Die Proteinfaltung ist ein Prozess der molekularen Selbstorganisation, bei dem sich eine lineare Kette von Aminosäuren zu einer definierten, funktionellen dreidimensionalen Struktur zusammensetzt. Der Prozess der Faltung ist ein thermisch getriebener diffusiver Prozess durch eine Gibbs-Energie-Landschaft im Konformationsraum für die Struktur der minimalen Energie. Während dieses Prozesses zeigt die freie Enthalpie des Systems nicht immer eine monotone Abnahme; stattdessen führt eine suboptimale Kompensation der Enthalpie- und der Entropieänderung während jedes Faltungsschrittes zur Bildung von Freien-Enthalpie-Faltungsbarrieren. Diese Barrieren und damit verbundenen hochenergetischen Übergangszustände, die wichtige Informationen über Mechanismen der Proteinfaltung enthalten, sind jedoch kinetisch unzugänglich. Um den Prozess der Barrierebildung und die strukturellen Merkmale von Übergangszuständen aufzudecken, werden Proteine genutzt, die über barrierefreie Pfade falten – so genannte “downhill folder“. Aufgrund der geringen Faltungsbarrieren werden wichtige Interaktionen der Faltung zugänglich und erlauben Einblicke in die ratenbegrenzenden Faltungsvorgänge. In dieser Arbeit vergleichen wir die Faltungsdynamiken von drei verschiedenen Varianten eines Lambda-Repressor-Fragments, bestehend aus den Aminosäuren 6 bis 85: ein Zwei-Zustands-Falter λWT (Y22W) und zwei downhill-folder-artige Varianten, λYA (Y22W/Q33Y/ G46,48A) und λHA (Y22W/Q33H/G46,48A). Um auf die Kinetik und die strukturelle Dynamik zu greifen zu können, werden Einzelmolekülkraftspektroskopische Experimente mit optische Pinzetten mit Submillisekunden- und Nanometer-Auflösung verwendet. Ich fand, dass die niedrige denaturierende Kraft die Mikrosekunden Faltungskinetik von downhill foldern auf eine Millisekunden-Zeitskala verlangsamt, sodass das System für Einzelmolekülstudien gut zugänglich ist. Interessanterweise zeigten sich unter Krafteinwirkung die downhill-folder-artigen Varianten des Lambda-Repressors als kooperative Zwei-Zustands-Falter mit deutlich unterschiedlicher Faltungskinetik und Kraftabhängigkeit. Drei Varianten des Proteins zeigten ein hoch konformes Verhalten unter Last. Die modellfreie Rekonstruktion von Freien-Enthalpie-Landschaften ermöglichte es uns, die feinen Details der Transformation des Zwei-Zustands-Faltungspfad direkt in einen downhill-artigen Pfad aufzulösen. Die Auswirkungen von einzelnen Mutationen auf die Proteinstabilität, Bildung der Übergangszustände und die konformationelle Heterogenität der Faltungs- und Entfaltungszustände konnten beobachtet werden. Interessanterweise zeigen unsere Ergebnisse, dass sich die untersuchten Varianten trotz der ultraschnellen Faltungszeit im Bereich von 2 μs in einem kooperativen Prozess über verbleibende Energiebarrieren falten und entfalten, was darauf hindeutet, dass wesentlich schnellere Faltungsraten notwendig sind um ein downhill Limit vollständig zu erreichen. / Protein folding is a process of molecular self-assembly in which a linear chain of amino acids assembles into a defined, functional three-dimensional structure. The process of folding is a thermally driven diffusive search on a free-energy landscape in the conformational space for the minimal-energy structure. During that process, the free energy of the system does not always show a monotonic decrease; instead, sub-optimal compensation of enthalpy and entropy change during each folding step leads to formation of folding free-energy barriers. However, these barriers, and associated high-energy transition states, that contain key information about mechanisms of protein folding, are kinetically inaccessible. To reveal the barrier-formation process and structural characteristics of transition states, proteins are employed that fold via barrierless paths – so-called downhill folders. Due to the low folding barriers, the key folding interactions become accessible, yielding insights about the rate-limiting folding events. Here, I compared the folding dynamics of three different variants of a lambda repressor fragment, containing amino acids 6 to 85: a two-state folder λWT (Y22W) and two downhill-like folding variants, λYA (Y22W/Q33Y/G46,48A) and λHA (Y22W/Q33H/G46,48A). To access the kinetics and structural dynamics, single-molecule optical tweezers with submillisecond and nanometer resolution are used. I found that force perturbation slowed down the microsecond kinetics of downhill folders to a millisecond time-scale, making it accessible to single-molecule studies. Interestingly, under load, the downhill-like variants of lambda repressor appeared as cooperative two-state folders with significantly different folding kinetics and force dependence. The three protein variants displayed a highly compliant behaviour under load. Model-free reconstruction of free-energy landscapes allowed us to directly resolve the fine details of the transformation of the two-state folding path into a downhill-like path. The effect of single mutations on protein stability, transition state formation and conformational heterogeneity of folding and unfolding states was observed. Noteworthy, our results demonstrate, that despite the ultrafast folding time in a range of 2 µs, the studied variants fold and unfold in a cooperative process via residual barriers, suggesting that much faster folding rate constants are required to reach the full-downhill limit.

O processo de auto-organização da estrutura proteica a partir da cadeia de aminoácidos é conhecido como enovelamento. Apesar de conhecermos a estrutura tridimencional de muitas proteínas, para a maioria delas, não possuímos uma compreensão suficiente para descrever em detalhes como a estrutura se organiza a partir da sequência de aminoácidos. É bem conhecido que a formação de núcleos de estruturas locais, conhecida como estrutura secundária, apresenta papel fundamental no enovelamento final da proteína. Desta forma, o desenvolvimento de métodos que permitam não somente predizer a estrutura secundária adotada por um dado resíduo, mas também, a maneira como esse processo deve ocorrer ao longo do tempo é muito relevante em várias áreas da biologia estrutural. Neste trabalho, desenvolvemos dois métodos de predição de estruturas secundárias utilizando modelos com o potencial de fornecer informações mais detalhadas sobre o processo de predição. Um desses modelos foi construído utilizando autômatos celulares, um tipo de modelo dinâmico onde é possível obtermos informações espaciais e temporais. O outro modelo foi desenvolvido utilizando redes neurais residuais profundas. Com este modelo é possível extrair informações espaciais e probabilísticas de suas múltiplas camadas internas de convolução, o que parece refletir, em algum sentido, os estados de formação da estrutura secundária durante o enovelamento. A acurácia da predição obtida por esse modelo foi de ~78% para os resíduos que apresentaram consenso na estrutura atribuída pelos métodos DSSP, STRIDE, KAKSI e PROSS. Tal acurácia, apesar de inferior à obtida pelo PSIPRED, o qual utiliza matrizes PSSM como entrada, é superior à obtida por outros métodos que realizam a predição de estruturas secundárias diretamente a partir da sequência de aminoácidos. / The process of self-organization of the protein structure is known as folding. Although we know the structure of many proteins, for a majority of them, we do not have enough understanding to describe in details how the structure is organized from its amino acid sequence. In this work, we developed two methods for secondary structure prediction using models that have the potential to provide detailed information about the prediction process. One of these models was constructed using cellular automata, a type of dynamic model where it is possible to obtain spatial and temporal information. The other model was developed using deep residual neural networks. With this model it is possible to extract spatial and probabilistic information from its multiple internal layers of convolution. The accuracy of the prediction obtained by this model was ~ 78% for residues that showed consensus in the structure assigned by the DSSP, STRIDE, KAKSI and PROSS methods. Such value is higher than that obtained by other methods which perform the prediction of secondary structures from the amino acid sequence only.

This paper addresses folding the circle in half and discussing some of over one hundred different mathematical terms and functions generated in that one fold. The simplicity of process in understanding fundamentals of mathematics by folding circles and observing what is generated is unknown because we only draw pictures of circles. Examples are given about observing and exploring relationships in the circle that are appropriate for first, second, third grade level and beyond. The traditional educational ‘parts-towhole’ approach can only be fully realized through the comprehensive frame of Whole-to-parts by folding the circle. Wholemovement of the circle is not only direct; it is the only context inclusive to progressively understanding parts within unity of the Whole.

Background: RNA secondary structure prediction by energy minimization is the central computational tool for the analysis of structural non-coding RNAs and their interactions. Sparsification has been successfully applied to improve the time efficiency of various structure prediction algorithms while guaranteeing the same result; however, for many such folding problems, space efficiency is of even greater concern, particularly for long RNA sequences. So far, spaceefficient sparsified RNA folding with fold reconstruction was solved only for simple base-pair-based pseudo-energy models. Results: Here, we revisit the problem of space-efficient free energy minimization. Whereas the space-efficient minimization of the free energy has been sketched before, the reconstruction of the optimum structure has not even been discussed. We show that this reconstruction is not possible in trivial extension of the method for simple energy models. Then, we present the time- and space-efficient sparsified free energy minimization algorithm SparseMFEFold that guarantees MFE structure prediction. In particular, this novel algorithm provides efficient fold reconstruction based on dynamically garbage-collected trace arrows. The complexity of our algorithm depends on two parameters, the number of candidates Z and the number of trace arrows T; both are bounded by n2, but are typically much smaller. The time complexity of RNA folding is reduced from O(n3) to O(n2 + nZ); the space complexity, from O(n2) to O(n + T + Z). Our empirical results show more than 80 % space savings over RNAfold [Vienna RNA package] on the long RNAs from the RNA STRAND database (≥2500 bases). Conclusions: The presented technique is intentionally generalizable to complex prediction algorithms; due to their high space demands, algorithms like pseudoknot prediction and RNA–RNA-interaction prediction are expected to profit even stronger than \"standard\" MFE folding. SparseMFEFold is free software, available at http://www.bioinf.unileipzig. de/~will/Software/SparseMFEFold.

Thesis (MTh)--Stellenbosch University, 2011. / ENGLISH ABSTRACT: This dissertation is a literary study with a qualitative component, provoked by family 'crises' and escalating single parenting, predominantly by mothers in default family structures beset by many childcare issues. It investigates- through tacit elimination of weak paradigms, a developmental mindset, empirical research and biblical consultation- a holistic family paradigm best suited for individual human development in care consciousness in society. The study assumes that, at grassroots levels of society, monogamy, faithfully practiced by morally responsible, natural, parental agencies, is ideal for holistic child care and is suitable for human development. It can also serve as a pre-emptive strategy against the following: delinquency, father absence, abuse, neglect, divorce, separation, indifference, family disintegration, relational poverty, pathological disorders, feminized poverty calling for government intervention, and general societal unrest. However, the monogamous family set up of the nuclear family variety requires relational adjustment. Through studies in ethics and theology, 'care' emerged as a fundamental concept of what it means to be human and is a potential entry point to relational conflicts and lack of development sustainability. Care can spread through inclusion, affirmation, participation and empowerment of the formerly marginalized sectors. Perlas‘ social three-folding strategy, engages the power of politics and economics to care for civil society‘s needs in tripartite partnerships. Similarly, family three-folding units can be effective, at grass root levels, in bringing about holistic child care. Appropriate interpretation, contextual and responsible application of biblical principles for family life from both the OT and NT is part of the interdisciplinary research process. Ephesians 5:21- 6:4; Genesis 1:27-28, 2:24; Deuteronomy 6:6-9 and other appropriate texts will be analyzed in this regard. Holistic child care should contribute significantly to improvement in quality of family life leading to sustainable societies where human rights are respected and caring attitudes promoted globally. The empirical research sought data triangulation, of outstanding family and child care issues, through a phenomenological design that engaged mothers as the units of analysis. Variables were, among others, mothers‘ sentiments and perspectives of men, fathers and husbands. Samples of 10 single mothers, using a mixed sampling methodology and 10 married mothers (the focus group), were selected. In-depth interviews using standardized open-ended questions were utilized. The projective technique was effective in eliciting hidden, negative and bitter sentiments on gender issues requiring urgent attention. Work-overloaded mothers perceived men as self-centered pleasure seekers who are disinterested in child care. Abusive, controlling and economically non-contributing husbands are a burden to their spouses. Spousal rape, enforcement of government restraining orders and 'ukhutwala' issues also surfaced. On the other hand, seasoned, respectful affirmations of men were voiced by a few mothers who have experienced the godly power of forgiveness. Consequently, a frame of reference for family three-folding was outlined in chapter 5, based on biblical teachings, participant mothers‘ conciliatory mindsets, Christian single mothers‘ experiences, human rights considerations, good parenting strategies and relevant generic literature contributions. Conclusions: By analogy, family three-folding indirectly reflects, the relational and functional aspects of the Triune God; reconciliation is a crucial part of the Christian calling; care consciousness is God consciousness and no family is ideal enough out of union/ fellowship [koinonia] with the Lord. Consequently, a believing single mother and her children also constitute a three-folding family, with God as Father to the fatherless. Single parent families deserve support and encouragement. Family three-folding recommends, through dialogues in communities, that: - Men learn to curb their domineering tendencies and practice service [diakonia] to others, guided by biblical principles of servanthood and the "One Man Can…"manual; - women welcome responsible male headship in families for peaceful co-existence and holistic child care; - decision-making be inclusive of family members on issues that concern them; - awareness campaigns on sound family three-folding principles, values and models be initiated through the media, formal education and dialogues at all levels of the society. / AFRIKAANSE OPSOMMING: Die studie is 'n verduidelikende argument met 'n kwalitatiewe komponent, aangespoor deur gesinskrisisse, stygende enkel ouerskap, hoofsaaklik van moeders in gebroke gesinstrukture en gekenmerk deur baie kindersorgprobleme. Deur eliminasie van nie-holistiese situasies word 'n ontwikkelende houding, empiriese navorsing en Bybelse verwysings gebruik om 'n holistiese gesinsparadigma daar te stel vir die optimale menslike ontwikkeling en gemeenskapsbewuste sorg. Die studie veronderstel dat holistiese kindersorg deur 'n moreel verantwoordelike en natuurlike ouerlike agentskap ideaal is vir menslike ontwikkeling en dien as'n voorkomende strategie teen sosio-ekonomiese onrus, veroorsaak deur familie disintegrasie, verarmde verhoudings, misdaad, psigies-sosiale versteurings, mishandeling, verwaarlosing, egskeiding, skeiding, afwesige vaders, onverskilligheid, selfgesentreerde moeders, veramde vroue, wat tussenkoms van die regering noodsaak. Deur 'n studie van etiek en teologie het 'sorg' na vore gekom as 'n fundamentele konsep van wat dit beteken om menslik te wees en is 'n potensiale toegangspunt tot konflik in verhoudings en volgehoue ontwikkeling. Sorg kan deur insluiting, bevestiging, deelname en bemagtiging van die voorheen verstotenes bevorder word. Perlas se sosiale driepunt strategie kombineer die tussenkoms van politiese en ekonomiese invloed om in 'n driebeengenootskap na die burgerlike gemeenskap se behoeftes om te sien. Op dieselfde manier kan drievoudige gesinsverhoudings effektief wees op grondvlak om holistiese kindersorg te weeg te bring. Toepaslike interpretasie en kontekstuele en verantwoordelike toepassing van Bybelse beginsels vir gesinslewe uit beide die OT en NT is noodsaaklik. Efesiërs 5:21-6:4; Genesis 1:27-28 en 2:24 Deuteronomium 6:6-9 en ander toepaslike teksverwysings sal in hierdie verband geanaliseer word. Holistiese kindersorg behoort grootliks by te dra om die kwaliteit van gesinslewe te verbeter en te lei tot standhoudende gemeenskappe, waar menseregte gerespekteer word en omgee-verhoudings globaal bevorder word. Die empiriese navorsing het driebeen data van uitstaande gesins- en kindersorg situasies gesoek, deur 'n fenomenologiese ontwerp wat moeders betrek as analiseringseenhede. Veranderlikes was, onder andere, moeders se houdings en perspektief van mans, vaders en eggenote. 'n Steekproef van 10 enkel moeders, deur 'n gemengde steekproef metodologie, en 10 getroude moeders (die fokus groep), is gekies. Die projektiewe tegniek was effektief in die verkryging van die verborge, negatiewe en bitter sentimente omtrent gesalgskwessies wat dringende aandag vereis. Werk-oorlaaide moeders het mans beskou as selfgesentreerde plesiernajaers sonder enige belang in kindersorg. Mishandelende, oorheersende en ekonomiese nie-bydraende mans is 'n las vir hul gades. Eggenootverkragting, die afdwing van beperkingsbevele deur die regering en 'ukhutwla' sake het ook na vore gekom. Aan die ander kant is tydige, respekvolle ondersteuning van mans, wat die goddelike krag van vergifnis ondervind het, deur 'n paar moeders genoem. 'n Verwysingsraamwerk vir drievoudige gesinsverhoudings is gevolglik uiteengesit in hoofstuk 5, gebaseer op Bybelse lering, deelnemende moeders se versoenende ingesteldheid, Christelike enkel moeders se ondervindings, mense regtelike oorwegings, goeie strategieë vir kinderopvoeding en toepaslike generiese literatuur bydraes. Die gevolgtrekkings is: driebeen-gesinsverhoudings is kontekssensitief, holisties en weerspieël indirek die beeld van ons relasionele, funksionele, liefdevolle Drie-enige God; versoening is 'n belangrike deel van die Christelike roeping; sorgbewustheid is God bewussyn en geen gesin is ideaal genoeg buite die vereniging / gemeenskap [Koinonia] met die Here nie. Gevolglik behels 'n gelowige enkelmoeder met haar kinders ook 'n driebeenverhouding, met God as Vader vir die Vaderlose. Enkel-ouer gesinne verdien ondersteuning en aanmoediging. Gesin drie-vou beveel aan dat deur dialoog in gemeenskappe: - mans hulle dominerende tendense leer bekamp en diens aan ander leer lewer [diakonia], met Bybelse beginsels van diens en die "One Man Can…" handleiding as riglyn; - vroue verantwoordelik manlike hoofskap verwelkom in gesinne vir vredevolle saambestaan en holistiese kindersorg - besluitneming ingesluit word by gesinslede omtrent sake wat op hulle van betrekking is - bewusmakingveldtogte oor gesonde, versoendende driebeen gesinsverhoudings, waardes en modelle deur die media, formele onderrig en dialoog bekendgestel word aan alle vlakke van die samelewing.

Das Formdrücken findet seine industrielle Anwendung in der Herstellung rotationssymmetrischer Hohlbauteile für kleine und mittlere Losgrößen. Diese Bauteile werden häufig in einem weiteren Verfahrensschritt als Vorform für die Herstellung profilierter Hohlkörper genutzt. Verfahrensbedingt tritt bereits bei der Vorformherstellung eine ungewollte Blechdickenabnahme auf. Um diese Blechdickenabnahme zu minimieren, wurde anhand numerischer Methoden das Verfahren des Rotationsschwenkbiegens an der Professur Virtuelle Fertigungstechnik der TU Chemnitz entwickelt. Das Prinzip dieses inkrementellen Umformprozesses basiert auf einer Verfahrenskombination des konventionellen Drückens und des Schwenkbiegens, mit dem Ziel der faltenfreien Herstellung von Hohlbauteilen bei gleichzeitiger minimaler Blechausdünnung. Die als Halbzeug verwendete Ronde wird zu Beginn des Prozesses auf eine formgebende Matrize gespannt und in Rotation versetzt. Durch die Schwenkbewegung eines zylindrischen Umformwerkzeuges wird das ebene Blech an die Kontur der Matrize angelegt, wobei keine Relativbewegung zwischen Blech und Werkzeug stattfindet. Demzufolge entstehen minimale Zugspannungen in der Blechebene und die Blechausdünnung wird deutlich verringert. Durch die Durchmesserreduzierung bilden sich jedoch ebenso tangentiale Druckspannungen aus, welche zu einer ungewollten Faltenbildung führen können. Im Rahmen des Vortrages werden anhand von FEM-Simulationen Möglichkeiten vorgestellt, um diese Druckspannungen zu reduzieren oder gezielt zur Vorformherstellung für profilierte Hohlbauteile zu nutzen.

Les virus Nipah (NiV) et Hendra (HeV) appartiennent au genre Henipavirus au sein de la famille des Paramyxoviridae. Cette famille comporte de nombreux pathogènes tel que le virus de la rougeole (MeV). Les paramyxovirus possèdent un génome de type ARN simple brin encapsidé par la nucléoprotéine (N) au sein d'une nucléocapside hélicoïdale. N interagit avec la phosphoprotéine (P) et cette dernière recrute la polymérase (L) qui assure la transcription et la réplication du génome viral. L'objectif de mon projet de thèse était de caractériser les protéines N et P ainsi que les interactions qui existent entre elles chez les trois virus, NiV, HeV et MeV. A la différence du MeV, qui a été intensivement étudié au cours des dernières années, les données moléculaires et structurales sur les Henipavirus étaient très limitées. A l'aide d'analyses computationnelles, nous avons pu déchiffrer l'organisation modulaire de N et de P, et nous avons montré que les régions, C-terminale de N (NTAIL) et N-terminale de P (PNT), sont prédites comme intrinsèquement désordonnées (RIDs). Les RIDs sont des régions fonctionnelles dépourvues de structures secondaires et tertiaires stables dans des conditions physiologiques. En utilisant des approches biochimiques et biophysiques, nous avons confirmé que NTAIL et PNT sont désordonnées. Elles conservent toutefois des structures secondaires transitoires qui pourraient correspondre à des éléments de reconnaissance moléculaire (ou MoREs) impliqués dans de transitions structurales en présence d'un partenaire. / The Paramyxoviridae family includes many important human and animal pathogens, such as measles virus (MeV), a morbillivirus, and the emerging Nipah (NiV) and Hendra (HeV) viruses, members of the Henipavirus genus. Paramyxoviruses possess a negative-strand RNA genome that is encapsidated by the nucleoprotein (N) into a helical nucleocapsid. N interacts with the phosphoprotein (P), and this latter recruits the polymerase that ensures genome replication and transcription. My PhD project has mainly focused on the characterization of the N and P proteins and on the interactions between these two proteins from the three cognate viruses, namely NiV, HeV and MeV. While MeV has been extensively studied through the past years, structural and molecular information on Henipavirus N and P proteins were rather scarce. Using computational analyses, we deciphered the modular organization of Henipavirus N and P. Intrinsically disordered regions (IDRs) were predicted within these proteins, notably at the C-terminus of N (referred to as NTAIL), and at the N-terminus of P (referred to as PNT). IDRs are functional despite they lack of a well-defined 3-D structure under physiological conditions. Biochemical and biophysical approaches pointed out a mostly disordered state for both NTAIL and PNT, although they were shown to contain short-order prone segments (i.e. molecular recognition elements, MoREs). These latter are involved in partner recognition and in disorder-to-order transitions. The C-terminal domains of the P proteins (referred to as PXD) were found to bind to NTAIL and to induce an α-helical transition thereof.

Les nanocavités à cristal photonique ont été largement étudiées au cours de la dernière décennie du fait de leur aptitude à fortement confiner la lumière (faible volume modal) et de leurs faibles pertes optiques (grand facteur de qualité). Parmi le grand nombre de géométries proposées, nous nous intéressons ici au cas de la cavité L3 étudiée par Noda et al. (trois trous manquants dans la direction K du réseau triangulaire sous-jacent) utilisée dans plusieurs applications et notamment pour la réalisation de nano-lasers et d’interrupteurs optiques. Cependant, l’injection ou l’extraction de lumière dans de telles nanocavités s’avère extrêmement difficile du fait de la diffraction importante dont souffrent ces structures. Différentes approches en champ proche ont été récemment développées et notamment le couplage évanescent utilisant des guides d’onde nanostructurés ou des fibres optiques étirées. Dans le but de pallier à la faible efficacité de couplage à l’espace libre, nous développons une conception récemment proposée par De Rossi et al. afin de changer radicalement le profil du diagramme de rayonnement. Cette approche utilise la méthode de repliement des bandes qui consiste à introduire au sein d’un réseau triangulaire de période (a), un sous-réseau de trous de période (2a) qui améliore considérablement l’efficacité de couplage dans la direction verticale. Bien que certaines mesures de l’efficacité de collection et du coefficient de qualité aient déjà été mentionnées dans la littérature, aucune mesure directe des diagrammes de rayonnement de ces nanocavités n’a été réalisée jusqu’alors. Nous étudions dans ce travail différents types de nanocavités et de molécules L3 à cristaux photoniques présentant des profils de champ lointain optimisés. Les diagrammes de rayonnement de cavités non-repliées et repliées incorporées dans des membranes actives suspendues en InP sont systématiquement mesurés et comparés. Un bon accord entre les simulations numériques et les diagrammes de champ lointain mesurés expérimentalement est obtenu, montrant des lobes d’émission très directionnels le long de la normale à l’échantillon. En outre, des expériences de couplage à l’espace libre ont été réalisées montrant des efficacités de couplage d’environ 15% pour des coefficients de qualité supérieurs à 10 000. Ces résultats valident ainsi la technique de repliement des bandes dans les cavités L3 qui, une fois repliées, conservent un faible volume modal et un coefficient de qualité élevé ainsi qu’une grande efficacité de couplage à l’espace libre, à la fois dans les configurations nanocavité unique et nanocavités couplés. Nous montrons aussi expérimentalement que l’écart spectral inter-modal dans deux cavités L3 couplées de manière évanescente peut être contrôlé grâce à l’ingénierie de la barrière photonique. La « barrière de potentiel » est formée par les trous d’air séparant les deux cavités. L’écart en fréquence entre les modes peut être fortement réduit et augmentée via une diminution ou une augmentation du rayon des trous de la rangée centrale de la barrière jusqu’à ∼ −30% ou ∼ 30% de sa valeur initiale. En outre, le signe de la l’écart spectral entre les modes peut être inversé de telle sorte que le mode fondamental peut être soit symétrique ou anti-symétrique et ce, sans modifier ni la géométrie de la cavité, ni la distance inter-cavité. / Photonic crystal (PhC) nanocavities have been intensively investigated during the last decade due to their capabilities of achieving tight light confinement and low optical losses simultaneously. Among the different geometries, the cavity proposed by Noda et al., namely a L3 cavity (three holes missing in the K direction of the underlying triangular lattice) with shifted end-holes has been widely used in several applications including laser emission and switching devices. However, input/output free space light coupling of such nanocavities is quite challenging. In this regard, near field coupling schemes have been recently developed, such as evanescent coupling using tapered optical fibers. In order to overcome the poor free space coupling, a new cavity design has been recently proposed by De Rossi et al. that totally changes the radiation pattern. This is based on a band folding approach introducing a modulation of the holes size at twice the period of the underlying PhC, which considerably increases the coupling efficiency in the vertical direction. While some measurements of the Q-factor and coupling efficiency were performed, no direct characterization of the far-field of such cavities has been performed so far. In this work we have studied different types of L3 photonic crystal cavities and L3 photonic molecules with optimized far-field profiles. Radiation patterns from « folded » and « unfolded » cavities incorporated in suspended InP active membranes were systematically measured and compared. Good agreement between simulations and experimental far-field patterns has been found, demonstrating highly directional emission lobes along the sample normal. Furthermore, free space input coupling experiments have been performed showing coupling efficiency of about 15% of contrast with quality factors exceeding 10 000. These results validate the « folded » L3 cavities as good candidates for small volume and high Q cavities with efficient free space coupling, either in single or coupled cavity configurations. We also experimentally show that the mode splitting in two-evanescently coupled Photonic Crystal L3 cavities can be controlled through photonic barrier engineering. The « potential barrier » is formed by the air-holes in between the two cavities. By changing the hole radius of the central row in the barrier up to ∼ 30% or down to ∼ −30% , the frequency splitting can be strongly increased or reduced. Moreover, the sign of the splitting can be reversed in such a way that the fundamental mode can be either the symmetric or the anti-symmetric one without altering neither the cavity geometry nor the inter-cavity distance.

Nous avons étudié le couplage dépliement-transport de la Maltose Binding Protein (MBP ou MalE), une protéine périplasmique d'E. Coli et d'un mutant instable, le MalE219, en fonction de la concentration d'un agent dénaturant, le chlorure de guanidium (GdnHCl) à l'échelle de la molécule unique. La technique utilisée est basée sur la détection électrique du transport de macromolécules à travers un nanopore protéique (l'Aérolysine d'Aeromonas Hydrophila) inséré dans une bicouche lipidique plane. Les résultats obtenus ont été comparés à ceux obtenus lors d'une précédente étude réalisée à travers un autre nanopore protéique, l'alpha-hémolysine du Staphylocoque doré, de géométrie et de charge nette différente. Nous avons montré l'existence de temps courts et longs de blocage du courant associés à des protéines dépliées ou partiellement repliées. La fréquence des blocages du courant permet d'obtenir la fraction de protéine dépliée passant à travers le pore en fonction de la concentration en GdnHCl. Les courbes de dénaturation obtenues avec les deux pores montrent un comportement sigmoïdale très similaire. Le type de pore n'influence donc pas la dénaturation des protéines, mais uniquement leur dynamique de transport. En revanche, la courbe de dénaturation du mutant instable présente un déplacement vers les concentrations plus faibles en GdnHCl. Il a été montré également que la présence du maltose comme ligand sur le MalE219 stabilise nettement sa structure. Pour La MBP, les temps de blocages longs diminuent avec l'augmentation de la concentration de GdnHCl montrant une dynamique de transition vitreuse . Cette technique est appropriée à l'étude du dépliement et des changements de conformation de protéines, mais ne permet pas d'obtenir des informations structurales sur les états intermédiaires de repliement. Ainsi, la spectroscopie RMN a été utilisée pour tenter de caractériser ces états intermédiaires de repliement, notamment par la méthode d'échange proton-deutérium. Elle consiste à suivre les cinétiques d'échange des résidus de la protéine sur des spectres 2D 1H-15N HSQC à différentes concentrations de GdnHCl.Ainsi 180 résidus sur les 370 que compte la MBP ont été suivis lors de la dénaturation en présence de GdnHCl. Les deux hélices en C-terminal sont très accessibles au solvant et se dénaturent facilement. La MBP est composée de deux domaines globulaires, le domaine N-ter et le domaine C-ter. Les éléments de structures secondaires situés dans la zone intermédiaire entre les deux domaines (principalement des brins β) sont particulièrement affectés par l'agent dénaturant. D'autres structures secondaires dans les domaines globulaires sont très protégées et plutôt stables. Il est donc proposé que les protéines partiellement dépliées s'insèrent dans le pore par l'extrémité C-terminal et que des parties de structuration tertiaire restent stable entraînant le blocage du pore. / We study the unfolding-transport mechanism of the Maltose Binding Protein (MBP or MalE), a periplasm protein of E. Coli and a destabilised variant, the MalE219, as the function of the concentration of denaturing agent, Guanidine Hydrochloride(GdnHCl) at the single molecule level. The technique is based on the electrical detection of the macromolecule transport through a nanometer-scale channel, Aerolysin channel, inserted into a planar lipid bilayer. Results obtained were compared to previous data with another channel, the alpha-Hemolysin. Both channels have different geometry and net charge.We show that we can distinguish unfolded states from partially folded ones with aerolysin pore.Unfolded proteins induce short current blockades, their duration is constant as a function of the concentration of denaturing agent. Partially folded proteins exhibit long blockades whose life times decrease as the concentration of GdnHCl increase, this indicates a possible glassy dynamics.The frequency of the short current blockades increases as the concentration of denaturing agent increases, following a sigmoidal denaturation curve.The unfolding curve of native MBP with Aerolysin pore is similar to the one previously measured with Hemolysin channel. The denaturation curve of the destabilized variant obtained with Aerolysin is shifted towards lower value of GdnHCl concentration in agreement with bulk measurements. We show also that the addition of maltose stabilizes the structure of MalE219. This nanopore recording technique is also suitable for the study of unfolding and conformation changes of proteins.In order to obtain structural informations that nanopore recording cannot provides, the structure of MBP along its denaturation curve was studied by NMR spectroscopy. The Hydrogen-exchange method known to be sensitive to folding intermediates was specially used. It consists in tracking hydrogen-deuterium exchange rates for amino on the 2D 1H-15N HSQC spectra.Thus, 180 residus of 370 for MBP was followed during denaturation in the presence of GdnHCl. The two last helices in C-terminal of MBP are accessible to the solvent and are denaturated easily. MBP is a two domains protein, N-ter domain and C-ter domain. It was found out that the C- and D-domain of MBP (mainly alpha-helices) could be relatively stable in presence of denaturing agent and that beta strands which make the link between the two domains would be affected by the denaturing agent. It was proposed that partially unfolded proteins enter the pore by the C-terminal end and that stable tertiary structure still present block the pore.

I en kantviksmaskin som används för plåtbockning sker oönskade deformationer i mekanismen som klämmer fast arbetsmaterialet. Risken finns att deformationerna gör så arbetsmaterialet flyttas och det kan påverka positionen för bockningen.Målet med studien var att mäta laster och deformationer i kantviksmaskinen och sammanställa mätdata för att jämföra med FEM-analyser av konstruktionen och till grund för framtida arbete med maskinen. Problemet undersöktes genom att utföra mätningar med LVDT-givare och en lastcell. Mätresultatet visade att det blev en förskjutning och vid fastklämningen av arbetsmaterialet varierade klämkraften. FEM-analyserna kom upp i en lägre förskjutning än den uppmätta. Det finns då misstanke om att en del av förskjutningen kan bero på en mekanism för verktygsbyte. För att bekräfta detta behöver mätningar genomföras som kan visa bidraget av deformation från denna mekanism. FEM-analyserna gjordes med olika lastfördelning för att motsvara klämkraften. Analysen med en uppdelad last var baserad på klämkraftens fördelning som var uppmätt och det gav en fördelning av förskjutningen som var lik den uppmätta. För framtida analyser rekommenderas att använda denna eller en liknande lastfördelning. Utifrån mätningar och analyser konstateras det att överprismat böjs och vrids under klämningen. Detta i sin tur ändrar öververktygens position samt bidrar till att klämning inte sker i mittenpositionerna. / In an edge folding machine, used for sheet metal bending, which have undesired deformations in the mechanism that clamps the work material there is a risk that the deformations will cause the work material to be moved and this can affect the position of the bending. The aim of the study was to measure loads and deformations in the edge folding machine and compile measurement data to compare with FEM-analyzes of the design to get a basis for future work with the machine. The problem was investigated by carrying out measurements with LVDT-sensors and a load cell. The results showed that there was a displacement in the clamping of the work material and that the clamping force varied. The FEM-analyzes came up in a lower displacement than the measured one. A possible conjecture could be that a part of the displacement may be due to the tool change mechanism. To confirm this, measurements need to be performed which can show the contribution of deformation from this mechanism. The FEM-analyzes were made with different load distribution to correspond to the clamping force. The analysis with a divided load where the sectioning was based on the distribution of the clamping force that was measured gave a distribution of the displacement that was similar to the measured. For future analyzes it is recommended to use this or a similar load distribution. Based on measurements and analyzes it is found that the upper prism is bent and twisted during the clamping. This changes the position of the top tools and contribute to no clamping in the middle positions.