Bulletin of the American Physical Society
2005 72nd Annual Meeting of the Southeastern Section of the APS
Thursday–Saturday, November 10–12, 2005; Gainesville, FL
Session CE: Poster Session I |
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Room: Hilton Cypress |
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CE.00001: Thermodynamically Correct G\={o} Models: Incorporating Entropic Interactions into Minimalist Models Alexander Chew, Hugh Nymeyer G\={o}-like or ``native-centric'' protein models have been very successful in describing folding behavior. These models typically treat all atomic interactions as purely enthalpic in origin; however, many interactions, such as the hydrophobic effect at room temperature, are known to be largely entropic. We construct a new G\={o}-like model that treats atomic interactions as arising from a combination of enthalpic and entropic forces between various hydrophobic and hydrophilic groups. This new model captures the correct temperature dependent behavior of protein contacts, allowing us to observe cold denaturation and derive heat capacity curves that can be compared directly against experimental data. [Preview Abstract] |
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CE.00002: The Role of Backbone Desolvation in Helix Folding Hugh Nymeyer Replica exchange molecular dynamics simulations are used to study the helix-coil transition in different peptides with the amino-acid sequence YKAAXAKAAXAKAAXAK, where X is a substitutable site. Although numerous studies have compared the average helical propensity of different force-fields, little attention has been given to the ability of force-fields to capture the relative helical propensity of different amino-acids. Comparisons are made using two commonly used force- fields (GROMOS and AMBER). Beta-branched amino-acids are found to be destabilizing to helical structure, but this destabilization is consistently overestimated. The temperature dependence of this destabilization is also used to determine the difference in the enthalpy of helix-formation for different amino-acid substitutions. Although the enthalpic component of this destabilization is too strong, it appears sensitive to the particular force-field, which suggests that it may be useful for force-field parameterization. [Preview Abstract] |
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CE.00003: Multiple frequency MR implantable coil system for \textit{in vivo} studies of bioartificial pancreas at 11.1 T N.A. Volland, C.A. Taylor, T.H. Mareci, I. Constantinidis Bioartificial pancreatic macroconstructs may deliver insulin secreting cells for blood glucose regulation. Non-invasively monitoring \textit{in vivo} is key to understanding its function and efficacy. Initial NMR imaging {\&} spectroscopy showed great promise with surface coils at 4.7 T. Sensitivity limitations restrict measurements so we developed an inductively-coupled multiple-frequency coil system for 11.1 T. This system contains an implantable loop-gap resonator, inductively coupled to an external coil, resonating at 471 MHz for $^{1}$H and optimized for $^{31}$P at 191 MHz. This system has a sensitivity gain of $\sim $5.2 ($\pm $2.3) over a surface coil. Images were acquired for both frequencies. Ongoing work focuses on: 1) a receive-only coil system, 2) adding a third resonance (443 MHz for $^{19}$F), and 3) developing coating material and embedding the implantable coil in the macroconstruct. This system will be characterized in vitro prior to its use in vivo. [Preview Abstract] |
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CE.00004: Folding stability analysis of FKBP12 by mutation of charged residues. Jyotica Batra, Huan-Xiang Zhou The folded conformation of a protein is stabilized by hydrophobic and electrostatic interactions. Our group has developed theoretical methods for calculating effects of charged residues on folding stability. To test these methods and to better understand electrostatic effects, we have carried out measurements of wild-type and charge-mutated variants of the 12 kD FK506-binding protein (FKBP12). The charge mutations were selected based on sequence comparison with a close homologue, FKBP12.6. The experimental results provide some support of theoretical calculations but also identify shortcomings for further improvement. We are in the process of generating a hyper-stable variant of FKBP12 by accumulating individual stabilizing substitutions with FKBP12.6. [Preview Abstract] |
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CE.00005: Folding and binding stability of the \textit{$\varepsilon $} and \textit{$\theta $} subunits of DNA polymerase III. Daniel Spencer, Ah Young Park, Nicholas E. Dixon, Huan-Xiang Zhou The \textit{$\varepsilon $} subunit of DNA polymerase III is responsible for the proofreading and repair functions of the holoenzyme during DNA replication. The \textit{$\theta $} subunit binds to the \textit{$\varepsilon $} subunit. This binding has been suggested to provide additional folding stability to the \textit{$\varepsilon $} subunit. We have studied the folding stability and the binding affinity of the two subunits at 15 \r{ }C. The midpoint of urea denaturation of the \textit{$\varepsilon $} subunit was low, at 2.4 M urea, but the slope of the unfolding free energy versus urea was high (at 2.9 kcal/mol/M). The sensitivity to urea echoes the low thermal stability. In contrast, the midpoint of urea denaturation of the \textit{$\theta $} subunit was high, at 3.8 M urea, but the slope of the unfolding free energy versus urea was low (at 1.0 kcal/mol/M). Both proteins thus showed marginal stability with respect to denaturation. Their complex exhibited much greater resistance to denaturation, with a midpoint of urea denaturation at 4.3 M. [Preview Abstract] |
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CE.00006: Diffusion tensor magnetic resonance imaging of regeneration/degeneration after rat sciatic nerve injury Min Sig Hwang, George Perrin, David Muir, Thomas Mareci Diffusion tensor imaging was performed to investigate myelination and demyelination spatiotemporally in cut or crushed excised rat sciatic nerves in a 17.6 T magnet with a solenoid RF coil. Orientation independent measures of water diffusion, fractional anisotropy (FA) and averaged diffusivity ($<$D$>)$, were examined as MR parameters for the quantification of the myelin within the major peripheral nerve. Crushed nerves initially demonstrated decreased FA, followed by increase to FA of normal nerve with time. At 14 days post injury, FA of the nerve is high, 0.85, at the site proximal to the injury then FA decreases in a proximodistal gradient because the nerve remains more demyelinated toward the distal area. Cut sciatic nerves displayed a prolonged decrease of FA with time after injury. Also FA correlates with $<$D$>$ in these nerves. Therefore FA or $<$D$>$ may be a good indicator of myelination and demyelination in rat sciatic nerves and FA appears to be a more sensitive indicator of myelin. [Preview Abstract] |
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CE.00007: Experimental studies of protein binding affinity by different methods. Debangshu Samanta, Daniel Spencer, Huan-Xiang Zhou Protein-protein binding is central to most protein functions; convenient assays of binding affinity are thus invaluable for elucidating mechanisms of biological processes. We are carrying out different assays on the binding of the 12 kD FK506-binding protein (FKBP12) with target peptides. The methods include affinity chromatography, isothermal titration calorimetry, and fluorescence spectroscopy. The goal is to identify a convenient protocol for identifying peptides that form part of the binding site on the target protein of FKBP12. FKBP12 is a multiple-function protein. For example, it regulates the ryanodine receptor, a calcium release channel implicated in excitation-contraction coupling. Our approach is expected to have wide applicability in identifying target peptides. [Preview Abstract] |
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CE.00008: Study of aggregation in polysaccharides by triple detection HPLC David Norwood, Liz Serpas, Erica Sharp It has been observed that various species of the polysaccharide carrageenan undergo a change in conformation under varying conditions of temperature and added salt. The change is from a random coil (under conditions of high temperature or low salt) to a helix (under conditions of low temperature or high salt). It is a point of contention as to whether the helix is formed of one coil wrapping upon itself or two coils wrapping around one another. We present the results of a study of this conformation change using viscometry and multi-angle laser light scattering (MALLS) incorporating size-exclusion chromatography (SEC). In previous research, our batch light scattering results showed a clear increase in molecular weight and radius of gyration when NaCl was added to varying concentrations of iota-carrageenan, which could be interpreted as the conformation change described. However, estimates of persistence length ($\sim $ R$_{G}^{2}$ / M$_{W})$ calculated using MALLS data show no strong variation when increasing added salt. This suggests that the molecular weight increase reflects an aggregation of polymer molecules instead of a change in conformation. However, SEC results show very little variation in molecular weight and radius of gyration, and instead, show behavior typical of linear polyelectrolytes. Resolution of these different results suggests a loose aggregation of polymer molecules that preserves the overall structure rather than a significant change in polymer architecture. We present viscometry and dynamic light scattering results that confirm these conclusions. [Preview Abstract] |
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CE.00009: Dynamics and intramolecular ligand binding of DtxR studied by MD simulations and NMR spectroscopy Myunggi Yi, Nilakshee Bhattacharya, Timothy Logan, Huan-Xiang Zhou Diphtheria toxin repressor (DtxR) regulates the expression of the diphtheria toxin gene through intramolecular ligand binding (Wylie et al., Biochemistry 2005, 44:40-51). Protein dynamics is essential to the binding process of the Pro-rich (Pr) ligand to the C-terminal SH3 domain. We present MD and NMR results on the dynamics and ligand interactions of a Pr-SH3 construct of DtxR. NMR relaxation data (T1, T2, and NOE) showed that the Pr ligand is very flexible, suggesting that it undergoes binding/unbinding transitions. A 50-ns MD trajectory of the protein was used to calculate T1, T2, and NOE, reproducing the NMR results for the SH3 domain but not for the Pr segment. During the MD simulation, the ligand stayed bound to the SH3 domain; thus the simulation represented the bound state. The NMR data for the Pr-segment could be explained by assuming that they represented the average behavior of a fast binding/unbinding exchange. Though unbinding was not observed in the MD simulation, the simulation did show large fluctuations of a loop which forms part of the wall of the binding pocket. The fluctuations led to opening up of the binding pocket, thus weakening the interaction with the Pr segment and perhaps ultimately leading to ligand unbinding. [Preview Abstract] |
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CE.00010: Electrical Detection of Immobilized Proteins With Ungated AlGaN/GaN High Electron Mobility Transistors Byoung Sam Kang, Fan Ren, Lin Wang, Charles Lofton, Weihong Tan, Stephen Pearton, A. Dabiran, A. Osinsky, P. Chow Ungated AlGaN/GaN High Electron Mobility Transistor structures were functionalized in the gate region with aminopropyl silane. This serves as a binding layer to the AlGaN surface for attachment of fluorescent biological probes. Fluorescence microscopy shows that the chemical treatment creates sites for specific absorption of probes. Biotin was then added to the functionalized surface to bind with high affinity to streptavidin proteins. The HEMT drain-source current showed a clear decrease of 4 uA as this protein was introduced to the surface, showing the promise of this all-electronic detection approach for biological sensing. [Preview Abstract] |
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CE.00011: Modeling of the Effects of Beam Fluctuations from LIGO's Mode Cleaner Nafis Jamal, Sanichiro Yoshida LIGO's mode cleaner (MC) is a triangular laser cavity that forms the Input Optics (IO) along with the subsequent mode matching telescopes (MMT). The output beam from the MC travels through the MMT chain to the core optics, the heart of LIGO, which consists of the power recycling mirror, beam splitter and the two arm cavities. If the incoming beam to the core optics is flawed, LIGO's sensitivity becomes degraded. In my research, we model the MC's effect on the laser beam and the performance of the core optics. To appropriately model the MC, seismic perturbations as well as stabilizing control forces must be simulated. Using the LIGO's End-to-End simulator, we model the MC's length sensing control (LSC) to adjust the overall optical path length to resonance. To complement the LSC, we model the Alignment Sensing Control (ASC) system to correct the angular misalignment of the MC mirrors, minimizing the beam pointing angle (by a factor of 3) as well as maximizing power coupled in the cavity (from $>$99{\%} to $>$99.9{\%}). We will analyze how the beam pointing and amplitude fluctuations at the MC's output affect LIGO's overall performance. [Preview Abstract] |
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CE.00012: Numerical simulation of LIGO input optics Shivanand none, Nafis Jamal, Sanichiro Yoshida Numerical analysis has been carried out to understand the performance of the Input Optics used in the first generation of LIGO (Laser Interferometer Gravitational-wave Observatory) detector. The input optics is a subsystem consisting of a mode cleaner and mode-matching telescope, where all the optics are suspended and installed in vacuum. Using the end-to-end package (LIGO programming language), computer codes have been made to simulate the input optics. Giving realistic seismic noise to the suspension point of the optics and using the length sensing/alignment sensing control for the mode cleaner, the performance of the input optics has been simulated under various scenarios such as with an order of magnitude higher seismic noise than the normal level, and with/without the alignment sensing control feedback from the arm cavity to the mode-matching telescope. The results are assessed in terms of the beam pointing fluctuation of the laser beam going into the arm cavities, and its influence on the optical coupling to the arm cavities and the noise level at the gravitational wave port signal. [Preview Abstract] |
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CE.00013: Light Scattering as a Diagnostic of Asteroid Structure Ashley Espy, Bo Gustafson With the identification of the Veritas family as the source of the 9.35 degree dust band of the Zodiacal cloud (Nesvory, et al. 2003), we are presented with a new means to study this family and its precursor asteroid. When an asteroid breaks up, the larger pieces remain together on similar orbits, but the smaller (sub-mm to micron) particles, experience a stronger perturbation from the solar radiation pressure and migrate to the zodiacal cloud. Light scattered by this corresponding dust band can yield information, on the structure of the material in the dust and thus also the precursor. Using the Microwave Scattering Facility (Gustafson 1996), models of these dust particles are created and the scattering intensities and polarizations measured. One hypothesis is that the Veritas precursor was NOT differentiated, but rather an aggregate of interstellar grains like the Bird's Nest model proposed by Greenberg and Gustafson (1981). If so, we expect to find structure in the dust on the scale of the interstellar grains. Else, if the precursor WAS fully or partially differentiated, then the bulk material in the dust should appear homogeneous or show structure on a larger scale. [Preview Abstract] |
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CE.00014: Development of ultra-high frequency microwave instrumentation for low-loss magnetic resonance spectroscopy at high magnetic fields. S.-S. Kim, S.-C. Lee, A. Wilson, S. Takahashi, S. Hill, R. Wylde, P. Goy We have developed a range of techniques for performing high-field angle-dependent microwave spectroscopies of low-dimensional conductors, superconductors and magnets. A combination of methods enables wide frequency coverage (8-700 GHz, 0.3-23 cm$^{-1})$, and all instrumentation is fully compatible with the high field facilities at the National High Magnetic Field Laboratory (NHMFL).We employ two kinds of probe: (1) a cavity perturbation technique, where the cavity is coupled to the spectrometer via rectangular waveguides (8-350 GHz); and (2) a broadband non-resonant technique, employing corrugated waveguide and a quasioptical bridge ($>$ 170 GHz). The corrugated waveguides are optimized for propagation of the HE11 cylindrical mode more commonly associated with high-power plasma applications. The losses are extremely low at high frequencies, enabling detection of small signals. The sample is coupled to the bottom of the waveguide via a near-field perturbation. All components associated with these instruments are insensitive to the stray fields found in proximity to the high-field magnets at the NHMFL. We will present brief examples of applications of these instruments. [Preview Abstract] |
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CE.00015: Long-wave infrared absorption spectrum of U:CaF$_{2}$ Justin Cleary, Robert Peale High-resolution transmission spectroscopy at liquid-helium sample temperatures was performed on a single crystal of CaF$_{2}$ doped to 1 atomic percent with uranium. Uranium concentration was verified by Rutherford backscattering spectroscopy, which revealed no significant concentrations of other heavy impurity ions. A previously unreported group of sharp lines was found in the spectral region of 900 - 3500 cm$^{-1}$. Temperature dependence reveals the presence of a low-lying level 10 cm$^{-1}$ above the ground level. Ultraviolet laser irradiation of the sample at 248 nm and 355 nm wavelengths and annealing at 100 C induced changes in absorption-line strengths and revealed independent behavior of at least 5 groups of lines. These results indicate the presence of at least five different crystal-field environments for the uranium center. [Preview Abstract] |
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CE.00016: Scalar potential model (SPM) of redshift and discrete redshift John Hodge On the galactic scale the universe is inhomogeneous and redshift z is occasionally less than zero. Several differences among galaxy types suggest that spiral galaxies are Sources and that early type galaxies are Sinks of a scalar potential field (SPF). The morphology-radius and intragalactic medium cluster observations support a cell structure of galaxies. The SPF causes the mass expected by Newtonian mechanics to measure less in Source galaxies and more in Sink galaxies. The cell structure allows the universe to be bounded and flat without collapsing. An equation is derived relating z of particle photons and the distance D to galaxies. The calculated z has a correlation coefficient of 0.88 with the measured z for a sample of 32 spiral galaxies with a Cepheid based D. The equation is consistent with z <0 observations of close galaxies. At low cosmological distances, the equation reduces to z»KD, where K is a constant, positive value. The model qualitatively suggests the discrete variations in z, which was reported by W. G. Tifft, 1997, ApJ 485, 465 and others, are consistent with the SPM. Full text: http://web.infoave.net/~scjh. [Preview Abstract] |
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CE.00017: Source for a Temperature-Controlled Metal Cluster Beam Wei Jiang, Forrest Payne, Louis Bloomfield Metal clusters can be produced easily by laser vaporization of a sample into an inert cooling gas. We have used a pulsed Nd:YAG laser to evaporate cobalt from a rotating rod into a 20cm-long narrow pipe filled with helium gas, injected by a pulsed gas valve. The outgoing part of the pipe (15cm long) is attached to a helium refrigerator and an electrical heater, which allow us to control the pipe's temperature over the range from 60K to room temperature. If the gas-cluster mixture stays in the pipe long enough before supersonic expansion, it reaches thermal equilibrium with the pipe. [Preview Abstract] |
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CE.00018: Ionization and Charge Transfer in Collisions of Singly and Doubly Charged Heavy Ions with Gaseous Targets Nicholas Evans, Larry Toburen, Jefferson Shinpaugh, Robert DuBois While energetic atomic collisions can be well described for few electron systems, collisions involving many electrons are more difficult to model. Understanding these collision systems is essential to modeling energy deposition in the irradiation of materials. Experimental measurements of absolute total and partial cross sections for charge transfer and ionization have been made for collisions of $C^{+}$,$Cl^{+}$, and $Cl^{2+}$ in the energy range of 1-4 MeV with various gaseous targets including Ar, Ne, $N_{2}$, $H_{2}O$, and $CH_{4}$. The measurements were taken at the tandem Van de Graaff accelerator facility at East Carolina University. Post-collision projectile ions were electrostatically analyzed, and total cross sections are determined by measuring the final charge fraction of the projectile beam as a function of target density. Recoil target ions were electrostatically extracted, and their final charge was determined using time of flight methods. The final charge of the projectiles were then measured in coincidence with the recoil ion charge to determine partial cross sections. [Preview Abstract] |
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CE.00019: Impurity Deionization Effects on Surface Recombination DC Current-Voltage Charateristics on Oxidized Silicon Zuhui Chen, Bin B. Jie, Chih-Tang Sah Impurity deionization effects on the electron-hole recombination DC base-current gate-voltage (R-DCIV) at the SiO$_{2}$/Si interface traps are investigated. It is shown that impurity deionization does not significantly affect 90{\%} of the bell-shaped R-DCIV curve. The R-DCIV lineshape distortion due to impurity deionization is still small when recombination current is several decades smaller than its peak current for device and material parameters such as impurity concentration and oxide thickness in their practical ranges. Thus, full impurity ionization approximation can be employed without loss of accuracy in using the R-DCIV methodology to extract the parameters. [Preview Abstract] |
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CE.00020: Structural and Mophological Studies of Precolombine Au-Based Craftsmanships Jairo Roa-Rojas, Jos\'{e} Humberto Molina Aranguren We report crystallographic and morphological analysis of pre-Columbian craftsmanship for evaluation and restoration after 500 years of production by native artisan. Gold pieces of the pre-Columbian culture from the \textit{andine} plateau were studied. Carefully Rietveld refinement of the X-ray diffraction patterns showed the characteristic Au structural phase, with incipient additional peaks, which correspond to non reactive Ni, Cr and Pt elements, to conform a microgranular composite. EDX spectrum reveals the presence of those elements and the semi quantitative analysis supplies values of 88{\%} Au, 6{\%} Ni, 4.5{\%} Cr and 1.5 Pt. SEM show three well recognized types of grain: one majority obscure topology of 8 -- 10 $\mu $m grain size; second with slightly more brightness of grains, 3 $\mu $m size; and a third kind of grains with mean size smaller than 3 $\mu $m. These results were corroborated by using AFM studies. We interpret the first grain regime as corresponding to Au; second to Ni and Cr; and third to Pt. Similar mixture was prepared by utilizing Aldrich 99.99{\%} precursors in order to perform the restoration of pre-Columbian pieces. The X-ray analysis of mixture showed the same behavior of initial studies of pieces. [Preview Abstract] |
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CE.00021: Monte Carlo Simulations for a Photomultiplier's One-Photoelectron Response Alejandro de la Puente, Brian Beckford$^2$, Naipy Perez, Joerg Reinhold Currently, we are conducting small prototype tests as well as Monte Carlo simulations (MC) to investigate the feasibility of employing wavelength shifting plastic and low cost photomultipliers (PMT) for constructing ring imaging Cherenkov detectors (RICH). As the expected light yield is low, a realistic model for the one-photoelectron response of the PMTs is needed. Two Monte Carlo programs were written, one with a realistic description of the amplification chain, and a second approximating the process. Because a fully realistic description is very computing intensive and therefore impractical for implementation into large-scale detector simulations the goal was to determine suitable approximations to the amplification process. Employing the Central Limit Theorem, it was found that the lower stages of the PMT are well described by Gaussian distributions rather than the more realistic Poissonian distributions. This reduces significantly the computing time. In the future, the MC will be used for characterization of the PMTs as well as a generator in a full detector simulation. [Preview Abstract] |
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CE.00022: The Diffusion Orientation Transform (DOT) for MR Imaging Evren Ozarslan, Timothy Shepherd, Baba Vemuri, Stephen Blackband, Thomas Mareci Diffusion-weighted signal attenuation in pulsed field gradient MRI experiments provides a powerful means to extract microstructural information, such as anisotropy, from porous media and biological tissues. However, in fibrous media, it remains challenging to find the preferred orientations of water diffusion when there are more than one fiber orientations inside a voxel. We describe a novel technique, the diffusion orientation transform that provides a direct link between the apparent diffusion coefficients and the water displacement probabilities along different directions. The transform can be applied to data collected on a single spherical shell with the assumption of monoexponential attenuation. Alternatively, data acquired on several spherical shells can be reconstructed to yield more accurate probability values on the sphere. Both simulations and real experiments demonstrate that the parameterized surfaces constructed from the probability values are able to resolve crossing fibers accurately. The developed methods will improve the reliability of schemes used to map the anatomical connectivities within nervous tissue. [Preview Abstract] |
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