Dissertations / Theses on the topic 'Structural dynamics'

This thesis is about how our syntactic choice changes with linguistic experience. Studies on syntactic priming show that our decisions are influenced by sentences that we have recently heard or recently spoken. They also show that not all sentences have an equal amount of influence; that repetition of verbs increases priming (the lexical-boost effect) and that some verbs are more susceptible to priming than others. This thesis explores how and why syntactic decisions change with time and what these observations tell us about the cognitive mechanism of speaking. Specifically, we set out to develop a theoretical account of syntactic priming. Theoretical accounts require mathematical models and this thesis develops a sequence of mathematical models for understanding various aspects of syntactic priming. Cognitive processes are modelled as dynamical systems that can change their behaviour when they process information. We use these dynamical systems to investigate how each episode of language comprehension or production affects syntactic decisions. We also use these systems to investigate how long priming persists, how groups of consecutive sentences affect structural decisions, why repeating words leads to greater syntactic priming and what this tells us about how words, concepts and syntax are cognitively represented. We obtain two kinds of results by simulating these mathematical models. The first kind of results reveal how syntactic priming evolves over time. We find that structural priming itself shows a gradual decay with time but the lexical enhancement of priming decays catastrophically – a result consistent with experimental observations. We also find that consecutive episodes of language processing add up nonlinearly in memory, which challenges the design of some existing psycholinguistic experiments. The second kind of results reveal how our syntax module might be connected to other cognitive modules. We find that the lexical enhancement of syntactic priming might be a consequence of how the modules of attention and working memory influence syntactic decisions. These models suggest a mechanism of priming that is in contrast to a previous prediction-based account. This prediction-based account proposes that we actively predict what we hear and structural priming is due to error-correction whenever our predictions do not match the stimuli. In contrast, our account embodies syntactic priming in cognitive processes of attention, working memory and long-term memory. It asserts that our linguistic decisions are not based solely on abstract rules but also depend on the cognitive implementation of each module. Our investigations also contribute a novel theoretical framework for studying syntactic priming. Previous studies analyse priming using error-correction or Hebbian learning algorithms. We introduce the formalism of dynamical systems. This formalism allows us to trace the effect of information processing through time. It explains how residual activation from a previous episode might play a role in structural decisions, thereby enriching our understanding of syntactic priming. Since these dynamical systems are also used to model neural processes, this theoretical framework brings our understanding of priming one step closer to its biological implementation, bridging the gap between neural processes and abstract thoughts.

Med utviklingen som har funnet sted innenfor den norske oljebransjen de siste årene har både teknologien og utfordringene blitt mer komplekse. Subsea-operasjoner har blitt mer vanlig og gir utslag i at det på havbunnen i mange felt er sammenkoblede systemer av konstruksjoner. I relasjon til seismisk aktivitet reises da spørsmålet om disse systemene med brønner, rør og andre konstruksjoner kan tåle å bli utsatt for et jordskjelv av en viss størrelse. For å ta et steg i retningen av å besvare dette spørsmålet, dreier denne hovedoppgaven seg om studien av en beskyttelseskonstruksjon som utsettes for grunnakselerasjoner funnet ved probabilistisk evaluering av valgte jordskjelvdata tilgjengelig for den norske kontinentalsokkelen.Den valgte konstruksjonen er lokalisert i Åsgårdfeltet på Haltenbanken vest for midt-Norge. Det er en ganske liten og slank konstruksjon hvis funksjon er å beskytte oljeinstallasjoner fra eventuelle skader forårsaket fra trål og fallende objekter i forbindelse med fiskeriindustrien. I modelleringen av konstruksjonen vurderes den som et produkt av tre forskjellige systemer. Det første systemet er konstruksjonen alene, det andre systemet er jordsystemet og det tredje er fluidsystemet. Dermed ble tre modeller laget der de forskjellige systemegenskapene (fjærer/dempere, hydrodynamiske krefter) ble introdusert stegvis.For å undersøke konstruksjonens respons i forhold til påsatte grunnakselerasjoner, måtte representative tidsrekker for jordskjelv brukes. Disse tidsrekkene ble funnet ved hjelp av probabilistisk vurdering av en syntetisk jorskjelvkatalog. Denne jordskjelvkatalogen ble generert ved å bruke Gutenberg-Richter relasjonen, og de tilhørende parametrene og områdene de gjelder for ble funnet i en rapport angående seismisk inndeling av Norge \cite{zonation}. Jordskjelvparameteren som ble valgt var maksimum grunnakselerasjon (PGA) i både horisontal og vertikal retning estimert ved en relasjon funnet av Ambraseys, med flere \cite{ambhor}\cite{ambver}. Videre ble ordningsstatistikk brukt på de genererte PGA-verdiene ved å bruke Gumbels fordeling for maksima. De resulterende PGA-verdiene i horisontal og vertikal retning ble så brukt for å finne en passende tidsrekke for akselerasjon i en database over jordskjelv for Europa og Midtøsten \cite{esmd}. Deretter ble disse akselerasjonene påsatt de tre modellene og responsen ble evaluert ved ikkelineær direkte implisitt integrasjon. Videre ble en modal analysis av responene utført på den fullt neddykkede modellen for sammenlikningens skyld. Enda en tidsserie ble også påsatt den fullt neddykkede modellen som ble generert basert på det området med høyest seismisk aktivitet, funnet i rapporten nevnt ovenfor for å vurdere det verst tenkelige tilfellet.Resultatene av disse analysene viste at med introduksjon av jord-konstruksjon-interaksjon modellert ved fjærer og dempere, så økte forskyvningene sammenliknet med den fast innspente modellen (konstruksjonen alene). Videre så økte forskyvningene ytterligere ved å introdusere hydrodynamiske krefter. På grunn av små forskyvninger dominerte treghetskreftene responsen for den neddykkede modellen. Med tanke på konstruksjonens oppførsel så ble konstruksjonen nesten ikke affisert av de påsatte grunnakselerasjonene - som er et godt tegn. Imidlertid er det vanskelig å konkludere hvordan andre typer konstruksjoner som rør og platformer ville ha respondert hvis de ble utsatt for de samme grunnakselerasjonene ettersom disse har mye større dimensjoner og annerledes geometri.

In the development of engineering products, it is necessary to predict dynamic properties of the modified structures. Achieving such predictions by using the structural properties of the original structure and information on the modifications is commonly referred to as structural modification analysis. In this thesis, Ö
zgü
ven&rsquo
s Structural Modification Method and Sherman-Morrison Method are selected as exact methods for structural modifications to predict the dynamics of a locally modified structure. Also, a new structural modification method named as &ldquo
Extended Successive Matrix Inversion Method&rdquo
is developed in this study. These three methods are implemented in a software developed herein, called &ldquo
Structural Modification Toolbox&rdquo
. The software uses modal analysis results of MSC Nastran©
for the original structure and calculates the modified frequency response functions by any of the methods above. In order to validate the software, direct modal analysis results of MSC Nastran©
for the frequency response functions of the modified structure are used. The methods are compared in terms of computational time, and the effectivity of each method is studied as a function of modification size to determine which of these methods is more suitable. In order to investigate the application of the methods and compare their results with experimental ones, modal tests are conducted on a scaled aircraft structure. The solutions are compared with test results obtained from modified test structure. Additionally, the software is used for comparison of real aircraft test results and frequency response functions of the modified structure.

One of the main goals in structural biology is to understand the folding mechanisms and three-dimensional structure of biomolecules. Many biomolecular systems adopt multiple structures as a function of their microenvironment, which makes them difficult to be characterized by traditional structural biology tools (e.g., NMR, X-ray crystallography). As an alternative, complementary tools that can capture and sample multiple conformations needed to be developed. In the present work, we pioneered the application of a new variant of ion mobility spectrometry, trapped ion mobility spectrometry (TIMS), which provides high mobility resolving power and the possibility to study kinetically trapped intermediates as a function of the starting solution (e.g., pH and organic content) and gas-phase conditions (e.g., collisional activation, molecular dopants, hydrogen/deuterium back-exchange). When coupled to mass spectrometry (TIMS-MS), action spectroscopy (IRMPD), molecular dynamics and biochemical approaches (e.g., fluorescence lifetime spectroscopy), a comprehensive description of the biomolecules dynamics and tridimensional structural can be obtained. These new set of tools were applied for the first time to the study of Flavin Adenine Dinucleotide (FAD), Nicotineamide Adenine Dinucleotide (NAD), globular protein cytochrome c (cyt c), the 31 knot YibK protein, 52 knot ubiquitin C terminal hydrolase (UCH) protein, and the 61 knot halo acid dehydrogenase (DehI) protein.

A casual look at regional unemployment rates reveals that there are vast differences, which cannot be explained by different institutional settings. Our paper attempts to trace these differences in the labor market performance back to the regions' specialization in products that are more or less advanced in their product cycle. The model we develop shows how individual profit and utility maximization endogenously yields higher employment levels in the beginning. In later phases, however, employment decreases in the presence of process innovation. Our model suggests that the only way to escape from this vicious circle is to specialize in products that are at the beginning of their "economic life". The model is based on an interaction of demand and supply side forces.

Les structures protéiques sont de nature hautement dynamique contrairement à leur représentation dans les structures cristallines. Une composante majeure de la dynamique structurelle est la flexibilité des protéines inhérentes. L'objectif principal de cette thèse est de comprendre le rôle de la dynamique inhérente dans les structures protéiques et leur propagation. La flexibilité des protéines est analysée à différents niveaux de complexité structurelle, du niveau d'organisation primaire au niveau quaternaire. Chacun des cinq premiers chapitres traite un niveau différent d'organisation structurelle locale avec le premier chapitre traitant des structures secondaires classiques tandis que le second analyse la même chose en utilisant un alphabet structurel - les blocs protéiques. Le troisième chapitre se concentre sur l'impact d'événements physiologiques spéciaux comme les modifications post-traductionnelles et le désordre sur les transitions d'ordre sur la flexibilité des protéines. Ces trois chapitres indiquent une mise en œuvre dépendante du contexte de la flexibilité structurelle dans leur environnement local. Dans les chapitres suivants, des structures plus complexes sont prises en compte. Le chapitre 4 traite de l'intégrine αIIbβ3 impliquée dans des troubles génétiques rares. L'impact des mutations pathologiques sur la flexibilité locale est étudié dans deux domaines rigides de l'intégrine αIIbβ3 ectodomaine. La flexibilité inhérente dans ces domaines est montrée pour moduler l'impact des mutations vers les boucles. Le chapitre 5 traite de la modélisation structurelle et de la dynamique d'une structure protéique plus complexe du récepteur des chimiokines des antigènes du groupe Duffy incorporé dans un système de membrane mimétique érythrocytaire. Le modèle est soutenu par l'analyse phylogénétique la plus complète sur les récepteurs de chimiokines jusqu'à ce jour, comme expliqué dans le dernier chapitre de la thèse
Protein structures are highly dynamic in nature contrary to their depiction in crystal structures. A major component of structural dynamics is the inherent protein flexibility. The prime objective of this thesis is to understand the role of the inherent dynamics in protein structures and its propagation. Protein flexibility is analyzed at various levels of structural complexity, from primary to quaternary levels of organization. Each of the first five chapters’ deal with a different level of local structural organization with first chapter dealing with classical secondary structures while the second one analysis the same using a structural alphabet - Protein Blocks. The third chapter focuses on the impact of special physiological events like post-translational modifications and disorder to order transitions on protein flexibility. These three chapters indicate towards a context dependent implementation of structural flexibility in their local environment. In subsequent chapters, more complex structures are taken under investigation. Chapter 4 deals with integrin αIIbβ3 that is involved in rare genetic disorders. Impact of the pathological mutations on the local flexibility is studied in two rigid domains of integrin αIIbβ3 ectodomain. Inherent flexibility in these domains is shown to modulate the impact of mutations towards the loops. Chapter 5 deals with the structural modelling and dynamics of a more complex protein structure of Duffy Antigen Chemokine Receptor embedded in an erythrocyte mimic membrane system. The model is supported by the most comprehensive phylogenetic analysis on chemokine receptors till date as explained in the last chapter of the thesis

Photosynthesis is indisputably the primary biological process to introduce chemical energy and biomass into ecosystems by oxidizing water and reducing carbon dioxide into organic compounds. Photosystem II (PSII) is a unique protein complex, present in thylakoid membranes of all oxygenic photosynthetic organisms, able to catalyze the water-splitting reaction using sunlight as driving force, thus being responsible for the generation of all the molecular oxygen accumulated in the atmosphere for over three billion years. Although its catalytic core has been extremely conserved throughout evolution, from cyanobacteria to higher plants, the necessity of different photosynthetic organisms to cope with ever-changing environmental light conditions led to the emergence of a great variability among its peripheral antenna systems, differentiating in extrinsic phycobilisomes in cyanobacteria and intrinsic light harvesting complexes (LHCII) in green algae and higher plants. LHCII are integral membrane proteins that occur as heterotrimers of Lhcb1-2-3 subunits and monomeric Lhcb4-5-6 polypeptides and associate peripherally with the PSII core in variable numbers, thus forming large supramolecular assemblies called PSII‐LHCII supercomplexes. The minimal functional unit, found in all light conditions, consists of a dimeric PSII core (C2) with two strongly bound LHCII trimers (S2), made of Lhcb1 and Lhcb2, connected by two monomeric Lhcb4 and Lhcb5 subunits, and is called C2S2. In limiting light conditions, the C2S2 can further associate with one or two moderately bound LHCII trimers (M2) which consist of Lhcb1, Lhcb2 and Lhcb3 proteins connected by the monomeric Lhcb6, a peculiar subunit found only in higher plants, originating supercomplexes of type C2S2M1-2. A further supramolecular organization is due to the lateral association of PSII-LHCII supercomplexes within the thylakoid membrane plane, forming PSII-LHCII megacomplexes, or even higher ordered arrays. The LHCII fulfill a dual role by either quenching the excess light energy, often occurring in natural environments, or optimizing its harvesting in ecosystems where there is competition and mutual shading. The rearrangement of the PSII’s modular antenna system through its dynamic interaction with the PSII core, therefore, appears to be a key process in light harvesting regulation. Moreover, plant’s PSII and LHCII are spatially and functionally segregated into piled discs of thylakoid membranes (grana), where they occupy 80% of the surface. Their structural arrangement into PSII-LHCII supercomplexes interacting dynamically with each other appears to be critical in determining the overall membrane architecture and ultimately the efficiency of photosynthesis. Although the overall structure of the basic C2S2 supercomplex in plants has been recently resolved at nearly atomic resolution, there is still a lack of knowledge regarding its structural rearrangement in different light conditions as well as its specific interaction within the membrane plane and between adjacent membranes. During this thesis’ work we have been able to isolate pure PSII-LHCII super- and megacomplexes from pea plants grown in moderate light by mild solubilization of stacked thylakoid membranes. In order to assess their overall functional architecture, the full biochemical characterization of isolated PSII-LHCII supercomplexes, comprehensive of accurate proteomic analyses, was coupled with structural studies. Their structural characterization, performed by transmission electron microscopy (TEM) in cryogenic conditions (cryo-EM) and subsequent single particle analysis, led to a novel 3D structure at about 14 Å resolution of the supercomplexes of type C2S2M. The obtained electron density map revealed that under normal light conditions most of the supercomplexes within the grana are of type C2S2M and occur as paired supercomplexes, whose interactions are mediated by physical connections across the stromal gap of adjacent membranes. The specific overlapping of LHCII trimers facing each other in paired supercomplexes, as already observed in other studies, suggests that this conformation might be representative of their native state within the membranes. The physical connections observed across the stromal gap might be attributable to the mutual interaction between the long N-terminal loops of the monomeric Lhcb4 subunits. These subunits occupy a pivotal position in the 3D map of the paired supercomplexes and are clearly bridged across the stromal gap by electron densities attributable to these loops. In addition, despite the its structural flexibility, the remarkable sequence conservation of this region, even in distant phylogenetic photosynthetic organisms, may suggest its major involvement in structural dynamics. The specific interaction observed in paired supercomplexes seems to be mediated by cations present within the chloroplast in relatively low concentrations as their depletion from buffers used for isolation leads to the dissociation of the paired supercomplexes into single ones. Moreover, this evidence was also strongly supported by the decrease in the PSII excitonic connectivity measured in-vivo. The paired behavior has also been observed in higher oligomerization forms of isolated PSII-LHCII supercomplexes in which two paired supercomplexes laterally interact with each other in the membrane plane, thus forming paired megacomplexes. This novel structure has been obtained by EM and 2D reconstruction of negatively stained particles and, despite its low resolution, reveals how PSII-LHCII supercomplexes may laterally and stromally interact with each other in different ways. The observation of the potential overlapping of LHCII trimers in megacomplexes facing each other, as well as the occurrence of different geometries of interaction between supercomplexes within the membrane plane and between megacomplexes in adjacent membranes, provide intriguing insights on how PSII and LHCII might interact in a very stable manner within the thylakoid membrane and between different discs in the grana. In order to study the PSII-LHCII supercomplex remodeling in the context of ever-changing light environmental conditions, PSII-LHCII supercomplexes have been isolated from pea plants grown at different light intensities: low (LL), moderate (CL) and high light (HL). The accurate profiling and quantitation of the LHCII subunits in the isolated supercomplexes and in the native thylakoids, achieved by using a mass-spectrometry based proteomic approach, was coupled with the evaluation in-vivo of their functional antenna size (ASII). At increasing light intensities, the structural remodeling of the modular PSII’s antenna system led to the reduction of the amount of LHCII M-trimers in the isolated complexes, attested by the decreased level of Lhcb3 and Lhcb6. This specific remodeling does not occur at the same rate in the entire thylakoid membrane. The whole LHCII pool is downregulated only in plants grown in HL, suggesting the occurrence of different acclimation strategies. The remarkable decrease of the ASII observed in HL acclimated plants, when compared to LL plants, can be attributed to the significant increase of the Lhcb4 specific isoform Lhcb4.3, occurring both in isolated supercomplexes and in thylakoid membranes. Unlike isoforms Lhcb4.1-2, the Lhcb4.3 isoform, whose transcription is enhanced upon HL exposure, interestingly has a truncated C-terminus that is located at the binding interface with Lhcb6 within the supercomplex structure. The incorporation of Lhcb4.3 in the PSII-LHCII supercomplex might play a major role in decreasing its functional antenna size by reducing its affinity to bind additional M-trimers, thus regulating its light harvesting efficiency even at moderate light intensities. Conversely, the exposure to HL induces the decrease of the PSII antenna cross-section in isolated supercomplexes and the partial depletion of the whole antenna system of PSII in the thylakoid membranes, thus constitutively preventing damages to the reaction center when light continuously exceeds its energy-processing capacity. These results aim at broadening the current knowledge on how the light harvesting antenna system associated with the PSII core is finely regulated upon plants’ long term acclimation to different light intensities. The flexibility of the PSII’s modular antenna system, accompanied by its finely tuned structural interaction with the core complex, pivotal for the 3D organization of plant thylakoid membranes, certainly played a key role in determining its remarkable evolutionary outcome. Taken together, these results may provide new research directions while certainly broadening the knowledge on how PSII-LHCII assemblies and their supramolecular interaction contribute to maintain the complex architecture of thylakoid membranes and the overall efficiency of photosynthesis in ever changing environmental conditions.
La fotosintesi è indubbiamente il processo biologico principale che introduce energia chimica e biomassa negli ecosistemi ossidando l’acqua e riducendo l'anidride carbonica in composti organici. Il fotosistema II (PSII) è un complesso proteico presente nelle membrane tilacoidali di tutti gli organismi fotosintetici, l’unico in grado di catalizzare la reazione di lisi dell'acqua utilizzando la luce solare come forza motrice e di conseguenza responsabile della generazione di tutto l'ossigeno molecolare presente nell'atmosfera da più di tre miliardi di anni. Nonostante il centro catalitico del PSII sia rimasto fondamentalmente inalterato nel corso dell'evoluzione dai cianobatteri alle piante superiori, la necessità di far fronte alla continua variazione delle condizioni di luce ambientali ha portato all’evoluzione di sistemi di antenne periferiche altamente differenziate, distinte in ficobilisomi estrinseci nei cianobatteri e complessi di membrana intrinseci (LHCII) in alghe verdi e piante superiori. Gli LHCII sono complessi proteici di membrana presenti come etero-trimeri composti dalle subunità Lhcb1-2-3 e subunità monomeriche Lhcb4-5-6 associate perifericamente con il centro catalitico del PSII in numero variabile, formando così associazioni supramolecolari chiamate supercomplessi PSII-LHCII. L'unità funzionale minima, presente in ogni condizione di luce, detta C2S2, è costituita da un PSII centro di reazione dimerico (C2) legato strettamente a due complessi antenna trimerici (S2), composti da Lhcb1 e Lhcb2, mediante due subunità monomeriche Lhcb4 e Lhcb5. In condizioni di luce limitante il C2S2 può ulteriormente associare uno o due complessi antenna trimerici legati moderatamente (M2), costituiti dalle subunità Lhcb1, Lhcb2 e Lhcb3, mediante una peculiare subunità monomerica che si trova solo nelle piante superiori, Lhcb6, generando supercomplessi di tipo C2S2M1-2. I supercomplessi PSII-LHCII possono ulteriormente interagire lateralmente all'interno del piano della membrana tilacoidale formando megacomplessi PSII-LHCII o più estesi arrangiamenti ordinati semicristallini. I complessi antenna LHCII svolgono un duplice ruolo, la dissipazione efficiente dell'energia luminosa, spesso in eccesso negli ambienti naturali, e l’ottimizzazione della sua raccolta negli ambienti in cui vi è concorrenza tra organismi e ombreggiatura reciproca. Il riassetto del sistema di antenne modulari del PSII attraverso la sua interazione dinamica con il centro catalitico sembra quindi essere un processo chiave nella regolazione della raccolta della luce. Inoltre, i PSII e LHCII nelle piante sono spazialmente e funzionalmente segregati in dischi impilati di membrane tilacoidi (grana), dove occupano l'80% della superficie. La loro disposizione strutturale in supercomplessi PSII-LHCII che interagiscono dinamicamente tra loro sembra essere determinante per l'architettura complessiva della membrana tilacoidale e quindi per l'efficienza della fotosintesi. Sebbene la struttura del supercomplesso base C2S2 delle piante sia stata recentemente risolta ad una risoluzione quasi atomica, c'è ancora una lacuna conoscitiva riguardo al ri-arrangiamento strutturale dei PSII-LHCII che avviene in diverse condizioni di luce e alla loro interazione reciproca nel piano della membrana e tra membrane adiacenti dei grana. Durante il lavoro svolto in questa tesi, siamo stati in grado di purificare super- e megacomplessi PSII-LHCII isolati da piante di pisello coltivate in luce moderata mediante la completa solubilizzazione delle membrane tilacoidali. La caratterizzazione biochimica dei supercomplessi PSII-LHCII isolati, complementata da accurate analisi proteomiche, è stata accoppiata con studi strutturali al fine di comprendere la loro architettura funzionale. La caratterizzazione strutturale, eseguita mediante microscopia elettronica a trasmissione (TEM) in condizioni criogeniche (cryo-EM) e successiva analisi d’immagine sulle singole particelle, ha portato ad una nuova struttura tridimensionale (3D) a circa 14 Å di risoluzione del supercomplesso di tipo C2S2M. La mappa di densità elettronica ottenuta ha rivelato che, in condizioni di luce di crescita di intensità moderata, la maggior parte dei supercomplessi è di tipo C2S2M. Essi sono disposti in maniera accoppiata, interagendo mediante collegamenti fisici attraverso l’intervallo stromatico, verosimilmente di membrane adiacenti. La sovrapposizione specifica degli LHCII trimerici, uno di fronte all'altro in supercomplessi accoppiati, come già osservato in altri studi, suggerisce che questa conformazione potrebbe essere rappresentativa del loro stato nativo all'interno delle membrane. I collegamenti fisici osservati nell’intervallo stromatico potrebbero essere attribuibili all'interazione reciproca tra le lunghe porzioni N-terminali di subunità monomeriche Lhcb4 adiacenti. Queste subunità occupano una posizione chiave nella mappa 3D dei supercomplessi accoppiati e le densità elettroniche che attraversano l’intervallo stromatico connettendo i due supercomplessi sono chiaramente attribuibili alle loro porzioni flessibili N-terminali. La sequenza amminoacidica di questa regione, nonostante la sua flessibilità, è sorprendentemente conservata anche in organismi fotosintetici filogeneticamente distanti, il che suggerisce un suo coinvolgimento in dinamiche strutturali fisiologicamente rilevanti per l’apparato fotosintetico. L'interazione specifica osservata nei supercomplessi appaiati sembra essere mediata dai cationi presenti all'interno del cloroplasto in concentrazioni fisiologiche. La loro rimozione dai tamponi utilizzati per l'isolamento, infatti, ne provoca la dissociazione in singoli supercomplessi. Questa evidenza è inoltre sostenuta dalla stima della connettività funzionale misurata in-vivo tramite tecniche di induzione di fluorescenza. Nei supercomplessi appaiati infatti si è evidenziato un potenziale trasferimento di energia maggiore se confrontato con i supercomplessi singolarizzati mediante semplice diluizione dei cationi presenti. L’ appaiamento sul lato stromatico mediato da cationi è stato osservato anche in forme isolate di PSII-LHCII con forme di oligomerizzazione superiore ai supercomplessi, in cui due supercomplessi accoppiati interagiscono lateralmente tra loro nel piano di membrana, formando così megacomplessi appaiati. Questa nuova struttura è stata ottenuta con TEM e ricostruzione bidimensionale a partire da particelle colorate negativamente. Nonostante la bassa risoluzione ottenuta, questa struttura rivela come i supercomplessi PSII-LHCII possono interagire reciprocamente in modi diversi, sia lateralmente che attraverso l’intervallo stromatico. L'osservazione della potenziale sovrapposizione degli LHCII trimerici in megacomplessi accoppiati, così come la presenza di diverse geometrie di interazione tra supercomplessi all'interno del piano di membrana e tra megacomplessi nelle membrane adiacenti, forniscono informazioni interessanti su come PSII e LHCII potrebbero interagire in modo stabile e specifico all'interno della membrana tilacoidale e tra i vari dischi dei grana. Al fine di studiare il rimodellamento dei supercomplessi PSII-LHCII nel contesto di un continuo cambiamento delle condizioni ambientali di luce, sono stati isolati supercomplessi PSII-LHCII da piante di pisello cresciute a diverse intensità di luce: bassa (LL), moderata (CL) e alta (HL). La valutazione in-vivo delle dimensioni dell'antenna funzionale del PSII (ASII) è stata accoppiata con l’identificazione e la quantificazione, mediante analisi proteomiche, delle diverse subunità di LHCII presenti sia nei supercomplessi isolati che nei tilacoidi nativi. All’aumentare dell’intensità di luce di crescita, si evince il rimodellamento strutturale dell’antenna modulare del PSII dovuto alla riduzione della quantità di LHCII trimerici di tipo “M” nei complessi isolati, attestata da una ridotta presenza di Lhcb3 e Lhcb6. Questo rimodellamento specifico non avviene però con le stesse modalità in tutta la membrana tilacoidale. Infatti, la quantità totale di LHCII nei tilacoidi viene significativamente ridotta solo in piante cresciute in HL, suggerendo la presenza di diverse strategie di acclimatazione in grado di ridurre l’antenna funzionale nei tilacoidi. La notevole diminuzione dell’ASII osservata sia nei supercomplessi isolati che nelle membrane tilacoidi di piante cresciute in HL, rispetto alle piante LL, può essere attribuita al significativo incremento di Lhcb4.3, una isoforma di Lhcb4. A differenza delle isoforme Lhcb4.1-2, l'isoforma Lhcb4.3, la cui trascrizione è nota aumentare in seguito all'esposizione ad HL, presenta l’estremità C-terminale troncata. Questa porzione della proteina nella struttura del supercomplesso C2S2M si trova a livello dell’interfaccia di legame con Lhcb6, la subunità monomerica che funge da connettore specifico per l’LHCII trimerico di tipo “M”. L'incorporazione di Lhcb4.3 nel supercomplesso PSII-LHCII sembrerebbe svolgere quindi un ruolo importante nel ridurre le dimensioni dell'antenna funzionale, riducendo l’affinità di legame di antenne aggiuntive (tipo “M”) per ridurre l’efficienza di raccolta della luce già ad intensità moderate. L'esposizione ad HL invece, oltre ad indurre la diminuzione dell'antenna del PSII in supercomplessi isolati, determina anche la riduzione parziale di tutte le antenne del PSII presenti nelle membrane tilacoidi, impedendo quindi danni al centro di reazione quando la luce incidente supera costantemente la sua capacità di utilizzarla efficientemente. Questi risultati contribuiscono ad aumentare le conoscenze su come il sistema di antenne associate al PSII è attivamente regolata a lungo termine modulando l’espressione genica in piante acclimatate a diverse intensità di luce. La flessibilità del sistema modulare di antenne del PSII e la sua interazione strutturale con il centro catalitico, oltre ad essere fondamentale per l’architettura tridimensionale delle membrane tilacoidi delle piante, ha certamente giocato un ruolo chiave nel determinare la loro notevole diversificazione nel corso dell’evoluzione. Nel complesso questi risultati potrebbero fornire nuovi spunti per ampliare la conoscenza di come le associazioni di PSII e LHCII e la loro reciproca interazione contribuiscono a mantenere la complessa architettura delle membrane tilacoidi e quindi l'efficienza complessiva della fotosintesi in condizioni ambientali in continuo mutamento.

Many relationship-based studies focus on how businesses are maintained and developed. However, little attention focused on individuals as business initiators and the consequent processes. This study will bridge this gap. A theoretical model with two cases will answer two questions    -How individuals initiate business through personal network? -What is the consequent process?   The studies demonstrate that individual do play a very important role when initiating a new business and they set in motion relationship-building processes that change the network structure.   The contribution for research and management is clear. The netentrepruer is a new ‘actor’ and can be useful in future studies of business networks. Management can usefully become conscious of the possibilities they have in studying their network contacts before initiating new businesses. Managers should utilize managing individual’s networks as new competition strategies. This will modify the view of management strategy and also contribute to theory building.

[Truncated abstract] This thesis presents three different methods to investigate flexural wave propagation and scattering, power flow and transmission efficiencies, and dynamic stress concentration and fatigue failures in structural dynamics. The first method is based on the acoustical wave propagator (AWP) technique, which is the main part described in this thesis. Through the numerical implementation of the AWP, the complete information of the vibrating structure can be obtained including displacement, velocity, acceleration, bending moments, strain and stresses. The AWP technique has been applied to systems consisting of a one-dimensional stepped beam, a two-dimensional thin plate, a thin plate with a sharp change of section, a heterogeneous plate with multiple cylindrical patches, and a Mindlin?s plate with a reinforced rib. For this Mindlin?s plate structure, through the comparison of the results obtained by Mindlin?s thick plate theory and Kirchhoff?s classical thin plate theory, the difference of theoretical predicted results is investigated. As part of these investigations, reflection and transmission coefficients, power flow and transmission efficiencies in a onedimensional stepped beam, and power flow in a two-dimensional circular plate structure, are studied. In particular, this technique has been successfully extended to investigate wave propagation and scattering, and dynamic stress concentration at discontinuities. Potential applications are fatigue failure prediction and damage detection in complex structures. The second method is based on experimental techniques to investigate the structural response under impact loads, which consist of the waveform measuring technique in the time domain by using the WAVEVIEW software, and steady-state measurements by using the Polytec Laser Scanning Vibrometer (PLSV) in the frequency domain. The waveform measuring technique is introduced to obtain the waveform at different locations in the time domain. These experimental results can be used to verify the validity of predicted results obtained by the AWP technique. Furthermore, distributions of dynamic strain and stress in both near-field (close to discontinuities) and far-field regions are investigated for the study of the effects of the discontinuities on reflection and transmission coefficients in a one-dimensional stepped beam structure. Experimental results in the time domain can be easily transferred into those in the frequency domain by the fast Fourier transformation, and compared with those obtained by other researchers. This PLSV technique provides an accurate and efficient tool to investigate mode shape and power flow in some coupled structures, such as a ribbed plate. Through the finite differencing technique, autospectral and spatial of dynamic strain can be obtained. The third method considered uses the travelling wave solution method to solve reflection and transmission coefficients in a one-dimensional stepped beam structure in the time domain. In particular, analytical exact solutions of reflection and transmission coefficients under the given initial-value problem are derived. These analytical solutions together with experimental results can be used to compare with those obtained by the AWP technique.

Thesis (Ph. D.)--University of North Carolina at Chapel Hill, 2007.
Title from electronic title page (viewed Mar. 27, 2008). "... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Physics and Astronomy." Discipline: Physics and Astronomy; Department/School: Physics and Astronomy.

Le sujet de cette thèse est principalement ciblé sur l’étude du transport ionique dans les sulfates d’alcalins de la famille LIMSO₄, où M=Na, K, Rb, Cs. Une attention particulière est portée sur l’étude du système LiNaSO₄, le plus intéressant en termes de dynamique ionique, par RMN en fonction de la température. Dans le cadre de cette étude, nous avons effectué des mesures de temps de relaxation et de largeurs de raie pour toute la série de composés. Des mesures de coefficients d’autodiffusion du ₇li et du ²³Na, ont été menées depuis l’ambiante jusqu’à la température de fusion. Pour la première fois, nous avons pu mesurer la cinétique de transition de phase dans LiNaSO₄, à partir d’une nouvelle méthode basée sur la différence de temps de relaxation dans les deux phases de part et d’autre d e la transition, mais sans mesurer forcément le T₁. Cette technique élaborée dans le cadre de ce travail permet de mesurer l’évolution au cours du temps du volume de la phase qui apparait pour des vitesses de refroidissement contrôlées. Nous avons aussi mené une étude par RMN des réorientations des groupements sulfates dans la phase basse température. L’influence des réorientations des SO ₄² sur les couplages quadripolaires au noyau 7li, a été étudiée par un modèle de réorientation par sauts, qui n’avait encore jamais été utilisé pour les sulfates. La méthode proposée est une méthode à « bas couts » car elle permet d’atteindre l’information sur la dynamique des groupements sulfates sans enrichir l’échantillon en ¹⁷O ou de mener des expériences très longues pour le ³³S, ou sans passer par les mesures de temps de relaxation. Afin d’analyser le rétrécissement par le mouvement (motional narrowing) en fonction de la température dans les solides avec deux sous réseaux cationiques diffusant comme dans le cas du LiNaSO₄ , nous avons élaboré un modèle permettant de fitter l’évolution observée à deux marches de la largeur de raie RMN avec la température. La fonction analytique obtenue a été étendue au cas de distributions de temps de corrélation
The main goal of a present research is a detailed study of ionic transfer in double sulfates belonging to the LIMSO₄ family, where M = Na, K, Rb, Cs. The most attention has been paid to LiNaSO₄ as to the most interesting (in terms of the ion dynamics) compound among other double sulfates. We have carried out magnetic relaxation measurements and line width analysis for all compounds under consideration. Moreover, PGF NMR measurements of ₇li and ²³Na self-diffusion coefficients in LiNaSO4 have been carried out. For the first time, we have measured the phase transition kinetics in LiNaSO₄. For this purpose, we developed a new technique, which is based on the difference of spin-lattice relaxation times in the two phases, but which does not involve the direct measurement of T₁. Elaborated technique allows measuring time evolution of the volume of the appearing phase at controlled cooling rates. We have carried out NMR study of the sulfate ion reorientations in the low-temperature modification of LiNaSO₄. The influence of the SO ₄² reorientational jumps on the quadrupolar interactions of 7Li nuclei was investigated b y a j ump reorientational model, which has not previously been app lied to sulfates. The proposed method is a “low-cost” technique, since it does not require an ¹⁷O enriched sample and dispenses with time-consuming ³³S NMR. Other advantage of a given method is a possibility to probe reorientational motions without NMR relaxation measurements. To analyze motional narrowing in solids with two diffusing spin sublattices (such case occurs, e.g., in LiNaSO₄) we deduced a formula, which can be used for fitting of the two-step temperature dependencies of the NMR line width. The obtained function has been al so ex tended to the case, when a distribution of correlation times takes place. The advantage of this approach is that even in the case of distribution of correlation times, the fitting function could be expressed in the analytical form

The GntR super-family of transcriptional regulators are ubiquitously distributed throughout the prokaryotic world. There are currently 231,015 sequences in the Pfam database pertaining to GntR proteins (PF000392) from over 17,000 bacterial species. The proteobacteria, firmicutes and actinobacetria account for 95% of all GntR sequences in the database. Yet despite their wide distribution, very few have been studied in depth. The general structure of GntR proteins is a highly homologous helix-turn-helix (HTH) domain linked to a C-terminal effector binding/oligomerisation (Eb/O domain) by a flexible linker. Binding of effector molecules to the Eb/O domain causes conformational changes within the protein allowing binding or release of specific DNA operator sequences which controls gene transcription or repression. The work described here aims to address some of the unknowns relating to GntR-like regulators in terms of structural and dynamical information about their general mechanism of function of this highly diverse family of proteins. Thirty target GntR proteins were selected from sequence analysis of PF000392. These thirty targets were extensively analysed in silico revealing four proteins with novel C-terminal topologies (Gp26, FucR, Reut_B4779 and Colbol_00895) for which there is no structural information. Four proteins (HutC, DevA, DevE and Gp26) were also studied experimentally by using protein biochemistry and x-ray crystallography. The structure of HutC has been solved. However, it has not been fully refined due to the publication of a homologous structure during the course of this work. DevE crystals were obtained and examined by x-ray, further refinement of crystallography conditions and selenomethionine protein preparation resulted in poor phasing and low resolution defracting crystals. Work in this thesis also aimed to refine methodology of 2D-IR spectroscopy to examine protein molecular dynamics at femtosecond resolution with a view to applying this to GntR-like proteins. The model system for this work was InhA and isoniazid.

The penalty method is a versatile and widely used technique for imposing constraints in finite element analysis. Traditionally, it is implemented by adding artificial stiffness to the system equations. However, this leads to large eigenfrequencies being introduced, which, when used in explicit dynamics, can significantly decrease the critical time step of an analysis. This in turn vastly increases computational expense, increases the chances of instability, and generally leads to a less robust formulation. The mass penalty method, a less widely used penalty technique that operates on the mass matrix of a dynamic system, does not introduce large eigenfrequencies, but is less accurate and less versatile than the traditional stiffness penalty method. In this thesis, the two methods are combined to form the bipenalty method. A general formulation is provided that can be used to describe any number of arbitrary multipoint constraints. Mathematical proofs are developed that show that the bipenalty method, like the stiffness penalty method, introduces extra eigenfrequencies into the system, but that they can be carefully controlled by manipulation of the stiffness and mass penalty parameters. It is shown that it is a simple matter to select these parameters such that the critical time step is unaffected by the constraints. The constraint imposition accuracy of the method is analysed, and found to be comparable to that of the traditional stiffness penalty method. An algorithm is provided that describes how to select the penalty parameters for maximum accuracy. Low errors are attainable due to the fact that very large penalty parameters can be used without causing instability. The method is then applied for the first time to two problem types commonly solved using penalty methods: crack propagation (modelled using cohesive surfaces), and contact-impact. A series of examples are presented that demonstrate the stability and accuracy of the method.

A procedure is described for the redesign of undamped unforced linear structural systems to meet specified changes in natural frequency or mode shape. A baseline analysis is conducted using finite elements to obtain a subset of the natural frequencies and mode shapes. A two stage perturbation analysis is then used to obtain the structural changes required to meet the specified changes in natural frequency or mode shape.
Applied Science, Faculty of
Mechanical Engineering, Department of
Graduate

Methods for comprehensive structural dynamic analysis generally employ input-output modal analysis with a mathematical model of structural vibration using excitation and response data. Recently operational modal analysis methods using only vibration response data have been developed. In this thesis, both input-output and operational modal analysis, in the presence of significant unmeasured excitations, is considered. This situation arises when a test structure cannot be effectively isolated from ambient excitations or where the operating environment imposes dynamically-important boundary conditions. The limitations of existing deterministic frequency-domain methods are assessed. A novel time-domain estimation algorithm, based on the estimation of a discrete-time autoregressive moving average with exogenous excitation (ARMAX) model, is proposed. It includes a stochastic component to explicitly account for unmeasured excitations and measurement noise. A criterion, based on the sign of modal damping, is incorporated to distinguish vibration modes from spurious modes due to unmeasured excitations and measurement noise, and to identify the most complete set of modal parameters from a group of estimated models. Numerical tests demonstrate that the proposed algorithm effectively identifies vibration modes even with significant unmeasured random and periodic excitations. Random noise is superimposed on response measurements in all tests. Simulated systems with low modal damping, closely spaced modes and high modal damping are considered independently. The accuracy of estimated modal parameters is good except for degreesof- freedom with a low response level but this could be overcome by appropriate placement of excitation and response measurement points. These observations are reflected in experimental tests that include unmeasured periodic excitations over 200% the level of measured excitations, unmeasured random excitations at 90% the level of measured excitations, and the superposition of periodic and random unmeasured excitations. Results indicate advantages of the proposed algorithm over a deterministic frequency domain algorithm. Piezoceramic plates are used for structural excitation in one experimental case and the limitations of distributed excitation for broadband analysis are observed and characterised in terms of actuator geometry and modal deformation. The ARMAX algorithm is extended for use with response measurements exclusively. Numerical and experimental tests demonstrate its performance using time series data and correlation functions calculated from response measurements.

Mitochondrial cytochrome c (Cc) is a small haem protein, primarily involved in electron transfer, but is an example of an extreme multifunctional protein with roles in several stages of apoptosis through interaction with phospholipids and Apaf-1. The switch in function is associated with an interaction with cardiolipin (CL) and gain of peroxidase activity. Mutations in the Cc gene lead to Thrombocytopenia 4, a disease associated with enhanced apoptotic activity. The Y48H variant is found in the 40-57 W-loop, the lowest free-energy foldon. A 1.36 Å resolution X-ray structure of the Y48H variant reveals minimal structural changes to that of the wild-type protein and G41S variant (also associated with Thrombocytopenia 4). Despite this, the intrinsic peroxidase activity is enhanced, implying that a penta-coordinate haem species is more prevalent in the Y48H variant, corroborated through determination of a Met80 off-rate of > 125 s-1 compared with ~ 6 s-1 for the wild-type protein. Heteronuclear NMR experiments with the ferric Y48H variant have revealed heighted dynamics relative to the WT protein in the 40-57 and 71-85 W-loops, the latter being the loop containing the Met80 ligand, suggesting communication between these two substructures. When these results are considered in relation to the G41S variant, a dynamic picture emerges in which heightened dynamics in key substructures of the Cc fold facilitate an increased population of a penta-coordinate, peroxidase active species of the order wild-type < G41S < Y48H. Studying the alkaline transition through pH jump stopped-flow 2 spectroscopy has revealed that not only is the pK695 is reduced by ~ 1 pH unit compared to that of the wild-type protein, but also the pK of the trigger is lowered. In contrast, variants in the 71-85 W-loop do not alter the pK of the trigger but are nevertheless associated with enhanced peroxidase activity relative to the wild-type protein, due to enhanced local dynamics within the haem crevice.

The finite element method is a valuable tool for simulating complex physical phenomena. However, any finite element based simulation has an intrinsic amount of error with respect to the exact solution of the selected physical model. Being aware of this error is of notorious importance if sensitive engineering decisions are taken on the basis of the numerical results. Assessing the error in elliptic problems (as structural statics) is a well known problem. However, assessing the error in structural transient dynamics is still ongoing research. The present thesis aims at contributing on error assessment techniques for structural transient dynamics. First, a new approach is introduced to compute bounds of the error measured in some quantity of interest. The proposed methodology yields error bounds with better quality than the already available approaches. Second, an efficient methodology to compute approximations of the error in the quantity of interest is introduced. The proposed technique uses modal analysis to compute the solution of the adjoint problem associated with the selected quantity of interest. The resulting error estimate is very well suited for time-dependent problems, because the cost of computing the estimate at each time step is very low. Third, a space-time adaptive strategy is proposed. The local error indicators driving the adaptive process are computed using the previously mentioned modal-based error estimate. The resulting adapted approximations are more accurate than the ones obtained with an straightforward uniform mesh refinement. That is, the adapted computations lead to lower errors in the quantity of interest than the non-adapted ones for the same number of space-time elements. Fourth, a new type of quantities of interest are introduced for error assessment in time-dependent problems. These quantities (referred as timeline-dependent quantities of interest) are scalar time-dependent outputs of the transient solution and are better suited to time-dependent problems than the standard scalar ones. The error in timeline-dependent quantities is eficiently assessed using the modal-based description of the adjoint solution. The thesis contributions are enclosed in five papers which are attached to the thesis document.
El mètode dels elements finits és una eina valuosa per a simular fenòmens físics complexos. Tot i això, aquest mètode només proporciona aproximacions de la solució exacta del model físic considerat. Per tant, quantificar l'error comés en l'aproximació és important si la simulació numèrica s'utilitza per a prendre decisions que poden tenir importants conseqüències. Actualment, les eines que permeten avaluar aquest error són ben conegudes per a problemes estacionaris, però encara presenten importants limitacions per a problemes transitoris com la dinàmica d'estructures. L'objectiu d'aquest treball és contribuir a millorar les tècniques existents per estimar l'error en dinàmica d'estructures i proposar-ne de noves. La primera contribució és una nova metodologia per a calcular cotes de l'error en una quantitat d'interès del problema. Les cotes proposades són més precises i proporcionen una millor estima de l'error que les cotes calculades amb tècniques prèvies. La segona contribució és una una nova tècnica que proporciona aproximacions de l'error en una quantitat d'interès utilitzant càlculs eficients. La novetat principal d'aquesta proposta és aproximar la solució del problema adjunt associat a la quantitat d'interès utilitzant l'anàlisi modal. El resultat és un estimador de l'error indicat particularment per a problemes transitoris, ja que el cost de calcular l'estimador a cada pas de temps és molt baix. La tercera contribució és una tècnica que permet construir de manera adaptada tant la discretizació temporal com espacial amb l'objectiu de millorar l'eficiència de la simulació. Aquesta tècnica es basa en la informació proporcionada per l'estima de l'error amb anàlisi modal. Les aproximacions calculades utilitzant les discretitzacions adaptades són més precises que les obtingudes amb un simple refinament uniforme de la malla de càlcul. És a dir, les discretitzacions adaptades proporcionen un error en la quantitat d'interès menor que les discretizacions no adaptades per al mateix nombre d'elements espai-temps. Finalment, la quarta contribució és un nou tipus de quantitats d'interès especialment indicades per a estimar l'error en problemes transitoris. Aquest nou tipus de quantitats són funcions escalars dependents del temps que proporcionen una informació més completa sobre l'error en problemes transitoris que les quantitats d'interès estàndard. L'error en aquestes noves quantitats és estimat eficientment utilitzant la descripció modal de la solució del problema adjunt. Les contribucions d'aquest treball es troben recopilades en cinc articles que s'inclouen adjunts en el document de la tesi.

Cette thèse présente des travaux effectués dans le cadre de l'optimisation de forme de pièces mécaniques, sous critère dynamique, par approche isogéométrique. Pour réaliser une telle optimisation nous mettons en place dans un premier temps les éléments coque au travers des formulations Kirchhoff-Love puis Reissner-Minlin. Nous présentons une méthode permettant d'atteindre les vecteurs normaux aux fibres dans ces formulations au travers de l'utilisation d'une grille mixte de fonctions de base interpolantes, traditionnellement utilisées en éléments finis, et de fonction non interpolantes issues de la description isogéométrique des coques. Par la suite, nous détaillons une méthode pour le couplage de patch puis nous mettons en place la méthode de synthèse modale classique dans le cadre de structures en dynamique décrites par des éléments isogéometriques. Ce travail établit une base pour l'optimisation de forme sous critères dynamique de telles structures. Enfin, nous développons une méthode d'optimisation de forme basée sur le calcul du gradient de la fonction objectif envisagée. La sensibilité de conception est extraite de l'analyse de sensibilité au niveau même du maillage du modèle, qui est obtenue par l'analyse discrète de sensibilité. Des exemples d'application permettent de montrer la pertinence et l'exactitude des approches proposées
Isogeometric method is a promising method in bridging the gap between the computer aided design and computer aided analysis. No information is lost when transferring the design model to the analysis model. It is a great advantage over the traditional finite element method, where the analysis model is only an approximation of the design model. It is advantageous for structural optimization, the optimal structure obtained will be a design model. In this thesis, the research is focused on the fast three dimensional free shape optimization with isogeometric shell elements. The related research, the development of isogeometric shell elements, the patch coupling in isogeometric analysis, the modal synthesis with isogeometric elements are also studied. We proposed a series of mixed grid Reissner-Minlin shell formulations. It adopts both the interpolatory basis functions, which are from the traditional FEM, and the non-interpolatory basis functions, which are from IGA, to approximate the unknown elds. It gives a natural way to define the fiber vectors in IGA Reissner-Mindlin shell formulations, where the non-interpolatory nature of IGA basis functions causes complexity. It is also advantageous for applying the rotational boundary conditions. A modified reduce quadrature scheme was also proposed to improve the quadrature eficiency, at the same time, relieve the locking in the shell formulations. We gave a method for patch coupling in isogeometric analysis. It is used to connect the adjacent patches. The classical modal synthesis method, the fixed interface Craig-Bampton method, is also used as well as the isogeometric Kirchhoff-Love shell elements. The key problem is also the connection between adjacent patches. The modal synthesis method can largely reduce the time costs in analysis concerning structural dynamics. This part of work lays a foundation for the fast shape optimization of built-up structures, where the design variables are only relevant to certain substructures. We developed a fast shape optimization framework for three dimensional thin wall structure design. The thin wall structure is modelled with isogeometric Kirchhoff-Love shell elements. The analytical sensitivity analysis is the key focus, since the gradient base optimization is normally more fast. There are two models in most optimization problem, the design model and the analysis model. The design variables are defined in the design model, however the analytical sensitivity is normally obtained from the analysis model. Although it is possible to use the same model in analysis and design under isogeomeric framework, it might give either a highly distorted optimum structure or a unreliable structural response. We developed a sensitivity mapping scheme to resolve this problem. The design sensitivity is extracted from the analysis model mesh level sensitivity, which is obtained by the discrete analytical sensitivity analysis. It provides exibility for the design variable definition. The correctness of structure response is also ensured. The modal synthesis method is also used to further improve the optimization eficiency for the built-up structure optimization concerning structural dynamics criteria

Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 1998.
Includes bibliographical references (leaves 104-106).
by Yi-Mei Maria Chow.
M.Eng.

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 2003.
Includes bibliographical references (leaves 79-80).
Instructional Shake tables are an effective pedagogical tool for use in class room and lab, for teaching structural dynamics at advanced undergraduate and graduate level. A detailed study is carried out for a miniature shake table, currently used by the University Consortium of Instructional Shake Tables. A detailed description of the apparatus is given, followed by the system operation. Experiments that simulate different earthquakes are run, and response of a two degree of freedom structure model is noted. Issues regarding interpretation of the response are discussed. Finally an application of the apparatus is demonstrated by use of wavelets for extracting vibration modes of the structure and their damping.
by Muhammed Ali Ifran Baig.
S.M.

Prediction of the conditions required for the transformation of one phase of a mineral into another has long been a goal of condensed matter physics. This is especially desirable for phase transitions which are believed to be involved in geological processes, but for which the conditions of temperature or pressure are hard to reproduce experimentally. This thesis examines a number of structural phase transitions including those of MgSiO₃ perovskite, which is thought to form the largest part of the Earth's mantle and of ZrO₂ which plays an important role in inhibiting crack formation in ceramics. These phase transitions, in which an alternative phase may be reached by continuous distortions of the structure on an atomic level, are examined primarily through the use of first principles electronic structure calculations. Existing first principles techniques were extended to facilitate determination of the equilibrium structure by relaxation of the unit cell and the calculation of the lattice dynamics of complex phases. The distortion involved in most of the phase transitions studied is found to reflect the normal vibrational modes of one or both phases. The phase transitions of MgSiO₃ are found to be well described by only a few normal modes of the highest-symmetry cubic phase, dominated by two modes involving tilting of the SiO₆ octahedra. These modes resemble rigid unit modes, in which SiO₆ octahedra are assumed to remain perfectly rigid but may rotate with respect to other octahedra, whilst preserving linkages between them. The extent to which such simple modes are an accurate description of the dynamics of MgSiO₃, BaZrO₃ and SiO₂ is investigated by way of structural analysis and lattice dynamics of both stable and metastable phases. Both simple models deduced from the lattice dynamical analysis and molecular dynamics using forces calculated from first principles are used to estimate transition temperatures for thermally induced phase transitions in MgSiO₃.

This submission for the degree of Doctor of Science includes all the publications by the author and a description of his research, covering the period 1969-2015. The main contributions to knowledge made by the author concern his new approaches to structural dynamics, aeroelasticity, material science and related problems. In particular, the major activities of his research relate to the (i) free vibration and buckling analysis of structures, (ii) dynamic stiffness formulation, (iii) response of metallic and composite structures to deterministic and random loads, (iv) aeroelasticity of metallic and composite aircraft, (v) a unified approach to flutter, dynamic stability and response of aircraft, (vi) aeroelastic optimisation and active control, (vii) application of symbolic computation in structural engineering research, (viii) development of software packages for computer aided structural analysis and design and (ix) thermal properties of polymer nanocomposites and hot ductility of steel. The free vibration analysis of structures is a research topic which has been an age old companion of the author ever since he was working for his Master’s degree in Mechanical Engineering in the early 1970s, when he chose a crankshaft vibration problem of the Indian Railways as the research topic for his Master’s thesis. With increasing maturity and experience, he provided solutions to vibration and buckling problems ranging from a simple single structural element to a high capacity transport airliner capable of carrying more than 500 passengers and a large space platform with a plan dimension of more than 30 metres. To provide these solutions, he resorted to an elegant, accurate, but efficient method, called the dynamic stiffness method, which uses the so-called dynamic stiffness matrix of a structural element as the basic building block in the analysis. The author has developed dynamic stiffness matrices of a large number of structural elements including beams, plates and shells with varying degrees of complexity, particularly including those made of composite materials. Recently he published the dynamic stiffness matrices of isotropic and anisotropic rectangular plates for the most general case when the plate boundaries are free at all edges. Computation of natural frequencies of isotropic and anisotropic plates and their assemblies for any boundary conditions in an exact sense has now become possible for the first time as a result of this development. This ground-breaking research has opened up the possibility of developing general purpose computer programs using the dynamic stiffness method for computer-aided structural analysis and design. Such computer programs will be vastly superior to existing computer programs based on the finite element method, both in terms to accuracy and computational efficiency. This is in line with the author’s earlier research on free vibration and buckling analysis of skeletal structures which led to the development of the computer program BUNVIS (Buckling or Natural Vibration of Space Frames) and BUNVIS-RG (Buckling or Natural Vibration of Space Frames with Repetitive Geometry) which received widespread attention. Numerous research papers emerged using BUNVIS and BUNVIS-RG as research tools. The author’s main contributions in the Aeronautical Engineering field are, however, related to the solutions of problems in aeroelasticity, initially for metallic aircraft and in later years for composite aircraft. He investigated the aeroelastic problems of tailless aircraft for the first time in his doctoral studies about 40 years ago. In this research, a unified method combining two major disciplines of aircraft design, namely that of stability and control, and that of flutter and response, was developed to study the interaction between the rigid body motions of an aircraft and its elastic modes of distortion. The computer program CALFUN (CALculation of Flutter speed Using Normal modes) was developed by the author for metallic aircraft and later extended to cover composite aircraft. The associated theories for composite aircraft were developed and the allied problems of dynamic response to both deterministic and random loads were solved. With the advent of advanced composite materials, the author’s research turned to aeroelasticity of composite aircraft and then to optimization studies. New, novel and accurate methods were developed and significant inroads were made. The author broke new ground by applying symbolic computation as an aid to the solution of his research problems. The computational efficiency of this new approach became evident as a by-product of his research. The development of software based on his theories has paved the way for industrial applications. His research works on dynamic stiffness modelling of composite structures using layer-wise and higher order shear deformation theory are significant developments in composites engineering. Such pioneering developments were necessitated by the fact that existing methodologies using classical lamination theory are not sufficiently accurate, particularly when the structural components made from composite materials are thick, e.g. the fuselage of a transport airliner. Given the close relationship between structural engineering and material science, the author’s research has broadened into polymers and nano-composites, functionally graded materials and hot ductility of steel. His research activities are continuing and expanding with further diversification of his interests.

Over the last three decades the political economy debate abandoned its focus on manufacturing as the main engine of the technological dynamism and the source of the wealth of nations. However recent years have witnessed a renewed interest in manufacturing production. This has led analysts to announce and welcome a worldwide 'manufacturing renaissance' emerging in different contexts with multiple focuses. The thesis provides new analytical and empirical lenses for disentangling the dynamics of manufacturing development. We do this by showing how learning processes are the fundamental category responsible for production capabilities dynamics which in turn trigger structural change. Essay 1 'The Manufacturing Renaissance: Transforming Industrial Systems and the Wealth of Nations' presents a novel synthesis of two strands of economic research, Structural Economic Dynamics and the Economics of Capabilities. Within this framework we integrate structural change and production capabilities dynamics. The following Essays of this dissertation apply and extend this theoretical synthesis by focusing firstly on learning in production structures and cumulative (non-linear) structural change dynamics (Essays 2 and 3 respectively); secondly, in developing new diagnostics for industrial policies design (Essay 4); finally, in investigating industrial policies for manufacturing development (Essay 5). Essay 2 'Structural Learning: Embedding discoveries and the dynamics of production' extends the current framework by rembedding learning dynamics from which production capabilities are generated in the production structure itself. Essay 3 'Manufacturing Agrarian Change. Agricultural production, intermediate institutions and Intersectoral commons: Lessons from Latin America' than applies the concept of structural learning developed in Essay 2 to the intersectoral interdependencies on the interface of agriculture and manufacturing. Moreover, we show how in the context of Chile and Brazil intersectoral learning from which intersectoral commons derive was facilitated by the development of intermediate institutions. Essay 4 'Production Capability Indicators. Mapping countries' structural trajectories and the assessment of industrial skills in LDCs: The case of Tanzania' addresses the problem of capturing these learning dynamics through production capabilities indicators at the national level. Not only do we propose a new theoretically-sensitive methodology for quantifying learning dynamics but also we apply this to industrial skills assessment in Tanzania. Finally, Essay 5 'Industrial Policy for Manufacturing Development. Structural dynamics and institutional changes in a dual economy: A case of dependent industrialisation in the Italian Mezzogiorno' focuses on the development of industrial policies, the latter understood as mechanisms to trigger learning dynamics at the sectoral and intersectoral level. The Italian 'Mezzogiorno' case is presented to illustrate these dynamics in a context of dependent industrialisation.

This thesis investigates the host-guest chemistry and structural dynamics in three families of coordination frameworks – Prussian blue analogues (PBAs), zeolitic imidazolate frameworks (ZIFs), and lanthanoid metal-organic frameworks (MOFs). This was primarily achieved using in situ gas-loading neutron powder diffraction (NPD) to examine various guests in the pore space of these materials. Each of these frameworks contain structural motifs that have previously been identified as influential in the uptake of gases. Gas-loaded NPD of the PBA Fe¬3[Co(CN)6]2 revealed two CO2 adsorption sites, both of which interact with the coordinatively-unsaturated Fe(II) sites. A linear relationship was also observed between the material's thermal expansion behaviour when dosed with increasing amounts of CO2, suggesting the potential for controlled thermal expansion properties. NPD analysis of gas-loaded Co(nIm)2-RHO has revealed five adsorption sites each when this material was dosed with CO2 or D2. Host-guest interactions at CO2 and D¬2 adsorption sites are observed to be predominantly driven by electrostatic interactions with the nitro functional group of the 2 nitroimidazolate bridging ligand. Analysis of CO2-loaded NPD data for Co(mIm)2-SOD revealed only a single CO2 adsorption site that accounted for ca. 17% of the total amount of CO2 dosed. This comparison has helped to confirm the necessity of having ligands with strong charge polarisation in order to achieve guest interaction and crystallographic ordering. NPD analysis of gas-loaded Y(btc) has revealed multiple adsorption sites with dosed with CO2, CD4, and O2. These host-guest adsorption sites typically occur between the guest molecule and the carboxylate functional groups of the bridging ligand. Despite the presence of bare metal sites, only the O2 guest is seen to interact weakly. This has been attributed to the contraction in O-Y-O coordination angles upon desolvation of the host material.

This doctoral dissertation is divided in two parts. In part 1, we investigate, from a multi-sectoral perspective, one of the most important processes of structural change of the last fifty years, namely, the increase in relative importance of the financial sector, or financialisation. The term financialisation remains an unclear concept in social science. Our main innovation consists in conceptualise financialisation as an increase in the financial content in monetary terms of each unit of output produced. In this way, we are able to investigate changes in relative importance of financial activities considering interactions among sectors. In part 2, we extend Goodwin's growth cycle model to an open economy set up in a way that incorporates the balance-of-payments constraint to growth, i.e. Thirlwall's (1979) law.

The aim of this thesis is to describe a number of materials that have attracted interest due to their magnetic, electric or structural properties with the use of generalized models. In hexagonal multiferroic LuFeO3 the study of the magnetic excitations in the material reveals the presence of elusive topological objects (i.e. effective magnetic monopoles and toroidal moments) not previously reported as well ad the non-reciprocal character of particular magnons in the material. The model and the results can be generalized to the class of hexagonal multiferroics. In the case of TbMnO3 we analyze the excitation spectrum of a cycloidal spin system that exhibit improper ferroelectricity. The results reveal that soft electromagnons have a large contribution, due to domain wall-localized modes, to the static dielectric constant of the material and, in general, of the cycloidal systems. A study of the response of GaV4S8 to photoexcitation is performed through atomistic spin dynamics simulations. Thermal properties of GaV4S8 are discovered to be related to the magnetic phases of the material due to the changing magnon transport properties of different magnetic phases. A change of the order of 2 in the thermal conductivity is observed in the transition from cycloidal to ferromagnetic phases A study of improper ferroelectricity in hybrid organic-inorganic perovskites is performed by using a Landau type symmetry breaking theory. The theory shows a rich phase diagram and the presence of nested domain walls. The theory describes a molecular ordering mechanism as a possible explanation for weak improper ferroelectricity observed in NH2(CH3)2Fe(COOH)3. The decade-long problem of the stripe ordering in IrTe2 is addressed. The existing observations of different striped phases in the material are reproduced in this study through a combination of first principle calculations and a phenomenological model. The same model predicts a phase diagram for the dimerized phases in the shape of a Devil's Staircase. This result partially fills a gap in the knowledge about IrTe, up to date no exhaustive explanation is known for the dimerization mechanism, and no other information on the dimerized phase diagram was available aside of the results reproduced in this work. The essence of this work is that minimalistic models and general considerations about energy and symmetries are powerful tools to describe quite diverse problems. This thesis address the importance of the excitations in the properties of certain materials and points out features that have not been previously reported in literature.