Senior Projects of the Class of 2010
(updated October 7, 2009)
Cody Allen with Prof. Anthony Jack (Dept. of Cognitive Science)
Quantitative Metrics for Describing Topographic Organization in Individuals
Visual areas in the brain of both monkey and man contain organized maps of the visual field. These maps can be measured using fMRI while participants view visual stimuli presented at different locations relative to a fixation point. However, current methods for topographic mapping are purely qualitative in nature, and involve using visual inspection to search for consistent patterns in pseudo-colored figures. We seek to develop a method of quantitatively describing topographic organization on the cortical surface, so allowing us to describe differences between individuals, and between distinct visual areas in occipital, parietal, and frontal cortex. In addition to developing quantitative metrics, more meaningful color-coded topographic maps will be created with the use of overlaid gradient fields. A goal of this research is to identify the neural basis for individual differences in visuo-spatial ability.
Andrew Balko with Glenn Starkman
Controlling Eclipses to Improve X-Ray Angular Resolution
To improve X-ray angular resolution of existing and future telescopes, it is possible to use the properties of natural eclipses. An occulting satellite would facilitate the study of a wide variety of sources especially in the X-ray spectrum. The eclipses cast by an X-ray occulting steerable satellite would overcome the limitations of natural eclipses by being regulated and reproducible. The gains in angular resolution using this method would be significant in future space observatories and may be applied to other wavelengths, though X-ray interferometry should make vast improvements in the field in the long term. A type of Eclipse Mapping Method involving optimization techniques is implemented with a conjugate gradient algorithm, supplemented by laboratory test-bed experiments in order to help determine the usefulness of such an endeavor.
Frederick Davey with Charles Rosenblatt
Surface Memory Effect for Liquid Crystals
PRELIMINARY ABSTRACT: Samples of liquid crystals are prepared by sandwiching two pieces of glass coated with a polymer, and inserting the liquid crystals in between. The polymers act to orient the liquid crystal molecules relative to the glass surface, however not all angles of rotation are necessarily fixed. When only one surface has an azimuthal constraint (using a rubbed polyimide, for example), and the other does not (as with the polymer polymethyl methacrylate) the imposed azimuthal orientation propagates to the surface without the constraint. A memory effect has been observed where, after some time, the secondary surface begins to constrain the liquid crystals in the same orientation as the primary surface. The causes and extents of this effect are unknown, and of primary interest in this project is the time it takes for the memory effect to be noticeable. Analysis of the effect will be done by aligning the liquid crystal in the bulk by an external electric field. The resulting orientation distribution through the cell can be determined by analyzing the intensity and polarization of a beam of light passing through the sample.
Michael Ding with Timothy Atherton
Liquid Crystal Configurations from Conformal Mapping
The method of conformal mapping can be applied to solve Laplace's equation in complicated 2-D geometries. First approximations for nematic liquid crystals obey Laplace's equation and so we may apply a conformal map to determine the configuration of liquid crystal, and hence obtain the energy and consequently the phase diagram. Conformal mapping allows for the preservation of angles in the complex plane. Conformal maps for convex polygons have been explored. However, non-convex geometries are more problematic. Our research will be focused on investigating energy distributions of nematic liquid crystals in non-convex n-sided polygons. The Schwarz-Christoffel mapping, specific conformal map, will be applied to these non-convex polygons. Furthermore, we intend to apply a recently discovered formula due to Crowdy to consider nematic liquid crystals confined to multiply connected domains.
Steven Ewart with Andrea Romani (SOM, Dept. of Physiology & Biophysics)
Role of Cellular Mg2+ in Modulating Collagen Deposition and Interleukin Release in Ito and Kupffer Cells
Introduction: Magnesium ion (Mg2+) is the second most abundant cation after potassium within mammalian cells, including liver cells. At the cellular level, Mg2+ has been reported to regulate more than 180 enzymes, especially those involved in cell cycle regulation and glucose metabolism. Acute and chronic ethanol administration reduces total Mg2+ content in liver tissue. A decrease in cellular Mg2+ content has been associated with increased pro-inflammatory cytokines release and altered collagen deposition.
Hypothesis: In the present study I will test the hypothesis that a reduced cellular Mg2+ content within Kupffer and Ito (stellate) cells is sufficient to generate an increased production of Il-2 and Il-6 and an increased collagen deposition, respectively, or it predisposes to these changes in the presence of ethanol administration.
Methods: Kupffer and Ito cells isolated from rat livers will be maintained in culture in the presence of varying extracellular Mg2+ concentrations (i.e. 0.4, 0.8 and 2 mM). Cell cultures will be challenged by addition of different doses of ethanol ranging from 0.01% to 1% for varying period of time spanning from 15 min to 96 hours. Cellular Mg2+ content will be measured by atomic absorbance spectrophotometry (AAS). Release of IL-2 and IL-6 in the extracellular medium will be assessed by Elisa assay. Collagen deposition will be determined by 3H-proline incorporation. mRNA levels for Il-2, Il-6 and collagen will be determined by RT-PCR.
Matthew Hakes with Corbin Covault
Design and Construction of Optical Concentrators
When ultra high energy particles strike the upper atmosphere, they emit Cherenkov radiation. By studying the radiation, we hope to determine the direction of their travel and ultimately where they come from which is currently unknown. Optical concentrators are used to limit the viewing angle, allowing the experimenter to select a portion of the sky and focus the light from that portion into a detector. The main considerations in the design of a concentrator are performance characteristics and ease of construction. Computer simulations will be done to investigate the performance of various concentrator designs. The designs which exhibit desirable characteristics will be evaluated on how easily they can be built. The one which is the best compromise between performance and ease of construction will be built and tested to ensure it has the characteristics predicted in the simulation.
Kyle Helson with John Ruhl
Sapphire Half-Wave Plate Characteristics
The polarization of the cosmic microwave background radiation (CMB) contains imprints of gravity waves from the early universe. The Spider telescope is a balloon-borne telescope designed to extensively investigate this polarization. Using six rotating sapphire half-wave plates, the light from the CMB will be rotated before being measured by six separate bolometers. Characterization of these half-wave plates, along with their quartz anti-reflective coatings is necessary for their implementation. Spectra will be taken using a Fourier Transform Spectrometer and the ACBAR cryogenic test dewar. Data will be analyzed to determine whether the HWP's meet specifications.
Gareth Kafka with Robert Brown
Imaging by Magnetic Particles with a Nonlinear Field Response
Magnetic Particle Imaging (MPI) is a procedure akin to Magnetic Resonance Imaging (MRI) with a key fundamental difference. MRI is a noninvasive procedure which is used by doctors to form an image of the inside of a body. Aside from being expensive, however, the technique is fundamentally limited in resolution by the small signal-to-noise ratio (SNR). MPI would also be used as a method to image the body, but it also involves the introduction of magnetic particles into the sample. These particles have a nonlinear response to magnetic fields and could thus amplify the SNR and bind to the tissues of interest, giving very accurate spatial detail. The technique has the potential for very high resolution, but it is not yet a well understood effect. The goal of this project is to find a deeper understanding of this phenomenon. Also, we will investigate the extent to which we may test the technique, in collaboration with the physics group in the Radiology Department. In general, we aim to improve our understanding of the theoretical model and our experimental capabilities for investigating the technique.
Michael Kelley with Volodimyr Duzhko
Spectroscopic Studies of Charge and Energy Transfer Processes in Self-Organizing Heterogeneous Photovoltaic Materials
In response to growing needs for renewable and pollutant-free energy resources, conversion of sunlight into electricity by solar cells is one of the most promising alternatives. Utilization of organic photovoltaic materials allows for improving the cost-effectiveness of the fabrication approaches. However the cost-efficiency of state-of-the-art organic photovoltaic devices needs to be further improved. Self-assembled organic materials, such as liquid crystals, possess efficient electronic and optoelectronic properties due to a high degree of structural order and can be fabricated by inexpensive approaches. In this project, we study the structural, optoelectronic, and charge transfer properties of heterogeneous organic photovoltaic materials produced through the co-assembly of p-type and n-type semiconducting liquid crystals. When these liquid crystals are coaxed to self-assemble into nanostuctured blends, photo-generation of free charges at the p-n interface and their collection at the electrodes can be improved. This research will be concerned with the measurement of the self-assembly and charge transfer in mixtures of 2,3,9,10,16,17,23,24-Octakis(octyloxy)-29H,31H-phthalocyanine and N,N′-bis(1-hexylheptyl)-perylene-3,4:9,10-bis-(dicarboximide) or N,N’-Ditridecylperylene-3,4,9,10-tetracarboxylic diimide through steady-state and transient UV-vis-NIR optical absorption spectroscopy to determine the structure of the energy levels, photoluminescence spectroscopy to determine the charge transfer efficiency, and time-of-flight measurements to determine the charge transportation efficiency. Comparison of the measurements of these materials as solutions, aggregate fibers, and solid films will reveal changes in their properties at different levels of aggregation. This research will help determine the viability of using liquid crystal photovoltaic structures to satisfy the need for renewable energy in the near future.
Guozhi (Joe) Liang with Corbin Covault
Prototype Cherenkov Detector Design & Deployment
The High Energy Astrophysics lab at the university focuses much of its efforts in the Pierre Auger Observatory collaboration. As a new observatory, set to be deployed in Colorado, progresses through the design and development stage, one task, which would further enhance the data collection, is the prototyping, testing, and deployment of a Cherenkov radiation detector. The design of this detector involves light collection with a non-optical concentrator during a cosmic ray shower. A coincidence mechanism using scintillation and photomultiplier tubes triggers data collection on the main detector. Retooling and renewing the prototype detector and its auxiliary components is the primary task of this senior project. Replacing the scintillation material, building and testing mobile high voltage supplies, as well as assembly and testing of a new set of photomultiplier tubes are all early tasks which would retool the detector. Such retooling would involve thorough testing of the components in the detector. This renewing of the detector ultimately leads to field deployment and the data collection of cosmic ray shower events.
Michael Macdonald with Xuan Gao
Large Scale Graphene Transistor Arrays
Graphene, a single atomic sheet of carbon atoms, was recently isolated by separating single layers of graphite and received tremendous interest in electronic applications. The widely used mechanical exfoliation method used to obtain single layers of graphene, however, is uncontrolled and not useful for manufacturing large scale electronics. We will explore various contact printing methods for producing large scale graphene transistor arrays. The goal of this project is to achieve few layer or single layer graphene transistor arrays on centimeter size silicon wafer with high yield.
Benjamin McCabe with Rolfe Petschek
Animating Tessellations of the Plane with Statistical Models
(started in fall 2009 and will be resumed and completed in spring 2010)
Artists, particularly M.C. Escher, have made many attractive tessellations of the plane, incidentally illustrating many of the two dimensional space groups. Such pictures may have different space groups or attractiveness based on the patterning and symmetry of various colors in the pictures, and in defects in such symmetries. Many physical systems have "broken" symmetries in which an unspecified state (e.g. color) can be determined by the state of its neighbors, as in antiferromagnetism. Much is known about such ordering in various two dimensional cases, including various statistical models thereof. In this project we will combine art and physics by animating an Escher-like tessellation of the plane, using a Monte-Carlo or similar simulation of a statistical model to change the colors or other attributes of the tessellation. As the formation of long range order in such models, and the resulting potential fractional dimensionality of the patterns is thought to have aesthetic value, this will hopefully achieve all of providing an interesting illustration of two dimensional statistical models, an interesting piece of modifiable art, and a potential screen-saver.
Seraina Murphy with Robert Brown & Fraser Robb (GE Healthcare)
Going Beyond Protons for MR Study
Although high-field MRI coil testing has been a popular research subject for years, the use of carbon-13 in imaging is relatively new. The potential market for 13C dual-tuned coils has also increased due to the growing popularity of 3T magnets in medical imaging. However, the number of available dual-tuned coils is limited as much of the 13C research done today is at higher fields (7T and 11.7T). The goal of this project is the theoretical design and construction of carbon-13 coil prototype—to test a new high-frequency birdcage head coil for use in high-field MRI and for today’s high multiples of receive and transmit channels. The specific application is for a field strength of 3T and 32-channels. The aim is to see this new device through to a working model, and to model its performance with new circuit analysis techniques applicable to the higher frequencies, concluding in designing and implementing changes as needed for a successful prototype. Examples of challenges will involve altering the spacing between the end rings and legs to optimize the performance. The main physics challenge will be to find effective inductance and capacitance components to use for circuit analysis at high frequency. Lumped circuit analysis requires modifications when the magnetic field wavelengths inside of a dielectric human tissue become comparable to the coil size. Understanding the RF physics at high fields is at the cutting edge of MRI coil design today.
Nicholas Reinsvold with Charles Rosenblatt
Surface Orientation of Chiral Liquid Crystals
It is well documented that placing chiral liquid crystal molecules on an achiral surface causes the molecular orientation to twist locally due to the chirality of molecules. This experiment will use two distinct chiral molecular species in a mixture. One molecule will have a left twist while the other molecule will have a right twist, in an attempt to produce a mixture with no overall twist. The two chiral molecules must be distinct species in order to prevent twisting but still retain chiral properties which would be lost if the molecules were the same species. The mixture will be placed on an achiral surface treated for alignment along a specific azimuthal axis." The molecules will be examined to determine if rotation occurs after the initial alignment. This experiment will be supervised by Professor Charles Rosenblatt and Yoonseuk Choi.
Andrew Rosenberger with Kathleen Kash
STM Study of Self Arranging Hexagonal Nano-lattices
Hexagonal lattices of Benzene rings doped with sulfonic acid groups attached to substituted biphenyl units are promising, new structures being produced by Macromolecular Science and Engineering. When deposited on surfaces, these molecules can form stacked hexagonal arrays with a hole size of 20 to 500 nm, which could have applications in fuel cells, water desalinization, and as thermoelectric materials. In order to ascertain the usefulness of these materials and proper synthesis techniques, the use of scanning tunneling microscopy (STM) and an atomic force microscope (AFM) to analyze samples of these molecules deposited on surfaces is necessary. By determining the size, aggregation, and quality of shape of the molecule for various synthesis conditions, more can be learned about the properties and usefulness of these materials.
Joshua Rubin with Justin Sydnor (Dept. of Economics)
Projection of the Solar Tech Industry as Motivated by Underlying Principles
Within the United States, and elsewhere in the world, there is a growing concern over the limited resources that are useable as energy sources. Technologies such as mono-crystalline and poly-crystalline solar cells, well established low efficiency and high cost power sources, have begun to be replaced by a new generation of less efficient but significantly cheaper photovoltaic cells. New thin-thin film and photovoltaic collector arrays are just approaching parity in energy generation. This “grid parity”, the point at which it is economically identical between solar cells and “dirty” energy sources, is an important stage in the development of any electrical technology. By comparing the newer approaches to more traditional processes through the concept of the diffusion of innovations one should be able to project the role of these new technologies. Analysis of recent trends for these solar technologies might be able to predict the market structure of the solar industry well into the future. One might hope to observe recognizable technological adoption trends in data available from the EPA and other sources. This project will use baseline comparison of the adoption of thin film photovoltaics and collector photovoltaics, over regional and scale differences, to predict the future of this industry. Through statistical analysis techniques, run in a program such as Stata, this project will present time-series comparisons of the different technologies and their potential roles as components of the electrical grid.
Aaron Shojinaga with Jie Shan
AC Conductivity of Silver Nanoparticles
(started in fall 2009 and continuing into fall 2010)
The electrical conductivity for bulk metal is described by the well-known Drude model. As the size of the metal is reduced to the nanometer scale however, the energy levels become discrete, rather than continuous. The average spacing between adjacent energy levels in a metal nanoparticle is called the Kubo gap, and is related to the Fermi energy of the metal and the size of the nanoparticle. For instance, in a silver nanoparticle of 3-nm diameter containing ~103 atoms, the Kubo gap is around 5-10 meV. Therefore, at room temperature when the thermal energy is greater than this gap, the electrical conductivity will be the same as in bulk metal. As the temperature is lowered however, the Kubo gap becomes significant and the nanoparticle becomes an insulator. Although the DC properties of this metal-to-insulator transition are well understood, the experimental observations and theoretical description for AC conductivity are much less comprehensive. In this project I will investigate the AC conductivity of silver nanoparticles in an interesting frequency range that corresponds with the Kubo gap of the nanoparticles. Conductivity will be measured using terahertz (1 THz ~ 4.2 meV) time-domain spectroscopy based on a mode-locked laser. The frequency dependence of the complex conductivity will be investigated as a function of the sample temperature to understand the metal-to-insulator transition.
Lily Stanley with Xuan Gao
Nanowire Transistors for DNA Sensing
As electrical devices have gotten smaller nanowires have become a novel material for use in fabricating these devices. Using nanowires transistors can be made on the nano scale. I will be using these transistors to create a biomolecule sensor, with the goal of highly sensitive detection of DNA. The nanowires will be synthesized through a ‘bottom up’ (chemistry-based) approach and the nanowire transistors fabricated using lithography techniques. Both physical adsorption and covalent bonding will be explored to attach probe peptide nucleic acid (PNA) onto nanowire surface to capture the target DNA. Electrical measurement of the nanowire transistor will be used to detect and study DNA hybridization. Effects like base mismatch between probe and target strands and charge screening in ionic solutions will be investigated as DNAs hybridize/dehybridze on nanowire surface.
Kyle Strodtbeck with David Farrell
Measuring the Density of Bone
Density is a fundamental property of condensed matter and some recent work suggests that there may be a direct relationship between it and magnetic susceptibility for biological materials. Magnetic susceptibility may therefore provide a method to image the density of the human body, which would be of considerable value in medical diagnostics. However, checking this relationship requires measuring the in-vitro density of biological samples. Because of their porous structure, inhomogeneity, and restricted lifetime, this is a challenging task. The present investigation is focused on bone, which offers the most stable biological material for physical measurements. In preliminary studies, using the standard water immersion method, it has been found that changes in density of several percent can occur on immersing bone samples in water. Furthermore, these changes are not a monotonic function of immersion time, presumably reflecting a complex interplay between the diffusion of water into the sample, which tends to increase the density, and sample expansion, which has the opposite effect. Bone samples will be collected, for a variety of different species, and a specially designed container will be utilized to accurately determine their density at room temperature. Careful attention will be paid to reproducibility and experimental uncertainties. The non-monotonic behavior mentioned will be studied and compared between species to see if understandable patterns emerge. Depending on the progress made with these bone studies, the experiment may be extended to the more difficult case of (soft) biological material.
Daniel Thomson with Glenn Starkman
Dark Matter Capture by Binary Systems
Dark matter is thought to pervade the galaxy, making up over 90% of its total mass. Dark matter particles traveling through multi-body bound gravitational systems, such as binary star systems or planetary systems, can scatter off those bodies and become gravitationally bound. The rate of capture will depend on the relative masses of the star and planets as well as their orbital parameters. By numerically integrating the orbits of dark matter particles through such binary or multi-body systems we will characterize the capture efficiency. This will allow us to better determine the importance of dark matter capture to so-called indirect signals of dark matter, such as dark-matter-dark-matter annihilation.
Michal Usowicz with Volodimyr Duzhko
Self-Assembled Solar Cells of Nanostructured Architectures
(started in spring 2009 for completion in fall 2009)
Currently the most efficient solar cells are made of silicon and are not a viable technology due to high device fabrication costs. It is hoped that organic semiconductors and hybrid systems with nanostructured inorganic materials can be used to construct less expensive, yet efficient, solar cells. The purpose of this project is to develop a new fabrication approach that would enable self-assembly of organic electron-donor and electron-acceptor molecules into blends of a quasi one-dimensional architecture. We will study exciton dissociation at the donor-acceptor interfaces and transport of electrons and holes along the quasi one-dimensional donor and acceptor channels in photovoltaic device architectures as well as in a number of simpler model geometries. Better understanding these fundamental photo-physical processes would allow for further optimization of the device performance.
Corbett Walsh with Prof. George Dubyak (SOM, Dept. of Physiology & Biophysics)
Regulation of ATP release in Astrocytes
Cell volume regulation is of particular physiologic importance in neural tissues due to the adverse effects of even small changes in brain volume. In the brain, extracellular ATP acts as an autocrine / paracrine signaling molecule and participates in volume regulation by activating a family of P2 receptors. While significant advances have been made regarding the signaling controlling ATP release, the actual conduits for the export of ATP have not been clearly defined. Investigations of ATP release from astrocytes have identified several ubiquitously expressed large channels as candidate conduits for ATP release; non-junctional “gap-junction hemichannels” comprised of connexin or pannexin subunits, volume sensitive organic anion channels, and Maxi-anion channels. I plan to investigate what channel or channels are responsible for ATP release using the C6 rat line.
Alexander Wijangco with Glenn Starkman
Constraining Dark Matter with X-Rays
Dark matter is a generic term for an exotic class of particles that might explain the observed gravitational movements of stars and galaxies. However, despite the best efforts of several experiments, dark matter particles have gone undetected and the constraints which allow the possibility of these particles continue to become stricter. However, a possibility that has been less explored is whether dark matter particles can exist in excited states; particularly if they can reach these states by interacting with normal matter. If so, then evidence for such a process could be detected through byproducts of the eventual decay of a dark matter particle from an excited state to a ground state, such as x-ray emission. This project will examine the hypothetical possibility of such a process, constraints that can be placed upon it with existing data, and possible methods of the detection for such a process.
Sander Zandbergen with Tom Shutt
Reflectivity Measurements of Critical Materials for the LUX Dark Matter Experiment
The key component of the Large Underground Xenon (LUX) detector is measuring scintillation light from liquid xenon in order to detect particle dark matter in the form of Weakly Interacting Massive Particles (WIMPs). Optimal performance requires highly efficient transportation of photons to the photomultiplier tubes (PMTs), so all other materials must be highly reflective. The two prime materials are a large surface of polytetrafluoroethylene (PTFE) and some metal for electric field producing grids. I will use the group’s prototype liquid xenon detector in situ, with liquid xenon scintillation light at a vacuum ultraviolet (VUV) wavelength of 175 nm, to take measurements from samples of several critical LUX components. These measurements will be compared to a light collection Monte Carlo simulation, and reflectivity values will be extracted. This will allow for proper selection of materials and full understanding of LUX light collection.