Bulletin of the American Physical Society
2008 APS March Meeting
Volume 53, Number 2
Monday–Friday, March 10–14, 2008; New Orleans, Louisiana
Session Q9: Focus Session: DNA and Biofluid Analysis with Micro and Nanofluidic Devices |
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Sponsoring Units: DFD Chair: Dorian Liepmann, University of California, Berkeley Room: Morial Convention Center RO7 |
Wednesday, March 12, 2008 11:15AM - 11:51AM |
Q9.00001: Using hydrodynamics to control DNA conformation for genotyping, sorting, and analysis Invited Speaker: Understanding the dynamics of biopolymers in complex flows is critical for the successful design of lab-on-a-chip devices. Work by Chu, Shaqfeh, and others using both Brownian dynamics simulations and direct, single molecule visualization methods have yielded unprecedented insights into DNA dynamics in simple shear, planar extension, and a range of linear mixed flows. Here, we focus on two flows designed to stretch and manipulate DNA conformation for single molecule genotyping and analysis; that is, flows designed to produce specific conformation fields. First, we present results on DNA in pressure-driven flow through a post array, and discuss insights from direct comparisons with Brownian Dynamics simulations by Shaqfeh and co-workers. Second, we consider stagnation point flows and, through the use of sequence-specific probes, demonstrate the potential of these flows for target sequence identification, single molecule studies of enzyme kinetics, and sorting. [Preview Abstract] |
Wednesday, March 12, 2008 11:51AM - 12:03PM |
Q9.00002: Droplet-based microfluidics for high-throughput scanning of a large probe library. Adam Abate, Dave Weitz Droplet-based microfluidics can produce monodisperse picoliter size microreactors at 10 kHz speed. We use this technology to prepare and fuse two drop trains. The drops in one train each contain a unique biochemical probe. The drops in the other train contain a probe target, enzymes, proteins, and other biochemical reagents that are necessary to sufficiently mimic the cellular environment. We synchronize the trains hydrodynamically and use electro-coalescence to perform high-throughput controlled fusion of one of each type of droplet microreactor. Using a multicolor laser excitation and fluorescence polarization detector we monitor each fusion event to observe the state of the probe and extract information about the target. This allows us to scan through a large probe library in a matter of seconds using less than 1$\mu $L or reagent. [Preview Abstract] |
Wednesday, March 12, 2008 12:03PM - 12:15PM |
Q9.00003: Distant-ion dragging of polarizable nanodroplets and solvated DNA on nanotubes Boyang Wang, Petr Kral Long distance Coulombic coupling allows efficient molecular dragging at the nanoscale by moving electrons, ions and molecules [1]. We use molecular dynamics simulations to show that ions intercalated inside semiconducting single-wall carbon nanotubes (SWNT) can be solvated in polarizable nanodroplets adsorbed on the SWNTs, and the coupled systems can be dragged by electric fields [2]. We also demonstrate that solvated single-strand DNA molecules adsorbed on SWNTs can be driven by ionic solutions flowing inside the tubes. These phenomena could be applied in molecular delivery, separation, desalination and be integrated in modern lab-on-a-chip technologies. [1] Boyang Wang and Petr Kral, JACS 128, 15984 (2006). [2] Boyang Wang and Petr Kral, submitted. [Preview Abstract] |
Wednesday, March 12, 2008 12:15PM - 12:27PM |
Q9.00004: Spontaneous and coherent Raman spectroscopy of microfluidic flows Rajan Arora, Georgi Petrov, Vladislav Yakovlev Identifying protein structure and understanding its conformational dynamics are the grand challenges for biomedical science. The advent and most recent progress of microfluidics holds a promise of successfully addressing the major issues of structure determination---protein crystallization---by greatly multiplexing the evaluated number of crystallization conditions and protein dynamics---protein folding---by achieving a microsecond scale mixing. The further success of these approaches will strangely depend on the availability of remote probes capable of non-invasive interrogating the structure of biological molecules. Vibrational spectroscopy offers superior structural and chemical sensitivity, which can be successfully applied for characterizing transitional kinetics in microfluidic channels. In particular Raman and CARS give the molecular fingerprint along with structural information that is not possible with conventional fluorescence measurements. Here we are investigating the potential applicability of spontaneous and coherent Raman spectroscopy for protein folding and crystallization. Under suitable experimental conditions coherent Raman is seen to be 100 times more efficient than conventional Raman. [Preview Abstract] |
Wednesday, March 12, 2008 12:27PM - 12:39PM |
Q9.00005: Detection of Kinase Translocation Using Microfluidic Electroporative Flow Cytometry Chang Lu, Jun Wang, Ning Bao, Leela Paris, Hsiang-Yu Wang, Robert Geahlen Translocation of a protein between different subcellular compartments is a common event during signal transduction in living cells. Detection of these events has been largely carried out based on imaging of a low number of cells and subcellular fractionation/Western blotting. These conventional techniques either lack the high throughput desired for probing an entire cell population or provide only the average behaviors of cell populations without information from single cells. Here we demonstrate a new tool, referred to as microfluidic electroporative flow cytometry, to detect the translocation of an EGFP-tagged tyrosine kinase, Syk, to the plasma membrane in B cells at the level of the cell population. We combine electroporation with flow cytometry and observe the release of intracellular kinase out of the cells during electroporation. We found that the release of the kinase was strongly influenced by its subcellular localization. Cells stimulated through the antigen receptor have a fraction of the kinase at the plasma membrane and retain more kinase after electroporation than do cells without stimulation and translocation. This tool will have utility for kinase-related drug discovery and tumor diagnosis and staging. [Preview Abstract] |
Wednesday, March 12, 2008 12:39PM - 12:51PM |
Q9.00006: DNA/Protein Concentration and Identification by Nano-Channel Electrokinetics Gilad Yossifon, Hsueh-Chia Chang Electric field focusing into charged nano-channels can concentrate and filter charged biological molecules. This transport specificity is further enhanced with sequence or receptor specific DNA probes and antibodies functionalized onto the channel wall or nano-colloids. Our theoretical and experimental studies show, however, the same field-focusing phenomenon can discharge mobile ions from the channel and produce a growing polarized layer outside the channel, both of which can significantly affect the I-V characteristics and molecular migration rate within the channel. Conversely, the presence of trapped molecules or nano-colloids can be sensitively detected with nano-channel impedance spectroscopy due to such field-focusing phenomena. We present several DC and AC electrokinetic techniques for concentrating, filtering and detecting biomolecules in nano-channels based on this principle. [Preview Abstract] |
Wednesday, March 12, 2008 12:51PM - 1:03PM |
Q9.00007: DNA dynamics in sub-persistence length confinement Yeng-Long Chen, Arsen Grigoryan Recent advances in genomic science and microscopy have spurred extensive investigation of the dynamics of double stranded DNA molecules in bulk solution and micron- and nano-scale fluidic channels. On the length scale of the DNA molecule's radius of gyration, classical polymer physics has been extremely successful in predicting the macromolecule's conformation and dynamics. With the availability of sub-100nm channels, it has become possible to study with detail the conformation and dynamics of DNA at the length scale of the DNA persistence length ($\sim$50nm), as well as DNA interactions with other molecules such as proteins. We employ Brownian dynamics simulations to explore DNA dynamics confined in channels of the DNA persistence length scale. The bending and thermal energy, the conformational entropy, and the DNA-surface interactions all contribute to the macromolecular dynamics. We compare our simulation results to the predictions of the Odijk theory for confined polymers, and we find that the confinement strongly affects the chain conformation and dynamics and lead to non-monotonic extensional relaxation. [Preview Abstract] |
Wednesday, March 12, 2008 1:03PM - 1:15PM |
Q9.00008: Learning from the Jersey Turnpike:Cell Lysis, Labeling and Washing with Microfluidic Metamaterials Kevin Loutherback, Keith Morton, David Inglis, Opheli Tsui, James Sturm, Stephen Chou, Robert Austin Directing objects across functional streamlines at low Reynolds number is difficult but important since this motion can be used to label, lyse, and analyze complex biological objects on-chip without cross-contamination. Here we use an asymmeteric post array to move cells across coflowing reagents and show on-chip, immunofluorescent labeling of platelets with washing and \emph{E.Coli} cell lysis with simultaneous separation of bacterial chromosome from the cell contents. Furthermore, we develop the concept of a microfluidic metamaterial by using the basic asymmetric post array as a building block for complex particle handling modes. These modular array elements could be of great use for developing robust techniques for on-chip, continuous flow manipulation and analysis of cells, large bio-particles, and functional beads. [Preview Abstract] |
Wednesday, March 12, 2008 1:15PM - 1:27PM |
Q9.00009: Scaling of Polymer Diffusivity in Confined Colloid-Polymer Systems Amir Amini, Marc Robert We show how the diffusivity of a polymer chain in a colloidal suspension varies with the extent of confinement and the number of segments, as well as with concentration of colloids. These predications are compared with experimental results [Preview Abstract] |
Wednesday, March 12, 2008 1:27PM - 1:39PM |
Q9.00010: Dynamics of Individual Flexible Biopolymers in a Microvortex Flow Chao-Min Cheng, Philip LeDuc Research in single polymer dynamics has provided exciting insights including increasing the understanding of cellular structures. Additionally, advances in micro-scale technologies such as microfluidics have been widely used for analyzing biological responses at the cellular and molecular levels. We describe observations of the real-time dynamics of individual flexible polymers (fluorescently labeled DNA molecules) under a microvortex environment through a pressure-driven microfluidic approach. This allows us to create a microvortex flow on a single molecule, which can simultaneously be imaged to determine the structural response of the individual molecule. The DNA exhibits distinct conformations and controlled curvatures that are influenced by both extension and bending dynamics, which can be directly correlated to their location within the microvortex. We analyzed the dynamics of these individual molecules and determined the elongation strain rate and the curvature under the pressure-driven flow. Their overall orientation ranges from parallel in the main inlet channel to perpendicular while being deformed within the flow inside of the microvortex. These results provide insights that will be important in numerous areas such as single molecule dynamics and polymer physics. [Preview Abstract] |
Wednesday, March 12, 2008 1:39PM - 1:51PM |
Q9.00011: Microfluidic devices for separation of human blood samples Virginia VanDelinder, Alex Groisman We describe design and operation of microfluidic devices for separation of human blood. The first device separates plasma from the cellular elements of blood using size exclusion in a cross-flow. The device generates 1 uL of high-quality plasma four minutes after loading the blood sample and can operate continuously for at least one hour. The second device separates white bloods cells (WBC) from red blood cells (RBC) using perfusion in a continuous cross-flow. The microfluidic device is tested with a suspension of polystyrene beads and is shown to efficaciously exchange the carrier medium while retaining all beads. The RBC content of the blood sample is reduced about 4000-fold while 98 percent of WBCs are retained with a resultant WBC : RBC ratio of 2.4 at the device outlet. [Preview Abstract] |
Wednesday, March 12, 2008 1:51PM - 2:03PM |
Q9.00012: Cheaters and Cooperators: A Study of Bacterial Conflict on a Chip Guillaume Lambert, Peter Galajda, Juan Keymer, Robert Austin We study the interaction of cheating and cooperating {\it escherichia Coli} metapopulations under selective pressure on chip designed to create a landscape of metabolic pressures. Using micro- and nano-fabrication techniques, we create microfluidic chips with an effective `fitness landscape' for the bacterial cells at the population level in which we can tune their access to spatial and energetic resources. Our custom-made micro habitats allow us to study the local density distribution and subpopulation dynamics of bacterial cells subjected to social pressure. We show that the microscopic collective behavior of the cheaters and cooperators differ greatly depending on the fitness landscape they evolved in. Locally, subpopulations emerge and compete in a `tug-of-war' fashion. Globally, metapopulations rise, fall, evolve and adapt to their hostile environment. [Preview Abstract] |
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