abstract: The pace of exoplanet discoveries has rapidly accelerated in the past few decades and the number of planets with measured mass and radius is expected to pick up in the coming years. Many more planets with a size similar to earth are expected to be found. Currently, software for characterizing rocky planet interiors is lacking. There is no doubt that a planet’s interior plays a key role in determining surface conditions including atmosphere composition and land area. Comparing data with diagrams of mass vs. radius for terrestrial planets provides only a first-order estimate of the internal structure and composition of planets [e.g. Seager et al 2007]. This thesis will present a new Python library, ExoPlex, which has routines to create a forward model of rocky exoplanets between 0.1 and 5 Earth masses. The ExoPlex code offers users the ability to model planets of arbitrary composition of Fe-Si-Mg-Al-Ca-O in addition to a water layer. This is achieved by modeling rocky planets after the earth and other known terrestrial planets. The three distinct layers which make up the Earth's internal structure are: core, mantle, and water. Terrestrial planet cores will be dominated by iron however, like earth, there may be some quantity of light element inclusion which can serve to enhance expected core volumes. In ExoPlex, these light element inclusions are S-Si-O and are included as iron-alloys. Mantles will have a more diverse mineralogy than planet cores. Unlike most other rocky planet models, ExoPlex remains unbiased in its treatment of the mantle in terms of composition. Si-Mg-Al-Ca oxide components are combined by predicting the mantle mineralogy using a Gibbs free energy minimization software package called Perple\_X [Connolly 2009]. By allowing an arbitrary composition, ExoPlex can uniquely model planets using their host star’s composition as an indicator of planet composition. This is a proven technique [Dorn et al 2015] which has not yet been widely utilized, possibly due to the lack of availability of easy to use software. I present a model sensitivity analysis to indicate the most important parameters to constrain in future observing missions. ExoPlex is currently available on PyPI so it may be installed using pip or conda on Mac OS or Linux based operating systems. It requires a specific scripting environment which is explained in the documentation currently stored on the ExoPlex GitHub page. / Dissertation/Thesis / Masters Thesis Astrophysics 2018

Obesity is a severe concern worldwide and its prevalence is expected to continue to increase. Linked to diabetes, kidney disease, heart disease, and high blood pressure among other things, obesity has been identified as the forthcoming, largest preventable cause of mortality. Osteoarthritis, surgical consequences, distribution of subcutaneous adipose tissue, and alteration of joint biomechanics have vast implications in total joint repair (TJR). Previous studies have linked obesity to increased forces through weight-bearing lower extremities, alterations in gait, and risk of implant failure. The objectives of this study were to (1) provide a tool to predict lower extremity dimensions and shape variations of subcutaneous adipose tissue, (2) identify the degree to which obesity influences shape variation of the osseous anatomy of the knee joint, and (3) lay a foundation to compare the knee contact force of obese patients in activities of daily living. Long-leg EOS films were obtained, retrospectively over 5 years, from 232 patients that were being seen at the Adult Reconstruction Clinic at the University of Iowa. Using custom Matlab algorithms, measurements of soft tissue distribution and lower extremity osseous anatomy were obtained and analyzed. Additionally knee contact force measurements were obtained through motion capture analysis and modeling in Anybody Technology. Males and females had similar lower extremity shapes, with females having greater knee circumferences than males. The variability of PPT and PTT tended to be greater in females and increased with increasing BMI. Although similar in the anteroposterior direction, males tended to have on average 12mm wider proximal tibias in the mediolateral direction. Clinical observations of increased post-operative complications trend with these findings. The future of research into biomechanics of obesity will rely heavily on anatomic models of the obese lower extremities, which until this work did not exist.

While there is continuing interest in bioresorbable materials for orthopedic fixation devices, the major challenge in utilizing these materials in load-bearing applications is creating materials sufficiently stiff and strong to sustain loads throughout healing while maintaining fracture stability. The primary aim of this study is to quantify the degradation rate of a bioresorbable material system, then use this degradation rate to determine the material response of an orthopedic device made of the same material as healing progresses. The present research focuses on the development and characterization of a material system consisting of carbon foam infiltrated with hydroxyapatite (HA) reinforced poly(D,L-lactide)-co-poly(glycolide) (PDLGA). A processing technique is developed to infiltrate carbon foam with HA/PDLGA and material morphology is investigated. Additionally, short-term rat osteoblast cell studies are undertaken to establish a starting point for material biocompatibility. Degradation experiments are conducted to elicit the time-dependent properties of the material system at the material scale. These properties are then incorporated into computational models of an internal plate attached to a fractured human femur to design and predict the material response to applied physiological loads. Results from this work demonstrate the importance of material dissolution rate as well as material strength when designing internal fixation plates.

Cell shape is important to understanding the mechanics of three-dimensional (3D) cell aggregates. When an aggregate of embryonic cells is compressed between parallel plates, the cell mass and the cells of which it is composed flatten. Over time, the cells typically move past one another and return to their original, spherical shapes, even during sustained compression, although the profile of the aggregate changes little once plate motion stops. Although the surface and interfacial tensions of cells have been attributed to driving these internal movements, measurements of these properties have largely eluded researchers. Here, an existing 3D finite element model, designed specifically for the mechanics of cell-cell interactions, is enhanced so that it can be used to investigate aggregate compression. The formulation of that model is briefly presented and enhancements made to its rearrangement algorithms discussed. Simulations run using the model show that the rounding of interior cells is governed by the ratio between the interfacial tension and cell viscosity, whereas the shape of cells in contact with the medium or the compression plates is dominated by their respective cell-medium or cell-plate surface tensions. The model also shows that as an aggregate compresses, its cells elongate more in the circumferential direction than the radial direction. Since experimental data from compressed aggregates are anticipated to consist of confocal sections, geometric characterization methods are devised to quantify the anisotropy of cells and to relate cross sections to 3D properties. The average anisotropy of interior cells as found using radial cross sections corresponds more closely with the 3D properties of the cells than data from series of parallel sections. A basis is presented for estimating cell-cell interfacial tensions from the cell shape histories they exhibit during the cell reshaping phase of an aggregate compression test.

Language production depends upon the context in which words are named. Renaming previous items results in facilitation while naming pictures semantically related to previous items causes interference. A computational model (Oppenheim, Dell, & Schwartz, 2010) proposes that both facilitation and interference are the result of using naming events as “learning experiences” to ensure future accuracy. The model successfully simulates naming data from different semantic interference paradigms by implementing a learning mechanism that creates interference and a boosting mechanism that resolves interference. This study tested this model’s assumptions that semantic interference effects in naming are created by learning and resolved by boosting. Findings revealed no relationship between individual performance across semantic interference tasks, and measured learning and boosting abilities did not predict performance. These results suggest that learning and boosting mechanisms do not fully characterize the processes underlying semantic interference when naming.

Cell shape is important to understanding the mechanics of three-dimensional (3D) cell aggregates. When an aggregate of embryonic cells is compressed between parallel plates, the cell mass and the cells of which it is composed flatten. Over time, the cells typically move past one another and return to their original, spherical shapes, even during sustained compression, although the profile of the aggregate changes little once plate motion stops. Although the surface and interfacial tensions of cells have been attributed to driving these internal movements, measurements of these properties have largely eluded researchers. Here, an existing 3D finite element model, designed specifically for the mechanics of cell-cell interactions, is enhanced so that it can be used to investigate aggregate compression. The formulation of that model is briefly presented and enhancements made to its rearrangement algorithms discussed. Simulations run using the model show that the rounding of interior cells is governed by the ratio between the interfacial tension and cell viscosity, whereas the shape of cells in contact with the medium or the compression plates is dominated by their respective cell-medium or cell-plate surface tensions. The model also shows that as an aggregate compresses, its cells elongate more in the circumferential direction than the radial direction. Since experimental data from compressed aggregates are anticipated to consist of confocal sections, geometric characterization methods are devised to quantify the anisotropy of cells and to relate cross sections to 3D properties. The average anisotropy of interior cells as found using radial cross sections corresponds more closely with the 3D properties of the cells than data from series of parallel sections. A basis is presented for estimating cell-cell interfacial tensions from the cell shape histories they exhibit during the cell reshaping phase of an aggregate compression test.

The pre-Botzinger complex (pBC) is a sub-circuit of the respiratory central pattern generator. The pBC is required for eupnea and is contained in a transverse slice of the ventrolateral medulla. In the slice, pBC cells are responsible for generating the respiratory rhythm, and hypoglossal motoneurons (HMs) are responsible for transmitting the rhythm out of the brainstem to the muscles. Understanding how the transverse slice rhythm is generated and transmitted is a first step in understanding how this process occurs in vivo. To understand this network, we developed ionic current models of the individual network components and explored how the various ion channels affect single-cell firing characteristics and network dynamics. First, we used the considerable amounts of experimental data from neonatal HMs to develop an HM model. The model was used to explore the roles of ion channels in shaping the complex dynamics of the neonatal HM action potential (AP) and to investigate the age-dependent changes in HMs. We used a genetic algorithm to optimize the HM model to more closely fit experimental measures of AP shape. A comparison of feature-based and template-based fitness functions revealed that a feature-based fitness function performs best when optimizing the HM model to fit characteristics of the neonatal HM AP. Next, we used our existing pBC models to understand how different ionic currents affect rhythmogenesis in the pBC. Our results indicate that intrinsic bursters increase the robustness of rhythm generation in the pBC. Finally, we developed an improved pBC neuron model and explored how various ion channels affect bursting dynamics at the single-cell level. The HM and pBC models developed in this study will be used in future network models of the transverse slice.

While there is continuing interest in bioresorbable materials for orthopedic fixation devices, the major challenge in utilizing these materials in load-bearing applications is creating materials sufficiently stiff and strong to sustain loads throughout healing while maintaining fracture stability. The primary aim of this study is to quantify the degradation rate of a bioresorbable material system, then use this degradation rate to determine the material response of an orthopedic device made of the same material as healing progresses. The present research focuses on the development and characterization of a material system consisting of carbon foam infiltrated with hydroxyapatite (HA) reinforced poly(D,L-lactide)-co-poly(glycolide) (PDLGA). A processing technique is developed to infiltrate carbon foam with HA/PDLGA and material morphology is investigated. Additionally, short-term rat osteoblast cell studies are undertaken to establish a starting point for material biocompatibility. Degradation experiments are conducted to elicit the time-dependent properties of the material system at the material scale. These properties are then incorporated into computational models of an internal plate attached to a fractured human femur to design and predict the material response to applied physiological loads. Results from this work demonstrate the importance of material dissolution rate as well as material strength when designing internal fixation plates.

Coupling beams are structural elements used to connect two or more shear walls. The most common material used in the construction of coupling beam is reinforced concrete. The use of coupling beams along with shear walls require them to resist large shear forces, while possessing sufficient ductility to dissipate the energy produced due to the lateral loads. This study has been undertaken to produce a computational model to replicate the behavior of conventionally reinforced coupling beams subjected to cyclic loading. The model is developed in the finite element analysis software ABAQUS. The concrete damaged plasticity model was used to simulate the behavior of concrete. A calibration model using a cantilever beam was produced to generate key parameters in the model that are later adapted into modeling of two coupling beams with aspect ratios: 1.5 and 3.6. The geometrical, material, and loading values are adapted from experimental specimens reported in the literature, and the experimental results are then used to validate the computational models. The results like evolution of damage parameter and crack propagation from this study are intended to provide guidance on finite element modeling of conventionally reinforced concrete coupling beams under cyclic lateral loading.

Elevated levels of reactive oxygen species (ROS) cause or aggravate a variety of pathological conditions such as cardiovascular disease, cancer and rheumatoid arthritis. Despite known links between oxidative stress and disease, years of clinical studies have failed to show clear benefits of antioxidant therapy. It is now recognized that ROS such as hydrogen peroxide can act as signaling molecules and are required for physiological functioning of a number of signaling pathways. Therefore, a mechanistic basis of ROS-mediated regulation of cell signaling must be established to enable rational design of antioxidant-based therapies. The challenges in quantification of transient changes mediated by ROS during cell signaling have impeded investigation of redox-regulated signaling. In the present work, computational modeling is used to circumvent these technical challenges and to test competing hypotheses of redox regulation. Using a quantitative, systems level approach to study interactions between ROS dependent and independent regulatory mechanisms, the most comprehensive model of the IL-4 signaling pathway to date has been developed and validated with experimental data. The model is capable of predicting kinase phosphorylation dynamics under new oxidative conditions, and our analyses suggest that reversible oxidation of tyrosine phosphatases is the primary mechanism of redox regulation in this pathway. Additional computational methods have been developed to study ROS as mediators of crosstalk between signaling pathways, to optimize model parameters, and to interrogate model dynamics for the purpose of model selection. Collectively, these modeling tools provide a new systems-level perspective for investigating reversible protein oxidation as a means of control over cellular signal transduction.