Digital Commons Network^™

Computational Optogenetics: Empirically-Derived Voltage- And Light-Sensitive Channelrhodopsin-2 Model, John C. Williams, Jianjin Xu, Zhongju Lu, Aleksandra Klimas, Xuxin Chen, Christina M. Ambrosi, Ira S. Cohen, Emilia Entcheva

Department of Biomedical Engineering Faculty Publications

Channelrhodospin-2 (ChR2), a light-sensitive ion channel, and its variants have emerged as new excitatory optogenetic tools not only in neuroscience, but also in other areas, including cardiac electrophysiology. An accurate quantitative model of ChR2 is necessary for in silicoprediction of the response to optical stimulation in realistic tissue/organ settings. Such a model can guide the rational design of new ion channel functionality tailored to different cell types/tissues. Focusing on one of the most widely used ChR2 mutants (H134R) with enhanced current, we collected a comprehensive experimental data set of the response of this ion channel to different irradiances and voltages, …

Role Of Programmed Proteolysis During Meiosis, Vincent Matthews, G. Valentin Borner Ph.D.

Undergraduate Research Posters 2013

Meiosis is the process which forms gametes and spores for reproduction in eukaryotic cells. During the pachytene phase of meiosis I, a protein structure, called the Synaptonemal Complex (SC), forms between homologous chromosomes and creates a scaffold for genetic recombination. In yeast, the Zip1 protein is a major structural component of the SC. At restrictive temperature for meiosis, ZIP1 is required for completion of meiotic divisions. At permissive temperature ZIP1 is required for proper chromosome segregation. We observed that chemical inhibition of the proteasome, with MG132, results in arrest at prophase of meiosis I. Based on these results, we questioned …

Bioavailable Lead In Topsoil Collected From General Aviation Airports, Jerry H. Kavouras, Randal J. Demik, Allison C. Hopkins

Biology Department Faculty Articles

Representatives of the aviation community are interested in determining the environmental effects of leaded fuel emissions from general aviation flight operations. Soil is an environmental sink for lead to accumulate over time. This study measured bioavailable lead concentrations in topsoil at three general aviation airports and at one site with no general aviation operations in order to determine if general aviation aircraft operations are contributing to the contamination of airport topsoil at levels that require remediation by law. Bioavailable refers to substances that organisms can absorb, because they have access to them. Topsoil was collected from refueling areas, run-up areas, …

Stabilizing Nanostructured Solid Oxide Fuel Cell Cathode With Atomic Layer Deposition, Yunhui Gong, Diego Palacio, Xueyan Song, Rajankumar L. Patel, Xinhua Liang

Chemical and Biochemical Engineering Faculty Research & Creative Works

We demonstrate that the highly active but unstable nanostructured intermediate-temperature solid oxide fuel cell cathode, La_0.6Sr_0.4CoO_3-δ (LSCo), can retain its high oxygen reduction reaction (ORR) activity with exceptional stability for 4000 h at 700 C by overcoating its surfaces with a conformal layer of nanoscale ZrO₂ films through atomic layer deposition (ALD). The benefits from the presence of the nanoscale ALD-ZrO₂ overcoats are remarkable: a factor of 19 and 18 reduction in polarization area-specific resistance and degradation rate over the pristine sample, respectively. The unique multifunctionality of the ALD-derived nanoscaled ZrO₂ overcoats, …

Correlating Thomboembolism To Individual Platelet Aggregation Rate, Luke Werrett, Dr. Kenneth Solen

Journal of Undergraduate Research

The objective of this research project was to identify a correlation between a traditional platelet activity test using an aggregometer, and a new test that measures interactions between blood and man-made materials in a simulated blood flow environment. A correlation between these data would give artificial organ recipients and open-heart surgery candidates a more thorough risk analysis of their situation, and indicate the need for caution or additional medication.

Impedance Detection Of Biological Molecules In Microfluidic Channels, Daniel Evans, Dr. Aaron Hawkins

Journal of Undergraduate Research

At the current time, the most sensitive detection methods for biological molecules are based on fluorescent tags. This requires the use of optical sources and detectors as well as the introduction of a fluorophore that can be attached to a molecule of interest. In light of these challenges, my research goal was to create a sensitive method of detection based on electrical impedance measurements rather than optical measurements. In theory, this technique has the potential for providing a detection method that can be easily implemented on multiple parallel channels on a microfluidic chip.

Nanoemulsions Of Non-Toxic Fluorocarbon Liquids Used To Transfect Genes With Applied Ultrasound, Cody L. Martin, Dr. William Pitt

Journal of Undergraduate Research

Gene delivery has been an important topic of medical and scientific research today, due to its potential in aiding the fight against cancer, heart disease and many genetic disorders. By transfecting appropriate genes into diseased cells, specific proteins can be produced that will alleviate problems at the cellular level. In addition, if the gene delivery is done by a targeted non-viral approach, such as ultrasound combined with contrast agent bubbles, the efficiency of transfection always increases. The targeted non-viral approach consists of applying focused ultrasound to a specific tissue in the presence of microbubbles. The application of ultrasound will cause …

A Course Grain Model For Protein-Surface Interactions, Shuai Wei, Thomas A. Knotts Iv

Faculty Publications

The interaction of proteins with surfaces is important in numerous applications in many fields—such as biotechnology, proteomics, sensors, and medicine—but fundamental understanding of how protein stability and structure are affected by surfaces remains incomplete. Over the last several years, molecular simulation using coarse grain models has yielded significant insights, but the formalisms used to represent the surface interactions have been rudimentary. We present a new model for protein surface interactions that incorporates the chemical specificity of both the surface and the residues comprising the protein in the context of a one-bead-per-residue, coarse grain approach that maintains computational efficiency. The model …

Semi-Automated Curation Of Metabolic Models Via Flux Balance Analysis: A Case Study With Mycoplasma Gallisepticum, Eddy J. Bautista, Joseph Zinski, Steven M. Szczepanek, Erik L. Johnson, Edan R. Tulman, Steven J. Geary, Ranjan Srivastava

Open Access Author Fund Awardees' Articles

Primarily used for metabolic engineering and synthetic biology, genome-scale metabolic modeling shows tremendous potential as a tool for fundamental research and curation of metabolism. Through a novel integration of flux balance analysis and genetic algorithms, a strategy to curate metabolic networks and facilitate identification of metabolic pathways that may not be directly inferable solely from genome annotation was developed. Specifically, metabolites involved in unknown reactions can be determined, and potentially erroneous pathways can be identified. The procedure developed allows for new fundamental insight into metabolism, as well as acting as a semi-automated curation methodology for genome-scale metabolic modeling. To validate …

Characterization Of Secondary Organic Aerosol Precursors Using Two-Dimensional Gas Chromatography With Time Of Flight Mass Spectrometry (Gc×Gc/Tofms), Melissa Jordan Roskamp

Dissertations and Theses

The oxidation of volatile organic compounds (VOCs) plays a role in both regional and global air quality through the formation of secondary organic aerosols (SOA). More than 1000TgC/yr of non-methane VOCs are emitted from biogenic sources (significantly greater than from anthropogenic sources). Despite this magnitude and potential importance for air quality, the body of knowledge around the identities, quantities and oxidation processes of these compounds is still incomplete (e.g., Goldstein & Galbally, 2007; Robinson et al., 2009). Two-dimensional gas chromatography paired with time-of-flight mass spectrometry (GC×GC/TOFMS) is a powerful analytical technique which is explored here for its role in better …

Numerical Analysis Of Co-Flowing Immiscible Liquids In Co-Axial Microtubes, In-Hwan Yang

Chemical and Biological Engineering ETDs

This research developed dimensionless correlations, based on the numerical simulations, for the boundaries between the dripping, transition and jetting regimes. Additional correlations are also developed for the radius and formation frequency of disperse droplet in the dripping regime and the transition regime, when the total volume of the satellite droplets is less than 1% of the disperse primary droplets.

Adatom Emission From Nanoparticles: Implications For Ostwald Ripening, Tyne Johns

Chemical and Biological Engineering ETDs

To achieve clean air in our cities, all modern means of ground transportation make use of catalytic converters. Precious metal-based catalysts such as Pt and Pd are currently used in catalytic converters. To achieve higher fuel efficiency, combustion can be carried out in excess air resulting in a reduction of greenhouse gas (GHG) emissions. Reduction of these emissions has emerged as a major challenge. Most of the pollutants are emitted within the first 30 seconds after starting an engine because the catalyst is cold. The development of catalysts which achieve high activity at low temperatures will improve fuel efficiency and …

Novel Etch Studies And Passivation Techniques On Inas/Gasb Superlattice Based Infrared Detectors, Maya Narayanan Kutty

Electrical and Computer Engineering ETDs

Infrared (IR) detectors today are being utilized for a variety of imaging applications such as medical diagnostics, navigation instruments of automobiles and aircrafts, meteorological imaging, night-vision and fog/smoke imaging, surveillance, target acquisition and astronomical/space imaging. These wide ranging implementations have given rise to varied design requirements for these devices such as the required sensitivity, operating temperature, spectral sensitivity, peak wavelength and cost. Type-II band aligned InAs/Ga(In)Sb strained layer superlattice (SLS) material system proposed for the IR detection in the 1970s has been considered in recent years as an interesting alternative to the present day IR detection technologies. Type-II SLS technology …

Engineered Knottin Peptide Enables Noninvasive Optical Imaging Of Intracranial Medulloblastoma, Sarah J. Moore, Melanie G. Hayden Gephart, Jamie M. Bergen, You Rong S. Su, Helen Rayburn, Matthew P. Scott, Jennifer R. Cochran

Engineering: Faculty Publications

Central nervous system tumors carry grave clinical prognoses due to limited effectiveness of surgical resection, radiation, and chemotherapy. Thus, improved strategies for brain tumor visualization and targeted treatment are critically needed. We demonstrate that mouse cerebellar medulloblastoma (MB) can be targeted and illuminated with a fluorescent, engineered cystine knot (knottin) peptide that binds with high affinity to α β , α β , and α β integrin receptors. This integrin-binding knottin peptide, denoted EETI 2.5F, was evaluated as a molecular imaging probe in both orthotopic and genetic models of MB. Following tail vein injection, fluorescence arising from dye-conjugated EETI 2.5F …

Origami-Based Design For Engineering Applications, Kevin Campbell Francis

Theses and Dissertations

Origami can be a powerful source of design inspiration in the creation of reconfigurable systems with unparalleled performance. This thesis provides fundamental tools for designers to employ as origami-based designs are pursued in their respective fields of expertise. The first chapter introduces origami and makes connections between origami and engineering design through a survey of engineered applications and characterizing the relationship between origami and compliant mechanisms. The second chapter evaluates the creasing of non-paper sheet materials, such as plastics and metals, to facilitate origami-based compliant mechanism design. Although it is anticipated that most origami-based design will result from surrogate folds …

Dynamic Vegetation Roughness In The Riparian Zone, Tyler Gillihan

Civil Engineering ETDs

Vegetation in the floodplain plays an important role in dictating the hydraulics of an open channel river system. While vegetation is beneficial to the biological productivity of the river system, it can also increase flood risk due to increased channel roughness. Traditional means of predicting flow hydraulics involve applying a constant roughness value, while neglecting change in roughness due to flow characteristics and variation of vegetation parameters. The objective of this research was to develop and demonstrate techniques to hydraulically model an open channel river system while taking into account dynamic roughness due to vegetation. The Sedimentation and River Hydraulics …

Parallel Simulation Of Particle Dynamics With Application To Micropolar Peridynamic Lattice Modeling Of Reinforced Concrete Structures, Hossein Honarvar Gheitanbaf

Civil Engineering ETDs

As the first goal of this thesis, we will explain a general purpose parallel particle dynamics code (pdQ2). We describe the re-architecting of pdQ (the MD/PD code that was developed in [Sakhavand 2011]) as pdQ2. pdQ2 is completely non-domain-specific in that user files are clearly separated from non-user files and no #ifdefs exist in the code. Thus, it operates as a particle simulation engine that is capable of executing any parallel particle dynamics model. As in the original pdQ, users can customize their own physical models without having to deal with complexities such as parallelization, but the ease of extensibility …

Significance Of Nanosilica Incorporation In Type G Oil Well Cement Pastes, Andrew Griffin

Civil Engineering ETDs

Emergent interest in advanced hydrocarbon exploration and geological carbon dioxide (CO2) sequestration has brought about a requisite for improving existing oil well cementing materials and understanding the macro and microstructural characterization mechanisms of oil well cement (OWC). OWC slurries have stringent performance requirements, including low viscosity, rapid strength development, low permeability and enhanced degradation resistance. Preliminary research work showed that nanosilica is capable of reducing OWC porosity and therefore is was thought that nanosilica incorporation may have potential to improve the aforementioned performance requirements. In this research, Type G OWC paste specimens produced with water to binder (w/b) ratio of …

Fabrication And Characterization Of A Palladium/Porous Silicon Layer, Nicholas Hong Lui

Master's Theses

When porous silicon is plated with a catalytic metal, the two materials can act together as a single entity whose electrical properties are sensitive to its environment – the sensing component of an electrochemical gas sensor. Etching pores into silicon is an electrochemical process; and which type of doped silicon used is one of its key parameters. For nearly all reported porous silicon gas sensors, the silicon has been of the p-doped variety – because p-doped porous etching is better understood and the layers that result from it are more predictable – despite n-doped silicon having potentially significant benefits in …

Ua66 Ogden College Of Science & Engineering Newsletter, Cheryl Stevens, Dean

Ogden College of Science & Engineering Publications

No abstract provided.

On The Primitives Of Causality: From The Semantics Of Agonist And Antagonist To Models Of Accident Causation And System Safety, Loïc Brevault, Francesca Favaro, Joseph Saleh

Faculty Publications

Controversial discussions on causality have been present in ancient philosophy since the days of Aristotle. Despite the use of this concept in numerous subjects, there is no consensus on the definition of causality and its possible mathematization. Many authors have analyzed the relation between causes and effects; the predominant school of thought reduces causation to a physical relation (either deterministic or probabilistic) between two events. The distinction between causes and consequences is not always clear and meaningful as different “layers of understanding” may be applied to the notion of causality. From this point of view the cause-effect implication relation can …

All-Optical Photoacoustic Detection Of Absorbers In Tissue Phantoms, Jami Johnson, Michelle Sabick, Kasper Vanwijk

Mechanical and Biomedical Engineering Faculty Publications and Presentations

Visualizing and characterizing vascular structures is important for many areas of health care, from accessing difficult veins and arteries for laboratory testing, to diagnosis and treatment of cardiovascular disease. Photoacoustic (PA) imaging, one of the fastest growing fields of biomedical imaging, is well suited for this task. PA imaging is based on the photoacoustic effect, which starts with a pulsed laser source incident on biological tissue. If the wavelength of the source matches an absorption wavelength of a chromophore within the tissue, a portion of the pulse energy is absorbed by the chromophore and converted into heat. A subsequent increase …

Metal-Assisted Etching Of Silicon Molds For Electroforming, Ralu Divan, Dan Rosenthal '14, Karim Ogando, Leonidas E. Ocola, Daniel Rosenmann, Nicolaie Moldovan

Student Publications & Research

Ordered arrays of high-aspect-ratio micro/nanostructures in semiconductors stirred a huge scientific interest due to their unique one-dimensional physical morphology and the associated electrical, mechanical, chemical, optoelectronic, and thermal properties. Metal-assisted chemical etching enables fabrication of such high aspect ratio Si nanostructures with controlled diameter, shape, length, and packing density, but suffers from structure deformation and shape inconsistency due to uncontrolled migration of noble metal structures during etching. Hereby the authors prove that a Ti adhesion layer helps in stabilizing gold structures, preventing their migration on the wafer surface while not impeding the etching. Based on this finding, the authors demonstrate …

Design And Development Of A Low Cost Platform To Facilitate Post-Stroke Rehabilitation Of The Elbow/Shoulder Region, Stephen Curran

Masters

For post-stroke rehabilitation of the upper limbs, increased amounts of therapy are directly related to improved rehabilitation outcomes. As such, a low cost therapy platform is proposed suitable for facilitating active therapy and administering activeassist therapy to the shoulder/elbow region of the upper limbs of individuals post-stroke in a local clinic or domestic setting. Enabling a person to undergo intensive rehabilitation therapy outside of a rehabilitation hospital setting permits the amount of therapy administered to be maximised. While studies have shown that technological approaches to post-stroke rehabilitation do not produce better outcomes than equal amounts of traditional therapy in a …

The Role Of Mechanically Induced Erk Phosphorylation In Stem Cell Adipogenesis, Daniel E. Menter

Department of Engineering Mechanics: Dissertations, Theses, and Student Research

Mechanical cell stimulation has only recently been highlighted for its ability to direct cell function and fate. The development of techniques to apply controlled mechanical stimulation to cells has allowed researchers to examine the effects of forces on cell behavior. These studies have shown that cells, and in particular, stem cells are very sensitive to mechanical stimuli. While the potential impact of mechanical forces has been demonstrated by these studies, there have not been many studies that compare the differing effects of stimulation profiles and methods. Further, molecular mechanosensing mechanisms have not been identified. In this work, we compared the …

Hypoxia Preconditioning Increases Survival And Decreases Expression Of Toll-Like Receptor 4 In Pulmonary Artery Endothelial Cells Exposed To Lipopolysaccharide, Irshad Ali, Rahul Nanchal, Fouad Husnain, Said H. Audi, G. Ganesh Konduri, John C. Densmore, Meetha Medhora, Elizabeth R. Jacobs

Biomedical Engineering Faculty Research and Publications

Pulmonary or systemic infections and hypoxemic respiratory failure are among the leading causes of admission to intensive care units, and these conditions frequently exist in sequence or in tandem. Inflammatory responses to infections are reproduced by lipopolysaccharide (LPS) engaging Toll-like receptor 4 (TLR4). Apoptosis is a hallmark of lung injury in sepsis. This study was conducted to determine whether preexposure to LPS or hypoxia modulated the survival of pulmonary artery endothelial cells (PAECs). We also investigated the role TLR4 receptor expression plays in apoptosis due to these conditions. Bovine PAECs were cultured in hypoxic or normoxic environments and treated with …

Enzymatic Hydrolysis Of Biomass At High-Solids Loadings – A Review, Alicia A. Modenbach, Sue E. Nokes

Biosystems and Agricultural Engineering Faculty Publications

Enzymatic hydrolysis is the unit operation in the lignocellulose conversion process that utilizes enzymes to depolymerize lignocellulosic biomass. The saccharide components released are the feedstock for fermentation. When performed at high-solids loadings (≥ 15% solids, w/w), enzymatic hydrolysis potentially offers many advantages over conversions performed at low- or moderate-solids loadings, including increased sugar and ethanol concentrations and decreased capital and operating costs.

The goal of this review is to provide a consolidated source of information on studies using high-solids loadings in enzymatic hydrolysis. Included in this review is a brief discussion of the limitations, such as a lack of available …

Establishing Permanent Vegetation After Highway Construction, John C. Soper, Walter H. Schacht

Nebraska Department of Transportation: Research Reports

No abstract provided.

Modeling The Effect Of Apc Truncation On Destruction Complex Function In Colorectal Cancer Cells, Dipak Barua, William S. Hlavacek

Chemical and Biochemical Engineering Faculty Research & Creative Works

In colorectal cancer cells, APC, a tumor suppressor protein, is commonly expressed in truncated form. Truncation of APC is believed to disrupt degradation of β-catenin, which is regulated by a multiprotein complex called the destruction complex. The destruction complex comprises APC, Axin, β-catenin, serine/threonine kinases, and other proteins. The kinases CK1α and GSK-3β, which are recruited by Axin, mediate phosphorylation of β-catenin, which initiates its ubiquitination and proteosomal degradation. The mechanism of regulation of β-catenin degradation by the destruction complex and the role of truncation of APC in colorectal cancer are not entirely understood. Through formulation and analysis of a …

Novel Paradigms For Visual Field Mapping With Functional Magnetic Resonance Imaging, Yan Ma

Dissertations (1934 -)

The overall goal of this study is to evaluate the existing, and develop new visual field mapping paradigms, which consist of visual stimulation scheme, post-processing and displaying tools using fMRI for both research and clinical applications.

We first directly compared phase mapping and random multifocal mapping paradigms with respect to clinically relevant factors. Multifocal mapping was superior in immunity to noise and was able to accurately decompose the response of single voxels to multiple stimulus locations. In contrast, phase mapping activated more extrastriate visual areas and was more efficient per run in achieving a statistically efficient response in a minimum …