Tesis sobre el tema "Irreversibel"

Detta arbete görs i samarbete med IKEA of Sweden och behandlar färgförändringar på textilier. Hållbarhet är en av de största utmaningarna för vår tid och drastiska förändringar av våra vanor och attityder krävs. IKEA arbetar aktivt för att skapa en mer hållbar värld för ’de många människorna’ och en vision är att skapa en attitydförändring och omvärdera inställningen till en blekningsprocess, som generellt anses som något negativt, till en positiv uppfattning till färgförändringen. Genom att bygga upp färger på nya sätt kan en kulör börja med en distinkt färg och under en viss tid förändras genom en traditionell blekningsprocess och erhålla en ny distinkt färg. Förhoppningen är att med denna teknik skapa ett konstant nyhetsvärde som gör att kunder inte är benägna att kassera sina varor för att de tröttnat på dem, utan istället finner ett värde i att behålla textilier som förändras under sin livscykel på ett intressant sätt. För denna rapport var uppdraget att utveckla, studera och dokumentera färgförändringen hos textilier. För studien vävdes en bomulls- och hampaväv med bindning önskad av IKEA. Två färgkombinationer utvecklades, en blå/rosa och en gul/rosa. Dessa kombinationer bestod av anjoniskt svavelfärgstoff, blått respektive gult, samt ett rosa svavelpigment. Målet var att få det blå och gula färgstoffet att blekas över tiden och genom denna process göra det rosa pigmentet synligt och därmed bli den dominerande färgen. Detta sker eftersom det blå och gula svavelfärgstoffet har en lägre färghärdighet än det rosa svavelpigmentet. Totalt togs tre färgkompositioner fram för varje färgkombination. En utan tillsatser, en med silikon samt en med harts. Dessa kompositioner studerades för att eventuellt kunna påvisa hur tillsatser kan påverka färgförändringen. Därefter testades färgförändringen på IKEA Testlab i Älmhult genom simulering av inom- och utomhusmiljö, även tvätt- och gnidtester utfördes. Mätningarna visade att det sker en färgförändring över tiden och att de skiljer sig, dels mellan färgerna men även mellan kompositionerna. Den blå/rosa kombinationen påvisade en långsammare förändring än den gul/rosa och gemensamt för båda är att förändringen skedde exponentiellt över tiden inom de studerade tidsintervallen. Det påvisades även att tillsatserna påverkade förändringen, silikon visade den minsta skillnaden numeriskt, det vill säga de proven var närmast den rosa färg som det önskades att provet skulle övergå till. Förändringen är mer påtaglig hos de gul/rosa proverna där det rosa pigmentet är tydligt medan den blå/rosa kombinationen har en förändring inom samma färgspektrum där färgen gått från en distinkt mörk färg till en distinkt ljus färg.

Das Lektin aus Pisum sativum, der Gartenerbse, ist Teil der Familie der Leguminosenlektine. Diese Proteine haben untereinander eine hohe Sequenzhomologie, und die Struktur ihrer Monomere, ein all-ß-Motiv, ist hoch konserviert. Dagegen gibt es innerhalb der Familie eine große Vielfalt an unterschiedlichen Quartärstrukturen, die Gegenstand kristallographischer und theoretischer Arbeiten waren. Das Erbsenlektin ist ein dimeres Leguminosenlektin mit einer Besonderheit in seiner Struktur: Nach der Faltung in der Zelle wird aus einem Loop eine kurze Aminosäuresequenz herausgeschnitten, so dass sich in jeder Untereinheit zwei unabhängige Polypeptidketten befinden. Beide Ketten sind aber stark miteinander verschränkt und bilden eine gemeinsame strukturelle Domäne. Wie alle Lektine bindet Erbsenlektin komplexe Oligosaccharide, doch sind seine physiologische Rolle und der natürliche Ligand unbekannt. In dieser Arbeit wurden Versuche zur Entwicklung eines Funktionstests für Erbsenlektin durchgeführt und seine Faltung, Stabilität und Monomer-Dimer-Gleichgewicht charakterisiert. Um die spezifische Rolle der Prozessierung für Stabilität und Faltung zu untersuchen, wurde ein unprozessiertes Konstrukt in E. coli exprimiert und mit der prozessierten Form verglichen.

Beide Proteine zeigen die gleiche kinetische Stabilität gegenüber chemischer Denaturierung. Sie denaturieren extrem langsam, weil nur die isolierten Untereinheiten entfalten können und das Monomer-Dimer-Gleichgewicht bei mittleren Konzentrationen an Denaturierungsmittel auf der Seite der Dimere liegt. Durch die extrem langsame Entfaltung zeigen beide Proteine eine apparente Hysterese im Gleichgewichtsübergang, und es ist nicht möglich, die thermodynamische Stabilität zu bestimmen. Die Stabilität und die Geschwindigkeit der Assoziation und Dissoziation in die prozessierten bzw. nichtprozessierten Untereinheiten sind für beide Proteine gleich. Darüber hinaus konnte gezeigt werden, dass auch unter nicht-denaturierenden Bedingungen die Untereinheiten zwischen den Dimeren ausgetauscht werden.

Die Renaturierung der unprozessierten Variante ist unter stark nativen Bedingungen zu 100 % möglich. Das prozessierte Protein dagegen renaturiert nur zu etwa 50 %, und durch die Prozessierung ist die Faltung stark verlangsamt, der Faltungsprozess ist erst nach mehreren Tagen abgeschlossen. Im Laufe der Renaturierung wird ein Intermediat populiert, in dem die längere der beiden Polypeptidketten ein Homodimer mit nativähnlicher Untereinheitenkontaktfläche bildet. Der geschwindigkeitsbestimmende Schritt der Renaturierung ist die Assoziation der entfalteten kürzeren Kette mit diesem Dimer.
The lectin from Pisum sativum (garden pea) is a member of the family of legume lectins. These proteins share a high sequence homology, and the structure of their monomers, an all-ß-motif, is highly conserved. Their quaternary structures, however, show a great diversity which has been subject to cristallographic and theoretical studies. Pea lectin is a dimeric legume lectin with a special structural feature: After folding is completed in the cell, a short amino acid sequence is cut out of a loop, resulting in two independent polypeptide chains in each subunit. Both chains are closely intertwined and form one contiguous structural domain. Like all lectins, pea lectin binds to complex oligosaccharides, but its physiological role and its natural ligand are unknown. In this study, experiments to establish a functional assay for pea lectin have been conducted, and its folding, stability and monomer-dimer-equilibrium have been characterized. To investigate the specific role of the processing for stability and folding, an unprocessed construct was expressed in E. coli and compared to the processed form.

Both proteins have the same kinetic stability against chemical denaturant. They denature extremely slowly, because only the isolated subunits can unfold, and the monomer-dimer-equilibrium favors the dimer at moderate concentrations of denaturant. Due to the slow unfolding, both proteins exhibit an apparent hysteresis in the denaturation transition. Therefore it has not been possible to determine their thermodynamic stability. For both proteins, the stability and the rates of association and dissociation into processed or unprocessed subunits, respectively, are equal. Furthermore it could be shown that even under non-denaturing conditions the subunits are exchanged between dimers.

Renaturation of the unprocessed variants is possible under strongly native conditions with 100 % yield. The processed protein, however, can be renatured with yields of about 50 %, and its refolding is strongly decelerated. The folding process is finished only after several days. During renaturation, an intermediate is populated, in which the longer of the two polypeptide chains forms a homodimer with a native-like subunit interface. The rate limiting step of renaturation is the association of the unfolded short chain with this dimer.

In questa tesi tratteremo il problema di costruire una teoria termodinamica per trasformazioni su un sistema passante per stati di non-equilibrio. Cercando di generalizzare a sistemi che non sono all’equilibrio, rilasseremo la richiesta che siano in equilibrio globalmente. Lo stato termodinamico sarà univocamente determinato da un insieme di parametri termodinamici definiti localmente, della stessa natura e significato fisico dei parametri usati nella termodinamica classica. Le molteplici assunzioni necessarie al fine di avere una teoria mesoscopica comunque predittiva verranno giustificate a posteriori, quando possibile, in base alle predizioni che da tale modello nasceranno. In particolare ci concentreremo sugli effetti termoelettrici di Thompson, Seebeck e Peltier, esempi storici di grande rilevanza nel campo della termodinamica del non-equilibrio.

Diese Dissertation beschäftigt sich mit der rigorosen Herleitung effektiver Modelle zur Beschreibung von Schädigungsprozessen. Diese effektiven Modelle werden für verschiedene raten-unabhängige Schädigungsmodelle linear elastischer Materialien hergeleitet. Den Ausgangspunkt stellt dabei ein unidirektionales Mikrostrukturevolutionsmodell dar, dessen Fundament eine Familie geordneter zulässiger Mikrostrukturen bildet. Jede Mikrostruktur dieser Familie besitzt die gleiche intrinsische Längenskala. Zur Herleitung eines effektiven Modells wird das asymptotische Verhalten dieser Längenskala mittels Techniken der Zwei-Skalen-Konvergenz untersucht. Um das Grenzmodell zu identifizieren, bedarf es einer Mikrostrukturregularisierung, die als diskreter Gradient für stückweise konstante Funktionen aufgefasst werden kann. Die Mikrostruktur des effektiven Modells ist punktweise durch ein Einheitszellenproblem gegeben, welches die Mikro- von der Makroskala trennt. Ausgehend vom Homogenisierungsresultat für die unidirektionale Mikrostrukturevolution werden effektive Modelle für Zwei-Phasen-Schädungsprozesse hergeleitet. Die aus zwei Phasen bestehende Mikrostruktur der mikroskopischen Modelle ermöglicht z.B. die Modellierung von Schädigung durch das Wachstum von Inklusionen aus geschädigtem Material verschiedener Form und Größe. Außerdem kann Schädigung durch das Wachstum mikroskopischer Hohlräume und Mikrorissen betrachtet werden. Die Größe der Defekte skaliert mit der intrinsischen Längenskala und die unidirektionale Mikrostrukturevolution verhindert, dass bei fixierter Längenskala die Defekte für fortlaufende Zeit schrumpfen. Das Material des Grenzmodells ist dann in jedem Punkt als Mischung von ungeschädigtem und geschädigtem Material durch das Einheitszellenproblem gegeben. Dabei liefert das Einheitszellenproblem nicht nur das Mischungsverhältnis sondern auch die genaue geometrische Mischungsverteilung, die dem effektiven Material des jeweiligen Materialpunktes zugrunde liegt.
This dissertation at hand deals with the rigorous derivation of such effective models used to describe damage processes. For different rate-independent damage processes in linear elastic material these effective models are derived as the asymptotic limit of microscopic models. The starting point is represented by a unidirectional microstructure evolution model which is based on a family of ordered admissible microstructures. Each microstructure of that family possesses the same intrinsic length scale. To derive an effective model, the asymptotic behavior of this intrinsic length scale is investigated with the help of techniques of the two-scale convergence. For this purpose, a microstructure-regularizing term, which can be understood as a discrete gradient for piecewise constant functions, is needed to identify the limit model. The microstructure of the effective model is given pointwisely by a so-called unit cell problem which separates the microscopic scale from the macroscopic scale. Based on these homogenization results for unidirectional microstructure evolution models, effective models for brutal damage processes are provided. There, the microstructure consists of only two phases, namely undamaged material which comprises defects of damaged material with various sizes and shapes. In this way damage progression can be modeled by the growth of inclusions of weak material, the growth of voids, or the growth of microscopic cracks. The size of the defects is scaled by the intrinsic length scale and the unidirectional microstructure evolution prevents that, for a fixed length scale, the defects shrink for progressing time. According to the unit cell problem, the material of the limit model is then given as a mixture of damaged and undamaged material. In a specific material point of the limit model, that unit cell problem does not only define the mixture ratio but also the exact geometrical mixture distribution.

Environmental factors and lifestyle can alter the way our genes are expressed influencing a network of chemical switches within our cells collectively known as the Epigenome. Among the epigenetic mechanisms orchestrating the gene expression, methylation is of foremost importance and probably fair to say, still incompletely decoded. Dysregulations of histone methylation patterns lead to the repression or activation of signalling pathways that often promote the genesis and progression of disease states. Lysine specific demethylase 1 (LSD1) oxidatively removes methyl groups from histone H3 and its aberrant activity has been correlated with the development of a broad range of pathologies. Therefore, specific inhibitors of LSD1 have potential in pharmacological applications. Research into LSD1 and its functions in normal and abnormal cells has been hindered by the lack of a specific and potent suppressor. The development of a selective inhibitor could not only foster the understanding of the biological roles of LSD1 but also represent a breakthrough for the design of novel drugs for a range of burdensome diseases. Here we investigate on reversible and irreversible inhibitors of LSD1, with the hope of broadening the current knowledge on this epigenetic target. By analysing the LSD1 interaction with the transcription factor Snail-1, we generated a series of small peptides as potential reversible inhibitors. The synthetic peptides were then evaluated in cellular assays. In search of novel non-covalent LSD1 blockers, we next explored Phage Display technology. Thereafter, we targeted LSD1 covalently by synthesising multiple structural analogues of the clinically used antidepressant TCP (Parnate®), which is a known irreversible suppressor of LSD1 activity. We evaluated their ability of inhibiting LSD1 in a cell-free assay and the compounds showing enzymatic inhibition were tested as potential anti-proliferative and differentiating agents in leukaemia cell lines. Finally, we generated activity-based probes to fluorescently label LSD1 for biological applications.

Cette thèse analyse le rôle de l'irréversibilité de l'investissement sur la concurrence dynamique. Elle est composée de quatre articles théoriques et d'une introduction générale. Le deuxième chapitre s'intéresse à la possibilité de préemption en investissement irréversible, concurrence imparfaite et évolution de la demande aléatoire. Il montre qu'il n'y a pas de préemption sans sauts de demande. En effet, la linéarité des coûts d'investissement crée une incitation pour les entreprises à investir aussi vite que possible. Dès lors, il ne peut y avoir de préemption en l'absence d'évolution de la demande. Le troisième chapitre étudie la dynamique de la répartition de capacités au sein de l'oligopole, lorsque l'investissement est irréversible, la concurrence imparfaite et la demande aléatoire. Il montre que la dynamique de l'investissement a une propriété d'efficacité, et qu'une asymétrie entre capacité initiale peut se conserver à court terme, mais disparait à long terme. Le quatrième chapitre analyse les décisions d'investissement d'un duopole quand chaque entreprise peut investir dans deux types de capacités différentes. L'une des capacités permet de produire à un coût marginal plus faible, mais est plus chère à l'achat. Les entreprises sont contraintes financièrement en première période. A cause de cela, les entreprises peuvent utiliser les deux types de capacités en même temps, et il y a une possibilité de préemption. De plus, l'augmentation du prix de la capacité inefficace peut renforcer son utilisation. Le dernier chapitre étudie l'impact de l'irréversibilité de l'investissement sur la possibilité de collusion. L'irréversibilité de l'investissement réduit la profitabilité de la déviation de court terme, l'entreprise qui dévie ayant besoin d'augmenter sa capacité, mais crée aussi une incitation de long terme. En effet, l'investissement réalisé par l'entreprise qui dévie l'engage à un certain niveau de capacité dans le futur, permettant de préempter l'entreprise concurrente. A cause de cet effet de préemption, plus les entreprises sont patientes, plus la collusion peut être difficile à soutenir
This thesis studies the role of the irreversibility of investment on the dynamic imperfect competition. It is composed of four theoretical articles and a general introduction. The second chapter studies the role of demand evolution on the possibility of preemption under irreversible investment under imperfect competition. It shows there is no possibility of preemption when there is no jump of demand. Indeed, the linearity of investment cost creates no incentive for the firms to delay investment. When there is no demand evolution, this prevents preemption. The third chapter focuses on the dynamics of firms' capacity when the irreversibility of investment is partial. It shows that the investment dynamics exhibits an efficiency property, and that some initial asymmetry in capacity can be preserved in the short run, but disappears in the long run. The fourth chapter considers the investment choice of firms when there are two different productive capacities embodying different types of technology. One technology permits to produce at a lower marginal cost but the purchasing price of the capacity using this technology is higher. Due to the presence of a financial constraint, firms use different technologies at the same time, and a preemption equilibrium appears. Finally, this paper presents a counter intuitive policy result: an increase in the price of one of the capacities may increase its utilization. The last chapter studies the impact of the irreversibility of investment on collusion possibility. The irreversibility of investment reduces the profitability of short run deviation, as the deviating firm has to invest in order to increase its capacity, and it creates a long run effect. lndeed, once the deviating firr has invested, it is committed toits new capacity. The deviation may thus lead to a preemption of the punishing firm. This preemption effect can make collusion harder to sustain for more patient firms

L'objectif de notre recherche est le marquage irreversible du site de liaison de l'acide -aminobutyrique (gaba#a) en vue de sa caracterisation moleculaire. Le recepteur ionotrope gaba#a est un hetero-oligomere regroupant autour d'un canal chlorure plusieurs sites de liaison qui interagissent entre eux: gaba, benzodiazepine, canal, barbiturates, steroides, ainsi que d'autres moins bien definis. Le recepteur gaba#a aurait une structure pentamerique, composee d'au moins trois des seize sous-unites ( 1-6, 1-4, 1-3, , p1-2) que la biologie moleculaire a permis mettre en evidence a ce jour, sans qu'une (ou des) composition(s) definie(s) aient pu etre attribuees aux recepteur(s) natif(s) qui possede(nt) vraissemblablement une grande heterogeneite de constitution. La pharmacologie complexe du recepteur gaba#a, probablement liee a sa structure moleculaire, pourra etre mieux comprise lorsque les proteines receptrices auront ete caracterisees et la topologie des differents sites de liaison mieux cernee: c'est le but du marquage irreversible qui consiste a etablir une liaison covalente entre le recepteur et un ligand portant une fonction reactive en l'absence (marquage d'affinite) ou en presence de lumiere (marquage de photoaffinite). Nous avons synthetise une quinzaine de molecules photoactivables portant quatre fonctions photosensibles differentes. Trois d'entre elles ont ete retenues en fonction de leurs caracteristiques physico-chimiques, de leur stabilite en milieu physiologique et de leur affinite pour le recepteur: l'acide 2-diazo-4-(5)-imidazole acetique 35, le chlorure de m-sulfonate benzene diazonium (msbd) 41 et l'azidopyridazinyl-gaba 49 sont des marqueurs irreversibles du recepteur gaba#a. Les deux derniers ont ete retenus pour etre synthetises sous forme radioactive en raison de leur stabilite en presence du recepteur membranaire. L'azidopyridazinyl-gaba 49 (ic#5#0=6. 10#-#7 m) est un marqueur de photoaffinite efficace dont l'analogue radioactif permettra une etude topologique du recepteur par marquage de la proteine et sequencage des elements proteolyses et purifies. Le msbd est un marqueur d'affinite puissant dont le caractere d'antagoniste non-competitif a ete mis en evidence par electrophysiologie. Une methode de dissociation efficace a permis de caracteriser sa liaison irreversible avec le recepteur gaba#a membranaire par etude des cinetiques de marquage et d'acceder ainsi a sa constante de dissociation. Le radioligand #3hmsbd marque quatre bandes proteiques dont le poids moleculaire correspond a celui de sous-unites et du recepteur. Le msbd pourra, en raison de ses caracteristiques d'affinite, etre utilise soit sous forme radioactive de maniere classique comme l'azidopyridazinyl-gaba 49, soit sous forme non-radioactive comme marqueur d'un recepteur ayant subi des mutations choisies en fonctions de criteres bien particuliers

Nous présentons des approches théoriques et numériques pour deux dynamiques irréversibles et parallèles sur des modèles de mécanique statistique. Dans le premier chapitre, nous présentons les résultats théoriques sur un système de particules induite par une chaîne de Markov irréversible, à savoir le TASEP. Permettant des multiples retournements de spin \`à chaque itération, nous définissons un modèle avec une dynamique parallèle appartenant à la famille des PCA et nous dérivons sa mesure stationnaire. Dans ce cadre, nous traitons {\it le problème du blocage}, {\it i.e.} comprendre les effets d’une perturbation localisée dans le taux de transition des particules sur des systèmes irréversibles: le problème du blocage. Dans le deuxième chapitre, nous présentons une version unidimensionnelle du modèle d'Ising avec potentiel de Kac. Nous définissons une PCA avec une interaction asymétrique et nous trouvons sa mesure stationnaire avec condition aux limites périodique.Ensuite, nous prouvons la convergence, dans la limite thermodynamique, de cette mesure stationnaire vers la mesure de Gibbs pour toutes les températures supérieures à la température critique via les estimations de F\"ollmer et le théorème d'unicité de Dobrushin. Dans la seconde partie de la thèse, nous étudions ces deux dynamiques à travers des expériences numériques. Dans le cas du TASEP en exploitant des processeurs graphiques (GPU) et CUDA pour identifier une estimation raisonnable du {temps de m\'elange} et renforcer la conjecture qu’à la fois dans la version, la règle de mise à jour série ou parallèle, le courant peut ne pas être analytique dans l’intensité du blocage autour de la valeur $ \varepsilon = 0 $
In this thesis we present theoretical and numerical approaches for two irreversible and parallel dynamics on one-dimensional statistical mechanics models. In the first chapter we present theoretical results on a particles system driven by an irreversible Markov chain namely the totally asymmetric simple exclusion process (TASEP). Allowing multiples spin-flips in each time-step we define a model with a parallel dynamics that belongs to the family of the probabilistic cellular automata (PCA) and we derive its stationary measure. In this framework we deal with {\it the blockage problem}, {\it i.e.} to understand the effects of a localized perturbation in the transition rates of the particles on irreversible systems: the blockage problem. In the second chapter we present a one-dimensional version of the Ising model with Kac potential. Again we define a PCA dynamics with asymmetric interaction between particles and we find its stationary measure for periodic boundary condition. Then we prove the convergence, in the thermodynamic limit, of such stationary measure to the Gibbs measure for all temperatures above the critical one via F\"ollmer estimates and dobrushin's uniqueness theorem. In the second part of the thesis, we investigate these two dynamics through numerical experiments.In the case of the TASEP we exploit general purpose graphical processors unit (GPGPU) writing a parallel code in CUDA to identify a reasonable {\it mixing time} and reinforce the conjecture that in both version, serial or parallel update rule, the current may be non-analytic in the blockage intensity around the value $\varepsilon = 0$

Für mikroskopische Teilchen, die sich durch eine überdämpfte Fockker-Planck-Gleichung beschreiben lassen, werden thermodynamische Größen definiert. Es wird ein Ausdruck für die irreversible Arbeit berechnet. Weiterhin wird ein Kreisprozess konstruiert und für diesen der Wirkungsrad am Punkt maximaler Leistung berechnet. Als Spezialfall wird dann ein Teilchen in einem harmonischen Potential betrachtet. Alle Ergebnisse stammen bereits aus einer Veröffentlichung, es werden jedoch hier alle Berechnungen angegeben.

In this thesis, several stochastic models are investigated, which are subjected to irreversible dynamics. Motivation for the presented work stems, on the one hand, from particular physical systems under consideration, which are modeled by the studied stochastic processes. Besides that, the models discussed in this thesis are, on the other hand, generally interesting from the point of view of statistical physics, since they describe systems far from thermodynamic equilibrium. Interesting properties to be encountered are, e.g., dynamical scaling behavior or continuous phase transitions. The first issue to be addressed, is the investigation of irreversibly aggregating systems, where the main emphasis is laid on aggregation of monopolarly charged clusters suspended in a fluid. For this purpose, rate equations are analyzed and Brownian dynamics simulations are performed. It is shown that the system crosses over from power-law cluster growth to sub-logarithmic cluster growth. Asymptotically, the cluster size distribution evolves towards a universal scaling form, which implies a 'self-focussing' of the size distribution. Another emphasis of this thesis is the investigation of nonequilibrium critical phenomena, in particular, the study of phase transitions into absorbing states (states that may be reached irreversibly). To this end, the continuous nonequilibrium phase transition of directed percolation, which serves as a paradigm for absorbing-state phase transitions, is analyzed by a novel approach. Despite the lack of a partition function for directed percolation, this novel approach follows the ideas of Yang-Lee theory of equilibrium statistical mechanics, by investigating the complex roots of the survival probability. Stochastic models such as directed percolation mimic spreading processes, e.g., the spreading of an infectious disease. The effect of long-time memory, which is not included in directed percolation and which corresponds to immunization in epidemic spreading, is investigated through an appropriate model. This model includes dynamical percolation (perfect immunization) as a special case, as well as directed percolation (no immunization). The critical behavior of this model is studied by means of Monte Carlo simulations, in particular for weak immunization. A further generalization is investigated, which allows spontaneous mutations and different species of spreading agents (pathogens). Restricting the analysis to perfect immunization and two spatial dimensions, it is shown by Monte Carlo simulations, that immunization leads to a crossover from dynamical to directed percolation. Other properties of this model are discussed in detail.

Memoria (licenciado en ciencias jurídicas y sociales)
La presente memoria de investigación aborda la reparación del daño ambiental irreversible mediante una interpretación extensiva de la reparación como objeto de la acción ambiental contemplada en el inciso primero del artículo 53 de la Ley Nº 19.300. Al respecto, se sostiene que ante la imposibilidad de reparar in natura el daño ambiental ocasionado, y bajo la premisa de que no resulta posible reconocer normativamente en Chile un ámbito de irrestricta irresponsabilidad, resulta procedente, por analogía, la aplicación de medidas de compensación ambiental como forma de reparación en equivalencia frente a esta categoría de daños no previstas por el legislador. Se plantea que la solución acá ofrecida, además de resultar idónea en atención al bien jurídico tutelado por la acción ambiental, resulta coincidente con los principios que inspiran el sistema de responsabilidad civil por daño ambiental en Chile, en tanto concretiza la idea básica sobre la cual se articula cualquier sistema de responsabilidad: que quien resulte responsable de la ocasión de un daño ambiental se encuentre obligado a su reparación. Palabras

8-Cyclopentyl-3-(3-(4-fluorosulfonylbenzoyl)oxy)propyl-propylxanthine (44, FSCPX) has been reported to exhibit potent and selective irreversible antagonism of the A1 adenosine receptor when using in vitro biological preparations. However, FSCPX (44) suffers from cleavage of the ester linkage separating the reactive 4-(fluorosulfonyl)phenyl moiety from the xanthine pharmacophore when used in in vivo biological preparations or preparations containing significant enzyme activity, presumably by esterases. Cleavage of the ester linkage renders FSCPX (44) inactive in terms of irreversible receptor binding. In order to obtain an irreversible A1 adenosine receptor antagonist with improved stability, and to further elucidate the effects of linker structure on pharmacological characteristics, several FSCPX (44) analogues incorporating the chemoreactive 4-(fluorosulfonyl)phenyl moiety were targeted, where the labile ester linkage has been replaced by more stable functionalites. In particular, ether, alkyl, amide and ketone linkers were targeted, where the length of the alkyl chain was varied from between one to five atoms. Synthesis of the target compounds was achieved via direct attachment of the N-3 substituent to the xanthine. These compounds were then tested for their biological activity at the A1 adenosine receptor via their ability to irreversibly antagonise the binding of [3H]-8-cyclopentyl-1,3-dipropylxanthine ([3H]DPCPX, ( 9) to the A1 adenosine receptor of DDT1 MF-2 cells. For comparison, the xanthines were also tested for their ability to inhibit the binding of [3H]-4-(2-[7-amino-2-{furyl} {1,2,4}- triazolo{2,3-a} {1,3,5}triazin-5-ylamino-ethyl)]phenol ([3H]ZM241385, 36) to the A2A adenosine receptor of PC-12 cells. The results suggest that the length and chemical composition of the linker separating the reactive 4-(fluorosulfonyl)phenyl moiety from the xanthine ring contribute to the potency and efficacy of the irreversible A1 adenosine receptor ligands. Like FSCPX (44, IC50 A1 = 11.8 nM), all derivatives possessed IC50 values in the low nM range under in vitro conditions. Compounds 94 (IC50 A1 = 165 nM), 95 (IC50 A1 = 112 nM) and 96 (IC50 A1 = 101 nM) possessing one, three and five methylene spacers within the linkage respectively, exhibited potent and selective binding to the A1 adenosine receptor versus the A2A adenosine receptor. Compound 94 did not exhibit any irreversible binding at A1 adenosine receptors, while 95 and 96 exhibit only weak irreversible binding at A1 adenosine receptors. Those compounds containing a benzylic carbonyl separating the 4-(fluorosulfonyl)phenyl moiety from the xanthine ring in the form of an amide (119, IC50 A1 = 24.9 nM, and 120, IC50 A1 = 21 nM) or ketone (151, IC50 A1 = 14 nM) proved to be the most potent, with compound 120 exhibiting the highest selectivity of 132-fold for the A receptor over the A2A receptor. compounds 119, 120 and 151 also strongly inhibited the binding of [3H]DPCPX irreversibly (82%, 83% and 78% loss of [3H]DPCPX binding at 100 nM respectively). compounds 120 and 151 are currently being evaluated for use in in vivo studies. Structure-activity studies suggest that altering the 8-cycloalkyl group of A1 selective xanthines for a 3-substituted or 2,3-disubstituted styryl, combined with N-7 methyl substitution will produce a compound with high affinity and selectivity for the A2A adenosine receptor over the A1 adenosine receptor. Compound 167 (IC50 A2A = 264 nM) possessing 8-(m-chloro)styryl substitution and the reactive 4-(fluorosulfonyl)phenyl moiety separated from the xanthine ring via an amide linker in the 3-position (as for 119 and 120), exhibited relatively potent binding to the A2A adenosine receptor of PC-12 cells, with a 16-fold selectivity for that receptor over the A1 adenosine receptor. However, compound 167 exhibited only very weak irreversible binding at A2A adenosine receptors. Overall, at this stage of biological testing, compound 120 appears to possess the most advantageous characteristics as an irreversible antagonist for the A1 adenosine receptor. This can be attributed to its high selectivity for the A1 adenosine receptor as compared to the A2A adenosine receptor. It also has relatively high potency for the A1 adenosine receptor, a concentration-dependent and selective inactivation of A1 adenosine receptors, and unbound ligand is easily removed (washed out) from biological membranes. These characteristics mean compound 151 has the potential to be a useful tool for the further study of the structure and function of the A1 adenosine receptor.

Research into chemical sensors, and in particular colourimetric sensors, is an area of increasing interest. The instant access to important chemical information that such devices can bring is their most attractive feature. The aim of this project has been to develop such colourimetric indicators and to research their behaviour in detail such that their response to different environments can be known, and their formulation altered to suit the application.

[ES] En esta tesis se ha desarrollado una estrategia multidisciplinar que incluye la irradiación de complejos ligando/proteína junto con estudios de fluorescencia y/o espectroscopía de absorción transitoria, cromatografía de exclusión por tamaño seguida de espectroscopía de absorción y/o fluorescencia, análisis proteómico y modelización (docking y simulaciones de dinámica molecular) con el fin de profundizar y obtener información relevante en procesos relacionados con la formación de complejos irreversibles ligando-proteína. Ello ha permitido lograr la descripción del centro de reconocimiento molecular de albúminas séricas de distintas especies por el fármaco carprofeno, profundizar en procesos de fotoalergia producidos por el metabolito del fármaco triflusal y llevar a cabo el marcaje de residuos de lisina de la albúmina sérica humana por fotogeneración de electrófilos latentes "quinone methide". A continuación se describen brevemente cada uno de estos aspectos. En primer lugar, se ha estudiado la posible existencia de un centro de reconocimiento común en las albúminas séricas (AS) de diferentes especies empleando el fármaco antiinflamatorio no esteroideo (S)-carprofeno (CPF) como sonda fotoactiva. Así, se ha seguido la irradiación de los complejos de CPF/SA a ¿max = 320 nm por fluorescencia, mostrandose un aumento de la emisión debido a la deshalogenación. Tras la cromatografía de filtración en gel, la fracción proteica presentaba emisión proveniente del ligando, verificando la unión covalente del radical fotogenerado intermedio CBZ¿ a las AS. El análisis proteómico reveló la incorporación de CBZ¿ en varias posiciones en las diferentes albúminas. Se observaron modificaciones en la interfaz IB/IIIA en todos los casos (Tyr452 en las albúminas séricas humana, conejo y rata y Tyr451 en las albúminas séricas bovina, cerdo y oveja). Estudios de docking y de simulación de dinámica molecular el caso de albúmina sérica humana corroboraron las modificaciones covalentes observadas experimentalmente. Posteriormente, se ha investigado la unión fotoquímica del HTB, el metabolito del antiagregante plaquetario triflusal a albúmina sérica humana (ASH). El análisis proteómico de las disoluciones de HTB/ASH tras ser irradiadas mostró la adición de HTB en los grupos ¿-amino de los residuos Lys137, Lys199, Lys205, Lys352, Lys432, Lys541, Lys545 y Lys525 de la ASH. El mecanismo de reacción parece implicar la substitución del grupo CF3 del HTB por un nuevo residuo amida. Solo el residuo Lys199 se localiza en una cavidad interna de la proteína mientras que el resto de los residuos modificados resultaron estar situados en la parte externa. Los estudios computacionales revelaron que la unión supramolecular de HTB a ASH se produce en la región "V-cleft". Esta unión fotoquímica puede estar en la base de la aparición de efectos secundarios fotoalérgicos no deseados. Finalmente, se ha demostrado la utilidad de los 4-trifluorometilfenoles como pre-cursores de electrófilos latentes tipo "quinone methide" (QM) para la unión específica a residuos de lisina que se encuentran en los sitios de unión de la proteína. Así, se ha observado que estos aceptores de Michael, generados de modo fotoinducido, han sido capaces de realizar una modificación covalente específica de residuos de lisina en albúmina sérica humana (ASH). En concreto, los intermedios reactivos de tipo QM generados tras la irradiación de los complejos 4-trifluorometil-1-naftol o 4- (4-trifluorometilfenil) fenol con ASH exhibieron selectividad química hacia los residuos de lisina dando lugar a aductos de amida. Un estudio detallado realizado mediante análisis proteómico confirmó este hecho. Así, para el derivado de naftol se observó la modificación covalente de los residuos Lys106 y Lys414 (ubicados en los subdominios IA y IIIA, respectivamente), mientras que para el derivado de bife-nilol ocurrió la modificación
[CAT] En aquesta tesi s'ha desenvolupat una estratègia multidisciplinària que inclou la irradiació de complexos lligand/proteïna juntament amb estudis de fluorescència i/o espectroscopia d'absorció de transients, cromatografia d'exclusió de grandària se-guida d'espectroscòpia d'absorció i/o fluorescència, anàlisi i modelització proteòmica (docking i simulacions de dinàmica molecular) amb l'objectiu d'aprofundir i obtenir informació rellevant en els processos relacionats amb la formació de com-plexos lligand-proteïna irreversibles. Això ha permès la descripció del centre de reconeixement molecular d'albúmines sèriques de diferents espècies pel fàrmac carprofen, i aprofundir en processos de fotoal·lèrgia produïts pel metabolit del fàrmac triflusal i realitzar el marcatge de residus de lisina d'albúmina sèrica humana per fotogeneració d'electròfil "quinone methide" latent. Cadascun d'aquests aspectes es descriu breument a continuació. En primer lloc, s'ha estudiat la possible existència d'un centre de reconeixement comú en albúmines sèriques (AS) de diferents espècies utilitzant el fàrmac antiinflamatori no esteroïdal (S)-carprofèn (CPF) com a sonda fotoactiva. Així, s'ha se-guit la irradiació dels complexos de CPF/SA a un màxim de 320 nm per fluorescència, amb un augment de les emissions a causa de la deshalogenació. Després de la cromatografia de filtració de gel, la fracció de proteïna presentava emissió del lli-gand, verificant la unió covalent del radical fotogenerat intermedi CBZ¿ a les AS. L'anàlisi proteòmica va revelar la incorporació de CBZ¿ en diverses posicions en els diferents albúmines. En tots els casos s'han observat modificacions a la interfície IB/IIIA (Tyr452 en albúmina sèrica humana, conill i rata i Tyr451 en albúmines sèriques bovina, porc i ovella). Els estudis de docking i de simulació de dinàmiques moleculars en el cas d'albúmina sèrica humana van corroborar les modificacions covalents experimentalment observades. Posteriorment, s'ha investigat la unió fotoquímica del HTB, el metabòlit de l'antiagregant plaquetari triflusal a l'albúmina sèrica humana (ASH). L'anàlisi proteòmica de les solucions HTB/ASH després de ser irradiades mostraren l'addició de HTB en els grups ¿-amino dels residus Lys137, Lys199, Lys205, Lys352, Lys432, Lys541, Lys545 i Lys525 de la ASH . El mecanisme de reacció podria implicar la substitució del grup CF3 de la HTB amb un nou residu d'amida. Només el residu Lys199 està situat en una cavitat interna de la proteïna, mentre que la resta dels residus modificats van resultar estar situats a l'exterior. Els estudis computacionals van revelar que la unió supramolecular de HTB a ASH es produeix a la regió "V-cleft". Aquesta unió fotoquímica pot ser la base de l'aparició d'efectes secundaris fotoal·lèrgics no desitjats. Finalment, s'ha demostrat la utilitat de 4-trifluorometilfenols com a precursors d'electròfils latents "quinone methide" (QM) per a la unió específica a residus de lisina trobats en els llocs d'unió de la proteïna. Per tant, s'ha observat que els acceptors de Michael, generats de manera foto-induïda han pogut fer una modificació covalent específica de residus de lisina en albúmina de sèrica humana (ASH). Concretament, els intermedis reactius del tipus QM generats després de la irradiació dels complexos 4-trifluoromethyl-1-naftol o 4-(4-trifluoromethylphenyl) fenol amb ASH exhibiren selectivitat química als residus de lisina resultant en aductes ami-da. Un estudi detallat realitzat mitjançant anàlisi proteòmica confirmà aquest fet. Així, pel derivat del naftol, es va observar la modificació covalents de residus Lys106 i Lys414 (localitzada en subdominis IA i IIIA, respectivament), mentre que per al derivat de bifenil la modificació es va produir en el Lys195 (en subdomini IIA). Els estudis teòrics proporcionen una visió molecular més profunda de la selectivitat observada
[EN] In this thesis a multidisciplinary strategy has been developed that includes irradiation of ligand/protein complexes along with fluorescence and/or transient absorption spectroscopy, size-exclusion chromatography followed by absorption and/or fluorescence spectroscopy, proteomic analysis and modelling (docking and molecular dynamics simulations) in order to deepen and obtain relevant information in processes related to the formation of irreversible ligand-protein complexes. This has made it possible to achieve the description of the molecular recognition centre of serum albumin of different species by the carprofen drug, to deepen in photoallergy processes produced by the metabolite of the triflusal drug and to carry out the la-belling of lysine residues of human serum albumin by photogeneration of latent electrophiles "quinone methide". Each of these aspects is briefly described below. First, the possible existence of a common recognition centre in serum albumin (SA) of different species has been studied using the non-steroidal antiinflammatory drug (S)-carprofen (CPF) as a photoactive probe. Thus, irradiation of the CPF/SA complexes at ¿max = 320 nm has been followed by fluorescence, showing an increase in emission due to dehalogenation. After gel filtration chromatography, the protein fraction presented emission from the ligand, verifying the covalent bonding of the CBZ¿ intermediate photogenerated radical to the SA. Proteomic analysis revealed the incorporation of CBZ¿ in various positions in the different albumins. Modifications in the IB/IIIA interface were observed in all cases (Tyr452 in human, rabbit and rat serum albumin and Tyr451 in bovine, porcine and sheep serum albumin). Docking and molecular dynamics simulation studies in the case of human serum albumin corroborated the experimentally observed covalent modifications. Subsequently, the photochemical binding of HTB, the metabolite of the triflusal platelet antiaggregant to human serum albumin (HSA), has been investigated. Proteomic analysis of the HTB/HSA solutions after being irradiated showed the addition of HTB in the ¿-amino groups of residues Lys137, Lys199, Lys205, Lys352, Lys432, Lys541, Lys545 and Lys525 of the HSA. The reaction mechanism seems to involve replacing the CF3 group of HTB with a new amide residue. Only the Lys199 residue is located in an internal cavity of the protein whilst the rest of the modified residues were found to be located on the outside. Computational studies revealed that supramolecular binding of HTB to HSA occurs in the "V-cleft" region. This photochemical binding may be at the base of the appearance of unwanted photoallergic side effects. Finally, the utility of 4-trifluoromethylphenols as precursors of latent "quinone methide" (QM) type electrophiles for specific binding to lysine residues found at the protein binding sites has been demonstrated. Thus, it has been observed that these photogenerated Michael acceptors, have been able to perform a specific covalent modification of lysine residues in human serum albumin (HSA). Specifically, the QM type reactive intermediates generated after irradiation of the 4-trifluoromethyl-1-naphthol or 4- (4-trifluoromethylphenyl) phenol complexes with HSA exhibited chemical selectivity towards lysine residues giving rise to amide adducts. A detailed study conducted by proteomic analysis confirmed this fact. Thus, for the naphthol derivative the covalent modification of residues Lys106 and Lys414 (located in subdomains IA and IIIA, respectively) was observed, while for the biphenyl derivative the modification occurred in Lys195 (in subdomain IIA). Theoretical studies provided a deeper insight at the molecular level of the experimentally observed selectivity.
Molins Molina, Ó. (2020). Unión fotoquímica irreversible de ligandos a albúminas séricas [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/139676
TESIS

The importance of extremely slow retention and release has superseded the notion that sorption of pesticides to soil is an instantaneous and reversible process. A fraction of sorbed pesticide is also often reported to bind irreversibly to the soil matrix. This has important implications for pesticide mobility and bioavailability. It is essential to understand sorption phenomena to allow accurate prediction of pesticide fate within the soil environment. This thesis describes the result of applying a sequential extraction procedure, based on the principles of isotope or “self-exchange”, to nine pesticide/soil systems. The significance of irreversible sorption in controlling pesticide mobility was assessed using isotope exchange (12C and 14C) to characterise pesticide exchange kinetics in-situ over protracted time-scales. Sequential extraction increased in harshness in the order: isotope exchange < forced isotope exchange < solvent extraction. Three pesticides (one neutral, one basic, one acidic) and three temperate, arable soils (ranging in texture and pH) were studied. A three-site sorption model was developed to further interpret the data obtained. Although results showed the experimental design of the isotope exchange technique was not powerful enough to identify whether remaining sorbed pesticide was participating in slowly reversible or irreversible sorption, the forced isotope exchange procedure was able to provide an indication of amounts of pesticide not participating in exchange between the soil and solution. Under abiotic conditions, only minimal amounts of initial-applied pesticide were found to take part in irreversible binding. Soil combustion quantified irreversible sorption in the order: chlorotoluron (≤ 2.27 ± 0.36%) > prometryn (≤ 1.35 ± 0.60%) > hexaconazole (≤ 0.50 ± 0.06%). Varying the soil composition had little effect on amounts of irreversibly sorbed pesticide, probably due to the small amounts of irreversible sorption observed overall. These results suggest that the vast majority of sorbed chlorotoluron, prometryn and hexaconazole (in the parent form) participated in very slow but reversible binding, a result also confirmed by the three-site sorption model. Pesticide sorption behaviour is a complex process. Although sorption phenomena are still not fully understood, these results provide a greater insight into the significance of irreversible binding for predicting pesticide fate.

Tax uncertainty is often claimed to be harmful for investments. Capital taxes, such as property and wealth taxes, are particularly exposed to tax uncertainty. Capital tax un- certainty emerges from expected tax reforms, the unclear outcome of future tax audits, and simplified estimates of capital tax bases in investment models. Uncertain returns on investment as well as stochastic taxation contribute to overall uncertainty and may significantly affect investment decisions. Hitherto, it is unknown how capital tax uncertainty affects investment timing. However, it is well known that both uncertainty and capital tax may be harmful for investment and decelerate investment activities. We are the first to study the investment timing effects of stochastic capital taxes in a real options setting with risky investment opportunities. Our results indicate that even risk neutral investors are sensitive with respect to capital tax risk and may react in a surprising manner to a newly introduced stochastic capital tax. As an apparently paradoxical investment e¤ect, we find that increased capital tax uncertainty can accelerate risky investment if such uncertainty is such ciently low compared to cash flow uncertainty. In contrast, high capital tax risk delays high-risk innovative investment projects. To reduce unintended consequences of uncertain tax policy, tax legislators and tax authorities should avoid high levels of cap- ital tax uncertainty. Broadening the capital tax base or increasing the capital tax rate induces ambiguous timing effects. Furthermore, high-growth investments are likely to be postponed if they experience a capital tax cut. Since investment reactions upon tax reforms are well-known to affect income and wealth distribution, reliable estimations of the impact of taxes on economic decisions are necessary. (authors' abstract)
Series: WU International Taxation Research Paper Series

The role of elasticity and disorder and their interplay in plastic deformation processes is investigated on different length scales. Random disorder, in the form of impurities, fluctuations of defect densities and spatial heterogeneities, is responsible for a wealth of phenomena including surface roughening, non-linear dynamic response, stick-slip behaviour and temporal intermittency, which are observed in a wide variety of physical systems. A theoretical description of these phenomena is provided by theories of pinning and depinning transitions. In this work, these aspects are investigated in the context of plastic deformation of random media, such as real crystals with disordered microstructures or disordered elastic continua. Under the effect of an external force, these systems exhibit a complex behaviour arising form the competition between elasticity and disorder. Disorder tends to perturb the system, which reacts by opposing elastic restoring forces. This complex small scale dynamics determines the macroscopic behaviour of irreversibly deforming materials. These aspects are studied on different length scales. The problem of the depinning transition occurring in dislocation assemblies is first investigated. Dislocations are microstructure defects mediating plastic deformation. Under the effect of external forces, they are driven through disordered landscapes and rearrange into complex assemblies. A theory of pinning and collective behaviour of linear and planar dislocation arrays is formulated. Non-local elastic properties arise naturally form long-range dislocation interactions and influence dramatically statics and dynamics of these systems in the presence of disorder. Comparison with numerical results and experimental data confirms the validity of this approach. An application to vortex lattices in Type II superconductors is then considered. Dislocation assemblies such as low angle grain boundaries are often observed in these systems, determining the emergence of a polycrystalline phase. A theory of vortex polycrystals is proposed, in the conceptual framework of grain boundary pinning. Several aspects, including grain growth, transport properties, hysteretic behaviour and vortex lattice melting are investigated. Results are found in agreement with numerical simulations and experimental observations. On larger length scales, a theory of plastic flow in the presence of random stress fluctuations is discussed. The problem proves to be described by a continuum mean-field pinning model, where disorder is produced by randomness in dislocation densities. Such a description provides a theoretical framework to understand the origin of the critical behaviour often observed in plastically deforming crystals in the form of self-affine surface roughening and intermittent avalanche motion.

Irreversible electroporation (IRE) is an energy directed focal ablation technique. This procedure typically involves the placement of two or more electrodes into, or around, a region of interest within the tissue and administering a sequence of short, intense, pulsed electric fields (PEFs). The application of these PEFs results in an increase in the transmembrane potential of all cells within the electric field above a critical value, destabilizing the lipid bilayer of the cellular membrane and increasing the cell-tissue permeability. For years, many have used this phenomenon to assist the transport of macromolecules typically unable to penetrate the cell membrane with the intent of avoiding cell necrosis or irreversible electroporation. More recently, however, irreversible electroporation has proven to be a successful alternative for the treatment of cancer. Proper tuning of the pulse parameters has allowed for a targeted treatment of localized tumors, and has shown immense value in the treatment of surgically inoperable tumors located near major blood vessels and nerves. While it is critical to ensure sufficient treatment of the target tissue, it can be equally vital to the treatment and patients overall outcome that the pulsing conditions are set to moderate the associated thermal effects with the electroporation of biological tissue. The development of thermal mitigation strategies for IRE treatment is the focus of this dissertation. Herein, the underlying theory and thermal considerations of tissue electroporation in various scenarios are described. Additionally, new thermal mitigation approaches with the intention of maintaining tissue temperature below a thermally damaging threshold, while also preserving or improving IRE lesion volume are detailed. Further, numerical models were developed and ex vivo tissue experiments performed using a perfused organ model to examine three thermal mitigation strategies in their ability to moderate temperature. Tests conducted using thermally mitigating treatment delivery on live tissue confirm the capacity to deliver more energy to the tissue at a thermally acceptable temperature, and provide the potential for a replete IRE lesion.
Doctor of Philosophy

Perception in our everyday life takes place in multisensory environments, and hence involves the processing of a multitude of signals captured by various sensory modalities. Given the different nature of the signals, understanding how all the information is combined in the brain to form an integrated percept is not straightforward. One of the paramount questions is how the considerable timing differences between sensory information processing are managed. For example, in the last years there has been a tremendous surge in interest to understand how the perceptual system elicits the subjective impression of synchrony for stimuli coming from different sensory modalities. Yet, most evidence so far concerns stimulus-related properties in simple contexts. The present dissertation addresses the influence of cognitive factors and participants’ inner state (such as attention, action task demands, and ongoing brain rhythms) on synchrony perception between audio-visual events. In the first two studies of the dissertation, we have addressed the role of selective attention and action during cross-modal temporal recalibration. The results of these studies provide evidence that subjective simultaneity can be strongly modulated as a function of the focus of the observer’s endogenous attention, in otherwise identical stimulation conditions. In the third study, we have recorded electroencephalographic activity while participants performed an audio-visual simultaneity judgment task for stimuli presented at different asynchronies. Our results show that the phase of low frequency neural oscillations, reflecting brain states prior to the occurrence of an audio-visual event, can predict perceptual variability in synchrony judgments. Overall, our results shed new light on how cognitive factors can modulate multisensory perception.
La percepció del nostre entorn és multisensorial, és a dir, involucra el processament de senyals a través de diverses modalitats sensorials. Combinar aquesta informació en el cervell per tal de formar una percepció coherent i integrada és un procés complex, degut a la diferent naturalesa de les senyals. A més, això farà que el cervell hagi de resoldre diferències temporals durant el processament de la informació. En els últims anys, ha sorgit un profund interès per entendre com el sistema perceptiu genera la impressió de sincronia d’estímuls provinents de diferents modalitats sensorials. La major part dels estudis han examinat propietats de la percepció de sincronia relacionades directament amb els estímuls físics, en contexts molt simplificats. En aquesta tesi investigo la influència de factors cognitius i de l’estat intern de l’individu (com per exemple l’atenció, demandes en tasques motores, i els ritmes interns cerebrals) en la percepció de sincronia entre estímuls audiovisuals. En els primers dos estudis de la tesi, hem examinat la funció de l’atenció i les accions durant la recalibració temporal d’estímuls audiovisuals. Els resultats dels estudis mostren com la sincronia subjectiva pot ser fortament modulada en funció d’on es dirigeixi el focus atencional del participant, en condicions on l’estimulació física és idèntica. En el tercer estudi, hem enregistrat l’activitat electroencefalogràfica dels participants, mentres realitzaven una tasca de simultaneïtat. Durant aquesta tasca presentàvem diferentes asincronies entre estímuls audiovisuals per tal d’estudiar la percepció de sincronia (vs. asincronia). Els resultats indiquen que la fase de les oscil·lacions neuronals, que reflecteixen estats cerebrals abans de la presència d’un estímul audiovisual, poden predir la resposta en quan a percepció de sincronia. En resum, els nostres resultats aporten coneixement sobre com alguns factors cognitius poden modular la percepció multisensorial.

Thesis (Ph. D.)--University of California, San Diego, 2007.
Title from first page of PDF file (viewed June 8, 2007). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references (p. 69-72).

For almost 40 years, scholars have sought to determine how elections affect the economy. Recently, certain studies have focused on the effect of political uncertainty on the economy. This paper focuses specifically on the effect of political uncertainty on business investment. We use 30 years of data from the U.S. states to show that policy uncertainty leads to significant declines in business fixed investment, sometimes referred to as “irreversible investment.” Moreover, we find that the magnitude of the decline in investment depends on the level of policy uncertainty. These results support predictions for “Electoral Investment Theory” and the existence of reverse political business cycles more generally.

Proteases are present in all living organisms and are involved in various biological processes. Inhibition of protease activities in disease-causing agents is one strategy for rational drug design. Characterization of the protease inhibition processes is essential for understanding the inhibition mechanisms and for developing efficient therapeutics. This work represents a major challenge in analytical biochemistry. In this study, a strategy based on mass spectrometry has been developed to characterize irreversible inhibition of proteases. Five proteases representing three of the four protease classes were irreversibly inhibited by various irreversible inhibitors, some of which are potential drug candidates. In all the cases, the stoichiometry of each of the protease/inhibitor complexes was determined by electrospray ionization mass spectrometry through measurement of the complex's molecular weight. The inhibited proteases were then enzymatically cleaved and the resulting peptides isolated for further characterization by high performance tandem mass spectrometry. Attention was focused on the determination of the site(s) of the modification and the reaction mechanisms involved. High energy collision induced dissociation mass spectra of each modified peptide provided information on the exact modification site(s) and the detailed chemical nature of the covalent complex. The serine protease trypsin, the cysteine protease cruzain, and the aspartic proteases, HIV-2 protease and SIV protease, were covalently modified only at one amino acid residue, while the aspartic protease, HIV-1 protease, was found to be modified at three sites by the haloperidol derivative compounds. In addition, mass spectrometry has been applied to characterize the plasma glycoprotein, biotinidase, and to obtain partial peptide sequences of a membrane-bound protein, UDP-GalNac:polypeptide N-acetylgalactosaminyl transferase, using a low picomole quantity of sample.

Irreversible electroporation has recently emerged as an effective focal ablation technique. When performed clinically, the procedure involves placing electrodes into, or around, a target tissue and applying a series of short, but intense, pulsed electric fields. Oftentimes, patient specific treatment plans are employed to guide procedures by merging medical imaging with algorithms for determining the electric field distribution in the tissue. The electric field dictates treatment outcomes by increasing a cell's transmembrane potential to levels where it becomes energetically favorable for the membrane to shift to a state of enhanced permeability. If the membrane remains permeabilized long enough to disrupt homeostasis, cells eventually die. By utilizing this phenomenon, irreversible electroporation has had success in killing cancer cells and treating localized tumors. Additionally, if the pulse parameters are chosen to limit Joule heating, irreversible electroporation can be performed safely on surgically inoperable tumors located next to major blood vessels and nerves. As with all technologies, there is room for improvement. One drawback associated with therapeutic irreversible electroporation is that patients must be temporarily paralyzed and maintained under general anesthesia to prevent intense muscle contractions occurring in response to pulsing. The muscle contractions may be painful and can dislodge the electrodes. To overcome this limitation, we have developed a system capable of achieving non-thermal irreversible electroporation without causing muscle contractions. This progress is the main focus of this dissertation. We describe the theoretical basis for how this new system utilizes alterations in pulse polarity and duration to induce electroporation with little associated excitation of muscle and nerves. Additionally, the system is shown to have the theoretical potential to improve lesion predictability, especially in regions containing multiple tissue types. We perform experiments on three-dimensional in vitro tumor constructs and in vivo on healthy rat brain tissue and implanted tumors in mice. The tumor constructs offer a new way to rapidly characterize the cellular response and optimize pulse parameters, and the tests conducted on live tissue confirm the ability of this new ablation system to be used without general anesthesia and a neuromuscular blockade. Situations can arise in which it is challenging to design an electroporation protocol that simultaneously covers the targeted tissue with a sufficient electric field and avoids unwanted thermal effects. For instance, thermal damage can occur unintentionally if the applied voltage or number of pulses are raised to ablate a large volume in a single treatment. Additionally, the new system for inducing ablation without muscle contractions actually requires an elevated electric field. To ensure that these procedures can continue to be performed safely next to major blood vessels and nerves, we have developed new electrode devices that absorb heat out of the tissue during treatment. These devices incorporate phase change materials that, in the past, have been reserved for industrial applications. We describe an experimentally validated numerical model of tissue electroporation with phase change electrodes that illustrates their ability to reduce the probability for thermal damage. Additionally, a parametric study is conducted on various electrode properties to narrow in on the ideal design.
Ph. D.

Pancreatic and prostate cancer are both prevalent cancers in the United States with pancreatic being one of the most aggressive of all cancers and prostate cancer being one of the most common, ranking as the number one cancer in men. Treatment of both cancers can be quite challenging as the anatomy of the pancreas and prostate, as well as the development and diagnosis of the disease can greatly limit treatment options. Therefore, it is necessary to develop new cancer treatments to help manage and prevent these cancers. Irreversible electroporation is a new non-thermal focal ablation therapy utilizing short, pulsed electric fields to damage cell membranes leading to cell death. The therapy is minimally invasive, involving the insertion of needle electrodes into the region of interest and lasts less than two minutes. Heat sink effects that thermal therapies experience near large blood vessels do not affect irreversible electroporation. This allows the treatment to be used on tumors near vasculature as well as critical structures without harming these vital regions. While irreversible electroporation is a promising new cancer therapy, further developments are necessary to improve treatment planning models. This work aims to further understand the electric field thresholds necessary to kill different types of cancer cells with a focus on pancreatic and prostate cancer. The work is done using an in vitro tumor (hydrogel) model as this model is better than traditional cell suspension studies, with added benefits over the immediate use of tissue and animal models.
Master of Science

The current environment for drug discovery and disease treatment relies heavily on genomic analysis, structural biology and chemical biology techniques. With the enormous advances in genomic analysis and structural biology, the use of and desire for targeted therapies has increased. However, as more genomic data for cancer disease state pathology becomes available we must ask increasingly difficult questions and even produce new technologies, such as activity-based probes, to answer these questions. In particular, targeted kinase inhibitors for the treatment of cancer has become a mainstay for drug development for both industry and academia, but it is evident that the genomic data is not always indicative of protein expression. Additionally, protein expression alone does not completely characterize functional activity. Therefore, in order to more accurately validate drug targets and predict drug efficacy, we must not only identify possible targets but also determine their activity in vivo. The goal of this work was to develop a probe for Protein Kinase A that would act by alkylating a conserved cysteine in the substrate-binding pocket of the enzyme. We hypothesized that by targeting the substrate-binding pocket we could effectively utilize the natural substrate selectivity filters as well as take into account multiple endogenous regulatory mechanisms. We produced probes utilizing portions of the pseudosubstrate inhibitor PKI that demonstrate the ability to label the catalytic subunit of Protein Kinase A in an activity-dependent manner, thus making it an important first step in a new class of activity-based probes for the kinome.

The research presented in this dissertation is the result of our laboratory's effort to develop a microfluidic platform to interrogate, manipulate, isolate, and enrich rare mammalian cells dispersed within heterogeneous populations. Relevant examples of these target cells are stem cells within a differentiated population, circulating tumor cells (CTCs) in the blood stream, and tumor initiating cells (TICs) in a population of benign cancer cells. The ability to isolate any of these rare cells types with high efficiency will directly lead to advances in tissue engineering, cancer detection, and individualized medicine. This work lead directly to the development of a new cell manipulation technique, termed contactless dielectrophoresis (cDEP). In this technique, cells are isolated from direct contact with metal electrodes by employing fluid electrode channels filled with a highly conductive media. Thin insulating barriers, approximately 20 μ­m, serve to isolate the fluid electrode channels from the low conductivity sample buffer. The insulating barriers in a fluid-electrical system create a number of unique and interesting challenges from an electrical engineering standpoint. Primarily, they block the flow of DC currents and create a non-constant frequency response which can confound experimental results attempting to characterize the electrical characteristics of cells. Due to these, and other, considerations, the use of high-voltage high-frequency signals are necessary to successfully manipulate cells. The effect of these high frequency fields on cells are studied and applied to microfluidic and tissue level applications. In later chapters, theoretical and experimental results show how high frequency and pulsed electric fields can ablate cells and tissue. Understanding the parameters necessary to electroporate cells aids in the development of cDEP devices where this phenomenon is undesirable and gives insight towards the development of new cancer ablation therapies where targeted cell death is sought after. This work shows that there exists a finite frequency spectrum over which cDEP devices can operate in which cells are minimally affected by the induced electric fields. Finally, lessons learned in the course of the development of cDEP were adapted and applied towards cancer ablation therapies where electroporation are favorable. It was found that bursts of high frequency pulsed electric fields can successfully kill cells and ablate tissue volumes through a process termed High Frequency Irreversible Electroporation (H-FIRE). This technique is advantageous as these waveforms mitigate or eliminate muscle contractions associated with traditional IRE technologies. Similarly, the use of fluid electrodes in cDEP inspired the use of an organs vascular system as the conductive pathway to deliver pulses. This novel approach allows for the ablation of large volumes of tissue without the use of puncturing electrodes. These techniques are currently undergoing evaluation in tissue engineering applications and pre-clinical evaluation in veterinary patients.
Ph. D.

Acid related diseases like GERD, duodenal-and gastric ulcers and H. Pylori-positive peptic ulcer disease are primarily managed by reducing gastric acidity. Irreversible proton pump inhibitors (PPIs) inhibit gastric acid secretion effectively throughout the day by irreversibly inhibiting the gastric proton pump, H+, K+-ATPase, in the parietal cells. Reversible gastric proton pump inhibitors are under development, but have not yet reached clinical use.

The pharmacokinetic/pharmacodynamic (PK/PD) relationships of these compounds are nonlinear, with a delay in the effect-time profile compared to the plasma concentration-time course. PK/PD-modelling was used to characterize and quantify the pharmacological effect with regard to onset, intensity and duration of effect. Models based on functional data, that discriminate between drug-and system-specific parameters, were developed.

In general, the plasma concentration-time course for each individual was approximated by linear interpolation between time-points and served as input into the pharmacodynamic models. A turnover model of irreversible inhibition of gastric acid secretion by omeprazole in the dog described the data well. The model was challenged and found to be robust under different experimental conditions. This model could predict the effect following different exposure of omeprazole and following different histamine provocation. Different fitting approaches (naïve pooling, standard two-stage and nonlinear mixed effects modelling) were compared and resulted in similar parameter estimates. For the reversible inhibitors, a kinetic binding model was finally selected. With a binding model the delay in the effect-time profile is explained by prolonged binding to the enzyme.

Use of these results in drug development can be helpful with regard to selection of drugs for further development and to predict the first clinical dose.

Choline oxidase from Arthrobacter globiformis is a flavin-dependent enzyme that catalyzes the oxidation of choline to betaine aldehyde through two sequential hydride-transfer steps. The study of this enzyme is of importance to the understanding of glycine betaine biosynthesis found in pathogenic bacterial or economic relevant crop plants as a response to temperature and salt stress in adverse environment. In this study, chemical modification of choline oxidase using two irreversible inhibitors, tetranitromethane and phenylhydrazine, was performed in order to gain insights into the active site structure of the enzyme. Choline oxidase can also be inactivated irreversibly by freezing in 20 mM sodium phosphate and 20 mM sodium pyrophosphate at pH 6 and -20 oC. The results showed that enzyme inactivation was due to a localized conformational change associated with the ionization of a group in close proximity to the flavin cofactor and led to a complete lost of catalytic activity.

Le comportement photochimique de six anti-uv en solution dans le methanol a ete etudie: 4-amino benzoate d'ethyl hexyle ; 4-amino benzylidene camphre ; 4-amino benzal malonate de diisobutyle ; 1,3,5-tris-(p-(2-ethyl hex-1-yloxycarbonyl)-anilino)-s-triazine ; 2,4,6-tris-(4'-amino benzal malonate de diisobutyle)-s-triazine ; 2,4-bis-(4'-amino benzylidene camphre)-6-(2-ethyl hexyl amino)-s-triazine. L'amino benzylidene camphre et la triazine associee possedent une double liaison en alpha du cycle aromatique et sont le siege d'une photoisomerisation representant une voie importante de desactivation des etats excites. Les rendements quantiques initiaux de photoisomerisation ont ete mesures dans diverses conditions. Ils sont independants de la nature du solvant, de la presence ou l'absence d'oxygene et de la longueur d'onde d'irradiation. La photostabilite des six composes a ete estimee par mesure du rendement quantique de disparition irreversible. Les rendements sont de l'ordre de 10#-#6 a 10#-#4, ce qui reflete la photostabilite des molecules. Lors d'irradiations prolongees, plusieurs photoproduits ont ete mis en evidence et analyses: l'irradiation des composes comportant une amine primaire conduit a une imine par reaction avec le formaldehyde issu du methanol ; l'irradiation des triazines comportant une double liaison en alpha du cycle aromatique conduit a une fonction aldehyde par oxydation et coupure de la double liaison. Dans le cas de la triazine substituee par le benzal malonate, on assiste egalement a une tautomerisation ; l'irradiation de la triazine substituee par l'ester de l'acide para amino benzoique provoque la coupure d'une liaison entre le cycle triazine et l'amine secondaire et conduit a une amine primaire. Les composes etudies, bien que possedant une fonction amine primaire ou secondaire ne presentent aucune activite antioxydante. La determination des moments dipolaires des molecules a l'etat excite a permis de mettre en evidence l'existence d'un fort transfert de charge qui pourrait etre a l'origine de voies de desactivation importantes responsables de la photostabilite observee

Cette thèse étudie le comportement de la chaîne d'événements de Monte Carlo (ECMC) dans les systèmes de particules à interaction de longue portée. Les deux premiers chapitres présentent les méthodes actuelles de simulation moléculaire, en soulignant leurs difficultés à traiter l'interaction de Coulomb, et donnent les bases de l'ECMC. Le troisième chapitre présente notre cadre d'échantillonnage du système de Coulomb à l'aide de l'ECMC. Dans le cadre de la convention "tin-foil", la formulation constituée d’interaction à deux corps pour l'électrostatique peut être appliquée directement à la méthode "cell-veto". En ajoutant à cela, la factorisation dipolaire obtient un algorithme en O(NlogN)-par-balayage pour les systèmes dipolaires. Les chapitres quatre et cinq décrivent notre développement d'une application scientifique appelée JeLLyFysh pour la simulation moléculaire par ECMC. La conception de son médiateur et le traitement de toutes les opérations en flux continu sont les mieux adaptés aux extensions futures. Le chapitre six décrit les performances de l'ECMC pour les grands systèmes d'eau à l’aide de JeLLyFysh. La dynamique qui en résulte implique qu'un schéma plus sophistiqué est nécessaire pour équilibrer la polarisation. Enfin, au chapitre sept, on teste la stratégie d'échantillonnage avec changement de direction séquentiel. L'évolution du dipôle présente une dynamique particulière, et l'ensemble des choix de direction ainsi que l'ordre de sélection s'avèrent tous deux cruciaux pour atteindre la distribution stationnaire de l'orientation du dipôle
This thesis studies the behavior of event-chain Monte Carlo (ECMC) in long-range particle systems. In the first two chapters, we introduce established methods for molecular simulation, highlighting their difficulties in dealing with Coulomb interaction, and gives the basic of ECMC. The third chapter presents our framework of Coulomb system sampling using ECMC. Under the tin-foil convention, the formulation consisting of pairwise terms for electrostatics can be directly applied to the cell-veto method. Together with dipole factorization, we obtain an O(NlogN)-per-sweep algorithm for dipole systems. Chapters four and five describe our development of a scientific application called JeLLyFysh for molecular simulation through ECMC. Its mediator design and stream processing of all operations can best accommodate future extensions. Using JeLLyFysh, we profile the performance of ECMC for large water systems in chapter six. The resulting dynamics imply that a more sophisticated scheme is needed to equilibrate the polarization. Finally, in chapter seven, we test the sampling strategy with sequential direction change. The dipole evolution exhibits distinct dynamics, and the set of direction choices and the order to select prove both crucial in mixing the dipole's orientation