Within a polymer thin film, free-volume elements have a wide range of size and topology. This broad range of free-volume element sizes determines the ability for a polymer to perform molecular separations. Herein, the free volume and transport properties (diffusion, permeability, and selectivity) in both rubbery and glassy polymers were simulated using fully atomistic models. Extension of the computational tool to study the void structure in proteins is also included in this thesis. Six permeable thermally rearranged (TR) polymers and their precursors were studied. Using atomistic models, cavity size (free volume) distributions determined by a combination of molecular dynamics and Monte Carlo methods were consistent with experimental observation that TR polymers are more permeable than their precursors. The cavity size distributions determined by simulation were also consistent with free volume distributions determined by positron annihilation lifetime spectroscopy. The diffusion, solubility and permeation of gases in TR polymers and their precursors were also simulated at 308 K, with results that agree qualitatively with experimental data. A new hybrid Monte Carlo/Molecular Dynamics method is developed for estimating the slow diffusion processes of light gases transporting in glassy polymers. Diffusion coefficients, as small as 10⁻⁵ to 10⁻⁹ cm²/s are estimated for penetrants in four different polymers at 298 K. In all cases, agreement between literature experimental data and values obtained from the fast hybrid molecular dynamics method ranges from good to excellent. A new technique is developed using Monte Carlo methods to characterize the cavity size distribution and surface atoms in globular proteins. New statistical metrics have been defined for the structural characterization of globular proteins. Some of these metrics include volume, surface area, asymmetry ratio, interior cavity size distribution, and the identification of percolation channels. Wild-type (WT) myoglobin (Mb) and 5 Mb mutants have been studied in this research as examples. An analysis of cavity statistics provides an efficient method to quantify local properties such as packing density and transport pathways. The average cavity sizes of WT Mb and its mutants are around 4.0-5.0 Å. / text

The design, fabrication, and in-vivo testing of an implantable device to measure the pressure-volume (PV) relationship in the hearts of conscious, untethered rats is presented. Volume is measured using a tetrapolar catheter positioned in the left-ventricle which emits a 20kHz current field across the LV blood pool and parallel heart tissue and measures the resulting voltage. The admittance method is used to instantaneously remove the contribution of the parallel heart muscle and Wei’s non-linear blood conductance-to-volume equation is used to calculate volume. Pressure is measured with a strain gauge sensor at the tip of the catheter. The implant was designed to be small, light, and low-power. An average implant occupies 5 cm3, weighs 8g, and on a single charge collects data for 2 months taking 43 samples per day. Collected data is transmitted wirelessly via RF to a base station where it is recorded. The functionality of the implant and measurement system was verified in six rat experiments. In all experiments, ambulatory PV loops were measured on implantation day. Viable pressure data was recorded for 11 days in one rat; in another rat viable admittance data was collected for 10 days. Changing catheter position and non-constant blood resistivity are considered as sources of error in the volume measurement. Pressure drift due to changing atmospheric pressure is considered as a source of error in the pressure measurement. Lastly, alternative uses for the implant and directions for future improvement are considered. / text

Forces are increasingly recognized as major regulators of cell physiology and function, and the mechanical properties of cells are essential to the mechanisms by which cells sense forces, transmit them to the cell interior or to other cells, and transduce them into chemical signals that impact a spectrum of cellular responses. Furthermore, cells can sense their extracellular environment and regulate their own mechanics and biology. Due to limitation of methodology, the cortical property of cells has been extensively characterized; however, the mechanics and dynamics of cytoplasm which consists all key cellular organelles, remains poorly understood. Moreover, a basic understanding of cell mechanics, such as which parameters correlates with cell stiffness and therefore impact cell biology is unknown. In this thesis, we firstly present a thorough investigation of the mechanical and dynamic properties of the cytoplasm, including direct measurement of cytoplasmic material property using optical tweezers, and visualization of intracellular dynamics by tracer particles. By combining these two measurements we obtain a directly characterization of the cytoplasmic forces; we further apply this method to study cancer cells and cells without vimentin intermediate filament, and find that cancer cells have significantly stronger intracellular forces, which vimentin intermediate filament does not have effect on the force generation. Secondly, we present our result on the role of cell volume in cell mechanics and cell biology. We show that the volume of a cell changes upon the property of the extracellular environment; the change in cell volume directly induces change in the mechanical property of both cytoplasm and cell cortex. We further show that the change in cell volume is due to intracellular water influx/efflux, and this has significant impact on cell biology, such as stem cell differentiation. Finally, we present a direct characterization of the equation of state of living cells by measuring cell volume under increasing osmotic pressure. We show that a living cell, under osmotic compression, behaves as Van der Waals gas with a hard sphere excluded volume; the minimum volume of cells is determined by cellular proteins, which the equation of state of living cells is dominated by intracellular ions. / Engineering and Applied Sciences

Optimal large eddy simulation (OLES) is an approach to LES sub-grid modeling that requires multi-point correlation data as input. Until now, this has been obtained by analyzing DNS statistics. In the finite-volume OLES formulation studied here, under the assumption of small-scale homogeneity and isotropy, these correlations can be theoretically determined from Kolmogorov inertial-range theory, small-scale isotropy, along with the quasi-normal approximation. These models are expressed as generalized quadratic and linear finite volume operators that represent the convective momentum flux. These finite volume operators have been analyzed to determine their characteristics as numerical approximation operators and as models of small-scale effects. In addition, the dependence of the model operators on the anisotropy of the grid and on the size of the stencils is analyzed to develop idealized general operators that can be used on general grids. The finite volume turbulence operators developed here will be applicable in a wide range of LES problems. / text

Impedance has been used as a tool for cardiac research since the early 1940’s. Recently there have been many advances in this field in the diagnosis of human heart failure through the measurement of pacemaker and ICD coupled impedance detection to determine the state of pulmonary edema in patients through drops in lung impedance. These new detection methods are far downstream of the initial changes in physiology, which signify heart failure risk, namely, an increased left ventricular (LV) end-diastolic volume (also known as preload). This dissertation presents the first formal validation of the complex admittance technique for more accurate blood volume measurement in vivo in mice. It aims to determine a new configuration of admittance measurement in a large scale animal model (pigs). It also aims to prove that “piggybacking” an admittance measurement system onto previously implanted AICD and bi-ventricular pacemakers is a feasible and practical measurement that will serve as an early warning system for impending heart failure through the measurement of LV preload, which appears before the currently measured drop in lung impedance using previous techniques. / text

Not available / text

published_or_final_version / Mechanical Engineering / Master / Master of Philosophy

There is strong evidence that the skeletal muscles of pinnipeds are adapted for an aerobic, lipid-based metabolism under the hypoxic conditions associated with breath-hold diving. However, regional variations in mitochondrial density are unknown, and the few fiber typing studies performed on pinniped skeletal muscles are not consistent with an aerobic physiological profile. Thus, the objectives of this study were to (1) reexamine the fiber type distribution throughout the primary locomotory muscles of the harbor seal, and (2) to better understand the density and distribution of mitochondria in the locomotory muscles. Multiple samples from transverse sections of the epaxial muscles and a single sample of the pectoralis muscle of wild harbor seals were analyzed using immunohistochemical fiber typing and electron microscopy. Fiber typing results indicated that harbor seal epaxial muscles are composed of 47.4% type I (slow twitch, oxidative) fibers and 52.8%, IIa (fast twitch, oxidative) fibers. No fast twitch, glycolytic (type IIb) fibers were detected in the epaxial muscles or the pectoralis muscle. Mean volume density of mitochondria [Vv(mt,f)] was 5.6%, which is elevated over what would be predicted for a terrestrial mammal of similar mass. The elevated Vv(mt,f) had a high proportion of intermyofibrillar mitochondria, a trait not normally found in the muscles of terrestrial mammals with elevated Vv(mt,f). These results provide further evidence that the elevated mitochondrial volume density in pinniped muscle decreases the oxygen diffusion distance between myoglobin and mitochondria to facilitate aerobic respiration in working muscles. In addition, analyses of heterogeneity revealed that the regions of the epaxial muscles that were located deep within the muscle showed a significantly higher Vv(mt,f) relative to those regions that were superficially-located. In contrast, there was no significant heterogeneity of fiber type detected in either plane of the epaxial muscles. Thus, there was a fine-scale pattern of spatial heterogeneity of Vv(mt,f) within the epaxial muscles that does not manifest in fiber type distribution, indicating that the fibers have similar oxidative capacities.

No description available.

Current stoichiometric spark-ignited engine technologies require costly catalytic converters for reductions in tailpipe emissions. Load control is achieved by using a throttle, which is a leading contributor to reductions in efficiency. Spark-ignited lean burn natural gas engines have been proven to be more efficient and emit fewer pollutants than their stoichiometric counterparts. Load reduction in these engines can be achieved by regulating the air/fuel ratio of the intake charge thereby reducing the efficiency penalties inherent to throttling. Partially stratified charge (PSC) can provide further reductions in emissions and improvements in efficiency by extending the lean limit of operation. PSC is achieved by the ignition of a small quantity of natural gas in the vicinity of the spark plug. This creates an easily ignitable mixture at the spark plug electrodes, thereby providing a high energy ignition source for the ultra-lean bulk charge. Stratified charge engine operation using direct injection (DI) has been proposed as a method of bridging the throttleless load reduction gap between idle and ultra-lean conditions. A previous study was conducted to determine if PSC can provide a high-energy ignition source in a direct injected stratified charge engine. Difficulties with igniting the PSC injections in an air-only bulk charge were encountered. This study focuses on a fundamental Schlieren image-based analysis of PSC combustion. Natural gas was injected through a modified spark plug located in an optically accessible combustion bomb. The relationships between PSC injection timing, fuel supply pressure and spark timing were investigated. Spark timing is defined as the duration between commanded start of injection and the time of spark. As the fuel supply pressure was increased, the minimum spark timing that lead to successful combustion also increased. The largest spark timing window that led to successful combustion was determined to be 80 ms wide at an injection fuel supply pressure of 300 psi. The amount of unburned natural gas increased with increasing spark timing. A cold flow study of the PSC injection system was also conducted. The PSC injection solenoid was found to have a consistent average injection delay of 1.95 ms. The slope of the linear response region of observed injection duration to commanded injection duration was 8.4. Due to plenum effects, the average observed injection duration of the entire PSC system was an order of magnitude longer than the commanded injection duration and was found to vary significantly with fuel supply pressure.