Photosystem I (PSI) aus dem thermophilen Cyanobakterium Thermosynechococcus elongatus ist ein transmembraner Protein-Pigment-Superkomplex der photosynthetischen Elektronentransportkette. Er wandelt die Energie des Lichts in elektrische Energie mit einer Quanteneffizienz von nahezu 100 % um. Dazu uberträgt PSI Elektronen von Plastocyanin bzw. Cytochrom c6 (Cyt c6) auf Ferredoxin. Die Struktur des PSI wurde bereits 2001 mit einer Auflösung von 2,5 Å beschrieben (Jordan et al. 2001). Es lässt sich zur Generierung von Photoströmen auf Elektrodenoberflächen assemblieren und zur Produktion von Biokraftstoffen mit Enzymen koppeln. Die elektrische Kontaktierung des PSI mit Elektrodenoberflächen kann durch Komplexierung mit dem mitochondrialem Cytochrom c aus Pferdeherz (Cyt cHH) erhöht werden. Aufgrund der Nutzbarkeit dieses Proteinkomplexes sollte geklärt werden, wie PSI und Cyt cHH wechselwirken und wie sich die Interaktion von der des nativen PSI-Cyt c6-Komplexes unterscheidet. Deshalb lag der Fokus meiner Arbeit darauf, die Bindung des Cyt c6 und seines Analogons Cyt cHH an PSI mit kinetischen, kalorimetrischen, theoretischen und strukturellen Methoden zu untersuchen. Das Cyt c6 bindet im reduzierten Zustand an PSI und verringert nach erfolgtem Elektronentransfer seine Affinität. Das Cyt cHH bindet dagegen sowohl im reduzierten als auch im oxidierten Zustand an PSI. Mit Hilfe der kinetischen Messungen habe ich Bedingungen identifiziert, unter denen PSI mit dem jeweiligen Cytochrom c einen stabilen Komplex eingeht. Mit Hilfe eines rigid-body dockings wurden potenzielle Bindungsstellen der beiden Cytochrome berechnet. Fur Cyt c6 ergab sich eine spezifische Bindungsstelle, die eine gute Übereinstimmung mit den von mir gemessenen Kinetiken sowie mit weiteren Literaturdaten zeigt. Diese Bindungsstelle korreliert mit der veröffentlichten Kostruktur des bakteriellen Reaktionszentrums mit Cyt c2 aus Rhodobacter sphaeroides. Demgegenüber sind mehrere Cyt cHH-Bindungsstellen ... / Photosystem I (PSI) from the thermophilic cyanobacterium Thermosynechococcus elongatus is a membrane-bound, multipigment protein supercomplex. It converts light to electrochemical energy with a quantum efficiency of almost 100 %. It reduces the luminal proteins plastocyanin and cytochrome c6 (Cyt c6) to oxidize the stromal protein Ferredoxin. The structure of PSI has been solved in 2001 at a resolution of 2,5 Å (Jordan et al. 2001). PSI can be assembled on an electrode surface to produce photocurrents and the generated electrons can be used for the production of biofuels. The mitochondrial cytochrome c from horse heart (Cyt cHH) binds strongly to both, PSI and the electrode surface, and can therefore be applied to improve the electrical coupling. Due to the practical use of the PSI-Cyt c complex, the aim of my thesis is to characterize the interaction of PSI with Cyt c6 and the analog Cyt cHH. To this end, the binding of both cytochromes to PSI was analyzed by kinetic, calorimetric, theory-based and structural methods. Cyt c6 binds to PSI while being reduced and decreases its affinity after transferring its electron. In contrast, Cyt cHH binds to PSI in both oxidation states, reduced and oxidized, with identical affinity. By means of kinetic measurements, I identified conditions in which PSI forms a stable complex with either of the two cytochromes. The positions of the cytochrome binding sites at PSI were calculated by a rigid-body docking. For the calculation with Cyt c6, the majority of the potential binding sites are located at the luminal side of PSI, close to P700. The theoretic properties of one of these binding sites are in good agreement with my own kinetic measurements and literature data. The position and orientation of Cyt c6 in this theoretic binding site is almost identical to the localization of Cyt c2 in cocrystals with the bacterial reaction center from Rhodobacter sphaeroides. The potential Cyt cHH binding sites are uniformly distributed over ...

Molecular machines are essential components of living organisms. They are highly efficient and robust, much more than their macroscopic analogs. This stimulated growing interest in construction of artificial molecular machines with a set of functions which may be controlled in a specific way. Such man-made molecular complexes are designed as the building blocks for future nanotechnological devices. During the last decades many new molecular machines have been synthesized and characterized by various experimental techniques. This significantly increased our knowledge about systems of such kind and their functioning. However, there are only a few real applications of molecular machines. This is because the fundamental principles of operation of such single-molecule systems are not well understood. Existing theoretical studies, although very helpful, are still very sparse. This is because the molecular machines are very complex systems, comprising up to thousands atoms. Thus the progress in our understanding of nanoscale materials is tightly related to development of efficient computational and theoretical methodologies. In this work we studied two large classes of molecular machines: surface-moving nanocars and molecular rotors/motors, working on the surfaces and in crystalline state. In particular we studied the role of the internal interactions of these machines as well as their interactions with the environment. This included the flexibility of the molecules, including the rotation of the nanocars' wheels, effects of surface and rotors symmetry, charge transfer effects as well as many other factors. We have found out relations which determine the properties of studied classes of molecular machines. The development of computational and theoretical methods was another essential part of this work. In particular we have developed a family of the surface-molecule interaction potentials, aimed to performing long time scale and molecular simulations of complex systems. We also developed a physics-based model of the charge transfer happening between metals and the nanocars. This opened new ways to control such molecular machines. We also developed a theoretical framework to predict response of molecular rotors on various types of driving. Finally, we developed new and improved existing rigid-body molecular dynamics methods and extensively used them in our studies of molecular machines. / Only volume 2 has been digitized.

The wrist is one of the most complex joints in the human body. As such, the wrist joint is difficult to model due to the number of bones involved and its intricate soft tissue interactions. Many studies have attempted modeling the wrist previously; however, the majority of these studies simplify the joint into two-dimensions or idealized mechanical joints to reduce the complexity of the simulation. While these approaches still yield valuable information, the omission of a third-dimension or geometry defined movements limits the models’ usefulness in predicting joint function under non-idealized conditions. Therefore, the goal of this study was to develop a computational model of the wrist joint complex using commercially available software, whereby joint motion and behavior is dictated by highly accurate three-dimensional articular contact, ligamentous constraints, muscle loads, and external perturbations only. As such, a computational model of the human wrist was created using computed tomography (CT) images of a cadaver right upper extremity. Commercially available medical imaging software and three-dimensional computer aided design (CAD) software were used to reconstruct the osteoarticular surfaces and accurately add soft tissue constraints, as well as calculate kinematic motion simulations. The model was able to reproduce physiologic motion including flexion/extension and radial/ulnar deviation. Validation of the model was achieved by comparing predicted results from the model to the results of a published cadaveric experiment that analyzed wrist function under effects of various surgical procedures. The model was used to replicate the exact testing conditions prescribed for the experiment, and the model was able to accurately reproduce the trends and, in many instances, the magnitudes of the range of motion measurements in the study. Furthermore, the model can now be used to predict the magnitudes for the joint contact forces within the wrist as well as the tension developed in ligaments in hopes locating potential areas of concern after these surgical procedures have been conducted, including further development of arthritis in the wrist and ligament breakdown.

The glenohumeral joint is the most dislocated joint in the body due to the lack of bony constraints and dependence on soft tissue, primarily muscles and ligaments, to stabilize the joint. The goal of this study was to develop a computational model of the glenohumeral joint whereby joint behavior was dictated by articular contact, ligamentous constraints, muscle loading, and external perturbations. Validation of this computational model was achieved by comparing predicted results from the model to the results of a cadaveric experiment in which the relative contribution of muscles and ligaments to anterior joint stability was examined. The results showed the subscapularis to be critical to stabilization in both neutral and external rotations, the biceps stabilized the joint in neutral but not external rotation, and the inferior glenohumeral ligament resisted anterior displacement only in external rotation. Knowledge gained from this model could assist in pre-operative planning or the design of orthopedic implants. Use of this model as a companion to cadaveric testing could save valuable time and resources.

The aim of this study is to design a compliant lock mechanism for a dishwasher, using a systematic approach. Functionally binary pinned-pinned segment that exhibits bistable behavior is utilized. Pseudo-rigid-body model of the whole mechanism and the half segment is developed separately and the corresponding calculations are carried out. Among current solutions a different method namely &ldquo / arc fitting method&rdquo / is developed and it is utilized to construct the model. A software code is written to get the exact solutions, which require the evaluation of elliptic integrals. Results are compared with the analytical model and confirmed with physical prototype. Predefined tip forces are seen to provide the transition from one stable position to other. Durability, reliability and compactness characteristics are particularly considered.

This paper presents designs for Multistable Shape-Shifting Surfaces (MSSS) by introducing bistability into the Shape-Shifting Surface (SSS). SSSs are defined as surfaces that retain their effectiveness as a physical barrier while undergoing changes in shape. The addition of bistability to the SSS gives the surface multiple distinct positions in which it remains when shifted to, i.e. by designing bistability into a single SSS link, the SSS unit cell can change into multiple shapes, and stabilize within the resulting shape, while maintaining integrity against various forms of external assaults normal to its surface. Planar stable configurations of the unit cell include, expanded, compressed, sheared, half-compressed, and partially-compressed, resulting in the planar shapes of a large square, small square, rhombus, rectangle, and trapezoid respectively. Tiling methods were introduced which gave the ability to produce out-of-plane assemblies using planar MSSS unit cells. A five-walled rigid storage container prototype was produced that allowed for numerous stable positions and volumes. Applications for MSSSs can include size-changing vehicle beds, expandable laptop screens, deformable walls, and volume-changing rigid-storage containers. Analysis of the MSSS was done using pseudo-rigid-Body Models (PRBMs) and Finite Element Analysis (FEA) which ensured bistable characteristics before prototypes were fabricated.

This work extends a previously developed finite-volume overset-grid fluid flow solver to enable the characterisation of rigid-body-fluid interaction problems. To this end, several essential components have been developed and blended together. The inherent time-dependent nature of fluid-solid interaction problems is captured through the laminar transient incompressible Navier-Stokes equations for the fluid, and the Euler-Newton equations for rigid-body motion. First and second order accurate time discretisation schemes have been implemented for the former, whereas second and third order accurate time discretisation schemes have been made available for the latter. Without doubt the main advantage the overset-grid method offers regarding moving entities is the avoidance of the time consuming grid regeneration step, and the resulting grid distortion that can often cause numerical stability problems in the solution of the flow equations. Instead, body movement is achieved by the relative motion of a body fitted grid over a suitable background mesh. In this case, the governing equations of fluid flow are formulated using a Lagrangian, Eulerian, or hybrid flow description via the Arbitrary Lagrangian-Eulerian method. This entails the need to guarantee that mesh motion shall not disturb the flow field. With this in mind, the space conservation law has been hard-coded. The compliance of the space conservation law has the added benefit of preventing spurious mass sources from appearing due to mesh deformation. In this work, two-way fluid-solid interaction problems are solved via a partitioned approach. Coupling is achieved by implementing a Picard iteration algorithm. This allows for flexible degree of coupling specificationby the user. Furthermore, if strong coupling is desired, three variants of interface under-relaxation can be chosen to mitigate stability issues and to accelerate convergence. These include fixed, or two variants of Aitken’s adaptive under-relaxation factors. The software also allows to solve for one-way fluid-solid interaction problems in which the motion of the solid is prescribed. Verification of the core individual components of the software is carried out through the powerful method of manufactured solutions (MMS). This purely mathematically based exercise provides a picture of the order of accuracy of the implementation, and serves as a filter for coding errors which can be virtually impossible to detect by other means. Three instances of one-way fluid-solid interaction cases are compared with simulation results either from the literature, or from the OpenFOAM package. These include: flow within a piston cylinder assembly, flow induced by two oscillating cylinders, and flow induced by two rectangular plates exhibiting general planar motion. Three cases pertaining to the class of two-way fluid-interaction problems are presented. The flow generated by the free fall of a cylinder under the action of gravity is computed with the aid of an intermediate ‘motion tracking’ grid. The solution is compared with the one obtained using a vorticity based particle solver for validation purposes. Transverse vortex induced vibrations (VIV) of a circular cylinder immersed in a fluid, and subject to a stream are compared with experimental data. Finally, the fluttering motion of a rectangular plate under different scenarios is analysed.

Orientador: Auteliano Antunes dos Santos Junior / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia Mecânica / Made available in DSpace on 2018-08-16T12:15:36Z (GMT). No. of bitstreams: 1 Baruffaldi_LeonardoBartalini_M.pdf: 4986344 bytes, checksum: 359223cc9295f5b392b883e2841d037a (MD5) Previous issue date: 2010 / Resumo: Por 150 anos, os truques de três peças têm sido a estrutura padrão para o suporte de eixos e suspensões de trens de carga em diversos países. Embora sua robustez e facilidade de manutenção tenham conservado, em linhas gerais, a disposição e projeto dos componentes, novos requerimentos de carga e velocidade dos trens vêm mudando a forma como os projetistas enxergam o truque. Especial atenção tem sido dada ao modelo matemático da cunha de atrito, a peça fundida que é responsável pelo amortecimento dos vagões. A cunha de atrito promove a dissipação da energia mecânica por meio de contato de atrito seco com outros componentes do vagão. Devido às altas forças normais desenvolvidas nas superfícies de contato com características não suaves e, em geral, não lineares de atrito, as equações que regem o movimento da suspensão tornam-se de resolução difícil e surgem fenômenos como o de adesão escorregamento e o comportamento caótico típico de osciladores auto excitados. O presente trabalho tem como objetivo propor o uso de algoritmos de solução de problemas de complementaridade linear para resolver as forças de contato entre os corpos, visando a aprofundar a discussão sobre os modelos adotados para a cunha de atrito. Os resultados obtidos mostram que é possível modelar as forças de contato desse sistema utilizando um problema de complementaridade linear e que essa abordagem é, sob certas condições, mais eficiente do que o método das penalidades, normalmente aplicado para a resolução de problemas de contato / Abstract: For about 150 years now, three-piece trucks have been the standard axis' and suspensions' subframe used in freight railroad cars. The toughness and low maintenance costs of this system worked to maintain its basic design almost unchanged, but new requirements for loads and speed for freight cars are changing the way designers see the three-piece truck. Among the many interesting components of the three-piece truck, the friction wedge is getting some attention. The friction wedge is the main damping element in three-piece trucks and acts to dissipate mechanical energy via highly stiff contacts with friction. Due to the non-smooth and non-linear nature of frictional efforts, the equations of motion of the three-piece trucks become very awkward to deal with. Interesting phenomena of stick-slip, bifurcations, and limit cycle, typical of friction oscillators appear to some extent under normal operation. This work's main objective is to propose a new approach based on complementarity problems, used to solve for contact forces, to further extend the discussion on wedge dampers models. Results show that it is possible to model the problem using the linear complementarity problem and that, in some situations, this can be even more computationally efficient than the usual approach to solve contact problems: the penalty method / Mestrado / Mecanica dos Sólidos e Projeto Mecanico / Mestre em Engenharia Mecânica

Gegenstand dieser Arbeit ist die Simulation einer Wirkpaarung am Beispiel des innermaschinellen Transports von Stückgütern. Zur Schonung des Verarbeitungsgutes wird für das intermittierende Fördern ein neuartiger Bewegungsansatz betrachtet. Da sich der mit diesem Ansatz durchgeführte Prozess sehr sensitiv gegenüber den Eingangsparametern verhält, ist es notwendig, diesen zu simulieren, um somit eine stabile und robuste Bewegung zu synthetisieren. Als grundlegender Modellansatz wird die Diskrete Elemente Methode (DEM) gewählt, da diese es ermöglicht, den Kontakt von Starrkörpern realistisch abzubilden. Zur Umsetzung der Simulation wird die Modellbildung mit zwei unterschiedlichen Modellierungsumgebungen realisiert, die sich hinsichtlich der Umsetzung der DEM unterscheiden: Zum Einen mit Hilfe der kommerziellen Software MATLAB/Simulink und zum Anderen mit Hilfe der Open-Source-Software Woo DEM. Im Anschluss werden die damit erzeugten Modelle verifiziert und experimentell validiert, wodurch sich sowohl die Modellgüte als auch die Modelleignung ableitet. Dabei wird besonders auf die prozessentscheidende Rolle der Reibung eingegangen. Abschließend wird mit Hilfe des Vorzugsmodells an Hand zweier Beispiele die Modellanalyse vollzogen. Hierbei wird der neuartige Bewegungsansatz synthetisiert und simulativ hinsichtlich des Prozesserfolges überprüft. Dabei wird insbesondere auf die mit Hilfe des Modells quanitifizierbaren Prozessgrößen eingegangen. / The subject of this thesis deals with the simulation of an active unit demonstrated by the mechanical transport of pieced goods. To protect the processing goods, a novel motion approach for the intermittent transport is researched. Since the process performed with this approach is very sensitive to its input parameters, it is necessary to simulate it, with the aim to synthesize a stable and robust motion. The Discrete Element Method (DEM) is chosen as the basic model approach, because it allows the realistic representation of rigid body contacts. To implement the simulation the modelling is realised with two different modelling environments, which differ in the implementation of the DEM: Firstly, using the commercial software MATLAB/Simulink and secondly with the help of the open-source-software Woo DEM. Following that the generated models are verified and experimentally validated, whereby both the model goodness and the model suitability are derived. Special attention is dedicated to the role of the process relevant friction. Eventually, the model analysis is carried out with the help of two examples using the preferred model. Here, the novel motion approach is synthesized and verified by simulation in terms of process success. In particular it will address process variables, which are quantifiable because of the model.

Objects interacting with fluid are of high interest to visually present in three-dimensional applications, such as computer games and virtual environments. For presenting the interactions with high correctness, dynamic rigid body simulation may be used. This paper presents methods for efficient, physics-based real-time simulation of fluid-immersed rigid bodies, where the correctness of the simulation is maintained. Simulated forces include gravity, buoyancy, thrust, drag, and lift. To have the simulation run efficiently in real-time, discretization of the simulated rigid body is made by applying mentioned forces to a user-defined number of particles, sampled pseudo-randomly within the rigid body.