Bulletin of the American Physical Society
APS March Meeting 2019
Volume 64, Number 2
Monday–Friday, March 4–8, 2019; Boston, Massachusetts
Session X54: Polymers and Biopolymers in Very Strongly Confined Environments II: Polymers in Nanochannels and NanoporesFocus
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Sponsoring Units: DPOLY DBIO GSNP Chair: Ining Jou, University of Massachusetts Amherst Room: BCEC 254A |
Friday, March 8, 2019 8:00AM - 8:12AM |
X54.00001: Brownian Dynamics studies of a “Tug-of-War” of a DNA translocating through a two-nanopore system Swarnadeep Seth, Aniket Bhattacharya, Walter Reisner, William B Dunbar Two nanopore devices show potential for improved translocation control and error reduction through correlation of independent current channels accessed at each pore. We report Brownian dynamics (BD) simulation results for a dsDNA threading through a two-nanopore system using a coarse-grained model for the dsDNA and pore. Specifically, we study “tug-of-war” states, where the DNA is simultaneously present in both pores and the pores exert opposing electrophoretic forces. We extract the life-time of the tug-of-war as a function of biasing conditions, chain stiffness and inter-pore separation and investigate the correlation and cross-correlation functions of the chain translocation velocity through the pores. Our studies are expected to extend the single-pore translocation problem to dual nanopore pore systems and aide in the design of two-pore devices. |
Friday, March 8, 2019 8:12AM - 8:24AM |
X54.00002: Controlling DNA Tug-of-War in a Dual Nanopore Device Frank Liu, Yuning Zhang, Roland Nagel, Walter Reisner, William B Dunbar
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Friday, March 8, 2019 8:24AM - 8:36AM |
X54.00003: Simulations of extension distributions for DNA confined in nanochannels near the persistence length Aditya Bikram Bhandari, Kevin Dorfman DNA has been used extensively as a model system to study confined polymers. A particularly important application of strongly confined DNA is genome mapping, where DNA molecules labeled at sequence-specific sites along their backbone are stretched by confinement in nanochannels with widths close to the DNA persistence length. The distributions of the fractional extension obtained in genome mapping experiments are skewed-left from a Gaussian distribution. Mehlig and coworkers proposed an explanation for these skewed distributions by obtaining the asymptotic solution for a weakly correlated telegraph model of a channel-confined polymer in the limit of small channels and long chains. We have tested the predictions of this theory using pruned-enriched Rosenbluth method (PERM) simulations. The simulated distributions are in reasonable agreement with theory in the relevant asymptotic limits. However, deviations are observed as we move away from the strict inequalities in the limits of the theory, corresponding to situations that are more representative of experimental systems. |
Friday, March 8, 2019 8:36AM - 9:12AM |
X54.00004: Diffusion of DNA in confinement: From nanochannels to cells Invited Speaker: Kevin Dorfman The key challenge in understanding the diffusivity of DNA in strongly confined systems is accounting for the hydrodynamic interactions between the polymer and its environment. I will present both experimental and theoretical results on the diffusion of DNA in two highly confined systems that illustrate the complexity of this problem. |
Friday, March 8, 2019 9:12AM - 9:24AM |
X54.00005: Stochastic Resonance Behavior of DNA Translocation with an Oscillatory Electric Field Ining Jou, Rhys Duff, Murugappan Muthukumar Stochastic resonance (SR) describes the synchronization between noise of a system and an applied oscillating field to achieve an optimized response signal. In this work, we use simulations to investigate the phenomenon of SR of a single stranded DNA driven through a nanopore when oscillating electric field (OEF) is added. The system is comprised of a MspA protein nanopore embedded in a membrane and different lengths of DNA are driven from one end of the pore to the other via a constant potential difference. We superimposed an OEF over the existing electric field. The source of noise is due to thermal fluctuations, since the system is immersed in solution at room temperature. Here,the signal optimization we seek is an increase in translocation time (τ) of DNA through the protein pore. Normally, τ scales linearly with DNA length and inversely with driving force in a drift dominated regime. We found a nonmonotonic dependence of τ with the frequency of the oscillating field. This nonmonotonic behavior of τ is observed for all lengths of DNA, but SR occurs only for longer DNA. Furthermore, we also see evidence of DNA extension being influenced by the oscillating field while moving through the nanopore. |
Friday, March 8, 2019 9:24AM - 9:36AM |
X54.00006: Spontaneous Transport of Single-Stranded DNA through Graphene-MoS2 Heterostructure Nanopores Binquan Luan The effective transport of a single-stranded DNA (ssDNA) molecule through a solid-state nanopore is essential to the future success of high-throughput and low-cost DNA sequencing. Compatible with current electric sensing technologies, here, I propose and demonstrate by molecular dynamics simulations the ssDNA transport through a quasi-two-dimensional nanopore in a heterostructure stacked together with different 2D materials, such as graphene and molybdenum disulfide (MoS2). Due to different chemical potentials, U, of DNA bases on different 2D materials, it is energetically favorable for a ssDNA molecule to move from the low-U MoS2 surface to the high-U graphene surface through a nanopore. With the proper attraction between the negatively charged phosphate group in each nucleotide and the positively charged Mo atoms exposed on the pore surface, the ssDNA molecule can be temporarily seized and released thereafter through a thermal activation, that is, a slow and possible nucleotide-by-nucleotide transport. A theoretical formulation is then developed for the free energy of the ssDNA transiting a heterostructure nanopore to properly characterize the non-equilibrium stick-slip-like motion of a ssDNA molecule. |
Friday, March 8, 2019 9:36AM - 9:48AM |
X54.00007: Determining the Free Energy and Kinetics of a Translocating Polymer Chain Zachary Dell, Murugappan Muthukumar Polymer threading or translocation through nanopores is widely studied due to its ubiquity in biology and its recent use as a characterization method. In this work, we explored translocation of a chain from one spherical cavity to another, motivated by viruses and vesicles. The primary theoretical tool for studying a translocating chain is its free energy, which includes the free energy associated with the donor/acceptor compartments, and the polymer-pore interaction energy. In the first stage of the project, we focused on calculating chain free energy under spherical confinement, relevant for donor/acceptor compartments. Due to conflicting theoretical pictures, we implemented Monte Carlo simulations and investigated how the free energy relates to the confinement strength and how it varies when the chain is tethered. With the simulation results and previous translocation theories, we built a center of mass (CM) theory for polymer translocation. This theory establishes a physical interpretation for the translocation coordinate in terms of the CM. Also, our approach allows for the incorporation of hydrodynamics through the CM friction. Both the simulations and theory can be generalized to study other confined environments. |
Friday, March 8, 2019 9:48AM - 10:00AM |
X54.00008: Using capillaries with varying cross-section to study polymer dynamics and behavior under multiple confining length scales David Ring, Robert Riggleman, Daeyeon Lee Infiltrating polymers into cylindrical nanopores to induce confinement has led to the fabrication of a new class of nanostructured polymeric materials. The behavior of polymers during infiltration and under confinement has been elucidated with the help of computational studies, revealing a rich thermodynamic and kinetic landscape. These systems, however, focus on confinement with a single characteristic length scale. There are many situations in which polymers infiltrate into a porous medium with varying dimensions (e.g., a packing of nanoparticles). In this talk, we address the question of what happens when polymers are confined with more than one characteristic length scale. To that end, we have simulated capillaries with varying cross-sections and multiple well-defined points of confinement, including necks and voids. Using umbrella sampling, we can explore the free energy of an infiltrating polymer melt to characterize the impact of confinement on the driving force for infiltration. We also vary the diameter of the capillary mouths to characterize the effect of geometry on the start of infiltration as polymers move from the bulk to the confined pore. Lastly, we also investigate the effect of varying cross-section on the rheological components of the polymer. |
Friday, March 8, 2019 10:00AM - 10:12AM |
X54.00009: Polymer-Grafted Nanoparticle Translocation in Strongly Confining Nanochannels Michael Hore, William R Lenart, Gabriela T Justino The process of a particle moving from one region to another through a channel is central to many physical systems, including viral infection and water filtration. In this talk, we discuss the conformation of polymers that are grafted to a spherical nanoparticle surface, and the effect this has on the translocation of the particle through a single, confining nanochannel. Using self-consistent field theory (SCFT) coupled with Poisson-Nernst-Planck (PNP) theory, we investigate the distortion of the grafted polymer layer for nanoparticles undergoing translocation in strongly confining nanochannels, as well as the expected signatures that would be observed experimentally. |
Friday, March 8, 2019 10:12AM - 10:24AM |
X54.00010: Water mediated effects in alpha-helix formation inside nanotubes Dylan Suvlu, Dave Thirumalai, Jayendran C Rasaiah We present replica exchange molecular dynamics studies of the phase diagram for alpha-helix formation of capped polyalanine in nanotubes (NT) open to a water reservoir as a function of the NT diameter and hydrophobicity. A helix forms only in a narrow range of diameters. Helix formation in polyalanine is driven by a small negative enthalpy and a positive entropy change at 300 K, in contrast to the large negative entropy change that destabilizes the helix and favors the coiled state in bulk water. To understand the sequence dependence of helix formation inside the NT, solvation thermodynamics are determined by forming a thermodynamic cycle with liquid and gas phase MD simulations. Polyalanine forms a more thermodynamically favorable helix in the presence of water inside carbon and boron nitride NT. This is attributed to a favorable solvent reorganization energy and solvation entropy. In contrast, polyserine forms a stable helix in the gas phase but not in the presence of water while inside the CNT. This is attributed to unfavorable water-mediated interactions. However, polyserine forms a helix in a BNNT inside the gas phase but only over a narrow temperature range in the liquid phase. These data have implications for understanding helix formation inside the ribosome tunnel. |
Friday, March 8, 2019 10:24AM - 10:36AM |
X54.00011: Free energy cost of localizing an end-monomer of a confined polymer James Polson, Zakary R. N. McLure We develop and employ a simple Monte Carlo simulation method to calculate the free energy cost of localizing an end-monomer of a polymer to the inside surface of a confining cavity. The method is applied to a freely-jointed hard-sphere polymer chain confined to cavities of spherical, rectangular and cylindrical geometries. We consider cases where the other end of the polymer is free and where it is tethered to another point on the surface. We characterize the dependence of the free energy on the cavity size and geometry type, the localization position, the polymer length, and the effects of excluded volume interactions. The relevance of these results to the initial stages of polymer translocation through nanopores is discussed. |
Friday, March 8, 2019 10:36AM - 10:48AM |
X54.00012: Polymer Conformation & Diffusion in Symmetric Thin Film Confinement James Pressly, Robert Riggleman, Karen Winey Polymer conformation and dynamics in thin film nanoconfinement controls a variety of properties important for advanced coating technologies and nanoplatelet composites. In this study, we examine the effect of chain length and film thickness on polymer conformation, entanglement density, and center of mass polymer diffusion using coarse grained molecular dynamics simulations. Polymer chain lengths of N = 25-400 and were confined between parallel plates to create polymer film thicknesses of h = 5-40σ. The plates are composed of discrete beads with athermal polymer-plate interactions. The simulations indicate that the diffusion coefficient, D, increases as the film thickness decreases, with longer chains exhibiting a larger increase in D. This increase in the diffusion coefficient correlates with chain disentanglement as confinement increases, similar to previous simulations of polymers confined to cylindrical pores. While we observe slowed diffusion in the most confined cylindrical geometries associated with chain segregation, polymer diffusion confined in thin films increases monotonically with increasing confinement. |
Friday, March 8, 2019 10:48AM - 11:00AM |
X54.00013: Slit confinement effects on the Isotropic-Nematic-Smectic transition for semiflexible polymers: Structure, dynamics, and criticality Yeng-Long Chen, Dmytro Luzhbin, Supriya Roy Strong quasi-two dimensional confinement on semi-flexible polymer increases the polymer bending rigidity. In this study, we explored how confinement-induced change in the bending rigidity affects the phase transition of semi-flexible polymer solutions. We investigated the density induced isotropic to nematic to smectic phase transition for slit heights (H) comparable and smaller than the chain persistence length (P). |
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