Bulletin of the American Physical Society
2009 APS March Meeting
Volume 54, Number 1
Monday–Friday, March 16–20, 2009; Pittsburgh, Pennsylvania
Session W15: Biologically Inspired Physics: Self-Assembly, Filaments, Membranes |
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Sponsoring Units: DFD Chair: Norm Wagner, University of Delaware Room: 316 |
Thursday, March 19, 2009 11:15AM - 11:27AM |
W15.00001: Assembly and melting of DNA nanotubes and tile lattices Thomas Sobey, Stephan Renner, Friedrich Simmel Programmable molecular self-assembly using DNA is allowing the demonstration of increasingly novel nanoscale structures such as lattices and tubes. Understanding the assembly and melting pathways of these will allow us to develop more complex and/or stable structures, and potentially useful nanomaterials. We experimentally show differences in these pathways by correlating temperature-controlled UV absorption measurements with atomic force microscopy, fluorescence microscopy, and transmission electron microscopy measurements. The three-dimensional nanotubes assemble in several hierarchical steps but melt in a single step, and this contrast is proposed to arise from the fundamental distinction between three-dimensional closed tubes and two-dimensional open lattices. [Preview Abstract] |
Thursday, March 19, 2009 11:27AM - 11:39AM |
W15.00002: Response of a self-assembling to mechanical stress Yves Dubief, Ross Packard, Sreedhar Manchu, Leonie Cowley Coarse-grained molecular dynamics is used to characterize the mechanical properties of a solution of phospholipids and polyelectrolytes under shear and compression. DPPC (1,2-Dipalmitoylphosphatidylcholine), polyelectrolyes and water are coarse-grained using the MARTINI force field. Simulations are performed using both GROMACS and LAMMPS. In our simulation, the solution is confined by two rigid walls. The objective of this work is (i) to study influence of the electrostatic nature of the wall on the self-assembling structure of the solution and (ii) to define the rheological and structural response of the solution under shear and compression by moving one wall. [Preview Abstract] |
Thursday, March 19, 2009 11:39AM - 11:51AM |
W15.00003: Self-assembling structures resulting from the presence of polyelectrolytes in a solution of phospholipids Ross Packard, Yves Dubief The objective of this study is the characterization of self-assembled structures formed by the combination of phospholipids and polyelectrolytes. Coarse-grained molecular dynamics is used to simulate solutions of DPPC (1,2-Dipalmitoylphosphatidylcholine) and polyelectrolyes in three dimensional periodic domain. The MARTINI database defines the topology of coarse-grained macromolecules and water and simulations are performed using GROMACS. The interaction between negatively charged polyelectrolytes and positively charged hydrophilic heads of DPPC causes the disruption of lipid bilayer membranes and vesicles. The study attempts to define the conditions necessary for the formation of vesicles or organized networks of lipid bilayers that encapsulate the polyelectrolytes. Such structures are suspected to play an important role in biological fluids subject to large mechanical stress. [Preview Abstract] |
Thursday, March 19, 2009 11:51AM - 12:03PM |
W15.00004: Self-organized Gels in DNA/F-Actin mixtures without Crosslinkers John Butler, Ghee Hwee Lai, Olena Zribi, Ivan Smalyukh, Thomas Angelini, Kirstin Purdy, Ramin Golestanian, Gerard C. L. Wong Interactions between flexible chains and rigid rods govern a broad range of soft matter systems. As a model system of like-charged rigid rods and flexible chains, we examine mixtures of DNA and filamentous actin (F-actin). Confocal microscopy reveals the formation of elongated nematic F-actin domains reticulated via defect-free vertices into a network embedded in a mesh of random DNA. Synchrotron small-angle x-ray scattering (SAXS) indicates that the DNA mesh squeezes the F-actin domains into a nematic state with an inter-actin spacing that decreases with increasing DNA concentration. Salt strongly influences the domain sizes and transitions the system from a counterion-controlled regime to a depletion-controlled regime, both mechanisms of which are entropic in origin. [Preview Abstract] |
Thursday, March 19, 2009 12:03PM - 12:15PM |
W15.00005: Modeling the hydrophobic effect by coupling solutes to a lattice gas Amish Patel, David Chandler In problems of biological assembly, manifestation of the hydrophobic effect is complex depending on the size as well as the conformation of the solute. The solute disrupts the inherent structure of the solvent by causing an unbalancing of attractive interactions experienced by the solvent molecules The extent of this disruption determines the relative ease with which the solute is solvated. The theory of Lum, Chandler and Weeks (LCW) successfully describes this rich interplay between the solute and solvent structures by coarse-graining the solvent density and analytically integrating out solvent fluctuations on length-scales smaller than the coarse-graining length ($L_{c})$. Since the implementation of LCW theory can be computationally very demanding the coarse-grained solvent density was mapped onto a lattice gas by ten Wolde, Sun and Chandler. In this work, we further improve upon the theory by relaxing certain assumptions about the unbalancing of attractive interactions on length scales smaller than $L_{c}$. In addition to a brief overview of the theory, results obtained by application of the theory to several pertinent problems of hydrophobic assembly will be presented. [Preview Abstract] |
Thursday, March 19, 2009 12:15PM - 12:27PM |
W15.00006: Direct Measurement of Inter-filament Forces in Neurofilament Networks: Synchrotron X-ray Diffraction Study under Osmotic Pressure R. Beck, J. Deek, C.R. Safinya Neurofilaments (NFs) are the major protein constituents in neuronal processes (axons and dendrites) that impart mechanical stability and act as structural scaffolds. The filaments assemble from 3 different subunit proteins (NF-L, NF-M, NF-H) to form a 10 nm diameter flexible polymer with radiating unstructured sidearms. Recent work, showed that at high protein concentration, the NFs form a nematic hydrogel network with a well-defined interfilament spacing as can be measured by synchrotron small angle x-ray scattering (SAXS) [1]. In order to directly elucidate the interfilament forces responsible for the mechanical properties of NFs hydrogel, we conducted a SAXS-osmotic pressure study, which yielded pressure-distance curves at different subunit compositions and monovalent salts. We show that filaments composed with NF-L and NF-M strongly attract each other through their polyampholyte sidearms, in particularly at high monovalent salt. However, filaments comprised of NF-L and NF-H, show a distinctly different pressure-distance dependency, with much larger interfilament spacing and weaker salt dependence. Supported by DOE DE-FG-02-06ER46314, NIH GM-59288, NSF DMR-0803103, and the Human Frontier Science Program organization. [1] J.B. Jones, C.R. Safinya, Biophys. J. \textbf{95, }823 (2008) [Preview Abstract] |
Thursday, March 19, 2009 12:27PM - 12:39PM |
W15.00007: Flexible ferromagnetic filaments and the interface with biology Andrejs Cebers, Mihails Belovs, Kaspars Erglis Flexible ferromagnetic filaments exist in Nature (magnetotactic bacteria use them for the navigation purposes in the magnetic field of the Earth) and may be synthesized artificially by linking the functionalized ferromagnetic particles by DNA fragments of definite length. Ferromagnetic filaments allow to mimic self-propulsion of microorganisms by using AC magnetic fields. It is investigated both theoretically and experimentally. The elastic properties of the filaments are studied by kinetics of their orientation in an AC magnetic field of enough high frequency and allow to describe the observed deformation of the filaments at reversal of the magnetic field. By numerical analysis the Floquet coefficients for the dynamics of ferromagnetic filaments are calculated and the existence of stationary oscillations of U-like shapes is confirmed. These shapes self-propel perpendicularly to the AC magnetic field. [Preview Abstract] |
Thursday, March 19, 2009 12:39PM - 12:51PM |
W15.00008: Electrokinetic effects near a membrane David Lacoste We discuss the electrostatic and electrokinetic contribution to the elastic moduli of a cell or artificial membrane placed in an electrolyte and driven by a DC electric field. The field drives ion currents across the membrane, through specific channels, pumps or natural pores. In steady state, charges accumulate in the Debye layers close to the membrane, modifying the membrane elastic moduli. We first study a model of a membrane of zero thickness, later generalizing this treatment to allow for a finite thickness and finite dielectric constant. Our results clarify and extend the results presented in [D.\ Lacoste, M.\ Cosentino Lagomarsino, and J.\ F.\ Joanny, Europhys. Lett., {\bf 77}, 18006 (2007)], by providing a physical explanation for a destabilizing term proportional to $kps^3$ in the fluctuation spectrum, which we relate to a nonlinear ($E^2$) electro-kinetic effect called induced-charge electro-osmosis (ICEO). Recent studies of ICEO have focused on electrodes and polarizable particles, where an applied bulk field is perturbed by capacitive charging of the double layer and drives flow along the field axis toward surface protrusions; we predict similar ICEO flows around driven membranes, due to curvature-induced tangential fields within a non-equilibrium double layer, which hydrodynamically enhance protrusions. [Preview Abstract] |
Thursday, March 19, 2009 12:51PM - 1:03PM |
W15.00009: Piezoelectricity of Fluid Lipid Lamellar Phases and Their Chirality Dependence John Harden, Nicholas Diorio, Alexander Petrov, Antal Jakli The effects of chirality of membrane-forming lipids, has been largely ignored at present. Here we demonstrate that the chirality of phospholipids makes fluid lipid bilayers piezoelectric. This implies that chiral lipids would play a central role in the functioning of cell membranes as active mechano-transducers. By periodically shearing and compressing nonaqueous lamellar phases of left (L-alpha-Phosphatidylcholine), right (D-alpha-Phosphatidylcholine) and racemic (DL-alpha-Phosphatidylcholine) lipids, we induced a tilt of the molecules with respect to the bilayer's normal and produced an electric current perpendicular to the tilt plane with the chiral lipids but not with a racemic mixture. This effect occurs because the lipids from a SmA* phase liquid crystal structure of the bilayers. Under molecular tilt, a ferroelectric SmC* phase is formed, creating a polarization which is normal to the tilt plane. This coupling allows for a wide variety of sensory possibilities of cell membranes such as mechano-reception, magneto-sensitivity, as well as in-plane proton membrane transport and related phenomena like ATP-synthesis, soft molecular machine performance, etc. [Preview Abstract] |
Thursday, March 19, 2009 1:03PM - 1:15PM |
W15.00010: Biomotor-functionalized Nanowires for Nanobio-mechanical Applications Dong Shin Choi, Kyung-Eun Byun, Eunhee Cho, Moon-Sook Lee, Seunghun Hong Protein motors such as actomyosin have shown the possibility as a building block for bio-inspired nanomechanical applications such as protein motor-based nanoscale engines. For such applications, it is crucial to combine protein motors with inorganic nanostructure such as nanowires. However, it has been difficult to functionalize nanowires/nanotubes with biological motors due to the incompatibility of such nanostructures with biomotors. Herein, we present a method to functionalize nanowires with biomotors while maintaining their functionalities. Significantly, we successfully demonstrated various motility assays using biomotor-functionalized nanowires, such as the delivery of nanowires functionalized with actin filaments on solid substrates. [Preview Abstract] |
Thursday, March 19, 2009 1:15PM - 1:27PM |
W15.00011: Non-monotonic mobility vs. length dependence observed in electrophoretic separation of 25 bp DNA ladder in Pluronic gels. Seungyong You, David Van Winkle We electrophoresed a double-stranded DNA ladder first in an agarose gel, then in gels of Pluronic F-127 at room temperature. The DNA ladder consisted of 19 discrete fragments ranging in length from 25 to 450 bp at 25 bp increments plus 500 bp. The DNA fragments were first separated in agarose gel and stacked normally with 25 bp having the highest mobility. A single lane of the separated DNA ladder in the agarose gel was inserted at the edge of a Pluronic gel slab. The DNA was electrophoresed from the agarose into the Pluronic gels perpendicular to the original separation axis. Mobilities of DNA fragments increased from 25 bp to 175 bp and then decreased from 175 bp to 500 bp. The 25 bp and 500 bp bands of the ladder had approximately the same mobility in several different Pluronic gel concentrations. Both were slower than most bands in between. The highest mobility fragments with length of 175 bp have 59.5 nm contour length which is about 3.5 times the diameter of a micelle (17 nm). This result suggests a crossover from chromatographic separation to electrophoretic separation for these short DNAs. This research is supported by the state of Florida (Martech) and Research Corporation. [Preview Abstract] |
Thursday, March 19, 2009 1:27PM - 1:39PM |
W15.00012: Partition function and space-filling fractal-like networks of branching tubes Samir Lipovaca We may think of the probability in quantum mechanics as a sort of fluid that flows from one point to another continuously and without loss or gain. We will utilize this fluid idea and imagine that probability flows through a space-filling fractal-like networks of branching tubes similar to the networks of a general model for the origin of allometric scaling laws in biology. In the general model, scaling laws arise from the interplay between physical and geometric constraints. This model provides a complete analysis of scaling relations for mammalian circulatory systems that are in agreement with data. We will show that there is a connection between a quantum system in thermal equilibrium and space-filling fractal-like networks. The relationship will be revealed through the calculation of the total fluid (probability) network volume. We will show that this total volume is proportional to the partition function of the related quantum system. [Preview Abstract] |
Thursday, March 19, 2009 1:39PM - 1:51PM |
W15.00013: The impact of conformational fluctuations on self-assembly: Cooperative aggregation of archaeal chaperonin proteins Stephen Whitelam, Carl Rogers, Andrea Pasqua, Chad Paavola, Jonathan Trent, Phillip Geissler Protein complexes called rosettasomes self-assemble in solution to form large-scale filamentous and planar structures. The relative abundance of these aggregates varies abruptly with environmental conditions and sample composition. Our simulations of a model of patchy nanoparticles can reproduce this sharp crossover, but only if particles are allowed to switch between two internal states favoring different geometries of local binding. These results demonstrate how local conformational adaptivity can fundamentally influence the cooperativity of pattern-forming dynamics. [Preview Abstract] |
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