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Master of Science, Miami University, 2015, Computational Science and Engineering
Incoherent scatter radar (ISR) is a versatile tool to study the ionosphere by measuring the autocorrelation function (ACF). Accurate ACF in the E-region is difficult to obtain because the relative short range limits the length of a pulse. The short correlation time of the ionosphere renders the correlation using the pulse-to-pulse technique useless. In the thesis, we study a method that combines intra-pulse and inter-pulse techniques and apply it to the data taken at Arecibo Observatory. We show simultaneously measured ACF’s at short and long lags and summarize the merits of ACF. Applications of ACF and its advantages are discussed. The technique used here will make the derivation of ionosphere parameters more accurate.


Qihou Zhou (Advisor); Chi-Hao Cheng (Committee Member); Dmitriy Garmatyuk (Committee Member)


Aeronomy; Aerospace Engineering; Computer Engineering; Computer Science; Earth; Radiology


Incoherent scatter radar; ionosphere; E-region; parameters; autocorrelation function; accurate

Chen, XiaodongFluid-Structure Interaction Modeling of Epithelial Cell Deformation during Microbubble Flows in Compliant Airways
Doctor of Philosophy, The Ohio State University, 2012, Mechanical Engineering

The acute respiratory distress syndrome (ARDS) is a devastating lung disease. Patients with ARDS must be placed on a mechanical ventilator to survive. However, these ventilators also exacerbate the existing lung injury and as a result the mortality for ARDS is high (~25-40%). During ARDS, small pulmonary airways become occluded with fluid and mechanical ventilation of the fluid-filled lung involves the reopening of fluid-filled airways and the propagation of microbubbles over a layer of epithelial cells lining airway walls. Previous computational and experimental studies indicate that the large spatial gradients in pressure generated near the bubble tip may cause large-scale cellular deformation, rupture of the plasma membrane and cell necrosis. However, previous computational models do not account for the complex fluid-structure interactions that occur during in-vitro or in-vivo experiments. In addition, previous studies assumed rigid-wall conditions while pulmonary airways are in reality highly compliant and changes in airway wall mechanics may significantly influence the dynamics of airway reopening and cell deformation. Furthermore, the lung consists of a large network of bifurcating airways and different bifurcation patterns may influence both the hydrodynamics of airway reopening and cellular injury/deformation especially when the effect of gravity is considered. The objective of this particular thesis is to employ sophisticated computational fluid-structure interaction models to investigate how changes in the patient's biomechanical status such as airway wall compliance, fluid properties and bifurcation patterns influence the mechanics and hydrodynamics of microbubble induced cellular deformation and injury.

We have developed several sophisticated computational models that can better represent the in-vivo or in-vitro conditions of compliant airway walls, fully coupled fluid-structure interactions and 3D structure of pulmonary airways with epithelial cells lining airway walls. We will also develop a computational model that accounts for airway bifurcation and numerous physical forces (gravity, inertia and surface tension). The specific aims of this dissertation are:

1. Develop computational fluid dynamics models that better represent in-vitro microbubble flows conditions and can be extended to study cell deformation during airway reopening conditions.

2. Identify the influence of gravity, inertia and surface tension on liquid distribution and hydrodynamic forces in bifurcating pulmonary airways.

3. Evaluate how airway wall compliance influences cellular deformation during compliant airway reopening in a fully coupled two-dimensional fluid-structure interaction model.

4. Investigate how transient hydrodynamic forces generated during microbubble flows influence epithelial cell deformation in a three-dimensional computational model.

The innovative aspects of this research program include the development of a novel computational model that 1) considers the transient flow fields generated by airway wall deformation and fully coupled fluid-structure interactions at two free surfaces (air-liquid interface and compliant wall), 2) quantifies how airway wall compliance influences cellular deformation and 3) considers an additional levels of complexity such as bifurcation patterns and three-dimensional flow patterns that exists in-vivo. Our expectations are that the development of these more sophisticated computational models will help us understand how the complex structure of the lung epithelium and pulmonary airways influence microbubble-induced injury during mechanical ventilation. As such, this project could lead to important new information about the mechanisms responsible for ventilator-induced lung injury and the development of improved treatment and therapies of patients with ARDS.


Samir Ghadiali, PhD (Advisor); Terrence Conlisk, PhD (Committee Member); Yi Zhao, PhD (Committee Member); Ronald Xu, PhD (Committee Member)


Aeronomy; Biomedical Engineering; Mechanical Engineering


Fluid-Structure Interaction; microbubble; cell deformation; epithelial cell; free surface flow; curvature; gravity; inertial effect; surface tension; pressure gradient; compliant airway;

Wan, CaixiaMicrobial Pretreatment of Lignocellulosic Biomass with Ceriporiopsis Subvermispora for Enzymatic Hydrolysis and Ethanol Production
Doctor of Philosophy, The Ohio State University, 2011, Food, Agricultural and Biological Engineering

Pretreatment is a crucial step in the conversion of lignocellulosic biomass to fermentable sugars. Microbial pretreatment with white rot fungi can delignify lignocellulosic biomass under atmospheric conditions and, thus, has the potential to be applied to on-farm wet storage for cost-effective cellulosic ethanol production. The present research investigated the feasibility of solid-state microbial pretreatment of corn stover and other types of lignocellulosic biomass feedstocks with the white rot fungus Ceriporiopsis subvermispora.

The glucose and ethanol yields, based on the theoretical yield of untreated corn stover, reached 66.61% and 57.80%, respectively, after a 35-d pretreatment, which were more than three times of that obtained with the untreated corn stover. Washing of fungal-pretreated corn stover did not cause significant improvement in ethanol yield, suggesting no water insoluble inhibitory compounds were formed during fungal pretreatment. A high correlation was obtained between the remaining lignin content in the treated corn stover and its cellulose digestibility, indicating that lignin removal facilitated enzymatic hydrolysis.

The delignification process of corn stover was investigated throughout a 42-d pretreatment by monitoring changes in composition and enzyme production. Lignin degradation increased with pretreatment time, reaching 39.20% at the end of pretreatment while cellulose degradation was less than 4.52% throughout the process, indicating a high selectivity of the fungus for lignin in the corn stover. However, hemicellulose degradation, mainly xylose loss, was substantial with up to 27.52% hemicellulose simultaneously degraded with lignin. Manganese peroxidase (MnP) and laccase were two detected oxidative enzymes while xylanase was the major hydrolytic enzyme. Observation by scanning electron microscopy showed that fungal pretreatment changed the microstructure of corn stover significantly. At the later stage of pretreatment, corn stover became light, soft, and spongy and the color changed to whitish-yellow.

To evaluate the robustness of the fungal pretreatment process with C. subvermispora , other feedstocks, including wheat straw, soybean straw, switchgrass, and hardwood, were also examined. After pretreatment for 18 d, switchgrass and hardwood were effectively delignified with significant production of manganese peroxidase and laccase. Wheat straw was greatly resistant to fungal pretreatment unless glucose and malt extract were added to the substrate. In contrast, no fungal degradation occurred in soybean straw even with addition of external carbon sources and enzyme inducers (Mn2+, H2O2).

Hot water extraction and/or hydrothermal pretreatment were applied to improve fungal degradation of wheat straw and soybean straw. Hot water extraction removed extractives in substrates, which facilitated fungal degradation of wheat straw but not of soybean straw. Fungal degradation of soybean straw was finally improved by the liquid hot water pretreatment, which resulted in 36.70% lignin removal and 64.25% glucose yield.

Empirical models satisfactorily predicted fungal growth, oxygen uptake, holocellulose consumption, and lignin degradation; however, the prediction of enzyme production was poor.

The knowledge obtained from this study is important for the development of concurrent wet storage and microbial pretreatment with white rot fungi for lignocellulosic biomass and of a combined fungal and thermal/physical pretreatment process that can potentially overcome the problems associated with existing pretreatment methods.


Yebo Li (Advisor); Ann Christy (Committee Member); Fred Michel (Committee Member); Thaddeus Ezeji (Committee Member)


Aeronomy; Agricultural Engineering; Alternative Energy

Gong, YunIncoherent Scatter Study of Dynamics in the Ionosphere E- and F-Region at Arecibo
Master of Science, Miami University, 2012, Computational Science and Engineering
This thesis reports the investigation of the dynamics and associated phenomena occurring in the ionospheric E- and F-region heights above Arecibo. The observational data was derived with an incoherent scatter radar (ISR) from Arecibo Observatory, Puerto Rico. The thesis focuses primarily on two aspects. One is to study the atmospheric tidal and planetary waves. This is the first time that dual-beam ISR has been used for E- and F-region tidal and planetary wave studies. The vertical structures of the observed tidal and planetary waves are analyzed rigorously. This study is the first to report the existence and possible excitation mechanism of a terdiurnal tide in the F-region at low latitude. The second aspect is to give a more complete explanation of the midnight collapse phenomenon. The F-region electric field, ambipolar diffusion, and tidal components in the meridional wind all play a role in causing the midnight collapse at Arecibo.


Qihou Zhou, PhD (Advisor); Jade Morton, PhD (Committee Member); Dmitriy Garmatyuk, PhD (Committee Member)


Aeronomy; Engineering


incoherent scatter radar; the ionosphere; tidal and planetary waves; midnight collapse

Santana, JulioInvestigating Ionospheric Parameters Using the Plasma Line Measurements From Incoherent Scatter Radar
Master of Science, Miami University, 2012, Computational Science and Engineering
Because of deficiencies in sampling resolution and storage space, the plasma line frequency component of the incoherent scatter radar (ISR) spectrum has been neglected in experimentally verifying ionospheric parameters. Several incoherent scatter theories were independently developed with confirmation from low resolution data in the 1960s that used the plasma line resonant frequency and plasma line peak intensity to derive ionospheric parameters. Now that higher resolution measurement techniques exist, this thesis investigates three methods for obtaining plasma line resonant frequency, peak intensity, and spectral width. Following this study, several salient features endemic to the ISR experiment performed on January 15-17th, and January 22nd of 2010 are presented and analyzed.


Qihou Zhou, PhD (Advisor); Jade Morton, PhD (Committee Member); Chi Hao Cheng, PhD (Committee Member)


Aeronomy; Electrical Engineering; Plasma Physics


Plasma line; ionosphere; incoherent scatter radar; aeronomy; Arecibo Observatory; space weather