Browsing by Subject "College of Science & Engineering"

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Abstract Syntax Contextualization Framework for Debugging Attribute Grammar Specifications
(2024) Feraru, Matthew;
In this thesis, we explore an aspect of debugging attribute grammar (AG) specifications. AG frameworks in themselves are high-level languages that allow a programmer to specify the syntax rules and semantics of a new programming language. The debugging of AG specifications is often done by interactively traversing abstract syntax trees (ASTs) that represent a parsed program in a metaprogram. The goal of such debugging is to find AG specifications with semantic rules that observe correct inputs but incorrect outputs—the possible bugs of AG specifications we consider. For large programs, ASTs may be difficult to understand by a programmer; graphically rendering ASTs in a debugging interface is challenging and still does not make it straightforwardly easy to understand ASTs relative to source code. Resultantly, we propose a textual way to use source and source-like syntax to represent the location of a navigated-to AST node relative to its position in an entire AST and highlight any notable features of the tree, such as the application of rewrite rules. This contextualization framework of abstract syntax tree nodes has been prototyped to work on Silver [1] specifications, but it is applicable to any AG framework since it only relies on the core features of the AG paradigm itself.
Activation of the Inferior Olive
(2011-04-13) Walter, Camille
The inferior olive (IO) is a group of nuclei in the brainstem and is the sole origin of climbing fibers to the cerebellar cortex. While complete functions of the IO are unknown, it is believed to contribute to temporal processing. Functional magnetic resonance imaging (fMRI) studies have shown activation of the inferior olive by unexpected sensory stimuli. In this study, we tested the IO’s sensitivity to stimulus timing change to determine the time-change that is most efficient in activating the IO. We scanned normal human subjects while viewing sequences of visual stimuli and recognizing stimuli that deviated from isochronous stimuli by fifty to eight hundred milliseconds. The behavioral results showed that the subjects’ performance increased with timing change. The fMRI data were analyzed using event-related statistical parametric mapping of the hemodynamic responses; then we could see the activation of the inferior olive during all of the different stimulus timing changes. The 300 millisecond stimulus timing change produced the most activation of the IO, with time-changes of 200 to 600 (but not 50, 100, 700 or 800 ms) producing significant but less robust activation than 300 ms. These results were consistent with classical conditioning animal studies and indicate that reliable and robust activation of the inferior olive can be achieved in humans; they also can potentially be used to study diseases in which the IO is implicated.
Alcohol Dehydrogenases Deletion to Increase Yield of Isobutyrate
(2011-09-06) Zhou, Jun
Methacrylic acid is one of the most crucial chemical feedstocks in the material industry and there is a high quantity demand of methyl methacrylate (MMA) which is the ester form of methacrylic acid. Every year million tons of methyl methacrylate is produced to synthesize polymethyl metharylate (PMMA) which is a thermoplastic material and it is used as a light or shatter-resistant alternative to glass. Therefore, to come up with a method for producing methacrylic acid and methyl methacrylate becomes a popular topic of research in biosynthesis area. There are several traditional methods being used in the industry and the most common one is reacting acetone with hydrogen cyanide to generate acetone cyanohydrins and then treat it with sulfuric acid to form methyl methacrylate. However, because of side products and reaction condition, these two traditional methods require high quality of controlling harmful chemicals and hard to increase the yield of target product. What’s worse, the reactants are not renewable and emission will damage the environment. However, we have designed a new biosynthesis strategy to produce methacrylic acid. In this proposed work, glucose is converted to isobutyrate or 3-Hydroxyisobutyrate. By using oxidative dehydrogenation of isobutyrate and dehydration of hydroxyisobutyrate we could generate methacrylic acid
Assessment of O-ring Seal Performance by Measurement of Acoustic Emission Signals
(2011-04-13) Sun, Zhen
O-rings are commonly installed in fluid systems for sealing purpose. There is ongoing research towards improving O-rings’ sealing performances by using adaptive elastomeric materials at the Department of Mechanical Engineering at University of Minnesota. As part of seal development the performance of the seal has to be assessed. In this research a test stand for measuring leakage was constructed and leakage measurement was demonstrated as the seal leakage was measured by Monitoring Acoustic Emission (AE) signals. The test stand was constructed in which a specified load or a specified displacement can be applied to an O-ring held between flat plates, high pressure air introduced to the inside of the seal and AE due to leakage measured. The scope of this research was to try to quantify leakage rate of in use O-ring as a function of AE signals. The AE signals were measured as a function of volumetric air flow rate Q, working fluid pressure P, O-ring counterface force F and seal AE sensor distance d. Results showed that the Root Mean Square (RMS) values of AE signals increased with Q, P and F but decrease with d. Results also showed that the frequency spectrums of AE signals were wideband with multiple peaks at different frequencies. The physical interpretation of frequency spectrum was discussed but was not fully explained.
Biaxial Testing of Cadaveric and Decellularized Rat Heart Ventricles
(2011-08-11) Vanderheiden, Sarah
Whole organ decellularization is a promising technique to create 3D scaffolds necessary to generate bioartificial organs. However, due to the vital role of tissue mechanics in the contraction of the heart [3], it is necessary to assess the changes to the myocardium caused by decellularization. Previous studies have demonstrated that heart tissue is anisotropic [2]. Ventricle tissue fibers are aligned in the circumferential direction, and that orientation is preserved after decellularization [1]. The circumferential orientation of fibers is responsible for a higher stiffness in that direction than the longitudinal direction [1]. It has also been proved that decellularized tissues have a higher tangential modulus than cadaveric tissues [1].
Binding Residues of Intergrase (IN) and Its Host Cofactor Ini1
(2011-08-11) Wang, Nayi
Purpose Integration of viral DNA into its host chromosome is an important step in the HIV replication process (7). HIV integrase is an important enzyme which plays an essential role in inserting the vital DNA into the host chromosome and replicating HIV (6). It is one of the three enzyme will complement the therapeutic use of HIV protease and reverse transcriptase inhibitors. Though combining antiviral therapy with protease and reverse transcriptase inhibitors has proved the improvement of antiviral therapy for treatment of AIDS. However, because there are still some problems for drug resistance and toxicity, we still need to do some additional researches on the antiviral drugs. Integrase is a good target for antivirals due to its necessity for HIV replication. In addition, integrase can only use a single active site to accommodate two different configurations of DNA substrates, which will constrain the process of HIV to develop drug resistance to integrase inhibitors (7). To achieve the goal of crystallizing IN, our lab has been focusing much attention on the proteins that are binding partners of IN or host cofactors known to alter the biochemical characteristics of HIV-IN. One such host cofactor is SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 or also known as Ini1/SNF5. The goal of my research will be to express, purify, and characterize various Ini1 fragments as a potential chaperone in the crystallization of IN. And to find Ini1’s correct residues which binds to IN. Methods We cloned three different Ini1 constructs into the Sumo-Pro expression vector. We used PCR to get three lengths of fragments and inserted our construct into the SUMO vector which encodes a SUMO expression chaperone as well as a 6-Hisitidine affinity tag for IMAC purification. We tested for expression of the Sumo-Ini1 fragments through common methods utilizing the T7 based expression systems engineered into the Sumo-Pro vector. After small scale expression (5ml or 100ml cultures) and lysis via sonication, Ini1 was affinity purified with Ni-NTA and then by size-exclusion chromatography. Once the best behaved Ini1 construct was identified, we produced the protein in multiple 1L scale and purified to >90% purity. The SUMO tag includes an N-terminal recognition site that is recognized by the SUMO protease and will be removed. The purified protein then will be screened for crystal conditions. Results Size exclusion chromatography showed us a single, homogeneous, peak when Ini1 protein fragment from residue 170 to residue 250 was dialyzed with IN. In addition, after purification, both IN and Ini1 was contained in this single peak. This confirmed that we had a Ini1 fragment that was selectively binding to IN and forming a complex upon mixing and dialyzing. The discovery of this stable complex is the first step in our attempts to stabilize IN for our crystallographic pursuits.
CMOS Operational Amplifier
(2011-08-11) Wood, Sam
An operational amplifier (op-amp) is a voltage amplifier with a differential input and a single-ended output. Op amps are important building blocks for a wide range of electronic circuits. They are among the most widely used electronic devices today, being used in a large array of consumer, industrial, and scientific devices. They may be packaged as components, or used as elements in complex integrated circuits.
Comparison of carbonylation in young and old rat skeletal muscle
(2011-04-13) Willard, Isaac
Proteins, DNA, and lipids in most tissues become carbonylated due to oxidative stress. Skeletal muscles are particularly susceptible to such carbonylation because of the conversion from metabolic energy to mechanical energy during contraction. This project focuses on the relative levels of carbonylation in intermyofibrillar mitochondria (IFM), the subsarcolemmal mitochondria (SSM), the cytoplasm, and the extracellular space of skeletal muscle. The morphology and function of muscle cells change in response to ageing and development. To measure the variance in carbonylation patterns with respect to both development and age, muscle tissue from young and old animals is analyzed. A labeling agent is used to label mitochondria red and carbonyl groups green. Confocal microscopy can take images of the labeled tissue and overlay them to show the mitochondria that have been carbonylated. The amounts of uncarbonylated and carbonylated mitochondria are compared between young and old tissue to determine how carbonylation changes with age.
Computation of Defects in Materials
(2011-08-11) Veit, Max
Abstract The purpose of this project is to investigate and assess, using the MATLAB computer language, some numerical methods used in several elds of computational molecular dynamics. First a theoretical model of a one-dimensional chain of atoms was studied. The atoms in this chain would interact based on the Lennard-Jones potential energy function. Several algorithms were investigated that found con gurations of the chain where the total potential energy was lowest. Aspects of the one-dimensional chain were then carried over into a model of a two-dimensional system of atoms. For this model a full simulation of the movement of the atoms in the system was used to study the system. It was found that one of the simplest atom con gurations, a square lattice pattern, was unstable. In the simulation, this structure evolved over time into several disconnected regions, called grains," of a more stable triangular-hexagonal lat- tice pattern. These structures are similar to crystal grains in real-world polycrystalline materials. Some basic computational thermodynamics (more specically, Langevin dynamics) was also used in the simulation. It was found that by regulating the temperature, or average kinetic energy, of the system, the formation of grains could be controlled to some degree.
Coupling and Metathesis Copolymerization of Conjugated Polymers for Organic Photovoltaics
(2011-04-13) Slowinski, Bradley
In order to meet an ever increasing energy demand, photovoltaic technologies must be explored. As a low cost alternative to inorganic photovoltaics, organic photovoltaics offer a unique combination of flexibility and processability. Nevertheless, these devices should not be viable until their efficiency is improved.
Detecting Helium Vapor Pulses in Low Temperature Transmission Experiments
(2010-09-13) Maunu, Tyler
Bose-Einstein condensation, originally predicted in 1924 by S. Bose and A. Einstein, refers to a quantum configuration at low temperatures in which a large portion (the condensate fraction) of particles collapse into the ground state. Figure 1 shows the phenomena in Rb-87, a less complicated system that superfluid 4He, but the first experimental evidence of BEC . A superfluid is described as a phase of matter with zero viscosity, infinite conductivity, quantized vortices, and zero entropy. It is also characterized by the Cooper pairing of atoms and not electrons. It is generally accepted that superfluidity exhibited in Helium-4 is a consequence of composite boson exhibiting behavior that is associated with Bose-Einstein condensation. It has been proposed that experiments observing the transmission characteristics of a slab of Helium-4 superfluid that is subjected to a pulse of Helium-4 vapor. Figure 3 shows the set-up of our experimental cell. In the current experiment, we use a fiber optic cable to heat a slab of Helium-4 superfluid, which results in a pulse of vapor. This pulse of vapor is then allowed to impinge on the bottom of a slab of suspended Helium-4 atoms. The resultant atomic flux is then observed on a series of superconducting bolometers, which allow us to see the energy levels of transmitted Helium-4 atoms. Bolometers are essential for the detection system in this experiment because they are designed to function at the low temperatures needed to carry out this experiment, and allow for detection speeds on the order of 1 μs. Our experiment aims at pinning down Helium-4 superfluid as a Bose-Einstein condensate by observing the transmission characteristics of a Helium-4 superfluid slab. The purpose of my research was to understand and test the detection system being used to measure these transmission characteristics.
Dynamic Modelling and Control of Exoskeleton Gantry Robot
(2024) Hajare, Eesha;
This thesis presents the development and analysis of dynamic model of an exoskeleton gantry used to perform brain studies in freely moving mice for neuroscience experiments. The dynamic of model of the exoskeleton gantry comprised of X and Y stages is developed, and relevant system characteristics like bandwidth and stability are studied using theoretical model to predict the system behavior. The predicted bandwidth of the open loop system is found to be 1.9Hz and 3.8Hz for the Stage X and Y respectively using the theoretical model. The open loop system was further verified experimentally using LABVIEW and an experimental model was generated using computer software. According to the experimental results, the open-loop bandwidth of the X and Y stages was found to be 2.3 Hz and 2.76 Hz respectively. Furthermore, the open loop system is also used to gauge the stability of the closed-loop and the gain and phase margin are studied for the same purpose. According to theoretical studies, it is expected that the bandwidth of the open and closed loop system is expected to increase with a decrease in payload. The gain margin and phase margin are predicted theoretically and verified experimentally are well above the determined threshold of 2dB for gain margin and 450 for phase margin, this ensures the stability of the closed loop exoskeleton system. Moreover, the closed-loop bandwidth of the system is predicted using the theoretical model and an admittance control framework is proposed. The predicted closed-loop bandwidth for the exoskeleton gantry is found to be 19.2Hz and 16.4Hz for X and Y stages respectively. Furthermore, preliminary experimentation of the gantry with admittance control implementation suggests a closed loop bandwidth of 46Hz for Stage X.
The Effect of Anti-Epileptic Drugs on 4- AP Induced Seizures in Rat Brain Slices
(2011-04-13) Podritz, Courney; Rodenkirch, Rebecca
Epilepsy is a neurological disorder that affects an estimated 50 million people, nearly one-third of whom do not have sufficient control over its symptoms. It is characterized by the onset of hypersynchronous neuronal activity known as seizures. The Netoff lab is focused on understanding the dynamics of epilepsy at the cellular and neural network levels. Our project focuses on how certain antiepileptic drugs alter the connections between neurons to prevent seizures. In this project, we performed extracellular recordings in rat hippocampal brain slices using a microscope and micropipette electrode setup. The brain slices rested in low-magnesium artificial cerebrospinal fluid containing 4-aminopyridine, a potassium ion channel blocker that causes seizures. Once seizures began, we introduced the anti-epileptic drug ethosuximide to the fluid and observed the effect on the seizures. We have seen that the amplitude of the seizure activity is much lower overall after the drug is applied. Often the drug also reduces the length and/or frequency of the seizures. When we stop adding the drug, the original seizures resume, creating a “wash-out” effect as the drug is no longer present. If we can discover the precise cause of seizure onset and the mechanisms by which anti-epileptic drugs affect it, we can develop more effective treatments for epileptic patients.
Effects of Surfactants on The Yield and Size of Gold Nanorods
(2011-02-03) Lee, Kuang Chin
Evaluating and Monitoring BMPs with Networked Wireless Sensors
(2011-04-13) Winterhalter, Maia
Minnehaha Creek and the Mississippi River, like most other bodies of water, have contaminants flowing in them during all times of the year. These contaminants impact the environment differently depending on their nature; some are less harmful than others even though they might have a higher concentration in the water. Turbidity and high chloride concentrations are two indicators that a body of water is impaired, either for human use or ecologically. Best Management Practices, or BMPs, can help diminish these contaminants in many ways, such as settling small particles (turbidity) out of the water. I have been analyzing data collected from in-situ wireless sensors, comparing data upstream from various BMPs to downstream, and also analyzing the data to determine if water quality standards are violated. Stormwater outfalls into the Mississippi were monitored and compared with standards as well, in order to observe if these outfalls increased the concentrations of pollutants, particularly chloride or the turbidity, in the river over time. By determining the BMP performance, water quality around the metro can be monitored more accurately and the quality of its surface water will be secure into the future.
Evaluating Best Management Practices Using Wireless Sensor Networks
(2011-04-13) Thell, Kaitlin
The increase in urbanization has taking a toll on the quality of streams. Due to this, there has been an increased concentration of pollutants in urban streams. Pollutants including but are not limited to: herbicides, suspended solids, petroleum hydrocarbons, heavy metals, and pesticides. Storm water best management practices (BMPs) are tactics used to manage or lower pollutant loadings. Examples of BMPs are stormwater ponds used for settling particles and wetlands to remove organic pollutants. Currently, stream water quality is evaluated using a technique called grab sampling where the stream is sampled at a determined interval, which could be every week or every other week. However, this method is not the best because it does not capture the short term spikes of sediment or pollutants that occur during events such as rainstorms that could be problematic. In this project, grab sampling and a system of sensors called wireless sensor networks were used to capture real time data. By using these two techniques, the sort term spikes and how they were removed by the environment were able to be observed.
Exploration of Small Molecule Reduction via Transition Metal Complexes Supported by Novel Trianionic Cryptand Ligand Systems
(2011-04-13) Mullikin, Alex
The reductions of small molecules (CO2, CO, N2, and O2) have been studied as an interesting, cheap method for the formation of valuable chemical feedstocks. While prices of petroleum on the rise, processes such as the reduction of CO-2 into methanol are necessary to ease our use from non-renewable sources of fuel. To achieve these reductive processes, my research has been focused on the design and synthesis of novel ligands. Following the synthesis of these novel ligands, they will be metallated with late transition metals (Zn, Co, Fe, and Mn). A Zn complex which is supported by a trianionic, tetradentate cryptand ligand has been synthesized and characterized with X-Ray Crystallography. This metallated ligand, along with the fore mentioned metals, will be reacted with various small molecules and analyzed for the ligand’s ability to reduce these molecules.
Finding the Way With Cyclopath
(2011-04-13) Pitchford, David
In the past few years, Cyclopath has become an outstanding example of a geographic wiki, or "geowiki", and a valuable resource to Twin Cities cyclists. For site creator Reid Priedhorsky, it has also been an opportunity to study recommender systems in a new context. In his doctoral thesis, he studied a variety of possible heuristics for predicting users' ratings of byways in the cities. However, his research only compared these predictors at the lowest, node level. This project extends the research to study how different predictors lead to the recommendation of different routes to users. This leads to higher level questions such as: How 'different' are two predictors? How 'different' are the routes that they generate? Does one generate 'better' routes than others? The ensemble predictors tested call into four main groups, which are similar within themselves but distinct from each other in the routes they generate. Though quantification of the differences in routes has been simple, evaluating the routes holistically--and the predictors that generated them--is beyond the scope of automated analysis and will have to be done by cyclists themselves.
Formation and Aging of Ferrihydrite Nanoparticles in the Presence of Organics
(2010-10-11) Weber, Nolan R.
The object of this research project is to determine how adding organic compounds during crystal formation affects the physical properties of the ferrihydrite crystals that are formed. Ferrihydrite is a nanomaterial with no bulk counterpart and forms naturally in nature. Through these experiments, we hope to elucidate more details about out how the formation occurs in nature. Once we figure out how the formation occurs, we can manipulate it for various industrial and environmental applications.
Integrated Surface Acoustic Wave Device on an Aluminum Nitride Wafer
(2011-08-11) Ramirez, Johnny
Surface acoustic wave (SAW) devices are essential for many signal processing applications, ranging from filtering a signal, creating a device for military use, or using them to create a cell phone with better reception. Surface acoustic waves are generated by applying an electric signal to a piezoelectric substrate, which then turns the electric signal into an acoustic wave. SAW devices contain rectangular-looking figures known as interdigital transducers, essential for converting the acoustic wave back into an electric signal at the output. Therefore, two SAW devices are required for this effect to occur. The piezoelectric substrate used in this project is Aluminum Nitride (AlN), which allows the user to send a high frequency to the SAW device and operate at high temperatures.

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