Bulletin of the American Physical Society
APS March Meeting 2016
Volume 61, Number 2
Monday–Friday, March 14–18, 2016; Baltimore, Maryland
Session C41: Biopolymers in Confinement: IFocus
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Sponsoring Units: DBIO DPOLY DCOMP Chair: Kevin Dorfman, University of Minnesota - Minneapolis Room: 344 |
Monday, March 14, 2016 2:30PM - 2:42PM |
C41.00001: Flory theory or the two state cooperativity model: What describes backfolding of DNA in nanotubes? Kevin Dorfman, Abhiram Muraldihar Currently, there are two explanations available in the literature to describe the extension of semiflexible polymers, such as DNA, confined in nanotubes whose diameter is close to the persistence length. Almost a decade ago, Odijk (Phys. Rev. E, 2008, 77, 060901) used a Flory theory to derive a scaling law for the average extension of a semiflexible polymer confined in such a tube. More recently, Dai et al. (ACS Macro Lett. 1, 1046-1050) applied a two-state cooperativity model along the lines of the Zimm-Bragg model for helix coil transitions to explain the same phenomenon. Although the two theories are fundamentally different, there are simulation results supporting both approaches. In this talk, we will present results from Pruned-Enriched Rosenbluth Method (PERM) simulations of a discrete wormlike chain model, which show strong evidence supporting Odijk's Flory theory. Moreover, we will show that Odijk's scaling theory also predicts the contour length dependence of the chain extension. In contrast, we find that the cooperativity model predicts the average extension correctly only for the molecular weights used to parameterize the model. [Preview Abstract] |
Monday, March 14, 2016 2:42PM - 2:54PM |
C41.00002: Pore translocation of polymer chains with physical knots Antonio Suma, Angelo Rosa, Cristian Micheletti The driven traslocation of knotted chains through narrow pores has important implications for single-molecule manipulation contexts. Its complex phenomenology\footnote{A. Rosa, M. Di Ventra and C. Micheletti. \textit{Phys. Rev. Lett}, 2012, 109 , 118301} is, however, still largely unexplored, both as a function of knot complexity and the magnitude of the driving, translocating force. We accordingly report on a systematic theoretical and computational investigation of both aspects. In particular we consider the case of flexible chains accommodating a large repertoire of knots that are driven through pores too narrow to allow for their passage. We show that the observed rich translocation phenomenology can be rationalised in a transparent mechanical framework that can further be used for predictive purposes\footnote{A.Suma, A. Rosa and C. Micheletti. \textit{Pore translocation of knotted polymer chains, submitted}, 2015}. [Preview Abstract] |
Monday, March 14, 2016 2:54PM - 3:06PM |
C41.00003: Intramolecular Fluctuation of DNA in Nanochannels via High-throughput Video Microscopy Julian Sheats, Jeffrey G. Reifenberger, Han Cao, Kevin D. Dorfman Genome mapping is a promising technique that complements next generation sequencing. The distance between labels on barcoded DNA molecules is the main physical quantity employed by emerging nanochannel techonologies used to construct genome maps. Here we analyze time resolved data of {\it E. coli} DNA in a commercial nanochannel genome mapping system to obtain the probability distribution underlying the distance between labels. Improving upon a previous study of this type \footnote{Reinhart, W. F. et al., J. Chem. Phys. \bf{142}, 064902 (2015)}, this dynamic method avoids alignment to the reference genome, a process that is statistical in nature. The time-series analysis also allows for detection of a set of experimental artifacts present in static imaging, thereby filtering out several sources of potential systematic error. The resulting probability density remains left-skewed, supporting previous evidence. However, filtering out the artifacts resulted in a lower magnitude of skewness, which has implications for the statistical weights associated with the genome mapping algorithm. [Preview Abstract] |
Monday, March 14, 2016 3:06PM - 3:18PM |
C41.00004: Non-Equilibrium Dynamics of Nano-channel Confined DNA: A Brownian Dynamics Simulation Study Aniket Bhattacharya, Aiqun Huang, Walter Reisner We carry out Brownian dynamics (BD) simulation for a semi-flexible polymer chain characterized by a contour length $Na$ and a persistence length $\ell_p$ confined inside a rectangular nanochannel to study its compression and retraction dynamics while being pushed on one end at a constant velocity by a ``nano-dozer''. We study the evolution of one dimensional concentration profile $c(x,t)$ and the chain extension $R$ along the channel axis ($x$-axis) during both the contracting as well as the retracting phases as a function of the velocity of the nano-dozer, both in steady states and in transients. Furthermore, we measure the transverse fluctuations of the chain under contraction and retraction, and the amplitude of the density profile, and compare these simulation results with those obtained from an analytical model proposed by Khorshid {\em et al}. Our studies are guided by recent experimental results by Khorshid {\em et al.} (Phys. Rev. Lett, {\bf 113}, 268104 (2014)) and provide further justification to use a one dimensional PDE approach to understand the non-equilibrium dynamics of confined polymers. [Preview Abstract] |
Monday, March 14, 2016 3:18PM - 3:30PM |
C41.00005: Dynamics of topological events within single molecules of DNA confined in nanochannels. Jeffrey Reifenberger, Kevin Dorfman, Han Cao Genome mapping in nanochannels offers the ability to search for large genomic rearrangements within individual molecules of DNA often missed by sequencing techniques. This method labels DNA at specific sequence motifs such as `GCTCTTC' with a cy3-like fluorophore and then stains the backbone of dsDNA with an intercalating dye. DNA is electrophoretically loaded into an array of nanofluidic channels and linearized in physically confined narrow conduits fabricated on the silicon chip. The fluorescently labeled sequence motifs, unique to long genomic regions, are optically imaged and digitized reflecting structural changes that can occur within cancer. However, some molecules of DNA confined within the \textasciitilde 42 nm wide nanochannels contain topological structures: knots, S-folds, and end-folds that could appear as false genomic rearrangements. We present a technique in which thousands of molecules of \textit{E. coli} DNA are sequentially imaged in the nanochannels during several minutes allowing for topological events like diffusion of knots, unfolding at the ends, and spontaneous formation of S-folds to be measured. This technology will provide insights and a solution in error correction for making more accurate measurements. [Preview Abstract] |
Monday, March 14, 2016 3:30PM - 3:42PM |
C41.00006: Adsorption of annealed branched polymers on curved surfaces Jef Wagner, Gonca Erdemci-Tandogan, Roya Zandi Annealed branched polymers play important roles in many biological and industrial systems, notable among them single stranded RNA (ssRNA) that in solution takes on a branched secondary structure. Using a mean field theory, we both perturbatively and numerically examine the adsorption of annealed branched polymers on surfaces of several different geometries in a good solvent. Independent of the geometry of the wall, we observe that as branching density increases, surface tension decreases. However, we find a coupling between the branching density and curvature in that a further lowering of surface tension occurs when the wall curves towards the polymer, but the amount of lowering of surface tension decreases when the wall curves away from the polymer. This work was inspired by the idea of using functionalized gold nano-particles to bind RNA for gene delivery. Understanding the mechanisms involved with the adsorption of annealed branched polymers onto different surfaces will play a critical role in many biomedical technologies. [Preview Abstract] |
Monday, March 14, 2016 3:42PM - 3:54PM |
C41.00007: Depletion forces in collapsing a flexible chain molecule in a confined or free space Chanil Jeon, Bae-Yeun Ha A chain molecule can be entropically collapsed in a crowded medium whether confined or not. Qualitatively, the entropic (depletion) forces between monomers can be considered as effectively reducing the solvent quality, eventually making the excluded volume $v$ negative. Here, we characterize these forces in collapsing a flexible polymer in three distinct spaces: free, cylindrical, and (2-dimensional) slit-like. A few general features characterize flexible-chain collapse. Let $\phi_c$ is the volume fraction of crowders of size $a_c$ each (in units of the monomer size). In all three cases, chain compaction depends on a single parameter, i.e., the ratio $\phi_c/a_c$; there also exists a general relationship between $\phi_c/a_c$ and $v$. Our results suggest that the action of depletion forces is local and insensitive to the geometry of a confined space, as assumed in an effective-solvent picture. They also offer a physical sense of average crowder sizes in a poly-disperse crowded medium. [Preview Abstract] |
Monday, March 14, 2016 3:54PM - 4:06PM |
C41.00008: Detection of ATP hydrolysis through motion of nanoconfined DNA Maedeh Roushan, Gideon Livshits, Zubair Azad, Hong Wang, Robert Riehn Confinement of DNA to nanochannels with a cross-section of 100$\times$100 nm$^2$ and hundreds of micrometer long has previously been used to investigate the equilibrium binding properties of proteins to DNA. Here we report on the observation that a range of proteins which catalyze a modification of DNA, and that do so by hydrolyzing ATP, cause a net directed motion of nanochannel-confined DNA. We present a model for this observation that does not require any motor-like action of the protein and that is purely dependent on the catalytic properties. [Preview Abstract] |
Monday, March 14, 2016 4:06PM - 4:18PM |
C41.00009: Stochastic resonance during a polymer translocation process Debasish Mondal, Murugappan Muthukumar We study the translocation of a flexible polymer in a confined geometry subjected to a time-periodic external drive to explore stochastic resonance. We describe the equilibrium translocation process in terms of a Fokker-Planck description and use a discrete two-state model to describe the effect of the external driving force on the translocation dynamics. We observe that no stochastic resonance is possible if the associated free-energy barrier is purely entropic in nature. The polymer chain experiences a stochastic resonance effect only in presence of an energy threshold in terms of polymer-pore interaction. Once stochastic resonance is feasible, the chain entropy controls the optimal synchronization conditions significantly. [Preview Abstract] |
Monday, March 14, 2016 4:18PM - 4:54PM |
C41.00010: Strongly Non-equilibrium Dynamics of Nanochannel Confined DNA Invited Speaker: Walter Reisner Nanoconfined DNA exhibits a wide-range of fascinating transient and steady-state non-equilibrium phenomena. Yet, while experiment, simulation and scaling analytics are converging on a comprehensive picture regarding the equilibrium behavior of nanochannel confined DNA, non-equilibrium behavior remains largely unexplored. In particular, while the DNA extension along the nanochannel is the key observable in equilibrium experiments, in the non-equilibrium case it is necessary to measure and model not just the extension but the molecule's full time-dependent one-dimensional concentration profile. Here, we apply controlled compressive forces to a nanochannel confined molecule via a nanodozer assay, whereby an optically trapped bead is slid down the channel at a constant speed. Upon contact with the molecule, a propagating concentration ``shockwave'' develops near the bead and the molecule is dynamically compressed. This experiment, a single-molecule implementation of a macroscopic cylinder-piston apparatus, can be used to observe the molecule response over a range of forcings and benchmark theoretical description of non-equilibrium behavior. We show that the dynamic concentration profiles, including both transient and steady-state response, can be modelled via a partial differential evolution equation combining nonlinear diffusion and convection. Lastly, we present preliminary results for dynamic compression of multiple confined molecules to explore regimes of segregation and mixing for multiple chains in confinement. [Preview Abstract] |
Monday, March 14, 2016 4:54PM - 5:06PM |
C41.00011: Role of small ion dynamics in driven translocation of polyelectrolytes through nanopores Harshwardhan Katkar, Murugappan Muthukumar Nanopores have been proposed to be used for a variety of applications such as in DNA sequencing and as molecular separation devices. In the present study, we focus on the dynamics of small ions (counterions and salt ions) while a charged polymer translocates through a finite-length nanopore under the action of an externally applied electric field. Coarse-grained molecular dynamics simulations are performed to study the translocation process, taking both the long-range hydrodynamics and the long-range electrostatics into consideration. We address the role of small ion dynamics on the properties of a DNA in a confined region. [Preview Abstract] |
Monday, March 14, 2016 5:06PM - 5:18PM |
C41.00012: Free Energy of a Polymer in Slit-Like Confinement across the Odijk, moderate confinement, and Bulk Regimes Albert Kamanzi, Jason S. Leith, David Sean, Daniel Berard, Andrew C. Guthrie, Christopher M.J. McFaul, Gary W. Slater, Hendrick W. de Haan, Sabrina R. Leslie We directly measure the free energy of confinement for semi-flexible polymers from the nanoscale to bulk regimes in slit-like confinement. We use Convex Lens-induced Confinement (CLiC) microscopy of DNA to load and directly count molecules at equilibrium in a single chamber of smoothly increasing height. CLiC microscopy allows for direct visualization of polymers in free solution over long periods, as a function of tunable vertical confinement - from the millimeter to the nanometer scale, and within a single device. Our direct characterization of the free energy of confinement, across several orders of magnitude of applied confinement, agree with new simulations established in this work. We compare experimental results to the ``de Gennes blob model'', to theory published by Casassa, as well as to simulations by Chen and Sullivan, in appropriate regimes. This work establishes a robust platform for understanding and manipulating polymers at the nanoscale, with a wide range of applications to biomedical technologies. [Preview Abstract] |
Monday, March 14, 2016 5:18PM - 5:30PM |
C41.00013: Do Ions Flow Freely Through Confined DNA? Zubair Azad, Robert Riehn Double-stranded DNA in an aqueous solution is characterized by a strongly localized counter-ion cloud. Classical experiments have shown that the mobility of large DNA coils is independent of the number of basepairs, leading to an interpretation that the molecule can be understood as a collection of segments with constant mobility whose interactions are effectively screened from each other. This ``free-draining'' assumption posits that DNA and other electrolytes will not influence each other's mobility. In this talk, we call this assumption into question when the local concentration of DNA is increased beyond that of a self-avoiding random walk by nanoconfinement. We present translocation of DNA and fluorescent tracer ions under established chemical gradients, pressure-driven flow, and electrophoresis in nanochannels with cross sections that are 100 nm x 100 nm. We present evidence that interactions between the DNA and ionic tracers are a non-linear function of the applied fields. [Preview Abstract] |
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