Fiber beam-columns models with flexure-shear interaction for nonlinear analysis of reinforced concrete structures

The aim of this study was to develop a model capable to capture the different contributions which characterize the nonlinear behaviour of reinforced concrete structures. In particular, especially for non slender structures, the contribution to the nonlinear deformation due to bending may be not sufficient to determine the structural response. Two different models characterized by a fibre beam-column element are here proposed. These models can reproduce the flexure-shear interaction in the nonlinear range, with the purpose to improve the analysis in shear-critical structures. The first element discussed is based on flexibility formulation which is associated with the Modified Compression Field Theory as material constitutive law. The other model described in this thesis is based on a three-field variational formulation which is associated with a 3D generalized plastic-damage model as constitutive relationship. The first model proposed in this thesis was developed trying to combine a fibre beamcolumn element based on the flexibility formulation with the MCFT theory as constitutive relationship. The flexibility formulation, in fact, seems to be particularly effective for analysis in the nonlinear field. Just the coupling between the fibre element to model the structure and the shear panel to model the individual fibres allows to describe the nonlinear response associated to flexure and shear, and especially their interaction in the nonlinear field. The model was implemented in an original matlab® computer code, for describing the response of generic structures. The simulations carried out allowed to verify the field of working of the model. Comparisons with available experimental results related to reinforced concrete shears wall were performed in order to validate the model. These results are characterized by the peculiarity of distinguishing the different contributions due to flexure and shear separately. The presented simulations were carried out, in particular, for monotonic loading. The model was tested also through numerical comparisons with other computer programs. Finally it was applied for performing a numerical study on the influence of the nonlinear shear response for non slender reinforced concrete (RC) members. Another approach to the problem has been studied during a period of research at the University of California Berkeley. The beam formulation follows the assumptions of the Timoshenko shear beam theory for the displacement field, and uses a three-field variational formulation in the derivation of the element response. A generalized plasticity model is implemented for structural steel and a 3D plastic-damage model is used for the simulation of concrete. The transverse normal stress is used to satisfy the transverse equilibrium equations of at each control section, this criterion is also used for the condensation of degrees of freedom from the 3D constitutive material to a beam element. In this thesis is presented the beam formulation and the constitutive relationships, different analysis and comparisons are still carrying out between the two model presented.

Dynamics, rheology and critical properties of colloidal fluid mixtures

Liquids under the influence of external fields exhibit a wide range of intriguing phenomena that can be markedly different from the behaviour of a quiescent system. This work considers two different systems — a glassforming Yukawa system and a colloid-polymer mixture — by Molecular Dynamics (MD) computer simulations coupled to dissipative particle dynamics. The former consists of a 50-50 binary mixture of differently-sized, like-charged colloids interacting via a screened Coulomb (Yukawa) potential. Near the glass transition the influence of an external shear field is studied. In particular, the transition from elastic response to plastic flow is of interest. At first, this model is characterised in equilibrium. Upon decreasing temperature it exhibits the typical dynamics of glassforming liquids, i.e. the structural relaxation time τα grows strongly in a rather small temperature range. This is discussed with respect to the mode-coupling theory of the glass transition (MCT). For the simulation of bulk systems under shear, Lees-Edwards boundary conditions are applied. At constant shear rates γ˙ ≫ 1/τα the relevant time scale is given by 1/γ˙ and the system shows shear thinning behaviour. In order to understand the pronounced differences between a quiescent system and a system under shear, the response to a suddenly commencing or terminating shear flow is studied. After the switch-on of the shear field the shear stress shows an overshoot, marking the transition from elastic to plastic deformation, which is connected to a super-diffusive increase of the mean squared displacement. Since the average static structure only depends on the value of the shear stress, it does not discriminate between those two regimes. The distribution of local stresses, in contrast, becomes broader as soon as the system starts flowing. After a switch-off of the shear field, these additional fluctuations are responsible for the fast decay of stresses, which occurs on a time scale 1/γ˙ . The stress decay after a switch-off in the elastic regime, on the other hand, happens on the much larger time scale of structural relaxation τα. While stresses decrease to zero after a switch-off for temperatures above the glass transition, they decay to a finite value for lower temperatures. The obtained results are important for advancing new theoretical approaches in the framework of mode-coupling theory. Furthermore, they suggest new experimental investigations on colloidal systems. The colloid-polymer mixture is studied in the context of the behaviour near the critical point of phase separation. For the MD simulations a new effective model with soft interaction potentials is introduced and its phase diagram is presented. Here, mainly the equilibrium properties of this model are characterised. While the self-diffusion constants of colloids and polymers do not change strongly when the critical point is approached, critical slowing down of interdiffusion is observed. The order parameter fluctuations can be determined through the long-wavelength limit of static structure factors. For this strongly asymmetric mixture it is shown how the relevant structure factor can be extracted by a diagonalisation of a matrix that contains the partial static structure factors. By presenting first results of this model under shear it is demonstrated that it is suitable for non-equilibrium simulations as well.

Engineering Agent-Oriented Technologies and Programming Languages for Computer Programming and Software Development

Mainstream hardware is becoming parallel, heterogeneous, and distributed on every desk, every home and in every pocket. As a consequence, in the last years software is having an epochal turn toward concurrency, distribution, interaction which is pushed by the evolution of hardware architectures and the growing of network availability. This calls for introducing further abstraction layers on top of those provided by classical mainstream programming paradigms, to tackle more effectively the new complexities that developers have to face in everyday programming. A convergence it is recognizable in the mainstream toward the adoption of the actor paradigm as a mean to unite object-oriented programming and concurrency. Nevertheless, we argue that the actor paradigm can only be considered a good starting point to provide a more comprehensive response to such a fundamental and radical change in software development. Accordingly, the main objective of this thesis is to propose Agent-Oriented Programming (AOP) as a high-level general purpose programming paradigm, natural evolution of actors and objects, introducing a further level of human-inspired concepts for programming software systems, meant to simplify the design and programming of concurrent, distributed, reactive/interactive programs. To this end, in the dissertation first we construct the required background by studying the state-of-the-art of both actor-oriented and agent-oriented programming, and then we focus on the engineering of integrated programming technologies for developing agent-based systems in their classical application domains: artificial intelligence and distributed artificial intelligence. Then, we shift the perspective moving from the development of intelligent software systems, toward general purpose software development. Using the expertise maturated during the phase of background construction, we introduce a general-purpose programming language named simpAL, which founds its roots on general principles and practices of software development, and at the same time provides an agent-oriented level of abstraction for the engineering of general purpose software systems.

Topological aspects of the human protein interaction network

It is currently widely accepted that the understanding of complex cell functions depends on an integrated network theoretical approach and not on an isolated view of the different molecular agents. Aim of this thesis was the examination of topological properties that mirror known biological aspects by depicting the human protein network with methods from graph- and network theory. The presented network is a partial human interactome of 9222 proteins and 36324 interactions, consisting of single interactions reliably extracted from peer-reviewed scientific publications. In general, one can focus on intra- or intermodular characteristics, where a functional module is defined as "a discrete entity whose function is separable from those of other modules". It is found that the presented human network is also scale-free and hierarchically organised, as shown for yeast networks before. The interactome also exhibits proteins with high betweenness and low connectivity which are biologically analyzed and interpreted here as shuttling proteins between organelles (e.g. ER to Golgi, internal ER protein translocation, peroxisomal import, nuclear pores import/export) for the first time. As an optimisation for finding proteins that connect modules, a new method is developed here based on proteins located between highly clustered regions, rather than regarding highly connected regions. As a proof of principle, the Mediator complex is found in first place, the prime example for a connector complex. Focusing on intramodular aspects, the measurement of k-clique communities discriminates overlapping modules very well. Twenty of the largest identified modules are analysed in detail and annotated to known biological structures (e.g. proteasome, the NFκB-, TGF-β complex). Additionally, two large and highly interconnected modules for signal transducer and transcription factor proteins are revealed, separated by known shuttling proteins. These proteins yield also the highest number of redundant shortcuts (by calculating the skeleton), exhibit the highest numbers of interactions and might constitute highly interconnected but spatially separated rich-clubs either for signal transduction or for transcription factors. This design principle allows manifold regulatory events for signal transduction and enables a high diversity of transcription events in the nucleus by a limited set of proteins. Altogether, biological aspects are mirrored by pure topological features, leading to a new view and to new methods that assist the annotation of proteins to biological functions, structures and subcellular localisations. As the human protein network is one of the most complex networks at all, these results will be fruitful for other fields of network theory and will help understanding complex network functions in general.

Effect of mixing, particle interaction, and spatial dimension on the glass transition

In this thesis, the influence of composition changes on the glass transition behavior of binary liquids in two and three spatial dimensions (2D/3D) is studied in the framework of mode-coupling theory (MCT).The well-established MCT equations are generalized to isotropic and homogeneous multicomponent liquids in arbitrary spatial dimensions. Furthermore, a new method is introduced which allows a fast and precise determination of special properties of glass transition lines. The new equations are then applied to the following model systems: binary mixtures of hard disks/spheres in 2D/3D, binary mixtures of dipolar point particles in 2D, and binary mixtures of dipolar hard disks in 2D. Some general features of the glass transition lines are also discussed. The direct comparison of the binary hard disk/sphere models in 2D/3D shows similar qualitative behavior. Particularly, for binary mixtures of hard disks in 2D the same four so-called mixing effects are identified as have been found before by Götze and Voigtmann for binary hard spheres in 3D [Phys. Rev. E 67, 021502 (2003)]. For instance, depending on the size disparity, adding a second component to a one-component liquid may lead to a stabilization of either the liquid or the glassy state. The MCT results for the 2D system are on a qualitative level in agreement with available computer simulation data. Furthermore, the glass transition diagram found for binary hard disks in 2D strongly resembles the corresponding random close packing diagram. Concerning dipolar systems, it is demonstrated that the experimental system of König et al. [Eur. Phys. J. E 18, 287 (2005)] is well described by binary point dipoles in 2D through a comparison between the experimental partial structure factors and those from computer simulations. For such mixtures of point particles it is demonstrated that MCT predicts always a plasticization effect, i.e. a stabilization of the liquid state due to mixing, in contrast to binary hard disks in 2D or binary hard spheres in 3D. It is demonstrated that the predicted plasticization effect is in qualitative agreement with experimental results. Finally, a glass transition diagram for binary mixtures of dipolar hard disks in 2D is calculated. These results demonstrate that at higher packing fractions there is a competition between the mixing effects occurring for binary hard disks in 2D and those for binary point dipoles in 2D.

Between the scales: Water from different perspectives

In der vorliegenden Arbeit werden verschiedene Wassermodelle in sogenannten Multiskalen-Computersimulationen mit zwei Auflösungen untersucht, in atomistischer Auflösung und in einer vergröberten Auflösung, die als "coarse-grained" bezeichnet wird. In der atomistischen Auflösung wird ein Wassermolekül, entsprechend seiner chemischen Struktur, durch drei Atome beschrieben, im Gegensatz dazu wird ein Molekül in der coarse-grained Auflösung durch eine Kugel dargestellt.rnrnDie coarse-grained Modelle, die in dieser Arbeit vorgestellt werden, werden mit verschiedenen coarse-graining Methoden entwickelt. Hierbei kommen hauptsächlich die "iterative Boltzmann Inversion" und die "iterative Monte Carlo Inversion" zum Einsatz. Beides sind struktur-basierte Ansätze, die darauf abzielen bestimmte strukturelle Eigenschaften, wie etwa die Paarverteilungsfunktionen, des zugrundeliegenden atomistischen Systems zu reproduzieren. Zur automatisierten Anwendung dieser Methoden wurde das Softwarepaket "Versatile Object-oriented Toolkit for Coarse-Graining Applications" (VOTCA) entwickelt.rnrnEs wird untersucht, in welchem Maße coarse-grained Modelle mehrere Eigenschaftenrndes zugrundeliegenden atomistischen Modells gleichzeitig reproduzieren können, z.B. thermodynamische Eigenschaften wie Druck und Kompressibilität oder strukturelle Eigenschaften, die nicht zur Modellbildung verwendet wurden, z.B. das tetraedrische Packungsverhalten, welches für viele spezielle Eigenschaft von Wasser verantwortlich ist.rnrnMit Hilfe des "Adaptive Resolution Schemes" werden beide Auflösungen in einer Simulation kombiniert. Dabei profitiert man von den Vorteilen beider Modelle:rnVon der detaillierten Darstellung eines räumlich kleinen Bereichs in atomistischer Auflösung und von der rechnerischen Effizienz des coarse-grained Modells, die den Bereich simulierbarer Zeit- und Längenskalen vergrössert.rnrnIn diesen Simulationen kann der Einfluss des Wasserstoffbrückenbindungsnetzwerks auf die Hydration von Fullerenen untersucht werden. Es zeigt sich, dass die Struktur der Wassermoleküle an der Oberfläche hauptsächlich von der Art der Wechselwirkung zwischen dem Fulleren und Wasser und weniger von dem Wasserstoffbrückenbindungsnetzwerk dominiert wird.rn

Mental states monitoring through passive Brain-Computer Interface systems

The monitoring of cognitive functions aims at gaining information about the current cognitive state of the user by decoding brain signals. In recent years, this approach allowed to acquire valuable information about the cognitive aspects regarding the interaction of humans with external world. From this consideration, researchers started to consider passive application of brain–computer interface (BCI) in order to provide a novel input modality for technical systems solely based on brain activity. The objective of this thesis is to demonstrate how the passive Brain Computer Interfaces (BCIs) applications can be used to assess the mental states of the users, in order to improve the human machine interaction. Two main studies has been proposed. The first one allows to investigate whatever the Event Related Potentials (ERPs) morphological variations can be used to predict the users’ mental states (e.g. attentional resources, mental workload) during different reactive BCI tasks (e.g. P300-based BCIs), and if these information can predict the subjects’ performance in performing the tasks. In the second study, a passive BCI system able to online estimate the mental workload of the user by relying on the combination of the EEG and the ECG biosignals has been proposed. The latter study has been performed by simulating an operative scenario, in which the occurrence of errors or lack of performance could have significant consequences. The results showed that the proposed system is able to estimate online the mental workload of the subjects discriminating three different difficulty level of the tasks ensuring a high reliability.

Numerical modelling of fluid-structure interaction with application in hemodynamics

The thesis deals with numerical algorithms for fluid-structure interaction problems with application in blood flow modelling. It starts with a short introduction on the mathematical description of incompressible viscous flow with non-Newtonian viscosity and a moving linear viscoelastic structure. The mathematical model consists of the generalized Navier-Stokes equation used for the description of fluid flow and the generalized string model for structure movement. The arbitrary Lagrangian-Eulerian approach is used in order to take into account moving computational domain. A part of the thesis is devoted to the discussion on the non-Newtonian behaviour of shear-thinning fluids, which is in our case blood, and derivation of two non-Newtonian models frequently used in the blood flow modelling. Further we give a brief overview on recent fluid-structure interaction schemes with discussion about the difficulties arising in numerical modelling of blood flow. Our main contribution lies in numerical and experimental study of a new loosely-coupled partitioned scheme called the kinematic splitting fluid-structure interaction algorithm. We present stability analysis for a coupled problem of non-Newtonian shear-dependent fluids in moving domains with viscoelastic boundaries. Here, we assume both, the nonlinearity in convective as well is diffusive term. We analyse the convergence of proposed numerical scheme for a simplified fluid model of the Oseen type. Moreover, we present series of experiments including numerical error analysis, comparison of hemodynamic parameters for the Newtonian and non-Newtonian fluids and comparison of several physiologically relevant computational geometries in terms of wall displacement and wall shear stress. Numerical analysis and extensive experimental study for several standard geometries confirm reliability and accuracy of the proposed kinematic splitting scheme in order to approximate fluid-structure interaction problems.

Computer simulation studies of vector spin glasses

Die vorliegende Doktorarbeit befasst sich mit klassischen Vektor-Spingläsern eine Art von ungeordneten Magneten - auf verschiedenen Gittertypen. Da siernbedeutsam für eine experimentelle Realisierung sind, ist ein theoretisches Verständnis von Spinglas-Modellen mit wenigen Spinkomponenten und niedriger Gitterdimension von großer Bedeutung. Da sich dies jedoch als sehr schwierigrnerweist, sind neue, aussichtsreiche Ansätze nötig. Diese Arbeit betrachtet daher den Limesrnunendlich vieler Spindimensionen. Darin entstehen mehrere Vereinfachungen im Vergleichrnzu Modellen niedriger Spindimension, so dass für dieses bedeutsame Problem Eigenschaften sowohl bei Temperatur Null als auch bei endlichen Temperaturenrnüberwiegend mit numerischen Methoden ermittelt werden. Sowohl hyperkubische Gitter als auch ein vielseitiges 1d-Modell werden betrachtet. Letzteres erlaubt es, unterschiedliche Universalitätsklassen durch bloßes Abstimmen eines einzigen Parameters zu untersuchen. "Finite-size scaling''-Formen, kritische Exponenten, Quotienten kritischer Exponenten und andere kritische Größen werden nahegelegt und mit numerischen Ergebnissen verglichen. Eine detaillierte Beschreibung der Herleitungen aller numerisch ausgewerteter Gleichungen wird ebenso angegeben. Bei Temperatur Null wird eine gründliche Untersuchung der Grundzustände und Defektenergien gemacht. Eine Reihe interessanter Größen wird analysiert und insbesondere die untere kritische Dimension bestimmt. Bei endlicher Temperatur sind der Ordnungsparameter und die Spinglas-Suszeptibilität über die numerisch berechnete Korrelationsmatrix zugänglich. Das Spinglas-Modell im Limes unendlich vieler Spinkomponenten kann man als Ausgangspunkt zur Untersuchung der natürlicheren Modelle mit niedriger Spindimension betrachten. Wünschenswert wäre natürlich ein Modell, das die Vorteile des ersten mit den Eigenschaften des zweiten verbände. Daher wird in Modell mit Anisotropie vorgeschlagen und getestet, mit welchem versucht wird, dieses Ziel zu erreichen. Es wird auf reizvolle Wege hingewiesen, das Modell zu nutzen und eine tiefergehende Beschäftigung anzuregen. Zuletzt werden sogenannte "real-space" Renormierungsgruppenrechnungen sowohl analytisch als auch numerisch für endlich-dimensionale Vektor-Spingläser mit endlicher Anzahl von Spinkomponenten durchgeführt. Dies wird mit einer zuvor bestimmten neuen Migdal-Kadanoff Rekursionsrelation geschehen. Neben anderen Größen wird die untere kritische Dimension bestimmt.

Computer simulations of slowly relaxing systems in external fields

Eine der offenen Fragen der aktuellen Physik ist das Verständnis von Systemen im Nichtgleichgewicht. Im Gegensatz zu der Gleichgewichtsphysik ist in diesem Bereich aktuell kein Formalismus bekannt der ein systematisches Beschreiben der unterschiedlichen Systeme ermöglicht. Um das Verständnis über diese Systeme zu vergrößern werden in dieser Arbeit zwei unterschiedliche Systeme studiert, die unter einem externen Feld ein starkes nichtlineares Verhalten zeigen. Hierbei handelt es sich zum einen um das Verhalten von Teilchen unter dem Einfluss einer extern angelegten Kraft und zum anderen um das Verhalten eines Systems in der Nähe des kritischen Punktes unter Scherung. Das Modellsystem in dem ersten Teil der Arbeit ist eine binäre Yukawa Mischung, die bei tiefen Temperaturen einen Glassübergang zeigt. Dies führt zu einer stark ansteigenden Relaxationszeit des Systems, so dass man auch bei kleinen Kräften relativ schnell ein nichtlineares Verhalten beobachtet. In Abhängigkeit der angelegten konstanten Kraft können in dieser Arbeit drei Regime, mit stark unterschiedlichem Teilchenverhalten, identifiziert werden. In dem zweiten Teil der Arbeit wird das Ising-Modell unter Scherung betrachtet. In der Nähe des kritischen Punkts kommt es in diesem Modell zu einer Beeinflussung der Fluktuationen in dem System durch das angelegte Scherfeld. Dies hat zur Folge, dass das System stark anisotrop wird und man zwei unterschiedliche Korrelationslängen vorfindet, die mit unterschiedlichen Exponenten divergieren. Infolgedessen lässt sich der normale isotrope Formalismus des "finite-size scaling" nicht mehr auf dieses System anwenden. In dieser Arbeit wird gezeigt, wie dieser auf den anisotropen Fall zu verallgemeinern ist und wie damit die kritischen Punkte, sowie die dazu gehörenden kritischen Exponenten berechnet werden können.

Computer simulations of two-dimensional colloidal crystals under confinement and shear

In this thesis we are presenting a broadly based computer simulation study of two-dimensional colloidal crystals under different external conditions. In order to fully understand the phenomena which occur when the system is being compressed or when the walls are being sheared, it proved necessary to study also the basic motion of the particles and the diffusion processes which occur in the case without these external forces. In the first part of this thesis we investigate the structural transition in the number of rows which occurs when the crystal is being compressed by placing the structured walls closer together. Previous attempts to locate this transition were impeded by huge hysteresis effects. We were able to determine the transition point with higher precision by applying both the Schmid-Schilling thermodynamic integration method and the phase switch Monte Carlo method in order to determine the free energies. These simulations showed not only that the phase switch method can successfully be applied to systems with a few thousand particles and a soft crystalline structure with a superimposed pattern of defects, but also that this method is way more efficient than a thermodynamic integration when free energy differences are to be calculated. Additionally, the phase switch method enabled us to distinguish between several energetically very similar structures and to determine which one of them was actually stable. Another aspect considered in the first result chapter of this thesis is the ensemble inequivalence which can be observed when the structural transition is studied in the NpT and in the NVT ensemble. The second part of this work deals with the basic motion occurring in colloidal crystals confined by structured walls. Several cases are compared where the walls are placed in different positions, thereby introducing an incommensurability into the crystalline structure. Also the movement of the solitons, which are created in the course of the structural transition, is investigated. Furthermore, we will present results showing that not only the well-known mechanism of vacancies and interstitial particles leads to diffusion in our model system, but that also cooperative ring rotation phenomena occur. In this part and the following we applied Langevin dynamics simulations. In the last chapter of this work we will present results on the effect of shear on the colloidal crystal. The shear was implemented by moving the walls with constant velocity. We have observed shear banding and, depending on the shear velocity, that the inner part of the crystal breaks into several domains with different orientations. At very high shear velocities holes are created in the structure, which originate close to the walls, but also diffuse into the inner part of the crystal.

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.

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.

Sistemi Brain Computer Interface: dalla macchina al paziente

C’è un crescente interesse nella comunità scientifica per l’applicazione delle tecniche della bioingegneria nel campo delle interfacce fra cervello e computer. Questo interesse nasce dal fatto che in Europa ci sono almeno 300.000 persone con paralisi agli arti inferiori, con una età media piuttosto bassa (31 anni), registrandosi circa 5.000 nuovi casi ogni anno, in maggioranza dovuti ad incidenti automobilistici. Tali lesioni traumatiche spinali inducono delle disfunzioni sensoriali a causa dell’interruzione tra gli arti e i centri sopraspinali. Per far fronte a questi problemi gli scienziati si sono sempre più proiettati verso un nuovo settore: il Brain Computer Interaction, ossia un ambito della ricerca volto alla costruzione di interfacce in grado di collegare direttamente il cervello umano ad un dispositivo elettrico come un computer.

Mutagenesis and computer modeling studies of a GPCR conserved residue W5.43(194) in ligand recognition and signal transduction for CB2 receptor

W5.43(194), a conserved tryptophan residue among G-protein coupled receptors (GPCRs) and cannabinoid receptors (CB), was examined in the present report for its significance in CB2 receptor ligand binding and adenylyl cyclase (AC) activity. Computer modeling postulates that this site in CB2 may be involved in the affinity of WIN55212-2 and SR144528 through aromatic contacts. In the present study, we reported that a CB2 receptor mutant, W5.43(194)Y, which had a tyrosine (Y) substitution for tryptophan (W), retained the binding affinity for CB agonist CP55940, but reduced binding affinity for CB2 agonist WIN55212-2 and inverse agonist SR144528 by 8-fold and 5-fold, respectively; the CB2 W5.43(194)F and W5.43(194)A mutations significantly affect the binding activities of CP55940, WIN55212-2 and SR144528. Furthermore, we found that agonist-mediated inhibition of the forskolin-induced cAMP production was dramatically diminished in the CB2 mutant W5.43(194)Y, whereas W5.43(194)F and W5.43(194)A mutants resulted in complete elimination of downstream signaling, suggesting that W5.43(194) was essential for the full activation of CB2. These results indicate that both aromatic interaction and hydrogen bonding are involved in ligand binding for the residue W5.43(194), and the mutations of this tryptophan site may affect the conformation of the ligand binding pocket and therefore control the active conformation of the wild type CB2 receptor. W5.43(194)Y/F/A mutations also displayed noticeable enhancement of the constitutive activation probably attributed to the receptor conformational changes resulted from the mutations.