Bulletin of the American Physical Society
APS March Meeting 2011
Volume 56, Number 1
Monday–Friday, March 21–25, 2011; Dallas, Texas
Session V43: Focus Session: Translocation Through Nanopores II |
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Sponsoring Units: DPOLY DBP Chair: Johan Dubbeldam, Delft University of Technology, Netherlands Room: A306/307 |
Thursday, March 24, 2011 8:00AM - 8:12AM |
V43.00001: The Statistics of DNA Capture and Re-Capture by Solid-State Nanopores Mirna Mihovilovic, Erin Teich, Nick Hagerty, Jason Chan, Derek Stein We studied repeated electrophoretic translocations of the same DNA molecule through $\sim $10 nm nanopores using the voltage-reversal re-capture technique. Correlations were observed in the folding conformations of molecules re-captured within the Zimm relaxation time of the polymer. A trend was observed, whereby more compact conformations of DNA evolved over time. Consecutive event charge deficit measurements were narrowly distributed about a well defined mean, suggesting that the analysis of multiple translocations through a pore can be used to improve estimates of the length of long polymers. [Preview Abstract] |
Thursday, March 24, 2011 8:12AM - 8:24AM |
V43.00002: DNA translocation through a solid-state nanopore coated with a self-assembled monolayer Binquan Luan, Gustavo Stolovitzky, Glenn Martyna The translocation of DNA through a solid-state nanopore can be dramatically affected by surface properties of a pore, such as charge density, roughness and hydrophobicity, since the pore surface serves as a boundary for the hydrodynamic flow accompanying with DNA motion. Recent experiment demonstrated the coating of a self-assembled monolayer (SAM) on the surface of a nanopore, allowing an active control on the surface property. Using all-atom molecular dynamics simulation, we investigated the tribological effect on DNA translocation through a solid-state nanopore coated with a SAM. When DNA is confined to the center of a pore, i.e. no direct interaction between DNA and pore surface, charge density and roughness of a pore surface can affect electroosmotic and hydrodynamic flows inside a nanopore, respectively. When allowing direct interaction between DNA and a SAM, adhesive interaction via hydrogen bonds can substantially increase friction force on DNA during translocation but repulsive interaction permits a fast translocation of DNA. We found two types of motion of DNA, stick-slip and steady-sliding, that are qualitatively explained using a Langevin-like model. [Preview Abstract] |
Thursday, March 24, 2011 8:24AM - 8:36AM |
V43.00003: Nanopore DNA translocation studies of tri-oligomer DNA with two hybridization segments Venkat Balagurusamy, Paul Weinger, Xinsheng Ling We have earlier detected 12-base hybridizations in trimer DNA complexes formed by three single-stranded DNA oligomers hybridized at their ends sequentially, using nanopores of $\sim $ 10 nm diameter [1]. These complexes are connected to a polystyrene bead at one end to slow down their translocation. Here, we report translocation experiments at different voltages with nanopores $\sim $ 5 nm diameter. The measured time lapses between the passage of consecutive double-strand DNA segments in a trimer complex allow us to study the translocation dynamics. The measured mean-first-passage time between two consecutive hybridization segments is found to be consistent with theoretical estimates based on the Fokker-Planck equation.\\[4pt] [1] V.S.K.Balagurusamy, P.Weinger and X.S.Ling, \textit{Nanotechnology} \underline {21}, 335102 (2010). [Preview Abstract] |
Thursday, March 24, 2011 8:36AM - 8:48AM |
V43.00004: Dehydration and Ionic Conductance Quantization in Synthetic Nanopores James Wilson, Michael Zwolak, Massimiliano Di Ventra Synthetic nanopores and nanochannels create new opportunities - beyond biological ion channels - to study ionic transport at the nanoscale. One process that occurs at this scale is dehydration. Ions in water do not move freely, but are instead surrounded by tightly bound water molecules held by the charge-dipole interaction. These water molecules are organized into hydration layers. For the ion to move through a nanopore of sufficiently small radius, these hydration layers must be shed as there is not enough space within the pore to accommodate them. We use molecular dynamics simulations to develop a model of dehydration based on the energy cost associated with removing water molecules. We predict that the ionic current would show sudden drops as the pore radius is reduced due to the exclusion of the hydration layers. We also examine the effect of both the sign and magnitude of the ion charge, demonstrating that divalent ions will more clearly exhibit the effect of dehydration on the ionic current.\\[4pt] [1] M. Zwolak, J. Wilson, and M. Di Ventra, J. Phys.: Condens. Matter 22, 454126 (2010); See also M. Zwolak and M. Di Ventra, Phys. Rev. Lett. 103, 128102 (2009) [Preview Abstract] |
Thursday, March 24, 2011 8:48AM - 9:00AM |
V43.00005: Nanowire-nanopore transistor sensor for DNA detection during translocation Ping Xie, Qihua Xiong, Ying Fang, Quan Qing, Charles Lieber Nanopore sequencing, as a promising low cost, high throughput sequencing technique, has been proposed more than a decade ago. Due to the incompatibility between small ionic current signal and fast translocation speed and the technical difficulties on large scale integration of nanopore for direct ionic current sequencing, alternative methods rely on integrated DNA sensors have been proposed, such as using capacitive coupling or tunnelling current etc. But none of them have been experimentally demonstrated yet. Here we show that for the first time an amplified sensor signal has been experimentally recorded from a nanowire-nanopore field effect transistor sensor during DNA translocation. Independent multi-channel recording was also demonstrated for the first time. Our results suggest that the signal is from highly localized potential change caused by DNA translocation in none-balanced buffer condition. Given this method may produce larger signal for smaller nanopores, we hope our experiment can be a starting point for a new generation of nanopore sequencing devices with larger signal, higher bandwidth and large-scale multiplexing capability and finally realize the ultimate goal of low cost high throughput sequencing. [Preview Abstract] |
Thursday, March 24, 2011 9:00AM - 9:12AM |
V43.00006: How to improve the sensitivity in transverse electronic measurements of DNA for nucleobase distinction? Yuhui He, Ming Liu, Anton Grigoriev, Ralph H. Scheicher, Rajeev Ahuja In an attempt to realize third-generation whole-genome sequencing technologies, nanopores have been at the center of the research focus. Key issues with this approach involve how to slow down the translocation speed of DNA and how to achieve single-base resolution. We have previously proposed [arXiv:0708.4011; J. Phys. Chem. C 112, 3456 (2008)] the use of functionalized nanopore-embedded gold electrodes to address both these issues. More recently, we demonstrated [Appl. Phys. Lett. 97, 043701 (2010)] through molecular dynamics and electron transport simulations that the transverse differential conductance of a translocating DNA may allow for distinction between the four bases and can withstand electrical noise caused by DNA structure fluctuations. Our findings demonstrate several advantages of the transverse conductance approach, which may lead to realistic applications in rapid genome sequencing. [Preview Abstract] |
Thursday, March 24, 2011 9:12AM - 9:48AM |
V43.00007: Novel effects of chain flexibility, external force, and background stochasticity on polymer translocation Invited Speaker: The polymer translocation through membranes and the polymer crossing over activation barriers in general, are ubiquitous in cell biology and biotechnological applications. Because they are interconnected flexible systems, polymers in translocation incur entropic barriers but can thermally surmount them with unusual sensitivity to background biases. In the presence of non-equilibrium noises characteristic of living environments, the translocation can speed up much when resonant activation occurs. As a related issue, I will also discuss the problem of polymer surmounting a potential barrier, where the chain flexibility enhances the crossing. Furthermore, when the chain flexibility leads to conformational changes, the crossing rate can be even more dramatically increased. This conformational flexibility and variability enhance the stochastic resonance, where the chain crossing dynamics at an optimal temperature and chain length is maximally coherent and resonant to a minute periodic force. Utilizing the self-organizing behaviors mentioned above, we may learn about bio-molecular machinery of living as well as clever means of manipulating it. \\[4pt] [1] W. Sung and P. J. Park, Phys. Rev. Lett. \textbf{77}, 783 (1996) \\[0pt] [2] J. J. Kasianowicz, E. Branton and D. W. Deamer, Proc. Natl. Acad. Sci. USA \textbf{89},13370(1996) \\[0pt] [3] P. J. Park and W. Sung, J. Chem. Phys. \textbf{111}, 5239 (1999) \\[0pt] [4] M. Asfaw and W. Sung, Euro. Phys. Lett. \textbf{90}, 30008 (2010) [Preview Abstract] |
Thursday, March 24, 2011 9:48AM - 10:00AM |
V43.00008: Simulations of Single DNA Nucleotide Transport Through Nanoslits Brian Novak, Kai Xia, Dorel Moldovan, Dimitris Nikitopoulos, Steven Soper Transport of single molecules in nano-scale geometries might be used to identify them via their flight times. The motion of nucleotides in aqueous NaCl solution flowing through atomically smooth nanoslits composed of disordered carbon atoms was studied using nonequilibrium molecular dynamics simulations. The fluid was driven by gravity-like forces or the nucleotide was moved electrophoretically. Velocities were on the order of 1 m/s or 3 m/s, respectively. The relatively hydrophobic base parts of the nucleotides adsorbed to the walls multiple times while moving along the slit. The bases tended to adsorb/desorb with the sugar end of the base contacting the surface last/first. The distance required for separation of the flight time distributions (required channel length) was 8.8 $\mu $m for the gravity case. In the electrophoretic case with this surface, the nucleotides moved nearly as fast while adsorbed as while desorbed which made the separation more difficult than in the gravity case. [Preview Abstract] |
Thursday, March 24, 2011 10:00AM - 10:12AM |
V43.00009: Heat Treatment to Shrink Solid-State Nanopores Joseph Billo, Waseem Asghar, Samir M. Iqbal Solid-state nanopores have a promising application in the area of selective sensing of DNA. Therefore, it is imperative to have a simple and repeatable method for nano-fabrication of pores. This paper focuses on solid-state nanopore fabrication in a silicon-dioxide membrane with heat treatment. A 375 $\mu $m thick pre-oxidized silicon wafer with approximately 1 $\mu $m oxide is used. Photolithography followed by BHF etching, with well-cured photo-resist covering the back-side to preserve its oxide layer, was performed on the wafer in order to open square windows in the front-side oxide layer. Using the front-side oxide layer as a mask and the back-side oxide layer as an etch-stop, the silicon substrate underwent anisotropic etching to create SiO$_{2}$ membranes. The wafer was then cut into small squares approximately 1 cm on a side with each containing one membrane. A focused ion beam was used to open an initial pore in each membrane. Finally, a method for causing SiO$_{2}$ membranes to diffuse was used to shrink the pores to the desired diameter. [Preview Abstract] |
Thursday, March 24, 2011 10:12AM - 10:24AM |
V43.00010: The Nanofluidic Field-Effect in Electrically Actuated Nanopores Zhijun Jiang, Derek Stein We employed high-resolution milling techniques to create solid-state nanopores with integrated electrodes for exerting field-effect control over the transport of ions and single DNA molecules in solution. An embedded, annular gate electrode was used to voltage gate the ionic conductance through a nanopore. An absence of leakage currents confirms the electrostatic origin of this effect. The measurements also reveal strong dependencies on the pH and on the ionic strength of the fluid. These results reflect the crucial difference between the modulation of charge at a solid-liquid interface where surface chemistry plays an important role, versus at a chemically inert semiconductor interface. An electrochemical model of electro-fluidic gating that captures the gate-field-induced shift in the chemical equilibrium of the ionizable surface groups describes our measurements quantitatively. We seek to electrostatically control the translocation of DNA through such gated nanopores, and thereby mimic the single-molecule regulatory capabilities of biological transmembrane channels. [Preview Abstract] |
Thursday, March 24, 2011 10:24AM - 10:36AM |
V43.00011: FIB direct fabrication of sub-10 nm synthetic nanopores Jacques Gierak, Ali Madouri, Eric Bourhis, Jean-Yves Marzin, Ghani Oukhaled, Laurent Bacri, Benjamin Cressiot, Juan Pelta, Ralf Jede, Lars Bruchhaus, Lo\"Ic Auvray Nanopores in thin solid state membranes are used as single molecule electronic detectors or sensors. The membrane acts as a dividing wall in an electrolytic cell and draws charged molecules attracted by an electric field through the pore. Among the very few patterning techniques applicable to nanopores, one promising approach is to use a FIB system, which can produce small holes directly at specified locations with customized organization and shape into dielectric membranes. We detail an innovative FIB-based approach and the methodologies developed for sub-10 nm nanopore realization. Our method allows direct fabrication of nanometer-sized pores in relatively large quantities with excellent reproducibility. This approach offers the possibility to further process or to functionalize each pore on the same scale keeping the required nm-scaled positioning and patterning accuracies, for i.e. adding detection marks or local membrane thinning at nanopore site. Then we describe solutions for conditioning surface properties and for integrating such single nanopore devices for translocation experiments. Results involving DNA, proteins, polymers, colloids are presented. [Preview Abstract] |
Thursday, March 24, 2011 10:36AM - 10:48AM |
V43.00012: Incremental Mean First Passage Analysis of Unbiased Polymer Translocation Gary W. Slater, Hendrick W. de Haan To provide a measure of how translocation progresses, we have recently developed a method of mapping the process as a series of mean first passage processes of increasing displacement. Starting with a simplified, ``quasi-static'' model of translocation, exact numerical and analytic calculations using this Incremental Mean First Passage Time (IMFPT) approach yield insight into the robustness of the scaling of the translocation time \textit{$\tau $} with polymer length $N$ given by \textit{$\tau $}$\sim N^{2}$ as predicted in early theoretical studies of translocation. This approach reveals fundamental differences in the dynamics between absorbing and reflective boundary conditions when only one monomer is in the pore - both experimentally relevant scenarios. IMFPT is also applied to Langevin Dynamics simulations of a full polymer to test the impact of including features neglected in the simplified model. While the scaling for much of the process is now $\tau \sim N^{2.2}$ due to internal degrees of freedom, the exponent as measured by only the net translocation time is shown to depend greatly on the details of the simulation setup as a result of non-equilibrium effects. [Preview Abstract] |
Thursday, March 24, 2011 10:48AM - 11:00AM |
V43.00013: Nanoscale fluid transportation through individual carbon nanotubes Jin He, Di Cao, Pei Pang, Tao Luo, Stuart Lindsay, Predrag Kristic, Colin Nuckolls There are great interest in both simulation and experiment of fluid flow on the nanoscale. Carbon nanotubes, with their extremely small inner diameter (usually below 2 nm) and atomic smooth inner surface, are ideal materials for studying nanoconfinement and ion and molecule nanoscale translocation. The excellent electrical properties of CNTs can also be integrated to achieve nanoelectrofluidic device. This presentation describes our recent progress in studying fluid transport through individual carbon nanotubes, including simultaneously ionic and electronic measurements during water, ion and molecule translocation. [Preview Abstract] |
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