Bulletin of the American Physical Society
Joint Fall 2013 Meeting of the Texas Sections of the APS, AAPT, and Zone 13 of the SPS
Volume 58, Number 10
Thursday–Saturday, October 10–12, 2013; Brownsville, Texas
Session B4: Biological and Chemical Physics |
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Chair: Kwan Kelvin Cheng, Trinity University Room: Gran Salon |
Friday, October 11, 2013 10:30AM - 10:42AM |
B4.00001: Computational Search for Novel Endohedral Fullerenes Luis Basurto, Tunna Baruah, Rajendra Zope Carbon fullerenes are often used as electron acceptors due to their large electron affinity, low reorganization energy and three dimensional charge transport property. The open circuit voltage in organic photovoltaics is known to be related to the energy difference of the highest occupied molecular orbital (HOMO) energy of the donor and the lowest unoccupied molecular orbital (LUMO) of the electron acceptor. The use of endohedral fullerenes as electron acceptors offers an alternative way to manipulate its LUMO levels by varying the encapsulating unit. In recent years a few donor-acceptor complexes with endohedral units have been reported. We have recently designed a set of computational tools to search for stable endohedral fullerenes. Using this toolkit, we have optimized all 31924 isomers of C80fullerenes. Using the lowest 3000 and a few other promising candidate structures a set of 22000 endohedral complexes of Sc3N@C80 and 10000 complexes of Sc4O2@C80 was constructed. This set was subsequently optimized at PM6 level and the lowest few geometries were relaxed at the PBE-GGA level within DFT. These calculations confirm previously assigned fullerenes geometries and report a few new low energy isomers. This procedure is extended to search for novel endohedral fullerenes. [Preview Abstract] |
Friday, October 11, 2013 10:42AM - 10:54AM |
B4.00002: Biomechanical Discrimination of Diseased Cells for Cancer Diagnosis Azhar Ilyas, Muhammad Ahsan, Young-tae Kim, Samir Iqbal Biomechanical properties (size, shape, stiffness, viscosity, deformability) of cells change significantly in unhealthy cells and can be used to indicate the physiological state of the cells. Here, we report a simple and interesting strategy to identify cancer cells from biopsy samples. The detection scheme utilized single solid-state micropore as the biological transducer which translated the cell's viscoelastic behavior into electrical signals. As a model, bladder cancer cells and normal urothelial cells were investigated. The approach didn't require any staining, functionalization or availability of any biomarkers but relied on merely cellular mechanical properties. Temporal measurements of the ionic current were recorded across the micropore. Cancer cells gave distinctive pulse signals while passing through the micropore. The analysis of the pulses showed clear data clusters for cancer cells in contrast to their normal counterparts. On average, the bladder cancer cells showed one order of magnitude faster translocation time as compared to normal urothelial cells due to their softer nature. The cancer cells were easily identified from a mixture with a detection efficiency of more than 75{\%}. The statistical analysis of each single cell present in the probed sample demonstrated its capability to identify cancerous cells when they were very few in number. [Preview Abstract] |
Friday, October 11, 2013 10:54AM - 11:06AM |
B4.00003: Investigating Protein Conformation changes at a soft surface Ahmed Touhami, Marcela Alexander, Milena Corredig, John Dutcher Here we use AFM-single molecule force spectroscopy to probe the conformational changes in Beta-lactoglobulin (BLG) protein adsorbed onto the oil-in-water interface due to variations in pH. Single oil droplets are mechanically trapped in pores of polycarbonate filter and the AFM tip is used to grape and unfolds BLG molecules. The changes in the contour length upon each unfolding event were determined by fitting the WLC model of polymer elasticity to each of the BLG peaks of the force-extension profiles. Our results show clearly that BLG on the same oil droplet adopts different conformations at different pH regions. While at pH 2.5, the unfolded BLG has a contour length similar to the total length of single monomer with two large unfolding barriers, the protein exists mainly as a dimer formed of several smaller domains at pH 6.8. Furthermore, at pH 9 the interactions between the AFM tip and the BLG layer on the oil droplet surface are dominated by an important repulsion due to the highly negatively charged BLG layer. This study demonstrates a novel application of single molecule force spectroscopy to investigate the underlying mechanisms by which proteins can be used to stabilize food products. [Preview Abstract] |
Friday, October 11, 2013 11:06AM - 11:18AM |
B4.00004: Novel nanotechnology approach to target cancer disease by switching an alternative splicing Alexander Kazansky, Ivan Mendez, Karen Martirosyan High levels of activated STAT5B, a specific member of the STAT family, are intimately associated with prostate tumor progression, while the naturally occurring truncated form of STAT5B acts as a tumor suppressor. We have demonstrated that the truncated isoform of STAT5 is generated by insertion of an alternatively spliced exon and results in the introduction of an early termination codon. Recently, we have also demonstrated the feasibility of using steric-blocking splice-switching oligonucleotides (SSOs) with a complimentary sequence to the targeted exon-intron boundary to enhance alternative intron/exon retention. In this work we report the efficacy of the steric-blocking by splice-switching oligonucleotide (SSO) conjugates with pH insertion peptide (pHLIP) to block alternative splicing of STATs mRNA in vitro and in vivo. This technology would allow opening new pathways for chemotherapeutic disease intervention strategies based on the combination of pHLIP nanotechnology and a novel approach of switching expression from a proto-oncogene to a tumor suppressor. [Preview Abstract] |
Friday, October 11, 2013 11:18AM - 11:30AM |
B4.00005: Probing Conformational Changes in DNA by Force-Induced Melting of Double-Stranded DNA Carlos Jeziel Gonzalez, Ahmed Touhami The goal of this research is to study the thermodynamics and dynamics of conformational changes in double-stranded DNA (dsDNA) by single molecule stretching experiments using optical tweezers microscopy. Individual dsDNA molecules are attached to a chemically functionalized cover-slip and the force applied to the DNA, as a function of the extension, is measured via the motion of a trapped microsized bead. If a single dsDNA molecule is stretched to forces of about 65 pN, one observes a plateau in the force-extension curve. Very little additional force is required to stretch the molecule from its normal B-DNA contour length by a factor of 1.7 and more. The structural transition that occurs in this plateau is termed ``overstretching transition'' and is a transition from dsDNA to single-stranded DNA (ssDNA), closely similar to the thermal melting transition. However, the two strands do not separate completely at the end of the overstretching transition, but only at the much larger force of at least 150 pN. Our focus here is to investigate the helix-coil transition in dsDNA under various conditions. Our methodology provides an unprecedented opportunity for quantitative investigation of a wide range of physiologically important phenomena associated with DNA helix-destabilization. [Preview Abstract] |
Friday, October 11, 2013 11:30AM - 11:42AM |
B4.00006: Voronoi Tessellations Shell Analysis Sara Cheng, Campbell Compton, Hoa Nguyen, Kelvin Cheng In studies of lipid bilayer systems, disruptions caused by interaction of protein with lipid components are difficult to quantify. The purpose of our research project is to develop an analysis suite to analyze molecular dynamics (MD) trajectories of beta-amyloid on lipid bilayer systems containing POPC and cholesterol lipids. Using a combination of Python, Shell, and MATLAB scripts, we analyze multi-component, multi-shell, and multi-frame systems in order to better understand how beta-amyloid affects neuronal membrane mimics. The overall goal of our project is to gain insight on the damage caused by beta-amyloid and its role in the parthenogenesis of Alzheimer's disease. The focus of our presentation will be on the post-processing shell data generated from running our MD simulation results through a computer program, Voro$++$, which involves using Voronoi Tessellations generate shells around the protein. We will describe our method of extracting and analyzing MD simulations, including post-processing the results generated by a combination of GROMACS tools and in-house scripts. The results of our analysis suite, with a focus on density and order parameter, indicate strongest disruption of the lipid bilayer in the first shell surrounding the protein. [Preview Abstract] |
Friday, October 11, 2013 11:42AM - 11:54AM |
B4.00007: Physiological Changes in the Bacterial Behavior in Weak Magnetic Fields Samina Masood We study the effects of weak magnetic field on the bacterial growth. We use different type of magnetic field to find out that how the bacterial behavior changes if it grows in the magnetic field. This preliminary study includes a comparative study of different bacterial species to compare their shapes, their gram-staining and other structural differences. [Preview Abstract] |
Friday, October 11, 2013 11:54AM - 12:06PM |
B4.00008: Protection and inhibition of antibiotic-resistant mutants in structured bacterial populations Nalin Ratnayeke, Karishma Kaushik, Parag Katira, Vernita Gordon Antibiotic resistance is a major issue in public health. Populations of bacteria naturally generate mutants resistant to antibiotics, however the impact of population structure on the subsequent survival of mutants during antibiotic exposure is not well understood. Here we show that resistant mutant survival depends on population structuring such as population density and spatial organization of cells. Mixed populations of \textit{Pseudomonas aeruginosa} susceptible and resistant cells were exposed to antibiotics at various cell densities, and mutant survival was seen to vary non-monotonically with density. We hypothesize that cells in a population during antibiotic exposure are involved in both protection and inhibition of resistant mutants, and that population structure determines which of these processes is dominant. Through performing diffusion assays on agar growth plates, a diffusion constant of .86 $\pm$ .15 mm$^2$/hr and molecular weight of 950 $\pm$ 500 Da for a putative released inhibitory factor were estimated. Additionally, a model based on antibiotic reaction kinetics was developed in order to describe inhibition in mixed systems. Investigations into these phenomena will lead to an increased understanding of the development and maintenance of antibiotic resistance in nature. [Preview Abstract] |
Friday, October 11, 2013 12:06PM - 12:18PM |
B4.00009: Methodologies for Analyzing Motion Data in Humans Elizabeth Sizemore, Claire Sexton, Carey Davies, Anne Almeda, S.R. Slaughter Inertial measurement units (IMUs) are used to acquire acceleration, rotation, and magnetic field data in three dimensions. When attached to individual body segments these devices can wirelessly stream this data to computer workstations for analysis. The patterns seen can then be used to evaluate relative movements. In this study, rotation at the knee was analyzed by devices worn on the leg and thigh. Gait was studied over dissimilar surfaces, including flat, railroad ballast, and stairs. Image density, neural network, and fractal analysis techniques were employed to evaluate acquired data. Imaging software contributed to the quantification of rotation data in the X and Z axes. Error propagation neural networks create heuristic problem solvers that excel at analyzing non-linear relationships and capturing associations within a set. Fractal analysis gives us terms to express the degree of self similarity, which was applied to the different surface data. Determinations from these techniques will be presented. [Preview Abstract] |
Friday, October 11, 2013 12:18PM - 12:30PM |
B4.00010: Can single-cell behavior predict the structure and rheology of bacterial biofilms? Vernita Gordon, Benjamin Cooley, Travis Thatcher, Numa Dhamani, Sara Hashmi, William Waller, Ross Todd, Henry Lee, Daniel Hurwitz, Daniele Provenzano, Ahmed Touhami, Sheri Dellos-Nolan, Daniel Wozniak Biofilms are surface-mounted, multicellular communities of microbes. Biofilms are often associated with chronic infectins that resist treatment, evade the immune system, and damage host tissue. An essential characteristic of the biofilm state is that constituent organisms are bound in a polymeric matrix. This matrix, plus the native motility of bacteria, does much to control the structure that develops in the biofilm. The matrix plus the mechanics of embedded bacteria controls the rheology of the biofilm. Biofilm structure is important for biofilm function because it controls transport; biofilm rheology is important because it controls the response to mechanical removal strategies. Understanding structure and rheology are basic challenges, and measuring rheology of biofilms is itself very experimentally challenging. We present results that show that components of the biofilm matrix influence the single-cell behavior of bacteria on surfaces in component-specific ways. These results suggest that it may be possible to develop metrics that use single-cell behaviors as predictors of biofilms structure and rheology. [Preview Abstract] |
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