Coarse-graining and quantum-classical adaptive coupling in soft matter

Die vorliegende Arbeit untersucht den Zusammenhang zwischen Skalen in Systemen weicher Materie, der für Multiskalen-Simulationen eine wichtige Rolle spielt. Zu diesem Zweck wurde eine Methode entwickelt, die die Approximation der Separierbarkeit von Variablen für die Molekulardynamik und ähnliche Anwendungen bewertet. Der zweite und größere Teil dieser Arbeit beschäftigt sich mit der konzeptionellen und technischen Erweiterung des Adaptive Resolution Scheme'' (AdResS), einer Methode zur gleichzeitigen Simulation von Systemen mit mehreren Auflösungsebenen. Diese Methode wurde auf Systeme erweitert, in denen klassische und quantenmechanische Effekte eine Rolle spielen.rnrnDie oben genannte erste Methode benötigt nur die analytische Form der Potentiale, wie sie die meisten Molekulardynamik-Programme zur Verfügung stellen. Die Anwendung der Methode auf ein spezielles Problem gibt bei erfolgreichem Ausgang einen numerischen Hinweis auf die Gültigkeit der Variablenseparation. Bei nicht erfolgreichem Ausgang garantiert sie, dass keine Separation der Variablen möglich ist. Die Methode wird exemplarisch auf ein zweiatomiges Molekül auf einer Oberfläche und für die zweidimensionale Version des Rotational Isomer State (RIS) Modells einer Polymerkette angewandt.rnrnDer zweite Teil der Arbeit behandelt die Entwicklung eines Algorithmus zur adaptiven Simulation von Systemen, in denen Quanteneffekte berücksichtigt werden. Die Quantennatur von Atomen wird dabei in der Pfadintegral-Methode durch einen klassischen Polymerring repräsentiert. Die adaptive Pfadintegral-Methode wird zunächst für einatomige Flüssigkeiten und tetraedrische Moleküle unter normalen thermodynamischen Bedingungen getestet. Schließlich wird die Stabilität der Methode durch ihre Anwendung auf flüssigen para-Wasserstoff bei niedrigen Temperaturen geprüft.

"Offshore tower or platform foundations: numerical analysis of a laterally loaded single pile or pile group in soft clay and analysis of actions on a jacket structure"

Laterally loaded piles are a typical situation for a large number of cases in which deep foundations are used. Dissertation herein reported, is a focus upon the numerical simulation of laterally loaded piles. In the first chapter the best model settings are largely discussed, so a clear idea about the effects of interface adoption, model dimension, refinement cluster and mesh coarseness is reached. At a second stage, there are three distinct parametric analyses, in which the model response sensibility is studied for variation of interface reduction factor, Eps50 and tensile cut-off. In addition, the adoption of an advanced soil model is analysed (NGI-ADP). This was done in order to use the complex behaviour (different undrained shear strengths are involved) that governs the resisting process of clay under short time static loads. Once set a definitive model, a series of analyses has been carried out with the objective of defining the resistance-deflection (P-y) curves for Plaxis3D (2013) data. Major results of a large number of comparisons made with curves from API (America Petroleum Institute) recommendation are that the empirical curves have almost the same ultimate resistance but a bigger initial stiffness. In the second part of the thesis a simplified structural preliminary design of a jacket structure has been carried out to evaluate the environmental forces that act on it and on its piles foundation. Finally, pile lateral response is studied using the empirical curves.

The reconstruction of skeletal movement: the soft tissue artefact issue

In 3D human movement analysis performed using stereophotogrammetric systems and skin markers, bone pose can only be estimated in an indirect fashion. During a movement, soft tissue deformations make the markers move with respect to the underlying bone generating soft tissue artefact (STA). STA has devastating effects on bone pose estimation and its compensation remains an open question. The aim of this PhD thesis was to contribute to the solution of this crucial issue. Modelling STA using measurable trial-specific variables is a fundamental prerequisite for its removal from marker trajectories. Two STA model architectures are proposed. Initially, a thigh marker-level artefact model is presented. STA was modelled as a linear combination of joint angles involved in the movement. This model was calibrated using ex-vivo and in-vivo STA invasive measures. The considerable number of model parameters led to defining STA approximations. Three definitions were proposed to represent STA as a series of modes: individual marker displacements, marker-cluster geometrical transformations (MCGT), and skin envelope shape variations. Modes were selected using two criteria: one based on modal energy and another on the selection of modes chosen a priori. The MCGT allows to select either rigid or non-rigid STA components. It was also empirically demonstrated that only the rigid component affects joint kinematics, regardless of the non-rigid amplitude. Therefore, a model of thigh and shank STA rigid component at cluster-level was then defined. An acceptable trade-off between STA compensation effectiveness and number of parameters can be obtained, improving joint kinematics accuracy. The obtained results lead to two main potential applications: the proposed models can generate realistic STAs for simulation purposes to compare different skeletal kinematics estimators; and, more importantly, focusing only on the STA rigid component, the model attains a satisfactory STA reconstruction with less parameters, facilitating its incorporation in an pose estimator.

Patterning soft matter for cell culturing

In the search to understand the interaction between cells and their underlying substrates, life sciences are beginning to incorporate micro and nano-technology based tools to probe, measure and improve cellular behavior. In this frame, patterned surfaces provide a platform for highly defined cellular interactions and, in perspective, they offer unique advantages for artificial implants. For these reasons, functionalized materials have recently become a central topic in tissue engineering. Nanotechnology, with its rich toolbox of techniques, can be the leading actor in the materials patterning field. Laser assisted methods, conventional and un-conventional lithography and other patterning techniques, allow the fabrication of functional supports with tunable properties, either physically, or topographically and chemically. Among them, soft lithography provides an effective (and low cost) strategy for manufacturing micro and nanostructures. The main focus of this work is the use of different fabrication approaches aiming at a precise control of cell behavior, adhesion, proliferation and differentiation, through chemically and spatially designed surfaces.

EPR spectroscopy as a tool for the elucidation of non-covalent structuring principles in complex soft matter

This thesis aims at connecting structural and functional changes of complex soft matter systems due to external stimuli with non-covalent molecular interaction profiles. It addresses the problem of elucidating non-covalent forces as structuring principle of mainly polymer-based systems in solution. The structuring principles of a wide variety of complex soft matter types are analyzed. In many cases this is done by exploring conformational changes upon the exertion of external stimuli. The central question throughout this thesis is how a certain non-covalent interaction profile leads to solution condition-dependent structuring of a polymeric system.rnTo answer this question, electron paramagnetic resonance (EPR) spectroscopy is chosen as the main experimental method for the investigation of the structure principles of polymers. With EPR one detects only the local surroundings or environments of molecules that carry an unpaired electron. Non-covalent forces are normally effective on length scales of a few nanometers and below. Thus, EPR is excellently suited for their investigations. It allows for detection of interactions on length scales ranging from approx. 0.1 nm up to 10 nm. However, restriction to only one experimental technique likely leads to only incomplete pictures of complex systems. Therefore, the presented studies are frequently augmented with further experimental and computational methods in order to yield more comprehensive descriptions of the systems chosen for investigation.rnElectrostatic correlation effects in non-covalent interaction profiles as structuring principles in colloid-like ionic clusters and DNA condensation are investigated first. Building on this it is shown how electrostatic structuring principles can be combined with hydrophobic ones, at the example of host-guest interactions in so-called dendronized polymers (denpols).rnSubsequently, the focus is shifted from electrostatics in dendronized polymers to thermoresponsive alkylene oxide-based materials, whose structuring principles are based on hydrogen bonds and counteracting hydrophobic interactions. The collapse mechanism in dependence of hydrophilic-hydrophobic balance and topology of these polymers is elucidated. Complementarily the temperature-dependent phase behavior of elastin-like polypeptides (ELPs) is investigated. ELPs are the first (and so far only) class of compounds that is shown to feature a first-order inverse phase transition on nanoscopic length scales.rnFinally, this thesis addresses complex biological systems, namely intrinsically disordered proteins (IDPs). It is shown that the conformational space of the IDPs Osteopontin (OPN), a cytokine involved in metastasis of several kinds of cancer, and BASP1 (brain acid soluble protein one), a protein associated with neurite outgrowth, is governed by a subtle interplay between electrostatic forces, hydrophobic interaction, system entropy and hydrogen bonds. Such, IDPs can even sample cooperatively folded structures, which have so far only been associated with globular proteins.

Studio e sviluppo di un'infrastruttura di supporto alla schedulazione di hard/soft real-time tasks in ambiente QNX.

La tesi tratta lo studio del sistema QNX e dello sviluppo di un simulatore di task hard/soft real-time, tramite uso di un meta-scheduler. Al termine dello sviluppo vengono valutate le prestazioni del sistema operativo QNX Neutrino.

Nuovi elastomeri termoplastici "soft-hard" a base di pbs per applicazioni biomedicali

Nuovi elastomeri termoplastici "soft-hard" a base di PBS per applicazioni biomedicali

Characterization of a dual-energy X-ray absorptiometry system for soft tissues assessment and their correlations with metabolic state

Il crescente utilizzo di sistemi di analisi high-throughput per lo studio dello stato fisiologico e metabolico del corpo, ha evidenziato che una corretta alimentazione e una buona forma fisica siano fattori chiave per la salute. L'aumento dell'età media della popolazione evidenzia l'importanza delle strategie di contrasto delle patologie legate all'invecchiamento. Una dieta sana è il primo mezzo di prevenzione per molte patologie, pertanto capire come il cibo influisce sul corpo umano è di fondamentale importanza. In questo lavoro di tesi abbiamo affrontato la caratterizzazione dei sistemi di imaging radiografico Dual-energy X-ray Absorptiometry (DXA). Dopo aver stabilito una metodologia adatta per l'elaborazione di dati DXA su un gruppo di soggetti sani non obesi, la PCA ha evidenziato alcune proprietà emergenti dall'interpretazione delle componenti principali in termini delle variabili di composizione corporea restituite dalla DXA. Le prime componenti sono associabili ad indici macroscopici di descrizione corporea (come BMI e WHR). Queste componenti sono sorprendentemente stabili al variare dello status dei soggetti in età, sesso e nazionalità. Dati di analisi metabolica, ottenuti tramite Magnetic Resonance Spectroscopy (MRS) su campioni di urina, sono disponibili per circa mille anziani (provenienti da cinque paesi europei) di età compresa tra i 65 ed i 79 anni, non affetti da patologie gravi. I dati di composizione corporea sono altresì presenti per questi soggetti. L'algoritmo di Non-negative Matrix Factorization (NMF) è stato utilizzato per esprimere gli spettri MRS come combinazione di fattori di base interpretabili come singoli metaboliti. I fattori trovati sono stabili, quindi spettri metabolici di soggetti sono composti dallo stesso pattern di metaboliti indipendentemente dalla nazionalità. Attraverso un'analisi a singolo cieco sono stati trovati alti valori di correlazione tra le variabili di composizione corporea e lo stato metabolico dei soggetti. Ciò suggerisce la possibilità di derivare la composizione corporea dei soggetti a partire dal loro stato metabolico.

Moduli stabilisation and soft supersymmetry breaking in string compactifications

In this thesis, we shall work in the framework of type IIB Calabi-Yau flux compactifications and present a detailed review of moduli stabilisation studying in particular the phenomenological implications of the LARGE-volume scenario (LVS). All the physical relevant quantities such as moduli masses and soft-terms, are computed and compared to the phenomenological constraints that today guide the research. The structure of this thesis is the following. The first chapter introduces the reader to the fundamental concepts that are essentially supersymmetry-breaking, supergravity and string moduli, which represent the basic framework of our discussion. In the second chapter we focus our attention on the subject of moduli stabilisation. Starting from the structure of the supergravity scalar potential, we point out the main features of moduli dynamics, we analyse the KKLT and LARGE-volume scenario and we compute moduli masses and couplings to photons which play an important role in the early-universe evolution since they are strictly related to the decay rate of moduli particles. The third chapter is then dedicated to the calculation of soft-terms, which arise dynamically from gravitational interactions when moduli acquire a non-zero vacuum expectation value (VeV). In the last chapter, finally, we summarize and discuss our results, underling their phenomenological aspects. Moreover, in the last section we analyse the implications of the outcomes for standard cosmology, with particular interest in the cosmological moduli problem.

Progettazione e sintesi di coppie ioniche ("soft salts") basate su complessi Ir(III) tetrazolici.

In questo lavoro di tesi sperimentale si è sintetizzata e caratterizzata la prima classe di complessi tetrazolici di Ir(III) anionici con formula generale [Ir(C^N)2(L)2]-, in cui oltre ai leganti ciclometallanti ”C^N” quali 2-fenilpiridinato (ppy) o 2-(2,4-difluorofenil)piridinato (F2ppy), sono stati introdotti due anioni tetrazolato (L) come il 5-fenil tetrazolato (Tph) oppure 5-(4-cianofenil) tetrazolato (TphCN). I complessi di Ir(III) anionici ottenuti si sono mostrati intensamente fosforescenti, con emissioni centrate nella regione del blu o del verde (460 < λmax<520 nm). I derivati anionici sono stati poi combinati con complessi Ir(III) tetrazolici cationici in grado di fornire emissione nella regione del rosso (λmax > 650 nm), formando così i primi esempi di coppie ioniche (“soft salts”) a matrice puramente tetrazolica. In tutti i casi si è osservato come il colore emesso da parte dei soft salts sia il risultato di una vera propria sintesi additiva delle emissioni derivanti da componenti ioniche con proprietà fotoemittive differenti. La sostanziale assenza di fenomeni di energy o electron transfer tra la componente anionica e cationica e il giusto bilancio tra le emissioni blu o verdi e rosse si sono tradotte, in taluni casi, nell’ottenimento di luce bianca, con la possibilità di variare ulteriormente i colori emessi in seguito all’allontanamento dell’ossigeno molecolare disciolto nelle soluzioni dei soft salts stessi.

Palatal swelling as the first and only manifestation of extranodal follicular non-Hodgkin lymphoma: a case presentation

Non-Hodgkin lymphomas (NHLs) in the head and neck region are malignant lymphoid neoplasms that usually originate from B-lymphocytic cell lines. Primary extranodal manifestations of this hematolymphoid tumor in the oral cavity are rare and involve the maxillary jaw including the palatal soft tissues, the mandible, and gingival tissues in patients between 60 and 70 years of age without sex predilection. This case report of an extra-nodal NHL in the palate of a 75-year-old patient emphasizes the importance of accurate clinical, radiographic, and histologic diagnostic procedures to avoid delayed diagnosis or inappropriate treatment strategies. Chemotherapy, radiotherapy, or a combination of the two with a regular clinical and hemic follow-up is recommended.

Comparison of two scoring systems for evaluation of treatment outcome in patients with complete bilateral cleft lip and palate

Objective : To compare two scoring systems: the Huddart/Bodenham system (HB system) and the Bauru-BCLP yardstick (BCLP yardstick), which classify treatment outcome in terms of dental arch relationships in patients with complete bilateral cleft lip and palate (CBCLP). The predictive value of these scoring systems for treatment outcome was also evaluated. Design : Retrospective longitudinal study. Patients : Dental arch relationships of 43 CBCLP patients were evaluated at 6, 9, and 12 years. Setting : Treatment outcome in BCLP patients using two scoring systems. Main Outcome Measures : For each age group, the HB scores were correlated with the BCLP yardstick scores using Spearman's correlation coefficient. The predictive value of the two scoring systems was evaluated by backward regression analysis. Results : Intraobserver Kappa values for the BCLP yardstick scoring for the two observers were .506 and .627, respectively, and the interobserver reliability ranged from .427 and .581. The intraobserver reliability for the HB system ranged from .92 to .97 and the interobserver reliability from .88 to .96. The BCLP yardstick scores of 6 and 9 years together were predictors for the outcome at 12 years (explained variance 41.3%). Adding the incisor and lateral HB scores in the regression model increased the explained variance to 67%. Conclusions : The BCLP yardstick and the HB system are reliable scoring systems for evaluation of dental arch relationships of CBCLP patients. The HB system categorizes treatment outcome into similar categories as the BCLP yardstick. In case a more sensitive measure of treatment outcome is needed, selectively both scoring systems should be used.

A new yardstick for rating dental arch relationship in patients with complete bilateral cleft lip and palate

Objective: To develop yardsticks for assessment of dental arch relationship in young individuals with repaired complete bilateral cleft lip and palate appropriate to different stages of dental development. Participants: Eleven cleft team orthodontists from five countries worked on the projects for 4 days. A total of 776 sets of standardized plaster models from 411 patients with operated complete bilateral cleft lip and palate were available for the exercise. Statistics: The interexaminer reliability was calculated using weighted kappa statistics. Results: The interrater weighted kappa scores were between .74 and .92, which is in the "good" to "very good" categories. Conclusions: Three bilateral cleft lip and palate yardsticks for different developmental stages of the dentition were made: one for the deciduous dentition (6-year-olds' yardstick), one for early mixed dentition (9-year-olds' yardstick), and one for early permanent dentition (12-year-olds' yardstick).

Dental arch relationship in children with complete unilateral cleft lip and palate following one-stage and three-stage surgical protocols

The objective of this study is to compare dental arch relationship following one-stage and three-stage surgical protocols of unilateral cleft lip and palate. Dental casts of 61 children (mean age, 11.2 years; SD, 1.7), consecutively treated in one center with one-stage closure of the complete cleft at 9.2 months (SD, 2.0), were compared with a sample of 97 patients (mean age, 8.7 years; SD, 0.9), consecutively treated with a three-stage protocol including delayed hard palate closure in another center. The dental casts were assigned random numbers to blind their origin. Four raters graded dental arch relationship and palatal morphology using the EUROCRAN index. The strength of agreement of rating was assessed with kappa statistics. Independent t tests were run to compare the EUROCRAN scores between one-stage and three-stage samples, and Fisher's exact tests were performed to evaluate differences of distribution of the EUROCRAN grades. The intra- and inter-rater agreement was moderate to very good. Dental arch relationship in the one-stage sample was less favorable than in three-stage group (mean scores, 2.58 and 1.97 for one-stage and three-stage samples, respectively; p?

A longitudinal three-center study of dental arch relationship in patients with bilateral cleft lip and palate

OBJECTIVE: To compare and evaluate longitudinally the dental arch relationships from 4.5 to 13.5 years of age with the Bauru-BCLP Yardstick in a large sample of patients with bilateral cleft lip and palate (BCLP). DESIGN: Retrospective longitudinal intercenter outcome study. PATIENTS: Dental casts of 204 consecutive patients with complete BCLP were evaluated at 6, 9, and 12 years of age. All models were identified only by random identification numbers. SETTING: Three cleft palate centers with different treatment protocols. MAIN OUTCOME MEASURES: Dental arch relationships were categorized with the Bauru-BCLP yardstick. Increments for each interval (from 6 to 9 years, 6 to 12 years, and 9 to 12 years) were analyzed by logistic and linear regression models. RESULTS: There were no significant differences in outcome measures between the centers at age 12 or at age 9. At age 6, center B showed significantly better results (p=.027), but this difference diminished as the yardstick score for this group increased over time (linear regression analysis), the difference with the reference category (center C, boys) for the intervals 6 to 12 and 9 to 12 years being 10.4% (p=.041) and 12.9% (p=.009), respectively. CONCLUSIONS: Despite different treatment protocols, dental arch relationships in the three centers were comparable in final scores at age 9 and 12 years. Delaying hard palate closure and employing infant orthopedics did not appear to be advantageous in the long run. Premaxillary osteotomy employed in center B appeared to be associated with less favorable development of the dental arch relationship between 9 and 12 years.