Bulletin of the American Physical Society
APS March Meeting 2015
Volume 60, Number 1
Monday–Friday, March 2–6, 2015; San Antonio, Texas
Session S33: Focus Session: Conformations and Dynamics of Biopolymers I |
Hide Abstracts |
Sponsoring Units: DBIO DPOLY Chair: Aniket Bhattacharya, University of Central Florida Room: 208 |
Thursday, March 5, 2015 8:00AM - 8:12AM |
S33.00001: Comparison of the Single Molecule Dynamics of Linear and Circular DNAs in Planar Extensional Flows Yanfei Li, Kai-Wen Hsiao, Christopher Brockman, Daniel Yates, Gregory McKenna, Charles Schroeder, Michael San Francisco, Julie Kornfield, Rae Anderson Chain topology has a profound impact on the flow behaviors of single macromolecules [1]. The absence of free ends separates circular polymers from other chain architectures, i.e., linear, star, and branched. In the present work, we study the single chain dynamics of large circular and linear DNA molecules by comparing the relaxation dynamics, steady state coil-stretch transition, and transient molecular individualism behaviors for the two types of macromolecules. To this end, large circular DNA molecules were biologically synthesized [2] and studied in a microfluidic device that has a cross-slot geometry to develop a stagnation point extensional flow [3]. Although the relaxation time of rings scales in the same way as for the linear analog, the circular polymers show quantitatively different behaviors in the steady state extension and qualitatively different behaviors during a transient stretch. The existence of some commonality between these two topologies is proposed. [1] M. Kapnistos et al., Nat. Mater. 7, 997 (2008). [2] S. Laib et al., Macromolecules 39, 4115 (2006). [3] M. Tanyeri et al., Lab Chip 11, 1786 (2011). [Preview Abstract] |
Thursday, March 5, 2015 8:12AM - 8:24AM |
S33.00002: Ratchet rectification effect on the translocation of a flexible polyelectrolyte chain induced by spatial asymmetry of the channel Debasish Mondal, Murugappan Muthukumar We report a three dimensional Langevin dynamics simulation of a uniformly charged flexible polyelectrolyte, translocating through a asymmetric narrow channel with periodically varying cross-sections, under the influence of a periodic external electric field. When reflection symmetry of the channel is broken, rectification effect is observed with a favored direction for the chain translocation. For a given volume of the channel unit and polymer length, the rectification occurs only after a threshold frequency of the external periodic driving. We also observe that the extent of the rectification depends on the length of the polyelectrolyte, geometric parameters of the channel governing the spatial asymmetry, and the strength of the external periodic driving field. The observed rectification process is interpreted in terms of an effective asymmetric periodic potential along the direction of the polymer translocation. [Preview Abstract] |
Thursday, March 5, 2015 8:24AM - 8:36AM |
S33.00003: Comparison of Translocations of Ring and Linear Polymers Ning Ouyang, Murugappan Muthukumar We compare the translocation dynamics of ring and linear polymer chains (pertinent to circular and linear DNA) through a nanopore under a driving force, using the Fokker-Planck formalism and scaling arguments. We report qualitatively different dynamics between these topologies arising from the conformational entropy of the polymer and pore-polymer interaction. [Preview Abstract] |
Thursday, March 5, 2015 8:36AM - 8:48AM |
S33.00004: Increasing polymer diffusivity by increasing the contour length: The surprising effect of YOYO-1 on DNA dynamics Seunghwan Shin, Kevin Dorfman, Xiang Cheng Double-stranded DNA (dsDNA) labeled with cyanine dyes such as YOYO-1 has been extensively used as a model to study equilibrium and dynamic properties of semiflexible polyelectrolytes. The ability to directly visualize the polymer dynamics is an attractive feature of these experiments, but positively charged cyanine dyes affect the physical properties of dsDNA, distorting the double helix and counterbalancing the intrinsic negative charge of the backbone. A variety of studies have been conducted to reveal the effect of the dye on the contour length and the persistence length of dsDNA. However, fewer efforts have been made to directly quantify the effect of dye on the diffusion behavior of dsDNA. In order to resolve this issue, we measured the in-plane diffusion coefficient of unconfined dsDNA using confocal microscopy. Although there is widespread consensus that intercalation increases the contour length of dsDNA, we find that increasing the dye:base pair ratio for YOYO-1 actually enhances the diffusion of dsDNA. This enhancement is more significant at lower ionic strengths, which implies that the increase in the diffusion coefficient by dye-DNA intercalation is mainly due to a reduction of excluded volume effect resulting from charge neutralization on the backbone. [Preview Abstract] |
Thursday, March 5, 2015 8:48AM - 9:00AM |
S33.00005: Using an effective dimensionality to map the force-extension relation for a semi-flexible polymer in a nanoslit Hendrick de Haan The force-extension relation for a semi-flexible polymer is well described by the Marko-Siggia equation in both two and three dimensions. However, while of interest for experimental systems such as DNA in nanopits, the behaviour between these limiting dimensionalities is less understood. I will present results from simulations of a polymer subject to a stretching force $F$ confined in nanoslits of varying heights $h$. Going from the 3D case to the 2D case, both the coefficients of the equation and the relevant persistence length are shown to change. This observation leads to the definition of an effective dimensionality, $d_{eff}$, to characterize the system. At low $F$, using $d_{eff}$ in a generalized form of the Marko-Siggia relation provides good agreement with the simulation curves. However, at high $F$, $d_{eff}$ drifts back towards $d=3.0$. The reason behind this $F$ dependence is discussed. Semi-empirical forms for strong and weak confinement regimes will be presented and shown to give good agreement across all slit heights and stretching forces. $d_{eff}$ is thus dependent on $h$ and $F$ and provides a cohesive physical picture for all regimes. [Preview Abstract] |
Thursday, March 5, 2015 9:00AM - 9:12AM |
S33.00006: Correlated Fluctuations of DNA Between Nanofluidic Traps Alexander Klotz, Lyndon Duong, Mikhail Mamaev, Walter Reisner Nanoconfined polymer physics has been the subject of intense investigation, yet experimental efforts have focused almost exclusively on quantifying equilibrium confined chain conformation in simple nanoslit (2D) and nanochannel (1D) geometries. Complex nano environments, defined as spaces composed of interlinked nanoscale regions of varying confinement and dimensionality, are also technologically significant and have qualitatively distinct physics. Here, a single DNA molecule is suspended between two adjacent nanocavity structures embedded in an open nanoslit. A portion of the molecule occupies each cavity with a third linker segment connecting the two. Contour fluctuates between the cavities, giving rise to observed fluctuations in the fluorescence intensity measured for each cavity. Cross-correlation of the time-dependent cavity intensities enables a noise insensitive measurement of the relaxation times for the segmental transfer modes. We explore how these relaxation times scale with cavity width and spacing and compare our results to a simple free energy model incorporating a slit-dependent linker spring energy and cavity self-exclusion cost. [Preview Abstract] |
Thursday, March 5, 2015 9:12AM - 9:24AM |
S33.00007: Metastable Tight Knots in DNA Liang Dai, C. Benjamin Renner, Patrick Doyle Knotted structures can spontaneously occur in polymers such as DNA and proteins, and the formation of knots affects biological functions, mechanical strength and rheological properties. In this work, we calculate the equilibrium size distribution of trefoil knots in linear DNA using off-lattice simulations. We observe metastable knots on DNA, as predicted by Grosberg and Rabin. Furthermore, we extend their theory to incorporate the finite width of chains and show an agreement between our simulations and the modified theory for real chains. Our results suggest localized knots spontaneously occur in long DNA and the contour length in the knot ranges from 600 to 1800 nm. [Preview Abstract] |
Thursday, March 5, 2015 9:24AM - 9:36AM |
S33.00008: Translocation of a Polymer Chain Through a Nanopore Starting From a Confining Nanotube: The Limit of high Peclet Numbers Gary W. Slater, David Sean, Hendrick de Haan We use Langevin Dynamics simulations to study a scenario where a confining nanotube is used as a way to limit the range of conformations available to a polymer chain prior to driven translocation. We find that the tube not only reduces the variance in translocation times (a useful result for practical applications), but also that the elongated polymer conformations yield longer translocation times (also a useful result) that can be dominated by the post-propagation process when the diameter of the nanotube is smaller than a universal critical value. We adapt the tension propagation theory for this geometry and find agreement with the simulations using a single friction parameter to model the roles of both the nanopore and the crowding. To gain insight into the physical mechanisms behind this effective friction, we systematically remove i) crowding on the trans-side and/or ii) monomer collisions with the membrane containing the nanopore. We find that higher Peclet numbers increase the impact of crowding on the trans side but diminish the impact of the friction between the nanopore and the polymer. [Preview Abstract] |
Thursday, March 5, 2015 9:36AM - 9:48AM |
S33.00009: Dynamics of a fluctuating semi-flexible membrane Nathaniel Tukdarian, Aiqun Huang, Ramesh Adhikari, Aniket Bhattacharya We report our preliminary studies of conformations and dynamics of a fluctuating semi-flexible membrane. Our model of membrane with linear dimension $L$ consists of $N^2$ ($L=Nb_l$) excluded volume beads connected by anharmonic springs. The stiffness of the membrane is controlled by adjusting the strength $\kappa_b$ of the bending potential $U_{\rm bend} = \kappa_b \left(1 - \hat{n}_i\cdot \hat{n}_j\right)$ between adjacent elementary plaquettes consisting of three beads at the corners connected by bonds and characterized by normal unit vectors $ \hat{n}_i$ and $\hat{n}_j$. We study the conformations and dynamic fluctuations of the membrane using Brownian dynamics simulation. We show how the radius of gyration scales with $N$ and $\kappa_b$, and study characteristics of the transverse fluctuations, the root-mean-square displacement of the center of mass, and the dynamics of the end monomers at each corner. [Preview Abstract] |
Thursday, March 5, 2015 9:48AM - 10:00AM |
S33.00010: Expanded experimental parameter space of semiflexible polymer assemblies through programmable nanomaterials David Smith, Carsten Schuldt, Jessica Lorenz, Teresa Tschirner, Maximilian Moebius-winkler, Josef Kaes, Martin Glaser, Tina Haendler, Joerg Schnauss Biologically evolved materials are often used as inspiration in the development of new materials as well as examinations into the underlying physical principles governing their behavior. For instance, the biopolymer constituents of the highly dynamic cellular cytoskeleton such as actin have inspired a deep understanding of soft polymer-based materials. However, the molecular toolbox provided by biological systems has been evolutionarily optimized to carry out the necessary functions of cells, and the inability modify basic properties such as biopolymer stiffness hinders a meticulous examination of parameter space. Using actin as inspiration, we circumvent these limitations using model systems assembled from programmable materials such as DNA. Nanorods with comparable, but controllable dimensions and mechanical properties as actin can be constructed from small sets of specially designed DNA strands. In entangled gels, these allow us to systematically determine the dependence of network mechanical properties on parameters such as persistence length and crosslink strength. At higher concentrations in the presence of local attractive forces, we see a transition to highly-ordered bundled and ``aster'' phases similar to those previously characterized in systems of actin or microtubules. [Preview Abstract] |
Thursday, March 5, 2015 10:00AM - 10:12AM |
S33.00011: Molecular stress sensors constructed from DNA Meenakshi Prabhune, Jonathan Bath, Andrew J. Turberfield, Florian Rehfeldt, Christoph F. Schmidt Molecular stress generation in cells is spatially and temporarily organized in complex patterns to drive meso-scale active processes such as intracellular transport, cell migration, or cell division. To quantitatively understand how these processes are driven, it is necessary to map local stresses inside cells, which is hard due to the lack of appropriate probes. We have designed a molecular-scale probe consisting of a self-assembled DNA hairpin with a fluorophore - quencher pair that responds to small forces (pN) applied to its ends. We demonstrate the working of this force sensor \textit{in vitro }and explore possibilities for \textit{in vivo} application to map local stress fields in cells. [Preview Abstract] |
Thursday, March 5, 2015 10:12AM - 10:24AM |
S33.00012: AFM Studies of Conformational Changes in Proteins and Peptides Nicoleta Ploscariu, Pinakin Sukthankar, John Tomich, Robert Szoszkiewicz Here, we present estimates of molecular stiffness and mechanical energy dissipation factors for some examples of proteins and peptides. The results are obtained from AFM force spectroscopy measurements. To determine molecular stiffness and mechanical energy dissipation factors we developed a model based on measuring several resonance frequencies of an AFM cantilever in contact with either single protein molecule or peptides adsorbed on arbitrary surface. We used compliant AFM cantilevers with a small aspect ratio - a ratio of length to width - in air and in liquid, including biologically relevant phosphate buffered saline medium. [Preview Abstract] |
Thursday, March 5, 2015 10:24AM - 11:00AM |
S33.00013: Reptation Theory and Many Body Effects in Semiflexible Polymer Dynamics Invited Speaker: Erwin Frey |
Follow Us |
Engage
Become an APS Member |
My APS
Renew Membership |
Information for |
About APSThe American Physical Society (APS) is a non-profit membership organization working to advance the knowledge of physics. |
© 2024 American Physical Society
| All rights reserved | Terms of Use
| Contact Us
Headquarters
1 Physics Ellipse, College Park, MD 20740-3844
(301) 209-3200
Editorial Office
100 Motor Pkwy, Suite 110, Hauppauge, NY 11788
(631) 591-4000
Office of Public Affairs
529 14th St NW, Suite 1050, Washington, D.C. 20045-2001
(202) 662-8700