A theoretical model describing the motion of a small, fast rare gas atom as it passes over a liquid surface is developed and discussed in detail. A key feature of the model is its reliance on coarse-grained capillary wave and local mode descriptions of the liquid surface. Mathematically, the model is constructed with several concepts from probability and stochastic analysis. The model makes predictions that are quantitative agreement with neon-liquid surface scattering data collected by other research groups. These predictions include the dominance of single, rather than multiple, neon-liquid surface collision dynamics, an average of 60 % energy transfer from a neon atom upon colliding with a non-metallic surface, and an average of 25 % energy transfer upon colliding with a metallic surface. In addition to this work, two other investigations into the gas-liquid interface are discussed. The results of an experimental investigation into the thermodynamics of a gas flux through an aqueous surface are presented, and it is shown that a nitrous oxide flux is mostly due to the presence of a temperature gradient in the gas-liquid interface. Evidence for a reaction between a carbon dioxide flux and an ammonia monolayer on an aqueous surface to produce ammonium carbamate is also found. The second of these is an investigation into the mechanism of bromine production from deliquesced sodium bromide aerosol in the presence of ozone, and involves a sensitivity and uncertainty analysis of the computer aerosol kinetics model MAGIC. It is shown that under dark, non-photolytic conditions, bromine production can be accounted for almost exclusively by a reaction between gas-phase ozone and surface-bound bromide ions. Under photolytic conditions, bromine production instead involves a complicated interplay between various gas-phase and aqueous-phase reactions.

The Onsager heat of transport for p-tert-butyltoluene was measured, as part of a series of preliminary experiments towards the determination of the importance of temperature gradients on the air-sea flux of carbon dioxide. The results presented in this thesis imply that the temperature gradient is a major contributor to the magnitude of the air-sea flux. The heat of transport has been measured for the p-tert-butyltoluene system by measuring stationary-state pressure changes for known temperature differences on the vapour side of the interface. At the pressure ranges used the number of mean free paths was always outside the Knudsen zone, but the values of Q* were approximately 100 % of the latent heat of vaporisation. Departures from linearity of plots of P against ΔT are attributed to temperature jumps at the surface of the dry upper plate. Both the results taken for p-tert-butyltoluene and the earlier results for water from this laboratory fit to a Type III BET isotherm, where the c parameter is not constant. They also reveal the importance of the temperature gradient in determining the value of the thermal accommodation coefficient, and provide a new method of measuring thermal accommodation coefficients for a variety of surfaces and vapours

This thesis investigates the design, synthesis and biological assay of cysteine protease inhibitors within the papain superfamily of cysteine proteases. This is achieved by examining the effect of inhibitor design, especially warheads, on IC₅₀ values and structureactivity relationships between cysteine protease inhibitors of the papain superfamily. The representative proteases used are m-calpain, μ-calpain, cathepsin B and papain. Chapter One is an introductory chapter; Chapters Two-Four describe the design and synthesis of cysteine protease inhibitors; Chapter Five discusses assay protocol; and Chapter Six contains the assay results and structure-activity relationships of the synthesised inhibitors. Chapter One introduces cysteine proteases of the papain family and examines the structure, physiology and role in disease of papain, cathepsin B, m-calpain and μ-calpain. The close structural homology that exists between these members of the papain superfamily is identified, as well characteristics unique to each protease. Covalent reversible, covalent irreversible and non-covalent warheads are defined. The generic inhibitor scaffold of address region, recognition and warhead, upon which the inhibitors synthesised in this thesis are based, is also introduced. Chapter Two introduces reversible cysteine protease inhibitors found in the literature and that little is known about the effect of inhibitor warhead on selectivity within the papain superfamily. Oxidation of the dipeptidyl alcohols 2.6, 2.26, 2.29, 2.30, 2.35 and 2.36 utilising the sulfur trioxide-pyridine complex gave the aldehydes 2.3, 2.27, 2.19, 2.2, 2.21 and 2.22. Semicarbazones 2.37-2.40 were synthesised by a condensation reaction between the alcohol 2.3 and four available semicarbazides. The amidoximes 2.48 and 2.49 separately underwent thermal intramolecular cyclodehydration to give the 3-methyl-1,2,4- oxadiazoles 2.41 and 2.50. The aldehydes 2.3 and 2.27 were reacted with potassium cyanide to give the cyanohydrins 2.51 and 2.52. The cyanohydrins 2.51 and 2.52 were separately reacted to give 1) the α-ketotetrazoles 2.43 and 2.55; 2) the α-ketooxazolines 2.42 and 2.58; 3) the esterified cyanohydrins 2.60 and 2.61. A two step SN2 displacement reaction of the alcohol 2.6 to give the azide 2.62, an example of a non-covalent cysteine protease inhibitor. Chapter Three introduces inhibitors with irreversible warheads. The well-known examples of epoxysuccinic acids 3.1 and 3.5 are discussed in detail, highlighting the lack of irreversible cysteine protease specific inhibitors. The aldehydes 2.3 and 2.27 were reacted under Wittig conditions to give the α,β-unsaturated carbonyls 3.14-3.18. Horner- Emmons-Wadsworth methodology was utilised for the synthesis of the vinyl sulfones 3.20- 3.23. The dipeptidyl acids 2.24 and 2.28 were separately reacted with diazomethane to give the diazoketones 3.25 and 3.26. The diazoketones 3.25 and 3.26 were separately reacted with hydrogen bromide in acetic acid (33%) to give the α-bromomethyl ketones 3.27 and 3.28, which were subsequently reduced to give the α-bromomethyl alcohols 3.29-3.32. Under basic conditions the α-bromomethyl alcohols 3.29-3.32 ring-closed to form the peptidyl epoxides 3.33-3.36. Chapter Four introduces the disadvantages of peptide-based inhibitors. A discussion is given on the benefits of constraining inhibitors into the extended bioactive conformation known as a β-strand. Ring closing metathesis is utilised in the synthesis of the macrocyclic aldehyde 4.4, macrocyclic semicarbazone 4.15, the macrocyclic cyanohydrin 4.16, the macrocyclic α-ketotetrazole 4.18 and the macrocyclic azide 4.19. Chapter Five introduces enzyme inhibition studies. The BODIPY-casein fluorogenic assay used for establishing inhibitor potency against m-calpain and μ-calpain is validated. Assay protocols are also established and validated for cathepsin B, papain, pepsin and α- chymotrypsin. A discussion of the effect of solvent on enzyme activity is also included as part of this study. Chapter Six presents the assay results for all the inhibitors synthesised throughout this thesis and an extensive structure-activity relationship study between inhibitors is included. The alcohols 2.26 and 2.30 are unprecedented examples of non-covalent, potent, cathepsin B inhibitors (IC₅₀ = 0.075 μM selectivity 80-fold and 1.1 μM, selectivity 18-fold). The macrocyclic semicarbazone 4.15 is an unprecedented example of a potent macrocyclic cysteine protease inhibitor (m-calpain: IC₅₀ = 0.16 μM, selectivity 8-fold). The cyanohydrin 2.51 contains an unprecedented cysteine protease warhead and is a potent and selective inhibitor of papain (IC₅₀ = 0.030 μM, selectivity 3-fold). The O-protected cyanohydrin 2.61 is a potent and selective inhibitor of pepsin (IC₅₀ = 1.6 μM, selectivity 1.5-fold). The top ten warheads for potent, selective cathepsin B inhibition are: carboxylic acid, methyl ester, diazoketone, esterified cyanohydrin, α-bromomethyl ketone, α,β- unsaturated aldehyde, vinyl sulfones, α-bromomethyl-C₃-S,R-alcohol, alcohol and α,β- unsaturated ethyl ester. The selectivity of these warheads was between 5- and 130-fold for cathepsin B. The best inhibitors for cathepsin B were the α-bromomethyl ketone 3.26 (IC₅₀ = 0.075 μM, selectivity 16-fold), the α,β-unsaturated aldehyde 3.18 (IC₅₀ = 0.13 μM, selectivity 13-fold) and the esterified cyanohydrin 3.59 (IC₅₀ = 0.35 μM, selectivity 22- fold). Chapter Seven outlines the experimental details and synthesis of the compounds prepared in this thesis.

Ce travail de thèse porte sur les conditions économiques nécessaires à l’émergence d’une filière bioénergie par l’intermédiaire de la biomasse torréfiée. Cette recherche a été menée suivant deux approches complémentaires, l’une normative, portant sur l’étude du comportement des acteurs de cette filière, et l’autre positive, portant sur les conditions d’existence du marché de la biomasse torréfiée. Nous étudions les valeurs que l’offreur et le demandeur associent à la décision économique d’investissement dans de nouvelles technologies énergétiques et d’achat de la biomasse. Nous avons mesuré la demande des secteurs énergétiques afin de la confronter à l’offre et en déduire un prix d’échange en fonction de la flexibilité des industriels dans leur procédé de production et des contraintes environnementales auxquelles ils sont soumis. La thèse est composée de trois articles (chapitres 2, 3 et 4 en anglais) et de deux études confidentielles (chapitres 1 et 5 en français). Le chapitre 1 présente une enquête de terrain qualitative menée au niveau national, identifiant les demandeurs potentiels et déterminant les facteurs technico-économiques qui peuvent l’influencer. Le chapitre 2 étudie la décision d’investissement et de production d’un agent averse à l’ambiguïté faisant face à des incertitudes de marché telles que le nombre d’acteurs et l’effet de la concurrence des autres énergies fossiles sur le prix de vente de sa biomasse. Nous observons des effets asymétriques des deux incertitudes sur les montants optimaux de production et nous montrons théoriquement puis numériquement que l’aversion à l’ambiguïté tend à diminuer les niveaux optimaux d’investissement et de production. Le chapitre 3 présente le modèle que nous avons développé pour estimer la pénétration de la biomasse prétraitée dans le marché de la production d’électricité en fonction des politiques climatique et énergétiques modélisées. Nous en déduisons la fonction de demande en biomasse torréfiée. Dans le chapitre 4, nous développons un modèle en équilibre partiel d’offre provenant du secteur torréfaction et de demande en biomasse issue des secteurs électrique et raffinage pour estimer un prix d’équilibre d’échange de la biomasse torréfiée en fonction du prix du CO2 `a long terme. Enfin, cette approche positive est complétée par une étude logistique présentée dans le chapitre 5 afin de déterminer la stratégie d’approvisionnement et la taille optimale des unités de prétraitement implantées dans un bassin de production de biomasse. Le travail de recherche réalisé permet d’élaborer des recommandations destinées aux investisseurs et aux institutions en charge du développement des bioénergies. / This thesis focuses on the economic conditions required for the emergence of a bioenergy supply chain based on torrefied biomass. This research was conducted by using two complementary approaches: the normative one deals with the actors’ behavior in this sector and the positive one deals with the conditions necessary to trigger the torrefied biomass market in France. We study the supplier and demander behaviors regarding the investment in new energy technologies and the purchase of biomass. Then, the biomass demand per sector is modeled in order to compare it to the offer. We deduce an equilibrium selling price which depends on the flexibility of the industry in their production process and the environmental constraints under which they operate. This Ph.D. dissertation is composed of 3 articles (chapters 2, 3 and 4 in English) and 2 confidential studies (chapters 1 and 5 in French). Chapter 1 presents a survey driven at national level, to measure the potential demand and to determine the technical and economic factors influencing it. Chapter 2 analyzes the production and investment decisions of an ambiguity averse agent facing market uncertainties such as demand uncertainty (in terms of number of buyers) and competitive effect uncertainty (in terms of other energy resource). We apply our model on the bioenergy industries. We show that the investment decision of an agent depends on the effects of both the capital investment and the level of production on the cost and the uncertainty the agent is confronted with. Moreover, we find that ambiguity aversion tends to decrease the agent’s optimal levels of production and investment. Chapter 3 studies the penetration of green electricity production from biomass and its impacts on the future electricity generation mix for France incorporating different scenarios of emission allowance prices. The model is applied to the French power market under consideration of the neighboring countries and we determine the torrefied biomass demand function from our model. In chapter 4, we develop a partial equilibrium model of torrefied biomass supply and demand coming from the power sector and the refinery sector on the long term under CO2 price constraints. Our main results are the equilibrium selling prices of torrefied biomass and the break-even CO2 price which triggers the demand. A last chapter aims at studying the strategy of supply and the optimal size of pre-treatment units located in a pool of biomass production. The research carried out allows to propose recommendations for investors and institutions in charge of the development of bioenergies.

Les gaz à effet de serre (GES) sont en partie responsables du changement climatique. L'humanité est donc confrontée à un choix : soit de réduire les émissions des gaz qui sont la cause du problème, ou bien de prendre de mesures pour permettre aux populations de surmonter les conséquences de ces changements. Dans cette thèse, nous nous concentrons sur la première solution sous la prémisse selon laquelle une grande partie de l'effet de serre provient des activités humaines. Plus précisément, nous proposons quelques essais sur la modélisation des déterminants des investissements ayant pour objet la réduction des GES, en particulier des investissements dans l'amélioration de l'efficacité énergétique, et des investissements dans la substitution de ressources (fossiles) non-renouvelables par des ressources renouvelables. Tout d'abord nous essayons et expliquons la lente diffusion de certains investissements dans l'efficacité énergétique dans un cadre d'équilibre général. Ensuite, nous étudions les déterminants de la substitution des ressources non-renouvelables par des ressources renouvelables lorsque celles-ci sont des substituts parfaits. Enfin, nous tenons compte de la nécessité permanente de ressources sales, même si des technologies plus propres sont disponibles. Toutes ces questions sont basées sur des modèles qui ne peuvent être entièrement résolus analytiquement. Par conséquent, nous proposons dans cette thèse une méthodologie basée sur les propriétés des polynômes de Chebyshev pour calculer les solutions. / Greenhouse gases (GHG) are responsible for some climate change. Humanity faces a choice: either reducing the emissions of these gases or adapt to climate change. In this dissertation we focus on the first solution under the premise that a large part of the greenhouse effect comes from human activities. More precisely, we propose some essays on modeling the determinants of investing in reducing GHG through improving energy efficiency and substituting non-renewable resources (fossil fuels) by renewable resources. We first try and explain the slow diffusion of some energy efficient investments in a general equilibrium framework. We then study the determinants of switching from non-renewable resources to renewable resources when these are perfect substitutes. Finally, we account for the need of dirty resources even if cleaner technologies are available. All these issues are based on models that cannot be fully solved analytically, therefore we also propose in this dissertation a methodology based on the properties of Chebyshev polynomials to compute the solutions.

Submitted by Lucienne Costa (lucienneferreira@ufcg.edu.br) on 2018-05-11T22:51:17Z No. of bitstreams: 1 JOSÉ ETIMÓGENES DUARTE SEGUNDO – TESE (PPGEQ) 2017.pdf: 3042948 bytes, checksum: e0c377da642dbbf1ba0a1022f463d9de (MD5) / Made available in DSpace on 2018-05-11T22:51:17Z (GMT). No. of bitstreams: 1 JOSÉ ETIMÓGENES DUARTE SEGUNDO – TESE (PPGEQ) 2017.pdf: 3042948 bytes, checksum: e0c377da642dbbf1ba0a1022f463d9de (MD5) Previous issue date: 2018-08-31 / Para satisfazer aplicações industriais e o crescente consumo de combustíveis fósseis, têm-se realizado várias pesquisas sobre o desenvolvimento de materiais e tecnologias para o armazenamento de energia de forma sustentável e renovável. O grafeno é um material que despertou interesse de estudos recentes devido às suas excelentes propriedades físico-químicas, mecânicas, térmicas, elétricas e ópticas. Em uma bateria de íons de lítio, o grafeno supera as limitações de capacidade do grafite, comumente usado como material anódico. Neste trabalho, estudou-se o uso de monocamada de grafeno como ânodo em uma bateria de íons de lítio para verificar a influência da densidade de corrente e da composição do eletrólito no desempenho eletroquímico do material. A densidade de corrente foi aplicada em três níveis diferentes: 3, 5 e 10 μA/cm2. O eletrólito testado foi LiPF6 1M em etilenocarbonato/dietilcarbonato (50/50v) (EC-DEC), etilmetilcarbonato (EMC) ou propilenocarbonato (PC). As análises de microscopia de força atômica e Raman exibiram uma monocamada de grafeno uniforme sobre a superfície do substrato. Os espectros de impedância eletroquímica da célula descarregada foram analisados para investigar a cinética do processo de eletrodo nos diferentes eletrólitos. Os resultados mostraram um processo controlado pela transferência de carga, mas com grande contribuição da difusão de íons de lítio. Na caracterização eletroquímica, os melhores resultados foram obtidos para o eletrólito EC-DEC. A capacidade irreversível no 1º ciclo variou de 11,39 a 77,47%, em função da densidade de corrente aplicada, e maior capacidade de descarga foi de 21 575 mAh/g, para 3 μA/cm2. Com a aplicação dessa mesma densidade de corrente, a eficiência coulômbica média foi de 67,12% e a capacidade de descarga sofreu redução de 87,90%, ao longo de 20 ciclos. Os resultados obtidos confirmaram o grande potencial do grafeno para aplicação em sistemas de armazenamento de energia. / To satisfy industrial applications and the growing consumption of fossil fuels, researches have been performed on the development of materials and technologies for energy storage in a renewable and sustainable way. Graphene is a material that has interested recent studies due to its excellent physical-chemical, mechanical, thermal, electrical and optical properties. In a lithium-ion battery, graphene overcomes the capacity limitations of graphite, commonly used as anode material. In this work, monolayer graphene using as anode was studied in a lithium-ion battery to verify the influence of current density and electrolyte composition on the electrochemical performance of electrode material. Current density was applied in three different levels: 3, 5 and 10 μA/cm2. The electrolyte tested was LiPF6 1M in ethylene carbonate/diethyl carbonate (50/50v) (EC-DEC), ethyl methyl carbonate (EMC) or propylene carbonate (PC). AFM and Raman microscopy analysis exhibited a uniform monolayer graphene over substrate surface. The EIS spectra of discharged cell were analyzed to investigate the kinetics of electrode process in different electrolytes. Results showed a process controlled by charge transfer but with great contribution of lithium-ion diffusion in case of EC-DEC solvent. Irreversible capacity in the 1st cycle ranged from 11.39 to 77.47%, as function of applied current density, and the highest discharge capacity was 21,575 mAh/g, for 3 μA/cm2. With application of this current density value, the average coulombic efficiency was 67.12% and the discharge capacity was reduced by 87.90% over 20 cycles. Results confirmed the great potential of graphene for application in energy storage systems.

Given a graph G and an initial colouring of its vertices with two colours, say black and white, an irreversible k-threshold conversion process on G is an iterative process in which a white vertex becomes permanently coloured black at time t if at least k of its neighbours are coloured black at time t-1. A set S of vertices is an irreversible k-threshold conversion set (k-conversion set) of G if the initial colouring in which the vertices of S are black and the others are white results in the whole vertex set becoming black eventually. In the case where G is (k+1)-regular, it can be shown that the k-conversion sets coincide with the so-called feedback vertex sets, or decycling sets. In this dissertation we study the size and structure of minimum k-conversion sets in several classes of graphs. We examine conditions that lead to equality and inequality in existing bounds on the minimum size of a k-conversion set of G, for k- and (k+1)-regular graphs G. Furthermore, we derive new sharp lower bounds on this number for regular graphs of degree ranging from k+1 to 2k-1 and for graphs of maximum degree k+1. We determine exact values of the minimum size of a k-conversion set for certain classes of trees. We show that every (k+1)-regular graph has a minimum k-conversion set that avoids certain structures in its induced subgraph. These results lead to new proofs of several known results on colourings and forest partitions of (k+1)-regular graphs and graphs of maximum degree k+1. / Graduate

Dans cette thèse nous présentons les résultats sur l'emploi des systèmes Hamiltoniens à port et des systèmes de contact commandés pour la modélisation et la commande de systèmes issus de la Thermodynamique Irréversible. Premièrement nous avons défini une classe de pseudo-systèmes Hamiltoniens à port, appelée systèmes Hamiltoniens à port irréversibles, qui permet de représenter simultanément le premier et le second principe de la Thermodynamique et inclut des modèles d'échangeurs thermiques ou de réacteurs chimiques. Ces systèmes ont été relevés sur l'espace des phases thermodynamiques muni d’une forme de contact, définissant ainsi une classe de systèmes de contact commandés, c'est-à-dire des systèmes commandés non-linéaires définis par des champs de contacts stricts. Deuxièmement, nous avons montré que seul un retour d'état constant préserve la forme de contact et avons alors résolu le problème d'assignation d'une forme de contact en boucle fermée. Ceci a mené à la définition de systèmes de contact entrée-sortie et l'analyse de leur équivalence par retour d'état. Troisièmement, nous avons montré que les champs de contact n'étaient en général pas stables en leur zéros et avons alors traité du problème de la stabilisation sur une sous-variété de Legendre en boucle fermée. / This doctoral thesis presents results on the use of port Hamiltonian systems (PHS) and controlled contact systems for modeling and control of irreversible thermodynamic processes. Firstly, Irreversible PHS (IPHS) has been defined as a class of pseudo-port Hamiltonian system that expresses the first and second principle of Thermodynamics and encompasses models of heat exchangers and chemical reactors. These IPHS have been lifted to the complete Thermodynamic Phase Space endowed with a natural contact structure, thereby defining a class of controlled contact systems, i.e. nonlinear control systems defined by strict contact vector fields. Secondly, it has been shown that only a constant control preserves the canonical contact structure, hence a structure preserving feedback necessarily shapes the closed-loop contact form. The conditions for state feedbacks shaping the contact form have been characterized and have lead to the definition of input-output contact systems. Thirdly, it has been shown that strict contact vector fields are in general unstable at their zeros, hence the condition for the the stability in closed-loop has been characterized as stabilization on some closed-loop invariant Legendre submanifolds

Various distillates are treated with hydrogen gas during hydrotreatment in the presence of catalyst in order to reduce the sulfur and aromatic content of the product. Optimal hydrotreater performance is essential for producing Nynas specialty oils, in order to fulfill the planned production volume and to meet the product specification. Loss of catalyst activity is inevitable during the production. To adjust for the impact of catalyst deactivation, different process variables are manipulated. Different distillates affect the catalyst in different ways due to the variation in distillate composition. Distillates with higher organic nitrogen content and running at a lower temperature tend to deactivate the catalyst more due to the adsorption of nitrogen compounds on the active sites of the catalyst and their slow nature of desorption. In this master thesis, different catalyst deactivation mechanisms with a focus on nitrogen deactivation have been studied. Since nitrogen is not normally measured at Nynas, nitrogen content of different distillates and products and how these values change during operation was not known. Different distillates, blend of distillates and different products were measured to estimate roughly the typical nitrogen value of the distillates and products. The temperature data inside the reactors were analyzed to calculate and plot WABT (weighted average bed temperature) during different product runs and to see whether there is a correlation between the nitrogen content of the feed and operation severity (increase in WABT). Historical process data from hydrotreater unit 2 (mostly from 2013-2014) were analyzed with a view to finding out signs of catalyst deactivation. Similar product runs were also analyzed and compared to see how the catalysts performed at different periods of time. A kinetic model, based on HDS kinetics, has been used for following up two product runs. To do so, sulfur content of the feed and product were measured. Aromatic content of the product was also measured to see whether the product was on specification. .From the calculation and plotting of WABTs, it could be seen that there is an increase in WABT during the product runs operating at lower temperatures and with higher nitrogen content. From the comparison of two P3 product runs at two different time periods, it could be seen that ∆T development over one bed (amount of reaction over the bed) was much lower at one time. This can possibly be a sign of catalyst deactivation since it contributed to lesser amount of reaction over the bed. From the calculations by using the kinetic model, it could be seen that the actual temperatures were higher than the predicted temperatures. The increase in WABTs could also be noticed. These observations can possibly be coupled with nitrogen deactivation of the catalysts.  However, more tests are required to verify whether the temperature differences were significant or not. Other parameters which are also important from product selling point of view such as viscosity, color, flash point, acid number etc. and have not been covered in this degree project need to be taken into consideration before making further conclusions.

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