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Leuty, Gary MAdsorption and Surface Structure Characteristics Toward Polymeric Bottle-Brush Surfaces via Multiscale Simulation
Doctor of Philosophy, University of Akron, 2014, Polymer Science
For decades, device design has focused on decreasing length scales. In computer and electronic engineering, small feature sizes allow increasing computational power in ever-smaller packages; in medicine, nanoscale in vivo devices and sensors and coatings have myriad applications. These applications all focus strongly on material/component interfaces. While recent advances in experimental techniques probing interfaces at nanometer and sub-nanometer scales have improved dramatically, computational simulation remains vital to obtaining detailed information about structure and energetics in nanometer-scale interactions at interfaces and the physical properties arising from interactions at larger scales. We start with all-atom molecular dynamics simulations of methane and chloromethane adsorption on the (100) surface of molybdenum to understand adsorbate polarity/geometry and substrate interaction potential effects on interfacial structure, packing and energetics. For featureless substrates, adsorbate geometry and orientation do not influence packing and affinity. Substrates with explicit surface structure show cooperation between substrate and adsorbate geometry via adsorption-site preference. Methane prefers sites over unit cell faces, roughly commensurate with the Mo surface, whereas chloromethane invites disorder, orienting its long axis along ”bridges” between surface Mo atoms. In the second phase, we used a coarse-grained bead-spring model to perform simulations of bottle-brush homopolymers tethered to a wall substrate at long time/length scales. We studied the intra- and intermolecular accumulation of tension in tethered bottle-brush backbones vs. bottle-brush dimensions and surface grafting density. Variations in bond force and bottle-brush/component shape and size descriptors uncovered three tension ”regimes”: (i) an isolated-brush regime (low surface grafting density), where intramolecular interactions dominate and tension is minimal; (ii) a ”soft-contact” regime, where neighboring bottlebrushes’ side chains overlap, compressing side chains and transmitting moderate tension to backbones; and (iii) a ”hard-contact” regime, where increased side-chain overlap forces reorientation, accumulating significant backbone tension. We then performed a small number of simulations of tethered bottle-brushes with two different side chain types to illustrate the morphologies available as a result of microphase separation, varying the strength of the interactions between side chain types. Continuing this work in the future should help discover other possible applications arising from varying the chemical nature of the side chains.

Committee:

Mesfin Tsige, Dr. (Advisor); Mark Foster , Dr. (Committee Member); Shi-Qing Wang, Dr. (Committee Member); Gustavo Carri, Dr. (Committee Member); Jutta Luettmer-Strathmann, Dr. (Committee Member)

Subjects:

Condensed Matter Physics; Materials Science; Molecular Physics; Physical Chemistry; Physics; Polymers; Theoretical Physics

Keywords:

Molecular dynamics simulation; bottle-brush polymers; adsorption; computer simulation; coarse-grained bead-spring molecular dynamics; all-atom molecular dynamics; surfaces and interfaces

Jamali, SafaRheology of Colloidal Suspensions: A Computational Study
Doctor of Philosophy, Case Western Reserve University, 2015, Macromolecular Science and Engineering
Computational studies have emerged as a key class of scientific approached to solving different problems of interest in the past few decades. Dissipative Particle Dynamics, DPD, a mesoscale simulation technique based on Molecular Dynamics has been established as a powerful technique in recovering a wide range of physical and chemical processes. Nevertheless, absence of robust bridge between the computational parameters to the physical characteristics of a system has limited applications of DPD. Thus in the second chapter of this dissertation (after a brief introduction and organizational guideline in chapter 1) a systematic study will be presented, providing several routes for setting the simulation parameters based on the real experimental measures. Although computational and theoretical works have always been a crucial areas of research in the rheology society, DPD has not been employed in rheological studies. This is mainly due to the fact that a step-by-step guideline does not exist for rheological measurements in DPD. Another reason for this lack of success in rheological community is that the built-in thermostat in DPD is not capable of providing a stable control over the thermodynamics of the system under flow conditions. Thus, firstly in chapter 3 different methods of viscosity measurement and rheological studies will be discussed in detail, and consequently in chapter 4 a novel thermostat is presented to modify the natural shortcomings of DPD under flow. For decades now, scientists across different disciplines have attempted at identifying the nature of versatile rheological response of colloidal suspensions. Exhibiting Newtonian behavior at very low, shear-thinning at intermediate, and shear-thickening at high flow rates in dense colloidal suspensions exemplifies a broad range of rheological regimes within a simple solid-liquid system. Despite numerous experimental and computational efforts in explaining the underlying mechanism of these behavior, there is still an ongoing debate in the scientific community on the subject. Hence, in final chapter a comprehensive study on rheology of colloidal suspensions (including a complete flow curve, normal stress measurements and microstructural evolutions) is presented, based on the results and foundations in prior chapters as well as in the literature.

Committee:

Joao Maia (Advisor); Wnek Gary (Committee Member); Daniel Lacks (Committee Member); Michael Hore (Committee Member)

Subjects:

Chemical Engineering; Mechanical Engineering; Physics; Polymers

Keywords:

Fluid Dynamics, Rheology, Colloidal Suspensions, Mesoscale Simulations, Dissipative Particle Dynamics, Computational Fluid Dynamics

LI, ZHENLONGDYNAMICS OF POLYMER SELF-ASSEMBLY BY COMPUTER SIMULATION
Doctor of Philosophy, Case Western Reserve University, 2011, Macromolecular Science and Engineering

We studied the self-assembly dynamics of two polymeric systems, block copolymer micelles and supramolecular polymer solutions using computer simulation.

Dissipative Particle Dynamics simulations were applied to study the equilibrium properties, kinetics of micellization and equilibrium chain-exchange in A2B3 and A4Bx(x=4,6,8) diblock copolymer micelle solutions. The critical micelle concentration, micelle aggregation number distribution and micelle structure were found to agree well with previous experimental and theoretical studies. The time-evolution of micelles from unimers is found to follow three stages: unimer consumption, equilibration of the number of micelles progressing mainly by the fusion/fission mechanism and slow adjustment of the weight-average aggregation number by micelle fusion, unimer and small aggregate exchange. The effect of polymer concentration, hydrophobic interaction energy and block length on the kinetics of micellization were also considered. By performing micelle hybridization simulations, we found the equilibrium chain exchange follows a first-order kinetic process and the characteristic time, mainly determined by chain expulsion and does not depend on polymer concentration. The chain exchange characteristic time, τ, increases exponentially with core block length, NA and interaction parameter between blocks, χAB as τ ~ exp(0.67χABNA). We also found that in contrast to theoretical predictions, chain exchange between micelles occurs more rapidly for micelles with a longer corona-block length due to a higher compatibility of diblock copolymers and therefore a lower potential barrier for chain expulsion.

Using coarse-grained molecular dynamics simulations we studied the equilibrium and rheological properties of dilute and semi-dilute solutions of head-to-tail associating supramolecular polymers with our newly-developed model for spontaneous reversible association. We found that for a given spacer length all shear-rate-dependent reduced viscosity data collapse into one master curve with two power-law regions with increasing slopes due to change of the degree of self-assembling under shear. The equilibrium viscosity is found to obey a power-law scaling dependence with exponent 1.5 on oligomer volume fraction, in agreement with experimental observations for several dilute or semi-dilute solutions of supramolecular polymers, implying that dilute and semi-dilute supramolecular polymer solutions exhibit high polydispersity, but may not be sufficiently entangled to follow the reptation mechanism of relaxation, expected for wormlike micelles.

Committee:

Elena Dormidontova (Advisor); Alexander Jamieson (Committee Member); Jay Mann (Committee Member); Lei Zhu (Committee Member)

Subjects:

Polymers

Keywords:

self-assembly dynamics; block copolymer micelles; supramolecular polymer; computer simulation; DPD simulation; Molecular Dynamics simulation; micelle dynamics; viscosity;

Zagorski, Scott B.Modeling, Control and State Estimation of a Roll Simulator
Doctor of Philosophy, The Ohio State University, 2012, Mechanical Engineering

This research involved the modeling, control and state estimation of a Roll Simulator. The focus of this study was on the Roll Simulator's application in emulating rollovers for vehicles such as ROVs. The Roll Simulator was designed to study occupant kinematics during a vehicle rollover in a laboratory setting. Little research has been performed where the focus has been on the vehicle rolling over to 90 degrees and the interaction of the occupant with the road plane at this instance has been closely examined. The Roll Simulator allows for these types of analyses to occur.

In this dissertation, a two (2) degree-of-freedom model, describing the dynamics of the Roll Simulator, is developed. Equations of motion, derived using Lagrange's energy methods, describe the dynamics of the sled-platform assembly. Additional sub-system modeling is also performed to capture the dynamics of a hydraulic system, electro-magnetic particle brake and electric roll motor. The validity of the full simulation is corroborated by comparisons with experimental data from the Roll Simulator.

Control strategies for the Roll Simulator are also discussed. The strategies are derived utilizing simple physics of the system. This allows for desired trajectories to be met using feed-forward terms. Application of feedback is limited due to the configurations of the actuators and the short duration maneuever.

A variety of linear observers are introduced to estimate states within the Roll Simulator. A Kalman Filter is developed to estimate sled speed. To tune the filter, the Kalman Filter is applied to a higher fidelity model which has four (4) degrees-of-freedom. To capture the non-linear behavior of the sled-platform assembly, an Extended Kalman Filter (EKF) is used. When applied to experimental data, the observed sled speed exhibits gross over-estimation of the true speed. This is due to a disturbance in the system. A disturbance observer is used to estimate rolling resistance between the sled and floor and account for any uncertainties in system parameters. When using the disturbance observer, the linear Kalman Filter is able to more accurately estimate sled speed. For low-load low-speed applications, the output of a Kalman Filter using an accelerometer and measured drum speed, closely agrees with sled speed, when appropriate gain scheduling is introduced.

Lastly, a feedback linearization technique is investigated. This studies the versatility of the Roll Simulator when the limitations of its actuators are increased.

Committee:

Dennis Guenther (Advisor); Gary Heydinger (Committee Member); Ahmet Kahraman (Committee Member); Gary Kinzel (Committee Member)

Subjects:

Mechanical Engineering

Keywords:

Roll Simulator; Vehicle Dynamics; System Dynamics; Recreational Off-Highway Vehicles; Lagrange's Energy Equation; Dynamics; Kalman Filter; Extended Kalman Filter; Disturbance Observer; Feedback Linearization

Saxena, ChaitanyaUltrafast dynamics of energy and electron transfer in DNA-photolyase
Doctor of Philosophy, The Ohio State University, 2007, Biophysics
One of the detrimental effects of UV radiation on the biosphere is the formation of cyclobutane pyrimidine dimers (Pyr<>Pyr) between two adjacent thymine bases in DNA. Pyr<>Pyr dimers bring DNA repair machinery in the cell to a standstill and may result in mutation or cell death. Photolyase which is a photoenzyme that exists in all three branches of life, harnesses blue or near-UV light energy to cleave the cyclobutane ring of the Pyr<>Pyr and, thus, prevents the harmful effects of UV radiation. Photolyase obtained from E.coli is a monomeric protein with two noncovalently attached cofactors: one is a light-harvesting photoantenna, a pterin molecule in the form of methenyltetrahydrofolate (MTHF), and the other one is the catalytic cofactor, a fully reduced deprotonated flavin molecule (FADH -). In the proposed hypothesis for the catalysis, the enzyme binds a Pyr<>Pyr in DNA, independent of light. The antenna chromophore MTHF harvests UV/blue-light photon, and transfers the excitation energy (dipole-dipole interaction) to FADH -. Excited FADH -*then transfers an electron to the Pyr<>Pyr, which consequently splits the Pyr<>Pyr into two pyrimidines and hence repairs the damaged DNA. The repair cycle ends when the excess electron is transferred from the repaired pyrimidine back to the nascent-formed FADH and regenerates the active FADH -form. The complex mechanism of energy and electron transfer in photolyase enzyme was investigated using state-of-the-art femtosecond laser spectroscopy in this study. The photophysics of FADH -cofactor was also studied in aqueous solution. Dramatic shortening of the excited state lifetime of FADH -in aqueous solution compare to its lifetime in protein environment compelled us to propose that enzyme photolyase modulates photophysical properties of the flavin cofactor to perform the essential biological function of electron transfer to repair damaged DNA.

Committee:

Dongping Zhong (Advisor)

Keywords:

ultrafast dynamics; Biological dynamics; Femtosecond; Photolyase; Enzyme dynamics; Cryptochrome; Electron transfer in proteins; Energy transfer in proteins

Bazow, Dennis P.Fluid dynamics for the anisotropically expanding quark-gluon plasma
Doctor of Philosophy, The Ohio State University, 2017, Physics
Local momentum anisotropies are large in the early stages of the quark-gluon plasma created in relativistic heavy-ion collisions, due to the extreme difference in the initial longitudinal and transverse expansion rates. In such situations, fluid dynamics derived from an expansion around an isotropic local equilibrium state is bound to break down. Instead, we resum the effects of the slowest nonhydrodynamic degree of freedom (associated with the deviation from momentum isotropy) and include it at leading order, defining a local anisotropic quasi-equilibrium state, thereby treating the longitudinal/transverse pressure anisotropy nonperturbatively. Perturbative transport equations are then derived to deal with the remaining residual momentum anisotropies. This procedure yields a complete transient effective theory called viscous anisotropic hydrodynamics. We then show that the anisotropic hydrodynamic approach, especially after perturbative inclusion of all residual viscous terms, dramatically outperforms viscous hydrodynamics in several simplified situations for which exact solutions exist but which share with realistic expansion scenarios the problem of large dissipative currents. Simulations of the full three-dimensional dynamics of the anisotropic quark-gluon plasma are then presented.

Committee:

Ulrich Heinz (Advisor); Michael Lisa (Committee Member); Yuri Kovchegov (Committee Member); Junko Shigemitsu (Committee Member)

Subjects:

Physics

Keywords:

Relativistic fluid dynamics; Quark-gluon plasma; Anisotropic dynamics; Viscous hydrodynamics; Boltzmann equation; GPU; CUDA; Parallel computing

Bourke, Jason MichaelImplications of Airflow Dynamics and Soft-Tissue Reconstructions for the Heat Exchange Potential of Dinosaur Nasal Passages
Doctor of Philosophy (PhD), Ohio University, 2015, Biological Sciences (Arts and Sciences)
This study seeks to restore the internal anatomy within the nasal passages of dinosaurs via the use of comparative anatomical methods along with computational fluid dynamic simulations. Nasal airway descriptions and airflow simulations are described for extant birds, crocodylians, and lizards. These descriptions served as a baseline for airflow within the nasal passages of diapsids. The presence of shared airflow and soft-tissue properties found in the nasal passages of extant diapsids, were used to restore soft tissues within the airways of dinosaurs under the assumption that biologically unfeasible airflow patterns (e.g., lack of air movement in olfactory recess) can serve as signals for missing soft tissues. This methodology was tested on several dinosaur taxa. Restored airways in some taxa revealed the potential presence and likely shape of nasal turbinates. Heat transfer efficiency was tested in two dinosaur species with elaborated nasal passages. Results of that analysis revealed that dinosaur noses were efficient heat exchangers that likely played an integral role in maintaining cephalic thermoregulation. Brain cooling via nasal expansion appears to have been necessary for dinosaurs to have achieved their immense body sizes without overheating their brains.

Committee:

Lawrence Witmer, PhD (Advisor)

Subjects:

Anatomy and Physiology; Animal Sciences; Biology; Biomechanics; Fluid Dynamics; Paleontology; Scientific Imaging; Zoology

Keywords:

dinosaurs; computational fluid dynamics; CFD; anatomy; reptiles; birds; biomechanics; turbinates; brain cooling; thermoregulation; fluid dynamics; Stegoceras; Euoplocephalus; Panoplosaurus; bony-bounded; airway; nasal passage; nasal cavity

Ickes, JacobImproved Helicopter Rotor Performance Prediction through Loose and Tight CFD/CSD Coupling
Master of Science, University of Toledo, 2014, Mechanical Engineering
Helicopters and other Vertical Take-Off or Landing (VTOL) vehicles exhibit an interesting combination of structural dynamic and aerodynamic phenomena which together drive the rotor performance. The combination of factors involved make simulating the rotor a challenging and multidisciplinary effort, and one which is still an active area of interest in the industry because of the money and time it could save during design. Modern tools allow the prediction of rotorcraft physics from first principles. Analysis of the rotor system with this level of accuracy provides the understanding necessary to improve its performance. There has historically been a divide between the comprehensive codes which perform aeroelastic rotor simulations using simplified aerodynamic models, and the very computationally intensive Navier-Stokes Computational Fluid Dynamics (CFD) solvers. As computer resources become more available, efforts have been made to replace the simplified aerodynamics of the comprehensive codes with the more accurate results from a CFD code. The objective of this work is to perform aeroelastic rotorcraft analysis using first-principles simulations for both fluids and structural predictions using tools available at the University of Toledo. Two separate codes are coupled together in both loose coupling (data exchange on a periodic interval) and tight coupling (data exchange each time step) schemes. To allow the coupling to be carried out in a reliable and efficient way, a Fluid-Structure Interaction code was developed which automatically performs primary functions of loose and tight coupling procedures. Flow phenomena such as transonics, dynamic stall, locally reversed flow on a blade, and Blade-Vortex Interaction (BVI) were simulated in this work. Results of the analysis show aerodynamic load improvement due to the inclusion of the CFD-based airloads in the structural dynamics analysis of the Computational Structural Dynamics (CSD) code. Improvements came in the form of improved peak/trough magnitude prediction, better phase prediction of these locations, and a predicted signal with a frequency content more like the flight test data than the CSD code acting alone. Additionally, a tight coupling analysis was performed as a demonstration of the capability and unique aspects of such an analysis. This work shows that away from the center of the flight envelope, the aerodynamic modeling of the CSD code can be replaced with a more accurate set of predictions from a CFD code with an improvement in the aerodynamic results. The better predictions come at substantially increased computational costs between 1,000 and 10,000 processor-hours.

Committee:

Chunhua Sheng, Ph.D. (Advisor); Abdeh Afjeh, Ph.D. (Committee Member); Ray Hixon, Ph.D. (Committee Member); Glenn Lipscomb, Ph.D. (Committee Member)

Subjects:

Aerospace Engineering; Fluid Dynamics; Mechanical Engineering

Keywords:

Computational Fluid Dynamics; Computational Structural Dynamics; CFD; CSD; Helicopter; Rotor; Coupling; UH-60A; Rotorcraft; Aerodynamics

Yang, JunyiNonlinear Dynamics of Driveline Systems with Hypoid Gear Pair
PhD, University of Cincinnati, 2012, Engineering and Applied Science: Mechanical Engineering

This dissertation research focuses on evaluating the nonlinear dynamics of driveline systems employed in motor vehicles with emphasis on characterizing the excitations and response of right-angle, precision hypoid-type geared rotor structure. The main work and contribution of this dissertation is divided into three sections. Firstly, the development of an asymmetric and nonlinear gear mesh coupling model will be discussed. Secondly, the enhancement of the multi-term harmonic balance method (HBM) is presented. Thirdly and as the final topic, the development of new dynamic models capable of evaluating the dynamic coupling characteristics between the gear mesh and other driveline structures will be addressed.

A new asymmetric and nonlinear mesh model will be proposed that considers backlash, and the fact that the tooth surfaces of the convex and concave sides are different. The proposed mesh model will then be fed into a dynamic model of the right-angle gear pair to formulate the dimensionless equation of motion of the dynamic model. The multi-term HBM will be enhanced to simulate the right-angle gear dynamics by solving the resultant dimensionless equation of motion. The accuracy of the enhanced HBM solution will be verified by comparison of its results to the more computationally intensive direct numerical integration calculations. The stability of both the primary and sub-harmonic solutions predicted by applying multi-term HBM will be analyzed using the Floquent Theory. In addition, the stability analysis of the multi-term HBM solutions will be proposed as an approximate approach for locating the existence of sub-harmonic and chaotic motions.

In this dissertation research, a new methodology to evaluate the dynamic interaction between the nonlinear hypoid gear mesh mechanism and the time-varying characteristics of the rolling element bearings will also be developed. The time-varying mesh parameters will be obtained by synthesizing a 3-dimensional loaded tooth contact analysis (TCA) results. The time-varying stiffness matrix approach will be used to represent the dynamic characteristics of the rolling element bearings.

An overall nonlinear dynamic model of the hypoid gear box considering elastic housing structure will be developed as well. A lumped parameter model of the flexible housing will be extracted form an appropriate set of frequency response functions through modal parameter identification method. In order to obtain the rotational coordinates, a rigid body interpolation of the translational responses at the bearing locations on the housing structure will be applied. The reduced model will be then coupled with the hypoid gear-shaft-bearing assembly model by applying a proposed dynamic coupling procedure.

Finally, a hypoid geared rotor system model considering the propeller shaft flexibility will be established. The propeller shaft bending flexibility will be modeled as lumped parameter model through using the component mode synthesis (CMS). The torsional flexibility of propeller shaft will be simplified as a torsional spring connecting the inertia of moment of engine and pinion. Physically, the pinion input shaft is driven by the propeller shaft through a universal joint, which will be modeled as a flexible simple supported boundary condition as well as fluctuating rotation speed and torque excitation.

Committee:

Teik Lim, PhD (Committee Chair); Sundaram Murali Meenakshi, PhD (Committee Member); Dong Qian, PhD (Committee Member); David Thompson, PhD (Committee Member)

Subjects:

Mechanics

Keywords:

Nonlinear gear dynamics;Multi-term harmonic balance;Asymmetric mesh;Gear backlash;Nonlinear driveline dynamics;Sub-harmonic and chaotic motions;

Kastner, Jeffrey F.Far-field radiated noise mechanisms in high reynolds number and high-speed jets
Doctor of Philosophy, The Ohio State University, 2007, Mechanical Engineering
The present research examines the relationship between the large-scale structure dynamics of a jet and the far-field sound. This was achieved by exploring the flowfield and the far field of an axisymmetric Mach 0.9 jet with a Reynolds number of approximately 0.76 million. The jet is controlled by eight plasma actuators, which operate over a large frequency range and have independent phase control allowing excitation of azimuthal modes (m) 0, 1, 2, and 3. The jet’s far field is probed with a microphone array positioned at 30 degrees with respect to the downstream jet axis. The array is used to estimate the origin of peak sound events in space, and find the sound pressure level (SPL) and overall sound pressure level (OASPL). The lower forcing Strouhal numbers (StDF’s) increase the OASPL and move noise sources upstream while higher StDF’s decrease the OASPL and have noise source distributions similar to the baseline jet. The flowfield was investigated using particle image velocimetry (PIV). A Reynolds decomposition of the PIV data emphasized the importance of the streamwise velocity fluctuations for the symmetric azimuthal modes (m = 0 and 2) and the cross-stream velocity fluctuations for the asymmetric azimuthal modes (m = 1 and 3). A proper orthogonal decomposition of the PIV data was performed to extract information about how forcing affects the large-scale flow features and conditionally average the PIV data. When forcing at StD’s other than the preferred mode, the conditional-averaged images show large-scale flow features that grow, saturate, and decay closer to the nozzle exit. When exciting a symmetric azimuthal mode, m = 0, near the preferred StDF, the streamwise phase-averaged velocity grows quickly and saturates over a relatively long spatial range. When exciting an asymmetric azimuthal mode, m = 1, near the preferred StDF, the cross-stream phase-averaged velocity grows slowly, saturates, and then decays relatively quickly. The noise source distribution occurred in the decay region for both m = 0 and m = 1, and the distribution changed in accordance with changes in the decay rate.

Committee:

Mo Samimy (Advisor)

Subjects:

Engineering, Mechanical

Keywords:

Fluid Dynamics; Gas Dynamics; Aeroacoustics; Optical Diagnostics

Thurow, Brian SOn the convective velocity of large-scale structures in compressible axisymmetric jets
Doctor of Philosophy, The Ohio State University, 2005, Mechanical Engineering
The role of compressibility on the convective velocity of large-scale structures in axisymmetric jets is studied using a home-built pulse burst laser system and newly developed high-repetition rate experimental diagnostics. A pulse burst laser system was designed and constructed with the ability to produce a burst of short duration (10 nsec), high energy (order of 10 -100 mJ/pulse) pulses over a ~150 microsecond period with inter-pulse timing as low as 1 microsecond (1 MHz). The application of the pulse burst laser for flow measurements was investigated through the development of MHz rate flow visualization and MHz rate planar Doppler velocimetry (PDV). MHz rate PDV is a spectroscopic technique that produces 28 time-correlated realizations of the velocity over a plane with a maximum repetition rate of up to 1 MHz and accuracies on the order of 5%. Space-time correlations were used to track structures within the flow field and determine their convective velocity. Data produced using flow visualization images agrees with previous research and indicates a strong departure of the convective velocity from theory. Data produced using velocity data, however, shows starkly different trends and does not produce the same measurements of convective velocity. This difference in measurement is attributed to a misinterpretation of the use of space-time correlation for tracking structures. The presence of a distinct boundary between the mixing layer and the jet core as well as the mixing layer and ambient air in the flow visualization data and some of the velocity data leads to a bias in the measurement. The space-time correlation is found to preferentially follow these boundaries, thus leading to faster and/or slower measurements of convective velocity. For the Mach 2.0 jet, velocity data was obtained with seed particles marking the jet core and the mixing layer, but not the ambient air. This lack of velocity measurements on the low-speed side of the jet’s mixing layer biased the space-time correlation results. An algorithm was developed to extrapolate the velocity into unseeded regions of the flow. Space-time correlation results based on the extrapolated data indicate a convective velocity close to the theoretical value.

Committee:

Mo Samimy (Advisor)

Keywords:

compressibility; compressible free shear layers; experimental fluid mechanics; fluid dynamics; aerodynamic measurement techniques; lasers; high-repetition rate lasers; advanced optical diagnostics; compressible fluid dynamics

Barnes, Caleb J.Unsteady Physics and Aeroelastic Response of Streamwise Vortex-Surface Interactions
Doctor of Philosophy (PhD), Wright State University, 2015, Engineering PhD
Streamwise vortex-surface interactions can occur in aviation intentionally in the context of formation flight as an energy saving mechanism, unintentionally in wake crossings when aircraft fly in close proximity, and as a consequence of aircraft design through the interaction of fluid dynamics between different aerodynamic surfaces. The bulk of past work on streamwise vortex-surface interactions has focused on steady inviscid analysis for optimizing aerodynamic loads in the context of formation flight or experimental analysis on fin buffeting problems. A fundamental understanding of the viscous and unsteady effects that may occur is both important and currently lacking in the literature. This dissertation seeks to fill this need by using a high-fidelity implicit large-eddy simulation approach coupled with geometrically non-linear finite elements to identify and analyze important physics that may occur. Simple, canonical configurations are employed in order help disentangle the many interrelated factors of a very complex problem. Analysis of a tandem wing configuration elucidated mutual induction between the incident vortex from the leader wing and tip vortex of the follower wing that resulted in a broad taxonomy of flow structure, wake evolution, and unsteady behaviors for several lateral impingement locations. Interaction of an isolated streamwise vortex with a wing revealed a robust helical instability develops when a strong vortex impinges directly with the leading-edge. This spiraling behavior was found to occur as a result of the upstream influence of adverse pressure gradients provided by the wing that drive the vortex into its linearly unstable regime allowing for the growth of shortwave perturbations. Stability can be augmented through vertical positioning of the vortex. A negative offset can enhance stability by providing a stronger adverse pressure gradient while a positive offset exploits a favorable gradient and removes the upstream instability altogether. The effects of wing compliance were revealed through full aeroleastic simulations. Essentially static, vortex-induced bending deformations reposition the vortex and drive it further into its unstable regime. Static and dynamic components of the aeroelastic response were systematically isolated where the static deformations were shown to provide the greatest influence. Dynamic effects provide some influence to the incident vortex behavior but these are secondary to the static behavior.

Committee:

George Huang, Ph.D. (Advisor); Joseph Shang, Ph.D. (Committee Member); Zifeng Yang, Ph.D. (Committee Member); Miguel Visbal, Ph.D. (Committee Member); Aaron Altman, Ph.D. (Committee Member)

Subjects:

Aerospace Engineering; Fluid Dynamics; Mechanical Engineering

Keywords:

formation flight; streamwise vortex interaction; fluid structure interaction; aeroelasticity; unsteady fluid dynamics; vortex dynamics; vortex surface interaction

Gonzalez, David RDevelopment of a Semi-Lagrangian Methodology for Jet Aeroacoustics Analysis
Doctor of Philosophy, The Ohio State University, 2016, Aero/Astro Engineering
A novel analysis technique is developed for the time-accurate analysis of noise sources in compressible jet flows. By adopting a Lagrangian point of view, the finite-time Lyapunov exponent (FTLE) method provides a means of linking discrete events in the vicinity of a high-subsonic jet shear layer to aft- and sideline-radiated noise. The FTLE is first validated in the compressible flow regime, as it was originally developed for incompressible flows, where it has shown substantial success in analyzing the dynamics of Lagrangian coherent structures. It is demonstrated by theoretical and numerical experiments that judicious choice of temporal intergration parameters highlights distinct features in the flow field. Due to the non-solenoidal nature of compressible flows, Lagrangian FTLE coefficients computed in forward and backward time can extract wave dynamics from the velocity field in addition to the flow-organizing convective features. Integration time, thus, acts as a pseudo-filter, smoothly separating coherent (convective) structures from propagating waves. Results are confirmed by first examining forward and backward FTLE coefficients for several simple, well-known acoustic fields and in the propagation of a two-dimensional acoustic pulse. Each coefficient is shown to capture a distinct portion of the traveling acoustic waves, with the forward FTLE (sf) focusing on the positive stroke and the negative portion extracted by the backward- integrated (sb) coefficient. Analysis of the mono-chromatic acoustic flow fields shows the peak FTLE magnitudes directly scale with the acoustic frequency and a complete reconstruction of the underlying dilatational field can be achieved by conducting the Lagrangian analysis over a single time step for each time instant. An increase in integration time subsequently leads to both damping and phase-shifting of the resolved acoustic waves as a consequence of the contribution from multiple temporal snapshots. Having established the theoretical foundation of the Lagrangian dynamics in compressible flows, the technique is then applied to identify events associated with intermittency in jet noise pressure probe data. Although intermittent events are known to be dominant causes of jet noise, their direct source in turbulent jet flows has remained unexplained. To this end, Large-Eddy Simulation (LES) data of several Mach 0.9 jets are subjected to FTLE to simultaneously examine, and thus expose, the causal relationship between coherent structures and the corresponding acoustic waves. The analysis illustrates that intermittent events are associated with entrainment in the initial roll up region and emissive events downstream of the potential-core collapse. Instantaneous acoustic disturbances are observed to be primarily induced near the collapse of the potential core and continue propagating towards the far-field at the experimentally-observed, approximately thirty-degree angle relative to the jet axis. Analysis of a fully-turbulent jet LES, where inflow turbulence was accounted for with a Reynolds- averaged-Navier-Stokes-initiated digital filter, further demonstrates that repelling Lagrangian structures given by the forward-integrated FTLE play a dominant role in establishing the near-acoustic field. By examining the evolution of the FTLE coefficients and the Lagrangian reconstruction of dilatation along the direction of maximum noise directivity, it is shown that sf contributes the bulk of the acoustic energy in the LES 'far-field'; and is also better correlated with the Eulerian dilatation at these locations than the backward-integrated field, despite the fact that the latter field is associated with the large-scale coherent structures. A two- point correlation analysis between the farfield dilatation and the Lagrangian coefficients along the time-mean potential core and shear layer boundaries further demonstrates that the farfield signals are intimately linked to the dynamics of coherent structures in these regions. Vortex merging events in the turbulent jet are also shown to be significant contributors to the genesis of farfield-radiating disturbances. In particular, they play a key role in establishing and modulating wavepackets within the potential core, which are known to be an important component of aft-radiated noise. The modulation of the wavepackets and the entrainment and emmission of acoustic energy to and from the ambient is highly influenced by the presence of strong repelling structures in the turbulent shear layer.

Committee:

Datta Gaitonde (Advisor); Jen-Ping Chen (Committee Member); Mark Lewis (Committee Member); Mohammad Samimy (Committee Member); Mei Zhuang (Committee Member)

Subjects:

Aerospace Engineering

Keywords:

Jet noise, finite-time Lypaunov exponents, Lagrangian dynamics, computational fluid dynamics

Calvitti, AlanPhase Locking in Coupled Oscillators as Hybrid Automata
Doctor of Philosophy, Case Western Reserve University, 2004, Systems and Control Engineering
Cruse's model of leg coordination (CCM) was derived to account for gaits and gait transitions in arthropods (analogous to, e.g. walktrotgallop in some quadrupeds). It has also been adapted to control locomotion in a series of hexapod robots. CCM is a systems-level, kinematic model that abstracts key physiological and dynamical properties in favor of tractability. A key feature is that gaits emerge from interaction among pairs of legs as effected by a set of coordination mechanisms acting at discrete points in time. We represent CCM networks as systems of coupled hybrid oscillators. Gaits are quantified by a temporal (discrete) phase vector. System trajectories are polyhedral, hence solvable over finite-time, but the presence of the switching automaton renders infinite horizon properties harder to analyze. Via numerical and symbolic simulations, we have mapped out the synchronization behavior of CCM networks of various topologies parametrically. We have developed a section-map analysis approach that exploits the polyhedral geometry of the hybrid state space. Our approach is constructive. Once switching boundaries are appropriately parameterized, we can extract periodic orbits, their domains of admissibility and stability, as well as expressions for the period of oscillation and relative phase of each cycle, parametrically. Applied to 2-oscillator networks, our approach yields excellent agreement with simulation results. A key emergent concept is that of a virtual periodic orbit (VPO). Distinguished from admissible periodic orbits, VPOs do not correspond to any in the underlying hybrid dynamics. However, when stable and close to being admissible, they are canonical precursors for a class of nonsmooth bifurcations and predictive of long transient behavior. Last, we take into consideration the possibility and difficulties of extending our approach to larger networks and to related oscillator-like hybrid dynamical systems with polyhedral trajectories.

Committee:

Randall Beer (Advisor)

Keywords:

bifurcations in hybrid systems; coupled oscillators; discrete event control; distributed control; entrainment; gaits and gait transitions; geometry of hybrid systems; hybrid dynamics; hybrid systems; phase locking; piecewise linear dynamics

Sheer, Francis JosephMulti-Scale Computational Modeling of Fluid-Structure Interactions and Adhesion Dynamics in the Upper Respiratory System
Doctor of Philosophy, The Ohio State University, 2011, Mechanical Engineering
Otitis Media (OM) is a disease that is characterized by inflammation of the Middle Ear (ME) mucosa. This disease is the most frequent reason that children in the US are prescribed antibiotics, accounting for 25% of all prescriptions filled annually. It has been estimated that in the US, an annual health related cost of ~$4 billion is associated with the diagnosis and treatment of OM. Most past studies support a casual role for poor Eustachian Tube (ET) function in the pathogenesis of OM. Therefore, Chapters 2 through 5 focus research on developing new treatments for OM though a better understanding of ET function. The ET is a collapsible airway that connects the Nasopharynx (NP) with the Middle Ear (ME) and is primarily responsible for clearance and pressure regulation of the ME. In Chapters 2 and 3, we use decoupled fluid-structure interaction (FSI) models to simulate ET function. Then in Chapter 4, we then use fully coupled FSI models to better simulate the highly non-linear, transient behavior associated with ET function. During inflammatory OM, the epithelial cells that line the ET lumen can up-regulate the apical expression of mucus glycoproteins. These glycoprotien interactions lead to adhesion forces within the lumen that seals the ET closed, hindering the regulation function of the ET. In Chapter 5 we therefore develop computational models that include these adhesive bonds and investigate how they influence overall ET function. The adhesive forces were first characterized with steered molecular dynamics simulations and then integrated into the tissue scale models. In every case, ET function was shown to be independent of LVPM force magnitudes, while TVPM force magnitudes were always of critical importance. Tissue mechanics, i.e., Young's modulus of both the cartilage and PMT tissue, were also shown to have a significant effect on ET function in all cases. Chapter 5 specifically shows that the ET is highly sensitive to these adhesive forces and different levels of adhesion can change the relative importance of all the different parameters of the system. Nearly 9.5 million people per year present to their primary care physician with the complaint of nasal obstruction. Of this large group of patients, over 600,000 sinonasal operations are performed annually in the US, and over 260,000 of these procedures are septoplasties. Even with this large number of surgeries performed every year, it has been estimated that septoplasty is only successful in 63-85% of cases. Chapter 6 unveils the details for a novel 'virtual surgery' technique to allow for better planned, and personalized surgical interventions for every patient. The approach uses geometries reconstructed from CT images and analyzed with a custom program to perform virtual surgery. The virtual surgery is performed by a surgeon and simulates the same procedures that are to be performed, but provides objective quantification, through the use of Computational Fluid Dynamics (CFD), of whether or not the intervention will benefit the patient. The program was then used in two case studies which illustrate the true diagnostic benefits of performing personalized surgeries.

Committee:

Samir Ghadiali, PhD (Advisor); Richard Hart (Committee Member); Alan Litsky (Committee Member); Robert Siston (Committee Member)

Subjects:

Biomedical Engineering; Mechanical Engineering

Keywords:

finite element analyis; computational fluid dynamics; multi-scale; fluid-strucutre interaction; adhesion dynamics; upper respiratory system; nasal aiways; Eustachian Tube; virtual surgery;

Berry, Eric J.Population ecology of the harvested understory palm Chamaedorea radicalis: pollination biology, female fecundity, and source-sink population dynamics
Doctor of Philosophy, Miami University, 2006, Botany
The harvest of non-timber forest products (NTFP) is an important source of income for rural communities worldwide, and as such there is concern over the sustainability of NTFP extraction. One example is concern over reduced yields from harvested populations of Chamaedorea, a large genus of dioecious understory palms whose leaves are sold commercially for use in floral displays. To accurately assess the sustainability of harvest, however, requires an understanding of the population biology of harvested species. In this study, I investigated factors that influence female fecundity and population growth in harvested populations of C. radicalis within the El Cielo Biosphere Reserve (Mexico). Pollinator exclusion and scanning electron microscopy of pollen grains revealed that C. radicalis is primarily wind-pollinated. Fruit number and fruit set of females were not dependent on sex ratio or density of males at either the neighborhood or population scale. Female fecundity was most dependent on palm size, as larger individuals produced the most flowers and fruits. These large palms were more abundant on rock outcrops than the forest floor, suggesting that rock outcrops are better microsites for C. radicalis. However, field experiments revealed that differences between the substrates were not from natural variation in microsite conditions, but rather due to differences in browsing by free-range livestock, which negatively affects palm survival, growth, and fecundity. I modeled populations exposed to livestock by incorporating field data into a source-sink transition matrix model that linked the demography of non-browsed palms on rock outcrops (source) and browsed palms on the forest floor (sink) via seed migration. Models projected that seed dispersal from rock outcrops was both necessary and sufficient to sustain the subpopulation on the forest floor. Adding leaf harvest reduced the survival and fecundity of all non-browsed adults, including important ‘source’ palms, with the result that rock outcrops were no longer a sufficient source of recruitment for the entire population. This finding indicates that the combination of harvest and browse is not sustainable. Based on these results, I recommend conservation efforts that improve reproduction and seedling recruitment in harvested populations, such as fencing livestock and protecting fruiting females from harvest.

Committee:

David Gorchov (Advisor)

Keywords:

Chamaedorea radicalis; dioecy; fruit set; Mexico; plant demography; population dynamics; seed dispersal; source-sink dynamics; wind pollination

Ding, YifuInfluence of Molecular Weight and Architecture on Polymer Dynamics
Doctor of Philosophy, University of Akron, 2005, Polymer Science
Molecular weight (MW) and architecture are two important parameters of a synthetic polymer. Their roles on polymer properties including dynamics have not been well understood yet. In this thesis, we have used various techniques including light, neutron scattering and dielectric spectroscopy to elucidate their influences on polymer dynamics within a broad time (frequency) range, covering chain, segmental relaxation and fast dynamics. Comparisons between different polymers were made to understand the role of chemical structure in determining MW dependence of the dynamic behavior. Experimental results showed that different physical properties studied appear to have similar molecular weight dependence in the sense that they all saturate when chains approach Gaussian coil behavior. We demonstrate that the difference in the molecular weight dependence for various polymers does not correlate with either the difference in the Kuhn segment length or molecular weight between entanglements. Instead, we propose to introduce an additional parameter, mR (molecular weight associated with each step of the Random walk in the approximation of Gaussian chain) that might be important for characterizing the molecular weight dependence of chain statistics and many physical properties. The most intriguing result is that the molecular weight dependence of the fast dynamics, sound velocity and fragility observed in polystyrene is opposite to the one observed in polyisobutylene, although Tg increases with molecular weight in both cases. We speculate that difference in symmetry of the monomer structures is responsible for the opposite behavior. Studies of the influence of architectures on fast and segmental relaxation were also carried out. We found that in the case of polybutadiene both of them scale better with total molecular weight instead of the molecular weight of each arm, as suggested by the chain end free volume model. Analysis of the branching effect on the segmental relaxation illustrates similarity to the blending of the same polymer with different molecular weights.

Committee:

Alexei Sokolov (Advisor)

Keywords:

Polymer Dynamics; Glass Transition; Fast dynamics; Fragility; Molecular Weight Effect; Depolarized Light Scattering

Garimella, SureshActuator Modeling and Control For a Three Degrees of Freedom Differential Thrust Control Testbed
Master of Science (MS), Ohio University, 2007, Electrical Engineering & Computer Science (Engineering and Technology)
This thesis presents an improvement in the performance of a three degrees of freedom differential thrust control testbed by considering the actuator dynamics. The testbed consists of three propellers that are used to produce thrust as well as attitude control for vertical takeoff and landing flight. Actuator dynamics consist of the motor-propeller dynamics and the nonlinear mapping relating the aerodynamic torques to the propeller speed. A previous controller was designed by neglecting the motor-propeller dynamics and the control allocation was done assuming a linear static relationship between aerodynamic torques and motor voltages. This work will determine the nonlinear control allocation mapping and model the motor-propeller dynamics as a first-order linear system. Simulation and real-time results showing an improvement in the performance of the testbed are presented by replacing the linear control allocation with nonlinear control allocation and by compensating for the motor-propeller dynamics. Further, the existing controller is redesigned considering the gyroscopic effects produced due to the spinning propellers.

Committee:

Jianchao Zhu (Advisor)

Keywords:

Nonlinear Control Allocation; Actuator Dynamics; DC Motor-propeller dynamics; Differential thrust control testbed; Trajectory Linearization Control; MATLAB/Simulink; Open-loop control; Closed-loop control

Gu, YinaProtein Dynamics, Loop Motions and Protein-Protein Interactions Combining Nuclear Magnetic Resonance (NMR) Spectroscopy with Molecular Dynamics (MD) Simulations
Doctor of Philosophy, The Ohio State University, 2016, Chemistry
Functional protein motions covering a wide range of timescales can be studied by NMR and molecular dynamics (MD) computer simulations. Nuclear magnetic resonance (NMR) spectroscopy of uniformly 15N-labeled proteins provides unique insights into protein backbone motions on the pico- to nanosecond timescale. Nuclear spin relaxation parameters (R1, R2, and heteronuclear {1H}-15N NOE) are routinely measured by well-established multidimensional relaxation experiments, which can be time-consuming typically taking on the order of a week. Recently, NMR chemical exchange saturation transfer (CEST) has emerged as a useful method to probe slow millisecond motions complementing spin relaxation in the rotating frame (R1ρ) and Carr-Purcell-Meiboom-Gill (CPMG) type experiments. CEST also provides site-specific R1 and R2 relaxation parameters requiring only short measurement times of the order of a few hours. We demonstrate that the CEST-derived relaxation parameters accurately reflect relaxation parameters obtained using the traditional method. A “lean” version of the model-free analysis (MFA) is introduced for the interpretation of R1 and R2 resulting in S2 order parameters that closely match those obtained using a standard MFA. The new methodology is demonstrated with experimental data of ubiquitin and arginine kinase and backed up with simulated data derived from microsecond MD simulations of ten different proteins. MD simulations of proteins now routinely extend into the hundreds of nanoseconds time scale range exceeding the overall tumbling correlation times (τc) of proteins in solution. However, presently there is no consensus on how to rigorously validate these simulations by quantitative comparison with model-free order parameters derived from NMR relaxation experiments. For this purpose we conducted MFA of NMR relaxation parameters computed from 500-ns MD trajectories of ten proteins. The resulting model-free S2 order parameters are then used as targets for S2 values computed directly from the trajectories by the isotropic Reorientational Eigenmode Dynamics (iRED) method by either averaging over blocks of variable lengths or by using exponentially weighted snapshots (wiRED). We find that the S2iRED values are capable of reproducing the target S2 with high accuracy provided that the averaging window is chosen as five times the length of τc. These results provide useful guidelines for the derivation of NMR order parameters from MD for a meaningful comparison with their experimental counter parts. Protein loops with their flexible nature on a wide range of timescales are critical for many biologically important events at the molecular level, such as protein interaction and recognition processes. To obtain a predictive understanding of the dynamic properties of loops, we performed long MD simulations of 38 proteins and validated the simulations using NMR chemical shifts. A total of 169 loops were analyzed and classified into three types (fast, slow, static) according to the correlation times computed from the trajectory. Chemical and biophysical loop descriptors, such as amino-acid sequence, average 3D structure, charge distribution, hydrophobicity, and local contacts were used to develop and parameterize a novel algorithm (ToeLoop) for the prediction of the flexibility and motional timescale of every protein loop, which is also implemented as a public web server. The results demonstrate that loop dynamics with their timescales can be predicted rapidly with reasonable accuracy, which will allow the screening of average protein structures to understand the dynamic properties of loops in protein-protein interactions (PPI) and allostery. We reported the loop motions and their dominant timescales for a database of 230 proteins that form protein-protein complexes using the ToeLoop predictor of loop dynamics. We observe a clear tendency of loops that move on relatively slow timescales of tens of ns to sub-µs to be directly involved in binding and recognition processes. Complex formation leads to a significant reduction in loop flexibility at the binding interface, but in a number of cases it can also trigger increased loop flexibility at distal sites in response to allosteric conformational changes. We explored the relationship between loop dynamics and experimental binding affinities and found that a prevalence of high loop rigidity at the binding interface is an indicator of increased binding strength. The importance of loop dynamics and allostery is highlighted by case studies of antibody-antigen complex, K-Ras GTPases, adenylate kinase, and ubiquitin-conjugating E2 enzyme.

Committee:

Rafael Br├╝schweiler (Advisor); Marcos Sotomayor (Committee Member); Steffen Lindert (Committee Member)

Subjects:

Biochemistry; Chemistry

Keywords:

Protein Dynamics, Loop Motions, Protein-Protein Interactions, Combining Nuclear Magnetic Resonance Spectroscopy with Molecular Dynamics Simulations

Rinehart, Aidan WalkerA Characterization of Seal Whisker Morphology and the Effects of Angle of Incidence on Wake Structure
Master of Science in Mechanical Engineering, Cleveland State University, 2016, Washkewicz College of Engineering
Seal whiskers have been found to produce unique wake flow structures that minimize self-induced vibration and reduce drag. The cause of these wake features are due to the peculiar three-dimensional morphology of the whisker surface. The whisker morphology can be described as an elliptical cross section with variation of diameter in the major and minor axis along the length and, angle of incidence, rotation of the elliptical plane with respect to the whisker axis, α at the peak and β at the trough. This research provided a more complete morphology characterization accomplished through CT scanning and analysis of 27 harbor and elephant seal whisker samples. The results of this study confirmed previously reported values and added a characterization of the angle of incidence finding that the majority of angles observed fall within ±5° and exhibit a random variation in magnitude and direction along the whisker length. While the wake effects of several parameters of the whisker morphology have been studied, the effect of the angle of incidence has not been well understood. This research examined the influence of the angle of incidence on the wake flow structure through series of water channel studies. Four models of whisker-like geometries based on the morphology study were tested which isolate the angle of incidence as the only variation between models. The model variations in angle of incidence selected provided a baseline case (α = β = 0°), captured the range of angles observed in nature (α = β = -5°, and α = β = -15°), and investigated the influence of direction of angle of incidence (α = -5°, β = -5°). The wake structure for each seal whisker model was measured through particle image velocimetry (PIV). Angle of incidence was found to influence the wake structure through reorganization of velocity field patterns, reduction of recovery length and modification of magnitude of Tu. The results of this research helped provide a more complete understanding of the seal whisker morphology relationship to wake structure and can provide insight into design practices for application of whisker-like geometry to various engineering problems.

Committee:

Wei Zhang, PhD (Advisor); Ibrahim Mounir, PhD (Committee Member); Shyam Vikram, PhD (Committee Member)

Subjects:

Aerospace Engineering; Aquatic Sciences; Engineering; Fluid Dynamics; Mechanical Engineering

Keywords:

seal; whisker; PIV; biomimicry; fluid dynamics; particle image velocimetry; bio-engineering; engineering; mechanical engineering; aerospace engineering; experimental fluid dynamics;

Barnes, Caleb J.An Implicit High-Order Spectral Difference Method for the Compressible Navier-Stokes Equations Using Adaptive Polynomial Refinement
Master of Science in Engineering (MSEgr), Wright State University, 2011, Mechanical Engineering
A high/variable-order numerical simulation procedure for gas dynamics problems was developed to model steep grading physical phenomena. Higher order resolution was achieved using an orthogonal polynomial Gauss-Lobatto grid, adaptive polynomial refinement and artificial diffusion activated by a pressure switch. The method is designed to be computationally stable, accurate, and capable of resolving discontinuities and steep gradients without the use of one-sided reconstructions or reducing to low-order. Solutions to several benchmark gas-dynamics problems were produced including a shock-tube and a shock-entropy wave interaction. The scheme's 1st-order solution was validated in comparison to a 1st-order Roe scheme solution. Higher-order solutions were shown to approach reference values for each problem. Uniform polynomial refinement was shown to be capable of producing increasingly accurate solutions on a very coarse mesh. Adaptive polynomial refinement was employed to selectively refine the solution near steep gradient structures and results were nearly identical to those produced by uniform polynomial refinement. Future work will focus on improvements to the diffusion term, complete extensions to the full compressible Navier-Stokes equations, and multi-dimension formulations.

Committee:

George Huang, PhD (Advisor); George Huang, PhD (Committee Member); Joseph Shang, PhD (Committee Member); Miguel Visbal, PhD (Committee Member)

Subjects:

Fluid Dynamics; Mechanical Engineering

Keywords:

high-order; spectral difference; CFD; computational fluid dynamics; Euler equations; Euler; gas dynamics; polynomial refinement; adaptive polynomial refinement; artificial dissipation

Al-Saidi, Wissam AbdoTopics in the Theory of Small Josephson Junctions and Layered Superconductors
Doctor of Philosophy, The Ohio State University, 2003, Physics

Small Josephson junctions are fascinating quantum systems with numerous potential applications, especially in the still infant field of quantum computation. In the first part of the thesis, I have studied some of the quantum aspects of these systems. Specifically, I have investigated their interactions with a resonant cavity, the Berry phase of a superconducting nanocircuit, and some properties of small Josephson junction arrays. I found that at specific values of the gate voltage of a Cooper pair box, there will be a strong coupling between the Josephson junction and the cavity mode; in this case the junction behaves as a two level atom. I also, verified that if there are N identical junctions in the cavity and are tuned on resonance, the cavity-junction interaction is enhanced by a factor √ N. This behavior is a clear sign of a cooperative phenomena. Also I found that if a Josephson junction is on resonance with one of the modes of a two-mode cavity, there will be a coupling between the two modes and ultimately a frequency-up or down conversion. I have also studied the spin-wave-like excitations of a disordered two and three dimensional array of small Josephson junctions. I consider a simple form of diagonal disorder and solve for the spin-wave spectral functions using the coherent potential approximation. Finally, using quantum Monte Carlo techniques, I have constructed the phase diagram of a disordered two dimensional array of small Josephson junctions.

In the second part of the thesis, I have studied the dynamics of vortices in a clean layered high-temperature superconductor. I found that the c-axis conductivity at nonzero frequencies shows a strong but not divergent increase as the vortex lattice freezing temperature is approached from above, followed by an apparently discontinuous drop. The discontinuity is consistent with the occurrence of a first-order freezing of the vortex lattice. The calculated equilibrium properties agree with previous Monte Carlo studies of the system.

Committee:

David Stroud (Advisor)

Subjects:

Physics, Condensed Matter

Keywords:

Small Josephson junctions; Layered superconductors; Langevin dynamics; Vortex dynamics; Berry phase

Teeling-Smith, Richelle MarieSingle Molecule Electron Paramagnetic Resonance and Other Sensing and Imaging Applications with Nitrogen-Vacancy Nanodiamond
Doctor of Philosophy, The Ohio State University, 2015, Physics
Electron paramagnetic resonance (EPR) is an established and powerful tool for studying atomic-scale biomolecular structure and dynamics. Yet it requires a homogeneous sample size of approximately 10^15 spin-labeled biomolecules. In contrast, single molecule measurements provide improved insights into heterogeneous behaviors that can be masked by ensemble measurements and are often essential for illuminating the molecular mechanisms behind the function of a biomolecule. In this dissertation, I report EPR measurements of a single labeled biomolecule demonstrating the merging of these two powerful techniques. We have selectively labeled individual double-stranded DNA molecules with nanodiamonds containing nitrogen-vacancy (NV) centers, and optically detected the paramagnetic resonance of the NV nanodiamond probe. Analysis of the spectrum reveals that the characteristic time scale for reorientation of the labeled molecule relative to the applied magnetic field is slow compared to the spin relaxation time of the nanodiamond probe. This demonstration of EPR spectroscopic determination of the dynamics of an individual labeled biomolecular construct provides the foundation for single molecule magnetic resonance studies of complex biomolecular systems. In addition to this single-molecule EPR study, I report on the use of the NV center in diamond as a probe for in-vivo magnetometry, in-vivo fluorescence imaging and temperature sensing, and a tool for the measure of spin resonances in neighboring systems. The NV center in diamond has proven to be powerful tool for sensing and imaging in various systems, with a broad array of undeveloped or underdeveloped applications. The studies included in this dissertation provide a brief overview of a select few experiments that explore these capabilities.

Committee:

P. Chris Hammel (Advisor); Ezekiel Johnston-Halperin (Committee Member); Michael G. Poirier (Committee Member); Ralf Bundschuh (Committee Member)

Subjects:

Biochemistry; Biophysics; Condensed Matter Physics; Molecular Physics; Nanoscience; Nanotechnology; Optics; Physics; Scientific Imaging

Keywords:

NV diamond; Nitrogen-Vacancy Diamond; EPR; Electron Paramagnetic Resonance; DNA; DNA dynamics; confocal microscopy; single molecule spectroscopy; single-molecule measurements; biophysics; biomolecular dynamics; ODMR; Optically detected magnetic resonance

Thapa, Mahendra B.Molecular Dynamics Simulation of Calbindin D-9k in apo, Singly and Doubly Loaded States in Various Side-chains
PhD, University of Cincinnati, 2016, Arts and Sciences: Physics
Calbindin D9k (CAB) is a single domain calcium-binding protein and is the smallest members of the calmodulin superfamily, possessing a pair of calcium-binding EF-hands, and structures for all four states have been determined and extensively characterized experimentally. Because of the tremendous advancement in hardware and software computer technologies in recent years, longer and more realistic molecular dynamics (MD) simulations of a protein are possible now in reasonable periods of time. These advances were exploited to generate multiple, all-atom MD simulations of CAB via the AMBER software package, and the resulting trajectories were employed to calculate backbone order parameters of the apo, the singly and the doubly loaded states of calcium in CAB. The results are in very good agreement with corresponding experimental NMR-based (Nuclear Magnetic Resonance spectroscopy) results, and are improved in comparison to those calculated over a decade ago; use of modified force fields played a key role in the observed improvements. The apo state is the most flexible, and the singly loaded and the doubly loaded states are similar, thus supporting positive cooperativity in line with the experimental results. Further, B-factor calculations of backbone atoms for these calcium-binding states of calbindin D9k also support such cooperativity. Although changes in side-chain motions are not necessarily correlated to changes in protein backbone mobility, past studies on the comparison of experimental and simulated methyl side-chain NMR relaxation parameters of CAB for the doubly-loaded state reported significant improvements in the quantitative representation of side-chain motion by MD simulation. In this project, the order parameters for various side chains in apo, singly loaded and doubly loaded states of CAB were calculated. The primary goal of this work was to determine whether or not the allosteric effect of calcium binding, as observed via the backbone order parameters, also extended to the amino acid side chains, and if so, to what extent. Such information could be useful in better understanding the physical basis of cooperative calcium binding in CAB. Most of the residues which provide ligands to bind calcium at the binding sites support positive cooperativity, as observed when Ca-Cß, Cß-C?, C-C bond and C-O bonds of COO groups of aspartic and glutamic acid residues, the C-N bond of the side-chain amide group in asparagine and glutamine residues, and the N-H bonds of amide (NH2) group order parameters were studied. There are only a few residues containing methyl groups that are involved in providing ligands to the calcium, and the studies of order parameters of C-C bond and C-H bond of these methyl groups did not exhibit the cooperativity effect upon calcium binding; the simulated C-C bond order parameter of the methyl group symmetry axis did correlate well with the experimental results for the fully loaded state of CAB (4ICB). Analysis of the MD trajectories using GSATools and MutInf, provided valuable insights into possible pathways for communicating allosteric effects between the two calcium-binding sites of CAB.

Committee:

Mark Rance, Ph.D. (Committee Chair); Eric Johnson, Ph.D. (Committee Member); Thomas Beck, Ph.D. (Committee Member); David Mast, Ph.D. (Committee Member); Rostislav Serota, Ph.D. (Committee Member)

Subjects:

Physics

Keywords:

Calbindin D-9k;Side-chain dynamics;Molecular Dynamics;4ICB;AMBER;NMR

Guarendi, Andrew NNumerical Investigations of Magnetohydrodynamic Hypersonic Flows
Master of Science, University of Akron, 2013, Mechanical Engineering
Numerical simulations of magnetohydrodynamic (MHD) hypersonic flow are presented for both laminar and turbulent flow over a cylinder and flow entering a scramjet inlet. ANSYS CFX is used to carry out calculations for steady flow at hypersonic speeds (Mach number > 5). The low magnetic Reynolds number (<<1) calculated based on the velocity and length scales in this problem justifies the quasistatic approximation, which assumes negligible effect of velocity on magnetic fields. Therefore the governing equations employed in the simulations are the compressible Navier-Stokes and the energy equations with MHD-related source terms such as Lorentz force and Joule dissipation. Turbulence effects are accounted for when applicable and multiple turbulence models are compared. The results demonstrate the ability of the magnetic field to affect the flowfield, and variables such as location and magnitude of the applied magnetic field are examined. An examination of future work is provided through the implementation of a semi-discrete central scheme in-house code toward the solution of the Orszag-Tang vortex system.

Committee:

Abhilash Chandy, Dr. (Advisor); Scott Sawyer, Dr. (Committee Member); Alex Povitsky, Dr. (Committee Member)

Subjects:

Aerospace Engineering; Engineering; Fluid Dynamics; Mechanical Engineering

Keywords:

Hypersonic; Hypersonic Flow; Flow over a cylinder; Magnetohydrodynamic; MHD; Lorentz; Hypersonic MHD; Numerical Methods; CFD; Computational fluid dynamics; fluid dynamics; Aerospace;

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