Archive: CAP REU Project Offerings, 2013
Follow links below for more details on individual projects:
Thermodynamics of Strongly Coupled Matter — From Ultracold Atoms to Neutron Stars
Particle Astrophysics Monte Carlo Simulations and Real-Time Data Acquisition
Disentangling the Physics of Evolving Galaxies: Gas Flows and Black Hole Growth
Statistics of Galaxies in Cosmic Context
Visualizing Cellular Motility
Jellyfish Neuromechanical Pumping Triggered by Pacemakers
Fluid Flow in Valveless Heart Tubes
Parachuting in Stratified Fluids
Water Wave Motion and Mathematical Modelling
Model Construction and Analysis for Yeast Mitotic Spindle Structure
Model Verification and Analysis for Pediatric Airways Airflow
Microelectromechanical Device for Viscometric Diagnostics
- Thermodynamics of Strongly Coupled Matter — From Ultracold Atoms to Neutron Stars (Drut/Anderson)The calculation of thermodynamic properties from microscopic interactions (a Hamiltonian) represents a significant challenge for many-body theory. A variety of solution techniques can be used which are applicable in specific temperature regimes ranging from zero to “low,” “intermediate,” and “high” temperature. At low temperature, for example, a variety of Monte Carlo solution techniques are employed, whereas at high temperature a virial expansion can be used.
- Project #1 – Inverting Quantum Operators. To calculate properties in the low-temperature regime, one needs to compute the inverse of certain quantum operators. However, these are very ill-condititioned and therefore require preconditioning. This is a big problem in lattice quantum chromodynamics, and it remains largely unexplored in other areas of many-body physics. In this project you will investigate the design and application of preconditioners for strongly interacting fermions in multiple dimensions.
- Project #2 – The Quantum Virial Expansion. At high temperatures one of the most efficient methods is the virial expansion. In this project you will calculate the virial coefficients from first principles for a variety of thermodynamic observables. This will be done for a number of different interactions, and you will use the results to analyze their connection to solutions found by methods in low temperature regimes.
The thermodynamic properties of quantum systems are relevant to experimentally realizable systems in condensed matter physics involving for example quantum wires, ultracold atoms as well as multiple problems in low energy nuclear physics, like neutron matter in the crust of neutron stars. This effort will serve as a prototype for a larger effort to calculate the properties of 3D thermodynamic systems across a full range of temperatures. Here we will be able to see how the results from the various methods connect at the limits of their applicability in much easier to solve systems. These projects will involve use of numerical linear-algebra methods for the solutions of quantum few-body systems, fast Fourier transforms in multiple dimensions, and iterative linear solvers. [Will use: Matlab, Fortran, C++, or python, plus Linux.]
- Particle Astrophysics Monte Carlo Simulations and Real-Time Data Acquisition (Wilkerson/Howe)The Experimental Neutrino and Particle Astrophysics 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). Opportunities for computational projects include:
- Project #1 – Simulations. Develop and implement simulations for the Majorana Demonstrator or KATRIN detector systems. Learn to use a large scale Monte Carlo simulation code, including graphical displays. [Will use: GEANT4 and ROOT (both written in C++), python/Mac OS X, Unix.]
- Project #2 – Real-Time Data Acquisition. 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 tables. [Will use: ORCA (Object-oriented Real-time Control and Acquisition, written in Objective C), python/Mac OS X.]
- Disentangling the Physics of Evolving Galaxies: Gas Flows and Black Hole Growth (Kannappan/Hoversten)The RESOLVE survey is acquiring unprecedented spectroscopic data in a census of all galaxies over a wide range in mass within a large volume of the nearby universe. The two projects below involve working on RESOLVE’s core spectroscopic pipeline to optimize extraction of information with specific scientific goals.
- Project #1 – Unmasking Supermassive Black Hole Activity. Recent work has highlighted the presence of supermassive black holes actively accreting gas in the nuclei of dwarf galaxies, which are the most common type of galaxy. Usually, such active galactic nuclei (AGN) are detected by examining ratios of spectroscopic emission lines. In this project, the student will classify AGN vs. normal galaxies in the RESOLVE Survey. Initially the student will implement traditional line-fitting techniques for the classification and examine how the results correlate with independent evidence of AGN activity and/or its potential drivers. In dwarf galaxies this effort may be complicated by strong star formation, which can produce the same spectroscopic emission lines, mixing with the AGN lines and thus masking their signature. Therefore the ultimate goal of this project is to define a new spectral line fitting technique to decompose star formation and AGN emission and thereby more consistently identify AGN in dwarf galaxies.
- Project #2 – Searching for Tracers of Outflowing Gas. Gas flows into galaxies provide the raw materials for new star formation as well as the fuel for supermassive black hole growth. Yet strong bursts of star formation and energetic black hole growth also cause gas to flow out of galaxies, in the form of jets and winds. Understanding the interplay of gas inflows and outflows is one of the key challenges for modern studies of galaxy evolution. In this project, the student will explore independent and complementary signatures of gas outflows, for example high-velocity “wings” in the spectroscopic emission lines emitted by ionized gas, two-dimensional flow patterns in the galaxy velocity field, and/or spectroscopic absorption lines from outflowing gas backlit by a bright galaxy nucleus. The most promising technique(s) will be applied to data for galaxies in the RESOLVE survey, which will enable analysis of how outflow strength relates to inflow strength, an important but largely unexplored connection, especially for
dwarf galaxies.
Computational techniques used in these projects may include alternative fitting algorithms, extrapolation, spectroscopic stacking, 2D velocity field modeling, error analysis using Monte Carlo techniques, statistical tests, and code run time optimization. [Will use: IDL (a programming language built on C), Linux, possibly also python or IRAF.]
- Statistics of Galaxies in Cosmic Context (Kannappan/Stark)The RESOLVE survey is a multi-wavelength galaxy census spanning a large volume of the nearby universe, including diverse cosmic environments ranging from clusters of galaxies to large-scale filaments and walls. The two projects below involve application of statistical methods to interpret the distribution of shapes and masses of galaxies and larger cosmic structures in RESOLVE.
- Project #1 – Reconstructing the 3D Shapes of Galaxies. Galaxy shapes reflect their evolutionary history, especially for the smallest galaxies called “dwarfs.” For example, ultra-thin flat dwarf galaxies may live in “quiet” parts of the universe where no other galaxies disturb their disk-like shapes. On the other hand, rounder dwarf galaxies may live in places where other galaxies disturb them more often. Alternatively, a galaxy’s shape may depend more on its mass, as random motions tend to become more regular with increasing galaxy mass. In this project the student will test these hypotheses using data for galaxies in the RESOLVE survey. Building on this analysis, the student will use statistical computational methods to infer whether the intrinsic 3D shapes of galaxies (as opposed to the 2D shapes we see in projection) represent one basic type or multiple types, and further determine whether the answer depends on mass or environment. A possible extension would be to compare multi-wavelength and kinematic data to infer the typical amplitude of intrinsic galaxy asymmetries.
- Project #2 – Characterizing Large-Scale Cosmic Structure. The cosmic clustering of galaxies in the Universe has traditionally been quantified either using the number density of galaxies per unit volume or using the masses of distinct groups of galaxies, typically estimated from their collective light. In this project, the student will explore alternative metrics using data from the RESOLVE survey. Initially we will work with an existing code to compute the galaxy number density with the relevant volume for averaging defined in different ways. These results can then be used to compare and contrast with new metrics developed by the student, which will take advantage of our unique compilation of complete mass and velocity data. For example these data allow computation of group masses from galaxy orbital velocities (as opposed to just collective light) and densities from galaxy masses (as opposed to just galaxy numbers). We will use visualization and statistical techniques to identify metrics that offer new insight into the physical mechanisms underlying changes in galaxy properties in the context of cosmic structure.
Computational techniques used in these projects may include fitting and statistical tests, Monte Carlo techniques, 3D visualization, and code run time optimization. [Will use: IDL (a programming language built on C), visualization software, Linux, possibly python.]
- Visualizing Cellular Motility (Oldenburg)Methods for acquiring high-speed images of cells have become commonplace in the laboratory. While simply playing a “movie” of the cellular motion can be useful, we can gain even better insight into cellular processes by using computational algorithms to selectively “contrast” certain types of movement. In my laboratory, we use Optical Coherence Tomography (OCT) to visualize breast cancer cells as they proliferate in 3D tissue models. We have been monitoring fluctuations in these cellular clusters, with the aim of correlating them with the progression of the cancer. These fluctuations occur at different, characteristic time scales depending upon the mechanism underlying the fluctuation. This project will involve exploring different ways of characterizing the time-dependent data in terms of its Fourier spectrum to render parametric images of the tissue models. [Will use: Matlab on any OS.]
- Jellyfish Neuromechanical Pumping Triggered by Pacemakers (Miller/Hoover)Jellyfish movement is governed by coordinated pacemakers that trigger bell pulses. Understanding the coupled action of the nerves and muscles that govern the contraction and relaxation of the bell are central to understanding jellyfish locomotion. Also central to understanding the pumping mechanism are the signals generated by pacemakers that are then propagated through the nervous system. In addition to triggering muscular contraction, these signals also regulate the activity of the other pacemakers. The dynamics of pacemaker-pacemaker interaction are responsible for forward swimming and turning, but mathematical models for this system are still in need of development. The REU student will test and develop new pacemaker models that will be validated with measurements taken of live jellyfish in our lab. We will be numerically modeling (using C++/Data Tank) the biological models that describe the signals transmitted from jellyfish neurons and muscular tissue, along with the pacemakers associated with these pulses. Models developed in this project will later be used to trigger force generation in a fluid dynamic model of jellyfish swimming. [Will use: C++, Matlab, Data Tank, Mac/Linux.]
- Fluid Flow in Valveless Heart Tubes (Miller/Baird)Fluid flow is essential in transporting blood within most macroscopic animals. The adult human heart uses values to create unidirectional flow through the body. When our embryonic heart first forms, it has no valves but still produces flow in one direction. This is also similar to many invertebrate hearts that pump blood without the use of valves. This project will focus on several mechanisms for producing unidirectional flow in valveless hearts. The student will run immersed boundary code to simulate blood pumping, visualize the resulting flows, and analyze video footage of live invertebrate hearts. Three major pumping mechanisms will be investigated, with results analyzed via a number of techniques. Questions that will be addressed include 1) How do animals transport fluid without the use of valves? 2) Which pumping mechanisms work best for a range of parameters? 3) How does the size of the tube play a role in transport? 4) What is the best way to visualize large data sets to answer these specific questions? This project will involve running fluid structure interaction code to investigate a range of parameters, extracting relevant data using python scripts, and visualizing data with Visit, Paraview, and python. [Will use: C, C++, python, IBAMR, Visit, Paraview, Matlab, OSX, Linux, bash Shell scripting.]
- Parachuting in Stratified Fluids (McLaughlin/Falcon)We will study the behavior of parachutes falling through stratified fluids experimentally and theoretically and in particular focus on timescales for descent as functions of the geometry and stratifications. The modeling will use elementary fluid dynamics, and the computing will involve data analysis and digitization of video and still images. [Will use: Matlab, Data Tank, possibly FORTRAN or C, Mac.]
- Water Wave Motion and Mathematical Modelling (Camassa/McLaughlin/Khatri)Wave motion is ubiquitous throughout the physical world. Participants in this project will learn the fundamentals of wave propagation by a combination of experiments, mathematical and numerical modeling with what is arguably the most familiar type of wave propagation, that occurring at the surface of water. The student will begin by observing experiments in the Joint Fluids Lab 36m wavetank, assisting with both the preparation (setting water depths, instrumentation etc,) and data collection. Parameters corresponding to several regimes, in order of increasing complexity, from small to large amplitude waves, from narrow and wide channel dynamics, etc., will be explored and data will be visualized with the help of the DataTank software (available on the lab’s computers), thereby identifying trends, “discovering” physical laws, and predicting outcomes. For each regime realization, students will help set up simple Matlab codes to model the wave propagation and capture its essential qualitative and quantitative elements in mathematical formulations (such as dispersion of wave-trains, learning how to isolate main frequencies and wavelengths etc.). No previous background in programming with Matlab is assumed, and students unfamiliar with it will learn the basics on site working with simple assignments designed to develop confidence and explore the possibilities offered by both DataTank and Matlab numerical environments. This project will involve basics of data collection and visualization, Fourier decomposition of signals, and simple “method of lines” tools to simulate surface displacement is long wave models of wave propagation. [Will use: Matlab, DataTank.]
- Model Construction and Analysis for Yeast Mitotic Spindle Structure (Taylor/Hsiao)Construct geometric models to feed into Brownian-motion and nonlinear-spring simulations of the yeast mitotic spindle. Run these simulations on UNC’s BASS supercomputer (Brownian) or interactively on lab machine (mass/spring). Analyze the results (statistical analysis) to determine the behavior of different models and how well they compare to experimental results from confocal microscopy. Augment simulators as required to model new phenomena or structures. This project will involve writing custom code to produce geometric input files to match current models, running existing simulation programs on supercomputer and interactively, writing custom analysis code to parse the results of the simulations, and perhaps extending the simulation codes to handle new phenomena. [Will use: C++, python/SOFA, Blender, custom/Linux, Windows.
- Model Verification and Analysis for Pediatric Airways Airflow (Taylor/Quammen)Construct geometric models of specified test geometries for lattice-Boltzmann flow simulation being used on segmented 3D CT scans of infants with obstructed airways. Run GPU-based flow simulation codes on the resulting models. Compare the results to what is expected to evaluate the correctness and accuracy of the simulation. Work with mathematicians and medical collaborators to determine an effective set of analysis techniques for the resulting flow simulations run on patient data. Work with computer scientists to produce calculations of the resulting techniques. This project will involve writing custom code to produce geometric input files to specifications, running existing simulation programs interactively on GPU through 3D user interface, writing custom analysis code to parse the results of the simulations, and perhaps extending the simulation codes to handle new phenomena. [Will use: C++, Matlab / VTK, ITK, Qt / Windows.]
- Microelectromechanical Device for Viscometric Diagnostics (Superfine/Judith)There is a great need for miniaturized devices for point of care testing of patients for infectious disease, glucose monitoring and bleeding disorders. We are developing a technology that can measure the mechanical properties of fluids and can be miniaturized for convenient application in diverse settings such as the patient home, the surgical suite and the ambulance. The device consists of microfabricated posts that rotate about their surface connection point to move the fluid around them. When the fluid changes its viscosity, the posts do not move as much, and they then provide a quantitative assessment of the fluid rheology. This project will involve modeling the mechanical and actuation properties of this device, and understand how we can best design the device for actuation, apply drive signals to calibrate the device, and understand the sensitivity and range of its measurement capabilities. [Will use: COMSOL, Matlab.]
