Characterization of structure and dynamics of submicrometric systems via fluorescence correlation spectroscopy

The presented thesis revolves around the study of thermally-responsive PNIPAAm-based hydrogels in water/based environments, as studied by Fluorescence Correlation Spectroscopy (FCS).rnThe goal of the project was the engineering of PNIPAAm gels into biosensors. Specifically, a gamma of such gels were both investigated concerning their dynamics and structure at the nanometer scale, and their performance in retaining bound bodies upon thermal collapse (which PNIPAAm undergoes upon heating above 32 ºC).rnFCS’s requirements, as a technique, match the limitations imposed by the system. Namely, the need to intimately probe a system in a solvent, which was also fragile and easy to alter. FCS, on the other hand, both requires a fluid environment to work, and is based on the observation of diffusion of fluorescents at nanomolar concentrations. FCS was applied to probe the hydrogels on the nanometer size with minimal invasivity.rnVariables in the gels were addressed in the project including crosslinking degree; structural changes during thermal collapse; behavior in different buffers; the possibility of decreasing the degree of inhomogeneity; behavior of differently sized probes; and the effectiveness of antibody functionalization upon thermal collapse.rnThe evidenced results included the heightening of structural inhomogeneities during thermal collapse and under different buffer conditions; the use of annealing to decrease the inhomogeneity degree; the use of differently sized probes to address different length scale of the gel; and the successful functionalization before and after collapse.rnThe thesis also addresses two side projects, also carried forward via FCS. One, diffusion in inverse opals, produced a predictive simulation model for diffusion of bodies in confined systems as dependent on the bodies’ size versus the characteristic sizes of the system. The other was the observation of interaction of bodies of opposite charge in a water solution, resulting in a phenomenological theory and an evaluation method for both the average residence time of the different bodies together, and their attachment likelihood.

Design and experimental characterization of antennas and wireless systems for innovative wearable and implantable ultra low–power applications

The present PhD thesis exploits the design skills I have been improving since my master thesis’ research. A brief description of the chapters’ content follows. Chapter 1: the simulation of a complete front–end is a very complex problem and, in particular, is the basis upon which the prediction of the overall performance of the system is possible. By means of a commercial EM simulation tool and a rigorous nonlinear/EM circuit co–simulation based on the Reciprocity Theorem, the above–mentioned prediction can be achieved and exploited for wireless links characterization. This will represent the theoretical basics of the entire present thesis and will be supported by two RF applications. Chapter 2: an extensive dissertation about Magneto–Dielectric (MD) materials will be presented, together with their peculiar characteristics as substrates for antenna miniaturization purposes. A designed and tested device for RF on–body applications will be described in detail. Finally, future research will be discussed. Chapter 3: this chapter will deal with the issue regarding the exploitation of renewable energy sources for low–energy consumption devices. Hence the problem related to the so–called energy harvesting will be tackled and a first attempt to deploy THz solar energy in an innovative way will be presented and discussed. Future research will be proposed as well. Chapter 4: graphene is a very promising material for devices to be exploited in the RF and THz frequency range for a wide range of engineering applications, including those ones marked as the main research goal of the present thesis. This chapter will present the results obtained during my research period at the National Institute for Research and Development in Microtechnologies (IMT) in Bucharest, Romania. It will concern the design and manufacturing of antennas and diodes made in graphene–based technology for detection/rectification purposes.

Numerical study of homogeneous and heterogeneous crystal nucleation in colloidal systems

Im Rahmen dieser Arbeit wurden Computersimulationen von Keimbildungs- und Kris\-tallisationsprozessen in rnkolloidalen Systemen durchgef\"uhrt. rnEine Kombination von Monte-Carlo-Simulationsmethoden und der Forward-Flux-Sampling-Technik wurde rnimplementiert, um die homogene und heterogene Nukleation von Kristallen monodisperser Hart\-kugeln zu untersuchen. rnIm m\"a\ss{ig} unterk\"uhlten Bulk-Hartkugelsystem sagen wir die homogenen Nukleationsraten voraus und rnvergleichen die Resultate mit anderen theoretischen Ergebnissen und experimentellen Daten. rnWeiterhin analysieren wir die kristallinen Cluster in den Keimbildungs- und Wachstumszonen, rnwobei sich herausstellt, dass kristalline Cluster sich in unterschiedlichen Formen im System bilden. rnKleine Cluster sind eher l\"anglich in eine beliebige Richtung ausgedehnt, w\"ahrend gr\"o\ss{ere} rnCluster kompakter und von ellipsoidaler Gestalt sind. rn rnIm n\"achsten Teil untersuchen wir die heterogene Keimbildung an strukturierten bcc (100)-W\"anden. rnDie 2d-Analyse der kristallinen Schichten an der Wand zeigt, dass die Struktur der rnWand eine entscheidende Rolle in der Kristallisation von Hartkugelkolloiden spielt. rnWir sagen zudem die heterogenen Kristallbildungsraten bei verschiedenen \"Ubers\"attigungsgraden voraus. rnDurch Analyse der gr\"o\ss{ten} Cluster an der Wand sch\"atzen wir zus\"atzlich den Kontaktwinkel rnzwischen Kristallcluster und Wand ab. rnEs stellt sich heraus, dass wir in solchen Systemen weit von der Benetzungsregion rnentfernt sind und der Kristallisationsprozess durch heterogene Nukleation stattfindet. rn rnIm letzten Teil der Arbeit betrachten wir die Kristallisation von Lennard-Jones-Kolloidsystemen rnzwischen zwei ebenen W\"anden. rnUm die Erstarrungsprozesse f\"ur ein solches System zu untersuchen, haben wir eine Analyse des rnOrdnungsparameters f\"ur die Bindung-Ausrichtung in den Schichten durchgef\"urt. rnDie Ergebnisse zeigen, dass innerhalb einer Schicht keine hexatische Ordnung besteht, rnwelche auf einen Kosterlitz-Thouless-Schmelzvorgang hinweisen w\"urde. rnDie Hysterese in den Erhitzungs-Gefrier\-kurven zeigt dar\"uber hinaus, dass der Kristallisationsprozess rneinen aktivierten Prozess darstellt.

Simulation of Smart Materials

The aim of this thesis is the elucidation of structure-properties relationship of molecular semiconductors for electronic devices. This involves the use of a comprehensive set of simulation techniques, ranging from quantum-mechanical to numerical stochastic methods, and also the development of ad-hoc computational tools. In more detail, the research activity regarded two main topics: the study of electronic properties and structural behaviour of liquid crystalline (LC) materials based on functionalised oligo(p-phenyleneethynylene) (OPE), and the investigation on the electric field effect associated to OFET operation on pentacene thin film stability. In this dissertation, a novel family of substituted OPE liquid crystals with applications in stimuli-responsive materials is presented. In more detail, simulations can not only provide evidence for the characterization of the liquid crystalline phases of different OPEs, but elucidate the role of charge transfer states in donor-acceptor LCs containing an endohedral metallofullerene moiety. Such systems can be regarded as promising candidates for organic photovoltaics. Furthermore, exciton dynamics simulations are performed as a way to obtain additional information about the degree of order in OPE columnar phases. Finally, ab initio and molecular mechanics simulations are used to investigate the influence of an applied electric field on pentacene reactivity and stability. The reaction path of pentacene thermal dimerization in the presence of an external electric field is investigated; the results can be related to the fatigue effect observed in OFETs, that show significant performance degradation even in the absence of external agents. In addition to this, the effect of the gate voltage on a pentacene monolayer are simulated, and the results are then compared to X-ray diffraction measurements performed for the first time on operating OFETs.

Synthesis and conformational analysis of heteroaromatic atropisomeric systems

The research work reported in this Thesis was held along two main lines of research. The first and main line of research is about the synthesis of heteroaromatic compounds with increasing steric hindrance, with the aim of preparing stable atropisomers. The main tools used for the study of these dynamic systems, as described in the Introduction, are DNMR, coupled with line shape simulation and DFT calculations, aimed to the conformational analysis for the prediction of the geometries and energy barriers to the trasition states. This techniques have been applied to the research projects about: • atropisomers of arylmaleimides; • atropisomers of 4-arylpyrazolo[3,4-b]pyridines; • study of the intramolecular NO2/CO interaction in solution; • study on 2-arylpyridines. Parallel to the main project, in collaboration with other groups, the research line about determination of the absolute configuration was followed. The products, deriving form organocatalytic reactions, in many cases couldn’t be analyzed by means of X-Ray diffraction, making necessary the development of a protocol based on spectroscopic methodologies: NMR, circular dichroism and computational tools (DFT, TD-DFT) have been implemented in this scope. In this Thesis are reported the determination of the absolute configuration of: • substituted 1,2,3,4-tetrahydroquinolines; • compounds from enantioselective Friedel-Crafts alkylation-acetalization cascade of naphthols with α,β-unsaturated cyclic ketones; • substituted 3,4-annulated indoles.

Severe Accident Simulation of Small Modular Reactors

Since the Three Mile Island Unit 2 (TMI-2), accident in 1979 which led to the meltdown of about one half of the reactor core and to limited releases of radioactive materials to the environment, an important international effort has been made on severe accident research. The present work aims to investigate the behaviour of a Small Modular Reactor during severe accident conditions. In order to perform these analyses, a SMR has been studied for the European reference severe accident analysis code ASTEC, developed by IRSN and GRS. In the thesis will be described in detail the IRIS Small Modular Reactor; the reference reactor chosen to develop the ASTEC input deck. The IRIS model was developed in the framework of a research collaboration with the IRSN development team. In the thesis will be described systematically the creation of the ASTEC IRIS input deck: the nodalization scheme adopted, the solution used to simulate the passive safety systems and the strong interaction between the reactor vessel and the containment. The ASTEC SMR model will be tested against the RELAP-GOTHIC coupled code model, with respect to a Design Basis Accident, to evaluate the capability of the ASTEC code on reproducing correctly the behaviour of the nuclear system. Once the model has been validated, a severe accident scenario will be simulated and the obtained results along with the nuclear system response will be analysed.

Simulation of visible light communications in vehicular networks

The rapid development in the field of lighting and illumination allows low energy consumption and a rapid growth in the use, and development of solid-state sources. As the efficiency of these devices increases and their cost decreases there are predictions that they will become the dominant source for general illumination in the short term. The objective of this thesis is to study, through extensive simulations in realistic scenarios, the feasibility and exploitation of visible light communication (VLC) for vehicular ad hoc networks (VANETs) applications. A brief introduction will introduce the new scenario of smart cities in which visible light communication will become a fundamental enabling technology for the future communication systems. Specifically, this thesis focus on the acquisition of several, frequent, and small data packets from vehicles, exploited as sensors of the environment. The use of vehicles as sensors is a new paradigm to enable an efficient environment monitoring and an improved traffic management. In most cases, the sensed information must be collected at a remote control centre and one of the most challenging aspects is the uplink acquisition of data from vehicles. My thesis discusses the opportunity to take advantage of short range vehicle-to-vehicle (V2V) and vehicle-to-roadside (V2R) communications to offload the cellular networks. More specifically, it discusses the system design and assesses the obtainable cellular resource saving, by considering the impact of the percentage of vehicles equipped with short range communication devices, of the number of deployed road side units, and of the adopted routing protocol. When short range communications are concerned, WAVE/IEEE 802.11p is considered as standard for VANETs. Its use together with VLC will be considered in urban vehicular scenarios to let vehicles communicate without involving the cellular network. The study is conducted by simulation, considering both a simulation platform (SHINE, simulation platform for heterogeneous interworking networks) developed within the Wireless communication Laboratory (Wilab) of the University of Bologna and CNR, and network simulator (NS3). trying to realistically represent all the wireless network communication aspects. Specifically, simulation of vehicular system was performed and introduced in ns-3, creating a new module for the simulator. This module will help to study VLC applications in VANETs. Final observations would enhance and encourage potential research in the area and optimize performance of VLC systems applications in the future.

Computer simulation methods to study interfacial tensions : from the Ising model to colloidal crystals

In condensed matter systems, the interfacial tension plays a central role for a multitude of phenomena. It is the driving force for nucleation processes, determines the shape and structure of crystalline structures and is important for industrial applications. Despite its importance, the interfacial tension is hard to determine in experiments and also in computer simulations. While for liquid-vapor interfacial tensions there exist sophisticated simulation methods to compute the interfacial tension, current methods for solid-liquid interfaces produce unsatisfactory results.rnrnAs a first approach to this topic, the influence of the interfacial tension on nuclei is studied within the three-dimensional Ising model. This model is well suited because despite its simplicity, one can learn much about nucleation of crystalline nuclei. Below the so-called roughening temperature, nuclei in the Ising model are not spherical anymore but become cubic because of the anisotropy of the interfacial tension. This is similar to crystalline nuclei, which are in general not spherical but more like a convex polyhedron with flat facets on the surface. In this context, the problem of distinguishing between the two bulk phases in the vicinity of the diffuse droplet surface is addressed. A new definition is found which correctly determines the volume of a droplet in a given configuration if compared to the volume predicted by simple macroscopic assumptions.rnrnTo compute the interfacial tension of solid-liquid interfaces, a new Monte Carlo method called ensemble switch method'' is presented which allows to compute the interfacial tension of liquid-vapor interfaces as well as solid-liquid interfaces with great accuracy. In the past, the dependence of the interfacial tension on the finite size and shape of the simulation box has often been neglected although there is a nontrivial dependence on the box dimensions. As a consequence, one needs to systematically increase the box size and extrapolate to infinite volume in order to accurately predict the interfacial tension. Therefore, a thorough finite-size scaling analysis is established in this thesis. Logarithmic corrections to the finite-size scaling are motivated and identified, which are of leading order and therefore must not be neglected. The astounding feature of these logarithmic corrections is that they do not depend at all on the model under consideration. Using the ensemble switch method, the validity of a finite-size scaling ansatz containing the aforementioned logarithmic corrections is carefully tested and confirmed. Combining the finite-size scaling theory with the ensemble switch method, the interfacial tension of several model systems, ranging from the Ising model to colloidal systems, is computed with great accuracy.

Agent-based simulation for renewable energy incentive design

In this thesis, we propose a novel approach to model the diffusion of residential PV systems. For this purpose, we use an agent-based model where agents are the families living in the area of interest. The case study is the Emilia-Romagna Regional Energy plan, which aims to increase the produc- tion of electricity from renewable energy. So, we study the microdata from the Survey on Household Income and Wealth (SHIW) provided by Bank of Italy in order to obtain the characteristics of families living in Emilia-Romagna. These data have allowed us to artificial generate families and reproduce the socio-economic aspects of the region. The families generated by means of a software are placed on the virtual world by associating them with the buildings. These buildings are acquired by analysing the vector data of regional buildings made available by the region. Each year, the model determines the level of diffusion by simulating the installed capacity. The adoption behaviour is influenced by social interactions, household’s economic situation, the environmental benefits arising from the adoption and the payback period of the investment.

Modelling and simulating in systems biology: an approach based on multi-agent systems

Systems Biology is an innovative way of doing biology recently raised in bio-informatics contexts, characterised by the study of biological systems as complex systems with a strong focus on the system level and on the interaction dimension. In other words, the objective is to understand biological systems as a whole, putting on the foreground not only the study of the individual parts as standalone parts, but also of their interaction and of the global properties that emerge at the system level by means of the interaction among the parts. This thesis focuses on the adoption of multi-agent systems (MAS) as a suitable paradigm for Systems Biology, for developing models and simulation of complex biological systems. Multi-agent system have been recently introduced in informatics context as a suitabe paradigm for modelling and engineering complex systems. Roughly speaking, a MAS can be conceived as a set of autonomous and interacting entities, called agents, situated in some kind of nvironment, where they fruitfully interact and coordinate so as to obtain a coherent global system behaviour. The claim of this work is that the general properties of MAS make them an effective approach for modelling and building simulations of complex biological systems, following the methodological principles identified by Systems Biology. In particular, the thesis focuses on cell populations as biological systems. In order to support the claim, the thesis introduces and describes (i) a MAS-based model conceived for modelling the dynamics of systems of cells interacting inside cell environment called niches. (ii) a computational tool, developed for implementing the models and executing the simulations. The tool is meant to work as a kind of virtual laboratory, on top of which kinds of virtual experiments can be performed, characterised by the definition and execution of specific models implemented as MASs, so as to support the validation, falsification and improvement of the models through the observation and analysis of the simulations. A hematopoietic stem cell system is taken as reference case study for formulating a specific model and executing virtual experiments.

Modeling and simulation of fibrinogen and its adsorption behavior

In this thesis different approaches for the modeling and simulation of the blood protein fibrinogen are presented. The approaches are meant to systematically connect the multiple time and length scales involved in the dynamics of fibrinogen in solution and at inorganic surfaces. The first part of the thesis will cover simulations of fibrinogen on an all atom level. Simulations of the fibrinogen protomer and dimer are performed in explicit solvent to characterize the dynamics of fibrinogen in solution. These simulations reveal an unexpectedly large and fast bending motion that is facilitated by molecular hinges located in the coiled-coil region of fibrinogen. This behavior is characterized by a bending and a dihedral angle and the distribution of these angles is measured. As a consequence of the atomistic detail of the simulations it is possible to illuminate small scale behavior in the binding pockets of fibrinogen that hints at a previously unknown allosteric effect. In a second step atomistic simulations of the fibrinogen protomer are performed at graphite and mica surfaces to investigate initial adsorption stages. These simulations highlight the different adsorption mechanisms at the hydrophobic graphite surface and the charged, hydrophilic mica surface. It is found that the initial adsorption happens in a preferred orientation on mica. Many effects of practical interest involve aggregates of many fibrinogen molecules. To investigate such systems, time and length scales need to be simulated that are not attainable in atomistic simulations. It is therefore necessary to develop lower resolution models of fibrinogen. This is done in the second part of the thesis. First a systematically coarse grained model is derived and parametrized based on the atomistic simulations of the first part. In this model the fibrinogen molecule is represented by 45 beads instead of nearly 31,000 atoms. The intra-molecular interactions of the beads are modeled as a heterogeneous elastic network while inter-molecular interactions are assumed to be a combination of electrostatic and van der Waals interaction. A method is presented that determines the charges assigned to beads by matching the electrostatic potential in the atomistic simulation. Lastly a phenomenological model is developed that represents fibrinogen by five beads connected by rigid rods with two hinges. This model only captures the large scale dynamics in the atomistic simulations but can shed light on experimental observations of fibrinogen conformations at inorganic surfaces.

Computer simulation of rod-coil block copolymers and tetrapod,polymer mixtures

In this thesis I present a new coarse-grained model suitable to investigate the phase behavior of rod-coil block copolymers on mesoscopic length scales. In this model the rods are represented by hard spherocylinders, whereas the coil block consists of interconnected beads. The interactions between the constituents are based on local densities. This facilitates an efficient Monte-Carlo sampling of the phase space. I verify the applicability of the model and the simulation approach by means of several examples. I treat pure rod systems and mixtures of rod and coil polymers. Then I append coils to the rods and investigate the role of the different model parameters. Furthermore, I compare different implementations of the model. I prove the capability of the rod-coil block copolymers in our model to exhibit typical micro-phase separated configurations as well as extraordinary phases, such as the wavy lamellar state, percolating structuresrnand clusters. Additionally, I demonstrate the metastability of the observed zigzag phase in our model. A central point of this thesis is the examination of the phase behavior of the rod-coil block copolymers in dependence of different chain lengths and interaction strengths between rods and coil. The observations of these studies are summarized in a phase diagram for rod-coil block copolymers. Furthermore, I validate a stabilization of the smectic phase with increasing coil fraction.rnIn the second part of this work I present a side project in which I derive a model permitting the simulation of tetrapods with and without grafted semiconducting block copolymers. The effect of these polymers is added in an implicit manner by effective interactions between the tetrapods. While the depletion interaction is described in an approximate manner within the Asakura-Oosawa model, the free energy penalty for the brush compression is calculated within the Alexander-de Gennes model. Recent experiments with CdSe tetrapods show that grafted tetrapods are clearly much better dispersed in the polymer matrix than bare tetrapods. My simulations confirm that bare tetrapods tend to aggregate in the matrix of excess polymers, while clustering is significantly reduced after grafting polymer chains to the tetrapods. Finally, I propose a possible extension enabling the simulation of a system with fluctuating volume and demonstrate its basic functionality. This study is originated in a cooperation with an experimental group with the goal to analyze the morphology of these systems in order to find the ideal morphology for hybrid solar cells.

Modelling, simulation and optimization of maintenance considerations on condition based maintenance

Globalization has increased the pressure on organizations and companies to operate in the most efficient and economic way. This tendency promotes that companies concentrate more and more on their core businesses, outsource less profitable departments and services to reduce costs. By contrast to earlier times, companies are highly specialized and have a low real net output ratio. For being able to provide the consumers with the right products, those companies have to collaborate with other suppliers and form large supply chains. An effect of large supply chains is the deficiency of high stocks and stockholding costs. This fact has lead to the rapid spread of Just-in-Time logistic concepts aimed minimizing stock by simultaneous high availability of products. Those concurring goals, minimizing stock by simultaneous high product availability, claim for high availability of the production systems in the way that an incoming order can immediately processed. Besides of design aspects and the quality of the production system, maintenance has a strong impact on production system availability. In the last decades, there has been many attempts to create maintenance models for availability optimization. Most of them concentrated on the availability aspect only without incorporating further aspects as logistics and profitability of the overall system. However, production system operator’s main intention is to optimize the profitability of the production system and not the availability of the production system. Thus, classic models, limited to represent and optimize maintenance strategies under the light of availability, fail. A novel approach, incorporating all financial impacting processes of and around a production system, is needed. The proposed model is subdivided into three parts, maintenance module, production module and connection module. This subdivision provides easy maintainability and simple extendability. Within those modules, all aspect of production process are modeled. Main part of the work lies in the extended maintenance and failure module that offers a representation of different maintenance strategies but also incorporates the effect of over-maintaining and failed maintenance (maintenance induced failures). Order release and seizing of the production system are modeled in the production part. Due to computational power limitation, it was not possible to run the simulation and the optimization with the fully developed production model. Thus, the production model was reduced to a black-box without higher degree of details.

A framework for cyber-physical system simulation

In these last years, systems engineering has became one of the major research domains. The complexity of systems has increased constantly and nowadays Cyber-Physical Systems (CPS) are a category of particular interest: these, are systems composed by a cyber part (computer-based algorithms) that monitor and control some physical processes. Their development and simulation are both complex due to the importance of the interaction between the cyber and the physical entities: there are a lot of models written in different languages that need to exchange information among each other. Normally people use an orchestrator that takes care of the simulation of the models and the exchange of informations. This orchestrator is developed manually and this is a tedious and long work. Our proposition is to achieve to generate the orchestrator automatically through the use of Co-Modeling, i.e. by modeling the coordination. Before achieving this ultimate goal, it is important to understand the mechanisms and de facto standards that could be used in a co-modeling framework. So, I studied the use of a technology employed for co-simulation in the industry: FMI. In order to better understand the FMI standard, I realized an automatic export, in the FMI format, of the models realized in an existing software for discrete modeling: TimeSquare. I also developed a simple physical model in the existing open source openmodelica tool. Later, I started to understand how works an orchestrator, developing a simple one: this will be useful in future to generate an orchestrator automatically.