On the Combination of Game-Theoretic Learning and Multi Model Adaptive Filters

This paper casts coordination of a team of robots within the framework of game theoretic learning algorithms. In particular a novel variant of fictitious play is proposed, by considering multi-model adaptive filters as a method to estimate other players’ strategies. The proposed algorithm can be used as a coordination mechanism between players when they should take decisions under uncertainty. Each player chooses an action after taking into account the actions of the other players and also the uncertainty. Uncertainty can occur either in terms of noisy observations or various types of other players. In addition, in contrast to other game-theoretic and heuristic algorithms for distributed optimisation, it is not necessary to find the optimal parameters a priori. Various parameter values can be used initially as inputs to different models. Therefore, the resulting decisions will be aggregate results of all the parameter values. Simulations are used to test the performance of the proposed methodology against other game-theoretic learning algorithms.</p

The role of dynamic hydrogen bond networks in protonation coupled dynamics of retinal proteins

Hydrogen bonds (H-bonds) are an essential interaction in membrane proteins. Embedded in complex hydrated lipid bilayers, intramolecular interactions through the means of hydrogen bonding networks are often crucial for the function of the protein. Internal water molecules that occupy stable sites inside the protein, or water molecules that visit transiently from the bulk, can play an important role in shaping local conformational dynamics forming complex networks that bridge regions of the protein via water-mediated hydrogen bonds that can function as wires for the transferring of protons as a part of the protein’s function. For example, the membrane-embedded channelrhodopsins which are found in archaea are proteins that couple light induced isomerization of a retinal chromophore with proton transfer reactions and passive flow of cations through their pore. I contributed to the development of a new algorithm package that features a unique approach to H-bond analyses. I performed analyses of long Molecular Dynamics (MD) trajectories of channelrhodopsin variants embedded in hydrated lipid membranes and large data sets of static structures, to detect and dissect dynamic hydrogen-bond networks. The photocycle of channelrhodopsins begins with absorption and isomerization of the retinal from an all-trans state to a 13-cis state and followed by the deprotonation of the Schiff base. Thus, the retinal is found in the epicenter of the analyses. Through the use of 2-dimensional graphs of the protein H-bond networks I identified protein groups potentially important for the proton transfer activity. Local dynamics are highly affected by point mutations of amino acids important for function. The interior of channelrhodopsin C1C2 hosts extensive networks of protein and H-bonded-water molecules, and a never reported before, network that can bridge transiently the two retinal chromophores in channelrhodopsin dimers. In a recently identified inward proton pump, AntR, I applied centrality measures on MD trajectories of the homology model I generated, to assess the communication of the amino acid residues within the networks. I detected a frequently sampled long water chain that connects the retinal with a candidate proton acceptor, as well as a conserved serine in the vicinity of the retinal chromophore plays a significant role in the connectivity and communication of the H-bond networks upon isomerization. A similar water bridge is sampled in independent simulations of ChR2, where a participant for the proton donor group connects to the 13-cis,15-anti retinal. Proton transfer reactions often take place through certain amino acids, forming patterns. I analyzed H-bond patterns or motifs in large hand-curated datasets of static structures of α-transmembrane helix proteins, organized according to the superfamilies they belong, their function and an alternative classification method. The presence of motifs in TM proteins is tightly related to their families/superfamilies of the host protein and their position along the membrane normal.Wasserstoffbrücken (H-Brücke) sind eine wesentliche Wechselwirkung in Membranproteinen. Eingebettet in komplexe hydratisierte Lipiddoppelschichten sind intramolekulare Wechselwirkungen über Wasserstoffbrückenbindungsnetzwerke oft entscheidend für die Funktion des Proteins. Interne Wassermoleküle, die stabile Stellen im Inneren des Proteins besetzen, oder Wassermoleküle, die vorübergehend aus der Masse zu Besuch kommen, können eine wichtige Rolle bei der Gestaltung der lokalen Konformationsdynamik spielen, indem sie komplexe Netzwerke bilden, die Regionen des Proteins über wasservermittelte Wasserstoffbrückenbindungen überbrücken, die als Drähte für den Transfer von Protonen als Teil der Proteinfunktion funktionieren können. Die in Archaeen vorkommenden, in die Membran eingebetteten Kanalrhodopsine sind beispielsweise Proteine, die die lichtinduzierte Isomerisierung eines Retinachromophors mit Protonentransferreaktionen und dem passiven Fluss von Kationen durch ihre Pore verbinden. Ich habe an der Entwicklung eines neuen Algorithmuspakets mitgewirkt, das einen einzigartigen Ansatz für H-Bindungsanalysen bietet. Ich habe lange Molekulardynamik-Trajektorien von Kanalrhodopsine-Varianten, die in hydratisierte Lipidmembranen eingebettet sind, sowie große Datensätze statischer Strukturen analysiert, um dynamische Wasserstoffbrücken-bindungsnetzwerke zu erkennen und zu zerlegen. Der Photozyklus der Kanalrhodopsine beginnt mit der Absorption und Isomerisierung des Retinals von einem all-trans-Zustand zu einem 13-cis-Zustand, gefolgt von der Deprotonierung der Schiff-Base. Somit steht das Retinal im Mittelpunkt der Analysen. Durch die Verwendung von 2-dimensionalen Graphen der Protein- H-Brückenetzwerke identifizierte ich Proteingruppen, die für die Protonentransferaktivität wichtig sein könnten. Die lokale Dynamik wird durch Punktmutationen der für die Funktion wichtigen Aminosäuren stark beeinflusst. Das Innere von Kanalrhodopsine C1C2 beherbergt ausgedehnte Netzwerke von Protein- und H-Brücke-Wassermolekülen und ein bisher unbekanntes Netzwerk, das die beiden retinalen Chromophore in Kanalrhodopsine-Dimeren vorübergehend überbrücken kann. In einer kürzlich identifizierten Protonenpumpe, AntR, wendete ich Zentralitätsmaße auf MD-Trajektorien des von mir erstellten Homologiemodells an, um die Kommunikation der Aminosäurereste innerhalb der Netzwerke zu bewerten. Ich fand, dass eine häufig gesampelte lange Wasserkette, die das Retinal mit einem Protonenakzeptor verbindet, sowie ein konserviertes Serin in der Nähe des Retinal-Chromophors eine wichtige Rolle bei der Konnektivität und Kommunikation der H-Brückesnetzwerke bei der Isomerisierung spielt. Eine ähnliche Wasserbrücke ist in unabhängigen Simulationen von Kanalrhodopsine-2 zu finden, wo ein Teilnehmer für die Protonendonorgruppe mit dem 13-cis,15-anti-Retinal verbunden ist. Protonenübertragungsreaktionen finden oft über bestimmte Aminosäuren statt und bilden Muster. Ich analysierte H-Brückemuster oder -motive in großen, von Hand kuratierten Datensätzen statischer Strukturen von α-Transmembranhelix-Proteinen, geordnet nach den Superfamilien, zu denen sie gehören, ihrer Funktion und einer alternativen Klassifizierungsmethode. Das Vorhandensein von Motiven in TM-Proteinen steht in engem Zusammenhang mit ihren Familien/Superfamilien des Wirtsproteins und ihrer Position entlang der Membrannormale

What makes for effective and meaningful online parliamentary public engagement?

This research primarily aims to develop evaluation methods to effectively harness citizen input from large unstructured data generated automatically through digital engagement activities. It is an interdisciplinary and collaborative project with the House of Commons which combines social science and data science to analyse the online engagement activities of the UK Parliament. Digital Engagement teams within Parliament have introduced various ways of engaging with the public online including consultations and digital debates. These have been popular since they started in 2015 but attract too many responses for staff to process manually and to get a clear picture of what the public is saying. I use machine learning and text mining approaches to analyse the data gathered by Parliament to summarise and reveal the network of participant interactions so Parliament can have a more informed idea of who is participating within which social/ideological clusters. This shows a public who have a diverse set of views but can be influenced based on the channel and type of engagement they are participating in. As the Members of Parliament are crucial to the engagement process, any way to encourage and facilitate their use of the online engagement is vital. Without input from officials overtly showing that they have listened to and incorporated the public’s opinions into their decisions, the online public engagement efforts from Parliament could be seen as insincere to many of the public. With this in mind, another aim is to explore how public opinion derived through the online engagement activities can be meaningfully incorporated into policy making. This entails working with different teams in Parliament to understand exactly how policy-makers are currently using the outputs of online engagement and how this can be improved. I conduct demonstration tests to test the methods of evaluation developed during the research and find that while these can be applied to digital engagement activities successfully to gain insights from the public, responsibility remains with the institution to ensure internal processes are equipped to make use of the public’s views

Tradition and Innovation in Construction Project Management

This book is a reprint of the Special Issue 'Tradition and Innovation in Construction Project Management' that was published in the journal Buildings

Revisiting the capitalization of public transport accessibility into residential land value: an empirical analysis drawing on Open Science

Background: The delivery and effective operation of public transport is fundamental for a for a transition to low-carbon emission transport systems’. However, many cities face budgetary challenges in providing and operating this type of infrastructure. Land value capture (LVC) instruments, aimed at recovering all or part of the land value uplifts triggered by actions other than the landowner, can alleviate some of this pressure. A key element of LVC lies in the increment in land value associated with a particular public action. Urban economic theory supports this idea and considers accessibility to be a core element for determining residential land value. Although the empirical literature assessing the relationship between land value increments and public transport infrastructure is vast, it often assumes homogeneous benefits and, therefore, overlooks relevant elements of accessibility. Advancements in the accessibility concept in the context of Open Science can ease the relaxation of such assumptions. Methods: This thesis draws on the case of Greater Mexico City between 2009 and 2019. It focuses on the effects of the main public transport network (MPTN) which is organised in seven temporal stages according to its expansion phases. The analysis incorporates location based accessibility measures to employment opportunities in order to assess the benefits of public transport infrastructure. It does so by making extensive use of the open-source software OpenTripPlanner for public transport route modelling (≈ 2.1 billion origin-destination routes). Potential capitalizations are assessed according to the hedonic framework. The property value data includes individual administrative mortgage records collected by the Federal Mortgage Society (≈ 800,000). The hedonic function is estimated using a variety of approaches, i.e. linear models, nonlinear models, multilevel models, and spatial multilevel models. These are estimated by the maximum likelihood and Bayesian methods. The study also examines possible spatial aggregation bias using alternative spatial aggregation schemes according to the modifiable areal unit problem (MAUP) literature. Results: The accessibility models across the various temporal stages evidence the spatial heterogeneity shaped by the MPTN in combination with land use and the individual perception of residents. This highlights the need to transition from measures that focus on the characteristics of transport infrastructure to comprehensive accessibility measures which reflect such heterogeneity. The estimated hedonic function suggests a robust, positive, and significant relationship between MPTN accessibility and residential land value in all the modelling frameworks in the presence of a variety of controls. The residential land value increases between 3.6% and 5.7% for one additional standard deviation in MPTN accessibility to employment in the final set of models. The total willingness to pay (TWTP) is considerable, ranging from 0.7 to 1.5 times the equivalent of the capital costs of the bus rapid transit Line-7 of the Metrobús system. A sensitivity analysis shows that the hedonic model estimation is sensitive to the MAUP. In addition, the use of a post code zoning scheme produces the closest results compared to the smallest spatial analytical scheme (0.5 km hexagonal grid). Conclusion: The present thesis advances the discussion on the capitalization of public transport on residential land value by adopting recent contributions from the Open Science framework. Empirically, it fills a knowledge gap given the lack of literature around this topic in this area of study. In terms of policy, the findings support LVC as a mechanism of considerable potential. Regarding fee-based LVC instruments, there are fairness issues in relation to the distribution of charges or exactions to households that could be addressed using location based measures. Furthermore, the approach developed for this analysis serves as valuable guidance for identifying sites with large potential for the implementation of development based instruments, for instance land readjustments or the sale/lease of additional development rights