Bulletin of the American Physical Society
2009 APS March Meeting
Volume 54, Number 1
Monday–Friday, March 16–20, 2009; Pittsburgh, Pennsylvania
Session A28: Bionanotechnology |
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Sponsoring Units: FIAP Chair: Xinsheng (Sean) Ling, Brown University Room: 330 |
Monday, March 16, 2009 8:00AM - 8:12AM |
A28.00001: Mesoscopic light reflection spectroscopy of weakly disordered dielectric media: Nanoscopic to mesoscopic light transport properties of a single biological cell and ultra-early detection of cancer Prabhakar Pradhan, Hariharan Subramanian, Dhwanil Damania, Hemant Roy, Vadim Backman We have developed a mesoscopic partial wave spectroscopy (PWS) method to measure the nanoscopic light transport properties of weakly disordered dielectric mesoscopic systems such as biological cells. Using mesoscopic theory, we have statistically quantified the light reflection coefficient and its correlation due to nanoscale refractive index fluctuations within a biological cell, and the results are consistent with the prediction of mesoscopic light transport theory. Finally, using these parameters, we have characterized the nanoscale optical disorder strength within the biological cell. Results of precancerous cell studies and cancer detection by the technique will be discussed. [Preview Abstract] |
Monday, March 16, 2009 8:12AM - 8:24AM |
A28.00002: Stick-Slip Motion of DNA in a Solid Nanopore Binquan Luan, Glenn Martyna Nanopore technology is a potential solution for the low-cost and high-throughput DNA sequencing. Till now, in a typical experiment DNA driven by an electric field translocates through a nanopore too fast to be detected at a single-base resolution. The recently proposed DNA transistor (Appl. Phys. Lett. 91, 153103 (2007)) holds the promise to trap DNA inside a nanopore and translocate single-stranded DNA (ssDNA) at a single-base resolution. Using extensive all-atom molecular dynamics simulations, we modeled the process of ssDNA's translocation through the DNA transistor when ssDNA is pulled by an optical tweezer. We found a stick-slip type of motions of DNA when both the stiffness of an optical tweezer and the pulling velocity are below critical values. This irregular motion of DNA is quantitatively characterized using the Tomlinson model. In a typical slip event, ssDNA advances one nucleotide spacing, while in a stick state the base of DNA can be conveniently measured. The duration of a stick state depends on the strength of a trapping field in the DNA transistor, the stiffness of an optical tweezer and the pulling velocity. Therefore, the controlled stick-slip motion of DNA is ideal for DNA sequencing methods using a solid nanopore. [Preview Abstract] |
Monday, March 16, 2009 8:24AM - 8:36AM |
A28.00003: Ionic Dependence of the Conformation and Dynamics of DNA Confined in Slit-like Nanofluidic Channels Yongqiang Ren, Walter Reisner, Derek Stein Due to the growth in nanobiofluidic technology for DNA manipulation and analysis there is growing interest in understanding the physics of DNA in nanoconfined environments. Using fluorescence video microscopy we study the ionic dependence of static and dynamic properties of DNA molecules confined in slit-like nanofluidic channels with varying channel height. We observe an abrupt transition from the de Gennes regime to the Odijk regime for three different ionic strengths for both the radius of gyration and the relaxation time. The cross-over channel height between the regimes increases with decreasing ionic strength. By direct measurement of the distribution function for the radius of gyration we can clearly show that the DNA molecules perform 2-D self-avoiding random walks for both the de Gennes and Odijk regimes. We also investigate the possible effects of electrostatic DNA-channel wall interactions. [Preview Abstract] |
Monday, March 16, 2009 8:36AM - 8:48AM |
A28.00004: Development of a nanopore-based electrical device for controlling the translocation of DNA with single base resolution and mass-production methods for sub-5 nm nanopores Hongbo Peng, Stephen Rossnagel, Stanislav Polonsky, Gustavo Stolovitzky During the last 10 years, nanopores have been proposed or demonstrated as sensors for rapid analysis of biomolecules (DNA, RNA, protein, etc.) or interactions between these biomolecules. Application of nanopores to low-cost DNA sequencing is particularly attractive as there is great need to reduce the cost for sequencing a whole human genome to \$1000. A key issue in the field of nanopore DNA sequencing is to control the DNA translocation. Here we will report the development of what we call a DNA transistor: a nanopore-based electrical device for controlling the translocation of DNA with single base resolution. The key part of this device is a free standing membrane, made of metal/dielectric/metal/dielectric/metal, with the thickness of each layer about 2 or 3 nm. A nanometer size (about 3 nm) pore is made through the membrane. Voltage biases are applied on the metal layers to modulate electrical field inside the nanopore. Our ongoing experiments test if the modulated electrical field can trap or translocate DNA in a controllable way. We will also report the development of methods to make uniform sub-5nm nanopores across standard 200 mm Si wafers using an industrial processing facility. [Preview Abstract] |
Monday, March 16, 2009 8:48AM - 9:00AM |
A28.00005: Single-Molecule Denaturation Mapping of Genomic DNA in Nanofluidic Channels Walter Reisner, Niels Larsen, Anders Kristensen, Jonas O. Tegenfeldt, Henrik Flyvbjerg We have developed a new DNA barcoding technique based on the partial denaturation of extended fluorescently labeled DNA molecules. We partially melt DNA extended in nanofluidic channels via a combination of local heating and added chemical denaturants. The melted molecules, imaged via a standard fluorescence videomicroscopy setup, exhibit a nonuniform fluorescence profile corresponding to a series of local dips and peaks in the intensity trace along the stretched molecule. We show that this barcode is consistent with the presence of locally melted regions and can be explained by calculations of sequence-dependent melting probability. We believe this melting mapping technology is the first optically based single molecule technique sensitive to genome wide sequence variation that does not require an additional enzymatic labeling or restriction scheme. [Preview Abstract] |
Monday, March 16, 2009 9:00AM - 9:12AM |
A28.00006: Translocation Studies of Single Strand-DNA Oligomer Complexes with ds-DNA Markers Using Solid-State Nanopores Venkat Balagurusamy, Paul Weinger, Sungcheol Kim, Xinsheng Sean Ling We have designed short oligomers of single strand DNA of about 130 bases long each with 12-bases long sticky ends that are complimentary to those on one end of other oligomers to form ds-DNA regions by Watson-Crick base-pairing in these regions. Such a design facilitates the formation of a chain of single strands of DNA with ds-DNA regions interspersed. In order to slow down the translocation speed of these complexes through solid-state nanopores that could enable one to identify the ds-DNA region markers in the blockage current signal during translocation, we have attached these ss-DNA complexes with a polystyrene bead on one end. We present the results of our preliminary studies that show that the signature of these ds-DNA region markers could be identified. [Preview Abstract] |
Monday, March 16, 2009 9:12AM - 9:24AM |
A28.00007: Magnetophoresis of Fe$_{3}$O$_{4}$ Nanorods David Tan, Jitkang Lim, Caitlin Lanni, Frederick Lanni, Robert Tilton, Sara Majetich The magnetophoretic motion of a nanorod is quite different from that of a nanosphere. In large particles, motion is predicted from the balance of magnetic and viscous drag forces, but for nanoparticles random thermal forces lead to Brownian motion as well. Due to magnetic and diffusive anisotropy, a nanorod has advantages over a nanosphere for the single particle guidance and tracking, which would be important for studies within living cells. We have investigated the magnetophoretic behavior of nanorods and nanospheres both theoretically and experimentally. Peclet number analysis shows that 300 nm x 20 nm nanorods are more likely to be in the convective than diffusive regime than nanospheres of equal volume, for the same field and field gradient. Experimental studies of nanorod motion were made using Fe$_{3}$O$_{4}$ nanorods coated with poly (diallyldimethylammonium chloride) and fluorescein-5-isothiocyanate (FITC) tagged bovine serum albumin (BSA) and dispersed in saline solution. The motion of the nanorods was observed with and without magnetic field gradients using fluorescence microscopy. Fluorescence micrograph showed the nanorods undergo magnetophoretic motion toward the higher field gradient region with a velocity of about 28$\mu $m/sec. The controlled motion of magnetic nanorods within HeLa cancer cells has been demonstrated. [Preview Abstract] |
Monday, March 16, 2009 9:24AM - 9:36AM |
A28.00008: Chip-based Magnetic Resonance System for Medical Diagnosis Hakho Lee, Tae-Jong Yoon, Ralph Weissleder We have developed a chip-based, diagnostic magnetic resonance (DMR) system that can perform rapid, quantitative and multi-channeled detection of biological targets. The measurement is based on the effect of molecularly targeted magnetic nanoparticles on NMR (nuclear magnetic resonance) signals. With magnetic nanoparticles bound to their intended detection targets, the overall spin-spin relaxation time of bulk samples will be significantly shortened, as the particles efficiently dephase spins of surrounding water protons. Because the signal detection relies on NMR, the interference from media becomes negligible, making it possible to perform measurements in native biological samples (e.g., blood, sputum and urine). As proof of concept, we have developed a first DMR prototype by integrating microcoils, microfluidic channels and a permanent magnet. The microcoils, used as an NMR probe, are arranged in an array format for multiplexed, parallel detection. The microfluidic channels provide on-chip mixing between magnetic nanoparticles and biological samples and confine the mixture to microcoils for high filling factor. Here, we demonstrate clinical utility of the DMR system by measuring proteins at exquisite sensitivities ($\sim $1 pM), identifying the disease condition of human sera, and profiling cancer cells according to their cell-surface markers. [Preview Abstract] |
Monday, March 16, 2009 9:36AM - 9:48AM |
A28.00009: Hyperpolarized Long-\emph T$\bf_1$ Silicon Nanoparticles for Magnetic Resonance Imaging Maja Cassidy, Jacob Aptekar, Alexander Johnson, Robert Barton, Menyoung Lee, Alexander Ogier, Chinh Vo, Chandrasekhar Ramanathan, David Cory, Alison Hill, Ross Mair, Matthew Rosen, Ronald Walsworth, Charles Marcus Nanoparticles are currently being widely investigated as targetable contrast agents for magnetic resonance imaging (MRI). Silicon is a promising material system for use as a magnetic resonance imaging agent due to its long bulk (T$\bf_1$) times and receptivity to hyperpolarization. We present studies of the nuclear relaxation (T$\bf_1$) times of silicon nanoparticles as a function of particle size, dopant concentration and fabrication method. The T$\bf_1$ times of these particles are found to be remarkably long (depending on size and dopant concentration), allowing for them to be transported and administered on practical time scales. In addition, we discuss the particles' receptivity to hyperpolarization, via low temperature microwave induced dynamic nuclear polarization. [Preview Abstract] |
Monday, March 16, 2009 9:48AM - 10:00AM |
A28.00010: Magnetic detection of biotin-streptavidin binding using InAs quantum well $\mu $-Hall sensor Khaled Aledealat, K. Chen, G. Mihajlovic, P. Xiong, G. Strouse, P.B. Chase, S. von Moln\'ar, M. Field, G.J. Sullivan Magnetic sensors are a key component in any high-sensitivity, rapid-response, and portable platform for magnetic biosensing. InAs quantum well micro-Hall sensors have shown high potential for such a role due to their low noise level and capability to detect single micron- sized or smaller superparamagnetic beads suitable for biosensing$^{1}$. Here we present successful selective biotinylation of InAs micro-Hall sensors and directed self-assembly of 350 nm streptavidin-coated superparamagnetic beads via the biotin-streptavidin interaction. Two Hall crosses with three and two beads produced detection signals with S/N ratio of 21.3 dB and 18.4 dB respectively. In addition, our progress for \textit{in situ} detection of micron-sized magnetic beads using microfluidic channel will be presented. $^{1}$G. Mihajlovic et al., APL 87, 112502 (2005) This work was supported by NIH NIGMS GM079592. [Preview Abstract] |
Monday, March 16, 2009 10:00AM - 10:12AM |
A28.00011: Single Nanometric Memory Unit Based On a Protein-Nanoparticle Hybrid Izhar Medalsy, Arnon Heyman, Oded Shoseyov, Danny Porath Proteins as an isolating template and nanoparticle (NP) as an electric storage component can form a single addressable unit cell isolated from the conductive surface and adjacent NPs. This setup gives rise to a wide range of nanoelectronic applications. Here we demonstrate, by Conductive AFM, a single nanometric memory unit using individual protein-NP hybrids. SP1 is a boiling-stable ring-shaped protein, 11 nm in diameter. Mutants of SP1 were synthesized allowing its selective attachment to gold surface and the formation of 2D arrays using methods such as phospholipids trough and Langmuir Blodgett. The SP1 inner pore was connected to Si NP forming a chargeable entity embedded in an isolating unit over a conductive surface. Each NP holds three charging states: natural, positive and negative. The charging life times are 10 min in ambient and days in vacuum. Using this setup, and the relative long charging time, we were able to apply a read and write operations on individual 5nm Si NP embedded in a stable protein. [Preview Abstract] |
Monday, March 16, 2009 10:12AM - 10:24AM |
A28.00012: Characterization of the Uptake of Quantum Dots by Algae Priyanka Bhattacharya, Sijie Lin, Xiaoqian Sun, David Brune, Pu-Chun Ke The exposure of living systems to nanoparticles is inevitable due to a dramatic increase in their release into the environment, the most likely pathways being through inhalation, ingestion and skin uptake. The extremely small size of the nanoparticles may facilitate their tissue and cellular uptake by plants and animals, resulting in either positive (drug delivery, antioxidation) or negative (toxicity, cellular dysfunction) effects. Here we report the effects of quantum dots uptake by algae, the single-celled plant species and major food sources for aquatic organisms. In our studies, the presence of quantum dots in algal cells was detected using fluorescence microscopy and electron microscopy. Using spectrophotometry we found a supralinear increase of the uptake with the concentration of quantum dots, with a saturation of the uptake occurring beyond a concentration of 15 mg/mL. Using a bicarbonate indicator we further evaluated the effects of quantum dots uptake on algal photosynthesis and respiration. Such study facilitates our understanding of the environmental impact of nanomaterials. [Preview Abstract] |
Monday, March 16, 2009 10:24AM - 10:36AM |
A28.00013: Thermochemical nanolithography of multi-functional templates for selective assembly of bioactive proteins Debin Wang, Vamsi Kodali, William Underwood, Jonas Jarvholm, Takashi Okada, Simon Jones, Mariacristina Rumi, Zhenting Dai, William King, Seth Marder, Jennifer Curtis, Elisa Riedo Atomic force microscopy based techniques have been successful in generating protein nano-arrays on various substrates. However, several challenges still exist in terms of resolution, writing speed, cost, substrate choice, protein bioactivity, multi-component patterning, and surface passivation. Recently, we have developed the use of thermochemical nanolithography combined with post covalent functionalization and molecular recognition on a polymer surface of a single chip to produce multiplexed nanopatterns at speeds of mm/s. These patterns can then be functionalized under native conditions to create tailored nano-assemblies of two different species of proteins coexisting on the same surface. The proteins attach selectively and strongly to the nanopatterns via covalent and/or specific interactions, while retaining their ability to interact specifically with other proteins in buffered solution. At present, this method has produced nanopatterns of bio-active proteins with features as small as 40 nm on polymer films. This technique opens up new possibilities in nanoscale manipulation of biological macromolecules as well as many molecular biophysics studies such as inter-protein interactions. [Preview Abstract] |
Monday, March 16, 2009 10:36AM - 10:48AM |
A28.00014: Directional Growth of Polymeric Nanowires Prem Thapa, Bret Flanders This work establishes an innovative electrochemical approach to the template free growth of conducting polypyrrole and polythiophene wires. These polymeric wires exhibit a knobby structure, but persistent growth in a given direction up to 30 $\mu $m in length. A long-range component of the applied voltage signal defines the growth-path. Moreover, the presence of this component enables the growth of amorphous nanowires with wire-like geometries. Such wires are employed in a non-invasive methodology for attaining strong mechanical attachments to live cells. This capability is of potential use in the electro-mechanical probing of cell physiological processes. [Preview Abstract] |
Monday, March 16, 2009 10:48AM - 11:00AM |
A28.00015: A novel nanoarchitecture with optical, solar, medical and biochemical utility M.J. Naughton, K. Kempa, Z.F. Ren We discuss a nanoscale platform offering widespread utility in nanophotonics, photovoltaics, visual prosthetics, and biological and chemical sensing. As a subwavelength wave-guide architecture, these nanostructures can be used in array form for high efficiency solar cells, as well as in a wide range of nanoscale manipulations of light without deleterious plasmonic effects. They are also being developed as a high electrode-density (10$^{8}$/cm$^{2})$ retinal implant. Finally, a modification of the basic structure enables the fabrication of a highly sensitive ``nanocavity'' biochemical sensor. We will report on aspects of each application. We also thank the following collaborators: N. Argenti, D. Cai, T.C. Chiles, P. Dhakal, Y. Gao, T. Kirkpatrick, Y.C. Lan, G. McMahon, J.I. Oh, B. Rizal, J. Rybczynski. [Preview Abstract] |
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