Molecular dynamics (MD) simulation is a powerful tool enabling researchers to gain insight into biological processes at the atomic level. There have been many advancements in both hardware and software in the last decade to both accelerate MD simulations and increase their predictive accuracy; however, MD simulations are typically limited to the microsecond timescale, whereas biological motions can take seconds or longer. Because of this, it remains extremely challenging to restrain simulations using ensemble-averaged experimental observables. Among various approaches to elucidate the kinetics of molecular simulations, Markov State Models (MSMs) have proven their ability to extract both kinetic and thermodynamic properties of long-timescale motions using ensembles of shorter MD simulation trajectories. In this dissertation, we have implemented an MSM path-entropy method, based on the idea of maximum-caliber, to efficiently predict the changes in protein folding behavior upon mutation. Next, we explore the accuracy of different MSM estimators applied to trajectory data obtained by adaptive seeding, in which new rounds of short MD simulations are collected from states of interest, and propose a simple method to build accurate models by population re-weighting of the transition count matrix. Finally, we explore ways to reconcile simulated ensembles with Hydrogen/Deuterium exchange (HDX) protection measurements, by constructing multi-ensemble Markov State Models (MEMMs) from biased MD simulations, and reconciling these predictions against the experimental data using the BICePs (Bayesian Inference of Conformational Populations) algorithm. We apply this approach to model the native-state conformational ensemble of apomyoglobin at neutral pH. / Chemistry

The typical research of Alzheimer's disease includes a series of cognitive states. Multi-state models are often used to describe the history of disease evolvement. Competing risks models are a sub-category of multi-state models with one starting state and several absorbing states. Analyses for competing risks data in medical papers frequently assume independent risks and evaluate covariate effects on these events by modeling distinct proportional hazards regression models for each event. Jeong and Fine (2007) proposed a parametric proportional sub-distribution hazard (SH) model for cumulative incidence functions (CIF) without assumptions about the dependence among the risks. We modified their model to assure that the sum of the underlying CIFs never exceeds one, by assuming a proportional SH model for dementia only in the Nun study. To accommodate left censored data, we computed non-parametric MLE of CIF based on Expectation-Maximization algorithm. Our proposed parametric model was applied to the Nun Study to investigate the effect of genetics and education on the occurrence of dementia. After including left censored dementia subjects, the incidence rate of dementia becomes larger than that of death for age < 90, education becomes significant factor for incidence of dementia and standard errors for estimates are smaller. Multi-state Markov model is often used to analyze the evolution of cognitive states by assuming time independent transition intensities. We consider both constant and duration time dependent transition intensities in BRAiNS data, leading to a mixture of Markov and semi-Markov processes. The joint probability of observing a sequence of same state until transition in a semi-Markov process was expressed as a product of the overall transition probability and survival probability, which were simultaneously modeled. Such modeling leads to different interpretations in BRAiNS study, i.e., family history, APOE4, and sex by head injury interaction are significant factors for transition intensities in traditional Markov model. While in our semi-Markov model, these factors are significant in predicting the overall transition probabilities, but none of these factors are significant for duration time distribution.

CALPHAD (CALculation of PHAse Diagrams) denotes the methodology used to assess thermodynamic data based on experiments as well as on first principles calculations. Essential for this method is the coupling of phase diagram and thermodynamic properties. It has been widely and successfully applied for decades in the field of materials science and engineering. Nevertheless, some shortcomings of the existing thermodynamic databases call for updated descriptions with improved thermodynamic modeling from unary, binary to ternary and higher-order systems. This thesis attempts to pioneer the development of a new generation of CALPHAD databases taking C-Co-Cr alloys with subsystems, unaries and binaries, as example. The present modeling and assessment work not only validate the new models applied in the development of the next, the 3rd, generation database, but also result in improved descriptions in a wider temperature range.In this 3rd generation database, thermodynamic descriptions are valid from 0 K up to high temperatures above liquidus. The Einstein model, rather than the polynomial basis functions used in the previous 2nd generation database, is applied to model the harmonic lattice vibration contribution to the heat capacity of condensed phases at low temperatures. In addition, terms describing the electronic excitations and anharmonic lattice vibrations, as well as the magnetic contribution, are added. A generalized two-state model is employed for the liquid phase to describe the gradual transition from the liquid to amorphous state. A revised magnetic model is adopted accounting for both the ferromagnetic and anti-ferromagnetic states explicitly. A newly suggested method to avoid violating the 3rd law of thermodynamics is adopted for e.g. stoichiometric phases. However, there is still some concern as Nernst’s heat theorem which states that 𝑑𝐶𝑃/𝑑𝑇 is zero at 0 K is not obeyed. All solution phases are modelled within the framework of the compound energy formalism (CEF).The task of the thesis is to construct an updated self-consistent thermodynamic description of the C-Co-Cr system for the third generation CALPHAD databases. The improvement is significant from a modeling point of view when compared to the second generation database. A good agreement between the calculated thermodynamic properties and the experimental data is achieved. The reliability of the extrapolations of unary and binary systems into higher order systems is demonstrated. / <p>QC 20170529</p>

<p>The overall aim of this thesis is to compare different methods for calculation of Core-Level shifts in metallic alloys. The methods compared are the Initial State model, the Complete screening and the Transition state model. Core-level shifts can give information of chemical bonding and about the electronic structure in solids.</p><p>The basic theory used is the so-called Density-Functional-Theory, in conjunction with the Local-Density Approximation and the Coherent-Potential- Approximation. The metallic alloys used are Silver-Palladium, Copper-Palladium, Copper-Gold and Copper-Platinum, all inface-centered-cubic configuration.</p><p>The complete screening- and the transition-state model are found to be in better agreement with experimental results than those calculated with the initial state model. This is mainly due to the fact that the two former models includes final-state effects, whereas the last one do not. The screening parameters within the Coherent-Potential approximation are also investigated. It is found that the Screened-Impurity Model can extend the validity of the Coherent-Potential-Approximation and increase it's accuracy.</p>

Eumelanin ist ein Fluorophor mit teilweise recht ungewöhnlichen spektralen Eigenschaften. Unter anderem konnten in früheren Veröffentlichungen Unterschiede zwischen dem 1- und 2-photonen-angeregtem Fluoreszenzspektrum beobachtet werden, weshalb im nichtlinearen Anregungsfall ein schrittweiser Anregungsprozess vermutet wurde. Um diese und weitere optische Eigenschaften des Eumelanins besser zu verstehen, wurden in der vorliegenden Arbeit vielfältige messmethodische Ansätze der linearen und nichtlinearen Optik an synthetischem Eumelanin in 0,1M NaOH verfolgt. Aus den Ergebnissen wurde ein Modell abgeleitet, welches die beobachteten photonischen Eigenschaften konsistent beschreibt. In diesem kaskadierten Zustandsmodell (Kaskaden-Modell) wird die aufgenommene Photonenenergie schrittweise von Anregungszuständen hoher Übergangsenergien zu Anregungszuständen niedrigerer Übergangsenergien transferiert. Messungen der transienten Absorption ergaben dominante Anteile mit kurzen Lebensdauern im ps-Bereich und ließen damit auf eine hohe Relaxationsgeschwindigkeit entlang der Kaskade schließen. Durch Untersuchung der nichtlinear angeregten Fluoreszenz von verschieden großen Eumelanin-Aggregaten konnte gezeigt werden, dass Unterschiede zwischen dem linear und nichtlinear angeregten Fluoreszenzspektrum nicht nur durch einen schrittweisen Anregungsprozess bei nichtlinearer Anregung sondern auch durch Unterschiede in den Verhältnissen der Quantenausbeuten zwischen kleinen und großen Aggregaten beim Wechsel von linearer zu nichtlinearer Anregung begründet sein können. Durch Bestimmung des Anregungswirkungsquerschnitts und der Anregungspulsdauer-Abhängigkeit der nichtlinear angeregten Fluoreszenz von Eumelanin konnte jedoch ein schrittweiser 2-Photonen-Anregungsprozess über einen Zwischenzustand mit Lebendsdauern im ps-Bereich nachgewiesen werden. / Eumelanin is a fluorophor with some special spectral properties. In earlier publications for instance a difference between 1- and 2-photons-excited fluorescence (OPEF and TPEF) was observed. Therefore in the nonlinear case a stepwise excitation process was supposed. In this thesis extensive linear and nonlinear optical examinations of synthetical Eumelanin / 0,1M NaOH were done in order to reach a better understanding of this and further optical properties. A theoretical model could be formulated that describes the measured fluorescence behaviour consistently. In this so called cascade model the photonic energy of the excited molecule relaxes by a stepwise energy transfer between a multitude of electronic states with continuously decreasing energy. Examination of the nonlinear excited fluorescence of different aggregate sizes showed, that differences between the spectra of linear and nonlinear excited fluorescence can not only be explained by an stepwise excitation process by nonlinear excitation but also by the difference in the relation of quantum yields between smaller and bigger aggregates by the change from linear to nonlinear excitation. In spite of this a stepwise 2-photons-excitation-process via an intermediate state with a lifetime in the picosecond-range had also been proved by determinations of the excitation cross section and the TPEF-intensity dependency on the pulse duration.

The overall aim of this thesis is to compare different methods for calculation of Core-Level shifts in metallic alloys. The methods compared are the Initial State model, the Complete screening and the Transition state model. Core-level shifts can give information of chemical bonding and about the electronic structure in solids. The basic theory used is the so-called Density-Functional-Theory, in conjunction with the Local-Density Approximation and the Coherent-Potential- Approximation. The metallic alloys used are Silver-Palladium, Copper-Palladium, Copper-Gold and Copper-Platinum, all inface-centered-cubic configuration. The complete screening- and the transition-state model are found to be in better agreement with experimental results than those calculated with the initial state model. This is mainly due to the fact that the two former models includes final-state effects, whereas the last one do not. The screening parameters within the Coherent-Potential approximation are also investigated. It is found that the Screened-Impurity Model can extend the validity of the Coherent-Potential-Approximation and increase it's accuracy.

Magistriniame darbe pristatomas Švedijos socialinės politikos modelis, apžvelgiama raida, nustatoma kokiam gerovės valstybės tipui jis priskiriamas. Nagrinėjamos gerovės valstybės formavimosi sąlygos, socialdemokratų politikos ideologijos įtaka socialiniam modeliui ir bedarbių integracijai. Darbe analizuojamas nedarbo paplitimas Švedijoje, rodikliai lyginami su ES. Tiriamos bedarbystės priežastys, nagrinėjamos nedarbo mažinimo priemonės. Prieita išvados, jog Švedijos socialiniam modeliui ir gerovės valstybei pamatus padėjo socialdemokratų politika ir ideologija, kurios vertybės išlaikytos iki šių dienų. Efektyvi socialdemokratų socialinė politika ir aktyvios darbo rinkos priemonės daro didelę įtaką bedarbių integracijos rezultatyvumui ir lemia žemą nedarbo lygį. Magistrinis darbas aktualus visos ES lygiu, nes socialinė politika Švedijoje plačiai išvystyta, o ES dar tik formuojama. Šalis jau pasiekė ES Lisabonos strategijos 2010 m. numatytus užimtumo tikslus. Čia daugelį metų nedarbo lygis mažesnis nei kitose ES šalyse. Švedija – universali valstybė, kurioje derinamas ekonomikos augimas, visiško užimtumo siekimas, nedarbo mažinimas kartu atidžiai rūpinantis gyventojų socialine apsauga. O Lietuvoje, kaip ir kai kuriose ES šalyse, trūksta gerovės valstybės elementų. / The model of social policy in Sweden is introduced in this Master‘s research work. Its evolution, the type of welfare state, conditions of formation are defined. The influence is established for social democratic ideology on the social model and for the integration process of unemployed persons. The prevalence of unemployment in Sweden is analysed, the rates are compared with EU. Unemployment reasons and means of unemployment reduction are considered. It was concluded, that the corner stone of Swedish social model and welfare state is social democratic politics and its values that are still significant and popular nowadays. Its operative social policy and active labour market actions influence the efficiency of unemployed persons’ integration process and determines the low rate of unemployment. This Master’s research work is significant in all EU, as the research field is relevant. Social policy is wide developed in Sweden, whereas it is in the initial stage period in EU. The country already succeeded in EU Lisbon Social Policy Agenda employment goals for 2010. A great while the unemployment rate was less than in other EU member countries. Sweden is the all-purpose state, where the economic growth, the pursuit of complete employment, the reduction of unemployed persons’ number are combined together with thorough citizens’ social security. And there is a lack of elements of welfare state in Lithuania and other EU countries.

Un des points cruciaux en pharmacoépidémiologie concerne le suivi longitudinal de l’exposition médicamenteuse dans les bases de données médico-administratives. Le parcours médicamenteux dans la « vraie » vie étant rarement linéaire, les trajectoires d’exposition médicamenteuses sont particulièrement complexes (notamment pour les médicaments psychoactifs) et difficilement mesurable par les méthodologies habituelles. Dans un premier temps nous avons ainsi étudié les trajectoires d’exposition à la méthadone notamment entre ses 2 formes galéniques à partir du SNIIRAM en région PACA-Corse. Cependant, la complexité des trajectoires d’exposition à la méthadone rendait leur description difficile. Pour modéliser précisément ces processus complexes un modèle multi-états a été construit. Dans ces travaux, nous avons pu identifier dans les bases de données des périodes ou l’exposition médicamenteuse ne peut être observée et pouvant engendrer un biais de classification des patients entre exposés et non exposés. Dans un second temps, nous avons donc étudié l’impact de ces périodes induites par les séjours hospitaliers a été évalué sur l’estimation du niveau d’exposition aux antipsychotiques de patients atteints de démence. En faisant l’hypothèse des « extrêmes » nous avons mis en évidence la variabilité importante induite par ces périodes. Enfin nous les avons modélisées et étudié leur impact sur la relation entre exposition aux benzodiazépines et mortalité toutes causes à 1 an à partir de l’EGB. L’ensemble de ce travail de thèse a permis de développer des méthodologies permettant une analyse plus précise de la dynamique d’exposition médicamenteuse. / In pharmacoepidemiology, one of the main concerns is analysis of drug exposure time in claim databases. In real-life settings, trajectories of patients ‘exposure are complex especially with psychoactive drugs and difficult to measure with traditional methodologies. In a first stage, we have highlighted the methadone exposure paths including between its two dosages formulations. This work underlined the multiplicity of exposure trajectories to methadone and the difficulty of making an accurate description. Consequently, we developed a multi-state model on a large claims database (SNIIR-AM) in order to investigate variations of methadone exposure with time. In this work, we identified the presence of periods or drug exposure cannot be observed in these databases. These periods lead to an unobservable or immeasurable exposure time bias in which patients are misclassified as unexposed. In a second stage, we assessed their impact on the prevalence of long-term antipsychotic use in community-dwelling patients with dementia considering hospitalization periods during which drugs administered are not available within almost all health insurance databases. Under extreme bias hypothesis the prevalence of long-term antipsychotic users almost doubled. Finally, we sought to model unobservable periods due to hospitalization and to apply several methods for addressing this bias and assess their impact on risk estimates. This approach was applied to the study of the association between benzodiazepines and mortality and was performed on the EGB database. In this thesis work we have developed methodologies for a more accurate analysis of the dynamics of drug exposure.

No description available.

This research introduces and applies the concept of digital state models for civil infrastructure condition assessment and structural testing. Digital state models are defined herein as any transient or permanent 3D model of an object (e.g. textured meshes and point clouds) combined with any electromagnetic radiation (e.g., visible light, infrared, X-ray) or other two-dimensional image-like representation. In this study, digital state models are built using visible light and used to document the transient state of a wide variety of structures (ranging from concrete elements to cold-formed steel columns and hot-rolled steel shear-walls) and civil infrastructures (bridges). The accuracy of digital state models was validated in comparison to traditional sensors (e.g., digital caliper, crack microscope, wire potentiometer). Overall, features measured from the 3D point clouds data presented a maximum error of ±0.10 in. (±2.5 mm); and surface features (i.e., crack widths) measured from the texture information in textured polygon meshes had a maximum error of ±0.010 in. (±0.25 mm). Results showed that digital state models have a similar performance between all specimen surface types and between laboratory and field experiments. Also, it is shown that digital state models have great potential for structural assessment by significantly improving data collection, automation, change detection, visualization, and augmented reality, with significant opportunities for commercial development. Algorithms to analyze and extract information from digital state models such as cracks, displacement, and buckling deformation are developed and tested. Finally, the extensive data sets collected in this effort are shared for research development in computer vision-based infrastructure condition assessment, eliminating the major obstacle for advancing in this field, the absence of publicly available data sets. / Ph. D.