Bulletin of the American Physical Society
APS March Meeting 2013
Volume 58, Number 1
Monday–Friday, March 18–22, 2013; Baltimore, Maryland
Session F46: SPS Undergraduate IV |
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Sponsoring Units: SPS Chair: Crystal Bailey, American Physical Society Room: Hilton Baltimore Holiday Ballroom 5 |
Tuesday, March 19, 2013 8:00AM - 8:12AM |
F46.00001: Density Functional Study of the structural properties in Tamoxifen Romeo de Coss-Martinez, Jorge A. Tapia, Ramiro F. Quijano-Qui\~nones, Gabriel I. Canto Using the density functional theory, we have studied the structural properties of Tamoxifen. The calculations were performed with two methodological approaches, which were implemented in SIESTA and Spartan codes. For SIESTA, we considerate a linear combination of atomic orbitals method, using pseudopotentials and the van der Waals approximation for the exchange-correlation potential. Here we analyzed and compared the atomic structure between our results and other theoretical study. We found differences in the bond lengths between the results, that could be attributed to code approaches in each one. [Preview Abstract] |
Tuesday, March 19, 2013 8:12AM - 8:24AM |
F46.00002: Cytotoxicity of Gold Nanoparticles with Varying Concentration and Under Low Dose Environmental Radiation on Human Embryonic Kidney 293 Cells (HEK-293) Shalana Crudup, Bruce Braender, Cristina Iftode, Tabbetha Dobbins Nanomaterials are increasingly being used in medicine. Most research surrounding the health and safety effects of nanomaterials examine the cytotoxicity of nanoparticles alone. Few studies, as this one does, examines the combined effects of nanoparticle concentration and radiation exposure on cytotoxicity to human embryonic kidney 293 cells (HEK-293). Nanoparticles injected in the body are supposed to undergo biodegradation once they are done their specified task, however, some do not and accumulate in the cells (particularly at the liver and kidney) and this causes intracellular changes. Examples of intracellular changes are the disruption of organelle integrity or gene alterations. This will cause the cells to die because the cells are very sensitive to changes in their pH. The experiments reported here focus on the cytotoxicity of gold nanoparticles as a function of varying particle concentrations and also with and without exposure to UV radiation. [Preview Abstract] |
Tuesday, March 19, 2013 8:24AM - 8:36AM |
F46.00003: Migration Modes in Cancer Cell Motility Di Wu, Helim Aranda-Espinoza Cancer cell metastasis is a result of secondary tumor proliferation after single or collective cancer cell migration from a primary tumor. The biophysical mechanisms of cancer cell migration and transmigration through the body vasculature, while investigated, is not extensively quantified. In general, directed cell motility is traditionally viewed as the result of lamellipodia generation through which the cell moves by extending an actin protrusion and adhesion beneath its plasma membrane. However, cancer cells also exhibit motility through blebbing, which involves momentary membrane detachment from the actin cortex, membrane expansion and retraction. While blebbing, cancer cells do not form cell-substrate attachments as with lamellipodia. In vitro studies of single cancer cell migration through microfluidic microchannels of constant or linearly changing widths model in vitro conditions of single cell migration through capillary pores. We study both modes of motility and observe that cancer cell migration using lamellipodia or blebbing depends on channel width. Drug treatments to manipulate the cytoskeleton demonstrate that cancer cell migration changes speed but not the mode of migration. [Preview Abstract] |
Tuesday, March 19, 2013 8:36AM - 8:48AM |
F46.00004: Developing a Novel, Interdisciplinary Approach to Study Protein Unfolding Ian Bentley, Justin Link The ability of a protein to function is a direct result of its ability to properly obtain its native, folded structure. In order to determine the structural stability of proteins and to gain knowledge of their folding mechanism, we must develop protocols that allow us to monitor the controlled unfolding of proteins. Here, we investigate the stability of cytochrome $c$, a well-studied, model protein, under denaturing conditions using circular dichroism (CD) and fluorescence. Using either a chemical denaturant (Guanidine HCl) or heat, we can cause a protein to gradually unfold. The changes in the fluorescence and CD spectra can provide insight into the stability of proteins by providing us with thermodynamic parameters such as the Gibbs free energy, melting temperature and enthalpy. Research in this lab has been explored with mutant proteins and change in CD signal, however further work must still be done to observe their unfolding monitored by fluorescence. This technique will allow us to determine which regions of native cytochrome $c$ have the greatest impact on the protein folding process. The objective of this session is to present recent work in developing a protocol to observe the unfolding of wild type and mutant proteins with fluorescence. [Preview Abstract] |
Tuesday, March 19, 2013 8:48AM - 9:00AM |
F46.00005: Optimization of radiation damage to proteins using X-ray nanofocusing optics Selwa Boularaoui, K. Evans-Lutterodt, S. Lee, A.F. Isakovic The need to understand protein structure and perform treatment lead to the use of X-ray and particle-based radiation. Since the use of such radiation has undesirable side effects, mostly through the damage to proteins, it is important to continuously work on decreasing radiation damage. We outline the proposal to use the kinoform refractive optics to focus X-rays on the nanoscale to minimize the radiation damage to protein crystals under study. These optics devices are nanofabricated from low-Z elements (silicon, diamond) and can be used at synchrotron X-ray radiation facilities. We discuss the automated setup that performs nanopositioning of the nanofocusing element, and collects the chemical and structural protein solution under study. We offer simple mathematical models in irradiation and in treatment that help optimize the radiation parameters. [Preview Abstract] |
Tuesday, March 19, 2013 9:00AM - 9:12AM |
F46.00006: Driving Sodium-Potassium Pumps With An Oscillating Electric Field: Effects On Muscle Recovery In The Human Biceps Brachii Matt Bovyn, Wei Chen, Olivia Lanes, Jason Mast Dr. Chen has developed a technique called synchronization modulation, which uses an oscillating electric field to increase the rate at which the sodium-potassium pumps in the cell membrane work. Because the sodium-potassium pump is integral in the recovery of skeletal muscle fibers after an action potential, we investigated the effects of applying synchronization modulation to muscles which had already undergone fatigue due to repeated action potentials during exercise. Fatigue was induced in human subjects' biceps brachii through isometric contraction. Surface electromyography measurements of fatigue index were used to quantify how the muscle recovered over the minutes following fatigue, both when synchronization modulation was applied and when it was absent. The preliminary results were inconclusive, but it is hoped that in later work it will be shown that applying synchronization modulation is effective in increasing the rate at which the muscle recovers to its initial state. This would demonstrate not only that synchronization modulation can be successfully applied to human muscle, but also that it has many potential applications in sports medicine and novel disease treatments. [Preview Abstract] |
Tuesday, March 19, 2013 9:12AM - 9:24AM |
F46.00007: Driving Sodium/Potassium Pumps with an Oscillating Electric field: Effects on Muscle Fatigue Olivia Lanes, Matthew Bovyn, Wei Chen Dr. Chen has developed a technique called Synchronization Modulation, which has already been proven to be an effective tool in synchronizing and speeding up the sodium/potassium pumps in cell membranes. When synchronized, it is thought that these pumps are more efficient because they require less ATP. We hypothesized that if this was correct, this technique may be used to reduce muscle fatigue. To test our hypothesis, we had multiple test subjects hold a 15 lb weight for as long as they could while isolating the bicep muscle and applying an oscillating electric field. We compared the EMG data we took during these trials to the control, which was done the same way but without applying the electric field. To compare how fatigued subjects were, we did a Fast Fourier Transform on the first and last 10 seconds of each trial to measure the Fatigue Index. Our preliminary results suggest that the Fatigue Index decreased at a slower rate in the trials where the subject held the weight with Synchronization Modulation. [Preview Abstract] |
Tuesday, March 19, 2013 9:24AM - 9:36AM |
F46.00008: Multiscale MD Simulations of Folding Dynamics and Mobility of Beta-Amyloid Peptide on Lipid Bilayer Surfaces Scott Van Tilburg, Kelvin Cheng Early interaction events of beta-amyloid peptides with the neuronal membranes play a key role in the pathogenesis of Alzheimer's disease. We have used multiscale Molecular Dynamics (MD) simulations to study the protein folding dynamics and lateral mobility of beta-amyloid protein on the cholesterol-enriched and -depleted lipid nano-domains. Several independent simulation replicates of all-atom and coarse-grained MD simulations of beta-amyloid on different lipid bilayer nano-domains have been generated. Using Define Secondary Structure of Proteins (DSSP) algorithm and mean-square-distance (MSD) analysis, the protein conformation and the lateral diffusion coefficients of protein, as well as the lipid and water, were calculated as a function of simulation time up to 200 nanoseconds for atomistic and 2 microseconds for coarse-grained simulations per replicate in different bilayer systems. Subtle differences in the conformation and mobility of the protein were observed in lipid bilayers with and without cholesterol. The structural dynamics information obtained from this work will provide useful insights into understanding the role of protein/lipid interactions in the membrane-associated aggregation of protein on neuronal membranes. [Preview Abstract] |
Tuesday, March 19, 2013 9:36AM - 9:48AM |
F46.00009: The structure of immiscible lipid phases as revealed by the Anton special purpose supercomputer Michael Sandar, Edward Lyman We present simulation data for a bilayer composed of a ternary mixture of cholesterol, dioloeoyl phosphatidylcholine and dipalmitoyl phosphatidylcholine. The chosen composition is in the two-phase region and the temperature is in the vicinity of the miscibility transition. Using the Anton special purpose supercomputer to generate continuous trajectories longer than ten microseconds--- which admits complete lipid mixing ---we observe robust liquid-liquid phase coexistence. We characterize the phase separated state by considering the local composition fluctuations. Correlation functions of the position reveal that the structure of the domain is circular on average, but that the boundary is subject to significant fluctuations, as expected in the neighborhood of a critical point. The domain diffuses on a slower timescale than the lipids, but by way of lipid exchange, rather than as a well-defined cluster. [Preview Abstract] |
Tuesday, March 19, 2013 9:48AM - 10:00AM |
F46.00010: Computational Analysis of ECGs Kevin Waters Electrocardiogram is among the most powerful methods at present to diagnose heart conditions. Here we employed Fourier transform to analyze Electrocardiograms. The goal of the project is to find a way to isolate different wave signals in ways that today's technology is not capable of. Our focus was on building on a code that is capable of filtering out P, QRS, T waves and noise from the ECG, so we created frequency filters that omitted selected amount of data. We first deconstructed and then constructed the ECG this way to find an optimal code assembly for each ECG wave (P-wave, QRS-wave, T-wave). By focusing on one patient, we succeeded to disentangle the complicated ECG signal. We plan to extend this method to more patients. [Preview Abstract] |
Tuesday, March 19, 2013 10:00AM - 10:12AM |
F46.00011: Nonlinear Dynamical Analysis of Fibrillation John A. Kerin, Justin M. Sporrer, David A. Egolf The development of spatiotemporal chaotic behavior in heart tissue, termed fibrillation, is a devastating, life-threatening condition. The chaotic behavior of electrochemical signals, in the form of spiral waves, causes the muscles of the heart to contract in an incoherent manner, hindering the heart's ability to pump blood. We have applied the mathematical tools of nonlinear dynamics to large-scale simulations of a model of fibrillating heart tissue to uncover the dynamical modes driving this chaos. By studying the evolution of Lyapunov vectors and exponents over short times, we have found that the fibrillating tissue is sensitive to electrical perturbations only in narrow regions immediately in front of the leading edges of spiral waves, especially when these waves collide, break apart, or hit the edges of the tissue sample. Using this knowledge, we have applied small stimuli to areas of varying sensitivity. By studying the evolution of the effects of these perturbations, we have made progress toward controlling the electrochemical patterns associated with heart fibrillation. [Preview Abstract] |
Tuesday, March 19, 2013 10:12AM - 10:24AM |
F46.00012: Imaging The Genetic Code of a Virus Jenna Graham, Justin Link Atomic Force Microscopy (AFM) has allowed scientists to explore physical characteristics of nano-scale materials. However, the challenges that come with such an investigation are rarely expressed. In this research project a method was developed to image the well-studied DNA of the virus lambda phage. Through testing and integrating several sample preparations described in literature, a quality image of lambda phage DNA can be obtained. In our experiment, we developed a technique using the Veeco Autoprobe CP AFM and mica substrate with an appropriate absorption buffer of HEPES and NiCl$_{\mathrm{2}}$. This presentation will focus on the development of a procedure to image lambda phage DNA at Xavier University. [Preview Abstract] |
Tuesday, March 19, 2013 10:24AM - 10:36AM |
F46.00013: Single Molecule Study on the Direct Transfer of \textit{E. coli} Single-Stranded Binding protein between Single-Stranded DNA Molecules Teckla Akinyi, I-Ren Lee, Taekjip Ha Single molecule fluorescence resonance energy transfer (smFRET) techniques allow a direct study of the mechanism of the spontaneous transfer of \textit{Escherichia coli} Single-Strand Binding (SSB) protein from single-stranded DNA to a competitor single-stand (ss)DNA. This investigation attempts to understand the kinetics of dissociation and ultimately figure out how long can SSB remain bound to ssDNA in midst of competitor free ssDNA. Application of single molecule techniques as described by Taekjip Ha, (\textit{Ha. Methods 25, 78--86 (2001)}) allow the quantification of the rapid dissociation of SSB from ssDNA as a function of ssDNA length and concentration. We also examined, whether the dissociation occurs with the SSB subunits released simultaneously or consecutively with the possibility of an intermediate state. The variation of dissociation time with DNA length and concentration of the competitive ssDNA demonstrate direct proportionality implying SSB is transferred between ssDNA molecules with a ratio of 1:1, with an abrupt transition from a high FRET state to a low FRET state indicating instantaneous dissociation limited by our time resolution. [Preview Abstract] |
Tuesday, March 19, 2013 10:36AM - 10:48AM |
F46.00014: Images of Cone Photoreceptors Using Spatially Non-Coherent Light Allison Hartman, Changgeng Liu, Myung Kim In order to get clear images of the photoreceptors in a living human eye, we constructed a collimated beam of light with controllable spatial coherence. In the past, imaging techniques using coherent light have shown interference speckles that are the similar size and shape as photoreceptors; these experiments have been unable to differentiate the speckles and the photoreceptors that are in the retina of the eye. We used MatLab to create a simulation of the optical system using a light source with variable spatial coherence reflecting off of a resolution target and we were able to eliminate the speckle patterns. We then created an experimental setup to verify out simulation. We were able to get clear images of resolution targets and our future work will be to image retina samples using spatially non-coherent light and apply this technique in Digital Holography experiments. [Preview Abstract] |
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