Bulletin of the American Physical Society
APS March Meeting 2015
Volume 60, Number 1
Monday–Friday, March 2–6, 2015; San Antonio, Texas
Session G43: Focus Session: Fluids Under Confinement and in Biological Systems |
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Sponsoring Units: DPOLY DBIO GSOFT Chair: Erio Tosatti, International School for Advanced Studies Room: 214C |
Tuesday, March 3, 2015 11:15AM - 11:27AM |
G43.00001: Stiff Filamentous Viruses Probe the Mobility of Counterions During Nanopore Translocations Angus McMullen, Jay Tang, Derek Stein We study the electrophoresis of two different filamentous viruses and double-stranded DNA through solid-state nanopores. The two viruses we examine, \textit{fd} and M13, are both $880$\,nm in length, 6.6\,nm in diameter, very stiff, and monodisperse. They only differ in their linear charge density, which is 30\,\% lower for M13 than for \textit{fd}. Filamentous viruses are therefore ideal for testing transport models and for comparisons with DNA dynamics. We find that the mean translocation speed of \textit{fd} virus is related to the nanopore diameter, $D$, and the virus diameter, $d$, as $\ln(D/d)^{-1}$, in agreement with the conventional electrokinetic model of translocations. In order to obtain quantitative agreement between that electrokinetic model and the measured translocation dynamics, however, one must conclude that the mobility of counterions within a few Angstroms of the polymer surface is strongly reduced from the bulk value. Similar reductions in counterion mobility near \textit{fd}, M13, and dsDNA explain their dynamics over a wide range of ionic strengths. This work was supported by NSF Grant CBET0846505, NSF Grant PHYS1058375 and Oxford Nanopore Technologies. [Preview Abstract] |
Tuesday, March 3, 2015 11:27AM - 11:39AM |
G43.00002: Salmonella detection in a microfluidic channel using orbiting magnetic beads Matt Ballard, Zachary Mills, Drew Owen, Srinivas Hanasoge, Peter Hesketh, Alexander Alexeev We use three-dimensional simulations to model the detection of salmonella in a complex fluid sample in a microfluidic channel. Salmonella is captured using magnetic microbeads orbiting around soft ferromagnetic discs at the microchannel bottom subjected to a rotating external magnetic field. Numerical simulations are used to model the dynamics of salmonella and microbeads throughout the detection process. We examine the effect of the channel geometry on the salmonella capture, and the forces applied to the salmonella as it is dragged through the fluid after capture. Our findings guide the design of a lab-on-a-chip device to be used for detection of salmonella in food samples in a way that ensures that salmonella captured by orbiting microbeads are preserved until they can be extracted from the system for testing, and are not washed away by the fluid flow or damaged due to the experience of excessive stresses. Such a device is needed to detect bacteria at the food source and prevention of consumption of contaminated food, and also can be used for the detection of a variety of biomaterials of interest from complex fluid samples. [Preview Abstract] |
Tuesday, March 3, 2015 11:39AM - 11:51AM |
G43.00003: Sequencing proteins with transverse ionic transport Paul Boynton, Massimiliano Di Ventra {\it De novo} protein sequencing is essential for understanding cellular processes that govern the function of living organisms. By obtaining the order of the amino acids that composes a given protein one can determine both its secondary and tertiary structures through protein structure prediction, which is used to create models for protein aggregation diseases such as Alzheimer's Disease [1]. Mass spectrometry is the current technique of choice for {\it de novo} sequencing, but because some amino acids have the same mass the sequence cannot be completely determined in many cases. In this paper we propose a new technique for {\it de novo} protein sequencing that involves translocating a polypeptide through a synthetic nanochannel and measuring the ionic current of each amino acid through an intersecting perpendicular nanochannel, similar to that proposed in [2] for DNA sequencing. Indeed, we find that the distribution of ionic currents for each of the 20 proteinogenic amino acids encoded by eukaryotic genes is statistically distinct, showing this technique's potential for {\it de novo} protein sequencing. \newline [1] Kelley, Nicholas W., et al. The Journal of Chemical Physics 129 (2008): 214707. \newline [2] Wilson, James, and M. Di Ventra. Nanotechnology 24 (2013): 415101. [Preview Abstract] |
Tuesday, March 3, 2015 11:51AM - 12:03PM |
G43.00004: Nanoscale Electrospray Ion Sources and a New DNA Sequencing Technique William Maulbetsch, Joseph Bush, Derek Stein Electrospray ion sources are used to transfer biochemical samples from solution into a charged gas phase for analysis, especially by mass spectrometry. Traditional ion sources require a background gas and high voltages, and waste most of the sample passed through the source's micrometer-scale tip. However, by scaling down the ion source to the nanoscale, we greatly reduce voltage and sample volume requirements, while eliminating the need for a background gas to desolvate droplets. We report experiments investigating the onset and characteristics of electrospray from glass capillaries whose tips were pulled down to an inner diameter on the order of 100 nanometers. Nanoscale ion sources serve as an integral part of a DNA sequencing technique we will describe, whereby DNA bases are identified by the molecular masses of the nucleotides. This work was supported by NIH grant NHGRI 1R21HG005100-01 and by Oxford Nanopore Technologies, Ltd. [Preview Abstract] |
(Author Not Attending)
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G43.00005: Statics and dynamics of softly confined polymers Andrea Scagliarini, Mauro Sbragaglia, Marcello Sega A variety of biological and technological problems where long chain molecules are constrained in spaces small compared to the molecule size (like membrane nanopores or nanofluidic slits) motivated recently a growing effort to understand the dynamics and structural scaling properties of polymers confined by solid walls. Our focus is, instead, on polymers confined in different geometries by soft interfaces, mimicking, e.g., DNA packaging inside cell nuclei or, mutatis mutandis, viral capsids. Soft-confinement is achieved by a proper choice of the solvation energies such that the polymer is trapped in one of the two phases of a binary mixture of immiscible liquids. We perform Molecular Dynamics simulations of polymers coupled with a fluctuating lattice Boltzmann method for the embedding matrix. Slab and droplet configurations are considered. In the former case we address the transition among various regimes of size scaling at changing the slab width. Under shear, the droplet is distorted from its equilibrium spherical shape and we explore how the transition from an isotropic geometry to a quasi-tube-like one affects polymer size scaling and knotting degree. Finally, we show how the feedback on the solvent induces viscoelastic rheology that can be related to polymer entanglement. [Preview Abstract] |
Tuesday, March 3, 2015 12:15PM - 12:27PM |
G43.00006: Threading moieties play a significant role in determining the DNA binding properties of binuclear ruthenium complexes Thayaparan Paramanathan, Andrew Clark, Fredrik Westerlund, Per Lincoln, Micah J. McCauley, Ioulia Rouzina, Mark C. Williams Binuclear ruthenium complexes are of interest due to their selective DNA binding properties, which make them potential candidates for chemotherapy. These dumbbell shaped molecules have to thread through the DNA base pairs to reach their final threaded intercalation state. Here we study the binuclear ruthenium complex, $\Delta \Delta $-[$\mu $-bidppz(bpy)$_{4}$Ru$_{2}$]$^{4+}$ and compare it with the previously studied $\Delta \Delta $-[$\mu $-bidppz(phen)$_{4}$Ru$_{2}$]$^{4+}$. Both have the same intercalating bridge unit, but different threading moieties. In this study, we stretch a single DNA molecule held with optical tweezers in the presence of the ligand at various concentrations and hold the DNA at constant force until an equilibrium DNA elongation is reached. The extension of the DNA obtained as a function of time during binding yields the kinetics and equilibrium binding properties of the ligand. The preliminary data suggests that the binuclear complex with bpy in the threading moiety shows stronger affinity and an order of magnitude faster on rate, compared to its counterpart with phen in the threading moiety. This confirms the hypothesis that the extra aromatic ring of phen interferes with the threading intercalation process. [Preview Abstract] |
Tuesday, March 3, 2015 12:27PM - 1:03PM |
G43.00007: Physics and (patho)physiology in confined flows: from colloidal patterns to cytoplasmic rheology and sickle cell anemia Invited Speaker: L. Mahadevan I will discuss a few problems that involve the interaction of fluids and solids in confined spaces. (i) Jamming in pressure-driven suspension flows that show a transition from Stokes flows to Darcy flows as the solids start to lock, as in evaporative patterning in colloids (e.g. coffee stain formation) .(ii) Jamming and clogging of red blood cells, as in sickle-cell pathophysiology, with implications for other diseases that involve jamming. (iii) The mechanical response of crowded networks of filaments bathed in a fluid, as in the cytoskeleton, that can be described by poroelasticity theory. In each case, I will show how simple theories of multiphase flow and deformation can be used to explain a range of experimental observations, while failing to account for others, along with some thoughts on how to improve them. [Preview Abstract] |
Tuesday, March 3, 2015 1:03PM - 1:15PM |
G43.00008: Quantifying the molecular mechanism for highly stereo-selective DNA threading intercalation Ali Almaqwashi, Johanna Andersson, Per Lincoln, Ioulia Rouzina, Fredrik Westerlund, Mark C. Williams DNA threading intercalators, such as binuclear ruthenium complexes, are regarded as potential DNA-targeted therapeutic drugs because of slow kinetics and high affinity. Recent bulk studies reported that poly(dAdT) threading intercalation by the binuclear ruthenium complex [$\mu $-dppzip(phen)$_{4}$Ru$_{2}$]$^{4+}$(Piz) is highly stereo-selective. The largest fractional binding was achieved for $\Delta $,$\Lambda $-Piz, with the $\Delta $ (right handed) configuration at the intercalating dipyridophenazine (dppz) subunit and the $\Lambda $ (left handed) configuration at the distal imidazophenanthroline (ip) subunit. To quantify this highly stereo-selective molecular mechanism, we used optical tweezers to probe single $\lambda $-DNA molecules elongation due to the threading intercalation by each of $\Delta $,$\Delta $-Piz and $\Delta $,$\Lambda $-Piz. While maintaining a DNA stretching force of 30 pN and a ligand concentration of 5 nM, the elongation was traced until reaching equilibrium. Then it was traced back to the free DNA extension by rinsing out the bound ligands. We found that the equilibrium elongation for $\Delta $,$\Lambda $-Piz is 30{\%} larger, and the affinity is 50{\%} higher relative to $\Delta $,$\Delta $-Piz. Further force-dependent study will quantitatively determine the differences in the zero-force binding site size, affinity and the DNA structural dynamics for association and dissociation. [Preview Abstract] |
Tuesday, March 3, 2015 1:15PM - 1:27PM |
G43.00009: Improving signal-to-noise performance for DNA translocation in solid-state nanopores at MHz bandwidths Bartholomeus Machielse, Adrian Balan, David Niedzwiecki, Jianxun Lin, Peijie Ong, Rebecca Engelke, Kenneth Shepard, Marija Drndic DNA sequencing using solid-state nanopores is impeded by the relatively high noise and low bandwidth of the current state-of-the-art translocation measurements. We measure the ion current noise through Si$_{3}$N$_{4}$~nanopores at bandwidths up to 1 MHz. At these bandwidths, the input-referred current noise is dominated by the amplifier's voltage noise acting across the total capacitance at the amplifier input. By reducing the nanopore membrane capacitance we are able to transition to a regime in which current noise is dominated by the effects of the capacitance of the amplifier itself. Advances in bandwidth and signal-to-noise ratio necessary for DNA sequencing will require lower capacitance devices as well as new amplifier designs with reduced input capacitance and~~noise characteristics. [Preview Abstract] |
Tuesday, March 3, 2015 1:27PM - 1:39PM |
G43.00010: DNA translocation measurements through low-capacitance solid-state nanopore chips at high bandwidths Chen-Chi Chien, David Niedzwiecki, Bartholomeus Machielse, Adrian Balan, Jianxun Lin, Peijie Ong, Kenneth Shepard, Marija Drndic We perform DNA translocation measurements with low-noise solid state nanopore chips.~ We obtain higher ion current signal-to-noise ratio and better resolution in ion current signals than previously reported in solid state nanopores at high bandwidths with chip capacitance lowering techniques of applying extra insulation on the chip surface. We show measurements of ion current~ during translocation of DNA molecules through thin silicon nitride (SiN) nanopores of small diameters at megahertz bandwidths with enhanced ionic signal-to-noise ratios.~~We further discuss how these results possibly pave the way towards identifying intramolecular DNA sequences with solid-state nanopores. [Preview Abstract] |
Tuesday, March 3, 2015 1:39PM - 1:51PM |
G43.00011: Up and down events in nanoparticle translocation through solid-state nanopores Mehdi Zanjani, Rebecca Engelke, Jennifer Lukes, Marija Drndic We study translocation of nanoparticles through solid-state nanopores. Normally, nanoparticle passage is expected to decrease ion current inside the nanopores, as in the case of typical Coulter counters. However, recent experiments have reported translocation events that show an increase in the ion current. We refer to such decrease and increase in ion current as \textit{down events} and \textit{up events} respectively. We use theoretical methods to study such events and to determine the conditions under which they happen. A transition nanopore diameter, $d_{t}$, is calculated from the theoretical model; up events are observed for nanopore diameters smaller than $d_{t}$, while for nanopore diameters larger than $d_{t\thinspace }$down events will occur. We also discuss how a simple mechanism can be implemented to distinguish nanoparticles of different shapes and sizes based on such up and down translocation events. [Preview Abstract] |
Tuesday, March 3, 2015 1:51PM - 2:03PM |
G43.00012: Structural Integrity of Proteins under Applied Bias during Solid-State Nanopore Translocation Mohammad R. Hasan, Raja Raheel Khanzada, Mohammed A. I. Mahmood, Adnan Ashfaq, Samir M. Iqbal The translocation behavior of proteins through solid-state nanopores can be used as a new way to detect and identify proteins. The ionic current through a nanopore that flows under applied bias gets perturbed when a biomolecule traverses the Nanopore. It is important for a protein detection scheme to know of any changes in the three-dimensional structure of the molecule during the process. Here we report the data on structural integrity of protein during translocation through nanopore under different applied biases. Nanoscale Molecular Dynamic was used to establish a framework to study the changes in protein structures as these travelled across the nanopore. The analysis revealed the contributions of structural changes of protein to its ionic current signature. As a model, thrombin protein crystalline structure was imported and positioned inside a 6 nm diameter pore in a 6 nm thick silicon nitride membrane. The protein was solvated in 1 M KCl at 295 K and the system was equilibrated for 20 ns to attain its minimum energy state. The simulation was performed at different electric fields from 0 to 1 kCal/(mol.{\AA}.e). RMSD, radial distribution function, movement of the center of mass and velocity of the protein were calculated. The results showed linear increments in the velocity and perturbations in ionic current profile with increasing electric potential. [Preview Abstract] |
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