Bulletin of the American Physical Society
APS March Meeting 2013
Volume 58, Number 1
Monday–Friday, March 18–22, 2013; Baltimore, Maryland
Session M44: Focus Session: Translocation through Nanopores I |
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Sponsoring Units: DBIO Chair: Aniket Battacharya, University of Central Florida Room: Hilton Baltimore Holiday Ballroom 1 |
Wednesday, March 20, 2013 8:00AM - 8:12AM |
M44.00001: Stiff Filamentous Virus Translocations through Solid-State Nanopores Angus McMullen, Derek Stein, Jay Tang We present experimental results of filamentous virus translocations through a solid-state nanopore. A nanopore can easily detect fd virus due to its linear shape and high linear charge density. With a width of 6.6 nm, a monodisperse length of 880 nm, and a long persistence length of 2.2$\,\mu$m, fd is a model stiff polymer for testing theories of translocation dynamics. The distribution of measured ionic current blockade amplitudes indicates that fd virus does not fold during translocation. The mean fd translocation time was linearly proportional to the applied voltage in the range 75 mV to 500 mV. The dispersion in translocation times was much greater for fd virus than expected from Brownian motion or the conformation-dependent fluid drag. Possible explanations for the observed dispersion will be discussed in light of its dependence on voltage and the salt concentration. This work was supported by NSF Grant CBET0846505 and the Brown University IMNI. [Preview Abstract] |
Wednesday, March 20, 2013 8:12AM - 8:24AM |
M44.00002: Biomolecular translocation through nanopores: from an anonymous polymer to realistic DNA Maria Fyta, Simone Melchionna, Sauro Succi, Efthimios Kaxiras We have developed an efficient multiscale approach to treat biomolecular motion in a fluid solvent. This scheme has been applied to the problem of polymer translocation through a nanopore, an intensively studied subject due to its variety of applications with ultra-fast DNA sequencing being one of them. Our first results involve an anonymous polymer translocating in pure water. We habe obtained important insight into the statistics and dynamics of the process. The translocation time exponent compares well with the experimental values, while we were able to monitor multiconformational translocation, the signatures of which are also relevant to the experimental counterparts. As a next step, we have made our modelling more realistic by including electrokinetic effects, i.e. ions, as well as a realistic quantum-mechanically derived potential for double stranded DNA. We are now able to look more deeply into what happens in the pore. The ionic conductance and DNA blockade can be qualitatively and quantitatively observed and connected to the experiments. Finally, we also investigate the effect of pore geometry in the DNA translocation process. [Preview Abstract] |
Wednesday, March 20, 2013 8:24AM - 8:36AM |
M44.00003: Effect of charge patterns along nanopores on the translocation kinetics of flexible polyelectrolytes Harsh Katkar, Murugappan Muthukumar One of the major challenges in DNA sequencing with nanopore-based electrophoresis is to slow down the DNA translocation. In the present study, we investigate the effectiveness of charge patterns along the pore on translocation dynamics. We perform a coarse-grained, three-dimensional Langevin dynamics simulation of a uniformly charged flexible polyelectrolyte translocating under uniform external electric field through a patterned solid-state nanopore. We maintain the total charge along the pore to be constant, while varying its distribution by placing alternate charged and uncharged sections of different lengths along the pore length. We observe a translocation success ratio close to 100 percent due to the presence of an attractive section near the cis end of the pore in all studied patterns. Further, we observe a nonmonotonic dependence of the translocation time with the period of the pattern. The optimum period corresponding to the longest translocation time is independent of lengths of polyelectrolyte and pore within the range studied. Calculations of mean first passage time based on free energy are able to predict the optimum period of the pattern qualitatively. [Preview Abstract] |
Wednesday, March 20, 2013 8:36AM - 8:48AM |
M44.00004: Nanopore Translocation Dynamics of star polymers Rong Wang, Zhu Liu The translocation of polymers through a narrow channel or a nanopore has a significant impact on numerous biological systems and industrial process, examples including rapid DNA sequencing, controlling drug delivery, and designing nanopore sequencing device.We consider the dynamics of flow-induced translocation of star polymers through a nanopore in three dimensions by dissipative particle dynamics approach, focusing on the dependence of the translocation time on the polymer chain length. The scaling of the average translocation time $\tau $ \textit{vs.} the total length $N_{\mbox{tot}} $ of the star polymer with three arms, $\tau \sim N_{\mbox{tot}}^{1.09\pm 0.04}$, is obtained in our simulation. We establish that the overall translocation time, with the translocation probability $P_{i}^{\mbox{trans}} $ and the translocation time $\tau_{i}$ under different translocation paths. We demonstrate that the translocation time $\tau$ of star polymers through the nanopore increases with the increase of the total arm numbers, while $\tau$ decreases with increasing number the forward arms that are initially squeezed into the nanopore. Our findings may provide a valuable guidance for experimental studies on the conformational and dynamics behaviors of star polymer translocation for further applications. [Preview Abstract] |
Wednesday, March 20, 2013 8:48AM - 9:00AM |
M44.00005: ABSTRACT WITHDRAWN |
Wednesday, March 20, 2013 9:00AM - 9:12AM |
M44.00006: A Fluid Channel Coincident With Graphene Tunneling Leads for DNA sequencing Luke Somers, Manuel Schottdorf, Chris Farina, Meni Wanunu, Eva Andrei One of the strategies towards controlled DNA sequencing by electrical readout of individual bases has been to direct single-stranded DNA through a tunnel junction. For this method to be viable, the DNA must be severely constrained to minimize geometric factors. We present a method for creating fluid channels the size of tunnel junctions, with tunneling leads across them. The fluid channel is formed by Atomic Layer Deposition around a gold wire thinned by feedback-controlled electromigration. The channel itself is used as a mask to assist in defining the tunneling leads out of graphene by electroburning. The principal reasons for selecting graphene are its proven tunnelling sensing ability, stability, and exceeding thinness. [Preview Abstract] |
Wednesday, March 20, 2013 9:12AM - 9:48AM |
M44.00007: Dynamics of polymer translocation through a nanopore under an applied external field Invited Speaker: Kaifu Luo Polymer translocation is of considerable importance to many biological processes and is envisaged to be useful for rapid DNA sequencing. Using analytical techniques and Langevin dynamics simulations, we have investigated the following problems. (1) For polymer translocation into a long narrow channel driven by longitudinal flow,\footnote{K. Luo, and R. Metzler, J. Chem. Phys., {\bf 134}, 135102 (2011)} we find that the translocation time shows a linear scaling behavior with the chain length. (2) For polymer translocation through nanochannels with different lengths,\footnote{H. Yong, Y. Wang, S. Yuan, B. Xu, and K. Luo, Soft Matter, {\bf 8}, 2769 (2012)} we observe a minimum of translocation time as a function of the channel length. (3) We have examined polymer translocation into confined systems, such as a slit,\footnote{K. Luo, and R. Metzler, J. Chem. Phys., {\bf 133}, 075101 (2010)} a fluidic channel,\footnote{K. Luo, and R. Metzler, Phys. Rev. E, {\bf 82}, 021922 (2010)} nanocontainers with different shapes,\footnote{K. Zhang, and K. Luo, J. Chem. Phys., {\bf 136}, 185103 (2012); to be published} which shows different translocation dynamics compared with the translocation into an unconfined environment.\\[4pt] This work is supported by the ``Hundred Talents Program'' of CAS and the National Natural Science Foundation of China (Grant Nos. 21225421, 21074126, 21174140). [Preview Abstract] |
Wednesday, March 20, 2013 9:48AM - 10:00AM |
M44.00008: Polymer Translocation Through a Nanopore from a Crosslinked Gel to Free Solution David Sean, Hendrick W. de Haan, Gary W. Slater We present results from a computer simulation study of DNA translocation through a nanopore in a membrane that separates a gel region from free solution. The gel is modeled by a square lattice of fixed poles such that the pore size is set by the lattice spacing. Starting with the DNA on the gel side, we examine how the gel pore size affects the dynamics of translocation. We find that due to entropic and frictional forces, the mean translocation time is affected by gel pore size. Since the spatial restrictions imposed by the gel limit the dynamics to one-dimensional motion on the cis side, variations in the width of the distribution of translocations times are also observed. [Preview Abstract] |
Wednesday, March 20, 2013 10:00AM - 10:12AM |
M44.00009: Statistical Inference of DNA Translocation using Parallel Expectation Maximization Kevin Emmett, Jacob Rosenstein, David Pfau, Akiva Bamberger, Ken Shepard, Chris Wiggins DNA translocation through a nanopore is an attractive candidate for a next-generation DNA sequencing platform, however the stochastic motion of the molecules within the pore, allowing both forward and backward movement, prevents easy inference of the true sequence from observed data. We model diffusion of an input DNA sequence through a nanopore as a biased random walk with noise, and describe an algorithm for efficient statistical reconstruction of the input sequence, given data consisting of a set of time series traces. The data is modeled as a Hidden Markov Model, and parallel expectation maximization is used to learn the most probable input sequence generating the observed traces. Bounds on inference accuracy are analyzed as a function of model parameters, including forward bias, error rate, and the number of traces. The number of traces is shown to have the strongest influence on algorithm performance, allowing for high inference accuracy even in extremely noisy environments. Incorrectly identified state transitions account for the majority of inference errors, and we introduce entropy-based metaheuristics for identifying and eliminating these errors. Inference is robust, fast, and scales to input sequences on the order of several kilobases. [Preview Abstract] |
Wednesday, March 20, 2013 10:12AM - 10:24AM |
M44.00010: Thermophoretic Regulation of Molecular Flux through a Nanopore Maxim Belkin, Aleksei Aksimentiev Transport of ions, nucleic acids and other molecular species through pores in thin membranes is a process of fundamental importance to the biological function of a cell and practical applications in the field of molecular separation, filtering, and, recently, DNA sequencing. Various approaches to control the transport have been examined, including the effects of the geometry, charge and chemical functionalization of the nanopore surface. Thermophoresis in liquids, i.e. movement of molecules along a temperature gradient, was discovered more than a century ago and has already been employed in various applications, typically involving macroscopic systems. In this work, we explore the use of thermal gradients for regulation of nanoscale fluxes. Specifically, we use all-atom molecular dynamics simulations to examine the effect of thermal gradients on transport of ions, small organic solutes and long DNA molecules through solid-state nanopores. In our typical simulation, multiple thermostats are applied to different parts of the same simulation system, allowing steady-state temperature gradients to be established and the effective forces associated with the thermal gradients to be determined. The results of our simulations suggest that nanopore fluxes of molecular species can be regulated by means of thermal gradients. We expect our results to find applications in molecular separation and filtering technologies, nanofluidic electronics and nanopore sequencing of DNA. [Preview Abstract] |
Wednesday, March 20, 2013 10:24AM - 10:36AM |
M44.00011: The effects of diffusion on an exonuclease/nanopore-based DNA sequencing engine Joseph E. Reiner, Arvind Balijepalli, Joseph W.F. Robertson, Bryon S. Drown, Daniel L. Burden, John J. Kasianowicz The electronic detection and characterization of individual polynucleotides driven through a single protein nanopore holds promise for rapid and low-cost DNA sequencing. A variation on reading DNA in a ticker tape fashion was recently proposed. The pore would electrically detect single nucleotides that are cleaved sequentially by an exonuclease enzyme in close proximity to one pore entrance. We will present the results of an analytical and computational study of this scheme. The analysis examines the effects of diffusive motion on the capture probability for each nucleotide. The capture probability increases with the applied transmembrane potential, but this is offset by the reduction in the residence time of each nucleotide in the pore. The theoretical results demonstrate that these two effects limit the capability of a cleavage-based nanopore sequencing engine. We will discuss these constraints and speculate on how the system could be improved. [Preview Abstract] |
Wednesday, March 20, 2013 10:36AM - 10:48AM |
M44.00012: DNA translocation through graphene nanopores Slaven Garaj, Song Liu, Jene A. Golovchenk, Daniel Branton Nanopores are versatile platform for studying structure and behaviour of individual biopolymers. In a nanopore device, an individual DNA molecule in aqueous solution is electrophoretically threaded through the nano-scale pore in a linear fashion. Resulting modulation of the ionic current through the nanopore is characteristic of the geometrical and chemical properties of the translocating molecule. It has been shown that a new class of nanopore fabricated in free-standing single-layer graphene membrane -- graphene nanopores -- have excellent predisposition to achieve sub-nanometre resolution in discerning features along the length of individual DNA molecules [1]. In this talk, we will demonstrate very high sensitivity of the graphene nanopore current on small variation of the diameter of translocating molecule, and we will examine the dynamics of the DNA molecule within the graphene nanopore. The implications of those results on prospects of physical DNA sequencing will be discussed. \\[4pt] [1] S. Garaj \textit{et al.}, Nature \underline{467}, 190-193 (2010). [Preview Abstract] |
Wednesday, March 20, 2013 10:48AM - 11:00AM |
M44.00013: Ionosphere perturbation of single DNA molecules in a.c. electric fields Zubair Azad, Robert Riehn The collapse of DNA molecules under an a.c. electric field was recently established, but is little understood. We applied alternating electric fields (0 - 200 kV/cm) to fluorescently labeled $\lambda$-DNA confined in quasi 1-d nanochannels. DNA was dissolved in a buffer that contained anionic tracer dyes of varying mobilities. Under a.c. electric fields we obseved a depletion of the anionic fluorophores in the region occupied by the DNA, and enrichment in the regions directly flanking it. The critical field strength to induce expulsion of the fluorophores was above 60 kV/cm. We believe that double-sided isotachophoresis can model the ion distributions in our experiment. Furthermore, we will comment on the dynamics of fluorescent co-ions in the solution perturbed by the DNA by observing their dynamics. [Preview Abstract] |
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