4:15pm, Room 46 Culler Hall, unless otherwise noted
|Date||Speaker||Title and Abstract or Field of Research |
|January 29||No seminar|
|Biological Physics candidate #1||Local and global DNA remodeling within DNA repair mechanisms Abstract|
|Biological Physics candidate #2||Prospects for Nanopore Sequencing: Direct and Simultaneous Force and Current Measurements of Single-Stranded DNA in Synthetic Nanopores Abstract|
|Biological Physics candidate #3||Light in Medicine: Using quantitative optical spectroscopy for non-invasive in vivo sensing of biological tissues Abstract|
|February 13||Biological Physics candidate #4||The Physics of the Genome: 3D DNA Organization in Health and Disease Abstract|
|Biological Physics candidate #5||Terahertz pulses: from probing conductivity in nanomaterials to biomedical applications Abstract|
Miami University Career Services
|What Career Services can do for you|
University of Northern Iowa
Exploring the Electronic Properties of Layered Materials Abstract
Univ of Illinois at Champaign-Urbana
|The Physics of Baseball: You Can Observe A Lot By Watching Abstract|
|No seminar|| |
Illinois State University
|Physics education research|
Old Dominion University
|Ultra cold atomic gases and light meet in one dimension Abstract|
Penn State University
|Academic Integrity among physics and engineering students|
Wright State University
|Mathematics of musical harmony|
National High Magnetic Field Laboratory
|Magneto-optical spectroscopy in high magnetic fields|
Annual Physics Scholarships &
Titles and Abstracts
Biological Physics Candidate #1
Local and global DNA remodeling within DNA repair mechanisms
Exogenous and endogenous factors continually damage the genome, which encodes the instructions for synthesizing our biological machinery. Left unchecked, these damage sites – particularly double strand breaks – can result in deleterious mutations and chromosomal rearrangements that lead to cell death and cancer. Fortunately, cells have evolved several pathways to detect and repair damaged DNA. Using single-olecule approaches, we have gained insight into aspects of the local and global DNA remodeling that occurs within these repair mechanisms. First, the MRN complex serves as an initial responder to DNA damage, and we obtained direct evidence of an important early step in local DNA processing that is performed by MRN and is required for the recruitment of additional repair proteins. Second, Holliday junctions are structured genetic elements that are central intermediates within a repair pathway. We provide additional data on the global rearrangements of the junctions and propose a novel mechanism used by anti-microbial hexapeptides to inhibit a major repair pathway.
Biological Physics Candidate #2
Prospects for Nanopore Sequencing: Direct and Simultaneous Force and Current Measurements of Single-Stranded DNA in Synthetic Nanopores
Nanopore-based DNA sequencing has emerged as a rapid, low-cost single-molecule technique in which individual bases are identified as the DNA molecule passes through the pore. In order to determine the signal available for sequencing a single-molecule of DNA in a synthetic nanopore, direct and simultaneous measurements of the forces and currents associated with the translocation of a single-stranded DNA molecule tethered to an AFM cantilever (a) were performed. These measurements indicated that ssDNA either translocated the nanopore in a “stick-slip” motion characterized by multiple stretching and rupture events or the ssDNA translocated with a constant net force between 10 and 60 pN (b). Minute <1 pN fluctuations in the force and <20 pA fluctuations in the current while the molecule was extracted under a constant force were observed every 0.35-0.60 nm (c) in homopolyers and heteropolymers of ssDNA and is consistent with the spacing between unstretched or partially stretched ssDNA. These results imply that synthetic nanopores have sufficient resolution to sequence individual bases of ssDNA.
Biological Physics Candidate #3
Light in Medicine: Using quantitative optical spectroscopy for non-invasive in vivo sensing of biological tissues
Optical spectroscopic methods provide a non-invasive means to dynamically study structural and functional properties of living tissue in their native states. In this presentation I will describe two experimental optical techniques - diffuse reflectance spectroscopy and diffuse correlation spectroscopy - and discuss how experimentally measured signals are analyzed to extract biologically relevant information about blood oxygenation and flow in tissues. I will present results from experiments demonstrating the practical applications of these methods, particularly for detection and treatment-monitoring of cancers in animals and humans.
Biological Physics Candidate #4
The Physics of the Genome: 3D DNA Organization in Health and Disease
The two-meter-long DNA sequence that makes up the human genome must somehow be packaged into a microscopic nucleus while maintaining its important biological functions, such as serving as the template for gene transcription and eventual protein production. My research investigates the basic features of this genome folding and how it is disrupted in disease. Using a molecular technique called Hi-C, I capture and identify all the interactions between different sequence regions of the genome and then quantitatively characterize the structural features at different length scales. These experiments reveal the fractal nature of the 3D genome structure. To further characterize the structure, I first investigate how it responds to perturbation in two disease states: the potentially cancer-causing chromosomal translocations formed after a DNA double-strand break and the collapsed nuclear structure observed in the premature aging disease Progeria. In my future research directions, I plan to extend these perturbation studies by artificially exerting physical stresses on the cells and monitoring the properties of the genome structure’s response to these stresses.
Biological Physics Candidate #5
Terahertz pulses: from probing conductivity in nanomaterials to biomedical applications
Recent progress in the field of ultrashort pulsed lasers has led to the development of practical tabletop sources of broadband terahertz (THz) pulses as well as ultrasensitive THz detection techniques, allowing scientists to take advantage of this historically inaccessible region of the electromagnetic spectrum between the infrared and microwave bands. Ever since, THz technology has enjoyed rapid growth and has already made significant impact in many areas including materials science, security, quality control, as well as medicine. In materials, broadband THz pulses are ideal for probing dynamics of free carriers and collective excitations, phonon resonances, as well as other phenomena. I will discuss how we used THz spectroscopy to study percolative carrier transport in silicon nanocrystal films and dynamics of the insulator-metal phase transition in a nano-granular vanadium dioxide film over picosecond time scales. In biomedical applications, unique THz spectroscopic signatures of many important biomolecules and sensitivity of THz radiation to the cellular environment make THz imaging a promising new diagnostic approach. At the same time, we have recently demonstrated that exposure to intense, picosecond-duration THz pulses affects DNA integrity, cellular repair functions, and gene expression in human skin tissue, suggesting potential therapeutic applications. However, the mechanisms by which intense THz pulses induce those effects are presently not known, and future experiments analyzing interactions of various cellular constituents with broadband THz pulses is key to understanding them.
Andrew Stollenwerk, University of Northern Iowa
Exploring the Electronic Properties of Layered Materials
Layered materials such as graphite consist of two-dimensional molecular sheets held together by weak electrostatic forces. The weak interlayer binding makes it possible to separate the crystal into single molecular sheets. These two-dimensional crystals can have properties that differ significantly from the “mother crystal.” Perhaps the most well-known of these two-dimensional crystals is graphene, formed by peeling away a single layer of graphite. Graphene in its purest state is strong, light, and an excellent conductor of heat and electricity. The seemingly limitless potential applications combined with the need to understand the fundamental physics have made graphene a superstar of condensed matter physics. This makes other layered materials jealous. As such, this colloquium will explore some of the other similarly structured materials that have been overlooked as well as several techniques used to study the electronic properties of crystals that are inherently lacking in the third dimension.
Alan Nathan, Univ of Illinois at Champaign-Urbana
The Physics of Baseball: You Can Observe A Lot By Watching
Following Yogi Berra's words of wisdom, I will use high-speed video clips to highlight some of the interesting physics underlying the game of baseball. The talk will focus on the subtleties of the baseball-bat collision, the intricacies of the flight of a baseball, and many other things. I will investigate some very practical questions and show how a physicist goes about trying to answer these questions. Some examples:
• What is the "sweet spot" of a bat?
• How does the batter's grip affect the batted ball?
• Why does aluminum outperform wood?
• What determines how far a fly ball travels?
• How much does a curve ball break?
• What's the deal with the knuckleball?
The talk should have something for everybody, whether your interest is baseball, physics, or the connection between them.
Mark Havey, Old Dominion University
Ultra cold atomic gases and light meet in one dimension
Quantum optics in ultra cold and high-density but not quantum degenerate, atomic gases is a little explored and promising area of study. Among the fascinating possibilities are (a) quantum hologram creation in diffusive and optically dressed samples, (b) development of random lasing, or a photonic bomb, (c) Anderson localization of light, and (d) formation of superradiant and subradiant collective states of the atomic ensembles. A common feature of these dynamical systems is the role that spatial disorder can play on the light-atom dynamics. Particularly intriguing physics may occur when the spatial dimensionality of the systems is reduced such that light propagation is limited to a quasi – one dimensional configuration.
In this presentation the broad physics involved is discussed, with examples drawn from both classical and quantum systems. On the classical front, I present and discuss results from a project studying one-dimensional localization of light through scattering from microscope cover glass slips and also from a roll of transparency film. In a second area of application, transmission of a tightly focused light beam through a cold and dense atomic cloud is studied. We find that the eponymous Lorentz-Lorenz shift, a widely accepted result first published around 1880, is not a priori applicable to the case of a gas of nearly immobile atoms. The atomic density dependent effect expected to lower the atomic resonance frequency in fact increases it in a dense and ultracold atomic gas.
This research is supported by the National Science Foundation