Bulletin of the American Physical Society
2006 APS March Meeting
Monday–Friday, March 13–17, 2006; Baltimore, MD
Session G25: Structure and Dynamics of Functional Macromolecules |
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Sponsoring Units: DPOLY Chair: Xinyan Cui, University of Pittsburgh Room: Baltimore Convention Center 322 |
Tuesday, March 14, 2006 8:00AM - 8:36AM |
G25.00001: BREAK
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Tuesday, March 14, 2006 8:36AM - 8:48AM |
G25.00002: Structural Transitions of F-Actin:Espin Bundles Kirstin Purdy, James Bartles, Gerard Wong Espin is an actin bundling protein involved in the formation of the parallel bundles of filamentous actin in hair cell stereocilia. Mutations in espin are implicated in deafness phenotypes in mice and humans. We present measurements of the F-actin structures induced by wild type and by mutated espin obtained via small angle x-ray scattering and fluorescence microscopy. We found that wild type espin induced a paracrystalline hexagonal array of twisted F-actin, whereas the mutated espin only condensed the F-actin into a nematic-like phase. The possibility of coexisting nematic and bundled actin in mixtures containing both mutant and wild type espins was also investigated. [Preview Abstract] |
Tuesday, March 14, 2006 8:48AM - 9:00AM |
G25.00003: Nonequilibrium Self-Assembly of Linear Fibers Chenghang Zong, Ting Lu, Tongye Shen, Peter Wolynes From physical viewpoint, a dynamic bio-fiber represents an interesting one-dimensional nonequilibrium system. We construct a minimal dynamic model for this type of fibers. Our model incorporates features such as realistic dynamics rules and site resolution. The steady state solutions are obtained with the nonequilibrium variational principle. The projection of steady state distributions produces an effective potential for the pure dynamic system. We demonstrate how dynamic behaviors such as catastrophe, rescue, and dynamic instability can be analyzed under the effective reaction coordinate. [Preview Abstract] |
Tuesday, March 14, 2006 9:00AM - 9:12AM |
G25.00004: Energetics and Dynamics of Constrained Actin Filament Bundling Le Yang, David Sept, Anders Carlsson The formation of filopodia-like bundles from a dendritic actin network has been observed to occur in vitro as a result of branching induced by Arp2/3 complex. We study both the energetics and dynamics of actin filament bundling in such a network in order to evaluate their relative importance in bundle formation processes. Our model considers two semiflexible actin filaments fixed at one end and free at the other, described using a normal-mode approximation. This model is studied by both Brownian dynamics and Monte Carlo energetics methods. In the dynamic simulations, we evaluate the time required for the filaments to interact and bind, and examine the dependence of this bundling time on the filament length, the distance between the filament bases, and the crosslinking energy. For most of the cases we have studied, the energetics and dynamics simulations give similar results for critical distance. Over a broad range of conditions, we find that the times required for bundling from a network are compatible with experimental observations. [Preview Abstract] |
Tuesday, March 14, 2006 9:12AM - 9:24AM |
G25.00005: Evolution of growth modes for polyelectrolyte bundles G.H. Lai, Olena V. Zribi, Golestanian Ramin, Gerard C.L. Wong F-actin is a prototypical `hard rod' polyelectrolyte, with a charge density of $\sim $1e/2.5{\AA} and a persistence length of $\sim $5-10 $\mu $m. In the presence of multivalent ions, F-actin can condense into close-packed bundles. In this work, we use fluorescence microscopy to study the detailed growth mode of such bundles, and show how it evolves as a function of salt concentration. Preliminary results indicate that at sufficiently high salt concentrations, the bundle width is relatively insensitive to salt concentration. Moreover, the growth mode of the system changes as a function of salt concentration, varying from lateral growth (which increases the bundle width) to longitudinal growth (which increases the bundle length). [Preview Abstract] |
Tuesday, March 14, 2006 9:24AM - 9:36AM |
G25.00006: Nanoscopic tubulin rings* Hacene Boukari, Dan Sackett, Peter Schuck, Susan Krueger, Ralph Nossal We describe results of analysis of fluorescence correlation spectroscopy, small-angle neutron scattering, and sedimentation measurements of nanoscopic polymer rings formed following interactions of tubulin (100 kDa) and a small peptide, cryptophycin (340 Da). Tubulin is a ubiquitous dimeric protein found in eukaryotic cells, and is the building block of microtubules, which are dynamical biopolymers involved in many critical cell functions. The peptide, which is a marine natural product, inhibits the formation of microtubules and, instead, induces the formation of the rings. Under the studied conditions these rings appear rigid, have circular geometry ($\sim $ 25 nm dia.), are monodisperse in size (8 tubulin dimers/ring), and are stable even with tubulin concentration as low as 1 nM. Remarkably, no intermediate oligomers (partial rings or others) are observed. Further, structural and hydrodynamic modeling confirms the number (8) of tubulin dimers per ring and shows that the tubulin monomers are not spherical, consistent with their known crystallographic structure. *H. Boukari, R. Nossal, D. Sackett, and P. Schuck, PRL 93, 98106 (2004). [Preview Abstract] |
Tuesday, March 14, 2006 9:36AM - 9:48AM |
G25.00007: Deformation of DNA and Polymer Labels during End-Labelled Free-Solution Electrophoresis. Gary W. Slater, Laurette C. McCormick Recent advancements to DNA sequencing by End Labelled Free Solution Electrophoresis (ELFSE) show the promise of this novel technique which overcomes the need for a gel by using a label (or \textit{drag-tag}) to render the free solution mobility of the DNA size-dependent. It is the attachment of an uncharged drag-tag molecule of a set size to all the various lengths of DNA in the sample that selectively slows down smaller DNA chains which have less force to pull the drag-tag than larger DNA. Taking advantage of the modified hydrodynamic properties of tagged DNA, ELFSE has been used to successfully sequence up to about 100 bases of DNA in the absence of a gel or other sieving. So far, only globally random coil conformations have been associated with ELFSE, i.e. the DNA and the label together form a single, undeformed hydrodynamic unit. However, next generation labels combined with high field strengths may allow for deformation of the DNA and/or a polymer label. We present here the necessary conditions for stretching, and some of the subsequent effects on separation, highlighting possible improvements to ELFSE performance via stretching of DNA and/or the polymer label. [Preview Abstract] |
Tuesday, March 14, 2006 9:48AM - 10:00AM |
G25.00008: Ferroelectric-specific peptides as building blocks for bio-inorganic devices Brian Reiss, Guo-Ren Bai, Orlando Auciello, Lenidas Ocola, Millicent Firestone Combinatorial phage display methods have been used to identify a circularly constrained heptapeptide sequence, ISLLHST, that strongly associates with a perovskite ferroelectric, lead zirconium titanate, Pb(Zr$_{x}$Ti$_{1-x})$O$_{3}$ (PZT). The affinity and selectively of binding to polycrystalline MOCVD deposited PZT thin films supported on Si/SiO$_{2}$/Pt substrates were determined by titering and immunofluorescence microscopy, and the peptide was shown to selectively bind PZT in the presence of Pt, Si, Au, and several different photoresists. Ferroelectric properties were determined by measurement of the $P-E$ hysteresis loop on unmodified and phage bound PZT thin films, and no change in the coercive field, E$_{c}$, or the saturation polarization, P$_{s}$ was observed after contacting the PZT with aqueous buffer or phage binding. This work represents an important first step towards rendering perovskite ferroelectrics compatible with biological molecules. Work is currently underway to study how conformational and positional control of tethered biomolecules can be controlled by the surface charge and/or polarization state of PZT as well as integration into several proto-type device architectures. [Preview Abstract] |
Tuesday, March 14, 2006 10:00AM - 10:12AM |
G25.00009: Bio-based Polymer Foam from Soyoil Laetitia M. Bonnaillie, Richard P. Wool The growing bio-based polymeric foam industry is presently lead by plant oil-based polyols for polyurethanes and starch foams. We developed a new resilient, thermosetting foam system with a bio-based content higher than 80{\%}. The acrylated epoxidized soybean oil and its fatty acid monomers is foamed with pressurized carbon dioxide and cured with free-radical initiators. The foam structure and pore dynamics are highly dependent on the temperature, viscosity and extent of reaction. Low-temperature cure hinds the destructive pore coalescence and the application of a controlled vacuum results in foams with lower densities $\sim $ 0.1 g/cc, but larger cells. We analyze the physics of foam formation and stability, as well as the structure and mechanical properties of the cured foam using rigidity percolation theory. The parameters studied include temperature, vacuum applied, and cross-link density. Additives bring additional improvements: nucleating agents and surfactants help produce foams with a high concentration of small cells and low bulk density. Hard and soft thermosetting foams with a bio content superior to 80{\%} are successfully produced and tested. Potential applications include foam-core composites for hurricane-resistant housing, structural reinforcement for windmill blades, and tissue scaffolds. [Preview Abstract] |
Tuesday, March 14, 2006 10:12AM - 10:24AM |
G25.00010: Calculation of the Vibrational Continuum in Helical Polymers from First Principles: Application to Single-walled Carbon Nanotubes Hadley Lawler, Carter White, John Mintmire A first-principles method for calculation of the full vibrational continuum in helical polymers is presented, with application to chiral single-walled carbon nanotubes. The dynamical matrix is calculated within a helical symmetry, utilizing a cylindrical basis for nuclear displacements. Sum rules within a helical symmetry, helical speeds of sound and helical flexure modes are addressed. [Preview Abstract] |
Tuesday, March 14, 2006 10:24AM - 10:36AM |
G25.00011: Optimizing the Geometry of Patterned Polymer Separation Media David Hoagland, Helmut Strey A quantitative understanding of polymer transport in patterned polymer separation media would guide the design of media with optimized pattern geometries. For example, one might desire to know what confinement geometry best separates linear polymers by molecular weight as a driving field is applied to a polymer mixture. By asserting that transport is controlled by steric interactions with a periodic pore structure, and that the driving field is low enough for a linearity in the relationship between transport rate and field magnitude, we have derived a simple, general expression for polymer mobility as a function of parameters characterizing polymer and pattern. Our expression can be used to derive optimized separation geometries that can be produced by micro- or nano-lithography methods. Analysis will be discussed for several pattern geometries that exert periodic constriction on migrating polymers. Financial support: UMass MRSEC [Preview Abstract] |
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