# Archive: CAP REU Project Offerings, 2014

Follow links below for more details on individual projects:

- Biophysics: Statistical and Deterministic Analysis of Cell Mechanics
- Nuclear/Particle Astrophysics: Real-Time Data Acquisition
- Medical Physics: Improving nuclear spin polarization of 129Xe gas
- Quantum Theory: Signal and Noise in Many-Body Quantum Mechanics
- Quantum Theory: Phase Transitions in Strongly Interacting Systems
- Quantum Theory: Looking for the Wigner Crystal: Strongly Interacting Electrons
- Astrophysics: Populating Dark Matter Halos with Galaxies
- Applied Mathematics: GPU Random Walk Method for Elliptic and Hyperbolic Problems
- Biomedical Optics: Analyzing Dynamic Imaging Sequences of Airway Mucus Transport
- Biomedical Physics: Data Processing and User Interface Software Development for a Novel Blood Elastometer

**Biophysics: Statistical and Deterministic Analysis of Cell Mechanics (Prof. Superfine/Co-mentors Osborne and Cribb).**Cells are remarkable mechanical objects, able to move across substrates and in 3 dimensions, able to alter their shape to invade between other cells, able to divide into new cells and able to sense their mechanical environment to change their very identity. We are studying this behavior in a variety of ways including the application of forces to cells using magnetic beads, and monitoring the behavior of the cell shape, stiffness, tension, motility and cell differentiation. We need to develop methods for analyzing the 2d trajectories of the beads recorded as time series. Models for the motion include free diffusion, diffusion in a viscoelastic medium and confined diffusion. All of these relate to the motion of a bead or vesicle inside the cytosol of the cell. In addition, we seek to analyze directed motion of beads to learn about the activity of molecular motors used in active transport inside cells. The analysis routines developed will become part of an analysis pipeline for our high throughput system as applied to studies of basic cell biology as well as applied to cancer. [Will use: COMSOL and Matlab.]**Nuclear/Particle Astrophysics: Real-time Data Acquisition (Prof. Wilkerson/Co-mentor Howe).**The Experimental Nuclear and Astroparticle Physics group is involved in experiments aimed at understanding neutrino properties, searching for dark matter, and performing tests of fundamental symmetries. Currently our two major experimental efforts are the MAJORANA DEMONSTRATOR 76Ge based search for neutrinoless double beta decay and the Karlsruhe Tritium Beta Decay Neutrino Mass experiment (KATRIN). We have projects related to real-time data acquisition (DAQ) associated with our research activities. There are a variety of potential projects spanning development of code to control fast electronics hardware modules, advanced scripting, near-time display tools, and support of smart phones and tablets. The project will utilize ORCA (Object-oriented Real-time Control and Acquisition) software system designed for dynamically building flexible and robust data acquisition systems for nuclear and astroparticle physics experiments. [Will use (depending on project): JavaScript, PHP, CouchDB, CouchApp, D3.js, Web-based, iOS, Objective C, Mac OS X, and OpenGL.]

**Medical Physics: Improving nuclear spin polarization of 129Xe gas (Prof. Branca/Co-mentor Zhang).**In nuclear magnetic resonance experiments 99% of the time we detect the nuclear spin of the hydrogen atom. Other atoms are difficult to detect because of their lower abundance and because of the low nuclear spin polarization we can achieve at conventional magnetic field strengths. Spin hyper-polarization solve this problem by increasing the nuclear spin polarization of select atoms by several orders of magnitude. For noble gas atoms like 129Xe, nuclear polarization can be increased by a process called spin-exchange optical pumping (SEOP). The efficiency of this process depends on a variety of experimental factors among which are gas partial pressure, temperature distribution, and laser light distribution in the optical cell in which the SEOP process occurs. With this project, we want to achieve optimal SEOP efficiency through a simulation-guided optimization of temperature and flow conditions inside the hyper-polarization optical cell. The increased polarization will then allow us to use HP Xenon gas in MR experiments as a probe for tissue perfusion and oxygen exchange at the lung level. [Will use: COMSOL Multiphysics and Matlab.]**Quantum Theory: Signal and Noise in Many-Body Quantum Mechanics (Prof. Drut/Co-mentor Anderson).**In this project you will analyze methods to overcome the signal-to-noise problem in Monte Carlo simulations of quantum gasses. As such, various computational “estimators” will be explored to understand what characteristics lead an effective extraction of signals in quantum statistical distributions. Ultimately, your objective will be to determine the best strategy to compute physical observables such as the pressure and the energy, and to use quantum Monte Carlo data to demonstrate your results. [Will use: Mathematica, fundamental programming skills.]**Quantum Theory: Phase Transitions in Strongly Interacting Systems (Prof. Drut/Co-mentor Anderson).**Phase transitions of matter from one state to another are accompanied by discontinuities and/or divergences in their associated thermodynamic observables. A qualitative change will also occur in the quantum statistical distributions generated by Monte Carlo calculations of such systems near transition. [Will use: Mathematica, Fortran/C.]**Quantum Theory: Looking for the Wigner Crystal: Strongly Interacting Electrons (Prof. Drut/Co-mentor Anderson).**In this project you will attempt to find a low-density phase of an electron gas known as the “Wigner crystal”, where the Coulomb interaction dominates the physics. This phase has proven difficult to study theoretically with computers, and little is known about it. You will find this phase through adaptation of a quantum Monte Carlo code, and analysis of the quantum statistical distributions that it generates. This is a potentially long-range project that will start with simpler systems and build up towards the full thermodynamic many-body problem. [Will use: Mathematica, Fortran/C.]**Astrophysics: Populating Dark Matter Halos with Galaxies (Profs. Kannappan & Erickcek/Co-mentor Eckert).**The Cosmic structure reflects a competition between the expansion of the universe and the attractive power of gravity, leading to continual growth of both voids of empty space where the expansion wins and condensations of matter where gravity wins. Modern cosmology suggests that the visible matter collected into galaxies is embedded in vast dark matter “halos”, and galaxies in groups share common mega-halos within which “subhalos” – slight overdensities of dark matter within the larger shared halo – surround each galaxy. The masses of dark matter halos are difficult to estimate directly from observations, but theoretical simulations of structure formation provide clear predictions of how many halos of different masses should exist – this frequency distribution is called a “mass function.” One technique for comparing observations and numerical simulations is “halo abundance matching,” in which groups are rank-ordered by an observable property expected to trace total mass, such as the integrated luminosity of all the galaxies, and then assigned 1-to-1 to the halos found in a simulation, from the most massive halo on down. In this project, the student will first construct a code to analyze the “mega-halo” mass function using this approach, then explore extensions of the method to create a “subhalo abundance matching” code capable of matching galaxies within groups to subhalos in simulations. This work fits into a longer term effort to measure and understand variations in the galaxy-to-subhalo mass relation, especially as a function of the larger halo mass in which the subhalo is embedded, with important implications for when and how subhalos form within or merge into larger halos. [Will use: python, IDL, plus Linux.]**Applied Mathematics: GPU Random Walk Method for Elliptic and Hyperbolic Problems (Prof. Mitran/Co-mentor Malahe).**An intriguing alternative to grid based methods for solving partial differential equations is to reformulate the problem as an averaging operation over random walks in the computational domain. The approach is overly expensive for standard CPU implementation, but is inherently parallel and low-communication, and thus of interest for GPU coding. The two projects explore this method for elliptic problems (similar to the Laplace equation) and hyperbolic problems (similar to the wave equation). A typical example is electromagnetic waves propagating through media of complex shape, such as the tree configurations shown below from a photonic crystal application arising in photovoltaic cell design. Initial training in GPU coding will be provided. [Will use: CUDA, FORTRAN, Python]**Biomedical Optics: Analyzing Dynamic Imaging Sequences of Airway Mucus Transport (Prof. Oldenburg/Co-mentor Blackmon).**We inhale thousands of pathogens every day. These are trapped by a mucus layer that lines the surface of our airways and acts as a protective layer. Studying the properties of airway mucus allows us to understand and monitor the progression of diseases, such as COPD and cystic fibrosis, that affect the respiratory system. The Oldenburg lab has been measuring mucus properties by introducing gold nanoparticles and performing optical coherence tomography (OCT) imaging. We have been collecting OCT images of in vitro models of the airway where mucus, bronchial cells, and nanoparticles are all moving dynamically. These image “stacks”, comprised of spatial data over time, can reveal how each of these components is moving with a different characteristic time and light signature. In this project, the student will perform analysis of dynamic OCT images (in both space and time) to look for correlations between motions of the varying components. In particular, is there any relevance to the thickness of the mucus upon the rate at which is it moving? Are the nanoparticles more or less diffusive near the mucus surface? [Will use: MATLAB, some Mathematica and C++]**Biomedical Physics: Data Processing and User Interface Software Development for a Novel Blood Elastometer (Prof. Oldenburg/Co-mentor Li).**Instruments for monitoring blood coagulation are crucially important for patients undergoing surgery or who suffer from inherited coagulopathies. The Oldenburg laboratory has developed a novel blood elastometer that operates on the principle of resonant acoustic spectropy to analyze blood samples placed within a microwell. This project aims to integrate all instrumentation control and data analysis software into one single user interface to aid in our ongoing research efforts and to provide a user-friendly interface that may enable future clinical application. The existing software components are able to control hardware to send electromagnetic force waveforms upon the sample and to record subsequent damped driven harmonic oscillations, which is a fundamental physics problem. The current system runs under LabView with some Matlab-based analysis components. [Will use: LabView and MATLAB.]