaC (YrdC), and TsaE (YjeE).
Biochemical characterization of this pathway suggested that the formation of t6A proceeds through an unstable threonylcarbamoyl adenosine monophosphate (TC-AMP) intermediate, which is produced by TsaC from its substrates CO2, L-threonine and ATP. To investigate this reaction in more detail a coupled assay was developed, enabling sensitive detection of turn over. TsaC is a promiscuous enzyme which readily accepts several amino acids as substrates. The formation of t6A from TC-AMP is catalyzed by TsaD, TsaB, and TsaE. Of these three proteins only TsaD is universally conserved suggesting it is the protein catalyzing the transfer of the threonylcarbamoyl moiety to A37 of tRNA. This transfer is not promiscuous as only TC-AMP serves as an efficient substrate for t6A formation. Structural investigation of these proteins are consistent with the formation of a single protein complex potentially alleviating issues with the reactivity and instability of TC-AMP.
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Dinkeloo, Kasia. "New Tools to Understand Mechanisms of Nutrient Transfer from Plants to Biotrophic Pathogens." Diss., Virginia Tech, 2018. http://hdl.handle.net/10919/97521.
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The interaction between Arabidopsis and its natural downy mildew pathogen, Hyaloperonospora arabidopsidis (Hpa), provides a model for understanding how oomycetes colonize plants. Hpa is a model organism for many highly destructive oomycete pathogens and transcriptomics of this interaction have been well-documented. However, the material in these studies has been derived from infected leaves that contain a mix of pathogen-proximal and pathogen-distal plant cells. The most direct interactions between Arabidopsis and Hyaloperonospora arabidopsidis occur in haustoriated cells- where the pathogen can secrete effectors and acquire nutrients needed for successful colonization and reproduction. These cells are difficult to isolate due to their limited number and ephemeral nature. I have developed a method to isolate the translatome (i.e., mRNAs associated with ribosomes) of pathogen-proximal cells. This method utilizes translating ribosome immuno-purification technology (TRAP), regulated by both pathogen-responsive and tissue-specific promoters, to isolate mRNAs that are being translated in pathogen-proximal cells. Compared to "bulk" transcriptomics of material isolated from homogenized leaves, this method will enrich for transcripts that are differentially expressed, and translated, in pathogen-proximal cells. From this method, RNA was isolated in amount and quality sufficient for sequencing. This sequencing data will enable the discovery of plant genes that may be manipulated by the pathogen to suppress defense responses and extract nutrients.<br>Ph. D.
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Li, Changhui. "Radiative interactions: I. Light scattering and emission from irregular particles. II. Time dependent radiative coupling of an atmosphere-ocean system." Texas A&M University, 2006. http://hdl.handle.net/1969.1/4135.
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In the first part of this dissertation, radiative interactions with single irregular particles
are simulated. We first introduce the basic method and techniques of Finite-
Difference Time-Domain method(FDTD), which is a powerful method to numerically
solve Maxwell's equations with high accuracy. To improve the efficiency of FDTD,
we also develop a parallel FDTD code. Since FDTD can simulate light scattering
by arbitrary shape and compositions, we study several radiative interaction cases for
single particles in an external plane parallel light source: the surface roughness effects
on the scattering, electric and magnetic energy density distribution in irregular particles,
and backscattered Mueller images. We also develop an innovative and accurate
method to simulate the infinitesimal electric dipole radiation from inside a particle
with arbitrary shape and composition. Our research and results are very important
to study light scattering by irregular particles, Raman scattering and fluorescence.
In the second part of the dissertation, we study radiative interactions in an
atmosphere-ocean system. By using the so called Matrix operator method, not only
the radiance of the radiation field, but also the polarization of the radiation field
are obtained. Given the single layer information for the atmosphere, time dependent
ocean surface shapes, and the ocean with no interface, the Matrix operator method couples these three layers and provides both the radiance and polarization reaching
a certain detector in the time domain, which are essential for atmospheric science
and oceanography. Several simple cases are studied by this method to demonstrate
its accuracy and robustness. We also show the most difficulties in this method and
discuss what one need to do in future research works.
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Marquart, Kyle Anthony. "pH as a control on interactions of methanogens and iron reducers." Thesis, Kansas State University, 2017. http://hdl.handle.net/2097/35567.
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Master of Science<br>Department of Geology<br>Matthew Kirk<br>A growing body of evidence demonstrates that methanogenesis and Fe(III) reduction can occur simultaneously. However, environmental controls on interactions between each are poorly understood. In this study we considered pH as a control on interactions between Fe(III) reduction and methanogenesis in anoxic sediment bioreactors. The reactors consisted of 100mL of synthetic aqueous media, and 1 g of marsh sediment amended with goethite (1mmol). One set of reactors received acidic media (pH 6), and the other alkaline media (pH 7.5). Each set received media containing acetate (0.25 mM) to serve as an electron donor. Control reactors, deficient in acetate, were also included. We maintained a fluid residence time of 35 days by sampling and feeding the reactors every seven days.
For pH 6.0 and pH 7.5 reactors, the measured pH of effluent samples averaged 6.33 and 7.37, respectively. The extent of Fe(III) reduction and methanogenesis varied considerably between each set of reactors. More Fe(III) was reduced in the pH 6 reactors (646.39 μmoles on avg.) than the pH 7.5 reactors (31.32 μmoles on avg.). Conversely, more methane formed in pH 7.5 reactors (127.5 μmoles on avg.) than the pH 6 reactors (78.9 μmoles on avg.). Alkalinity concentrations during the middle and end of the experiment averaged 9.6 meq/L and 5.2 meq/L in pH 6 and pH7.5 reactors, respectively Although much less Fe(III) reduction occurred in pH 7.5 reactors, the relative abundance of Fe(III) reducers in them decreased little from levels observed in the pH 6 reactors. Sequences classified within Geobacter, a genus of bacteria known primarily as dissimilatory metal reducers, accounted for 22% and 13.45% of the sequences in the pH 6 and pH 7.5 reactors and only 0.8% of the sequences in the marsh sediment inoculum. In contrast, sequences classified within orders of methanogens were low in abundance, making up only 0.47% and 1.04% of the sequences in the pH 6 and pH 7.5 reactors, respectively.
Mass balance calculations demonstrate that the amount of electron donor consumed by each group varied considerably between the sets of reactors. Expressed as a quantity of acetate, the reactions consumed about 160μM of electron donor each in pH 6 reactors. In contrast, methanogenesis consumed over 30 times more electron donor than Fe(III) reduction in the pH 7.5 reactors. Thus, the results of our experiment indicate that the decrease in electron donor consumption by Fe(III) reduction at basic pH was nearly matched by the increase in electron donor consumption by methanogens. Results of geochemical modeling calculations indicate that more energy was available for Fe(III) reduction in the pH 6.0 reactors than the pH 7.5 reactors, matching variation in Fe(III) reduction rates, and that the density of sorbed ferrous iron was higher in pH 6 reactors than pH 7.5 reactors. Thus, the calculation results are consistent with bioenergetics, but not variation in ferrous iron sorption, as a potential mechanism driving variation in the balance between each reaction with pH.
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Roy, Subhradeep. "Multiscale Views of Multi-agent Interactions in the Context Of Collective Behavior." Diss., Virginia Tech, 2017. http://hdl.handle.net/10919/78615.
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In nature, many social species demonstrate collective behavior ranging from coordinated motion in flocks of birds and schools of fish to collective decision making in humans. Such distinct behavioral patterns at the group level are the consequence of local interactions among the individuals. We can learn from these biological systems, which have successfully evolved to operate in noisy and fault-prone environments, and understand how these complex interactions can be applied to engineered systems where robustness remains a major challenge. This dissertation addresses a two-scale approach to study these interactions- one in larger scale, where we are interested in the information exchange in a group and how it enables the group to reach a common decision, and the other in a smaller scale, where we are focused in the presence and directionality in the information exchange in a pair of individuals. To understand the interactions at large scale, we use a graph theoretic approach to study consensus or synchronization protocols over two types of biologically-inspired interaction networks. The first network captures both collaborative and antagonistic interactions and the second considers the impact of dynamic leaders in presence of purely collaborative interactions. To study the interactions at small scale, we use an information theoretic approach to understand the directionality of information transfer in a pair of individual using a real-world data-set of animal group motion. Finally, we choose the issue of same-sex marriage in the United States to demonstrate that collective opinion formation is not only a result of negotiations among the individuals, but also reflects inherent spatial and political similarities and temporal delays.<br>Ph. D.
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Bahner, Daniel T. "Interactions between faculty and Latina/o and White community college transfer students| A mixed methods study." Thesis, California State University, Fullerton, 2015. http://pqdtopen.proquest.com/#viewpdf?dispub=3663984.
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<p> Although the number of community college Latina/o students is steadily growing, their completion and transfer rates lag behind other groups. Because the majority of Latina/o students begin their postsecondary education in community colleges only to transfer at very low rates, the long-storied promise of community colleges serving as "democracy's colleges" is more rhetoric than reality. Drawing upon Stanton-Salazar's (2004, 2011) work on the potential roles that institutional agents can play in working against the forces of educational stratification by lending their social capital to minority students, the purpose of this convergent mixed methods research was to examine the differences Latina/o and White potential transfer students report about the ways that faculty have facilitated or impeded their negotiation of the transfer process and the roles institutional agents filled in facilitating students' transfer progress.</p><p> The study followed a convergent mixed methods design, whereby 233 potential students completed an original survey concerning their interactions with faculty, and 14 potential transfer students participated in semi-structured interviews concerning their interactions with faculty while negotiating the transfer process. Analysis of the quantitative data collected through the survey revealed that students are generally pleased with their interactions with HCC faculty; and furthermore that Latina/o students rate their interactions with faculty more highly than White students do. From the qualitative data collected through the interviews eight themes emerged, including the importance of community colleges, social capital, developing goals, accepting responsibility for one's decisions, and caring faculty. Three convergences arose from combining the findings of the two separate modes of inquiry: (a) students are generally pleased with HCC faculty; (b) the importance of caring faculty; and (c) faculty serving institutional agents for students.</p><p> After the interpretations of these findings were discussed, as well as their implications for policy, theory, practice, and future research, three recommendations for action were offered.</p>
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Cranswick, Matthew A. "Gas-phase Photoelectron Spectroscopy and Computational Studies of Metal-thiolate Interactions: Implications to Biological Electron Transfer." Diss., The University of Arizona, 2008. http://hdl.handle.net/10150/195569.
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The research outlined in this dissertation focuses on understanding the role of metal-sulfur interactions as applied to bioinorganic and organometallic systems. This metal-sulfur interaction is analyzed using both gas-phase photoelectron spectroscopy (PES) and density functional theory (DFT). Gas-phase photoelectron spectroscopy is the most direct probe of electronic structure and is used in these studies to probe the molecular orbital energy levels of these model compounds, giving rise to an understanding of the metal and sulfur orbital interactions and characters (i.e. is an orbital primarily metal or sulfur based). Using density functional theory, orbital energies, overlap, and characters can be calculated and complement the PES experiments allowing for a detailed understanding of the electronic structure. The first part of my dissertation explains the design and implementation of a dual source gas-phase ultraviolet/X-ray photoelectron spectrometer (UPS/XPS). This gas-phase UPS/XPS can be used to quantify the bonding/antibonding character of frontier molecular orbitals, with specific applications to metal-sulfur interactions, allowing for a thorough analysis of the metal-sulfur interaction. The second part of the dissertation explores using model complexes, of the type Cp₂V(dithiolate) (where Cp is cyclopentadienyl and dithiolate is 1,2-ethenedithiolate or 1,2-benzenedithiolate), along with PES and DFT calculations to investigate the role of the pyranopterindithiolate cofactor and the d¹ electron configuration in modulating the redox potential and electron transfer in the active sites of molybdenum enzymes. This study shows that the d¹ electronic configuration offers a low energy electron transfer pathway for the reoxidation of the active site molybdenum center. The third part of the dissertation explores the use of model compounds that specifically focus on iron-thiolate interactions in biological systems, and the effect of electronic energy matching and sterics on the oxidation potential of this interaction. This study has shown that the metal-sulfur interaction is sensitive to the orientation of the thiolate ligand, and that during oxidation an “electronic-buffering effect” makes assigning a formal oxidation state to the metal center almost meaningless. All of these studies illustrate how the thiolate ligand can modulate the electron density and oxidation potential of the metal-sulfur interaction and the implication of this interaction to biological electron transfer.
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Baranova, Maria V. "Protein-Protein Interactions and Electron Transfer Associated with Cytochrome F and Plastocyanin From the Cyanobacterium Prochlorothrix Hollandica." Bowling Green State University / OhioLINK, 2007. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1178243290.
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Baugh, Jeffrey Loren. "Structural changes of fibronectin during cell interactions and adsorption to surfaces measured using fluorescence resonance energy transfer /." Thesis, Connect to this title online; UW restricted, 2003. http://hdl.handle.net/1773/8083.
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Myagkiy, Andrey. "Mineralization of Nickel in saprolitic ore of New Caledonia : Dynamics of metal transfer and modeling of coupled geochemical and hydrodynamic processes." Thesis, Université de Lorraine, 2017. http://www.theses.fr/2017LORR0277/document.
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La Nouvelle-Calédonie détient d’importantes réserves de nickel latéritique et est devenue, en 2017, le cinquième producteur mondial de Ni. Ces dépôts sont habituellement considérés comme résultant d’altération latéritique intense de la péridotite, qui constitue la principale source de nickel. Ainsi, le principal modèle conceptuel de la formation des minerais de nickel latéritique en Nouvelle-Calédonie est un modèle per descensum où la plupart des éléments (Mg, Ni et Si) ont été lessivés depuis la surface, en particulier lors du développement du sol latéritique. Le nickel est ensuite reprécipité, soit dans la goethite de la latérite fine, soit au niveau de la saprolite, sous forme de goethite et de silicates Mg-Ni, dont des talc-like ou kérolite. Les observations minéralogiques et structurales récentes ainsi que les données minières ont cependant mis en évidence de nombreux types d’hétérogénéités dans les concentrations, et la distribution des porteurs de Ni. Comprendre les facteurs la mobilité de cet élément, ses mécanismes de piégeage ainsi que les paramètres chimiques et hydrodynamiques à l’origine de ce piégeage, est essentiel afin de prévoir la distribution du nickel dans les profils latéritiques en Nouvelle-Calédonie, et constitue l’objectif de cette thèse. Ce travail est basé sur le développement (i) d’un modèle 1D s’intéressant en particulier au comportement géochimique du nickel lors de l’altération de l’ophiolite, sa comparaison avec les observations in situ et une compréhension détaillée de la mobilité des éléments traces pendant le processus, et (ii) d’un modèle 2D hydro-géochimique couplé avec l’hydrodynamique complexe des profils latéritiques, améliorant ainsi la connaissance du contrôle structural sur la redistribution et la minéralisation du nickel. Tandis que les simulations 1D permettent de mieux comprendre les aspects chimiques contrôlant les processus de rétention du nickel au sein d’un profil, le modèle 2D se révèle être un outil puissant pour la compréhension de la formation des dépôts locaux les plus riches en nickel. Les résultats du modèle 2D montrent une remobilisation du nickel depuis les horizons supérieurs puis sa reprécipitation sous forme de silicates dans la saprolite. Le nickel remobilisé provient principalement de la zone saprolitique à cause de la dissolution des silicates de nickel formés précédemment ainsi que de l’olivine résiduelle de cette zone. Ce modèle a également révélé que l’horizon latéritique (et en particulier les oxy- hydroxydes de nickel) avait un faible impact dans la remobilisation du nickel. L’infiltration latérale de l’eau contenant le nickel dissout issu des formations surincombantes est à l’origine de la formation des zones les plus riches dans les parties inférieures du profil. Cette redistribution est entièrement contrôlée par l’hydrodynamique locale, la topographie ainsi que l’orientation et la position des fractures. Les modèles présentés permettent d’expliquer les processus de formation des minerais de nickel latéritique saprolitique, améliorant ainsi la compréhension des paramètres contrôlant la mobilité des éléments traces dans un environnement ultramafique. Ceci donne une nouvelle clé de distribution du nickel dans les profils actuels, qui peut devenir un outil pour la prospection minière, et la recherche de nouvelles ressources exploitables<br>New Caledonia hosts significant lateritic nickel reserves, and presently became the fifth largest Ni producer in the world. These deposits are generally thought to be closely as- sociated with the intense chemical and mechanical weathering of peridotite bedrock that is a principal source of nickel. Thus, the main ore genesis model for Ni ores in New Caledonia is based on a single per descensum model where most elements (Mg, Ni, and Si) are leached from the surface, particularly, during lateritic soil development. Nickel is then concentrated either in the fine-grained laterite where goethite is the main Ni bearer, the so-called ’lateritic ore’, or below the laterites, in the saprolite level, where nickel occurs as goethite and several types of Mg-Ni silicates, in particular kerolite. Recent mineralogical and structural observations together with mining data have revealed a lot of different types of heterogeneities associated with the distribution and mineralogy of Ni bearing minerals. Therefore, in depth investigations of Ni mobility, its retardation processes along with its governing chemical and hydrodynamic parameters are of big importance for understanding and subsequent prediction of Ni distribution in profiles of New Caledonia. Such an investigation is an objective of the present work. The concept is based on the development of i) a powerful 1D model with particular emphasis on Ni geochemical behavior during ophiolite weathering, its comparison with in situ observations, and detailed understanding of trace elements mobility, and ii) 2D hydro-geochemical model coupled with complex hydrodynamics, that would additionally provide new insight into the structural control on Ni redistribution and mineralization. While the 1D simulations provide a remarkable result for understanding the chemical features that drive Ni retention processes in a profile, 2D model appears to be a powerful tool for understanding how local Ni-enrichments may form. The results of this model show the reactivation of Ni from upper horizons and its concentration in neo-formed silicates in bottom of the saprolite. The reactivated Ni comes mostly from the saprolite horizon due to the redissolution of previously formed Ni-bearing silicates and still persisting in this olivine zone. Modeling has revealed minor contribution of the laterite horizon (Ni-oxi-hydroxides) into the Ni remobilization. The lateral infiltration of water with remobilized Ni from areas such as topographic highs to downstream slope areas leads to the formation of richest deposits in this lower part of profile. The manner of redistribution is fully governed by the topographic slopes, orientation and position of the fractures. Presented models appear to be of importance in attempt of explanation of Ni mineralization processes, revealing the main keys to understanding the control of trace elements mobility in ultramafic environment. The latter gives new insights into the Ni distribution in present day profiles and, therefore, may greatly help in mineral prospecting and forecasting the distribution of future resources
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Malatkar, Pramod. "Nonlinear Vibrations of Cantilever Beams and Plates." Diss., Virginia Tech, 2003. http://hdl.handle.net/10919/28301.
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A study of the nonlinear vibrations of metallic cantilever beams and plates subjected to transverse harmonic excitations is presented. Both experimental and theoretical results are presented. The primary focus is however on the transfer of energy between widely spaced modes via modulation. This phenomenon is studied both in the presence and absence of a one-to-one internal resonance. Reduced-order models using Galerkin discretization are also developed to predict experimentally observed motions. A good qualitative agreement is obtained between the experimental and numerical results.
Experimentally the energy transfer between widely spaced modes is found to be a function of the closeness of the modulation frequency to the natural frequency of the first mode. The modulation frequency, which depends on various parameters like the amplitude and frequency of excitation, damping factors, etc., has to be near the natural frequency of the low-frequency mode for significant transfer of energy from the directly excited high-frequency mode to the low-frequency mode.
An experimental parametric identification technique is developed for estimating the linear and nonlinear damping coefficients and effective nonlinearity of a metallic cantilever beam. This method is applicable to any single-degree-of-freedom nonlinear system with weak cubic geometric and inertia nonlinearities. In addition, two methods, based on the elimination theory of polynomials, are proposed for determining both the critical forcing amplitude as well as the jump frequencies in the case of single-degree-of-freedom nonlinear systems.
An experimental study of the response of a rectangular, aluminum cantilever plate to transverse harmonic excitations is also conducted. Various nonlinear dynamic phenomena, like two-to-one and three-to-one internal resonances, external combination resonance, energy transfer between widely spaced modes via modulation, period-doubled motions, and chaos, are demonstrated using a single plate. It is again shown that the closeness of the modulation frequency to the natural frequency of the first mode dictates the energy transfer between widely spaced modes.<br>Ph. D.