Bulletin of the American Physical Society
2007 APS March Meeting
Volume 52, Number 1
Monday–Friday, March 5–9, 2007; Denver, Colorado
Session H27: Focus Session: Computational Nanoscience III - DNA Translocation / Nanopores |
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Sponsoring Units: DMP DCOMP Chair: Abdelkader Kara, University of Central Florida Room: Colorado Convention Center 301 |
Tuesday, March 6, 2007 8:00AM - 8:12AM |
H27.00001: Ionic conductance in nanopores Johan Lagerqvist, Michael Zwolak, Massimiliano Di Ventra We study ionic transport through nanopores from the perspective of the microscopic electrostatics. We predict the existence of step-like structures in the ionic conductance as a function of both nanopore diameter and ionic concentration. This is due to the formation and breakage of hydration layers around the ions. In bulk water, there are a few of these layers around each ion. As an ion goes through the pore, some of the hydration layers break and thus create an energetic barrier for ion transport. The number of broken layers depends on the pore diameter and the ionic concentration. In this talk, we discuss various properties of the hydration layers and the parameter range necessary to experimentally observe quantized conductance of ions through nanopores. Work supported in part by NSF and NIH. [Preview Abstract] |
Tuesday, March 6, 2007 8:12AM - 8:24AM |
H27.00002: Electrophoretic speed of a polyelectrolyte in a nanopore Sandip Ghosal A hydrodynamic model for determining the electrophoretic speed of a polyelectrolyte through a nanopore is presented. It is assumed that the speed is determined by a balance of electrical and viscous forces arising from within the pore in the presence of co and counter ions. Further, classical continuum electrostatics and hydrodynamics as well as the mean field description of Poisson-Boltzmann is assumed to be applicable after accounting for Manning condensation on the polyelectrolyte. An explicit formula for the translocation speed as a function of the pore geometry and other physical parameters is obtained and is shown to be consistent with recent experimental measurements on DNA translocation through nanopores in silicon membranes. [Preview Abstract] |
Tuesday, March 6, 2007 8:24AM - 8:36AM |
H27.00003: ABSTRACT HAS BEEN MOVED TO A41.00013 |
Tuesday, March 6, 2007 8:36AM - 8:48AM |
H27.00004: ABSTRACT WITHDRAWN |
Tuesday, March 6, 2007 8:48AM - 9:00AM |
H27.00005: Transcription of ribosomal RNA: the role of antitermination of RNA polymerase Stefan Klumpp, Terry Hwa The genes encoding ribosomal RNA are transcribed at high rates of 1-2 transcripts per second. These high transcription rates are crucial to maintain the large concentration of ribosomes necessary in fast growing bacteria. To understand how transcription is regulated under these conditions, we developed a model for the traffic of transcribing RNA polymerases (RNAP). Our simulations show that the transcription rate is limited by the elongation stage of transcription rather than by transcript initiation. The maximal transcription rate is severly impaired by RNAP pausing with pause durations in the second range which is ubiquitous under single-molecule conditions. We propose that ribosomal antitermination reduces pauses and thereby increases the transcription rate. This idea is in quantitative agreement with the observed increase of the elongation rate due to antitermination and predicts a two-fold increase of the transcription rate. Antitermination must be highly efficient, since incomplete antitermination with only a few percent of non-antiterminated, i.e. slow, RNAPs completely abolishes its effect. This result suggests that rho-dependent termination may selectively terminate slow RNAPs. [Preview Abstract] |
Tuesday, March 6, 2007 9:00AM - 9:12AM |
H27.00006: Mechanically induced cis to trans reisomerization of azobenzene Robert Turansky, Martin Konopka, Ivan Stich, Dominik Marx Using density functional techniques we study mechanochemistry of the azobenzene molecule. Azobenzene is an optically switchable molecule. Laser light is normally used to achieve molecular switching between the cis and trans isomers. We use mechanochemistry to achieve the switching. Thiolate-gold bond can used to exert mechanical energy on the molecule bonded between two gold electrodes in static AFM apparatus. Our model consists of two realistic gold electrodes bridged by dithioazobenzene. We find that pulling the transisomer leads just to formation of gold nanowires and mechanical breakage of the electrodes. However, mechanochemistry with modest applied forces leads to cis $\leftrightarrow$ trans reisomerization via rotation mechanism. Contrary, use of simple constraints instead of realistic gold electrodes, leads to cis $\leftrightarrow$ trans reisomerization, albeit with significantly larger applied forces and via inversion mechanism. Important experimental and theoretical ramifications of these simulations will be discussed. [Preview Abstract] |
Tuesday, March 6, 2007 9:12AM - 9:48AM |
H27.00007: DNA translocation through protein and synthetic nano pores Invited Speaker: DNA translocation through narrow protein channels is recognized as an important process in biology. Recently it has attracted lot of attention in the biophysical community following several experiments on DNA translocation through protein nano-pores, and more recently, through synthetic silicon nano-pores. A fundamental understanding is needed for various biological processes, {\em e.g.}, entry and exit of a DNA in and out of a cell, efficient separation methods for macromolecules, and, possibly fast DNA sequencing. In this talk I will be presenting results for the DNA translocation using a coarse-grained model for an idealized DNA as well as the pore. I will consider several scenarios for the DNA translocation. First, I will show scaling of translocation time of a homopolymer as it escapes from the {\em trans} side to the {\em cis} side of an idealized thin membrane\footnote{A. Milchev, K. Binder, and Aniket Bhattacharya, J. Chem. Phys. {\bf 121}, 6042 (2004).} Then I will consider DNA dynamics subject to a driving force inside the pore. Next, I will consider heteropolymer threading through a nano-pore. Specifically we will consider both highly ordered and completely random sequences of the chain and relate specific sequences to the distribution of the translocation time and the residence time inside the pore. These studies also will include effects due to different environment on either side of the pore, specific DNA-pore interactions located at selective sites, {\em etc.}. I will discuss relevance of these simulation results to recent experiments and theoretical models. [Preview Abstract] |
Tuesday, March 6, 2007 9:48AM - 10:00AM |
H27.00008: DNA nucleoside interaction and identification with carbon nanotubes Sheng Meng, Paul Maragakis, Costas Papaloukas, Efthimios Kaxiras DNA and carbon nanotubes (CNTs) are prototypical one-dimensional structures. Segments of single-strand DNA are extremely flexible, strongly hydrophilic biopolymers while CNTs are extremely stiff, strongly hydrophobic nanorods. The interaction between DNA and CNTs is being intensely investigated for possible use in, e.g., DNA transporters or biosensors. Recent success in detecting DNA conformational changes and hybridization by near-infrared fluorescence of CNTs or CNT-- field-effect transistors has opened the possibility of DNA sequencing through electronic means. Here we investigate the interaction of individual DNA nucleosides with a CNT in vacuum and in the presence of external gate voltage. We propose a scheme to discriminate between nucleosides on CNTs based on measurement of electronic features through a local probe such as scanning tunnelling spectroscopy. We demonstrate through quantum mechanical calculations that these measurements can achieve 100\% efficiency in identifying DNA bases. Our results support the practicality of ultrafast DNA sequencing using electrical measurements. [Preview Abstract] |
Tuesday, March 6, 2007 10:00AM - 10:12AM |
H27.00009: Probing the Structure of DNA-Carbon Nanotube Hybrids with Molecular Dynamics Simulations Robert R. Johnson, Alan T. Johnson, Michael L. Klein DNA-carbon nanotube hybrids (DNA-NT) consist of a single-walled carbon nanotube (SWNT) wrapped with a self-assembled monolayer of single-stranded DNA (ssDNA). Recent experiments involving DNA-NT have shown that this material holds a wide range of technologically useful properties. However, a detailed understanding of its microscopic structure and interactions is lacking. To assist the interpretation of contemporary experiments, we have performed atomistic molecular dynamics (MD) simulations using empirical force fields. MD reveals the nature of the interactions and structural arrangements involved in DNA-NT. We find that the hybrid material spontaneously self-assembles via the attractive $\pi -\pi $ stacking interaction between ssDNA nucleobases and SWNT sidewall. Under ambient conditions, ssDNA adopts various wrapping conformations about SWNT including right- and left- handed helices as well as disordered, kinked structures. These conformations are energetically distinct with the compact right-handed helix the most favorable. [Preview Abstract] |
Tuesday, March 6, 2007 10:12AM - 10:24AM |
H27.00010: Finite size effect on hydrogen bond cooperativity in (Ala)$_n$ polypeptides: A DFT study using numeric atom-centered orbitals Volker Blum, Joel Ireta, Matthias Scheffler An accurate representation of the energetic contribution $E_{\rm hb}$ of hydrogen bonds to structure formation is paramount to understand the secondary structure stability of proteins, both qualitatively and quantitatively. However, $E_{\rm hb}$ depends strongly on its environment, and even on the surrounding peptide conformation itself. For instance, a short $\alpha$-helical polypeptide (Ala)$_4$ can not be stabilized by its single hydrogen bond, whereas an infinite $\alpha$-helical chain (Ala)$_\infty$ is clearly energetically stable over a fully extended conformation. We here use all-electron density functional calculations in the PBE generalized gradient approximation by a recently developed, computationally efficient numeric atom-centered orbital based code$^1$ to investigate this H-bond \emph{cooperativity} that is \emph{intrinsic} to Alanine-based polypeptides (Ala)$_n$ ($n$=1-20,$\infty$). We compare finite and infinite prototypical helical conformations ($\alpha$, $\pi$, 3$_{10}$) on equal footing, with both neutral and ionic termination for finite (Ala)$_n$ peptides. Moderately sized NAO basis sets allow to capture $E_{\rm hb}$ with meV accuracy, revealing a clear jump in $E_{\rm hb}$ (cooperativity) when two H-bonds first appear in line, followed by slower and more continuous increase of $E_{\rm hb}$ towards $n\rightarrow\infty$. $^1$ V. Blum, R. Gehrke, P. Havu, V. Havu, M. Scheffler, \emph{The FHI Ab Initio Molecular Simulations (aims) Project}, Fritz-Haber-Institut, Berlin (2006). [Preview Abstract] |
Tuesday, March 6, 2007 10:24AM - 10:36AM |
H27.00011: Electronic Structure of DNA: A Maximally-Localized Wannier Function Approach Arash Mostofi, Nicola Marzari We combine large-scale, \textit{ab initio} electronic structure calculations and the maximally-localized Wannier function approach in order to study the electronic properties of DNA strands. By performing full first-principles calculations on stacked DNA base-pairs, we determine the optimally localized, real-space basis set that is able to describe the infinite one-dimensional system efficiently and accurately. This work opens the way to obtaining a detailed understanding of charge transport and conductance in DNA, bringing closer the prospect of engineering its electronic structure for use in nano-electronic circuits and biotechnology applications. [Preview Abstract] |
Tuesday, March 6, 2007 10:36AM - 10:48AM |
H27.00012: Theoretical study the physical contribution to the signal to noise ratio (SNR) and sensitivity of Extraordinary Magnetoresistance (EMR) quantum well structures Y. Shao, S. A. Solin, A. Girgis , L. R. Ram-Mohan, Keon-Ho Yoo The application of EMR sensor performance requires ultra-thin films with very high mobility \textit{$\mu $}, and high electron concentration \textit{ n}, because the sensitivity of the EMR device is proportional to the \textit{$\mu $}$ ^{2}$ and the SNR depends on the \textit{ n}$_{3D}$$^{1/2}$\textit{$\mu $}$ ^{2}$ (1/\textit{f} noise) or \textit{ n}$_{3D}$$^{1/2}$\textit{$\mu $}$ ^{5/2}$ (thermal noise). We have modeled the electron concentration and mobility in a two dimensional electron gas (2DEG) layer located in a delta-doped InSb/AlInSb heterostructure. The non-parabolic band structure due to the nature of the small energy band gap of InSb is explicitly accounted for. The subband energy levels, electron wave functions and band-edge profiles were obtained using the $\textbf {\textit{k}$\cdot$ \textit{p}}$ method. The electron transport properties were calculated by including contributions of scattering from ionized impurities, the background neutral impurities, the deformation potential acoustic phonons, and the polar optical phonons. We have calculated the dependencies of \textit{$\mu $}$ ^{2}$, \textit{ n}$_{3D}$$^{1/2}$\textit{$\mu $}$ ^{2}$ and \textit{ n}$_{3D}$$^{1/2}$\textit{$\mu $}$ ^{5/2}$ on temperature, spacer layer thickness, doping density, and the quantum well thickness. This work will impact EMR sensor design. [Preview Abstract] |
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