Gas-expanded liquids (GXLs) are novel and environmentally benign solvent systems with applications in reactions, separations, nanotechnology, drug delivery, and microelectronics. GXLs are liquid mixtures consisting of an organic solvent combined with a benign gas, such as CO2, in the nearcritical regime. In this work, molecular dynamics simulations have been combined with experimental techniques to elucidate the cybotactic region or local environment in gas-expanded liquids. Molecular dynamics simulations show clustering of methanol molecules in carbon dioxide-methanol mixtures. This clustering was not observed in carbon dioxide-acetone mixtures. Furthermore, addition of carbon dioxide enhances diffusivity of solutes in gas-expanded media as shown by both simulations and Taylor-Aris dispersion experiments. Finally, local structure and local compositions around pyrene in carbon dioxide-methanol and carbon-dioxide acetone were investigated using simulations and UV-vis spectroscopy.

The objective of this research is to use atomistic simulations to investigate dislocation nucleation from grain boundaries in face-centered cubic aluminum and copper. This research primarily focuses on asymmetric tilt grain boundaries and has three main components. First, this research uses molecular statics simulations of the structure and energy of these faceted, dissociated grain boundary structures to show that Σ3 asymmetric boundaries can be decomposed into the structural units of the Σ3 symmetric tilt grain boundaries, i.e., the coherent and incoherent twin boundaries. Moreover, the energy for all Σ3 asymmetric boundaries is predicted with only the energies of the Σ3 symmetric boundaries and the inclination angle. Understanding the structure of these boundaries provides insight into dislocation nucleation from these boundaries. Further work into the structure and energy of other low order Σ asymmetric boundaries and the spatial distribution of free volume within the grain boundaries also provides insight into dislocation nucleation mechanisms. Second, this research uses molecular dynamics deformation simulations with uniaxial tension applied perpendicular to these boundaries to show that the dislocation nucleation mechanisms in asymmetric boundaries are highly dependent on the faceted, dissociated structure. Grain boundary dislocation sources can act as perfect sources/sinks for dislocations or may violate this premise by increasing the dislocation content of the boundary during nucleation. Furthermore, simulations under uniaxial tension and uniaxial compression show that nucleation of the second partial dislocation in copper exhibits tension-compression asymmetry. Third, this research explores the development of models that incorporate the resolved stress components on the slip system of dislocation nucleation to predict the atomic stress required for dislocation nucleation from single crystals and grain boundaries. Single crystal simulations of homogeneous dislocation nucleation help define the role of lattice orientation on the nucleation stress for grain boundaries. The resolved stress normal to the slip plane on which the dislocation nucleates plays an integral role in the dislocation nucleation stress and related mechanisms. In summary, the synthesis of various aspects of this work has provided improved understanding of how the grain boundary character influences dislocation nucleation in bicrystals, with possible implications for nanocrystalline materials.

Orientador: Robson Pederiva / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia Mecânica / Made available in DSpace on 2018-08-25T19:18:34Z (GMT). No. of bitstreams: 1 RubensGoncalvesSalsaJunior_M.pdf: 19298740 bytes, checksum: e9f9763c1d9d97af499156bb958078e0 (MD5) Previous issue date: 2014 / Resumo: O objetivo deste trabalho é apresentar uma forma computacional eficaz de manipular a curva que representa o perfil dos camos, objetivando a sua aplicação em simulações computacionais e rotinas de otimização de um trem de válvulas. Ao longo dos anos, os motores de combustão interna têm sido pesquisados e aprimorados, seja na busca de maior potência, seja na busca de menor consumo de combustível. Um subsistema automotivo que afeta diretamente o desempenho dos motores é o sistema de acionamento de válvulas, que permite controlar a entrada e saída dos gases da câmara de combustão. Diversos pesquisadores têm estudado a cinemática e dinâmica do sistema de acionamento de válvulas para melhorar o desempenho do motor, focando nas características construtivas do perfil dos camos: ele tem ação preponderante sobre a dinâmica do sistema. Neste trabalho foi aplicado o método de otimização da evolução diferencial de modo a otimizar a resposta dinâmica da válvula de exaustão de um motor Diesel, modelada por um sistema de cinco graus de liberdade, utilizando o perfil do camo como variável de projeto. Em um dos estudos de caso obteve-se redução de aproximadamente 60% nos picos de aceleração no fechamento da válvula. Em outro estudo de caso a área sob a curva de aceleração foi maximizada, aumentando aproximadamente 9%. Também Foi demonstrado um artifício matemático para que fossem considerados dois objetivos na otimização, já que os esforços para maximizar a área sob a curva de aceleração e minimizar a aceleração mostraram-se antagônicos. Por fim, mostrou-se que o perfil ótimo do camo varia com a rotação do motor / Abstract: The objective of this work is to present an efficient computational way to manipulate the curve representing the cam profile, aiming their application in computer simulations and optimization routines for a valvetrain. Over the years internal combustion engines have been researched and improved, be it in the search for more power or be it in the search for lower fuel consumption. An automotive subsystem that directly affects the performance of the engine is the valvetrain system. This system allows the control of the admittance and release of gases from the combustion chamber. Several researchers have studied the kinematics and dynamics of the valve actuation system to improve engine performance focusing in the design characteristics of the profile of the cams: it has a predominant action on the dynamics of the system. In this work the optimization method of differential evolution was applied to optimize a Diesel engine exhaust valve's dynamic response using the cam profile as a design variable. In one case of study the acceleration peak had a 60% reduction. In another case of study the area under the valve's displacement curve was increased by 9%. A mathematical scheme was demonstrated to consider tow objectives for the parameters acceleration and area showed to be ambivalent. In addition, it was also demonstrated that the optimal cam profile varies with the engine speed / Mestrado / Mecanica dos Sólidos e Projeto Mecanico / Mestre em Engenharia Mecânica

This paper presents an investigation of seven different flux splitting algorithms for the discretization of inviscid fluxes, which are the primary source for the non-linear behavior (eg. shocks, contact discontinuities). The aim of the present work is to enhance the accuracy and robustness of CHEM, a three-dimensional flow solver, which is capable of simulating a wide range of flow conditions, including chemical non-equilibrium. Five different test cases cases are considered and thoroughly analyzed. The overall goal is to find a numerical scheme that can meet some stringent specifications of efficiency, accuracy and robustness on the widest possible spectrum of flow conditions.

Proteins and DNA are essential to life as we know it and understanding their function is understanding their structure and dynamics. The importance of the latter is being appreciated more in recent years and has led to the development of novel interdisciplinary techniques and approaches to studying protein function. Three techniques to study protein structure and dynamics have been used and combined in different ways in the context of this thesis and have led to a better understanding of the three systems described herein. X-ray crystallography is the oldest and still arguably most popular technique to study macromolecular structures. Nuclear magnetic resonance (NMR) spectroscopy is a not much younger technique that is a powerful tool not only to probe molecular structure but also dynamics. The last technique described herein are molecular dynamics (MD) simulations, which are only just growing out of their infancy. MD simulations are computer simulations of macromolecules based on structures solved by X-ray crystallography or NMR spectroscopy, that can give mechanistic insight into dynamic processes of macromolecules whose amplitudes can be estimated by the former two techniques. MD simulations of the model protein GB3 (B3 immunoglobulin-binding domain of streptococcal protein G) were conducted to identify origins of discrepancies between order parameters derived from different sets of MD simulations and NMR relaxation experiments.The results highlight the importance of time scales as well as sampling when comparing MD simulations to NMR experiments. Discrepancies are seen for unstructured regions like loops and termini and often correspond to nanosecond time scale transitions between conformational substates that are either over- or undersampled in simulation. Sampling biases can be somewhat remedied by running longer (microsecond time scale) simulations. However, some discrepancies persist over even very long trajectories. We show that these discrepancies can be due to the choice of the starting structure and more specifically even differences in protonation procedures. A test for convergence on the nanosecond time scale is shown to be able to correct for many of the observed discrepancies. Next, MD simulations were used to predict in vitro thermostability of members of the bacterial Ribonuclease HI (RNase H) family of endonucleases. Thermodynamic stability is a central requirement for protein function and a goal of protein engineering is improvement of stability, particularly for applications in biotechnology. The temperature dependence of the generalized order parameter, S, for four RNase H homologs, from psychrotrophic, mesophilic and thermophilic organisms, is highly correlated with experimentally determined melting temperatures and with calculated free energies of folding at the midpoint temperature of the simulations. This study provides an approach for in silico mutational screens to improve thermostability of biologically and industrially relevant enzymes. Lastly, we used a combination of X-ray crystallography, NMR spectroscopy and MD simulations to study specificity of the interaction between Drosophila Hox proteins and their DNA target sites. Hox proteins are transcription factors specifying segment identity during embryogenesis of bilaterian animals. The DNA binding homeodomains have been shown to confer specificity to the different Hox paralogs, while being very similar in sequence and structure. Our results underline earlier findings about the importance of the N-terminal arm and linker region of Hox homeodomains, the cofactor Exd, as well as DNA shape, for specificity. A comparison of predicted DNA shapes based on sequence alone with the shapes observed for different DNA target sequences in four crystal structures when in complex with the Drosophila Hox protein AbdB and the cofactor Exd, shows that a combined ”induced fit”/”conformational selection” mechanism is the most likely mechanism by which Hox homeodomains recognize DNA shape and achieve specificity. The minor groove widths for all sequences is close to identical for all ternary complexes found in the different crystal structures, whereas predicted shapes vary between the different DNA sequences. The sequences that have shown higher affinity to AbdB in vitro have a predicted DNA shape that matches the observed DNA shape in the ternary complexes more closely than the sequences that show low in vitro affinity to AbdB. This strongly suggests that the AbdB-Exd complex selects DNA sequences with a higher propensity to adopt the final shape in their unbound form, leading to higher affinity. An additional AbdB monomer binding site with a strongly preformed binding competent shape is observed for one of the oligomers in the reverse complement strand of one of the canonical (weak) Hox-Exd complex binding site. The shape preference seems strong enough for AbdB monomer binding to compete with AbdB-Exd dimer binding to that same oligomer, suggested by the presence of both binding modes in the same crystal. The monomer binding site is essentially able to compete with the dimer binding site, even though binding with the cofactor is not possible, because its shape is very close to the ideal shape. A comparison of different crystal structures solved herein and in the literature as well as a set of molecular dynamics simulations was performed and led to insights about the importance of residues in the Hox N-terminal arm for the preference of certain Hox paralogs to certain DNA shapes. Taken together all these insights contribute to our understanding of Hox specificity in particular as well as protein-DNA interactions in general.

Yan, Changqing. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2009. / Includes bibliographical references (leaves 92-97). / Abstracts in English and Chinese. / ABSTRACT (ENGLISH) --- p.iii / ABSTRACT (CHINESE) --- p.iv / ACKNOWLEDGMENTS --- p.v / LIST OF ABBREVIATIONS --- p.vi / TABLE OF CONTENTS --- p.vii / LIST OF FIGURES --- p.ix / LIST OF TABLES --- p.x / Chapter CHAPTER ONE: --- BACKGROUND INFORMATION --- p.1 / Chapter 1.1 --- Introduction --- p.1 / Chapter 1.2 --- Deoxyribonucleic Acid --- p.2 / Chapter 1.3 --- DNA Studies --- p.9 / Chapter 1.4 --- Cisplatin Studies --- p.11 / Chapter 1.5 --- Scope of the Thesis --- p.13 / Chapter CHAPTER TWO: --- METHODOLOY AND COMPUTATION --- p.16 / Chapter 2.1 --- Introduction --- p.16 / Chapter 2.2 --- Molecular Dynamics Simulation --- p.16 / Chapter 2.3 --- Quantum Mechanics Calculation --- p.23 / Chapter 2.4 --- Verification of Methodology --- p.25 / Chapter 2.4.1 --- Backbone Torsion Angles --- p.25 / Chapter 2.4.2 --- N7-N7 Distance --- p.30 / Chapter 2.4.3 --- Location of HOMO --- p.33 / Chapter 2.5 --- Summary --- p.35 / Chapter CHAPTER THREE: --- UNDERSTANDING OF THE CISPLATIN-DNA CROSSLINKS --- p.36 / Chapter 3.1 --- Introduction --- p.36 / Chapter 3.2 --- MO Analysis --- p.37 / Chapter 3.3 --- Potential Binding Products with the Ligand --- p.37 / Chapter 3.3.1 --- "1,2-d(GpG) Intrastrand Crosslink" --- p.43 / Chapter 3.3.2 --- "l,2-d(ApG) Intrastrand Crosslink" --- p.43 / Chapter 3.3.3 --- "l,3-d(GpXpG) Intrastrand Crosslink" --- p.44 / Chapter 3.3.4 --- d(GpC)d(GpC) Interstrand Crosslink --- p.44 / Chapter 3.3.5 --- d(GpXpC)d(GpXpC) Interstrand Crosslink --- p.44 / Chapter 3.3.6 --- Summary --- p.45 / Chapter 3.4 --- Potential Binding Products Analysis --- p.47 / Chapter 3.4.1 --- Site Identification Convention --- p.47 / Chapter 3.4.2 --- Potential Binding Products Analysis --- p.48 / Chapter 3.4.3 --- Applications --- p.53 / Chapter 3.5 --- Cisplatin-DNA Crosslink Products Analysis --- p.56 / Chapter 3.5.1 --- "1,2-d(GpG) and l,2-d(ApG) Intrastrand Crosslinks" --- p.61 / Chapter 3.5.2 --- "l,3-d(GpXpG) Intrastrand and d(GpXpC)d(GpXpC) Interstrand Crosslinks" --- p.62 / Chapter 3.5.3 --- d(GpC)d(GpC) Interstrand Crosslinks --- p.63 / Chapter 3.5.4 --- Platination at Terminal Positions --- p.65 / Chapter 3.6 --- Summary --- p.65 / Chapter CAHPTER FOUR: --- CONCLUDING REMARKS --- p.67 / APPENDIX I: BACKBONE TORSION ANGLES AND SUGAR RING CONFORMATIONS OF THE OPTIMIZED GEOMETRIES --- p.69 / APPENDIX II: BACKBONE TORSION ANGLES OF THE EXPERIMENTAL SEQUENCES FROM NUCLEIC ACID DATABASE (NDB) --- p.77 / REFERENCES --- p.92

In the interest of furthering the understanding of hemodynamics, this study has developed a method for modeling fluid mechanics behavior in individual human carotid arteries. A computational model was constructed from magnetic resonance (MR) data of a phantom carotid bifurcation model, and relevant flow conditions were simulated. Results were verified by comparison with previous in vitro experiments. The methodology was extended to create subject-specific carotid artery models from geometry data and fluid flow boundary conditions which were determined from MR and phase contrast MR (PCMR) scans of human subjects. The influence of subject-specific boundary conditions on the flow field was investigated by comparing a model based on measured velocity boundary conditions to a model based on the assumption of idealized velocity boundary conditions. It is shown that subject-specific velocity boundary conditions in combination with a subject-specific geometry and flow waveform influence fluid flow phenomena associated with plaque development. Comparing a model with idealized Womersley flow boundary conditions to a model with subject-specific velocity boundary conditions demonstrated the importance of employing inlet and flow division data obtained from individual subjects in order to predict accurate, clinically relevant, fluid flow phenomena such as low wall shear stress areas and negative axial velocity regions. This study also illustrates the influence of the bifurcation geometry, especially the flow divider position, with respect to the velocity distribution of the common carotid artery on the development of flow characteristics. Overall it is concluded that accurate geometry and velocity measurements are essential for modeling fluid mechanics in individual human carotid arteries for the purpose of understanding atherosclerosis in the carotid artery bifurcation.

The mechanical and physical properties of polymers are determined primarily by the underlying nano-scale structures and characteristics such as entanglements, crystallites, and molecular orientation. These structures evolve in complex manners during the processing of polymers into useful articles. Limitations of available and foreseeable computational capabilities prevent the direct determination of macroscopic properties directly from atomistic computations. As a result, computational tools and methods to bridge the length and time scale gaps between atomistic and continuum models are required. In this research, an internal state variable continuum model has been developed whose internal state variables (ISVs) and evolution equations are related to the nano-scale structures. Specifically, the ISVs represent entanglement number density, crystal number density, percent crystallinity, and crystalline and amorphous orientation distributions. Atomistic models and methods have been developed to investigate these structures, particularly the evolution of entanglements during thermo-mechanical deformations. A new method has been created to generate atomistic initial conformations of the polymer systems to be studied. The use of the hyperdynamics method to accelerate molecular dynamics simulations was found to not be able to investigate processes orders of magnitude slower that are typically measurable with traditional molecular dynamics simulations of polymer systems. Molecular dynamics simulations were performed on these polymer systems to determine the evolution of entanglements during uniaxial deformation at various strain rates, temperatures, and molecular weights. Two methods were evaluated. In the first method, the forces between bonded atoms along the backbone are used to qualitatively determine entanglement density. The second method utilizes rubber elasticity theory to quantitatively determine entanglement evolution. The results of the second method are used to gain a clearer understanding of the mechanisms involved to enhance the physical basis of the evolution equations in the continuum model and to derive the models material parameters. The end result is a continuum model that incorporates the atomistic structure and behavior of the polymer and accurately represents experimental evidence of mechanical behavior and the evolution of crystallinity and orientation.

Despite numerous advances in experimental methodologies capable of addressing the various phenomenon occurring on metal surfaces, atomic scale resolution of the microscopic dynamics remains elusive for most systems. Computational models of the processes may serve as an alternative tool to fill this void. To this end, parallel molecular dynamics simulations of self-diffusion on metal surfaces have been developed and employed to address microscopic details of the system. However these simulations are not without their limitations and prove to be computationally impractical for a variety of chemically relevant systems, particularly for diffusive events occurring in the low temperature regime. To circumvent this difficulty, a corresponding coarse-grained representation of the surface is also developed resulting in a reduction of the required computational effort by several orders of magnitude, and this description becomes all the more advantageous with increasing system size and complexity. This representation provides a convenient framework to address fundamental aspects of diffusion in nonequilibrium environments and an interesting mechanism for directing diffusive motion along the surface is explored. In the ensuing discussion, additional topics including transition state theory in noisy systems and the construction of a checking function for protein structure validation are outlined. For decades the former has served as a cornerstone for estimates of chemical reaction rates. However, in complex environments transition state theory most always provides only an upper bound for the true rate. An alternative approach is described that may alleviate some of the difficulties associated with this problem. Finally, one of the grand challenges facing the computational sciences is to develop methods capable of reconstructing protein structure based solely on readily-available sequence information. Herein a checking function is developed that may prove useful for addressing whether a particular proposed structure is a viable possibility.

Liquid fragmentation phenomenon is explored from both a fundamental (fully resolved) and an engineering (modeled) perspective. The dual objectives compliment each other by providing an avenue to gain further understanding into fundamental processes of atomization as well as to use the newly acquired knowledge to address practical concerns. A compressible five-equation interface model based on a Roe-type scheme for the simulation of material boundaries between immiscible fluids with arbitrary equation of state is developed and validated. The detailed simulation model accounts for surface-tension, viscous, and body-force effects, in addition to acoustic and convective transport. The material interfaces are considered as diffused zones and a mixture model is given for this transition region. The simulation methodology combines a high-resolution discontinuity capturing method with a low-dissipation central scheme resulting in a hybrid approach for the solution of time- and space-accurate interface problems. Several multi-dimensional test cases are considered over a wide range of physical situations involving capillary, viscosity, and gravity effects with simultaneous presence of large viscosity and density ratios. The model is shown to accurately capture interface dynamics as well as to deal with dynamic appearance and disappearance of material boundaries. Simulation of atomization processes and its interaction with the flow field in practical devices is the secondary objective of this study. Three modeling requirements are identified to perform Large-Eddy Simulation (LES) of spray combustion in engineering devices. In concurrence with these requirements, LES of an experimental liquid-fueled Lean Direct Injection (LDI) combustor is performed using a subgrid mixing and combustion model. This approach has no adjustable parameters and the entire flow-path through the inlet swirl vanes is resolved. The inclusion of the atomization aspects within LES eliminates the need to specify dispersed-phase size-velocity correlations at the inflow boundary. Kelvin-Helmholtz (or aerodynamic) breakup model by Reitz is adopted for the combustor simulation. Two simulations (with and without breakup) are performed and compared with measurements of Cai et al. Time-averaged velocity prediction comparison for both gas- and liquid-phase with available data show reasonable agreement. The major impact of breakup is on the fuel evaporation in the vicinity of the injector. Further downstream, a wide range of drop sizes are recovered by the breakup simulation and produces similar spray quality as in the no-breakup case.