Dissertations / Theses on the topic '029902 Complex Physical Systems'

Properly representing the principle physical interactions of complex biological systems is paramount for building powerful, yet simple models. As an in depth look into different biological systems at different scales, multiple models are presented. At the molecular scale, an analytical solution to the (linearized) Poisson-Boltzmann equation for the electrostatic potential of any size biomolecule is derived using spherical geometry. The solution is tested both on an ideal sphere relative to an exact solution and on a multitude of biomolecules relative to a numerical solution. In all cases, the bulk of the error is within thermal noise. The computational power of the solution is demonstrated by finding the electrostatic potential at the surface of a viral capsid that is nearly half a million atoms in size. Next, a model of the nucleosome using simplified geometry is presented. This system is a complex of protein and DNA and acts as the first level of DNA compaction inside the nucleus of eukaryotes. The analytical model reveals a mechanism for controlling the stability of the nucleosome via changes to the total charge of the protein globular core. The analytical model is verified by a computational study on the stability change when the charge of individual residues is altered. Finally, a multiple model approach is taken to study bacteria that are capable of different responses depending on the size of their surrounding colony. The first model is capable of determining how the system propagates the information about the colony size to those specific genes that control the concentration of a master regulatory protein. A second model is used to analyze the direct RNA interference mechanism the cell employs to tune the available gene transcripts of the master regulatory protein, i.e. small RNA - messenger RNA regulation. This model provides a possible explanation for puzzling experimentally measured phenotypic responses.
Ph. D.

Over the past twenty years molecules capable of templating their own synthesis, so called self–replicating molecules have gained prominence in the literature. We show herein that mixing the reagents for replicating molecules can produce a network of self–replicators which coexist and that the networks can be instructed by the addition of preformed template upon initiation of the reaction. Whilst self–replicating molecules offer the simplest form of replication, nature has evolved to utilise not minimal self–replication but reciprocal replication where one strand templates the formation of not an identical copy of itself but a reciprocal strand. Efforts thus far at producing a synthetic reciprocal replicating system are discussed and an alternative strategy to address the problems encountered is proposed and successfully implemented. The kinetic behaviour of a self–replicating reaction bears two distinctive time periods. Upon initiation, the reaction proceeds slowly as no template exists to catalyse the reaction. Upon production of the template, the reaction proceeds more rapidly via template direction. During this slow reaction period, the system is prone to mistakes as the reaction is slow and unselective. The creation of an [A•B] binary complex through non–covalent recognition of reagents allows for the reaction to proceed at an accelerated rate upon initiation however products of such a reaction are usually catalytically inert and do not promote further template directed reaction. A strategy to combine the desired behaviour of an [A•B] binary complex with the further template directed autocatalytic self–replicating reaction is described and implemented. Supramolecular polymers consist of repeating monomers which are held together by non–covalent interactions. The strong association of a self–replicating template dimer is comparable to that of supramolecular polymers reported thus far in the literature which are produced by cumbersome standard linear synthetic procedures. Herein the application of self–replication to the field of supramolecular polymer synthesis is discussed. As the autocatalytic reaction to produce the template monomers occurs under the same conditions as required to allow polymerisation to proceed, the polymer is able to spontaneously form in situ by self–replicating supramolecular polymerisation.

Management of lake-catchment systems is a long-term challenge for prevention of hazard risk and further sustainable development. Climate change and human activities are two important factors that concurrently affect the hydrology and sediment regimes within systems. Many soil conservation and sediment control techniques are known and widely studied based on experimental field plots. Catchments are complex dynamic systems. Spatially-distributed and process-based models provide powerful tools to simulate the complex behaviour of hydro-geomorphological processes in response to climate change and human impact on fluvial systems. Accordingly, this study addresses the principles, testing and application of an established cellular automata landscape evolution model (CAESAR) to study the dynamic non-linear behaviour of complex systems, past and present interactions among landscape elements and environmental controls, and potential future impacts. The results from a series of simulations of different systems (simple catchment, Old Alresford Pond, UK and Holzmaar, Germany) over different timescales (50 years to 5000 years), demonstrate a rapid catchment response to climatic drivers. This is characterised by variations, particularly peaks of modelled sediment discharge controlled by the magnitude and frequency of floods and droughts happened in a single year or a period of time. The effect of vegetation cover also plays an important role in accelerating the delivery of sediment or protecting the catchment from soil erosion. This erosional response is validated by comparing modelled sediment discharge and system evolution to magnetic susceptibility and accumulation rates of lake sediments, as well as documented data. The non-linear properties of complex systems, such as thresholds, feedback mechanisms and self-organised capability, are shown to exist in these simulations. This study also provides the probabilistic results of potential erosion risks in terms of future natural and human pressures. The modelling application permits a better understanding of the relationship between environmental forcings and complex dynamic system evolution processes. In addition, it allows investigations of the extent to which past and present human-environmental interactions generate subsequent impacts for the purpose of effective landscape management.

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, February 2005.
Includes bibliographical references (p. 63).
Current cost estimation practices rely on statistically relating physical parameters of a system to historical cost data. Unfortunately, this method is unable to effectively communicate the increasing complexity of system design to cost data. Additionally, current cost estimation techniques have had a historical inability to produce credible and explainable results. It is often considered to be a "black art" with the recurring question: "Where did that number come from?" This thesis systematically links design and cost information together, and demonstrates the utility of that link by estimating the impact of functional and physical design changes on the life-cycle cost and determining key cost drivers. The ability to quickly estimate the cost impact of design changes is important for decision makers and serves as a medium of communication between customers and developers. Credible estimation is gained by intimately linking the axiomatic design framework to the already existing costing unit (or component) domain and providing design traceability. Development cost is predicted by determining the functional requirements (FRs) affected by a change in customer needs or constraints, then by determining the propagation of that change from FRs to design parameters (DPs) to costing units. The list of affected components and the magnitude of the impact on each component is found and then used to determine through a parallel iteration process model how much development labor will be necessary to implement those changes. The labor is directly related to development costs. A formal method to designing operations using axiomatic design is presented in this thesis. Operations exist due to the time-variant combinatorial complexity of FRs.
(cont.) Operations implement reinitialization procedures in order to maximize the probability of success of FRs. This provides the way that axiomatic design can derive operations and the related cost parameters. This information could then be plugged into the cost impact model of a design change to determine the list-of affected operations. A new method of estimating the change in cost parameters due to a design change will be the focus of future research. Two main forms of key cost drivers are identified: the most expensive FRs and design iteration. A method of mapping estimates from the costing unit domain to the FR-DP map is suggested in order to cost out FRs. Design iteration as a key cost driver can be seen from two points of view. Axiomatic design identifies small design ranges, coupling and imaginary complexity as contributors to cost. Design structure matrices identify the most iterative set of tasks in the development process and offer procedures to reduce or speed up the iteration.
by Peter Nicholas Jeziorek.
S.M.

Plus de 50% de la population mondiale vit dans des zones urbaines et cette proportion devrait augmenter dans les prochaines décennies. Comprendre ce qui régit l'évolution des systèmes urbains est donc devenu d'une importance fondamentale. Ce renouveau d'intérêt combiné avec la disponibilité de données à grande échelle, permet d'entrevoir l'avènement d'une nouvelle science des villes, interdisciplinaire et basée sur les données.Des études récentes ont montré l'existence de régularités statistiques et de lois d'échelle pour plusieurs indicateurs socio-économiques, tels que la consommation d'essence, la distance moyenne parcourue quotidiennement, le cout des infrastructures, etc. Malgré plusieurs tentatives récentes, la compréhension théorique de ces résultats observés empiriquement demeure très partielle.Le but de cette thèse est d'obtenir une modélisation simplifiée, hors-équilibre de la croissance urbaine, en s'appuyant sur un petit nombre de mécanismesimportants et qui fournit des prédictions quantitatives en accord avec lesdonnées empiriques. Pour cela, nous nous inspirerons des études en géographiequantitative et en économie spatiale et nous revisiterons certains de ces anciens modèles avec une nouvelle approche intégrant les outils et concepts de la physique
More than 50 % of the world population lives in urban areas and this proportion is expected to increase in the coming decades. Understanding what governs the evolution of urban systems has thus become of paramount importance.This renewed interest combined with the availability of large-scale data, allows a glimpse into the dawn of a new science of cities, interdisciplinary and based on data.Recent studies have shown the existence of statistical regularities and scaling laws for several socio-economic indicators such as fuel consumption, average commuting distance, cost of infrastructure, etc., and despite several recent attempts, the theoretical understanding of these results empirically observed remains very partial. The purpose of this thesis is to obtain a simplified, out of equilibrium model of urban growth, based on a small number of important mechanisms and which provides quantitative predictions in agreement with empirical data. For this, we will draw on studies in quantitative geography and spatial economy and we will revisit some of these old models with a new approach that integrates the tools and concepts of physics

Doctor of Philosophy
Computing and Information Sciences
Scott A. DeLoach
As sensor prices drop and computing devices continue to become more compact and powerful, computing capabilities are being embedded throughout our physical environment. Connecting these devices in cyber-physical systems (CPS) enables applications with significant societal impact and economic benefit. However, engineering CPS poses modeling, architecture, and engineering challenges and, to fully realize the desired benefits, many outstanding challenges must be addressed. For the cyber parts of CPS, two decades of work in the design of autonomous agents and multiagent systems (MAS) offers design principles for distributed intelligent systems and formalizations for agent-oriented software engineering (AOSE). MAS foundations offer a natural fit for enabling distributed interacting devices. In some cases, complex control structures such as holarchies can be advantageous. These can motivate complex organizational strategies when implementing such systems with a MAS, and some designs may require agents to act in multiple groups simultaneously. Such agents must be able to manage their multiple associations and assignments in a consistent and unambiguous way. This thesis shows how designing agents as systems of intelligent subagents offers a reusable and practical approach to designing complex systems. It presents a set of flexible, reusable components developed for OBAA++, an organization-based architecture for single-group MAS, and shows how these components were used to develop the Adaptive Architecture for Systems of Intelligent Systems (AASIS) to enable multigroup agents suitable for complex, multigroup MAS. This work illustrates the reusability and flexibility of the approach by using AASIS to simulate a CPS for an intelligent power distribution system (IPDS) operating two multigroup MAS concurrently: one providing continuous voltage control and a second conducting discrete power auctions near sources of distributed generation.

This thesis is concerned with creating and evaluating interactive art systems that facilitate emergent participant experiences. For the purposes of this research, interactive art is the computer based arts involving physical participation from the audience, while emergence is when a new form or concept appears that was not directly implied by the context from which it arose. This emergent ‘whole’ is more than a simple sum of its parts. The research aims to develop understanding of the nature of emergent experiences that might arise during participant interaction with interactive art systems. It also aims to understand the design issues surrounding the creation of these systems. The approach used is Practice-based, integrating practice, evaluation and theoretical research. Practice used methods from Reflection-in-action and Iterative design to create two interactive art systems: Glass Pond and +-now. Creation of +-now resulted in a novel method for instantiating emergent shapes. Both art works were also evaluated in exploratory studies. In addition, a main study with 30 participants was conducted on participant interaction with +-now. These sessions were video recorded and participants were interviewed about their experience. Recordings were transcribed and analysed using Grounded theory methods. Emergent participant experiences were identified and classified using a taxonomy of emergence in interactive art. This taxonomy draws on theoretical research. The outcomes of this Practice-based research are summarised as follows. Two interactive art systems, where the second work clearly facilitates emergent interaction, were created. Their creation involved the development of a novel method for instantiating emergent shapes and it informed aesthetic and design issues surrounding interactive art systems for emergence. A taxonomy of emergence in interactive art was also created. Other outcomes are the evaluation findings about participant experiences, including different types of emergence experienced and the coding schemes produced during data analysis.

This work discusses applications of computational simulations to a wide variety of chemical systems, to investigate intermolecular interactions to develop force field parameters and gain new insights into chemical reactivity and structure stability. First, we cover the characterization of hydrogen-bonding interactions in pyrazine tetracarboxamide complexes employing quantum topological analyses. Second we describe the use of quantum mechanical energy decomposition analysis (EDA) and non-covalent interactions (NCIs) analysis to investigate hydrogen-bonding and intermolecular interactions in a series of representative 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([bmim][Tf2N]) ion pairs extracted from classical equilibrium and non-equilibrium molecular dynamics simulations. Thirdly, we describe the use of multipolar/polarizable AMOEBA force field to study the extraction of benzene from a gasoline model employing 1,3-dimethylimidazolium tetrafluorobrorate, [DMIM][BF4], and ethylmethylimidazolium tetrafluorobrorate, [EMIM][BF4]. Fourthly, we cover the recent improvements and new capabilities of the QM/MM code "LICHEM". Finally, we describe the use of polarizable ab initio QM/MM calculations and study the reaction mechanism of N-tert-butyloxycarbonylation of aniline in [EMIm][BF4], and ground state destabilization in uracil DNA glycosylase (UDG).

In this work 23Na MAS NMR was validated as a successful quantitative method for studies of exchanging sodium in bentonites useful, in particular, for studies of ion-exchange kinetics. Na-enriched bentonites equilibrated in a re-circulated process water at iron-oxide pelletizing plants may acquire properties of Ca-bentonites after already 20 minutes of the equilibration time, since >50 % of sodium ions will be exchanged by calcium ions during first minutes of bentonite placed in contact with the process water. It was shown that all sodium activated bentonites used in this study exchange >50% of sodium in Na+/Ca2+ and ca 20 % of sodium in binary Na+/Mg2+ systems with the same bentonite/solution ratio and same concentrations of these ions in aqueous solutions as in the process water at a pelletizing plant. In total, approximately 50 % of the exchangeable sodium in original bentonites was exchanged after equilibrating of bentonites in the process water already after 20 minutes. Experimental Na+/Ca2+ exchange curves for ‘model’ Ca2+(aq) solutions and for process water are very similar as Ca2+ is the dominant constituent in the process water. Since bivalent ions (Ca2+ and Mg2+) that present in the process water readily replace Na+ ions, Na-bentonite transforms into Ca- or Mg- bentonite, which have worse rheological, swelling and, therefore, binding properties. This ion-exchange process can influence the binder performance in the pelletizing process. Taking into account that fluorapatite is one of the components present in a blend of minerals processed, possible interactions between orthophosphate (the principal anionic component of apatites) and bentonites in aqueous suspensions are considered. It was found that sorption of orthophosphate on Ca-montmorillonite follows a different pattern from sorption of orthophosphate on aluminum oxides and kaolinite. While there is a small amount of sorption below pH 7, which may involve inner-sphere complexation and precipitation of AlPO4 to Al-OH edge sites on the montmorillonite crystals, most sorption of orthophosphate occurs at higher pH. Both macroscopic sorption measurements and solid-state 31P MAS NMR suggest that above pH 7 there is precipitation of proton depleted calcium phosphate phases. Based on both 31P chemical shifts and 31P chemical shift anisotropies it was concluded that the principal precipitated phased are most likely ‘brushite-like’ phases. Very short spin-lattice T2(31P) relaxation times (≤100 μs) for the orthophosphate/bentonite systems can possibly be explained by the presence of paramagnetic Fe in bentonites. Since there are insufficient concentrations of soluble Fe species in the supernatant solution that may give rise to the observed effects, it is likely that orthophosphate is precipitated as thin layers on the surfaces of montmorillonite crystals, where phosphorus may interact with Fe atoms present in the crystal lattice. PO4-tetrahedra in sorbed species can be also distorted giving rise to a larger 31P CSA than for pure ‘apatite-like phases’. 29Si MAS and 1H-29Si CP/MAS NMR experiments on bentonite samples also performed in this work provide information about impurities of quartz in bentonites, a level of substitution of aluminum by iron atoms in the structure of montmorillonite and about the degree of hydration of montmorillonite. 29Si NMR experiments on bentonite incubated with waterglass in aqueous suspensions at concentrations of sodium silicates as in the process water demonstrated that one can follow the process of polymerization of waterglass in solutions and also detect sodium silicates polymerized on surfaces of bentonites already after 1 hour of incubation. Polymerized waterglass sorbed on bentonite surfaces may also alter rheological, swelling and, therefore, binding properties of sodium-activated bentonites used in pelletization of iron-oxide ores.

Godkänd; 2012; 20121011 (alegor); LICENTIATSEMINARIUM Ämne: Gränsytors kemi/Chemistry of Interfaces Examinator: Professor Oleg N. Antzutkin, Institutionen för samhällsbyggnad och naturresurser, Luleå tekniska universitet Diskutant: Professor emeritus Willis Forsling, Institutionen för samhällsbyggnad och naturresurser, Luleå tekniska universitet Tid: Onsdag den 5 december 2012 kl 13.00 Plats: C305, Luleå tekniska universitet

This thesis advances the theory of network specialization by characterizing the effect of network specialization on the eigenvectors of a network. We prove and provide explicit formulas for the eigenvectors of specialized graphs based on the eigenvectors of their parent graphs. The second portion of this thesis applies network specialization to learning problems. Our work focuses on training reservoir computers to mimic the Lorentz equations. We experiment with random graph, preferential attachment and small world topologies and demonstrate that the random removal of directed edges increases predictive capability of a reservoir topology. We then create a new network model by growing networks via targeted application of the specialization model. This is accomplished iteratively by selecting top preforming nodes within the reservoir computer and specializing them. Our generated topology out-preforms all other topologies on average.

Under de senaste åren har produkterna blivit mer invecklade beträffande anslutningen, prestanda och funktionalitet. Därför är syftet av denna studie att undersöka hur komplexa system utvecklas och leds genom att genomföra fallstudie på olika svenska företag som utvecklar mekatroniska och cyber-fysiska system. Resultatet av denna studie har lett till identifieringen av många utmaningar som de undersökta företagen har och som i sin tur har lett till framställningen av ett analytiskt ramverk som diskuterar hur och vad man bör göra för att utveckla komplexa produkter på ett effektivt sätt, så att onödig komplexitet i produktutvecklingen kan reduceras.
In recent years, products have become more complex in terms of connectivity, performance and functionality. Therefore, this study aims at studying how complex products are developed and managed through conducting multiple case studies at different Swedish companies that develop mechatronic or cyberphysical systems. The results of this study is the identification of many challenges that the investigated companies have, which have led to a presentation of an analytical framework that discusses how complex product development projects can and should be managed in order to be efficient, in order to reduce unnecessary complexity in the way companies develop these complex products.

Policy makers increasingly rely on computer models to aid policy judgements for complex systems. The climate system, for example, is extremely complicated and its reaction to changes in radiative forcing through CO2 emissions can only be explored using models. Bayesian methods for making inferences about physical systems that combine information from computer simulators and system observations have become increasingly well studied. We apply some of these methods to the policy problem where the decisions to be made are inputs to the computer model. Particular features of our methodologies include: the provision of Bayesian decision support for the policy problem when it is known that policy may be adapted in reaction to future observations of the complex system; and careful integration of the knowledge that our computer simulators will evolve and improve over time, which may affect downstream strategies and, hence, current policy. Our methods also allow research investment questions to be explored in the context of the wider policy problem. For example, the question of whether or not an improved version of a computer simulator should be built and how much it should be run can be addressed as part of the policy problem.

Coating colors are applied to the base paper in order to maximize the performance of the end product. Coating colors are complex colloidal systems, mainly consisting of water, binders, and pigments. To understand the behavior of colloidal suspensions, an understanding of the interactions between its components is essential.

Many of the present problems that we are facing arise as unanticipated side-effects of our own actions. Moreover, the solutions implemented to solve important problems often create new problems. To avoid unintended consequences, understanding complex systems is essential in devising policy instruments and in improving environmental management. Thus, this thesis investigated systems modeling approaches to under- stand complex systems and monitor the environmental performance of management actions. The overall aim of the work was to investigate the usefulness of different systems modeling approaches in supporting environmental management. A driver- based, pressure-oriented approach was adopted to investigate systems modeling tools. Material/substance flow analysis, environmental footprinting, input-output analysis, process-based dynamic modeling, and systems dynamics modeling approaches were applied in different cases to investigate strengths and weaknesses of the tools in generating an understanding of complex systems. Three modeling and accounting approaches were also tested at different systems scales to support environmental mon- itoring. Static modeling approaches were identified as fundamental to map, account, and monitor physical resource metabolism in production and consumption systems, whereas dynamic modeling showed strengths in understanding complex systems. The results suggested that dynamic modeling approaches should be conducted on top of static analysis to understand the complexity of systems when devising and testing policy instruments. To achieve proactive monitoring, a pressure-based assessment was proposed instead of the mainstream impact/state-based approach. It was also concluded that the LCA community should shift the focus of its assessments to pressures instead of impacts.
Många nuvarande miljö- och utvecklingsproblem har uppstått som oförutsedda biverkningar av människans egna handlingar. De lösningar som prövats har i sin tur ofta skapat  nya problem. Det därför viktigt att förstå hur komplexa system fungerar och att utforma styrmedel och ledningssystem som minimerar risken för oönskade bieffekter. Den här avhandling har använt olika modelleringsmetoder för att öka förståelsen för komplexa system och bidra med kunskaper om hur miljöprestanda och förvaltningsåtgärder kan följas upp på ett mer effektivt sätt. Det övergripande syftet med arbetet var att undersöka användbarheten av olika modelleringsmetoder för att effektivisera den fysiska resurshanteringen i samhället. I arbetet har ett flödesbaserat och aktörsinriktat arbetssätt (pressure based and driver oriented approach) använts i modelleringen.  Material- och substansflödesanalys, miljöfotavtryck, input-output analys, processbaserad dynamisk modellering och systemdynamiska modelleringsmetoder studerades för att undersöka styrkor och svagheter hos de olika metoderna/verktygen.  Tre olika modellerings- och redovisningsmetoder för att stödja miljöövervakning testades också i olika systemskalor. Statiska modelleringsmetoder (räkenskaper) identifierades som grundläggande för att kartlägga, kontoföra och övervaka den fysiska resursmetabolismen i produktions- och konsumtionssystem, medan dynamisk modellering visade sin styrka i att skapa förståelse för komplexa system. Resultaten pekar på att dynamiska modelleringsmetoder bör användas som ett komplement till statiska analyser för att förstå komplexiteten i systemen när man utformar och testar styrmedel. För att uppnå proaktiv övervakning bör flödesbaserade räkenskaper utnyttjas i större utsträckning i stället för den vanliga tillstånds- och påverkansövervakningen (state/impact monitoring). En viktig slutsats är därför att LCA-samfundet bör flytta fokus i sina bedömningar från påverkan till flöden.

QC 20160830

The increasing complexity and size of modern Cyber-Physical Systems (CPS) has led to a sharp decline in productivity among CPS designers. Requirements on safety aggravate this problem further, both by being difficult to ensure and due to their high importance to the public. Tools, or rather efforts to facilitate the automation of development processes, are a central ingredient in many of the proposed innovations to mitigate this problem. Even though the safety-related implications of introducing automation in development processes have not been extensively studied, it is known that automation has already had a large impact on operational systems. If tools are to play a part in mitigating the increase in safety-critical CPS complexity, then their actual impact on CPS development, and thereby the safety of the corresponding end products, must be sufficiently understood. An survey of relevant research fields, such as system safety, software engineering and tool integration, is provided to facilitate the discussion on safety-related implications of tool usage. Based on the identification of industrial safety standards as an important source of information and considering that the risks posed by separate tools have been given considerable attention in the transportation domain, several high-profile safety standards in this domain have been surveyed. According to the surveyed standards, automation should primarily be evaluated on its reliable execution of separate process steps independent of human operators. Automation that only supports the actions of operators during CPS development is viewed as relatively inconsequential. A conceptual model and a reference model have been created based on the surveyed research fields. The former defines the entities and relationships most relevant to safety-related risks associated with tool usage. The latter describes aspects of tool integration and how these relate to each other. By combining these models, a risk analysis could be performed and properties of tool chains which need to be ensured to mitigate risk identified. Ten such safety-related characteristics of tool chains are described. These safety-related characteristics provide a systematic way to narrow down what to look for with regard to tool usage and risk. The hypothesis that a large set of factors related to tool usage may introduce risk could thus be tested through an empirical study, which identified safety-related weaknesses in support environments tied both to high and low levels of automation. The conclusion is that a broader perspective, which includes more factors related to tool usage than those considered by the surveyed standards, will be needed. Three possible reasons to disregard such a broad perspective have been refuted, namely requirements on development processes enforced by the domain of CPS itself, certain characteristics of safety-critical CPS and the possibility to place trust in a proven, manual development process. After finding no strong reason to keep a narrow perspective on tool usage, arguments are put forward as to why the future evolution of support environments may actually increase the importance of such a broad perspective. Suggestions for how to update the mental models of the surveyed safety standards, and other standards like them, are put forward based on this identified need for a broader perspective.
Den ökande komplexiteten och storleken på Cyber-Fysiska System (CPS) har lett till att produktiviteten i utvecklingen av CPS har minskat kraftigt. Krav på att CPS ska vara säkra att använda förvärrar problemet ytterligare, då dessa ofta är svåra att säkerställa och samtidigt av stor vikt för samhället. Mjukvaruverktyg, eller egentligen alla insatser för att automatisera utvecklingen av CPS, är en central komponent i många innovationer menade att lösa detta problem. Även om forskningen endast delvis studerat säkerhetsrelaterade konsekvenser av att automatisera produktutveckling, så är det känt att automation har haft en kraftig (och subtil) inverkan på operationella system. Om verktyg ska lösa problemet med en ökande komplexitet hos säkerhetskritiska CPS, så måste verktygens påverkan på produktutveckling, och i förlängningen på det säkra användandet av slutprodukterna, vara känd. Den här boken ger en översikt av forskningsfronten gällande säkerhetsrelaterade konsekvenser av verktygsanvändning. Denna kommer från en litteraturstudie i områdena systemsäkerhet, mjukvaruutveckling och verktygsintegration. Industriella säkerhetsstandarder identifieras som en viktig informationskälla. Då riskerna med användandet av enskilda verktyg har undersökts i stor utsträckning hos producenter av produkter relaterade till transport, studeras flera välkända säkerhetsstandarder från denna domän. Enligt de utvalda standarderna bör automation primärt utvärderas utifrån dess förmåga att självständigt utföra enskilda processteg på ett robust sätt. Automation som stödjer operatörers egna handlingar ses som tämligen oviktig. En konceptuell modell och en referensmodell har utvecklats baserat på litteraturstudien. Den förstnämnda definierar vilka entiteter och relationer som är av vikt för säkerhetsrelaterade konsekvenser av verktygsanvändning. Den sistnämnda beskriver olika aspekter av verktygsintegration och hur dessa relaterar till varandra. Genom att kombinera modellerna och utföra en riskanalys har egenskaper hos verktygskedjor som måste säkerställas för att undvika risk identifierats. Tio sådana säkerhetsrelaterade egenskaper beskrivs. Dessa säkerhetsrelaterade egenskaper möjliggör ett systematiskt sätt att begränsa vad som måste beaktas under studier av risker relaterade till verktygsanvändning. Hypotesen att ett stort antal faktorer relaterade till verktygsanvändning innebär risk kunde därför testas i en empirisk studie. Denna studie identifierade säkerhetsrelaterade svagheter i utvecklingsmiljöer knutna både till höga och låga nivåer av automation. Slutsatsen är att ett brett perspektiv, som inkluderar fler faktorer än de som beaktas av de utvalda standarderna, kommer att behövas i framtiden. Tre möjliga orsaker till att ett bredare perspektiv ändå skulle vara irrelevant analyseras, nämligen egenskaper specifika för CPS-domänen, egenskaper hos säkerhetskritiska CPS och möjligheten att lita på en beprövad, manuell process. Slutsatsen blir att ett bredare perspektiv är motiverat, och att den framtida utvecklingen av utvecklingsmiljöer för CPS sannolikt kommer att öka denna betydelse. Baserat på detta breda perspektiv läggs förslag fram för hur de mentala modellerna som bärs fram av de utvalda säkerhetstandarderna (och andra standarder som dem) kan utvecklas.

QC 20141001

This thesis presents a theoretical and computational approach to the accurate description of magnetic exchange interactions in a variety of complex systems. These include two main families of compounds. The first family is formed by inorganic coordination complexes, presenting localized magnetic centres and well-defined crystal structures. The second family consists of purely organic, π−conjugated odd alternant neutral polyradicals, which display a much larger structural flexibility and greater delocalization of the unpaired electrons over the π system. The thesis has two main parts. The first one refers to the adopted strategy for the accurate extraction of magnetic exchange interactions. The systems used to investigate this issue are coordination compounds of increasing complexity, including heterobinuclear and homotrinuclear complexes, for which experimental crystal structures and magnetic data are available. The adopted strategy is based on the mapping approach, which relies on a one to one correspondence between the non-relativistic, time-independent exact Hamiltonian and two model spin Hamiltonians, the so-called HDVV and Ising. Ultimately, the mapping approach consists on describing both the energy and the wave function of the pure spin states by means of broken symmetry functions, using a spin projector to establish a univocal relation. In this thesis, a detailed analysis of the mapping approach has enabled establishing an alternative and accurate manner for extracting magnetic interactions in complex systems. By pointing out two main deficiencies that make the standard mapping approach proposed by Noodleman not appropriate to certain systems, and following previous work in our group, we propose an alternative approach. This is based on a direct use of the energy of the broken symmetry solutions which are mapped into the energy expectation values of the corresponding broken symmetry solutions of the HDVV Hamiltonian. This strategy relies on the one-to-one correspondence of the diagonal terms of the HDVV and Ising matrix representations. This proposal has been applied to the three-centre three-electron problem, and is further verified by comparison of the calculated coupling constants with the available experimental data and by means of effective Hamiltonian theory. The exchange coupling constant values obtained with this approach are consistent. Additionally, effective Hamiltonian theory offers the possibility to check whether the system can be described as a Heisenberg system. The second part of the thesis deals with purely organic π−conjugated neutral radicals interacting through-bond, and applies the strategy developed for inorganic molecules to extract the magnetic coupling constants between the unpaired electrons in these compounds. On the basis of chemical stability, different building blocks are investigated. Then, by considering different coupling schemes (strategies to assemble them leading to different dimensionalities) and the role of structural flexibility, the main goal of the investigation is to establish the main electronic and structural factors to enhance the stability of the radical centres and promote a robust ferromagnetic interaction among them. Thus, Chapter 1 compares explicitly through-space and through-bond interacting organic radicals, providing experimental arguments for the choice of the latter as building blocks. Chapter 2 introduces the theoretical foundations on which all computational methodologies used in this thesis are based. Chapter 3 provides an analysis of electronic structure methods to establish an accurate scheme to compute magnetic coupling constants in complex systems with well-defined structural parameters. Based on different studies on organic polyradicals, Chapter 4 offers reliable arguments to design purely π−conjugated organic polyradical interacting through-bond, with large S value, high-spin ground state, robust ferromagnetic properties, strong magnetic anisotropy and chemical stability. The appearance of a secondary structure in these flexible molecules is found to be crucial for stabilizing the polyradical high-spin ground state. Altogether, the main conclusions of this thesis are that the proposed strategy for the extraction of magnetic exchange interactions provides consistent results and the proposal for using linear π-conjugated polyradicals, based on molecular units derived from triarylmethyl radicals, to achieve robust ferromagnetic properties in stable purely organic systems.
Esta tesis presenta un estudio teórico y computacional sobre la predicción precisa de constantes de acoplamiento magnético en una serie de sistemas complejos. Estos incluyen dos familias de compuestos principales. La primera familia está formada por complejos de coordinación inorgánicos, los cuales presentan centros magnéticos localizados sobre los átomos metálicos y estructuras cristalinas bien definidas. El segundo grupo se trata de radicales puramente orgánicos, con conjugación del sistema π, los cuales presentan una flexibilidad estructural mucho mayor y una deslocalización de los electrones desapareados más extensa. La tesis tiene dos partes principales. La primera se dedica a establecer una estrategia para la extracción de constantes de acoplamiento magnético, lo cual se lleva a cabo en una serie de complejos de coordinación heterodinucleares y homotrinucleares. La estrategia se basa la propuesta de una formulación alternativa del mapping approach, que evita el uso de un proyector de espín y con ello las deficiencias derivadas de ello, en comparación con la formulación inicial propuesta por Noodleman. Esta propuesta es aplicada al problema de tres-electrones tres-centros, y validada por comparación con el experimento y a través de le teoría del Hamiltoniano efectivo. La segunda parte de la tesis se centra en compuestos radicalarios puramente orgánicos π—conjugados, que presentan interacción entre los electrones desapareados a través de enlace. Con el objetivo de promover la estabilidad química de los centros radicalarios, diferentes unidades básicas son consideradas. En base a diferentes esquemas de acoplamiento de estas unidades, y del papel de la flexibilidad estructural, el principal objetivo es establecer los principales factores electrónicos y estructurales para aumentar la estabilidad del radical y promover una interacción ferromagnética robusta entre ellos. Las principales conclusiones de la tesis son dos: primero, la propuesta para extraer constantes de acoplamiento en sistemas complejos resulta en valores consistentes; segundo, esta tesis propone utilizar poliradicales lineales π-conjugados, basados en unidades moleculares derivados de poliarylmethyl radicales, para lograr propiedades ferromagnéticas robustas en sistemas puramente orgánicos estables.

Complex biogenic habitats created by large canopy-forming macroalgae on intertidal and shallow subtidal rocky reefs worldwide are increasingly affected by degraded environmental conditions at local scales and global climate-driven changes. A better understanding of the mechanisms underlying the impacts of complex suites of anthropogenic stressors on algal forests is essential for the conservation and restoration of these habitats and of their ecological, economic and social values. This thesis tests physical and biological mechanisms underlying the impacts of different forms of natural and human-related disturbance on macroalgal assemblages dominated by fucoid canopies along the east coast of the South Island of New Zealand. A field removal experiment was initially set up to test assemblage responses to mechanical perturbations of increasing severity, simulating the impacts of disturbance agents affecting intertidal habitats such as storms and human trampling. Different combinations of assemblage components (i.e., canopy, mid-canopy and basal layer) were selectively removed, from the thinning of the canopy to the destruction of the entire assemblage. The recovery of the canopy-forming fucoids Hormosira banksii and Cystophora torulosa was affected by the intensity of the disturbance. For both species, even a 50% thinning had impacts lasting at least eighteen months, and recovery trajectories were longer following more intense perturbations. Independently of assemblage diversity and composition at different sites and shore heights, the recovery of the canopy relied entirely on the increase in abundance of these dominant fucoids in response to disturbance, indicating that functional redundancy is limited in this system. Minor understory fucoids, which could have provided functional replacement for the dominant habitat formers, had reduced rates of growth or recruitment when the overlying canopy was disturbed. I then used a combination of field and laboratory experiments to test the impacts of physical and biotic stress sources on the dominant fucoids H. banksii and C. torulosa. The large fucoid Durvillaea antarctica was also included in one of the laboratory investigations. I assessed how altered physical and biotic conditions affect these important habitat formers, both separately and in combination. Physical stressors included increased sedimentation, nutrient enrichment and warmer water temperatures. Biotic stress originated from interspecific competition with turfs of articulated coralline algae and ephemeral, fast-growing green and brown algae. Sediment deposition severely reduced the survival and growth of recently settled H. banksii, C. torulosa and D. antarctica germlings in laboratory experiments. In the field, the recruitment of H. banksii on unoccupied substrates was significantly higher than in treatments in which sediments or mats of turf-forming coralline algae covered the substrate. This shows that sediment deposition and space pre-emption by algal turfs can synergistically affect the development of fucoid beds. Further impacts of sediment accumulation in the benthic environment were investigated using in situ and laboratory photorespirometry techniques to assess the contribution of coralline algae to assemblage net primary productivity (NPP), both in the presence and absence of sediment. The NPP of articulated corallines was reduced by sediment. Sediment accumulation among the thalli limited the access of the corallines to the light and induced photoinhibitive mechanisms. In the absence of sediment, however, coralline algae enhanced the NPP of assemblages with a fucoid canopy, showing the importance of synergistic interactions among the components of multi-layered assemblages in optimizing light use. Nutrient enrichment had a less pervasive influence on the dominant fucoids H. banksii and C. torulosa than sedimentation. In laboratory experiments, nutrients stimulated the growth of H. banksii and C. torulosa germlings. However, negative impacts of high nutrient levels were observed for the early life stages of D. antarctica. The abundance of opportunistic, fast-growing algae rapidly increased in response to nutrient enrichment both in the laboratory and in the field. Impacts of ephemeral species on fucoid early life stages were only evident in laboratory contexts, where green algae of the genus Ulva impaired both the settlement of H. banksii zygotes and the growth of its germlings. Fucoid recruitment in the field was not affected by increased covers of ephemeral algae caused by enhanced nutrient regimes, indicating that H. banksii and C. torulosa may be resistant to short-term (one year) nutrient pollution. In the laboratory, increased temperatures within the range predicted for the end of the 21st century caused increased mortality in the H. banksii, C. torulosa and D. antarctica germlings. In a separate experiment, a combination of warmer water temperatures and nutrient enrichment enhanced the growth of ephemeral green algae. These results suggest that opposite responses to altered climate conditions may contribute to shifts from complex biogenic habitats dominated by macroalgal canopies to simplified systems monopolized by a limited number of stress-tolerant species. This research contributes to a clearer mechanistic understanding of biotic and physical mechanisms shaping the structure of coastal marine hard bottom communities under increasingly stressful conditions worldwide. These findings may provide insights for other studies investigating the complex mosaic of challenges facing marine coastal ecosystems.

Introdução: Grande parte das ações para promover a atividade física no lazer em populações tem apresentado tamanhos de efeito pequenos ou inexistentes, ou resultados inconsistentes. Abordar o problema a partir da perspectiva sistêmica pode ser uma das formas de superar esse descompasso. Objetivo: Desenvolver um modelo baseado em agentes para investigar a conformação e evolução de padrões populacionais de atividade física no lazer em adultos a partir da interação entre atributos psicológicos dos indivíduos e atributos dos ambientes físico construído e social em que vivem. Métodos: O processo de modelagem foi composto por três etapas: elaboração de um mapa conceitual, com base em revisão da literatura e consulta com especialistas; criação e verificação do algoritmo do modelo; e parametrização e análise de consistência e sensibilidade. Os resultados da revisão da literatura foram consolidados e relatados de acordo com os domínios da busca (aspectos psicológicos, ambiente social e ambiente físico construído). Os resultados quantitativos da consulta com os especialistas foram descritos por meio de frequências e o conteúdo das respostas questões abertas foi analisado e compilado pelo autor desta tese. O algoritmo do modelo foi criado no software NetLogo, versão 5.2.1., seguindo-se um protocolo de verificação para garantir que o algoritmo fosse implementado acuradamente. Nas análises de consistência e sensibilidade, utilizaram-se o Teste A de Vargha-Delaney, coeficiente de correlação de postos parcial, boxplots e gráficos de linha e de dispersão. Resultados: Definiram-se como elementos do mapa conceitual a intenção da pessoa, o comportamento de pessoas próximas e da comunidade, e a percepção da qualidade, do acesso e das atividades disponíveis nos locais em que atividade física no lazer pode ser praticada. O modelo representa uma comunidade hipotética contendo dois tipos de agentes: pessoas e locais em que atividade física no lazer pode ser praticada. As pessoas interagem entre si e com o ambiente construído, gerando tendências temporais populacionais de prática de atividade física no lazer e de intenção. As análises de sensibilidade indicaram que as tendências temporais de atividade física no lazer e de intenção são altamente sensíveis à influência do comportamento atual da pessoa sobre a sua intenção futura, ao tamanho do raio de percepção da pessoa e à proporção de locais em que a atividade física no lazer pode ser praticada. Considerações finais: O mapa conceitual e o modelo baseado em agentes se mostraram adequados para investigar a conformação e evolução de padrões populacionais de atividade física no lazer em adultos. A influência do comportamento da pessoa sobre a sua intenção, o tamanho do raio de percepção da pessoa e a proporção de locais em que a atividade física no lazer pode ser praticada são importantes determinantes da conformação e evolução dos padrões populacionais de atividade física no lazer entre adultos no modelo.
Introduction: Most of the actions to promote leisure-time physical activity at the population level has shown small or null effect sizes, or inconsistent results. Approaching the problem from a systemic perspective can be one way to overcome this gap. Objective: To develop an agent-based model to explore how the interaction between psychological traits and built and social environments leads to the formation and evolution of leisure-time physical activity population patterns in adults. Methods: The modeling process consisted of three stages: development of a conceptual map, based on literature review and expert-based consultation; creation and verification of the models algorithm; and parametrization and consistency and sensitivity analyses. The results of the literature review were consolidated and reported by search domain (psychological, social and built environment aspects). The quantitative results of the expert-based consultation were described using frequency and the content of the open ended questions were analyzed and compiled by the author. The models algorithm has been created using NetLogo, version 5.2.1., following a verification protocol to ensure that the algorithm has been implemented accurately. The Vargha-Delaney test, partial rank correlation coefficients, boxplots, and line and scatterplot graphs were used during the consistency and sensitivity analysis. Results: The elements of the conceptual map are the persons intention, the behavior of the persons social network and the community at large, and the perception of quality, access and available activities of places where leisure-time physical activity is practiced. The model is a hypothetical community with containing two types of agents: people and places where leisure-time physical activity is practiced. People interact with each other and with the built environment, generating population temporal trends of leisure-time physical activity and intention. Sensitivity analysis indicated that the temporal trends of leisure-time physical activity and intention are highly sensitive to the influence of the persons current behavior on her future intention, the persons perception radius size, and the proportion of places where leisure-time physical activity leisure is practiced. Final considerations: The conceptual map and the agent-based model are suitable to investigate the formation and evolution of leisure-time physical activity population patterns in adults. The influence of the persons behavior on her intention, the persons perception radius size, and the proportion of places where leisure-time physical activity leisure is practiced seem to be important determinants of the formation and evolution of population patterns of leisure-time physical activity in this model.

Проблема людини в усьому розмаїтті характеристик її сутності й існування завжди виступала актуальним питанням в філософії науки. Проте, сьогодні вона набуває особливого значення. Сучасність характеризується небувалими за своїми масштабами економічними, науково-технологічними, соціально-політичними, духовними потрясіннями, які проявляються у конфлікті між людиною та її соціальним середовищем. Це підкреслює важливість правильного розуміння проблеми тілесності людини в фізкультурноспортивному концепті. Мета дослідження. Провести логіко-методологічний аналіз людської тілесності в фізкультурно-спортивному концепті. Для реалізації поставленої мети було проаналізовано питання феномену людської тілесності, досліджено сутність синергетичної парадигми та її роль в розвитку фізичної культури та розкрито вплив NBICS-конвергенції та трансгуманістичної еволюції на розвиток людини. Виклад матеріалу дослідження. Тілесність, на наш погляд, – це набір інформаційних, енергетичних, системноструктурних та функціональних властивостей, що належать кожній окремій біосистемі людини. Тілесність – це субстрат людської життєдіяльності, що являє собою багатомірне утворення, яке існує в трьох вимірах: біологічне (природне) тіло, внутрішня тілесність, зовнішня тілесність і конструюється на їхньому перетині. Тому тілесність – це змістовна складова людини, що забезпечує саму можливість соціального буття. Феноменом є той факт, що власне тілесність здійснює важливий вплив на структуру фізичної культури та забезпечує її існування та розвиток.

Swarm robotics is the study of developing and controlling large groups of robots. Collectives of robots possess advantages over single robots such as being robust to mission failures due to single-robot errors. Experimental research in swarm robotics is currently limited by swarm robotic technology. Current swarm robotic systems are either small groups of sophisticated robots or large groups of simple robots due to manufacturing overhead, functionality-cost dependencies, and their need to avoid collisions, amongst others. It is therefore useful to develop a swarm robotic system that is easy to manufacture, that utilises its sensors beyond standard usage, and that allows for physical interactions. In this work, I introduce a new type of low-friction locomotion and show its first implementation in the HoverBot system. The HoverBot system consists of an air-levitation and magnet table, and a HoverBot agent. HoverBots are levitating circuit boards which are equipped with an array of planar coils and a Hall-effect sensor. HoverBot uses its coils to pull itself towards magnetic anchors that are embedded into a levitation table. These robots consist of a Printed Circuit Board (PCB), surface mount components, and a battery. HoverBots are easily manufacturable, robots can be ordered populated; the assembly consists of plugging in a battery to a robot. I demonstrate how HoverBot's low-cost hardware can be used beyond its standard functionality. HoverBot's magnetic field readouts from its Hall-effect sensor can be associated with successful movement, robot rotation and collision measurands. I build a time series classifier based on these magnetic field readouts, I modify and apply signal processing techniques to enable the online classification of the time-variant magnetic field measurements on HoverBot's low-cost microcontroller. This method allows HoverBot to detect rotations, successful movements, and collisions by utilising readouts from its single Hall-effect sensor. I discuss how this classification method could be applied to other sensors and demonstrate how HoverBots can utilise their classifier to create an occupancy grid map. HoverBots use their multi-functional sensing capabilities to determine whether they moved successfully or collided with a static object to map their environment. HoverBots execute an "explore-and-return-to-nest" strategy to deal with their sensor and locomotion noise. Each robot is assigned to a nest (landmark); robots leave their nests, move n steps, return and share their observations. Over time, a group of four HoverBots collectively builds a probabilistic belief over its environment. In summary, I build manufacturable swarm robots that detect collisions through a time series classifier and map their environment by colliding with their surroundings. My work on swarm robotic technology pushes swarm robotics research towards studies on collision-dependent behaviours, a research niche that has been barely studied. Collision events occur more often in dense areas and/or large groups, circumstances that swarm robots experience. Large groups of robots with collision-dependent behaviours could become a research tool to help invent and test novel distributed algorithms, to understand the dependencies between local to global (emergent) behaviours and more generally the science of complex systems. Such studies could become tremendously useful for the execution of large-scale swarm applications such as the search and rescue of survivors after a natural disaster.

Physical systems modeled by networks are fully dynamic in the sense that the process of adding edges and vertices never ends, and no edge or vertex is necessarily eternal. Temporal networks enable to explicitly study systems with a changing topology by capturing explicitly the temporal changes. The controllability of temporal networks is the study of driving the state of a temporal network to a target state at deadline t_f within △t = t_f - t₀ steps by stimulating key nodes called driver nodes. In this research, the author aims to understand and analyze temporal networks from the controllability perspective at the global and nodal scales. To analyze the controllability at global scale, the author provides an efficient heuristic algorithm to build driver node sets capable of fully controlling temporal networks. At the nodal scale, the author presents the concept of Complete Controllable Domain (CCD) to investigate the characteristics of Maximum Controllable Subspaces (MCSs) of a driver node. The author shows that a driver node can have an exponential number of MCSs and introduces a branch and bound algorithm to approximate the CCD of a driver node. The proposed algorithms are evaluated on real-world temporal networks induced from ant interactions in six colonies and in a set of e-mail communications of a manufacturing company. At the global scale, the author provides ways to determine the control regime in which a network operates. Through empirical analysis, the author shows that ant interaction networks operate under a distributed control regime whereas the e-mails network operates in a centralized regime. At the nodal scale, the analysis indicated that on average the number of nodes that a driver node always controls is equal to the number of driver nodes that always control a node.

Photosynthesis involves the absorption of photons by light-harvesting pigments and the subsequent transfer of excitation from the absorption centre to the reaction centre. This highly efficient phenomenon of excitation transfer has traditionally been explained by the Forster mechanism of incoherent hopping of excitation from one chromophore to another. Recently 2D electronic spectroscopic evidences were gathered by Fleming and coworkers on the photosynthetic Fenna-Matthews-Olson (FMO) complex in green sulfur bacteria [1]. Subsequent simulation studies by the same group [2] led to the proposition of a quantum-mechanical, coherent, wave-like transfer of excitation among the chromophores. However, Fleming's conclusions regarding retention of coherence appeared surprising because, the complex would interact with the numerous degrees of freedom of the protein scaffold surrounding it, leading to decoherence, which is expected to be rapid. Thus, we were interested in proposing an analytical treatment to rationalize the excitation transfer. Traditional approaches employed for studying excitation energy transfer involve the master equation techniques where the system-bath coupling is perturbative and is truncated after a few orders. It is important to note that the system-bath coupling causes both decoherence and population relaxation. Such a perturbative approximation is difficult to justify for the photosystem, as the system-bath coupling and the interchromophoric electronic coupling have comparable values. Also, these treatments are largely numerical studies and demand involved calculations. Thus, exact calculations for such a system (7-level) are very difficult. Consequently, we were interested in developing an analytical approach where the coupling is treated as non-perturbative. We devised a novel analytical treatment which employs a unitary transformation analogous to the one used for the theory of nonadiabatic effects in chemical reactions [3]. Our treatment rests on an adiabatic basis which are eigenstates calculated at each nuclear position (i.e. at each configuration of the bath) bearing a parametric dependence in Qi, where Qi denotes the shift of the exciton at site `i' due to the environment. The treatment is justified because in the case of coherent transfer, the excitation would travel mostly amongst the adiabatic states and the effects of non-adiabaticity are small. We observed that the system-bath coupling, after the unitary transformation, could be decoupled at the lowest order into two parts: a) an adiabatic contribution, which accounts solely for decoherence (this is evaluated almost exactly in our approach) and b) a non-adiabatic contribution which accounts for population relaxation from one adiabatic state to another (treated by a Markovian master equation). When we applied our technique to the FMO complex, our prediction for population evolution at the chromophores showed excellent correspondence with those obtained by Nalbach and coworkers using path-integral calculations [4], which are exact. These were calculations where the environment was modelled using a Drude spectral density. Our method allowed the calculations to be readily performed for different temperatures as well. It should be specifically emphasized that, unlike the involved and cumbersome path-integral calculations by Nalbach and coworkers [4] or the hierarchical equation calculations by Ishizaki et al. [2], our method is simple, easy to apply and computationally expedient. Further it became evident that the ultra-efficiency of energy transfer in photosynthetic complexes is not completely captured by coherence alone but is the result of an interplay of coherence and the dissipative influence of the environment (also known as ENAQT or Environment Assisted Quantum Transport [5]). An added advantage of our analytical treatment was the flexibility it offered. Thus, we could use our formalism to perform expedient analyses on the behavior of the system under various conditions. For example, we may wish to evaluate the consequences of introducing correlations among the bath degrees of freedom on the efficiency of transfer to the reaction centre. To this end, we applied our formalism by introducing correlations among the bath degrees of freedom and then by introducing anticorrelations among the bath degrees of freedom. The conclusions were interesting, for they suggested that the efficiency of transfer to the reaction centre was enhanced by the presence of anti-correlations, when compared with an uncorrelated bath. Uncorrelated baths, in turn, had a higher efficiency of energy transfer than correlated baths [6]. Thus, the population evolution is fastest for the anti-correlated bath, followed by the uncorrelated bath and is slowest for the correlated bath. Similar conclusions have been reached at by Tiwari et al. [7]. We could also extend the formalism for studying the system under different spectral densities for the environment, apart from just the Drude spectral density which is popularly used in literature associated with FMO calculations. For instance, the FMO system could be analyzed for the Adolphs-Renger spectral density [3, 8]. Once again our results showed excellent agreement with those reported by Nalbach. We also analyzed the FMO system under the spectral density proposed by Kleinekathofer and coworkers [9]. It was found that these latter spectral densities had more profound participation from the environment, therefore coherences were destroyed more effectively and population relaxation was faster. The excitation transfer to the final site (site closest to the reaction centre in the FMO complex) was found to be faster for the Adolphs and Renger spectral density and the spectral density proposed by Kleinekathofer and coworkers, when compared to the Drude spectral density. Also, the excitation transfer was fastest when we modelled the environment using the Kleinekathofer spectral density. This reinforced the previous conclusions that the dissipative effects of the environment promote a faster energy transport. Being an almost analytical approach, our technique could be applied to systems with larger number of levels as well. A good example of such a case is the MEH-PPV polymer. 2D electronic-spectroscopic experiments performed on this polymer in solution speculate that the excitation energy transfer might be coherent even at physiological temperatures [10]. A prototype for studying this system might be a conjugated polymer with around 80-100 chromophores. Linewidths and Lineshapes in the vicinity of Graphene It has been reported that a vibrating dipole may de-excite by transferring energy non-radiatively to a neighboring metal surface [11]. It is also understood that due to its delocalized pi-cloud, graphene has a continuum of energy states and can behave like a metal sheet and accept energies. Thus, we proposed that if a vibrationally excited dipole de-excites in the vicinity of a graphene sheet, graphene may get electronically excited and thus serve as an effective quencher for such vibrational excitations. Depending on the distance of the dipole from the graphene sheet, the transfer might be intense enough to be spectroscopically probed. We have investigated the rate of such an energy transfer. We use the Dirac cone approximation for graphene, as this enables us to obtain analyt-ical results. The Fermi Golden rule was used to evaluate the rate of energy transfer from the excited dipole to the graphene sheet [12]. The calculations were performed for both the instances: a) energy transfer from a dipole to undoped graphene and, b) energy trans-fer from a dipole to doped graphene. For undoped graphene, the carrier (electron) charge density in the conduction band is zero and we would only have transitions from the valence band to the conduction band. As a consequence of absence of carrier charge density in CB (conduction band), the screening of Coulombic interactions in the graphene plane is ineffective. Thus, one could use the non-interacting polarizability for undoped graphene in the rate expression [13]. However, when we consider the case of doped graphene where EF is shifted upwards into CB, the conduction band electrons will contribute to screening. In this case, we have two sets of transitions: a) from ki in VB (valence band) to kf in CB and b) ki in CB to kf in CB, where ki and kf are the wavevectors which correspond to the initial and final electronic states in graphene. So we have used the polarizability propagator in the random phase approximation [14] to calculate the rate following the approach of [13]. It is also known that the imaginary part of the frequency domain dipole-dipole corre-lation function is a measure of the lineshape [15]. We were, thus, interested in evaluating the lineshape for these transitions. For evaluating the correlation function, we used the partitioning technique developed by L•owdin [16] and subsequently extracted the lineshape from its imaginary part. Using this method, we calculated lineshape for the vibrational excitation of CO molecule in the vicinity of an undoped graphene lattice. The linewidth for this system also was obtained. It could be seen that the vibrational linewidth for 1 CO in the vicinity (5 A) of undoped graphene (EF = 0:00eV ) is small (0:012 cm ) but could be observed experimentally. The lineshape calculations were also extended to cases where it is possible to have atomic transitions by placing an electronically excited atom in the vicinity of the graphene sheet. We considered the following two cases: a) 3p ! 2s transition in hydrogen atom, at a distance of 12 A from the graphene sheet and, b) 4p ! 3s transition in hydrogen atom, at a distance of 20 A from the graphene sheet. The linewidths for atomic transitions could be easily probed in these cases ( 55 cm 1 for 3p ! 2s and 56 cm 1 for 4p ! 3s). In the preceding calculations, the transi-tion dipoles were considered perpendicular to the graphene surface. It is worthwhile to note that if the transition dipoles are considered parallel to the graphene surface, the respective linewidths would be half of those obtained for the case where the transition dipoles are perpendicular. Another interesting possibility would be to consider a lanthanide metal complex placed within a few nanometers from graphene. Lanthanides are known to have sharp f-f transitions [17] and consequently, one could easily observe the effects of broadening due to energy transfer to the electronic system of graphene. Energy Eigenmodes for arrays of Metal Nanoparticles In the final part of the thesis we consider organized assemblies of metal nanoparti-cles, specifically helical and cylindrical assemblies and investigate the plasmonic excitation transfer across these assemblies. These were motivated by recent studies which reported growth of chiral asymmetric assemblies of nanoparticles on D and L- isomers of dipheny-lalanine peptide nanotubes [18]. The plasmons in the helical/cylindrical assemblies are expected to couple with each other via electromagnetic interactions. We construct the Hamiltonian for such systems and evaluate the eigenmodes and energies pertaining to these modes in the wave vector space. We also perform calculations for the group velocity for each eigenmode as this gives us an idea of which eigenmode transports excitation the fastest.

Associated to any finite simple graph Γ is the chromatic polynomial PΓ(q) whose complex zeros are called the chromatic zeros of Γ. A hierarchical lattice is a sequence of finite simple graphs {Γ_n}∞_n-0 built recursively using a substitution rule expressed in terms of a generating graph. For each n, let μn denote the probability measure that assigns a Dirac measure to each chromatic zero of Γ_n. Under a mild hypothesis on the generating graph, we prove that the sequence μn converges to some measure μ as n tends to infinity. We call μ the limiting measure of chromatic zeros associated to {Γ_n}∞_n-0. In the case of the Diamond Hierarchical Lattice we prove that the support of μ has Hausdorff dimension two.

Emulsions are advantageous in many applications including healthcare, food science, and detergency due to their ability to disperse one fluid in another, otherwise immiscible fluid. For the same reason, emulsions are also problematic when mixtures of oil and water are undesirable like in industrial wastewater pollution and fuel systems. Whether an emulsion is desirable or not, both benefit from understanding the fundamental relationship of emulsion formation and stability to the physical and chemical properties of the oil-water-surfactant mixture. This work identifies the formation and stability mechanisms of model emulsion systems through the perspective of emulsion prevention for applications in shipboard wastewater (bilge water) treatment. Although experiments in this study were designed to model bilge water systems, their fundamental approach makes them practical for many different applications like food science, pharmaceuticals, and detergency.

The impact of salts on emulsion formation and stability to coalescence were studied to understand how emulsions stabilized by ionic surfactant behave in saltwater environments. Droplet size analysis revealed that emulsion stability to coalescence improved with salt concentration. Through interfacial tension and zeta potential measurements, it was found that the addition of salt promoted close surfactant packing and faster surfactant adsorption kinetics at the oil-water interface. This aided in preventing coalescence and created conditions favorable for the formation of a stable Newton black film. Extended DLVO calculations were used to model the interaction energy between droplets and suggested that hydration forces play an important role in stabilizing these systems. These emulsions were then studied under dynamic ageing conditions to observe the impact of motion on emulsion stability. While statically aged emulsions were stable to coalescence, dynamic ageing induced coalescence (increased droplet size) or emulsified the oil droplets (decreased droplet size) depending on the surfactant concentration and energy input during ageing.

Formation mechanisms and stability of spontaneous emulsion systems were also investigated. Low molecular weight oils (e.g., toluene, xylenes, and cyclohexane) were found to spontaneously emulsify with nonylphenol polyethoxylated (NPE) and sodium dodecylbenzene sulfonate (SDBS). NPE emulsions spontaneously emulsified via diffusion and micelle swelling and displayed limited stability due to Ostwald ripening. SDBS emulsions also spontaneously emulsified with toluene but only in saltwater environments. As the concentration of salt in the aqueous phase increased, the spontaneity of these emulsions also increased. These systems were analyzed using the hydrophilic lipophilic difference (HLD) theory to evaluate its efficacy for predicting the conditions favorable for spontaneous emulsification. Limitations and practicality of using the HLD model for these systems were also explored.

abstract: What can classical chaos do to quantum systems is a fundamental issue highly relevant to a number of branches in physics. The field of quantum chaos has been active for three decades, where the focus was on non-relativistic quantumsystems described by the Schr¨odinger equation. By developing an efficient method to solve the Dirac equation in the setting where relativistic particles can tunnel between two symmetric cavities through a potential barrier, chaotic cavities are found to suppress the spread in the tunneling rate. Tunneling rate for any given energy assumes a wide range that increases with the energy for integrable classical dynamics. However, for chaotic underlying dynamics, the spread is greatly reduced. A remarkable feature, which is a consequence of Klein tunneling, arise only in relativistc quantum systems that substantial tunneling exists even for particle energy approaching zero. Similar results are found in graphene tunneling devices, implying high relevance of relativistic quantum chaos to the development of such devices. Wave propagation through random media occurs in many physical systems, where interesting phenomena such as branched, fracal-like wave patterns can arise. The generic origin of these wave structures is currently a matter of active debate. It is of fundamental interest to develop a minimal, paradigmaticmodel that can generate robust branched wave structures. In so doing, a general observation in all situations where branched structures emerge is non-Gaussian statistics of wave intensity with an algebraic tail in the probability density function. Thus, a universal algebraic wave-intensity distribution becomes the criterion for the validity of any minimal model of branched wave patterns. Coexistence of competing species in spatially extended ecosystems is key to biodiversity in nature. Understanding the dynamical mechanisms of coexistence is a fundamental problem of continuous interest not only in evolutionary biology but also in nonlinear science. A continuous model is proposed for cyclically competing species and the effect of the interplay between the interaction range and mobility on coexistence is investigated. A transition from coexistence to extinction is uncovered with a non-monotonic behavior in the coexistence probability and switches between spiral and plane-wave patterns arise. Strong mobility can either promote or hamper coexistence, while absent in lattice-based models, can be explained in terms of nonlinear partial differential equations.
Dissertation/Thesis
Ph.D. Electrical Engineering 2012

Cette thèse porte sur le rôle de l’espace dans l’organisation et dans la dynamique des communautés écologiques multi-espèces. Deux carences peuvent être identifiées dans les études théoriques actuelles portant sur la dimension spatiale des communautés écologiques : l’insuffisance de modèles multi-espèces représentant la dimension spatiale explicitement, et le manque d’attention portée aux interactions positives, tel le mutualisme, en dépit de la reconnaissance de leur ubiquité dans les systèmes écologiques. Cette thèse explore cette problématique propre à l’écologie des communautés, en utilisant une approche théorique s’inspirant de la théorie des systèmes complexes et de la mécanique statistique. Selon cette approche, les communautés d’espèces sont considérées comme des systèmes complexes dont les propriétés globales émergent des interactions locales entre les organismes qui les composent, et des interactions locales entre ces organismes et leur environnement. Le premier objectif de cette thèse est de développer un modèle de métacommunauté multi-espèces, explicitement spatial, orienté à l’échelle des individus et basé sur un réseau d’interactions interspécifiques générales comprenant à la fois des interactions d’exploitation, de compétition et de mutualisme. Dans ce modèle, les communautés locales sont formées par un processus d’assemblage des espèces à partir d’un réservoir régional. La croissance des populations est restreinte par une capacité limite et leur dynamique évolue suivant des mécanismes simples de reproduction et de dispersion des individus. Ces mécanismes sont dépendants des conditions biotiques et abiotiques des communautés locales et leur effet varie en fonction des espèces, du temps et de l’espace. Dans un deuxième temps, cette thèse a pour objectif de déterminer l’impact d’une connectivité spatiale croissante sur la dynamique spatiotemporelle et sur les propriétés structurelles et fonctionnelles de cette métacommunauté. Plus précisément, nous évaluons différentes propriétés des communautés en fonction du niveau de dispersion des espèces : i) la similarité dans la composition des communautés locales et ses patrons de corrélations spatiales; ii) la biodiversité locale et régionale, et la distribution locale de l’abondance des espèces; iii) la biomasse, la productivité et la stabilité dynamique aux échelles locale et régionale; et iv) la structure locale des interactions entre les espèces. Ces propriétés sont examinées selon deux schémas spatiaux. D’abord nous employons un environnement homogène et ensuite nous employons un environnement hétérogène où la capacité limite des communautés locales évoluent suivant un gradient. De façon générale, nos résultats révèlent que les communautés écologiques spatialement distribuées sont extrêmement sensibles aux modes et aux niveaux de dispersion des organismes. Leur dynamique spatiotemporelle et leurs propriétés structurelles et fonctionnelles peuvent subir des changements profonds sous forme de transitions significatives suivant une faible variation du niveau de dispersion. Ces changements apparaissent aussi par l’émergence de patrons spatiotemporels dans la distribution spatiale des populations qui sont typiques des transitions de phases observées généralement dans les systèmes physiques. La dynamique de la métacommunauté présente deux régimes. Dans le premier régime, correspondant aux niveaux faibles de dispersion des espèces, la dynamique d’assemblage favorise l’émergence de communautés stables, peu diverses et formées d’espèces abondantes et fortement mutualistes. La métacommunauté possède une forte diversité régionale puisque les communautés locales sont faiblement connectées et que leur composition demeure ainsi distincte. Par ailleurs dans le second régime, correspondant aux niveaux élevés de dispersion, la diversité régionale diminue au profit d’une augmentation de la diversité locale. Les communautés locales sont plus productives mais leur stabilité dynamique est réduite suite à la migration importante d’individus. Ce régime est aussi caractérisé par des assemblages incluant une plus grande diversité d’interactions interspécifiques. Ces résultats suggèrent qu’une augmentation du niveau de dispersion des organismes permet de coupler les communautés locales entre elles ce qui accroît la coexistence locale et favorise la formation de communautés écologiques plus riches et plus complexes. Finalement, notre étude suggère que le mutualisme est fondamentale à l’organisation et au maintient des communautés écologiques. Les espèces mutualistes dominent dans les habitats caractérisés par une capacité limite restreinte et servent d’ingénieurs écologiques en facilitant l’établissement de compétiteurs, prédateurs et opportunistes qui bénéficient de leur présence.
This thesis is a study of the role of space in the organization and dynamics of multi-species ecological communities. Two weaknesses can be identified from previous theoretical studies concerned with the spatial dimension of ecological communities: the scarcity of multi-species models based on a spatially explicit representation of space, and the lack of attention toward positive interspecific interactions, such as mutualism, despite the recognition of their ubiquity in ecological systems. This thesis explores this problematic by adopting a theoretical framework based on complex system theory and statistical mechanics. Following this approach, ecological communities can be viewed as complex systems whose global properties emerge from the local interactions between the organisms that composed them, and between the organisms and their environment. The first objective of this thesis is to develop a multi-species metacommunity model which is spatially explicit, individual-based, and centered on a general interspecific interaction web containing exploitation, competition as well as mutualism. In this model, local communities are created by an assembly process whereby species are drawn from a regional pool. Population growth is restricted by a carrying capacity and its dynamics is driven by simple reproduction and dispersal mechanisms acting at the level of single individual. These mechanisms depend on the biotic and abiotic conditions of the local communities and their effect varies with species, time and space. The second objective of this thesis is to determine the impact of an increasing spatial connectivity on the dynamics, and structural and functional properties of this metacommunity. More precisely, we set out to evaluate different community properties under changes in the level of species dispersal: i) the similarity in local community composition and its patterns of spatial correlations, ii) the local and regional diversity and the local species abundance, iii) the local and regional biomass, productivity and dynamical stability, and iv) the structure of the local interaction webs. These properties are examined under two spatial schemes. First, we employ a homogeneous environment, and second we employ a heterogeneous environment whereby the carrying capacity of local communities evolves along a gradient. In general, our results reveal that spatially distributed ecological communities are extremely sensitive to the modes and levels of species dispersal. Their spatiotemporal dynamics as well as their structural and functional properties can undergo profound changes in the form of significant transitions under slight changes of the level of dispersal. These changes are also highlighted by the emergence of spatiotemporal patterns in the spatial distribution of the populations, which are characteristics of phase transition generally observed in physical systems. The metacommunity presents two dynamical regimes. In the first regime, corresponding to weak levels of species dispersal, the assembly dynamics promotes the emergence of species-poor but stable communities made of abundant and strongly mutualistic species. The metacommunity has a high regional diversity since weakly connected communities conserve a distinct assemblage of species. On the other hand, in the second regime, corresponding to strong dispersal rates, regional diversity decreases at the benefit of an increase in local diversity. Local communities are more productive but their stability is reduced due to the important migration of individuals. This regime is also characterized by assemblages containing a richer diversity of interspecific interactions. These results suggest that an augmentation in the level of species dispersal permits organisms to couple local communities together which increases local coexistence and promotes the organization of richer and more complex ecological communities. Finally, our results suggest that mutualism is fundamental to the organization and persistence of ecological communities. Mutualistic species dominate in habitats characterized by a restricted carrying capacity and serve as ecological engineer by facilitating the establishment of competitors, predators and opportunists which benefit from their presence.