Bulletin of the American Physical Society
2006 APS March Meeting
Monday–Friday, March 13–17, 2006; Baltimore, MD
Session V16: Nanotechnology: Biological and Polymer |
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Sponsoring Units: FIAP Chair: Robert Austin, Princeton University Room: Baltimore Convention Center 312 |
Thursday, March 16, 2006 11:15AM - 11:27AM |
V16.00001: Microfluidic device for bacterial genome extraction and analysis Peter Galajda, Robert Riehn, Yan-Mei Wang, Juan Keymer, Ido Golding, Edward C. Cox, Robert H. Austin Although single molecule DNA manipulation and analysis techniques are emerging, methods for whole genome extraction from single cells, genomic length DNA handling and analytics is still to be developed. Here we present a microfabricated device to address some of these needs. This microfluidic chip is suitable for culturing bacteria and subsequently retrieve their genetic content. As a next step, the extracted DNA can be introduced in a nanostructured segment of the chip for precise handling, stretching and analysis. We hope that similar microdevices can be useful in studying genetic aspects of the cell lifecycle in a variety of organisms. [Preview Abstract] |
Thursday, March 16, 2006 11:27AM - 11:39AM |
V16.00002: Virus-Mimetic DNA Encapsulation Using Novel ABC Triblock Copolymers Rahul Sharma, You-Yeon Won To address the challenge of developing a safe and effective delivery system currently faced in gene therapy technologies, our research explores a novel approach for improving DNA encapsulation and delivery using a novel three-component block copolymer which by design has the self-assembling properties tailored for virus-like encapsulation of DNA. Our approach utilizes an ABC triblock copolymer composed of (A) \textit{hydrophilic }poly(ethylene oxide) (PEO), (B) \textit{hydrophobic} poly(n-butyl acrylate) (PnBA) and (C) \textit{cationic} poly(ethyleneimine) (PEI). With such an ABC sequence of blocks, the C block primarily interacts with the negatively charged phosphates on DNA, and the viral capsid-like morphology of the nanometers-thick membrane can be derived from the A and B blocks at the outer surface of collapsed DNA. In this presentation, we will discuss our recent experiments that establish a proof of concept and processing strategies for achieving the desired virus-mimetic DNA-encapsulating morphology composed of a compact DNA core covered with a layer of protective coating created by the ABC triblock copolymer. [Preview Abstract] |
Thursday, March 16, 2006 11:39AM - 11:51AM |
V16.00003: Electron Binding Energies in DNA Modified Surfaces: Theory and Experiment James Sullivan, Dmitri Petrovykh, George Schatz, Lloyd Whitman X-ray photoelectron spectroscopy is emerging as a powerful method for characterizing DNA on surfaces.[1] The relative positions of core electron binding energies (CBEs) suggest likely binding geometries and strength of chemical bonds, and the peak areas provide a quantitative measure of the coverage. Although CBEs for simple molecules can often be readily assigned to specific adsorption sites and bonding configurations based on historical data, such interpretation for CBEs of DNA is not generally possible. We are using density functional theory to determine the geometric and electronic configuration of DNA nucleobases, nucleosides, and nucleotides. We find the theoretical XPS spectra for isolated nucleic components are surprisingly similar to experimental spectra measured on DNA films, suggesting that---although the films are adsorbed on the surface---the underlying electronic structure of the nucleobases is ``free-like.'' 1. D. Y. Petrovykh, et al., J. Am. Chem. Soc. 125, 5219 (2003); D. Y. Petrovykh, et al., Langmuir 20, 429 (2004). [Preview Abstract] |
Thursday, March 16, 2006 11:51AM - 12:03PM |
V16.00004: Sequencing by Hybridization with Noisy Inputs Richard Yeh Sequencing by hybridization (SBH) is a proposed method for obtaining the base-by-base sequence of an unknown nucleic acid molecule in two steps: hybridization of fragments of the unknown DNA molecule to known subsequences, and reconstruction of the entire unknown sequence from the hybridization spectrum. Work in computer science has produced algorithms for the reconstruction process approaching information-theoretic bounds, but most treatments have ignored the effect of physical hybridization noise. I have been working on this problem by modeling the effect of noisy inputs on SBH algorithms and by calculating bounds on their reconstruction fidelity. This talk will give the progress of this effort. [Preview Abstract] |
Thursday, March 16, 2006 12:03PM - 12:15PM |
V16.00005: Surface Electrophoresis of DNA on Microporous Materials Eli Hoory, Andrew Dubitsky, John Frenna, Michael Ding, Jonathan Sokolov, Miriam Rafailovich Separation of single strand DNA molecules on solid surfaces can potentially be used for genomic research and diagnostic applications. Feasibility of DNA electrophoresis on solid surfaces has been demonstrated using insulating and semi-conducting substrates. Microporous membranes can offer advantages in separation because of the variety of surface-DNA interactions and surface morphologies. Droplets of Lambda Hind III DNA were applied to surfaces containing 0.2 to 2ng DNA. Results showed that variations in the electric field and Tris Borate EDTA buffer concentration both affected efficiency of separation. Significant differences in separation were found between different membrane types, including polyethersulfone and polyvinylidene fluoride. Better separation was obtained on low binding, small pore size membranes which could retain the DNA molecules on the surface. Further work includes sputter coating and other surface modifications of best candidate membranes to optimize efficiency of separation. [Preview Abstract] |
Thursday, March 16, 2006 12:15PM - 12:27PM |
V16.00006: Design of Mao Tensegrity Triangles -- Successful Prediction of Stable DNA Nanostructures. William B. Sherman, Jens Kopatsch, Pamela E. Constantinou, Nadrian C. Seeman One of the most promising motifs for crystal formation is the tensegrity triangle first developed by Mao and co-workers. This structure consists of three duplex domains ``woven'' across each other. Because the three edges of the triangle are not coplanar, it can serve as a fundamentally three-dimensional motif. This nonplanarity, however, makes the design of tensegrity triangles more complicated than most of the other DNA motifs built to date. We present a geometry-based method for estimating the strain associated with various tensegrity triangle edge lengths. Experiments confirm that the predicted low-strain structures form stably, while structures with strain larger than about 5{\%} tend to form multimers easily. [Preview Abstract] |
Thursday, March 16, 2006 12:27PM - 12:39PM |
V16.00007: Co-electrospinning of bacteria and viruses Wael Salalha, Jonathan Kuhn, Shmuel Chervinsky, Eyal Zussman Co-electrospinning provides a novel and highly versatile approach towards composite fibers with diameters ranging from a few hundred nm down to 30 nm with embedded elements. In the present work, co-electrospinning of poly(vinyl alcohol) (PVA) and viruses \textit{(T7, T4, $\lambda $}) or bacteria (\textit{Escherichia coli}, \textit{Staphylococcus albus}) was carried out. These preparations should have applications for tissue engineering, gene therapy, phage therapy and biosensing. The average diameter of the co-spun nanofibers was about \textit{300 nm}. We found that the encapsulated viruses and bacteria manage to survive the electrospinning process, its pressure buildup in the core of the fiber and the electrostatic field in the co-electrospinning process. Approximately 10{\%} of the \textit{Escherichia coli} and 20{\%} of \textit{Staphylococcus} \textit{albus }cells are viable after spinning. Approximately 5{\%} of the bacterial viruses were also viable after the electrospinning. It should be noted that the encapsulated cells and viruses remain stable for two months without a further decrease in number. These results demonstrate the potential of the co-electrospinning process for the encapsulation and immobilization of bio-objects and the possibility of adapting them to technical applications (e.g., bio-chips). [Preview Abstract] |
Thursday, March 16, 2006 12:39PM - 12:51PM |
V16.00008: The Design of Potent Liposome-Based Inhibitors of Anthrax Toxin Prakash Rai, Chakradhar Padala, Vincent Poon, Arundhati Saraph, Saleem Basha, Sandesh Kate, Kevin Tao, Jeremy Mogridge, Ravi Kane Several biological processes involve the recognition of a specific pattern of binding sites on a target surface. Theoreticians have predicted that endowing synthetic biomimetic structures with statistical pattern matching capabilities may impact the development of sensors and separation processes. We demonstrated for the first time that statistical pattern matching significantly enhances the potency of a polyvalent therapeutic -- an anthrax toxin inhibitor. We functionalized liposomes with an inhibitory peptide at different densities and observed a transition in potency at an inter-peptide separation that matches the distance between ligand-binding sites on the heptameric subunit of anthrax toxin. Pattern-matched polyvalent liposomes neutralized anthrax toxin \textit{in vitro} at concentrations four orders of magnitude lower than the corresponding monovalent peptide.~ We also showed that polyvalent liposome-based inhibitors can neutralize a microbial toxin \textit{in vivo}. Statistical pattern matching represents a facile strategy to enhance the potency of therapeutics targeting toxins or pathogens. Our results also illuminate other fundamental aspects of polyvalent recognition --specifically we found that the efficiency of polyvalent inhibition is influenced by the competition between the rates of ligand dissociation and diffusion. [Preview Abstract] |
Thursday, March 16, 2006 12:51PM - 1:03PM |
V16.00009: Submicrometer Hall sensors for detection of magnetic nanoparticles in biomolecular sensing Goran Mihajlovic, P. Xiong, S. von Molnar, K. Ohtani, H. Ohno, M. Field, G.J. Sullivan Significant progress has been made in the recent years in synthesis and biomolecular functionalization of magnetic nanoparticles. These magnetic bio-nanolabels can be utilized as protein or gene markers in biomolecular sensing assays, in contrast to the much larger micron sized magnetic beads that are usually limited to cell labeling. However, the low magnetic moments of individual nanoparticles (10$^{4}$-10$^{5 }$\textit{$\mu $}$_{B})$ render their sensitive detection still a challenging task. In order to address this issue we are developing miniaturized Hall sensors from InAs/AlSb quantum well semiconductor heterostructures with active Hall cross areas down to 300 nm $\times $ 300 nm. Our preliminary characterization measurements performed at room temperature show functional devices with magnetic field resolution $<$ 100 \textit{$\mu $}T/$\sqrt {\mbox{Hz}} $ at frequencies above 100 Hz, yielding a moment sensitivity $\sim $ 10$^{5}$ \textit{$\mu $}$_{B}$. In addition to the progress in improving the moment sensitivity of the submicrometer Hall detectors, we will also present efforts in device integration with on-chip microcoils for the generation of local magnetic excitation fields. Results on nanoparticle detection will also be presented. [Preview Abstract] |
Thursday, March 16, 2006 1:03PM - 1:15PM |
V16.00010: Novel glucose biosensor based on organic thin-film transistors. Maria Nikolou, Seiichi Takamatsu, Daniel Macaya, George Malliaras, Graciela Blanchet We report on a novel design of an organic thin-film transistor which utilizes a double channel transistor configuration. This electrochemical sensor-transistor is based on conducting polymers and operates at low voltages. The sensor response is measured as the drain-source current of one channel while a potential is applied on the other channel. The behavior of the transistor can be understood in terms of an electrochemical mechanism which is proven to depend on the ionic concentration of the electrolyte. The possible applications of these devices in biological sensing are explored as the advantages of their use are many, e.g. high sensitivity and selectivity, and low manufacturing cost. We present results from devices exploiting different conducting polymers, e.g. PEDOT:PSS, PANI, on a variety of substrates, e.g. glass, plastic, and demonstrate the capability of this type of device to sense glucose in a neutral pH buffer solution by a mechanism involving sensing of hydrogen peroxide. These devices can also be used effectively in the detection of other biological analytes. [Preview Abstract] |
Thursday, March 16, 2006 1:15PM - 1:27PM |
V16.00011: Application of hydroxyapatite thin film as a biosensor Hiroaki Nishikawa, Daichi Okumura, Masanobu Kusunoki, Shigeki Hontsu Hydroxyapatite (HAp) surface has an excellent ability of adsorption for functional biomolecules such as protein, DNA and so on. The surface electronic state of the HAp is affected by the adsorption of biomolecules. Thus, the electric properties of the surface such as resistivity and capacitance will vary. Because the property is effective for a receptor and transducer of biomolecule, we have investigated the application of the HAp as a suitable material for a biosensor. In this study, thin film of the sodium-doped HAp (Na-HAp) is prepared. The sodium doping is to decrease the resistivity of the HAp because the stoichiometric HAp is a good insulator. When bovine serum albumin of 1 ml was dropped to a Na-HAp thin film in a 100 ml pure water, the sample shows the drastic change of the AC resistance (at 120 kHz). This result shows that the Na-HAp will be one of the most effective materials for the biosensor applications. [Preview Abstract] |
Thursday, March 16, 2006 1:27PM - 1:39PM |
V16.00012: Directed Diblock Copolymer Self-Assembly Using Engineered Topologies To Drive Defect Motion. Ricardo Ruiz, Charles Black, Robert Sandstrom Self-organizing materials hold great promise for delineating the critical nanometer-scale elements of future integrated circuits. While self assembly provides a pathway to defining sub-lithographic dimensions, its Achilles’ heel lies in minimizing defects. Unlike lithographic processes, self assembly involves optimization of thermodynamic free energy, which can require prohibitively long equilibration times and may never reach pattern perfection. We have begun to address this intrinsic limitation by engineering surfaces to influence the assembly process. In this way we eliminate defects in the critical device areas, while driving unavoidable imperfections to predefined, non-crucial regions. We discuss this approach within the context of lamellar-phase poly(styrene-b-methylmethacrylate) diblock copolymer films, which possess excellent material characteristics for use as lithographic templates. Understanding the dynamics of pattern formation in these materials is crucial to optimizing their performance. We use correlation length measurements of lamellar diblock copolymer domains to extract information about mechanisms of defect annihilation. We also quantify the quality of these self-assembled materials within a framework of resist performance metrics, including resist profile, line-edge roughness, and etch characteristics. [Preview Abstract] |
Thursday, March 16, 2006 1:39PM - 1:51PM |
V16.00013: Conformational molecular architecture in alkylthiolate monolayer using atomic force microscopy electrostatic nanolithography Olga Mayevska, Sergei Lyuksyutov, Pavel Paramonov, Kazuo Umemura, Shane Juhl, Richard Vaia We propose a simple approach to form 50-nm raised structures based on conformational changes of organomercaptan molecules assembled in monolayer on surface of gold. Manipulation of amphifunctional molecules may be performed using a strong electric field (10$^{8}$-10$^{10}$ Vm$^{-1})$ induced by an atomic force microscope (AFM) tip. Such a field leads to re-arrangement of alkylthiolates assembled on Au (111) resulting in nano-patterning of raised nanostructure (1.5-9 nm high, 20-50 nm wide) arrays on a second-time scale by manipulating the tip above the monolayer. It is suspected, that as a result of the oxidative cleavage initiated by a weak bias of the tip, the S-end of the chain carrying a sulfenium cation is attracted to the tip forming a bi-layer, and the higher-layer structures in monolayer. Stabilization of the multiple-layered structures is accomplished via mutual attraction and entanglement of the hydrocarbon chains. [Preview Abstract] |
Thursday, March 16, 2006 1:51PM - 2:03PM |
V16.00014: Neutron Reflectometry Measurements of the Depth Profile of Water in a Fuel Cell Membrane. Joseph Dura, Charles Majkrzak, Sushil Satija, Norman Berk, Jon Owejan, Thomas Trabold Specular neutron reflectometry (NR) measurements have been performed on a prototypical polymer electrolyte membrane (PEM) for fuel cell application, e.g., Nafion. The samples were formed by spin coating onto a variety of substrates, and annealing in vacuum. The measurements are designed to reveal the water distribution across the thickness of the membrane material, as a function of relative humidity and for the case in which the film is in contact with a liquid water reservoir. Data from several samples indicates how the water profile for a given humidity changes with annealing temperature of the polymer film. Finally, we consider the application of phase-sensitive methods to eliminate potential ambiguity in the scattering length density profile of the membrane obtained from NR. [Preview Abstract] |
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