Bulletin of the American Physical Society
2007 APS March Meeting
Volume 52, Number 1
Monday–Friday, March 5–9, 2007; Denver, Colorado
Session J27: Focus Session: DNA Translocation / Nanopores - Experiments |
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Sponsoring Units: DMP DBP Chair: Aniket Bhattacharya, University of Central Florida Room: Colorado Convention Center 301 |
Tuesday, March 6, 2007 11:15AM - 11:27AM |
J27.00001: A tunable DNA spring in a nanochannel Robert Riehn, Rory Staunton, Shuang Fang Lim, Robijn Bruinsma, Walter Reisner, Robert Austin dsDNA becomes linearized when it is confined to nanofluidic channels with a cross-section of (100 nm)$^2$ or less, which has made them interesting for genomic DNA analyses. DNA is typically manipulated by means of electric fields. We have found that DNA undergoes a phase transition to a condensed state if an a.c. electric field is applied along the channel direction. The molecule collapses to about 1/4 of it's initial contour length. We will discuss how the effect depends on parameters such as frequency, field strength, channel dimensions, and will discuss the origin of the effect. Interestingly, DNA behaves like an artifical muscle that can be triggered by an a.c. electric field. Since the interaction is expected to hold for any solubilized polyelectrolyte, we speculate that the mechanism may lead to a new class of polymer-based mechanical actuators. These would not suffer from depolarization like piezo transducers. [Preview Abstract] |
Tuesday, March 6, 2007 11:27AM - 11:39AM |
J27.00002: dsDNA and nanobubble studies using solid-state nanopores Ralph Smeets, Ulrich Keyser, Diego Krapf, Meng-Yue Wu, Nynke Dekker, Cees Dekker DNA transport through fabricated solid-state nanopores is studied at various salt concentrations. dsDNA translocation at 1M KCl results in current blokkades, whereas by contrast current enhancements are observed at low salt concentrations. These current changes can be understood by taking both the volume and the counter ions of the molecule into account. Nanopore conductance and noise is studied as a nanopore is moved through a laser beam. The resulting conductance profiles show strong variations in the magnitude of the conductance and the low-frequency noise. In addition, we measure an unexpected double-peak conductance profile. A nanometer-sized gaseous bubble (nanobubble) explains this profile. Our data suggest that such nanobubbles act as the dominant source of low-frequency noise and conductance variability. Currently, translocation of RecA-coated DNA is employed to detect local protein structures and test translocation models. We will report on the latest status of these experiments. [Preview Abstract] |
Tuesday, March 6, 2007 11:39AM - 11:51AM |
J27.00003: Protein translocating as unfolded chains through solid-state nanopores Thomas Aref, Alexey Bezryadin We have detected translocation of the protein shrimp alkaline phosphatase (SAP) through a solid-state nanopore. The nanopores were fabricated in a silicon nitride membrane using a highly focused electron beam in a transmission electron microscope. Once formed, the nanopore was wet with an electrolytic solution and current was driven through it by application of an electric potential. When introduced to the negative side of the nanopore, the negatively charged SAP produced current blockages as the protein molecules were driven through the pore by the electric field. No current blockages occurred when protein had not been added to the electrolytic solution nor when polarity of the applied electric field was reversed. Furthermore, this globular protein does not appear to translocate as a sphere as might be expected, but rather goes through as an unfolded chain. Our current blockage events are similar to signals produced by lambda DNA translocating through a nanopore significantly larger than the DNA's diameter. This has implications for future experiments using nanopores to probe proteins. [Preview Abstract] |
Tuesday, March 6, 2007 11:51AM - 12:03PM |
J27.00004: Fabrication of sealed nanofluidic channels with single wall carbon nanotube electrodes for electronic DNA detection and analysis Chih-kuan Tung, Robert Riehn, Lukas Urban, Ali Yazdani, Robert Austin Detection of entropically elongated polymer molecules such as DNA in nanotubes by electronic means is a challenging task. SWCNT's are attractive nanoelectrode detection elements but cannot withstand many nanofabrication techniques commonly used in making nanochannels, such as dry etching. We have used near room temperature parylene deposition to create self-sealed nanochannels which pass over SWCNTs on the substrate surface. The process is totally e-beam compatible, and therefore allows us great flexibility in addressing problems and opportunities in nanoscale electronics. We will demonstrate applications such as electronic length measurement of elongated dsDNA molecules in the sealed nanochannels. [Preview Abstract] |
Tuesday, March 6, 2007 12:03PM - 12:15PM |
J27.00005: Capturing and Expulsion Processes of DNA Translocations in Solid-State Nanopores James Uplinger, Daniel Fologea, Brian Thomas, Ryan Rollings, John Wang, Jiali Li We study the DNA translocation dynamics through voltage biased solid-state nanopores. Our study examines the capturing and expulsion process of translocation events at various conditions, and compares them to artificial events. For events with translocation time on the order of 100 $\mu $s a significant portion of the translocation event corresponds to the transitory process of the DNA entering and exiting the nanopore, which is normally included in the overall translocation time. Our study reveals that DNA enter the nanopore with a higher speed than on exit. The limitations of the electronic response of the measurement system will also be discussed. [Preview Abstract] |
Tuesday, March 6, 2007 12:15PM - 12:27PM |
J27.00006: Manipulating DNA molecules inside nanopores using magnetic tweezers Hongbo Peng, Sean Ling There has been intense interest recently in using solid-state nanopores for DNA sequencing. A key to this goal is to develop the capability to control the motion or translocation of DNA molecules through the pore. Magnetic tweezers provide the possibility for manipulating multiple DNA molecules through addressable nanopore arrays. We will report our experimental design as well as the preliminary results on manipulating DNA molecules inside nanopores using magnetic tweezers. [Preview Abstract] |
Tuesday, March 6, 2007 12:27PM - 12:39PM |
J27.00007: Controlling DNA translocation through nanopores using optical tweezers Shanshan Wu, Xinsheng Sean Ling One of the key questions regarding DNA translocation studies is the ultimate limit to the spatial resolution of using ionic conductance measurement. We propose a method to improve on the spatial resolution by holding DNA under tension during translocation using optical tweezers. We will discuss the experimental setup and preliminary results. [Preview Abstract] |
Tuesday, March 6, 2007 12:39PM - 12:51PM |
J27.00008: Metastability and capillary condensation hysteresis in nearly ideal cylindrical alumina nanopores Felix Casanova, Casey E. Chiang, Chang-Peng Li, Igor V. Roshchin, Anne M. Ruminski, Michael J. Sailor, Ivan K. Schuller Nanoporous materials can be used as chemical and biological sensors. Anodized alumina, in which ordered cylindrical nanopores can be tuned in size, is a nearly ideal system to study gas adsorption and capillary condensation occurring in mesopores. Porous alumina with tunable pore diameters in the 10 to 60 nm range and a narrow distribution ($<$20{\%}) were dosed with several organic vapors. Capillary \textbf{\textit{evaporation}} occurs at equilibrium pressure for all pore sizes and gases, as predicted by the Kelvin equation. On the other hand, capillary \textbf{\textit{condensation}} occurs within a range of metastability of the gas phase, in agreement with theoretical models. Such a hysteresis in the condensation-evaporation process is a signature of metastability and depends on the gas adsorbed. Isopropanol (with stronger surface interactions) always condenses at the same pressure, whereas for toluene (with weaker interactions), the condensation pressure is less reproducible. [Preview Abstract] |
Tuesday, March 6, 2007 12:51PM - 1:03PM |
J27.00009: Natural Gas Storage on Nanoporous Carbon. Jacob Burress, Mikael Wood, Sarah Barker, John Flavin, Cintia Lapilli, Parag Shah, Galen Suppes, Peter Pfeifer Powdered and monolithic activated carbons have been made that have a large methane storage capacity (Alliance for Collaborative Research in Alternative Fuel Technology, http://all-craft.missouri.edu). The current best performer stores 115-119 grams methane per liter carbon at ambient temperature and 34 bar, compared to the DOE target of 118 g/L. Results are reported for the structure of the pore space (small angle x-ray scattering, nitrogen adsorption isotherms, methane adsorption isotherms, scanning and transmission electron microscopy), the methane binding energy (methane adsorption isotherms), and computer simulations of pore formation (probabilistic cellular automata). Most pores are centered about a width of 1.1 nm. At length scales larger than 100 nm, the samples are surface fractals with fractal dimension 2.4-2.6. [Preview Abstract] |
Tuesday, March 6, 2007 1:03PM - 1:15PM |
J27.00010: ABSTRACT WITHDRAWN |
Tuesday, March 6, 2007 1:15PM - 1:27PM |
J27.00011: Anisotropy of photoluminescence from dye molecules and zeolite-dye composites Hyunjin Lim, Hyeonsik Cheong, Jin Seok Lee, Kyung Byung Yoon The dynamics of photoluminescence from dye molecules in solvents and dye-containing zeolite rods were studied using polarized photoluminescence spectroscopy. We used nanoporous zeolites and pyronine dyes as the host and guest materials, respectively. The effects of concentration of dye molecules and zeolite-dye composites in various solvent were studied systematically. The anisotropy value ($\sim $2.8) reached the theoretical value ($\sim $3.0) in a highly viscous solvent (glycerol), whereas the anisotropy value is $\sim $1 in a low viscosity solvent (DMSO). The PL peak also shows a blue-shift in strongly polar solvents. In the case of zeolite-dye composites, we obtained a lower anisotropy value ($\sim $2.2) in glycerol. This result is interpreted in terms of energy transfer from dye molecules inside the zeolite pores to dye molecules on the surface of zeolite crystals. We also prepared a more advanced system, dye-containing zeolite rods in uniform orientations, using pyronine B and Y and zeolite L. The polarized PL spectra from vertically oriented monolayer of zeolite rods containing dye molecules show that the anisotropy ratio is $\sim $9 when the polarization direction of excitation light and the c-axis of zeolite rods are parallel. [Preview Abstract] |
Tuesday, March 6, 2007 1:27PM - 1:39PM |
J27.00012: How conductive polymer/nano-conductive filler composites can be? SuPing Lyu, Darrel Untereker, James Schley How conductive can polymer/filler composites be? It was thought the conductivity of composites could be increased by reducing the sizes of the fillers or increasing their aspect ratios, for example, by using carbon nanotubes. Invention of numerous conductive nanomaterials provides opportunity to verify this idea and to achieve higher conductivity. However, the highest conductivity of composites achieved was just a few percents of that of bulk materials of the fillers, regardless whether the filler was silver micron particles, platinum nano particles, carbon nano particles, or carbon nano tubes. The conductivity of filler-based composite is intrinsically limited by the micro-contact between the conductive fillers. Reducing the filler size or increasing aspect ratio did not yield significant improvements in conductivity although percolation may occur earlier. [Preview Abstract] |
Tuesday, March 6, 2007 1:39PM - 1:51PM |
J27.00013: Free-volume anomaly in confined glycerol. Duncan Kilburn, Victoria Garcia-Sakai, Ashraf Alam, Paul Sokol Glycerol is a small molecule glass-former which exhibits relatively high viscosity due to its extensive hydrogen bonding. Here we report the first measurements of local free volume and local mobility of glycerol confined in Vycor: a mesoporous silica glass with pores 70 Angstroms in diameter. We find that the lower molecular mobility in confinement (measured here using quasi-elastic neutron scattering) is accompanied by a higher mean free-volume size between molecules (as measured using positron annihilation lifetime spectroscopy). The strong wetting between glycerol and the glass surface appears to perturb the glycerol to such an extent that the normally observed free-volume/mobility relationship is reversed. Previous studies have come to similar conclusions (high glass transition temperature, low density) but this is the first to show that these effects originate locally. This is expected to have significant ramifications for the study of hydrogen-bonding liquids in confinement, for example water -- a topic of much current interest due to its application in hydration water in biological material. [Preview Abstract] |
Tuesday, March 6, 2007 1:51PM - 2:03PM |
J27.00014: Induced Thermal Dynamics in Aerosil Dispersed Glass Forming Liquid Dipti Sharma, Germano Iannacchione A high-resolution calorimetric spectroscopy study has been performed on pure glycerol and colloidal dispersions of an aerosil gel in glycerol covering a wide range of temperatures from $300$ to $380$~K, deep in the liquid phase of glycerol. The colloidal glycerol+aerosil samples with $0.07$, $0.14$, and $0.32 $~grams of silica per cm$^{3}$ of glycerol reveal activated energy (thermal) dynamics at temperatures well above the $T_g$ of the pure glycerol. The onset of these dynamics appears to be due to the frustration or pinning imposed by the silica gel on the glycerol liquid. Since this behavior occurs at relatively low silica density (large mean-void length compared to the size of a glycerol molecule), this induced dynamics is likely due to a cooperative mode of glycerol molecules with the aerosil gel via mutual hydrogen-bonding. However, the exact nature of these energy dynamics is not known. The study of such frustrated colloids may provide a unique avenue for illuminating the physics of glasses. [Preview Abstract] |
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