Browsing by Subject "Dynamics"
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Item A reverse osmosis treatment process for produced water: optimization, process control, and renewable energy application(2009-06-02) Mareth, BrettFresh water resources in many of the world's oil producing regions, such as western Texas, are scarce, while produced water from oil wells is plentiful, though unfit for most applications due to high salinity and other contamination. Disposing of this water is a great expense to oil producers. This research seeks to advance a technology developed to treat produced water by reverse osmosis and other means to render it suitable for agricultural or industrial use, while simultaneously reducing disposal costs. Pilot testing of the process thus far has demonstrated the technology's capability to produce good-quality water, but process optimization and control were yet to be fully addressed and are focuses of this work. Also, the use of renewable resources (wind and solar) are analyzed as potential power sources for the process, and an overview of reverse osmosis membrane fouling is presented. A computer model of the process was created using a dynamic simulator, Aspen Dynamics, to determine energy consumption of various process design alternatives, and to test control strategies. By preserving the mechanical energy of the concentrate stream of the reverse osmosis membrane, process energy requirements can be reduced several fold from that of the current configuration. Process control schemes utilizing basic feedback control methods with proportional-integral (PI) controllers are proposed, with the feasibility of the strategy for the most complex process design verified by successful dynamic simulation. A macro-driven spreadsheet was created to allow for quick and easy cost comparisons of renewable energy sources in a variety of locations. Using this tool, wind and solar costs were compared for cities in regions throughout Texas. The renewable energy resource showing the greatest potential was wind power, with the analysis showing that in windy regions such as the Texas Panhandle, wind-generated power costs are approximately equal to those generated with diesel fuel.Item A bond graph approach to analysis, synthesis, and design of dynamic systems(2003-12) Kim, Seyoon, 1967-; Longoria, Raul G.Item A comprehensive numerical model of Io's chemically-reacting sublimation-driven atmosphere and its interaction with the Jovian plasma torus(2012-05) Walker, Andrew Charles; Varghese, Philip L.; Goldstein, David Benjamin, doctor of aeronautics; Trafton, Laurence M.; Raja, Laxminarayan; Johnson, Robert; Spencer, JohnIo has one of the most dynamic atmospheres in the solar system due in part to an orbital resonance with Europa and Ganymede that causes intense tidal heating and volcanism. The volcanism serves to create a myriad of volcanic plumes across Io's surface that sustain temporally varying local atmospheres. The plumes primarily eject sulfur dioxide (SO₂) that condenses on Io's surface during the relatively cold night. During the day, insolation warms the surface to temperatures where a global partially collisional atmosphere can be sustained by sublimation from SO₂ surface frosts. Both the volcanic and sublimation atmospheres serve as the source for the Jovian plasma torus which flows past Io at ~57 km/s. The high energy ions and electrons in the Jovian plasma torus interact with Io's atmosphere causing atmospheric heating, chemical reactions, as well as altering the circumplanetary winds. Energetic ions which impact the surface can sputter material and create a partially collisional atmosphere. Simulations suggest that energetic ions from the Jovian plasma cannot penetrate to the surface when the atmospheric column density is greater than 10¹⁵ cm⁻². These three mechanisms for atmospheric support (volcanic, sublimation, and sputtering) all play a role in supporting Io's atmosphere but their relative contributions remain unclear. In the present work, the Direct Simulation Monte Carlo (DSMC) method is used to simulate the interaction of Io's atmosphere with the Jovian plasma torus and the results are compared to observations. These comparisons help constrain the relative contributions of atmospheric support as well as highlight the most important physics in Io's atmosphere. These rarefied gas dynamics simulations improve upon earlier models by using a three-dimensional domain encompassing the entire planet computed in parallel. The effects of plasma heating, planetary rotation, inhomogeneous surface frost, molecular residence time of SO₂ on the exposed non-frost surface, and surface temperature distribution are investigated. Circumplanetary flow is predicted to develop from the warm dayside toward the cooler nightside. Io's rotation leads to a highly asymmetric frost surface temperature distribution (due to the frost's high thermal inertia) which results in circumplanetary flow that is not axi-symmetric about the subsolar point. The non-equilibrium thermal structure of the atmosphere, specifically vibrational and rotational temperatures, is also examined. Plasma heating is found to significantly inflate the atmosphere on both the dayside and nightside. The plasma energy flux causes high temperatures at high altitudes, but plasma energy depletion through the dense gas column above the warmest frost permits gas temperatures cooler than the surface at low altitudes. A frost map (Douté et al., 2001) is used to control the sublimated flux of SO₂ which can result in inhomogeneous column densities that vary by nearly a factor of four for the same surface temperature. A short residence time for SO₂ molecules on the non-frost component is found to smooth lateral atmospheric inhomogeneities caused by variations in the surface frost distribution, creating an atmosphere that looks nearly identical to one with uniform frost coverage. A longer residence time is found to agree better with mid-infrared observations (Spencer et al., 2005) and reproduce the observed anti-Jovian/sub-Jovian column density asymmetry. The computed peak dayside column density for Io agrees with those suggested by Lyman-[alpha] observations (Feaga et al., 2009) assuming a surface frost temperature of 115 K. On the other hand, the peak dayside column density at 120 K is a factor of five larger and is higher than the upper range of observations (Jessup et al., 2004; Spencer et al., 2005). The results of the original DSMC simulations of Io's atmosphere show that the most important and sensitive parameter is the SO₂ surface frost temperature. To improve upon the original surface temperature model, we constrain Io's surface thermal distribution by a parametric study of its thermophysical properties. Io's surface thermal distribution is represented by three thermal units: sulfur dioxide (SO₂) frosts/ices, non-frosts (probably sulfur allotropes and/or pyroclastic dusts), and hot spots. The hot spots included in the thermal model are static high temperature surfaces with areas and temperatures based on Keck infrared observations. Elsewhere, over frosts and non-frosts, the thermal model solves the one-dimensional heat conduction equation in depth into Io's surface and includes the effects of eclipse by Jupiter, radiation from Jupiter, and latent heat of sublimation and condensation. The best fit parameters for the SO₂ frost and non-frost units are found by using a least-squares method and fitting to observations of the Hubble Space Telescope's Space Telescope Imaging Spectrograph (HST STIS) mid- to near-UV reflectance spectra and Galileo photo-polarimeter (PPR) brightness temperature. The thermophysical parameters are the frost Bond albedo, and thermal inertia, as well as the non-frost surface Bond albedo, and thermal inertia. The best fit parameters are found to be [equations] for the SO2 frost surface and [equations] for the non-frost surface. These surface thermophysical parameters are then used as boundary conditions in global atmospheric simulations of Io's sublimation-driven atmosphere using DSMC. The DSMC simulations show that the sub-Jovian hemisphere is significantly affected by the daily solar eclipse. The SO₂ surface frost temperature is found to drop ~5 K during eclipse but the column density falls by a factor of 20 compared to the pre-eclipse column due to the exponential dependence of the SO₂ vapor pressure on the SO₂ surface frost temperature. Supersonic winds exist prior to eclipse but become subsonic during eclipse because the collapse of the atmosphere significantly decreases the day-to-night pressure gradient that drives the winds. Prior to eclipse, the supersonic winds condense on and near the cold nightside and form a highly non-equilibrium oblique shock near the dawn terminator. In eclipse, no shock exists since the gas is subsonic and the shock only reestablishes itself an hour or more after egress from eclipse. Furthermore, the excess gas that condenses on the non-frost surface during eclipse leads to an enhancement of the atmosphere near dawn. The dawn atmospheric enhancement drives winds that oppose those that are driven away from the peak pressure region above the warmest area of the SO₂ frost surface. These opposing winds meet and are collisional enough to form stagnation point flow. The simulations are compared to Lyman-[alpha] observations in an attempt to explain the asymmetry between the dayside atmospheres of the anti-Jovian and sub-Jovian hemispheres. A composite "average dayside atmosphere" is formed from a collisionless simulation of Io's atmosphere throughout an entire orbit. The composite "average dayside" atmosphere without the effect of global winds indicates that the sub-Jovian hemisphere should have lower average column densities than the anti-Jovian hemisphere (with the strongest effect at the sub-Jovian point) due entirely to the diurnally averaged effect of eclipse. Lastly, a particle description of the plasma is coupled with the sophisticated surface thermal model and a final set of global DSMC atmospheric simulations are performed. The particle description of energetic ions from the Jovian plasma torus allows for momentum transfer from the ions to the neutral atmosphere. Also, the energetic ions (or solar photons) can dissociate the neutral atmosphere and cause sputtering of SO₂ on the surface. SO₂ remains the dominant dayside species (>90%) despite being dissociated by ions and photons to form O, O₂, S, and SO. SO₂ remains the dominant atmospheric species on the nightside between dusk and midnight due to sputtering of SO₂ surface frosts by energetic ions as well as the high thermal inertia of SO₂ frosts that cause the surface temperature to cool slowly and thus sublime a thicker SO₂ atmosphere. O₂ becomes the dominant atmospheric species above coldest areas of the surface because it is non-condensable at Io's surface temperatures and other species are sticking to the surface. SO and O are present in similar gas fractions because they are created together via the same ion and photo-dissociation reactions. Sulfur column densities are the lowest throughout the atmosphere because S is created slowly via direct dissociation of SO₂; it is instead created primarily through dissociation of SO. The momentum transfer from the plasma is found to have substantial effect on the global wind patterns. The interaction between the plasma pressure and day-to-night pressure gradient is highly dependent on Io's subsolar longitude. Similar to previous simulations, the westward winds reach higher Mach numbers and wind speeds than the eastward winds. This is because the westward winds are accelerated by a larger day-to-night pressure gradient due to the very cold surface temperatures that exist prior to dawn. Eastward equatorial winds on the nightside are accelerated by the plasma pressure and condense out near the dawn terminator after traveling ~3/4 of the circumference of Io. O₂ is pushed to the nightside by the circumplanetary winds where it builds-up until it reaches an equilibrium column density. On the nightside, O₂ is destroyed by ion dissociation. On the nightside, a shear layer develops between the equatorial eastward winds and stagnant non-condensable species at mid-latitudes. This shear layer generates lateral vorticity which is especially visible in O₂ streamlines. Large cyclones develop in the northern and southern hemispheres and are most apparent in the O₂ wind patterns because other species condense out on the nightside.Item Conformational dynamics of an unfolded biopolymer : theory and simulation(2012-12) Cheng, Ryan; Makarov, Dmitrii E.; Florin, Ernst-Ludwig; Elber, Ron; Henkelman, Graeme; Keatinge-Clay, Adrian T.The conformational dynamics of an unfolded biopolymer such as a polypeptide or DNA has attracted a significant amount of attention in the context of protein folding and the design of biomimetic technologies. To this end, recent advances in single-molecule experiments have allowed for biomolecules to be probed with an unprecedented level of detail, shedding light on their dynamics. Motivated by the need to interpret experimental data and to help guide future studies, we use concepts from polymer physics, computer simulations, and experimental data to study the timescales in which an unfolded biopolymer undergoes conformational rearrangement. First, we examine the end-to-end loop formation time in the experimentally relevant scenario where the dynamics are probed using a fluorescence probe and quencher. We show that the loop formation time in the experimentally relevant case is quantitatively dissimilar from the predictions of previous theoretical studies that neglect the quenching kinetics, which are often used to interpret experimental data. We additionally find that the loop formation times can be re-casted in a simple, universal dependence that is characteristic of random-coils. Furthermore, deviations from this universal dependence can be used as a sensitive tool for detecting structural order in unfolded biopolymers. We also consider a surface-tethered polymer chain and investigate the rate of a reaction between the free end and the surface. We explore this rate in the reaction-controlled limit and the diffusion-controlled limit, providing evidence for near-universal dependences of the rate in the respective limits. Next, we examine the transit time of end-to-end loop formation in a case study. We find that approximating the end-to-end dynamics as diffusion in a 1D potential of mean force fails dramatically to describe the transit time. Furthermore, we find that the transit time is uninfluenced by the average entropic force imposed by the polymer chain and is well described by a simple free-diffusion model. Finally, we explore the role of internal friction in the dynamics of an unfolded protein. Using simple polymer models that incorporate internal friction as an adjustable free parameter, we mimic typical single-molecule experiments that probe the unfolded state dynamics and make several experimentally verifiable predictions.Item Development of consistent nonlinear models of flexible body systems(Texas Tech University, 1998-12) Eskridge, Steven ENot availableItem Diagonal plus low rank approximation of matrices for solving modal frequency response problems(2010-12) Vargas, David Antonio; Bennighof, Jeffrey Kent, 1960-; Sirohi, JayantIf a structure is composed mainly of one material but contains a small amount of a second material, and if these two materials have significantly different levels of structural damping, this can increase the cost of solving the modal frequency response problem substantially. Even if the rank of the contribution to the finite element structural damping matrix from the second material is very low, the matrix becomes fully populated when transformed to the modal representation. As a result, the complex-valued modal matrix that represents the structure’s stiffness and structural damping is both full rank, because of the diagonal part contributed by the stiffness, and fully populated, because of off-diagonal imaginary terms contributed by the second material’s structural damping. Solving the modal frequency response problem at many frequencies requires either the factorization of a coefficient matrix at every frequency, or the solution of a complex symmetric eigenvalue problem associated with the modal stiffness/structural damping matrix. The cost of both of these approaches is proportional to the cube of the number of modes included in the analysis. This cost could be reduced greatly if the damping properties of the structure were handled carefully in modeling the structure, but in practical computation of the modal frequency response, the information that could potentially reduce the computational cost is often unavailable. This thesis explores the possibilities of obtaining a representation of the complex modal stiffness/structural damping matrix as a diagonal matrix plus a matrix of minimal rank. An algorithm for computing a “diagonal plus low rank” (DPLR) representation is developed, along with an iterative algorithm for using an inexact DPLR approximation in the solution of the modal frequency response problem. The behavior of these algorithms is investigated on several example problems.Item Dynamic Effects in Nucleophilic Substitution Reactions(2012-02-14) Bogle, Xavier SheldonIn order to rationally optimize a reaction, it is necessary to have a thorough understanding of its mechanism. Consequently, great effort has been made to elucidate a variety of reaction mechanisms. However, the fundamental ideas needed to understand reaction mechanisms are not yet fully developed. Throughout the literature, one encounters numerous examples of experimental observations that are not explainable by conventional mechanistic ideas and methods. The research described in this dissertation employs a unique approach towards the identification and analysis of systems whose observations cannot be explained by conventional transition state theory (TST). The nucleophilic substitution of 4,4-dichloro-but-3-en-2-one by sodium-para-tolyl-thiolate was explored. It was deduced that the reaction was concerted and consequently, the product selectivity observed in the reaction cannot be explained by TST. Dynamic effects play a major role in the observed selectivity and this is further supported by the results of dynamic trajectory simulations. Using computational studies, the ethanolysis of symmetric aryl carbonates was also shown to be concerted, provided that the substrate possesses good leaving groups. Furthermore, extensive precedence has been set by Gutthrie, Santos, Schelgel, and others, detailing concerted substitutions at acyl carbon. The Fujiwara hydroarylation is thought to occur by either a C-H activation mechanism or an electrophilic aromatic substitution (EAS). The KIEs associated with this reaction have been determined and provide strong support for the latter. Computational studies also displayed fair agreement with experimentally determined KIEs, further supporting the EAS mechanism. Isotopic perturbation of equilibria is invaluable in helping to determine whether a structure exists as a single structure or whether it is a time average of two equilibrating structures. The bromonium cation of tetramethylethylene and hydrogen pthalate have been wrongly reported as existing as equilibrating structures. The time averaged geometries have been determined in each case, via a variety of methods and the myth of equilibrating structures in the above cases has been debunked.Item Dynamic modeling and experimental verification of a flexible-follower quick-return mechanism(Texas Tech University, 1999-05) King, Steven A.In this thesis, the dynamics of flexible multibody systems is studied. In particular, a mathematical model of a flexible-follower quick-return mechanism is generated and verified experimentally. This mechanism is of special interest as the closed-loop constraint manifests itself as a time varying load in the domain of the flexible member. The motivation for modeling this type of system is the current trend in the design of industrial equipment toward lighter weight, more slender mechanism components used in order to achieve higher productivity and lower operating cost. As a result, the usual rigid body assumptions made in the dynamic analysis of these systems are no longer valid. Flexibility of the machine elements must be considered in order to produce useful system models. System equations of motion are generated using a hybrid parameter multiplebody system modeling technique. The methodology allows rigorous formulations of the complete nonlinear, hybrid diflferential equations with boundary conditions, no Lagrange multipliers are needed. To verify the model, an experimental mechanism was constructed and data was collected for several test runs with variations of the system parameters.Item Dynamic response and reliability analysis of an offshore wind turbine supported by a semi-submersible platform(2015-12) Thomas, Edwin, M.S. in Engineering; Manuel, LanceWind Energy is the fastest growing renewable energy source in the world. The trend is expected to continue with falling costs of technology, energy security concerns and the need to address environmental issues. Offshore wind turbines have a few important advantages over land-based turbines; offshore sites experience stronger and less turbulent winds, there are fewer negative aesthetic impacts in an offshore location, there is greater ease in the transport of wind turbine components over sea than on land, etc. Large offshore wind turbines mounted atop floating platforms offer a viable solution for deepwater sites. Of the various floating platform concepts that are being considered, a moored semi-submersible platform is considered in this study. The dynamic response and reliability analysis of a 13.2~MW offshore wind turbine supported by a moored semi-submersible platform is the subject of this study. A model for this integrated system has been developed and its various physical, geometric, and dynamic properties have been studied in this and another associated study. Loads data for the extreme and fatigue analysis of such systems are generally attained by running time-domain simulations for a range of sea states that are representative of the expected site-specific metocean conditions. The selected site of interest in the North Sea has a water depth of 200 m. The Environmental Contour (EC) method is used to identify sea states of interest that are associated with a target return period (50 years). These sea states are considered in short-term (1-hour) simulations of the integrated turbine-platform-mooring system. The dynamic behavior of the integrated wind turbine system is studied. Critical sea states for the various response loads are identified and the sensitivity of the system to the metocean conditions is discussed. Estimation of 50-year response levels (for turbine loads, platform motions, and the mooring line tension at the fairlead) associated with the target probability is subsequently carried out using 2D and 3D Inverse First-Order Reliability Method (FORM) approaches.Item Dynamical phenomena in multicomponent polymers(2006) Narayanan, Bharadwaj; Ganesan, VenkatThis research concerns with different aspects of dynamical phenomena in the context of multicomponent polymeric systems. The polymer melts under investigation include polymer blends of varying compositions of two homopolymers (A and B), polymer emulsions of homopolymers blended with block copolymers (AB) and pure block copolymer systems. A novel computation algorithm termed the Self-Consistent Brownian Dynamics (SCBD) was developed and employed to explore the flow effects encountered in the aforementioned polymeric systems. Our contributions in polymer blend systems include, quantification of the slip phenomena at the interface of phase separated symmetric and asymmetric blends. We have also quantified the slip suppression phenomena by the addition of copolymer compatibilizers to the polymer blend interfaces. We have also used the SCBD approach to study the effect of copolymer characteristics on the dynamics of an isolated polymer droplet embedded in a matrix of another polymer. In the case of ternary polymer blend systems, we have studied the flow-induced phase transitions in the microemulsion phases. We provide molecular viewpoint suggesting that the interplay between polymer chain conformations and their flow deformations can lead to novel flow effects upon the phase, structure and rheological behavior of ternary blend systems. In the case of pure copolymer systems, we have studied the effect of oscillatory shear on the lamellar orientation of phase separated multiblock copolymers.Item Electronic and Magnetization Dynamics of Cobalt Substituted Iron Oxide Nanocrystals(2011-02-22) Chen, Tai-YenKnowledge of energy dissipation and relaxation in electron, spin, and lattice degrees of freedom is of fundamental importance from both a technological and scientific point of view. In this dissertation, the electronic and magnetization dynamics of photoexcited colloidal cobalt substituted iron oxide nanocrystals, CoxFe3-xO4, were investigated through transient absorption and pump-probe Faraday rotation measurements. In this dissertation, linearly polarized femtosecond optical pulses at 780 nm were used to excite the weak absorption originating from the intervalence charge transfer transition (IVCT) between Fe2+ and Fe3+ ions of Fe3O4 nanocrystals. The timescale and corresponding relaxation processes of electronic relaxation dynamics of the excited IVCT state were first discussed. Size effect on electronic relaxation dynamics in Fe3O4 nanocrystals is not distinct on the basis of result from this study. One interesting feature of electronic dynamics data of photoexcited Fe3O4 nanocrystals is the creation of coherent acoustic phonons. Information on lattice temperature was obtained by measuring the period of coherent acoustic phonon as a function of excitation fluence and fit into a simple model based on Lamb?s theory. Since optical control of the magnetization can be either through optical or heating mechanisms, quantitative estimation of degree of demagnetization caused by lattice temperature is made by using Langevin function. The result from such estimation indicates the effect of lattice temperature rise on magnetization is too small to significantly affect the magnetization of Fe3O4 nanocrystals. Magnetization dynamics were studied via pump-probe Faraday rotation measurements. Optical excitation with near-infrared pulse resulted in an ultrafast demagnetization in 100fs. The energy of the excited state then relaxed through spin-lattice relaxation (SLR). Effects of surface spin and chemical tuning on the SLR were investigated by comparing the magnetization recovery timescales of nanocrystal with different particle sizes and cobalt concentration respectively. The experimental result is explained by a simple model where interior and surface spins contributed to the spin-lattice relaxation process differently. The observations suggest that spin-orbit coupling of the surface is stronger and less sensitive to stoichiometric variation than the interior spins of the nanocrystals.Item Estimation Strategies for Constrained and Hybrid Dynamical Systems(2012-10-19) Parish, Julie Marie JonesThe estimation approaches examined in this dissertation focus on manipulating system dynamical models to allow the well-known form of the continuous-discrete extended Kalman filter (CDEKF) to accommodate constrained and hybrid systems. This estimation algorithm filters sequential discrete measurements for nonlinear continuous systems modeled with ordinary differential equations. The aim of the research is to broaden the class of systems for which this common tool can be easily applied. Equality constraints, holonomic or nonholonomic, or both, are commonly found in the system dynamics for vehicles, spacecraft, and robotics. These systems are frequently modeled with differential algebraic equations. In this dissertation, three tools for adapting the dynamics of constrained systems for implementation in the CDEKF are presented. These strategies address (1) constrained systems with quasivelocities, (2) kinematically constrained redundant coordinate systems, and (3) systems for which an equality constraint can be broken. The direct linearization work for constrained systems modeled with quasi-velocities is demonstrated to be particularly useful for systems subject to nonholonomic constraints. Concerning redundant coordinate systems, the "constraint force" perspective is shown to be an effective approximation for facilitating implementation of the CDEKF while providing similar performance to that of the fully developed estimation scheme. For systems subject to constraint violation, constraint monitoring methods are presented that allow the CDEKF to autonomously switch between constrained and unconstrained models. The efficacy of each of these approaches is shown through illustrative examples. Hybrid dynamical systems are those modeled with both finite- and infinite-dimensional coordinates. The associated governing equations are integro-partial differential equations. As with constrained systems, these governing equations must be transformed in order to employ the CDEKF. Here, this transformation is accomplished through two finite-dimensional representations of the infinite-dimensional coordinate. The application of these two assumed modes methods to hybrid dynamical systems is outlined, and the performance of the approaches within the CDEKF are compared. Initial simulation results indicate that a quadratic assumed modes approach is more advantageous than a linear assumed modes approach for implementation in the CDEKF. The dissertation concludes with a direct estimation methodology that constructs the Kalman filter directly from the system kinematics, potential energy, and measurement model. This derivation provides a straightforward method for building the CDEKF for discrete systems and relates these direct estimation ideas to the other work presented throughout the dissertation. Together, this collection of estimation strategies provides methods for expanding the class of systems for which a proven, well-known estimation algorithm, the extended Kalman filter, can be applied. The accompanying illustrative examples and simulation results demonstrate the utility of the methods proposed herein.Item Evaluation of technologies for web-enabled chemical dynamics simulations(Texas Tech University, 2005-12) Chawla, Navdeep; Anderson, Per H.; Hase, William L.; Hernandez, Hector J.In the advancing world of Science & Technology, computer simulations have become an integral part of research and development in various fields. Chemical dynamics simulations describe the atomic level motions in molecules and chemical reactions, and they lead to a greater understanding of the properties of molecules and chemical reactions. The use of current chemical dynamics simulation software involves substantial human effort and expertise to create and execute simulation models. This limits the use of the software to experts. This research project proposed a generic framework for automating chemical dynamics simulations by abstracting complexity of creating and executing simulation models. The focus is on developing tools for creating & executing simulation models, generating animations and managing a simulation model repository through a graphical interface. These tools will be available through a web service. Extensibility and Scalability are important design considerations. In order to improve the accessibility of the system to non-experts, a web interface is developed which makes application easily and globally accessible by a web browser. Different High Performance Computing technologies are evaluated for interfacing with the simulation software to perform the simulations results and then animate the results with visualization tools. The proposed framework is implemented and tested using the chemical dynamics simulation software VENUS. This implementation provides a graphical-user interface for customizing simulation models and automats the process of job submission to different execution environments. Usability tests of the implementation have been conducted with a diverse group of users. Results of the usability tests are analyzed and recommendations are made for improvements in the proposed framework and implementation.Item Evaluation of technologies for web-enabled chemical dynamics simulations(2005-12) Chawla, Navdeep; Anderson, Per H.; Hase, William L.; Hernandez, Hector J.In the advancing world of Science & Technology, computer simulations have become an integral part of research and development in various fields. Chemical dynamics simulations describe the atomic level motions in molecules and chemical reactions, and they lead to a greater understanding of the properties of molecules and chemical reactions. The use of current chemical dynamics simulation software involves substantial human effort and expertise to create and execute simulation models. This limits the use of the software to experts. This research project proposed a generic framework for automating chemical dynamics simulations by abstracting complexity of creating and executing simulation models. The focus is on developing tools for creating & executing simulation models, generating animations and managing a simulation model repository through a graphical interface. These tools will be available through a web service. Extensibility and Scalability are important design considerations. In order to improve the accessibility of the system to non-experts, a web interface is developed which makes application easily and globally accessible by a web browser. Different High Performance Computing technologies are evaluated for interfacing with the simulation software to perform the simulations results and then animate the results with visualization tools. The proposed framework is implemented and tested using the chemical dynamics simulation software VENUS. This implementation provides a graphical-user interface for customizing simulation models and automats the process of job submission to different execution environments. Usability tests of the implementation have been conducted with a diverse group of users. Results of the usability tests are analyzed and recommendations are made for improvements in the proposed framework and implementation.Item Metal dependent structure, dynamics, and function in RNA measured by site-directed spin labeling and EPR spectroscopy(Texas A&M University, 2007-04-25) Kim, Nak-KyoonThe structure and function of RNA molecules are dependent on RNA-metal ion interactions in both diffusive and direct ways. Structural information for RNA has been obtained using various biophysical and biochemical methods. In this study, using site-directed spin labeling (SDSL) and EPR spectroscopy, distances in RNA duplexes, TAR RNA, and the hammerhead ribozyme have been measured to investigate RNA structures. Kinetic measurements have been performed in the extended hammerhead ribozyme to correlate the catalytic function with metal dependent ribozyme folding. As a basic model system for distance measurements, inter-spin distances in RNA duplexes with spin labels at various positions are measured using SDSL with continuous EPR and a Fourier deconvolution method. Divalent metal-ion dependent TAR RNA folding from bent to extended conformers is monitored by measuring inter-spin distances near the bulge region. In order to investigate a proposed loop-loop interaction in the extended hammerhead ribozyme which significantly enhances the ribozyme activity, distance measurements, dynamics studies, and kinetics measurements have been performed. We have introduced PELDOR long-distance measurements in order to investigate metal dependent folding of the hammerhead ribozyme. The dynamics of the spin labels attached to the hammerhead ribozyme with increasing mono- and divalent metal ion concentrations are monitored using CW EPR spectroscopy at room temperature. EPR data show that a loop-loop interaction occurs near the U1.6 nucleotide, and that in 0.1 M NaCl the docking occurs at submillimolar Mg2+ concentrations ([Mg2+]1/2, docking = ~ 0.7 mM). Kinetics measurements show that the hammerhead ribozyme requires high concentration of Mg2+ for the maximum cleavage activity ([Mg2+]1/2, cleavage = ~ 90 mM).Item Methodology for creating human-centered robots : design and system integration of a compliant mobile base(2012-05) Wong, Pius Duc-min; Sentis, Luis; Deshpande, AshishRobots have growing potential to enter the daily lives of people at home, at work, and in cities, for a variety of service, care, and entertainment tasks. However, several challenges currently prevent widespread production and use of such human-centered robots. The goal of this thesis was first to help overcome one of these broad challenges: the lack of basic safety in human-robot physical interactions. Whole-body compliant control algorithms had been previously simulated that could allow safer movement of complex robots, such as humanoids, but no such robots had yet been documented to actually implement these algorithms. Therefore a wheeled humanoid robot "Dreamer" was developed to implement the algorithms and explore additional concepts in human-safe robotics. The lower mobile base part of Dreamer, dubbed "Trikey," is the focus of this work. Trikey was iteratively developed, undergoing cycles of concept generation, design, modeling, fabrication, integration, testing, and refinement. Test results showed that Trikey and Dreamer safely performed movements under whole-body compliant control, which is a novel achievement. Dreamer will be a platform for future research and education in new human-friendly traits and behaviors. Finally, this thesis attempts to address a second broad challenge to advancing the field: the lack of standard design methodology for human-centered robots. Based on the experience of building Trikey and Dreamer, a set of consistent design guidelines and metrics for the field are suggested. They account for the complex nature of such systems, which must address safety, performance, user-friendliness, and the capability for intelligent behavior.Item Modeling and analysis of hybrid dynamic systems(Texas Tech University, 1996-12) Gotesman, MosheA modeling technique for hybrid dynamics systems, using high-level Petri nets, is presented. A hybrid dynamics system is a continuous dynamics system in which discrete events occur. Modeling of hybrid dynamics systems is difficult since continuous dynamics and discrete event dynamics have entirely different mathematics. The dissertation presents techniques for converting a hybrid dynamics system, represented mathematically or by means of a block diagram into a Petri net. The resulting Petri net. called the Hybrid Dynamics Petri Net (HDPN). captures both the continuous and discrete event phenomena in the system. This provides a single formalism for modeling hybrid dynamics systems. Procedures are also provided for converting a Petri net into a block diagram and into a mathematical representation. Some examples are implemented to demonstrate the capability of the Petri net formalism to correctly model hybrid dynamics systems. The examples demonstrate the modeling power of Petri nets for continuous and hybrid systems, including non-linear systems and MIMO systems.Item Particle dynamics and microrheology at liquid-liquid interfaces(Texas Tech University, 2009-05) Wu, Chih-yuan; Dai, Lenore L.Solid-stabilized emulsions, often refer to as Pickering Emulsions, have the ability to provide a simple and convenient experimental template to meet various requirements, such as changing property of solid particles, oil phase viscosity and interfacial curvature. The confocal laser scanning microscope (CLSM) is a useful and convenient tool to investigate the dynamics of particles at emulsions interfaces. Here we have employed Pickering emulsions as an experimental template and confocal laser scanning microscopy as a tool to study the dynamics of solid particles at liquid-liquid interfaces. In Chapter 4.1 and 4.2, the diffusion behavior of colloidal particles at oil-water interfaces is studied using Pickering emulsions as templates. The solid particles are sulfate modified polystyrene microparticles with diameters of 1.1 10-6 m and the oil phase is polydimethylsiloxane oil (PDMS) or octamethyltrisiloxane with different viscosities. The confocal laser scanning microscopy is used as a tool to observe the dynamics of microparticles at emulsions interfaces. The main discussion focuses on the effects of interfacial curvature, cluster size, and oil phase viscosity on the diffusive behavior of solid particles at oil-water interfaces. In Chapter 4.3 and 4.4, both of one-particle microrheology and two-particle microrheology are used to investigate the microrheologiccal data at the poly (dimethylsiloxane) oil-water interfaces. The dynamics of charged microparticles are observed using confocal laser scanning microscopy (CLSM) at the liquid-liquid interfaces. The experimental template is Pickering emulsions. For one-particle microrheology, the different charged sub-microparticles are used as tracers and mobility of the sub-microparticles depend largely on the viscoelastic properties of the oil phase and the wettability of the solid particles. However, those phenomena can be ignored in two-particle microrheology. In addition, the potential of microrheology at liquid-liquid interfaces is also developed in both two methodologies. The apparent loss modulus, storage modulus, and relaxation time of the oil-water interfaces are gathered at the liquid-liquid interfaces. Finally, the difference between the results of one- and two-particle microrheology is compared.Item Pounding and impact of base isolated buildings due to earthquakes(Texas A&M University, 2005-08-29) Agarwal, Vivek KumarAs the cost of land in cities increases, the need to build multistory buildings in close proximity to each other also increases. Sometimes, construction materials, other objects and any projections from a building may also decrease the spacing provided between the buildings. This leads to the problem of pounding of these closely placed buildings when responding to earthquake ground motion. The recent advent of base isolation systems and their use as an efficient earthquake force resisting mechanism has led to their increased use in civil engineering structures. At the same time, building codes that reflect best design practice are also evolving. The movement of these base isolated buildings can also result in building pounding. Since base isolation is itself a relatively new technique, pounding phenomenon in base isolated buildings have not been adequately investigated to date. This study looks at the base isolated response of a single two story building and adjacent two story building systems. Four earthquakes with increasing intensity were used in this study. It was found that it is difficult to anticipate the response of the adjacent buildings due to non- linear behavior of pounding and base isolation. The worst case for pounding was found to occur when a fixed base and base isolated buildings were adjacent to each other.Item Reinforcement Learning Control with Approximation of Time-Dependent Agent Dynamics(2013-04-30) Kirkpatrick, KentonReinforcement Learning has received a lot of attention over the years for systems ranging from static game playing to dynamic system control. Using Reinforcement Learning for control of dynamical systems provides the benefit of learning a control policy without needing a model of the dynamics. This opens the possibility of controlling systems for which the dynamics are unknown, but Reinforcement Learning methods like Q-learning do not explicitly account for time. In dynamical systems, time-dependent characteristics can have a significant effect on the control of the system, so it is necessary to account for system time dynamics while not having to rely on a predetermined model for the system. In this dissertation, algorithms are investigated for expanding the Q-learning algorithm to account for the learning of sampling rates and dynamics approximations. For determining a proper sampling rate, it is desired to find the largest sample time that still allows the learning agent to control the system to goal achievement. An algorithm called Sampled-Data Q-learning is introduced for determining both this sample time and the control policy associated with that sampling rate. Results show that the algorithm is capable of achieving a desired sampling rate that allows for system control while not sampling ?as fast as possible?. Determining an approximation of an agent?s dynamics can be beneficial for the control of hierarchical multiagent systems by allowing a high-level supervisor to use the dynamics approximations for task allocation decisions. To this end, algorithms are investigated for learning first- and second-order dynamics approximations. These algorithms are respectively called First-Order Dynamics Learning and Second-Order Dynamics Learning. The dynamics learning algorithms are evaluated on several examples that show their capability to learn accurate approximations of state dynamics. All of these algorithms are then evaluated on hierarchical multiagent systems for determining task allocation. The results show that the algorithms successfully determine appropriated sample times and accurate dynamics approximations for the agents investigated.