abstract: Conformational changes in biomolecules often take place on longer timescales than are easily accessible with unbiased molecular dynamics simulations, necessitating the use of enhanced sampling techniques, such as adaptive umbrella sampling. In this technique, the conformational free energy is calculated in terms of a designated set of reaction coordinates. At the same time, estimates of this free energy are subtracted from the potential energy in order to remove free energy barriers and cause conformational changes to take place more rapidly. This dissertation presents applications of adaptive umbrella sampling to a variety of biomolecular systems. The first study investigated the effects of glycosylation in GalNAc2-MM1, an analog of glycosylated macrophage activating factor. It was found that glycosylation destabilizes the protein by increasing the solvent exposure of hydrophobic residues. The second study examined the role of bound calcium ions in promoting the isomerization of a cis peptide bond in the collagen-binding domain of Clostridium histolyticum collagenase. This study determined that the bound calcium ions reduced the barrier to the isomerization of this peptide bond as well as stabilizing the cis conformation thermodynamically, and identified some of the reasons for this. The third study represents the application of GAMUS (Gaussian mixture adaptive umbrella sampling) to on the conformational dynamics of the fluorescent dye Cy3 attached to the 5' end of DNA, and made predictions concerning the affinity of Cy3 for different base pairs, which were subsequently verified experimentally. Finally, the adaptive umbrella sampling method is extended to make use of the roll angle between adjacent base pairs as a reaction coordinate in order to examine the bending both of free DNA and of DNA bound to the archaeal protein Sac7d. It is found that when DNA bends significantly, cations from the surrounding solution congregate on the concave side, which increases the flexibility of the DNA by screening the repulsion between phosphate backbones. The flexibility of DNA on short length scales is compared to the worm-like chain model, and the contribution of cooperativity in DNA bending to protein-DNA binding is assessed. / Dissertation/Thesis / Ph.D. Chemistry 2011

Entre as etapas do desenvolvimento de automóveis pode-se apontar a definição das características de suas suspensões. A fase de definição da suspensão pode ser dividida dentro do seguinte cenário: a escolha de um determinado tipo de suspensão, os pontos (geometria) e quais os valores de rigidez/amortecimento para todo o sistema irá resultar em um comportamento dinâmico desejado para o veículo, bem como a viabilidade de produção. Além disso, o entendimento da interação entre os parâmetros de suspensão, é crucial para a otimização do desempenho. Este trabalho pretende propor um método para aperfeiçoar a fase de \"tuning\" da suspensão, com foco principal no conforto. O veículo considerado é um caminhão comercial, e entre os seus parâmetros considerados estão rigidezes de molas da cabine e suspensão, amortecimento da suspensão de cabine e curvas do amortecedor da suspensão primária. O modelo virtual do veículo foi desenvolvido em ambiente ADAMS, o qual, previamente à otimização, foi validado contra dados experimentais. Métricas foram especialmente desenvolvidas levando em consideração aspectos subjetivos de conforto veicular, para dessa forma eliminar a variabilidade entre as avaliações subjetivas e análises das simulações. Os resultados mostraram expressivas melhorias no conforto e através de dados experimentais essas melhorias foram confirmadas. / Among the development phases of an automotive vehicle one can point out the definition of the characteristics of its suspensions. Suspension definition phase can be understood as the following scenario: given a suspension type, which hard points (geometric) and what values of stiffness/damping for the whole system will result in a desired dynamic behavior for the vehicle as well as production feasibility. Moreover, understanding the iteration among the suspension parameters, even considering just the tuning ones, is crucial for performance optimization. This work intends to propose a method for vehicle tuning characteristics optimization, having as a target the ride comfort. The vehicle considered here is a commercial truck, and among its parameters one considers cabin and suspension springs, cabin dampers and suspension damper curves. A vehicle model was developed in ADAMS environment and prior to the optimization the vehicle was validated against experimental data. Metrics were specially developed to take into account subjective aspects of ride, and, in this way, eliminating the gap between subjective evaluations and simulations analysis. Results showed improvements in ride comfort. The resulting setup was measured and the improvements were confirmed with experimental data.

Orientador: Auteliano Antunes dos Santos Júnior / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia Mecânica / Made available in DSpace on 2018-08-16T15:41:43Z (GMT). No. of bitstreams: 1 Idehara_AnneliseYuiko_M.pdf: 2161496 bytes, checksum: 55c604cc3cef545df951f0fbb8f2af19 (MD5) Previous issue date: 2009 / Resumo: Este trabalho tem como objetivo a análise do fenômeno de vibração na direção longitudinal de árvore de manivelas em motores de combustão interna, o cálculo de esforços sobre o mancal e o cálculo dos deslocamentos causados pela dinâmica do virabrequim. Essa vibração é apontada como uma das causas de desgaste precoce dos componentes acoplados ao virabrequim e do próprio componente. Reduzir essa vibração contribui para o aumento da vida útil e eficiência. A formulação proposta para estudo da dinâmica da estrutura é o modelo de múltiplos graus de liberdade com massas e inércias concentradas. Para o cálculo dos esforços de reação dos mancais, a equação de Reynolds é resolvida por diferenças finitas. Além disso, o programa comercial Excite (AVL) é utilizado para aferir resultados e fazer comparações. Os resultados são apresentados para diferentes condições de operação em um virabrequim comercial. Analisa-se de forma simples o efeito da redução de massa de 5% e de 10%. Por fim, conclui-se que a árvore de manivelas simulada não apresenta desgaste por contato metal-metal. / Abstract: This paper aims to analyze the phenomenon of vibration in the longitudinal direction of the crankshaft in internal combustion engines, the calculation of loads on the bearing and the calculation of displacements caused by the dynamics of the crankshaft. This vibration is identified as a cause of premature wear of the components coupled to the crankshaft and the component itself. Reduction in this vibration contributes to increased efficiency and life service time. The proposed formulation to study the dynamics of the structure is the model of multiple degrees of freedom with concentrated masses and inertias. The Reynolds equation is solved by Finite Differences Method to calculate the supported load of the bearing. In addition, the commercial program Excite (AVL) is used to evaluete results and make comparison. The results are presented for different operating conditions in a commercial crankshaft. A simple analysis of a crankshaft mass reduction of 5% and 10% is done. Finally, a conclusion that the crankshaft does not present a metal-metal contact is done. / Mestrado / Mecanica dos Sólidos e Projeto Mecanico / Mestre em Engenharia Mecânica

The motivation for this thesis was the need for further development of multibody dynamics simulation packages focused on detailed contact analysis. The thesis makes contributions in three different areas: Part I summarizes the equations, algorithms and design decisions necessary for dynamics simulation of flexible bodies with moving contacts. The assumed general shape function approach is presented. Additionally, the described technique enables studies of the residual stress release during grinding of flexible bodies. The proposed set of mode shapes was also successfully applied for modeling of heat flow. Part II is motivated by the need to reduce the computation time. The availability of the new cost-efficient multiprocessor computers triggered the development of the presented hybrid parallelization framework. The framework is designed to be easily portable and can be implemented without any system level coding or compiler modifications. Part III is motivated by the need for inter-operation with other simulation tools. A co-simulation framework based on the Transmission Line Modeling (TLM) technology was developed. The framework enables integration of several different simulation components into a single time-domain simulation. The framework has been used for connecting MSC.ADAMS and SKF BEAST simulation models. Throughout the thesis the approach was to present a practitioner roadmap. The detailed description of the theoretical results relevant for a real software implementation is put in focus. The software design decisions are discussed and the results of real industrial simulations are presented. This work has been supported by SKF, SSF/ProViking, ECSEL, KK-stiftelsen.

Multifunctional proteins that undergo major structural changes to perform different functions are known as “Transformer Proteins”, which is a recently identified class of proteins. One such protein that shows a remarkable structural plasticity and has two distinct functions is the transcription antiterminator, RfaH. Depending on the interactions between its N-terminal domain and its C-terminal domain, the RfaH CTD exists as either an all-α-helix bundle or all-β-barrel structure. Another example of a transformer protein is the Ebola virus protein VP40 (eVP40), which exists in different conformations and oligomeric states (dimer, hexamer, and octamer), depending on the required function.I performed Molecular Dynamics (MD) computations to investigate the structural conversion of RfaH-CTD from its all-a to all-b form. I used various structural and statistical mechanics tools to identify important residues involved in controlling the conformational changes. In the full-length RfaH, the interdomain interactions were found to present the major barrier in the structural conversion of RfaH-CTD from all-a to all-b form. I mapped the energy landscape for the conformational changes by calculating the potential of mean force using the Adaptive Biasing Force and Jarzynski Equality methods. Similarly, the interdomain salt-bridges in the eVP40 protomer were found to play a critical role in domain association and plasma membrane (PM) assembly. This molecular dynamic simulation study is supported by virus like particle budding assays investigated by using live cell imaging that highlighted the important role of these saltbridges. I also investigated the plasma membrane association of the eVP40 dimer in various PM compositions and found that the eVP40 dimer readily associates with the PM containing POPS and PIP2 lipids. Also, the CTD helices were observed to be important in stabilizing the dimer-membrane complex. Coarse-grained MD simulations of the eVP40 hexamer and PM system revealed that the hexamer enhances the PIP2 lipid clustering at the lower leaflet of the PM. These results provide insight on the critical steps in the Ebola virus life cycle.

My thesis aims several objectives. The first goal is to search the theoretical basis of management simulators and health management in order to create an overview of these two topics. Healthcare is an exceptional field, so as I set out to find specifics in health service management. Another aim of my thesis is to create a management simulator using Powersim software. Created management simulator is used as a modeling tool for simulation of processes and behavior of the upper or ward nurse on each shift the focus on utilization of subordinate nurses and supervisors themselves. The simulator is designed as a decision support system. The simulator has been tested and consulted on gastroenterology department of Nemocnice Milosrdných sester sv. Karla Boromejského in Prague. One of the goals is to make accessible the system thinking and its application to management. Using system dynamics approaches to case study to find appropriate recommendations for lower-level management in health care facilities in general. The last objective is the creation of test scenarios to verify the functionality of the simulator and testing hypotheses from which emerges a recommendation for hospital departments.

APOBEC3s (A3s) are a family of human cytidine deaminases that play important roles in both innate immunity and cancer. A3s protect host cells against retroviruses and retrotransposons by deaminating cytosine to uracil on foreign pathogenic genomes. However, when mis-regulated, A3s can cause heterogeneities in host genome and thus promote cancer and the development of therapeutic resistance. The family consists of seven members with either one (A3A, A3C and A3H) or two zinc-binding domains (A3B, A3D, A3D and A3G). Despite overall similarity, A3 proteins have distinct deamination activity and substrate specificity. Over the past years, several crystal and NMR structures of apo A3s and DNA/RNA-bound A3s have been determined. These structures have suggested the importance of the loops around the active site for nucleotide specificity and binding. However, the structural mechanism underlying A3 activity and substrate specificity requires further examination. Using a combination of computational molecular modeling and parallel molecular dynamics (pMD) simulations followed by experimental verifications, I investigated the roles of active site residues and surrounding loops in determining the substrate specificity and RNA versus DNA binding among A3s. Starting with A3B, I revealed the structural basis and gatekeeper residue for DNA binding. I also identified a unique auto-inhibited conformation in A3B that restricts access to the active site and may underlie lower catalytic activity compared to the highly similar A3A. Besides, I investigated the structural mechanism of substrate specificity and ssDNA binding conformation in A3s. I found an interdependence between substrate conformation and specificity. Specifically, the linear DNA conformation helps accommodate CC dinucleotide motif while the U-shaped conformation prefers TC. I also identified the molecular mechanisms of substrate sequence specificity at -1’ and -2’ positions. Characterization of substrate binding to A3A revealed that intra-DNA interactions may be responsible for the specificity in A3A. Finally, I investigated the structural mechanism for exclusion of RNA from A3G catalytic activity using similar methods. Overall, the comprehensive analysis of A3s in this thesis shed light into the structural mechanism of substrate specificity and broaden the understanding of molecular interactions underlying the biological function of these enzymes. These results have implications for designing specific A3 inhibitors as well as base editing systems for gene therapy.

Glycosaminoglycans (GAGs) are linear polysaccharides, built of periodically occurring disaccharide units. GAGs are ubiquitous in the extracellular matrix (ECM), where they exhibit multifarious biological activities. This diversity arises from - among others - their ability to interact with and regulate a large number of proteins, such as cytokines, chemokines, and growth factors. As of the huge variety in their chemical configuration, GAGs are further sub-classified into different types (heparin, for instance, is one of these sub-classes). Hence, GAGs are a diverse class of molecules, which surely contributes to the broadness of their spectrum of biological functions. Through varying arrangements of sulfate groups and different types of saccharide units, individual GAG molecules can establish specific atomic contacts to proteins. One of the best-studied examples is antithrombin-heparin, whose biologically relevant interaction requires a specific pentasaccharide sequence. It is valid to assume, however, that various proteins are yet to be discovered whose biological functions are in some way affected by GAGs. In other cases, and this is true for the cytokine interleukin-10 (IL-10), there are already experimental indications for a biologically relevant protein-GAG interaction, but the details are still obscure and the fundamental molecular interaction mechanism has still not been clarified. IL-10 has been shown to bind GAGs. So far, however, no structural detail about IL-10-GAG interaction is known. Function-wise, IL-10 is mainly considered to be immunosuppressive and therefore anti-inflammatory, but it in fact has the pleiotropic ability to influence the immune system in both directions, i.e. it constitutes a complex regulation system on its own. Therefore, the role of GAGs in this system is potentially substantial, but is yet to be clarified. In vitro experiments have yielded indications for GAGs being able to modulate IL-10\'s biological function, and obviously IL-10 and GAGs are simultaneously present in the ECM. This gives rise to the assumption that IL-10-GAG interaction is of biological significance, and that understanding the impact of GAGs on IL-10 biology is important - from the basic research point of view, but also for the development of therapies, potentially involving artificially designed ECMs. A promising approach for obtaining knowledge about the nature of IL-10-GAG interaction is its investigation on the structural level, i.e. the identification and characterization of the molecular interaction mechanisms that govern the IL-10-GAG system. In this PhD project it was my goal to reveal structural and molecular details about IL-10-GAG interaction with theoretical and computational means, and with the help of experiments performed by collaborators in the framework of the Collaborative Research Centre DFG Transregio 67. For achieving this, I developed three methods for the in silico investigation of protein-GAG systems in general and subsequently applied them to the IL-10-GAG system. Parts of that work have been published in scientific journals, as outlined further below. I proposed and validated a systematic approach for predicting GAG binding regions on a given protein, based on the numerical simulation and analysis of its Coulomb potential. One advantage of this method is its intrinsic ability to provide clues about the reliability of the resulting prediction. Application of this approach to IL-10 lead to the observation that its Coulomb attraction for GAGs is significantly weaker than in case of exemplary protein-GAG systems (such as FGF2-heparin). Still, a distinct IL-10-GAG binding region centered on the residues R102, R104, R106, R107 of the human IL-10 sequence was identified. This region can be assumed to play a major role in IL-10-GAG interaction, as described in chapter 3. Molecular docking methods are used to generate binding mode predictions for a given receptor-ligand system. In chapter 4, I clarify the importance of data clustering as an essential step for post-processing docking results and present a clustering methodology optimized for GAG molecules. It allows for a reproducible analysis, enabling systematic comparisons among different docking studies. The approach has become standard procedure in our research group. It has been applied in a variety of studies, and served as an essential tool for studying IL-10-GAG interaction, as described in chapter 3. Motivated by the shortcomings of classical docking approaches, especially with respect to protein-GAG systems, I worked on the development of a molecular dynamics-based docking method with less radical approximations than usually applied in classical docking. The goal was to make the computational model properly account for the special physical properties of GAGs, and to include the effects of receptor flexibility and solvation. The methodology was named Dynamic Molecular Docking (DMD) and published in the Journal of Chemical Information and Modeling-together with a validation study. The subsequent application of DMD in a variety of studies required enormous amounts of computational resources. For tackling this challenge, I established a graphics processing unit-based high-performance computing environment in our research group and developed a software framework for reliably performing DMD studies on this hardware, as well as on other computing resources of the TU Dresden. The investigation of the IL-10-GAG system via DMD was focused on the IL-10-GAG binding region predicted earlier, and made heavy usage of the optimized clustering approach named above. An important result of this endeavor is that IL-10's amino acid residue R107 significantly stands out compared to all other residues and supposedly plays a particularly important role in IL-10-GAG recognition. The collaboration with the NMR laboratory of Prof. Daniel Huster at the Universität Leipzig was fruitful: I post-processed nuclear Overhauser effect data and obtained heparin structure models, which revealed that IL-10-heparin interaction has a measurable impact on the backbone structure of the heparin molecule. These results were published in Glycobiology. In chapter 8, I propose two different scenarios about how GAG-binding to IL-10 might affect its biological function, based on the findings made in this thesis project. In conclusion, a set of methods has been developed, all of which are generically applicable for the investigation of protein-GAG systems. Regarding the IL-10-GAG system, valuable structural insights for increasing the understanding about its molecular mechanisms were derived. These observations pave the way towards unraveling GAG-mediated bioactivity of IL-10, which may then be specifically exploited, for instance in artificial ECMs for improved wound healing.

Flies are a widely distributed pest insect that poses a significant threat to food security. Flight is essential for the dispersal of the adult flies to find new food sources and ideal breeding spots. The supply of metabolic fuel to power the flight muscles of insects is regulated by adipokinetic hormones (AKHs). The fruit fly, Drosophila melanogaster, the flesh fly, Sarcophaga crassipalpis, and the oriental fruit fly, Bactrocera dorsalis all have the same AKH that is present in the blowfly, Phormia terraenovae; this AKH has the code-name Phote-HrTH. Binding of the AKH to the extracellular binding site of a G protein-coupled receptor causes its activation. In this thesis, the structure of Phote-HrTH in SDS micelle solution was determined using NMR restrained molecular dynamics. The peptide was found to bind to the micelle and be reasonably rigid, with an S 2 order parameter of 0.96. The translated protein sequence of the AKH receptor from the fruit fly, Drosophila melanogaster, the flesh fly, Sarcophaga crassipalpis, and the oriental fruit fly, Bactrocera dorsalis were used to construct two models for each receptor: Drome-AKHR, Sarcr-AKHR, and Bacdo-AKHR. It is proposed that these two models represent the active and inactive state of the receptor. The models based on the crystal structure of the β-2 adrenergic receptor were found to bind Phote-HrTH with a predicted binding free energy of –107 kJ mol–1 for Drome-AKHR, –102 kJ mol–1 for Sarcr-AKHR and –102 kJ mol–1 for Bacdo-AKHR. Under molecular dynamics simulation, in a POPC membrane, the β-2AR receptor-like complexes transformed to rhodopsin-like. The identification and characterisation of the ligand-binding site of each receptor provide novel information on ligand-receptor interactions, which could lead to the development of species-specific control substances to use discriminately against these pest flies.

Während CFD Simulationen für Metallschmelze im Rahmen des SFB920 fallen auf dem Taurus HPC Cluster in Dresden sehr große Datenmengen an, deren Handhabung den wissenschaftlichen Arbeitsablauf stark verlangsamen. Zum einen ist der Transfer in Visualisierungssysteme nur unter hohem Zeitaufwand möglich. Zum anderen ist interaktive Analyse von zeitlich abhängigen Prozessen auf Grund des Speicherflaschenhalses nahezu unmöglich. Aus diesen Gründen beschäftigt sich die vorliegende Dissertation mit der Entwicklung sog. Temporaler In-Situ Kompression für wissenschaftliche Daten direkt innerhalb von CFD Simulationen. Dabei werden mittels neuer Quantisierungsverfahren die Daten auf ~10% komprimiert, wobei dekomprimierte Daten einen Fehler von maximal 1% aufweisen. Im Gegensatz zu nicht-temporaler Kompression, wird bei temporaler Kompression der Unterschied zwischen Zeitschritten komprimiert, um den Kompressionsgrad zu erhöhen. Da die Datenmenge um ein Vielfaches kleiner ist, werden Kosten für die Speicherung und die Übertragung gesenkt. Da Kompression, Transfer und Dekompression bis zu 4 mal schneller ablaufen als der Transfer von unkomprimierten Daten, wird der wissenschaftliche Arbeitsablauf beschleunigt.