Дисертації з теми "Detailed kinetics model"

A one-dimensional, steady-state numerical model of the combustion of homogeneous solid propellant has been developed. The combustion processes is modeled in three regions: solid, two-phase (liquid and gas) and gas. Conservation of energy and mass equations are solved in the two-phase and gas regions and the eigenvalue of the system (the mass burning rate) is converged by matching the heat flux at the interface of these two regions. The chemical reactions of the system are modeled using a global kinetic mechanism in the two-phase region and an elementary kinetic mechanism in the gas region. The model has been applied to RDX, HMX and GAP. There is very reasonable agreement between experimental data and model predictions for burning rate, temperature sensitivity, surface temperature, adiabatic flame temperature, species concentration profiles and melt-layer thickness. Many of the similarities and differences in the combustion of RDX and HMX are explained from sensitivity analysis results. The combustion characteristics of RDX and HMX are similar because of their similar chemistry. Differences in combustion characteristics arise due to differences in melting temperature, vapor pressure and initial decomposition steps. A reduced mechanism consisting of 18 species and 39 reactions was developed from the Melius-Yetter RDX mechanism (45 species, 232 reactions). This reduced mechanism reproduces most of the predictions of the full mechanism but is 7.5 times faster. Because of lack of concrete thermophysical property data for GAP, the modeling results are preliminary but indicate what type of experimental data is necessary before GAP can be modeled with more certainty.

A detailed chemical kinetic model is developed and tested for the combustion of C2 and C3 oxygenated fuels such as ethanol, DME (dimethyl ether), acetone and n-propanol. It is validated by comparing predictions with experimental data on the structure of low pressure burner stabilised premixed flames and laminar burning velocities over a wide range of equivalence ratios. Data from shock tube and stirred reactor studies has also been considered. The elementary reactions of ethanol and DME oxidation have been studied extensively and were used as a starting point for extension to C3 oxygenated fuels. The chemistry of acetylene which is one of major intermediate species in higher hydrocarbon flames was also updated to improve the reliability of the present mechanism and acetylene laminar burning velocities and low-pressure premixed lean and rich flames were also computed. The detailed mechanism features more than 1500 reaction steps and 269 species. The structure of laminar premixed flames are predicted by using measured temperature profiles and conditions cover fuel-lean and fuel-rich mixtures at low pressure. The profiles of reactants, products and major intermediate species are compared to experimental data from mass spectrometry and the overall agreement between the kinetic model and experimental data is satisfactory. An analytic study of fuel consumption pathways is carried out to understand the detailed consumption pathways. The present mechanism is also tested against laminar flame speeds by calculating freely propagating premixed flames to extend the understanding of the combustion characteristics of oxygenated fuels. A sensitivity analysis is also performed.

Thesis (MSc)--Stellenbosch University, 2015.
ENGLISH ABSTRACT: Having caused the deaths of more than 10 million individuals since 2000 with most of them occurring in Africa, malaria remains a serious disease that requires undivided attention. To this end a detailed kinetic model of Plasmodium falciparum glycolysis was constructed, validated and used to determine potential drug targets for the development of novel, effective antimalarial therapies. The kinetic model described the behaviour of the glycolytic enzymes with a set of ordinary differential equations that was solved to obtain the steady state fluxes and concentrations of internal metabolites. The model included a glycerol branch represented in a single fitted equation. This present study set out to detect, characterise, and incorporate into the model the enzymes that constitute the glycerol branch of P. falciparum glycolysis. The kinetic parameters of glycerol 3-phosphate dehydrogenase (G3PDH), the first enzyme in the branch and catalyst of the dihydroxyacetone phosphosate (DHAP) reducing reaction, was determined and added to the detailed kinetic model. The model was subsequently validated by comparing its prediction of steady state fluxes with experimentally measured fluxes. Once it was evident that the predictions of the unfitted model agreed with experimentally measured fluxes, metabolic control analysis was performed on this branched system to ascertain the distribution of control over the steady state flux through the glycerol branch. The control G3PDH exercised over its own flux was less than expected due to the enzyme’s sensitivity to changes in NADH and thus the redox balance of the cell. Attempts were made to detect the enzymes responsible for the conversion of glycerol 3-phosphate (G3P) to glycerol. Very low levels of glycerol kinase activity was observed. Although G3P-dependent release of inorganic phosphate was detected results were inconclusive as to whether a non-specific phosphatase also mediated the conversion. Overall, the expansion of the model to include G3PDH did not affect the steady state metabolite concentrations and flux adversely.
AFRIKAANSE OPSOMMING: Vanaf die jaar 2000 het malaria die dood van meer as 10 miljoen mense veroorsaak. Die meeste sterftes het in Afrika voorgekom —’n aanduiding van hoe ernstige siekte dit is en een wat onverdeelde aandag moet geniet. Om hierdie rede is ’n gedetaileerde kinetiese model van glikoliese in Plasmodium falciparum gebou, gevalideer en gebruik om potensiële dwelm teikens te identifiseer vir die ontwikkeling van nuwe, meer effektiewe anti-malaria terapieë. Die kinetiese model beskryf die gedrag van die glikolitiese ensieme in terme van gewone differensiële vergelykings wat opgelos is om die bestendige toestand fluksies en interne metaboliet konsentrasies te bepaal. Die model sluit ’n gliserol-tak in wat deur ’n enkele aangepaste vergelyking verteenwoordig word. Hierdie studie het voorgeneem om die ensieme van die gliserol-tak van P. falciparum glikoliese te identifiseer, karakteriseer en in die model te inkorporeer. Ons het die kinetiese parameters van die eerste ensiem in die gliserol-tak, gliserol 3-fosfaat dehidrogenase (G3PDH), die katalis van die dihidroksiasetoon fosfaat(DHAP) reduserende reaksie, bepaal. Die kinetiese parameters is by die gedetaileerde model gevoeg. Validering het plaasgevind deur die model se voorspellings met eksperimenteel bepaalde waardes te vergelyk. Toe dit duidelik geword het dat die voorspellings van die model met die eksperimenteel bepaalde fluks ooreenstem, is metaboliese kontrole analiese op die vertakte sisteem uitgevoer. Dit is gedoen om vas te stel hoe die bestendige toestand fluks deur die gliserol-tak beheer word. G3PDH het nie volle beheer oor sy eie fluks nie, in teenstelling met ons vergewagtinge. Daar is gepoog om vas te stel watter ensieme verantwoordelik is vir die produksie van gliserol vanuit gliserol 3-fosfaat (G3P). ’n Lae gliserolkinase aktiwiteit is waargeneem. Alhoewel G3P afhanklike vrystelling van anorganise fosfaat waargeneem is, is dit nie duidelik vanuit die resultate of die proses deur ’n nie-spesifieke fosfatase uitgevoer word nie. Die uitbreiding van die model om ’n G3PDH vergelyking in te sluit het nie die bestendige toestand metaboliet konsentrasies en fluks negatief geaffekteer nie.

Thesis (PhD (Biochemistry))--University of Stellenbosch, 2009.
ENGLISH ABSTRACT: With the recent advances in the field of molecular biology, there is an increased need to integrate data on the various constituents of the cell in kinetic models that can predict and describe cellular behavior. When working towards a description of the entire cell using such kinetic models, the question arises: How do we compare different models for a given biological network? This is the central question addressed in my thesis and I developed and applied mathematical and computational methods for comparing dozens of existing models of erythrocyte and yeast glycolysis. To compare the steady-state behavior in models of erythrocyte glycolysis, I focussed on the function of the pathway, which is to supply the cell with Gibbs-free energy (γ- phosphate of ATP). I used supply-demand analysis in the framework of metabolic control analysis to make this comparison, which revealed that the ATP concentrations were homeostatically buffered at varying supply rates. I also applied this approach to compare steady-state behavior in models of yeast glycolysis, finding that they were not necessarily optimized for homeostatic maintenance of the ATP concentration and that in models for this organism the rate of ATP production is often determined by the supply reactions of glycolysis. In addition, I tested whether a kinetic model can describe novel behavior if it is adjusted to conditions different from those for which the model was originally constructed. More specifically, using a model of steady-state yeast glycolysis, I showed that small adjustments to the original enzyme concentrations are enough to obtain an oscillating model, which shows a remarkable resemblance to the experimentally observed oscillations. Importantly, some of these enzyme concentrations changes are known to occur during the pre-treatment of the cells which is necessary to obtain oscillatory behavior. To the best of my knowledge, the resulting model is the first detailed kinetic model that describes the experimentally observed strong synchronization of glycolytic oscillations in yeast populations. To analyze the dynamic behavior of yeast glycolytic models and to compare different models in terms of dynamics, I introduced a framework used in physics and engineering to create a vector based, two dimensional graphical representation of the oscillating metabolites and reactions of glycolysis. Not only was it possible to make a concise comparison of the set of models, but with the method I could also quantify the contribution of the interactions in the network to the transduction of the oscillations. Furthermore I could distinguish between different mechanisms of oscillation for each of the models, and demonstrated how the framework can be used to create such representations for experimental data sets.
AFRIKAANSE OPSOMMING: Met die onlangse vooruitgang in die veld van molekulere biologie, is daar ?n toenemende behoefte om data rakende die verskeie komponente van die sel in kinetiese modelle te integreer, om sodanig selgedrag te voorspel en te beskryf. As daar gepoog word om ’n beskrywing van die sel as geheel te verkry d.m.v. sulke kinetiese modelle, onstaan die vraag: Hoe vergelyk ons verskillende modelle van ’n gegewe biologiese netwerk? Dit is die sentrale vraag wat my tesis aanspreek en ek het wiskundige en numeriese metodes ontwikkel en toegepas om talle bestaande modelle van gis- en eritrosietglikolise te vergelyk. Om die bestendige-toestand gedrag in modelle van eritrosietglikolise te vergelyk, het ek gefokus op die funksie van die padweg, naamlik om die sel met Gibbs-vrye energie (γ-fosfaat van ATP) te voorsien. Ek het vraag-aanbod analiese in die raamwerk van metaboliese kontrole analiese gebruik om hierdie vergelyking te maak, wat getoon het dat die ATP konsentrasies homeostaties gebuffer was by verskillende aanbod tempos. Ek het ook hierdie aanpak gebruik om die bestendige-toestand gedrag in modelle van gisglikolise te vergelyk, en het bevind dat hulle nie noodwendig geoptimiseer is om ?n homeostatiese balans in die ATP konsentrasie te handhaaf nie, en dat in modelle vir hierdie organisme, die tempo van ATP produksie dikwels bepaal word deur die aanbod reaksies van glikoliese. Ek het verder ook bepaal of so ?n kinetiese model nuwe soorte gedrag kan beskryf, as dit aangepas word aan omstandighede wat verskil van dié waarvoor die model oorspronklik gekonstrueer was. Meer spesifiek, deur ?n model van bestendige-toestand gisglikolise te gebruik, kon ek wys dat klein veranderinge aan die oorspronkline ensiem konsentrasies genoeg was om ?n ossilerende model te verkry, wat opmerklik ooreenstem met die eksperimenteel waargenome ossilasies. Let ook daarop dat sommige van hierdie ensiem konsentrasie veranderinge plaasvind tydens die voorafbehandeling van die selle, wat essensieel is om die ossilasies waar te neem. Tot die beste van my kennis is die model wat ek met hierdie prosedures verkry het, die eerste gedetaileerde kinetiese model wat die eksperimenteel waargenome sterk sinkronisasie in ossilerende gis populasies voorspel. Om gis glikolitiese modelle te vergelyk in terme van hul dinamiese gedrag, het ek ?n raamwerk wat in fisika en ingeneurswese gebruik word, ingespan om ?n vektor-gebasseerde, twee dimensionele grafiese voorstelling van die ossilerende metaboliete en reaksies te maak. Hierdie raamwerk het dit nie net moontlik gemaak om ?n kompakte vergelyking van ?n stel modelle te maak nie, maar ek kon ook die bydrae van interaksies in die netwerk tot transduksie van die ossilasies kwantifiseer. Ek kon verder onderskeid tref tussen die verskillende ossilasiemeganismes vir elk van die modelle, en het ook gedemonstreer hoe die raamwerk gebruik kan word om sulke voorstellings vir eksperimentele datastelle te skep.

Thesis (MSc (Biochemistry))--University of Stellenbosch, 2009.
ENGLISH ABSTRACT: In Africa alone, Plasmodium, the causative agent of malaria is estimated to kill a child, under the age of five every thirty seconds140. The ability of the parasite to rapidly attain resistance, has resulted in immunity of the parasite to all, except one group of frontline drugs. The need to develop novel drugs, vaccines and prevention strategies that are accessible and affordable for third world countries is of the utmost importance to prevent needless human suffering and death. The glycolytic pathway is an attractive drug target since it is the principal source of ATP for the parasite. Many of the glycolytic enzymes have been studied and proposed as drug targets, but the importance of these enzymes for the function of the pathway as a whole has not been considered. It is known, from the frameworks of metabolic control analysis, that control of the flux and metabolite concentration can be divided among the individual steps. Differential control analysis of Plasmodium and erythrocyte glycolysis may reveal potential drug targets. These analyses require a detailed kinetic model of Plasmodium glycolysis, and the feasibility of constructing and validating such a model was the aim of this study. In this work we determined the feasibility of constructing and validating a detailed kinetic model for the Plasmodium falciparum glycolytic pathway. Whether the construction and validation of this kinetic model was feasible or not was decided on the basis of the ability to: i) culture and isolate sufficient asexual parasites for enzymatic and steady state assays , ii) obtain kinetic parameters such as Km and Vmax for each glycolytic enzyme, either from literature or experimentally, iii) measure glycolytic fluxes, iv) determine glycolytic intermediate concentrations, v) construct a kinetic model from the kinetic parameters and vi) validate it with steady state glycolytic fluxes and metabolite concentrations Each of the above criteria were successfully addressed. In summary, the kinetic parameters and glycolytic fluxes that were measured experimentally, were used to construct and partially validate a detailed kinetic model, respectively. Further validation of the model by means of steady state metabolite concentrations was shown to be possible with the development of a suitable protocol to measure the glycolytic intermediate concentrations. The model presented in this work may play an important role in drug target identification and improving the current understanding of host-parasite interactions and glycolytic regulation.
AFRIKAANSE OPSOMMING: Plasmodium, die parasiet wat malaria veroorsaak, is in Afrika alleen elke dertig sekondes verantwoordelik vir die afsterwe van ’n kind jonger as vyf jaar. Die parasiet se vermoë om vinnig weerstand op te bou het daartoe gelei dat Plasmodium weerstandbiedend is teen byna alle nuwe teen-malaria middels, behalwe vir ’n enkele toonaangewende groep. Die ontwikkeling van nuwe malaria teen-middels is van uiterste belang om lyding te voorkom. ’n Goeie teiken vir teen-malaria middels is die glikolitiese padweg omdat die metaboliese padweg essensieël is vir die produksie van ATP, die energiebron van die parasiet. Desondanks die feit dat meeste van die glikolitiese ensieme al goed bestudeer en as teiken voorgestel is, is dit steeds onduidelik hoe hierdie ensieme saam funksioneer om die metaboliese weg, as geheel, tot stand te bring. Metaboliese kontrole analise het aangetoon dat die glikolitiese beheer verdeel is tussen die onderskeie glikolitiese ensieme, m.a.w. geen enkele ensiematiese stap het volledige beheer oor die fluksie van die glikolitiese padweg nie. Die afsonderlike analise en vergelyking van Plasmodium - en rooibloedselglikolise met behulp van differensiële metaboliese kontrole analise sal moontlik gebruik kan word om gasheervriendelike teikens vir nuwe middels aan te toon. So ’n analise benodig ’n omvattende kinetiese model van Plasmodium glikolise. Derhalwe was die doel van hierdie studie om vas te stel hoe uitvoerbaar dit is om ’n kinetiese model van Plasmodium glikolise te konstrueer en te valideer. Die uitvoerbaarheid van die konstruksie en validering van die kinetiese model was geasseseer op grond van die vermoë om: i) parasietkulture te kweek en genoegsame parasiete, wat in die aseksuele fase is, te isoleer sodat ensiembepalings en bestendige toestand-bepalings gedoen kan word, ii) kinetiese parameters soos Km - en Vmax-waardes vir elke glikolitiese ensiem, hetsy vanuit literatuur of eksperimentele werk, te verkry, iii) glikolitiese fluksie te meet, iv) glikolitiese intermediaatkonsentrasies te bepaal, v) ’n kinetiese model van die bepaalde kinetiese parameters op te stel en vi) die model te valideer met glikolitiese flukswaardes en metaboliet- konsentrasies wat in die bestendige toestand verkry is. Elk van die bogenoemde kriteria was met sukses in hierdie studie aangespreek. Ter opsomming, die eksperimenteel bepaalde kinetiese parameters en glikolietiese flukswaardes was gebruik om onderskeidelik ’n gedetaileerde kinetiese model te konstrueer en gedeeltelik te valideer. Daar was getoon dat verdere validering van die model deur middel van bestendige toestand metabolietkonsentrasies moontlik is met die ontwikkeling van ’n geskikte protokol om glikolitiese intermediaatkonsentrasies te meet. Die model, soos opgestel in hierdie studie, kan moontlik ’n belangrike rol speel om teikens vir nuwe malaria teen-middels te identifiseer en om gasheer-parasiet interaksies en glikolitiese regulering beter te verstaan.

PONTIFÍCIA UNIVERSIDADE CATÓLICA DO RIO DE JANEIRO
Essa dissertação apresenta um estudo comparativo de quatro diferentes modelos de cinética química detalhada que envolvem as principais espécies químicas responsáveis pelo processo de formação e oxidação da fuligem, i.e., o oxigênio molecular, o radical hidroxila, o acetileno, o propargil, benzeno, fenil e pireno. Para este fim, considera-se a combustão de misturas de etileno/ar e metao/ar. Para analisar os modelos cinéticos são utilizados um reator perfeitamente misturado (PSR) e um reator parcialmente misturado (PaSR). No caso do reator perfeitamente misturado, um estudo sistemático da influência do tempo de residência e a riqueza da mistura sobre estas espécies químicas é apresentado. São discutidas as importantes discrepâncias obtidas, para o acetileno, o propargil, o benzeno, o fenil e o pireno, entre os modelos cinéticos analisados. As espécies oxidantes exibem menores discrepâncias dentre todas as espécies analisadas. No caso do reator parcialmente misturado, a razão entre o tempo de residência e o tempo de mistura é o parâmetro de análise. De modo geral, os resultados obtidos permitem avaliar o comportamento dos mecanismos cinéticos em uma situação representativa de combustão em escoamentos turbulentos.
In this dissertation a comparative study is presented of four different detailed kinetics models involving the main chemical species responsible for the soot formation and oxidation, i.e., the molecular oxygen, the hydroxyl, the acetylene, the propargyl, the benzene and the pyrene. To this purpose is considered the combustion of ethylene/air and metane/air. To analyze the kinetic models are used a perfect stirred reactor (PSR) and a partial stirred reactor (PaSR). In the case of a perfect stirred reactor a systematic study of the influence of the residence time and of the equivalence ratio on these chemical species is presented. Are discussed the important discrepancies obtained for acetylene, propargyl, benzene, phenyl and pyrene, between the kinetic models analyzed. The oxidizing species exhibit minor discrepancies only. In the case of the partially mixed reactor, the ratio between the residence time and the mixing time is the analysis parameter. Overall, the results obtained allow to evaluate the behavior of the kinetic mechanisms in situations representative of combustion in turbulent flows.

The effects on combustion derived by the blending of hydrogen with traditional fuels adopted for internal combustion engines have been studied. Results derived by emission tests of a gasoline-fed vehicle equipped with a system for the production of hydrogen on-board have been analysed. The energy balance for the engine was evaluated. It demonstrated the increase of fuel consumptions to perform electrolysis process on-board the vehicle. Afterwards, numerical simulations based on a detailed kinetic model have been performed to calculate pollutant emissions produced by methane and iso-octane (which represents gasoline) compared with a mixture composed of 10% mol/mol by hydrogen. Chemical species studied were residual hydrocarbons, nitrous oxides and carbon monoxide. Notable variations of pollutant has not been calculated for methane, wherease iso-octane showed a reduction of the aforementioned pollutants when hydrogen was introduced. In the end operating costs have been analysed. The use of stored hydrogen produced by methane steam reforming found a reduction by 7% of costs, compared to the production via electrolysis.

Les carburants dérivés du pétrole constituent la première source mondiale énergétique et leur approvisionnement constitue un défi actuel majeur impliquant des enjeux économiques et environnementaux cruciaux. Une des voies les plus efficaces pour peser simultanément sur ces deux enjeux passe par la diminution de la consommation en carburant. La simulation numérique constitue dès lors un outil précieux pour améliorer et optimiser les moteurs et les carburants. Les modèles chimiques détaillés sont nécessaires pour comprendre les phénomènes d’auto-inflammation et caractériser la nature et les quantités de polluants émis. Ces modèles mettent en jeu un nombre très important d’espèces et de réactions élémentaires, pour une espèce donnée et pour lesquelles la détermination des données thermodynamiques et cinétiques est un problème crucial. La chimie quantique constitue un outil précieux permettant d’une part de déterminer de façon précise les données thermocinétiques pour bon nombre de systèmes chimiques et d’autre part de mieux comprendre la réactivité de ces systèmes. Dans ce travail, les réactions unimoléculaires de décomposition d’hydrocarbures monocycliques et polycycliques (amorçages, réactions moléculaires, ß-scissions, formations d’éthers cycliques) ont été étudiées à l’aide des méthodes de la chimie quantique. Un mécanisme détaillé de pyrolyse d’un alcane polycyclique a été développé à partir des données thermodynamiques et cinétiques et des corrélations entre structure et réactivité déterminées pour les cyclanes à partir des calculs quantiques. Les simulations effectuées à partir de ce modèle sont en très bon accord avec les résultats expérimentaux de la littérature
Petroleum fuels are the world’s most important primary energy source and the need to maintain their supply is a major actual challenge involving both economical and environmental features. Decreasing fuels consumption is one of the more efficient ways to reconcile the goals of energy price and environmental protection. Numerical simulations become therefore a very important tool to optimize fuels and motors. Detailed chemical kinetic models are required to reproduce the reactivity of fuels and to characterize the amount of emitted pollutants. Such models imply a very large number of chemical species and elementary reactions, for a given species, and the determination of thermodynamic and kinetic data is a critical problem. Nowadays, quantum chemistry methods are able to calculate accurately thermodynamic data for a large number of chemical systems and to elucidate the reactivity of these systems. In this work we have used quantum chemistry to study the unimolecular reactions (initiation, molecular reactions, ß-scissions, cyclic ethers formations) involved in the decomposition of monocyclic and polycyclic hydrocarbons. From the results of quantum chemical calculations, a detailed chemical kinetic mechanism of the pyrolysis of a polycyclic alkane has been developed and validated against experimental data

La stabilité des carburants en phase liquide est de premier ordre dans le domaine du transport. Par exemple, les carburants, les lubrifiants ou les additifs doivent être stables de leur production jusqu'à leur utilisation. Cette thèse a pour but de développer et de valider une méthodologie alliant l’acquisition de données expérimentales et le développement de modèles cinétiques pour l'autoxydation en phase liquide.Expérimentalement, une approche complémentaire a été mise en place pour obtenir à la fois des données de réactivité globales via un appareil PetroOxy et des profils d’espèces via un autoclave instrumenté.Numériquement, une méthodologie basée sur un générateur de mécanismes est proposée pour obtenir une chimie détaillée en phase liquide. Les paraffines linéaires et branchées sont étudiées comme des carburants modèles représentatifs de l'autoxidation de carburants réels afin de valider l’approche proposée. Ces familles chimiques sont représentatives de la composition des carburants réels et alternatifs.La réactivité des n-paraffines de C8 à C16 ainsi que d’isomères de l’octane a été étudiée en PetroOxy sur la gamme de température 373-433 K. Puis, des profils d’espèces détaillés de la phase gaz et de la phase liquide ont été obtenus durant l’étude de l’oxydation du n-C8 et du 2-methylheptane dans un autoclave à 383 K et 10 bars. Des mécanismes cinétiques détaillés ont été développé pour toutes les molécules jusqu’à C14. Les mécanismes reproduisent qualitativement la formation des espèces majoritaires lors de l’autoxidation des alcanes ainsi que les tendances observées liées à la longueur de chaîne et la ramification. L’analyse des mécanismes cinétiques a mis en avant le rôle prédominant des radicaux peroxy (ROO) et peroxy-hydroperoxyde (HOOQOO) dans la consommation de carburants modèles.Cette étude a permis d’améliorer la compréhension des processus d’autoxidation des alcanes linéaires et branchés. L’étude de nouveaux systèmes permettra d’améliorer la compréhension globale des processus d’autoxidation et, de réduire l’écart de compréhension existant entre l’autoxidation des carburants réels et des carburants modèles
Liquid phase stability is a major concern in the transportation and the energy fields. Relevant examples are fuels, lubricants and additives which have to be stable from their production to their application (engine, combustors). This thesis aims to develop and validate a complete methodology combining both experimental data acquisition and the development of kinetic models for liquid phase autoxidation.The experimental methodology is based on a complementary approach to obtain (i) a global reactivity descriptor (Induction Periods) and (ii) detailed species profiles respectively using a PetroOxy device and an instrumented autoclave. Numerically, the presented methodology includes detailed liquid phase mechanisms generation with an automatic mechanism generator (RMG). Normal and iso-paraffins were selected as fuel surrogates for autoxidation to validate the developed methodology. They were selected regarding their large contribution in fuel composition and their growing interest as drop-in fuels.The reactivity of both n-paraffins from C8 to C16 and several C8 iso-paraffins was investigated over a wide temperature range (373-433 K) in the PetroOxy with liquid phase analyses. Then, detailed species profiles from the autoxidation of both n-octane and 2-methylheptane in autoclave were obtained at 383 K and 10 bars. Detailed liquid phase mechanisms were developed for all molecules tested up to C14. Mechanisms qualitatively reproduce the overall phenomenology of the chain length, the branching and the major species profiles observed experimentally. Mechanisms analysis allow to identify the main consumption pathways of alkanes through peroxy (ROO) and peroxy-hydroperoxide radicals (HOOQOO) over the temperature range investigated (373-473 K).This study permitted to increase the comprehension of autoxidation processes involved in normal and branched alkanes. The study of new chemical systems will increase the global comprehension of autoxidation processes and in fine it will reduce the gap between the current autoxidation knowledge and the real fuel autoxidation

Commercial fuels are mixtures with large numbers of components. Continuous thermodynamics is a technique for modelling fuel mixtures using a probability density function rather than dealing with each discreet component. The mean and standard deviation of the distribution are then used to model the chemical reactions of the mixture. This thesis develops the necessary theory to apply the technique of continuous thermodynamics to the oxidation reactions of hydrocarbon fuels. The theory is applied to three simplified models of hydrocarbon oxidation: a global one-step reaction, a two-step reaction with CO as the intermediate product, and the four-step reaction of Müller et al. (1992), which contains a high- and a low-temperature branch. These are all greatly simplified models of the complex reaction kinetics of hydrocarbons, and in this thesis they are applied specifically to n-paraffin hydrocarbons in the range from n-heptane to n-hexadecane. The model is tested numerically using a simple constant pressure homogeneous ignition problem using Cantera and compared to simplified and detailed mechanisms for n-heptane. The continuous thermodynamics models are able not only to predict ignition delay times and the development of temperature and species concentrations with time, but also changes in the mixture composition as reaction proceeds as represented by the mean and standard deviation of the distribution function. Continuous thermodynamics is therefore shown to be a useful tool for reactions of multicomponent mixtures, and an alternative to the "surrogate fuel" approach often used at present.

L'oxydation de l'éthylène, du propane et du propène a été étudiée dans un large domaine de température (900 à 1200 Kelvin), de pression (0,1 à 1 MPa) et de richesse (0,15 à 4) au moyen d'un réacteur auto-agité par jets gazeux. L'analyse chromatographique d'échantillons du milieu réactionnel permet de suivre la réaction d'oxydation dans son ensemble. Un mécanisme cinétique détaillé comportant 278 réactions et faisant intervenir 47 espèces chimiques, a été développé grâce à l'utilisation d'une technique d'analyse de sensibilité, et permet de modéliser correctement nos résultats expérimentaux.

Computational tools allow the simulation of biological processes giving results which can be used to build computational/experimental approaches for the study of cellular processes dynamics. In my Doctoral Thesis I described and applied calculation methods for the quantitative analysis of the dynamics of different cellular processes. The first chapter describes the mathematical and computational methods then used in the applications described in the following chapters: the first part describes the detailed kinetic models based on ordinary differential equations (ODEs) and the topographic and stoichiometric models to simulate the cellular metabolism of microorganisms. Particular attention is given to the application of an hybrid method: the structural kinetic modelling (SKM). The second part describes some computational methods proposed in literature for the time-series images analysis obtained with confocal microscopy on living cells. Calculation methods described allow the automated detection and tracking of microtubules comets. The second chapter describes my research activities in the application of the quantitative methods to the analysis of metabolic pathways in microorganisms. The application of ODEs and SKM methods are described and through computational simulations the output variation in kinetic parameters are analyzed respect to the perturbations in the input kinetic parameters. The parameter estimation is described through the comparison between experimental and simulation data and a method to build a difference index of kinetic parameters is suggested for build a computational/experimental approach to the analysis of cellular metabolism of microorganisms. The third chapter describes my research activities on the analysis of images obtained from confocal microscopy. Applications of computational methods for detection and tracking of microtubules comets are described. Microtubules dynamics are determined through the analysis of the growing of the microtubules plus ends by the study of EB3 protein made fluorescently by translational fusion with GFP. These methods have been applied to the study of the effects of the inactivation of the Citron kinase protein on the microtubules dynamics and on the angle of the mitotic spindle.

Gli strumenti di calcolo permettono la simulazione al calcolatore di processi biologici fornendo risultati che possono essere utilizzati per la costruzione di approcci computazionali/sperimentali per lo studio della dinamica dei processi cellulari. Nella mia Tesi di Dottorato ho descritto ed applicato metodi di calcolo per l’analisi quantitativa della dinamica di diversi processi cellulari. Il primo capitolo descrive i metodi matematici e computazionali utilizzati poi nelle applicazioni descritte nei capitoli successivi: la prima parte descrive i modelli cinetici dettagliati basati su equazioni differenziali ordinarie (ODEs) ed i modelli topografici e stechiometrici per simulare il metabolismo cellulare di microrganismi. Particolare attenzione è data all’applicazione di un metodo ibrido proposto in letteratura: lo Structural kinetic modeling (SKM). La seconda parte descrive alcuni metodi computazionali proposti in letteratura per l’analisi di serie di immagini su cellule viventi ottenute con la tecnologia della microscopia confocale. Sono descritti i metodi di calcolo che permettono il riconoscimento e la tracciatura automatica di comete di microtubuli. Il secondo capitolo descrive la ricerca che ho svolto con l’applicazione dei metodi quantitativi all’analisi dei percorsi metabolici cellulari di microrganismi. Si descrivono le applicazioni del metodo ODEs ed SKM e tramite simulazioni al calcolatore si analizzano le variazioni nell’output dei parametri cinetici considerando perturbazioni nell’input. Si descrive la stima di parametri attraverso il paragone tra dati sperimentali e simulati e si propone un metodo di costruzione di un indice di differenza parametrica che possa essere utile nella costruzione di un approccio computazionale/sperimentale all’analisi del metabolismo cellulare di microrganismi. Il terzo capitolo descrive la ricerca che ho svolto sull’analisi di immagini da microscopia confocale. Si descrivono le applicazioni dei metodi computazionali di rilevazione e tracciatura applicati allo studio della dinamica dei microtubuli, determinata a partire dall'analisi della crescita delle estremità positive grazie allo studio della proteina EB3, resa fluorescente mediante fusione traduzionale con GFP. Tali metodiche sono state applicate allo studio degli effetti dell'inattivazione della proteina Citron kinase sulla dinamica dei microtubuli e sull'angolo del fuso mitotico.
Computational tools allow the simulation of biological processes giving results which can be used to build computational/experimental approaches for the study of cellular processes dynamics. In my Doctoral Thesis I described and applied calculation methods for the quantitative analysis of the dynamics of different cellular processes. The first chapter describes the mathematical and computational methods then used in the applications described in the following chapters: the first part describes the detailed kinetic models based on ordinary differential equations (ODEs) and the topographic and stoichiometric models to simulate the cellular metabolism of microorganisms. Particular attention is given to the application of an hybrid method: the structural kinetic modelling (SKM). The second part describes some computational methods proposed in literature for the time-series images analysis obtained with confocal microscopy on living cells. Calculation methods described allow the automated detection and tracking of microtubules comets. The second chapter describes my research activities in the application of the quantitative methods to the analysis of metabolic pathways in microorganisms. The application of ODEs and SKM methods are described and through computational simulations the output variation in kinetic parameters are analyzed respect to the perturbations in the input kinetic parameters. The parameter estimation is described through the comparison between experimental and simulation data and a method to build a difference index of kinetic parameters is suggested for build a computational/experimental approach to the analysis of cellular metabolism of microorganisms. The third chapter describes my research activities on the analysis of images obtained from confocal microscopy. Applications of computational methods for detection and tracking of microtubules comets are described. Microtubules dynamics are determined through the analysis of the growing of the microtubules plus ends by the study of EB3 protein made fluorescently by translational fusion with GFP. These methods have been applied to the study of the effects of the inactivation of the Citron kinase protein on the microtubules dynamics and on the angle of the mitotic spindle.