Bulletin of the American Physical Society
75th Annual Meeting of the Southeastern Section of APS
Volume 53, Number 13
Thursday–Saturday, October 30–November 1 2008; Raleigh, North Carolina
Session DC: Biophysics II |
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Chair: Amy Oldenbrug, University of North Carolina Room: Holiday Inn Brownstone Lincoln |
Thursday, October 30, 2008 1:30PM - 1:42PM |
DC.00001: Dynamics of Individual cilia to external loading- A simple one dimensional picture Vinay Swaminathan, David Hill, R. Superfine From being called the cellular janitors to swinging debauchers, cilia have captured the fascinations of researchers for over 200 years. In cystic fibrosis and chronic obstructive pulmonary disease where the cilia loses it's function, the protective mucus layer in the lung thickens and mucociliary clearance breaks down, leading to inflammation along the airways and an increased rate of infection. The mechanistic understanding of mucus clearance depends on a quantitative assessment of the axoneme dynamics and the maximum force the cilia are capable of generating and imparting to the mucus layer. Similar to the situation in molecular motors, detailed quantitative measurements of dynamics under applied load conditions are expected to be essential in developing predictive models. Based on our measurements of the dynamics of individual ciliary motion in the human bronchial epithelial cell under the application of an applied load, we present a simple one dimensional model for the axoneme dynamics and quantify the axoneme stiffness, the internal force generated by the axoneme, the stall force and show how the dynamics sheds insight on the time dependence of the internal force generation. The internal force generated by the axoneme is related to the ability of cilia to propel fluids and to their potential role in force sensing. [Preview Abstract] |
Thursday, October 30, 2008 1:42PM - 1:54PM |
DC.00002: Directed Fluid Transport with Biomimetic ``Silia'' Arrays A.R. Shields, B.A. Evans, B.L. Carstens, M.R. Falvo, S. Washburn, R. Superfine We present results on the long-range, directed fluid transport produced by the collective beating of arrays of biomimetic ``silia.'' Silia are arrays of free-standing nanorods roughly the size of biological cilia, which we fabricate from a polymer-magnetic nanoparticle composite material. With external permanent magnets we actuate our silia such that their motion mimics the beating of biological cilia. Biological cilia have evolved to produce microscale fluid transport and are increasingly being recognized as critical components in a wide range of biological systems. However, despite much effort cilia generated fluid flows remain an area of active study. In the last decade, cilia-driven fluid flow in the embryonic node of vertebrates has been implicated as the initial left-right symmetry breaking event in these embryos. With silia we generate directional fluid transport by mimicking the tilted conical beating of these nodal cilia and seek to answer open questions about the nature of particle advection in such a system. By seeding fluorescent microparticles into the fluid we have noted the existence of two distinct flow regimes. The fluid flow is directional and coherent above the tips of the silia, while between the silia tips and floor particle motion is complicated and suggestive of chaotic advection. [Preview Abstract] |
Thursday, October 30, 2008 1:54PM - 2:06PM |
DC.00003: A Novel Silicone-Magnetite Composite Material Used in the Fabrication of Biomimetic Cilia B.L. Carstens, B.A. Evans, A.R. Shields, J. Su, S. Washburn, M.R. Falvo, R. Superfine We have developed a novel polymer-magnetite composite that we use to fabricate arrays of magnetically actuable biomimetic cilia. Biomimetic cilia are flexible nanorods 750 nm in diameter and 25 microns tall. They generate fluid flows similar to those produced by biological cilia. Polymer-magnetic nanoparticle materials such as ours are becoming increasingly useful in biomedical applications and microelectromechanical systems (MEMS). Comprised of magnetite (Fe3O4), the nanoparticles have a diameter of 5-7 nm and are complexed with a silicone copolymer and crosslinked into a flexible, magnetic solid. Amine groups make up 6-7 percent of the silicone copolymer, providing a simple means of functionalization. We present a detailed mechanical and magnetic analysis of our bulk crosslinked material. The high-aspect ratio biomimetic cilia we create with this magnetite-copolymer complex may have applications in microfluidic mixing, biofouling, and MEMS. [Preview Abstract] |
Thursday, October 30, 2008 2:06PM - 2:18PM |
DC.00004: In-situ AFM measurement of single fibrin fiber stiffness before and after addition of Factor XIII John Houser, E. Timothy O'Brien, Susan T. Lord, Richard Superfine, Michael R. Falvo Fibrin fibers are the main structural component of blood clots. Ligation of fibrin by native Factor XIII (FXIII) serves to fine tune the mechanical properties of the clot. Mechanical alteration is important because a clot must be stiff enough to resist forces from blood flow but compliant enough to prevent embolism (fracture). Cone and Plate measurements of fibrin gels, which represent the vast majority of mechanical measurements on fibrin, show that FXIII increases clot stiffness. More recently, measurements on individual fibrin fibers show that they exhibit remarkable extensibility, breaking at strains up to 300{\%}. As of yet, the origin of this extensibility is not fully understood. The different responses of ligated and unligated fibrin fibers can give us clues as to it's mechanism of extension. We use a combined fluorescence/atomic force microscope to stretch individual, isolated, fibrin fibers and then compare force extension curves of the same fiber before and after addition of FXIII. We found up to a 3.5-fold increase in fiber stiffness after addition of FXIII. We also show stiffening of individual fibrin fibers after crosslinking by gluteraldehyde. [Preview Abstract] |
Thursday, October 30, 2008 2:18PM - 2:30PM |
DC.00005: The role of single fiber strain stiffening in fibrin networks Nathan Hudson, Daniel Millard, John Houser, E. Timothy O'Brien, Susan Lord, Richard Superfine, Michael Falvo The mechanical properties of fibrin networks, the primary structural component of blood clots, are of great interest both from a biophysics and biomedical perspective. We take a novel approach to studying fibrin network mechanical properties using a combination fluorescence/atomic force microscope system to quantitatively manipulate and visualize the network. Many biological gels exhibit non-linear elasticity known as strain stiffening, but the origins of this behavior are not well understood. We hypothesized that the strain stiffening of individual fibers plays a role in the response of the overall network, and the data indicate that some of the individual fibers within a network do strain stiffen and distribute strain to less strained fiber segments. Each network pulled was also compared to a linear spring model of the same geometry. Preliminary analysis showing a difference between the strain distributions in the model and the actual network will be presented. [Preview Abstract] |
Thursday, October 30, 2008 2:30PM - 2:42PM |
DC.00006: Observation of molecular rings formed from DNA deposited on Au(111) Pengshun Luo, Michael S. Woody, Norman L. Bemelmans, Thomas P. Pearl Beside its biological functions, DNA has been used as a building block for biological sensors and a template for electronic nanostructures. These applications require a deep understanding of how DNA molecules organize on particular surfaces as well as the electronic properties of an individual DNA molecule. Using scanning tunneling microscopy (STM) and atomic force microscopy (AFM), we have successfully characterized DNA deposited on Au(111), of various strand lengths and sequences. Here we report the observation of ring-like structures formed on the Au(111) surface by adsorption of 45 bp long, double stranded DNA. To understand the nature of these structures, deposition parameters such as DNA concentration, exposure time, and buffer solution were varied. In an attempt to gain more insight into the structures, a computer model was constructed based on electrostatic interaction between the DNA molecules. This model provides additional information about the composition and formation mechanisms of the ring structures. [Preview Abstract] |
Thursday, October 30, 2008 2:42PM - 2:54PM |
DC.00007: An investigation of the structural transitions between different forms of DNA using the Adaptively Biased (ABMD) and Steered Molecular Dynamics Methods Mahmoud Moradi, Volodymyr Babin, Christopher Roland, Thomas A. Darden, Celeste Sagui Left-handed A-DNA and B-DNA along with right-handed Z-DNA, are believed to be the three main biologically active double-helix structures associated with DNA. The free energy differences associated with the A to B-DNA, and B to Z-DNA transitions in an implicit solvent environment have been investigated using the recently developed Adaptively Biased Molecular Dynamics (ABMD) method, with the RMSD as the collective variable associated with the former transition, and handedness and radius of gyration as the collective variables associated with the latter. The ABMD method belongs to the general category of umbrella sampling methods with a time-dependent potential, and allows for an accurate estimation of the free energy barriers associated with the transitions. The results are compared to those obtained using the Steered Molecular Dynamics method, and ultimately are used in order to gain insight into the microscopics of the DNA transitions. [Preview Abstract] |
Thursday, October 30, 2008 2:54PM - 3:06PM |
DC.00008: The free energy landscape of short polyproline peptides Mahmoud Moradi, Volodymyr Babin, Christopher Roland, Thomas A. Darden, Celeste Sagui Polyproline is a peptide whose configurations include both left- and right-handed helices. The free energy landscapes of polyproline peptides, as a function of the collective variables of handedness and radius of gyration, were calculated using the recently introduced Adaptively Biased Molecular Dynamics (ABMD) method. The ABMD method, which belongs to the general category of umbrella sampling methods with a time-dependent potential -- when combined with replica exchange, multiple walkers and umbrella correction runs -- allows for the efficient and accurate determination of the free energy maps. In turn, these free energy maps allow for an estimation of the transition pathways and barriers connecting the different helical structures, which are discussed for polyproline in vacuo, in implicit water, and the organic solvents hexane and propanol. [Preview Abstract] |
Thursday, October 30, 2008 3:06PM - 3:18PM |
DC.00009: Stochastic energetics of a Brownian motor driven by position dependent temperature Ronald Benjamin, Ryoichi Kawai We study the energetics of a Brownian motor driven by position dependent temperature, also known as the B{\"u}ttiker-Landauer motor. Overdamped models fail to predict the energetics when temperature is spatially inhomogeneous. Its found that the irreversible heat transfer via kinetic energy diverges as $\sqrt{M}$ (M being the mass of the Brownian particle) and cannot be accounted for by the overdamped model. The motor can never attain Carnot efficiency as evidenced by our results obtained from numerical solution of the Lahngevin equation and first principles molecular dynamics simulation. We also show that the motor can be converted into a refrigerator and find that the Coefficient of Performance (COP) of the refrigerator is far below the Carnot COP. Onsager symmetry relationship which links the motor to the refrigerator is confirmed in the presence of inhomogeneous temperature. Mechanisms to enhance the motor efficiency and refrigerator COP are also discussed. [Preview Abstract] |
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