Here are a few examples of excellent student work from summer 2013!


Field: Physical Oceanography

Title: Understanding Diffusivities and Bottom mixing in ocean models through programming and plotting model data

Student Researcher: Jumoke Opeyemi

Mentor: Vittorio Canuto, PhD, Adjunct Professor, Atmospheric Science, NASA Goddard Institute for Space Studies, Columbia University

Abstract: The main purpose of the project was to identify the strongest diffusivities within the bottom mixing in ocean model results and analyze why those areas receive such strong bottom mixing. To understand the biological systems of the Earth the best place to start is the oceans. Oceans are very important in the everyday processes that protect the Earth, but it most important to try to understand the tides, turbulence, the nature of hurricanes and tornadoes and lastly the controversial issue global warming. The research involved scrutinizing ocean bottom mixing to aid in understanding global warming and how to address it. Scientists James Lovelock and Chris Rapley found that mixing the oceans can reduce global warming as the ocean can be fertilized and decrease carbon dioxide in the air. This idea is not new and led to increased interest in ocean mixing. The research reported here is physical oceanography focusing on bottom mixing. The core of the research was identifying areas where ocean mixing was the strongest and seeking to understand why those areas were the strongest.


Field: Physics

Title: Effects of Demagnetization on Ferromagnetic Thin Films

Student Researcher: Mackenzie J. Coleman

Mentor: Andrew Kent, PhD, Professor of Physics, New York University

Abstract: An atomic force microscope was used to create images of nanoscopic ferromagnetic samples using magnetic force microscopy. Cobalt platinum multilayers were demagnetized to allow for random out of plane magnetic domain alignment. The samples were demagnetized along the easy axis, so there was an observable decrease in nominal domain size as the number of repeats in the cobalt platinum layers increased. This was due to the tendency of dipoles to align vertically through many planes instead of horizontally throughout one. While the data wasn’t entirely in conjunction with this tendency, overall it showed a slight trend towards an indirect relationship between domain size and number of erromagnetic and nonmagnetic repeated layers in the samples.


Field: Mathematics

Title: Nonlinear Dynamics and Music: The Appearance of Melodies in Chaotic Systems

Student Researcher: Sophie Connor

Mentor: Trushant Majmudar, PhD, Clinical Assistant Professor of Mathematics, New York University, Courant Institute of Mathematical Sciences

Abstract: Chaotic dynamics has been an area of great intrigue and discovery over the past four decades. Chaotic systems have been applied to a variety of fields of study, including cardiology, meteorology, engineering, and cryptology. Some have even ventured to explore the connections between music and nonlinear dynamics. Using a combination of basic MatLab and Java programming, this work employs several one-dimensional mapping strategies to display the numerous properties of nonlinear systems such as bifurcation, period-doubling, and both periodic and aperiodic behavior. Using these systems with the proper parameter values and initial coordinates, the values calculated with each successive iteration of the model are normalized and applied to generate pitch, tenor, and other musical properties. The extreme sensitivity of these systems to initial conditions and parameter variations allows them to produce values and, in turn, notes that cycle into a dramatic assortment of melodic or fugue-like lines recognizable as music. The compositions produced ranged from completely chaotic noise to free, jazz-like lines to regularly cyclic, melodic pieces.


Field: Chemistry

Title: The Use of Multiple Complementary Approaches including NMR Spectroscopy to Examine the Structure and Dynamics of Multidrug Resistant Proteins

Student Researcher: Nadia Bon

Mentor: Nathan Traaseth, PhD, Assistant Professor of Chemistry, New York University

Abstract: The structures of Small Multidrug Resistance (SMR) membrane proteins were analyzed using multiple complementary approaches to determine how the proteins are better able to eliminate antibiotics from bacteria. Techniques such as fluorescence are widely used to study how ligands, such as drugs, bind to proteins. However, these techniques do not penetrate the protein deeply enough to obtain a complete structural analysis. The Traaseth lab at New York University is using NMR (Nuclear Magnetic Resonance) spectroscopy to reconstruct proteins and examine protein residues using strip plots. Specifically, SugE which is a lesser known protein was purified and studied using a fluorescence and resistance assay as well as an isothermal titration calorimetry (ITC) with TPP and ethidium bromide. The results will be used in a comparative study to determine the adaptability of SugE and its potential as a transport agent.


Field: Chemistry

Title: Mixed Peroxyketals as Potential Intermediates for the Formation of Endocyclic Peroxides

Student Researcher: Amy Chan

Mentor: Keith A. Woerpel, PhD, Margaret and Herman Sokol Professor of Medicinal Chemistry, New York University

Abstract: Some natural and synthesized molecules with endocyclic peroxide functionality are biologically active as anti-cancer and anti-malarial agents. However, there are a limited number of methods to install peroxides into a molecule. Use of a cobalt-catalyzed peroxidation reaction to install a peroxide next to an alkyl group have been successful in the past. Attempts to install a peroxide next to a heteroatom using this method, have not been attempted, but could provide possible pathways to useful intermediates in endocyclic peroxide formation. This study shows that cobalt-catalyzed radical peroxidation reactions of silyl-protected enol ethers were successful, but peroxidation of a pivaloyl-protected enol ester was unsuccessful. Cobalt-catalyzed peroxidation of other functionalities is still being looked into.


Field: Chemistry

Title: Developing a Fluorescent Assay for Histone Deacteylases: Quantum Yield and Rates of Proposed Assays

Student Researcher: Olivia Iles

Mentor: Daniela Buccella, PhD, Assistant Professor of Chemistry, New York University

Abstract: Fluorescent probes are extremely valuable tools in the study of cell biology and biochemistry. They provide high sensitivity, minimal invasion, and the potential advantage of real-time analysis. These benefits explain the wide use of fluorescent assays in studying cell-level chemical activity. Due to the popularity of studying histone deacetylase (HDAC), an enzyme involved in post-transcriptional histone modifications, there is a high demand for accurate and effective HDAC assays, which could be provided by a fluorescent assay. This study seeks to develop a highly effective fluorescent probe to investigate the activity of histone deaceylases.