Bulletin of the American Physical Society
2006 Four Corners Section of the APS Fall Meeting
Friday–Saturday, October 6–7, 2006; Logan, Utah
Session D2: Bio-related Physics |
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Chair: Jean Francois Van Huele, Brigham Young University Room: Eccles Conference Center Room 205/207 |
Friday, October 6, 2006 1:30PM - 2:06PM |
D2.00001: Developing Serial Diffraction and Microdroplet Beams for Protein Structure Determination Invited Speaker: The first protein structure to be measured was that of myoglobin, in 1958 by John Kendrew, who then remarked ``Perhaps the most remarkable features of the molecule are its complexity and lack of symmetry.'' Indeed, it is this complexity that allows a protein to distinguish a specific molecular species from the thousands with which it might interact. Accordingly, protein structure can offer great insight into protein function but is very challenging to measure. As ``lensless imaging'' techniques are developed to extract real space structural information from nonperiodic diffraction measurements, serial diffraction of both electrons and x-rays become viable candidates for high-throughput measurement of protein structure. Both probe species require a vacuum environment and hence a means of injecting proteins from solution into vacuum while maintaining the protein in a hydrated form (water soluble proteins) or micellular form (membrane proteins) at all times. Microdroplet beams of the form proposed by Rayleigh in the 1880's offer the ideal tool. This talk will deliver a brief overview of protein structure, discuss the inversion of serial diffraction measurements by ``phase retrieval,'' and then present the requirements, challenges, and various experimental schemes currently directed towards protein structure determination by use of microdroplet beams. \newline \newline In collaboration with U. Weierstall, D. Starodub, K. Schmidt, P. Fromme, and J.C.H. Spence, Arizona State University. [Preview Abstract] |
Friday, October 6, 2006 2:06PM - 2:18PM |
D2.00002: Fabrication, Cleaning, and Filtering of Microscopic Droplet Beam Nozzles J. Warner, M. Hunter, U. Weierstall, J.C.H. Spence, R.B. Doak Structure determination of proteins is a subject of intense current interest. Most relevant is a protein's native conformation, which generally requires it be immersed in water (if water-soluble) or a lipid jacket (if a membrane protein). Emerging schemes of serial protein diffraction propose to embed proteins in microscopic water droplets (membrane proteins encased in a detergent micelle) and pass these in vacuum through an x-ray or electron beam. Droplet diameters of $<$2~$\mu $m and $<$200~nm are dictated by the respective probe penetration depths. Rayleigh nozzles of $<$1~$\mu $m and $<$100~nm can deliver such droplets, but clogging becomes a major hurdle at nozzle diameters below even 10~$\mu $m. This talk will present an extensive study of the cleaning, filtering, and operation of 4 $\mu $m diameter nozzles with intent to minimize clogging. Borosilicate and fused silica nozzles were investigated in both commercial and self-fabricated forms. Equipment was developed to flush the nozzles from both the tip and distal ends. A variety of solvents and detergents were tested, with and without sonication and both before and after the nozzle tip was formed. Flame burnishing was employed to smooth and clean the nozzles. \textit{In situ} formation of silicate filter frits was investigated. Still, only about 30{\%} of the 4 $\mu $m nozzles would run without clogging. An alternative to solid convergent nozzles will be described. [Preview Abstract] |
Friday, October 6, 2006 2:18PM - 2:30PM |
D2.00003: Breathing interplay effects during proton radiation therapy and development of repainting solutions Daniel Robertson, Joao Seco, Alexei Trofimov, Harald Paganetti The movement from passive scattering to active spot scanning in proton radiation therapy introduces the problem of interplay effects when elements of beam motion have a similar time scale to periodic tumor motion, as in a lung tumor. This can lead to significant deviations from the planned radiation dose. Although the repetition of a field over many treatment sessions tends to average out these inhomogeneities, the usual 30 fractions may still leave sizeable errors. These errors are characterized via computer simulation, and field `repainting' methods are developed to reduce them through increased dose averaging. [Preview Abstract] |
Friday, October 6, 2006 2:30PM - 2:42PM |
D2.00004: Lead Levels in Utah Eagles Michelle Arnold Lead is a health hazard to most animals, causing adverse effects to the nervous and reproductive systems if in sufficient quantity. Found in most fishing jigs and sinkers, as well as some ammunition used in hunting, this metal can poison wildlife such as eagles. Eagles are raptors, or predatory birds, and their lead exposure would most likely comes from their food -- a fish which has swallowed a sinker or lead shot in carrion (dead animal matter). As part of an ongoing project to investigate the environment lead levels in Utah, the bone lead levels in the wing bones of eagles have been measured for eagle carcasses found throughout Utah. The noninvasive technique of x-ray fluorescence was used, consisting of a Cd-109 radioactive source to activate lead atoms and a HPGe detector with digital electronics to collect the gamma spectra. Preliminary results for the eagles measured to date will be presented. [Preview Abstract] |
Friday, October 6, 2006 2:42PM - 2:54PM |
D2.00005: Modeling Wave Propagation in Cells and Tissues at the Microscopic Level Timothy Doyle, Keith Warnick Several proposed medical therapies and diagnostic methods are based on the interaction of ultrasonic or electromagnetic waves with cells and tissues at the microscopic level. To better understand these interactions, models are being developed to simulate wave propagation in tissues at the cellular level by incorporating a first-order approximation for the cell structure and multiple scattering between cells. The cells are modeled with a concentric spherical shell-core structure embedded in a medium, with the core, shell, and medium representing the nucleus, cytoplasm, and extracellular matrix respectively. Using vector multipole expansions and boundary conditions, scattering solutions are derived for a single cell with varying properties for each of the cell components. Multiple scattering between cells is simulated using addition theorems to translate the multipole fields from cell to cell and an iterative process to refine the scattering solutions. Results from ultrasonic scattering simulations are presented, including single-cell spectra and wave field images for up to several hundred cells. [Preview Abstract] |
Friday, October 6, 2006 2:54PM - 3:06PM |
D2.00006: Energy Computation for nanopore DNA sequencing with an AFM Shahid Qamar We are working on a technique to sequence the DNA with an atomic force microscope. Motivated by the experiment, we used an efficient technique to compute free energies of a DNA rotaxne molecule composed of a single strand DNA and a cyclodextrin molecule. Quantitative free energy computation involves milestoning technique with Arrhenius rate equation. The algorithm used computes the time scales of complex processes following the predetermined milestones along a reaction coordinate. A Markovian hopping mechanism was used. We performed the large scale molecular dynamics simulations at micro second level to compute the rare event kinetics which involves large scale distributed computational resources. We performed the molecular dynamics simulations for a DNA rotaxane in the absence of external force to compute the free energy differences among them. All the simulations were performed in aqueous solvent. The theoretical estimation of free energies qualitatively agrees with the experimental data obtained for nano pore DNA sequencing with an atomic force microscope. Initial results show the thermal fluctuations are dominant and the free energy differences between purine and pyrimidine is of the order of 1K$_{B}$T so the modification of DNA rotaxane is required to suppress the thermal fluctuations. [Preview Abstract] |
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