Bulletin of the American Physical Society
APS March Meeting 2011
Volume 56, Number 1
Monday–Friday, March 21–25, 2011; Dallas, Texas
Session Q43: Focus Session: Translocation through Nanopores I |
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Sponsoring Units: DPOLY DBP Chair: Aniket Bhattacharya, University of Central Florida Room: A306/307 |
Wednesday, March 23, 2011 11:15AM - 11:27AM |
Q43.00001: A Coupled-Dynamics Model for Polymer Translocation Timo Ikonen, Tapio Ala-Nissila, Aniket Bhattacharya, Wokyung Sung We study a coarse-grained model of driven translocation of biopolymers, which comprises coupled equations of motion for the translocation coordinate $s$ and the spatial coordinates for the first and the last bead of the translocating chain. We use Langevin dynamics simulations to solve the equations of motion and to study the dynamics of translocation through a nanopore, including the residence time distribution of the individual monomers and the average translocation time. In addition, we consider the time evolution of the spatial coordinates of the first and last bead, which underline the asymmetry of the dynamical chain conformations on the $cis$ and $trans$ sides. [Preview Abstract] |
Wednesday, March 23, 2011 11:27AM - 11:39AM |
Q43.00002: A new approach to polymer translocation Johan Dubbeldam, Vakhtang Rostiashvili, Andrey Milchev, Thomas Vilgis Polymer translocation is ubiquitous in nature. It plays a role in phenomena like virus infections and in trafficking of proteins through pores in a cell membrane. Many theoretical models have been developed to explain scaling properties of simple polymer chains through tiny nanopores. This has not resolved the controversies in this field, however. In this paper we employ novel methods to shed light on the results that were obtained using the different models that are in use today. We use, for example fractional Brownian motion to explain the scaling of the variance in the translocation length with time and find good agreement between simulation results and theoretical predictions. An extension of the theory to nanopores with more complex geometries are discussed. [Preview Abstract] |
Wednesday, March 23, 2011 11:39AM - 11:51AM |
Q43.00003: Stepping dsDNA through a solid-state nanopore one basepair at a time Anthony Ho, Jeffrey Comer, Aleksei Aksimentiev Solid-state nanopores hold great promise for single-molecule detection and manipulation, including low-cost, high-speed DNA sequencing. In a typical experiment, single molecules of DNA are driven through a nanopore by applying an electric potential difference across the membrane. As DNA passes through the pore, it modulates the ionic current, which potentially can be used to determine the DNA sequence. However, the typical rate of DNA transport in experiment is too high for detection of DNA sequences by ionic current measurement. It has been shown that it is possible to slow and weakly trap dsDNA in solid-state nanopores with diameters smaller than that of dsDNA [Nanotechnology 21:395501]. Using all-atom molecular dynamics simulations, we demonstrate that such pores can be used not only to trap but also to displace dsDNA in discrete steps using nanosecond-long pulses of electric field. Specifically, we have identified the pore geometry and pulse profiles that impel dsDNA by one basepair when the pulse is on and retain dsDNA in the same position when the pulse is off. Such nanopore traps may offer new means for manipulating single molecules in biophysics experiments. [Preview Abstract] |
Wednesday, March 23, 2011 11:51AM - 12:27PM |
Q43.00004: Universal and Non-Universal Translocation Dynamics of Coarse-Grained Biopolymers Invited Speaker: I will discuss recent progress on the dynamical scaling of coarse-grained models of (bio)polymers under spontaneous and forced translocation. [Preview Abstract] |
Wednesday, March 23, 2011 12:27PM - 12:39PM |
Q43.00005: DNA translocation through grapheme nanopores Christopher A. Merchant, Ken Healy, Meni Wanunu, Vishva Ray, Neil Peterman, John Bartel, Michael D. Fischbein, Kim Venta, Zhengtang Luo, A.T. Charlie Johnson, Marija Drndic We report on DNA translocations through nanopores created in graphene membranes. Devices consist of nanometer-thick graphene membranes with electron-beam sculpted nanopores. Due to the thin nature of the graphene membranes, we observe larger blocked currents than for traditional solid-state nanopores. Unlike traditional solid-state nanopore materials that are insulating, graphene is an excellent electrical conductor. Use of graphene as a membrane material opens the door to a new class of nanopore devices in which electronic sensing and control are performed directly at the pore. [Preview Abstract] |
Wednesday, March 23, 2011 12:39PM - 12:51PM |
Q43.00006: Characterization of DNA Translocation and Detection in Functionalized Nanopores Yaling Liu, Abhijit Ramachandran, Qingjiang Guo Functionalized nanopores have been used in selective detective of DNA. While the interaction between a bare nanopore and a DNA has been analyzed extensively, little is know for that of a functionalized nanopore. This work focuses on studying the DNA translocation dynamics and mechanism of DNA sequencing in a functionalized nanopore through a coarse-grained molecular dynamics model. Physical properties of chemically modified nanopores, i.e., the effective pore diameter under different bias voltages are characterized. The DNA translocation dynamics under different nanopore coatings and different bias voltages are studied. The simulation results reveal that molecular selective translocation larges lies on the flexibility and orientation of the coating molecules and their interaction with the translocating DNA. This research supports rational designs of DNA transportation- and manipulation-based diagnostic systems. [Preview Abstract] |
Wednesday, March 23, 2011 12:51PM - 1:03PM |
Q43.00007: Direct observation of DNA motions into solid state nanopore under applied electrical potentials on conductive surface Yoshitaka Hayashi, Genki Ando, Ichiro Idutsu, Toshiyuki Mitsui Solid state nanopore is one of emerging methods for rapid single DNA molecule detection because the translocation of the DNA though nanopore produces ionic current changes. One of issues in this method is clogging long DNA molecules. Once DNA molecules clogged, the molecules are rarely removed by varying or switching the polarity of applied bias voltages across the nanopore. We develop a modified nanopore by 50nm Au coating on top of the nanopore surface to be able to remove the clogged DNA molecules during the DNA translocation experiment. Fluorescence microscopy was implemented for observation of stained DNA molecules. The nanopores with diameters near 100 nm can be used initially. DNA translocation rates changes dramatically by tuning the applied electrical potentials on surface higher or lower than the potentials across the nanopore. Furthermore, the Au potentials modifies IV characteristic of the ionic current across the nanopore which is similar to the gate voltages controlling the SD current in FET. We will discuss the influence of surface potential on DNA motion and translocation and clogged DNA molecules. Finally, we will present the recent results of DNA translocation into the SiN-Au-SiO2 nanopore and discuss the effect of applied voltages on Au. [Preview Abstract] |
Wednesday, March 23, 2011 1:03PM - 1:15PM |
Q43.00008: Polymer Translocation through a Nanopore in the Presence of a Viscosity Gradient Hendrick W. de Haan, Gary W. Slater Of interest for both biological and technological applications, the translocation of a polymer across a membrane through a nanopore has been studied via simulations under a great variety of conditions. In this work, results will be presented from Langevin Dynamics (LD) simulations of polymer translocation where the viscosity on the $cis$ side of the membrane is different from the viscosity on the $trans$ side - a scenario both applicable to biological instances of translocation and replicable with artificial nanopores. Starting with the polymer halfway through the pore, the establishment of a preferential direction for large viscosity differences is observed. To investigate the origin of this effect, a simple model of the system as a 1D biased random walker in a viscosity gradient is explored by Monte Carlo and LD simulations. Good agreement between the simple model and the full polymer simulations for both the preferential direction and mean first passage time indicate that the effects that a viscosity difference across the membrane may have on translocation arise in the general case of a particle at a viscosity interface. [Preview Abstract] |
Wednesday, March 23, 2011 1:15PM - 1:27PM |
Q43.00009: Ionic Coulomb Blockade in Nanopores Matt Krems, Massimiliano Di Ventra Understanding the dynamics of ions in nanopores is essential for potential applications in molecule detection, DNA sequencing, and other technologies [1]. We show both analytically and by means of molecular dynamics simulations that ion-ion interactions in nanopores leads to the phenomenon of ionic Coulomb blockade, namely the build-up of ions inside a nanopore with specific capacitance impeding the flow of additional ions due to Coulomb repulsion. This is the classical counterpart of electronic Coulomb blockade in mesoscopic systems. We discuss the analogies and differences with the electronic case as well as experimental situations in which this phenomenon could be detected. \\[4pt] [1] M. Zwolak, M. Di Ventra, Physical Approaches to DNA sequencing and Detection, Rev. Mod. Phys. 80, 141 (2008). [Preview Abstract] |
Wednesday, March 23, 2011 1:27PM - 1:39PM |
Q43.00010: Modeling polyelectrolyte translocation through protein channels Jyoti Mahalik, Jing Hua, Yanbo Wang, Murugappan Muthukumar We will present results from Brownian Dynamics simulations of translocation of polyelectrolyte chains through alpha-hemolysin and MspA protein channels. Comparisons will be made between these two pores in terms of the various characteristics of translocation events. Specifically, we will discuss the distribution functions of blocked ionic current and translocation time. The critical roles played by the charge decorations and the geometries of these two protein pores will be presented. The sequence of the polymer will also be addressed. [Preview Abstract] |
Wednesday, March 23, 2011 1:39PM - 1:51PM |
Q43.00011: Polyelectrolyte translocation through a spherical cavity with tunable charge Alexander Eliseev, Murugappan Muthukumar We will present theoretical results on the free energy barrier for a translocating polyelectrolyte through a charge-decorated hole from a confining spherical cavity. Our results are based on self-consistent-field theory for the combined system of polyelectrolyte chain, counterions, electrolyte ions, and the dielectric mismatch between the cavity and the enclosing space. The effects of degree of ionization of the polymer and the net charge of the hole on the translocation barrier will be presented. [Preview Abstract] |
Wednesday, March 23, 2011 1:51PM - 2:03PM |
Q43.00012: Polymer translocation facilitated by Chaperones Aniket Bhattacharya, Tapio Ala-Nissila, Wokyung Sung We study translocation of biopolymers through a nanopore in a membrane facilitated by attractive binding particles (Chaperones) using Langevin dynamics simulation. Specifically we study how the density and attractive strength of these bindings particles affect the chain conformations at the $trans$ side and mean first passage time (MFPT). We also consider model larger chaperone that can bind reversibly on the multiple units of the translocating chain. Finally, we consider translocation of heteropolymers and how a specific sequence affect the translocation process. We discuss relevance of our studies in biological translocation processes.\\ $^1$R. Zandi, D. Reguera, J. Rudnick and W.~M. Gelbart, Proc. Natl. Acad. Sci. USA {\bf 100} 8649 (2003).\\ $^2$W. Sung and P.~J. Park, Phys. Rev. Lett. {\bf 77}, 783 (1996).\\ [Preview Abstract] |
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