Fluorescence spectroscopy and imaging have a very broad spectrum of applicationswithin the life sciences, in particular for detection and characterization ofbiomolecular dynamics and interactions in different environments. This thesis comprisesprojects that strive to further expand the information content extracted fromthe detected fluorescence, leading to sensitive readout parameters for studies ofbiomolecular dynamics and interactions. Two major strategies are presented toachieve this aim. The first strategy is based on the expansion of the availablereadout parameters beyond the "traditional" fluorescence parameters: intensity,wavelength, polarization and fluorescence lifetime. The additional parameters arebased on blinking properties of fluorescent labels. In particular on transitions betweensinglet and triplet states, and transitions between the trans- and cis-isomersof fluorophores. Two publications in the thesis are based on this strategy (paperI and IV). The second strategy is based on the utilization of fluorescence intensityfluctuations in order to detect the oligomerization mechanisms of fluorescentlylabeled peptides and proteins. This strategy combines the intensity fluctuationanalysis and the readout of distance dependent energy transfer between fluorescentmolecules together with the correlation analysis of fluorescence from two labeledproteins emitting at different wavelengths. Another two publications presented inthe thesis are based on the second comprehensive strategy (papers II and III).The work presented in this thesis shows that the blinking kinetics of fluorescentlabels contain significant information that can be exploited by a combination of fluctuationsanalysis with distance dependent excitation energy transfer between thefluorescent molecules, or by analysis of fluorescence covariance between moleculesthat emit at different wavelengths. These fluorescence-based methods have a significantpotential for molecular interaction studies in the biomedical field. / <p>QC 20160527</p>

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En els sistemes multiagent els models de confiança són una eina important perquè les interaccions entre agents siguin efectives. Ara bé, la confiança és una noció inherentment subjectiva, i per això els agents necessiten informació addicional per poder comunicar les avaluacions de confiança. Aquesta tesi doctoral se centra en dos mètodes per comunicar la confiança: l'alineament de la confiança i l'adaptació de la confiança. En el primer mètode, el problema de la comunicació de la confiança es modela com un problema d'alineament. Mostrem que les solucions actuals basades en ontologies comunes o en l'alineament d'ontologies generen problemes addicionals. Per això proposem com a alternativa alinear la confiança, basant-nos en les interaccions que dos agents comparteixen per tal d'aprendre un alineament. Fent servir el marc matemàtic de la teoria de canals formalitzem com les avaluacions subjectives de dos agents sobre la confiança es relacionen a través de les interaccions que fonamenten aquestes avaluacions. Com que els agents no poden accedir a les avaluacions de confiança dels altres, cal establir una comunicació. Especifiquem la rellevància i la consistència com a propietats necessàries per a aquesta comunicació. L'agent receptor de la confiança comunicada pot generalitzar els missatges fent servir la θ-subsumció, el que duu a un model predictiu que permet a un agent traduir futures comunicacions rebudes del mateix agent emissor. Mostrem aquest procés d'alineament a la pràctica fent servir TILDE, un algorisme de regressió de primer ordre, per tal d'aprendre un alineament. També il·lustrem la seva aplicació en un escenari d'exemple. De forma empírica demostrem: (1) que la dificultat d'aprendre un alineament depèn de la complexitat relativa dels diversos models de confiança; (2) que el nostre mètode millora altres mètodes existents d'alineament de la confiança; i (3) que el nostre mètode funciona bé sota condicions d'engany. El segon mètode per comunicar la confiança es basa en permetre que els agents raonin sobre llurs models de confiança i que personalitzin les comunicacions per adaptar-se millor a les necessitats d'un altre agent. Els mètodes actuals no permeten la suficient introspecció o adaptació del models de confiança. Per això presentem AdaptTrust, un mètode per incorporar un model computacional de confiança a l'arquitectura cognitiva d'un agent. En AdapTrust les creences i els objectius d'un agent influencien les prioritats entre aquells factors que són importants per a la computació de la confiança. Aquests al seu torn defineixen els valors dels paràmetres del model de confiança, i així l'agent pot dur a terme canvis en el seu model computacional de confiança a base de raonar sobre les seves creences i objectius. D'aquesta manera és capaç de modificar proactivament el seu model i produir avaluacions de confiança que millor s'adaptin a les seves necessitats actuals. Donem una formalització declarativa d'aquest sistema integrant-lo en una representació ⎯ fonamentada en un sistema multicontext ⎯ d'una arquitectura d'agent basada en creences, desitjos i intencions (BDI). També mostrem com amb el nostre marc es poden incorporar tres dels actuals models de confiança en el sistema de raonament d'un agent. Finalment fem servir AdapTrust en un marc d'argumentació que permet als agents construir una justificació per a llurs avaluacions de confiança. A través d'aquest marc els agents justifiquen les seves avaluacions segons unes prioritats entre factors, les quals al seu torn són justificades per les creences i objectius dels agents. Aquestes justificacions es poden comunicar a altres agents a través d'un diàleg formal. Així un agent, a base d'argumentar i raonar sobre les prioritats d'un altre agent, pot adaptar el seu model de confiança per oferir-li una recomanació de confiança personalitzada. Aquest sistema l'hem comprovat empíricament i hem vist que millora els actuals sistemes que permeten argumentar sobre avaluacions de confiança. / In open multi-agent systems, trust models are an important tool for agents to achieve effective interactions; however, trust is an inherently subjective concept, and thus for the agents to communicate about trust meaningfully, additional information is required. This thesis focuses on Trust Alignment and Trust Adaptation, two approaches for communicating about trust. The first approach is to model the problem of communicating trust as a problem of alignment. We show that currently proposed solutions, such as common ontologies or ontology alignment methods, lead to additional problems, and propose trust alignment as an alternative. We propose to use the interactions that two agents share as a basis for learning an alignment. We model this using the mathematical framework of Channel Theory, which allows us to formalise how two agents' subjective trust evaluations are related through the interactions that support them. Because the agents do not have access to each other's trust evaluations, they must communicate; we specify relevance and consistency, two necessary properties for this communication. The receiver of the communicated trust evaluations can generalise the messages using θ-subsumption, leading to a predictive model that allows an agent to translate future communications from the same sender. We demonstrate this alignment process in practice, using TILDE, a first-order regression algorithm, to learn an alignment and demonstrate its functioning in an example scenario. We find empirically that: (1) the difficulty of learning an alignment depends on the relative complexity of different trust models; (2) our method outperforms other methods for trust alignment; and (3) our alignment method deals well with deception. The second approach to communicating about trust is to allow agents to reason about their trust model and personalise communications to better suit the other agent's needs. Contemporary models do not allow for enough introspection into ⎯ or adaptation of ⎯ the trust model, so we present AdapTrust, a method for incorporating a computational trust model into the cognitive architecture of the agent. In AdapTrust, the agent's beliefs and goals influence the priorities between factors that are important to the trust calculation. These, in turn, define the values for parameters of the trust model, and the agent can effect changes in its computational trust model, by reasoning about its beliefs and goals. This way it can proactively change its model to produce trust evaluations that are better suited to its current needs. We give a declarative formalisation of this system by integrating it into a multi-context system representation of a beliefs-desires-intentions (BDI) agent architecture. We show that three contemporary trust models can be incorporated into an agent's reasoning system using our framework. Subsequently, we use AdapTrust in an argumentation framework that allows agents to create a justification for their trust evaluations. Agents justify their evaluations in terms of priorities between factors, which in turn are justified by their beliefs and goals. These justifications can be communicated to other agents in a formal dialogue, and by arguing and reasoning about other agents' priorities, goals and beliefs, the agent may adapt its trust model to provide a personalised trust recommendation for another agent. We test this system empirically and see that it performs better than the current state-of-the-art system for arguing about trust evaluations.

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Sverige står idag inför utmaningar för att minska koldioxidutsläppen inom transportsektorn. Bilen har länge varit en planeringsnorm i Sverige. Till följd av satsningar för hållbar utveckling har en omställning till mer hållbara transporter som kollektivtrafik blivit aktuell. Örebro och Västerås är två medelstora kommuner som har uttryckt ambitioner om att utveckla den lokala kollektivtrafiken. Respektive kommun har ett externt handelsområde som är viktigt både för den kommunala och regionala handeln. Arbetet syftar till att analysera planering och effektivisering av kollektivtrafik till och från externa handelsområden. I studien har kvalitativa intervjuer med planerare och politiker, samt dokumentanalys av olika plandokument genomförts. Vidare har planeringshandboken Kol-TRAST och teorier om Stigberoende använts som verktyg i analysen. Resultatet visar på att externa handelsområden ofta bortprioriteras i planering för kollektivtrafik, dels på grund av stigberoende, dels på grund av bristande politisk förankring. Trots goda ambitioner i plandokument finns det ofta en brist på praktiskt initiativtagande inom planeringen. / Today Sweden is facing challenges in reducing carbon dioxide emissions in the transport sector. Planning for car traffic has long been a norm in Sweden. As a result of initiatives for sustainable development, a shift to more sustainable transport such as public transport has become necessary. Örebro and Västerås are two medium-sized Swedish municipalities that have expressed ambitions to develop public transport on a local level. Each municipality has an out-of-town shopping area that is considered important for both municipal and regional trade. This study is based on qualitative interviews, as well as document analysis. The planning manual Kol-TRAST and theories of path dependency have been used to analyze the results. The results show that out-of-town shopping areas often are de-prioritized in planning for public transport, partly due to path dependence and partly due to a lack of political support. Despite ambitious planning documents, there is often a lack of practical initiative in planning.

In a society where everything must be within the vicinity and accessible, people face challenges like climate, segregation and inequality. All people have the right to services such as education, care, work and housing without being prevented by unsustainable urban planning. Sustainable urban planning can define several things, but something all definitions have in common is that they use strategic plans. One such well spoken about is the "15 minute city" which was introduced in 2016 by the urbanist and professor Carlos Moreno. The concept is about an accessible city, in terms of services, education, care, work and more, for residents within a 15 minute walk or bike ride. Attempts to apply the 15 minute city can be seen in several cities around the world and partially in Stockholm, Sweden. An example is in Södertälje, a suburb in Stockholm county, which is characterized by the car centric city. The swedish policy “ Trafik för en attraktiv stad” (TRAST) helps sektion with urban planning and sustainability with focus on traffic. Because of these guidelines and Södertäljes oversight plan over their whole urban area it would be of interest to investigate how well the 15 minute city can be applied in Södertälje and its relation to the district of Ronna. The purpose of this study is to examine the potential Södertälje has in becoming a 15 minute city, in regards to the swedish policy document TRAST. In addition, studying whether the strategic plan can complement Södertälje's oversight plan of the entire city. The method that was applied consisted of literature study and case study where literature was gathered, for example, via search engines like Web of Science and Diva Portal. The case study consisted of two site visits, one earlier and one later in the day. The result and the analysis indicate that several aspects in Södertäljes oversight planning of their area and TRAST match that of the 15 minute city. Introducing this type of planning in the city requires, for example, that several barriers or the carsdomination in the urban area be remedied or reduced, which can provide opportunities for pedestrians and cyclists. The conclusions drawn from the results are that the introduction of the 15-minute city concept in the urban area, Södertälje, is possible. At last at recommendation to continuation of the study is a case study would consist of a city that has recently applied the 15 minute city and compare the effects of this more concretely. / I ett samhälle där allting ska vara nära och tillgängligt möts människor av utmaningar om klimatet, segregation och ojämlikhet. Alla människor har rätten till funktioner som utbildning, vård, arbete och boende utan att förhindras av en dålig samhällsplanering. Hållbar samhällsplanering kan innebära flera saker men något alla definitioner har gemensamt är att de tillämpar planstrategier. En sådan är “15 minutersstaden” som introducerades år 2016 av urbanisten och professorn Carlos Moreno. Idén handlar om en tillgänglig stad, vad gäller just funktionerna, utbildning, vård, arbete och mer, för invånarna inom en kvarts promenad eller cykeltur. Försök att tillämpa 15 minutersstaden finns i flera städer runtom i världen och i Sverige kan man hitta det delvis i Stockholm. Ett exempel är i Södertälje tätort, i Stockholms län, som präglas av bilsamhället. Policyn “Trafik för en attraktiv stad” (TRAST), hjälper sektorer inom samhällsplaneringen att samarbeta för ett hållbart planerande med fokus på trafiken. med hjälp av dess riktlinjer och översiktsplanen i Södertälje skulle vara av intresse att undersöka hur väl 15 minutersstaden går att applicera, och detta i förhållande till en av dess stadsdelar Ronna.  Syftet med detta arbete är att undersöka potentialen Södertälje har i att bli en 15 minutersstad med hänsyn till policyn TRAST. Dessutom studerades likheter och skillnader mellan Södertäljes översiktsplan och 15 minutersstaden vad gäller planeringen. Metoden som tillämpades var kvalitativ och bestod av en litteraturstudie och en fallstudie. Fallstudien omfattade två platsbesök i stadsdelen Ronna, en tidigare och en senare på dygnet.  Resultatet och analysen tyder på att flera aspekter i översiktsplanen och TRAST:en stämmer överens med 15 minutersstaden. Det går dessutom att införa denna planeringstyp i Södertälje men kräver dock till exempel att flera barriärer åtgärdas, såväl bildominansen i tätorten. Detta för att ge möjlighet åt gående och cyklister att röra sig i staden. Slutsatserna som dras utifrån resultaten är att införandet av konceptet 15 minutersstaden i tätorten Södertälje är möjlig. Som en sista slutsats i arbetet finns framtid forskning vilket berör att studera en stad som nyligen applicerat 15 minutersstaden och jämföra effekterna av detta mer konkret.

Many human diseases including cancer have been associated with altered cellular metabolism and a changed oxygen consumption in cells. Fluorophores are sensitive to their local environment due to their long life times in transient dark states. A recent study successfully utilized this sensitivity to image differences in oxygen concentrations in cells using transient state (TRAST) microscopy together with fluorescent labels [1]. A natural continuation of this study is to investigate the possibilities of using this method with natural fluorophores already present in cells and thereby avoid articial labeling. Flavin adenine dinucleotide (FAD) is an auto fluorescent coenzyme that is naturally present in cells and involved in cellular metabolism. This project is an exploratory pilot study for cellular measurements with the aim to investigate if FAD can be used to probe oxygen concentrations in aqueous solution using transient state monitoring and fluorescence correlation spectroscopy (FCS). This thesis includes the results from FCS and TRAST experiments on FAD in aqueous solutions with different oxygen concentrations as well as different ascorbic acid concentrations. The performed experiments showed that FAD monitored with TRAST is sensitive to differences in oxygen concentrations for the aqueous solutions used in this study.

The thesis has been written on the basis of main architectural concepts and their application in real life within a historical context investigation. Main architectural concepts are represented in a harmony of architectural composition that deals with relations among form, structure and space in the unique art work. Genius loci play very important role in the architectural creation - it represents a special and extra-ordinary urban locality and its architectural value in the historical, geographical and cultural context. The origin of Ostravice village within the historical frame concept of Moravia domain is the topic of this thesis. Other historical documents gave information about Bruneswerde as the Brno Castle. That means Brno Castle had to be founded not in Brno (as it has been consid-ered for many years) but it was located in Beskydy at Ostravice. The sacred city – Civitas Dei had been located in Bruneswerde region in early ages as the centre of European culture, education and spiritual life. Civitas Dei – divine Jerusalem in the transcription of St. Augustine's book De civitate Dei – is not only glorification of God and religious fantasy. It is also one of significant clues for recognition of historical architecture. The depiction of unknown settlement from the book of unde-fined origin is a superb testimony about extinct architectural works. They are legible from cadastral maps. Brno Castle - residence of nobility and power served shelter to St. Vojtěch, St. Prokop, St. Václav and St. Ludmila as it is obvious for the mentioned picture. Three major temples, three com-position axes symbolized by three towers on coins are in analogical relation to Brno triangle of four saints - the Saint family of Brno temples. Powerful ambitions of Brno City principals and clergy are inscribed into the urban structure in the way of composition relations which are legible to them who devoted themselves to the mystery of harmony. The absence of historical continuity affects personal attitudes and also identity of the whole community. The architecture truly reflects the past state of polis and it is eloquent even after its death. The architectural composition relations influence the natural environment for long time, longer than the architectural work existence. The geometric order of Renaissance Brno existence has not been in attention of architects so far. The features were discovered in characteristic paintings by Albrecht Durer. They are evidently secret works of the genius. A meaningful collaborator and follower in the extensive project was also his friend Jan Čert from Brno and lately from Vienna. His noble genealogy played a significant role in history of Silesia and Moravia for centuries. It is tendency to consider him as Austrian or even German architect. It is because of the fact that the genealogy tree of his noble family had roots in Moravia. It is supposed that Durer with Jan Čert´s support created the extraordinarily monumental architectural and urban works in Brno. A remarkable consensus in the urban composition of two squares and transition of traditional urban structure of Ostravice Civitas Dei into the modern Brno is also confirmed due to the identification of noble creators and owners, who were at the foundation, transformation and extinction of elements of the Moravian urban structure.