Bulletin of the American Physical Society
APS March Meeting 2017
Volume 62, Number 4
Monday–Friday, March 13–17, 2017; New Orleans, Louisiana
Session F6: The Structure and Dynamics of Confined BiopolymersFocus
|
Hide Abstracts |
Sponsoring Units: DBIO DPOLY Chair: Greg Morrison, University of Houston Room: 265 |
Tuesday, March 14, 2017 11:15AM - 11:27AM |
F6.00001: Polymer Crowding in Confined Polymer-Nanoparticle Mixtures Wyatt J. Davis, Alan R. Denton Crowding can influence the conformations and thus functionality of macromolecules in quasi-two-dimensional environments, such as DNA or proteins confined to a cell membrane. We explore such crowding within a model of polymers as penetrable ellipses, whose shapes are governed by the statistics of a 2D random walk. The principal radii of the polymers fluctuate according to probability distributions of the eigenvalues of the gyration tensor. Within this coarse-grained model, we perform Monte Carlo simulations of mixtures of polymers and hard nanodisks, including trial changes in polymer conformation (shape and orientation). Penetration of polymers by nanodisks is incorporated with a free energy cost predicted by polymer field theory. Over ranges of size ratio and nanodisk density, we analyze the influence of crowding on polymer shape by computing eigenvalue distributions, mean radius of gyration, and mean asphericity of the polymer. We compare results with predictions of free-volume theory and with corresponding results in three dimensions*. Our approach may help to interpret recent (and motivate future) experimental studies of biopolymers interacting with cell membranes, with relevance for drug delivery and gene therapy.\\[1ex] *W. K. Lim and A. R. Denton, J. Chem. Phys. (2016). [Preview Abstract] |
Tuesday, March 14, 2017 11:27AM - 11:39AM |
F6.00002: Abstract Withdrawn
|
Tuesday, March 14, 2017 11:39AM - 11:51AM |
F6.00003: Translocation dynamics of pre-packaged polymers Chandra Bergmann, Ajay Gopinathan Cells contain polymers such as proteins and nucleic acids that, in many cases, translocate through pores only after being more tightly packaged by transport factors with an affinity for the inside of the pore. Examples include the export of large mRNA complexes and the import of the HIVĀ genome through the nuclear pore complex. Here, we use a Fokker-Planck formalism to model how the properties of these transport factors affect the time of translocation. In the simplest models, translocation time decreases as both the packaging fraction and transport factor affinity increase. If we take into account that the diffusion constant of the polymer is reduced both by increasing the packaging fraction and increasing the affinity of the transport factor with the pore interior, we are able to identify optimal and sub-optimal regimes of the parameter space, where deviations from the optimal regime can increase the time of polymer translocation drastically. In vivo, our results suggest that transport factor properties need to be carefully tuned to lie in the optimal regime in order to ensure function and that making relatively small changes to these properties can interfere with or enhance translocation. [Preview Abstract] |
Tuesday, March 14, 2017 11:51AM - 12:27PM |
F6.00004: Confined wormlike chains in external fields Invited Speaker: Greg Morrison The confinement of biomolecules is ubiquitous in nature, such as the spatial constraints of viral encapsulation, histone binding, and chromosomal packing. Advances in microfluidics and nanopore fabrication have permitted powerful new tools in single molecule manipulation and gene sequencing through molecular confinement as well. In order to fully understand and exploit these systems, the ability to predict the structure of spatially confined molecules is essential. In this talk, I describe a mean field approach to determine the properties of stiff polymers confined to cylinders and slits, which is relevant for a variety of biological and experimental conditions. I show that this approach is able to not only reproduce known scaling laws for confined wormlike chains, but also provides an improvement over existing weakly bending rod approximations in determining the detailed chain properties (such as correlation functions). Using this approach, we also show that it is possible to study the effect of an externally applied tension or static electric field in a natural and analytically tractable way. These external perturbations can alter the scaling laws and introduce important new length scales into the system, relevant for histone unbinding and single-molecule analysis of DNA. [Preview Abstract] |
Tuesday, March 14, 2017 12:27PM - 12:39PM |
F6.00005: Probing the Miscibility Phase Space of Two Nanochannel-Confined DNA Molecules Ahmed Khorshid, Walter Reisner While small identical particles always mix in equilibrium, self-avoiding polymers under transverse confinement can segregate or demix as a fundamental consequence of chain interconnectivity and entropy maximization. Demixing arises as mixed polymer conformations in confinement have a higher excluded-volume, and thus lower entropy, than non-mixed conformations. A wide range of simulation/scaling efforts have quantified the detailed segregation-mixing phase space for two confined chains, yet there are no quantitative experiments on two-polymer mixing in confinement. Here we use pneumatically actuated hydrodynamic flow to compress two differentially labeled nanochannel confined DNA molecules against dead-end nanoslit barriers. The differential labeling enables us to quantify separately the dynamic concentration profiles of each chain along the channel enabling precise determination of the degree of chain overlap. For 300x300 nm channels, we find that chains will resist mixing at low applied flow. At intermediate flow speeds, the two chains will partially overlap. At sufficiently high flow speeds the two chains fully mix. In addition, for smaller channels (200x200nm), the maximum chain overlap will decrease in comparison to wider channels with the two chains never fully overlapping. [Preview Abstract] |
Tuesday, March 14, 2017 12:39PM - 12:51PM |
F6.00006: Wall Depletion Length of a Channel-Confined Polymer Guo Kang Cheong, Xiaolan Li, Kevin Dorfman The use of DNA has been prevalent in studying channel-confined polymers. Commonly, the assumption of a wall depletion length is used to bring correspondence between experimental systems (a polyelectrolyte in a charged channel) to theoretical models (a neutral polymer in a hard wall). We tested this assumption by using pruned-enriched Rosenbluth method (PERM) to simulate a confined DNA in a tube. We used a two parameter, exponentially decaying, repulsive potential to model the polymer-wall electrostatics interaction. We are interested, in particular, on where this assumption breaks down and its implication on experimental studies under a low ionic strength. We have found that the depletion length for the confinement free energy differ from those of mean span while it is still an extensive property of the channel size. Conversely, the depletion length from mean span is tantamount to the depletion length from variance about the mean span through all channel sizes. [Preview Abstract] |
Tuesday, March 14, 2017 12:51PM - 1:03PM |
F6.00007: Manipulating and Visualizing Molecular Interactions in Customized Nanoscale Spaces Francis Stabile, Gil Henkin, Daniel Berard, Marjan Shayegan, Jason Leith, Sabrina Leslie We present a dynamically adjustable nanofluidic platform for formatting the conformations of and visualizing the interaction kinetics between biomolecules in solution, offering new time resolution and control of the reaction processes. This platform extends convex lens-induced confinement (CLiC), a technique for imaging molecules under confinement, by introducing a system for in situ modification of the chemical environment; this system uses a deep microchannel to diffusively exchange reagents within the nanoscale imaging region, whose height is fixed by a nanopost array. To illustrate, we visualize and manipulate salt-induced, surfactant-induced, and enzyme-induced reactions between small-molecule reagents and DNA molecules, where the conformations of the DNA molecules are formatted by the imposed nanoscale confinement. By using nanofabricated, nonabsorbing, low-background glass walls to confine biomolecules, our nanofluidic platform facilitates quantitative exploration of physiologically and biotechnologically relevant processes at the nanoscale. This device provides new kinetic information about dynamic chemical processes at the single-molecule level, using advancements in the CLiC design including a microchannel-based diffuser and postarray-based dialysis slit. [Preview Abstract] |
Tuesday, March 14, 2017 1:03PM - 1:15PM |
F6.00008: Brownian diffusion of single walled carbon nanotubes in highly confined rock-like porous media~ Zhao Tang, Shannon Eichmann, Frederick MacKintosh, Matteo Pasquali Despite its importance in biophysics and energy, the thermal motion of stiff filaments in crowded environments is not completely understood. Recent experiments on the motion of single-walled carbon nanotubes (SWCNT) in gels showed that SWCNTs slither and rotate as predicted by Odijk theory and that even minimal flexibility can speed up diffusion in highly confined environments. However, it is not clear whether the same behavior would translate to other classes of crowded environments. For example, in porous media, the narrow connections between rock pores (i.e., pore throat) cause an extra confinement effect. The dependence of filament motion on such pore shapes is still not understood.~ Here, we use near-infrared microscopy to image the SWCNT diffusion in a heterogeneous submicron sized porous system made of randomly close packed silica colloids to mimic the structure of rocks. We show that for short SWCNTs, whose length is up to a few times the diameter of the beads, pore throats negligibly affect the SWCNT motion. Conversely, long SWCNTs frequently bend due to the narrowness of the pore throat that limits the SWCNT orientations. These results are crucial to understand the diffusive dynamics of SWCNTs used for oil detection in highly-confined porous media. [Preview Abstract] |
Tuesday, March 14, 2017 1:15PM - 1:27PM |
F6.00009: Formatting biopolymers using adjustable nanoconfinement Daniel Berard, Marjan Shayegan, Francois Michaud, Gil Henkin, Shane Scott, Sabrina Leslie Sensitive visualization and conformational control of long, delicate biopolymers present critical challenges to emerging biotechnologies and biophysical studies. Next-generation nanofluidic manipulation platforms strive to maintain the structural integrity of genomic DNA prior to analysis but can face challenges in device clogging, molecular breakage, and single-label detection. We address these challenges by integrating the Convex Lens-induced Confinement (CLiC) technique with a suite of nanotopographies embedded within thin-glass nanofluidic chambers. We gently load DNA polymers into open-face nanogrooves in linear, concentric circular, and ring array formats and perform imaging with single-fluorophore sensitivity. We use ring-shaped nanogrooves to access and visualize confinement-enhanced self-ligation of long DNA polymers. We use concentric circular nanogrooves to enable hour-long observations of polymers at constant confinement in a geometry which eliminates the confinement gradient which causes drift and can alter molecular conformations and interactions. Taken together, this work opens doors to myriad biophysical studies and biotechnologies which operate on the nanoscale. [Preview Abstract] |
Tuesday, March 14, 2017 1:27PM - 1:39PM |
F6.00010: Overlap free energy of polymers under cylindrical confinement James Polson, Aidan Tremblett, Deanna Kerry Polymers subject to cylindrical confinement can experience intramolecular overlap due to internal folding or intermolecular overlap with other polymers, and the free energy cost of chain overlap drives single-chain unfolding or multi-chain segregation, respectively. Theoretical treatments of such dynamical processes often employ analytical approximations of the conformational free energy. In this study, Monte Carlo simulations are used to measure the overlap free energy of polymers subject to cylindrical confinement. The calculated free energy functions are used to test the predictions of scaling theories and quantify the finite-size effects. We calculate the conformational free energy of a single folded polymer as a function of the position of the fold along the tube for both flexible and semi-flexible hard-sphere chains. We also examine the cases of arm retraction in star polymers and the segregation of ring polymers under cylindrical confinement. The scaling of the free energy functions with chain length and stiffness, as well as confinement diameter, are generally consistent with theoretical predictions, though appreciable deviations due to finite-size effects persist for chains up to $N$=500 monomers. [Preview Abstract] |
Tuesday, March 14, 2017 1:39PM - 1:51PM |
F6.00011: Thermodynamics of helix-coil transitions of polyalanine in open carbon nanotubes. Dylan Suvlu, Seneviratne Samaratunga, Dave Thirumalai, Jayendran Rasaiah Understanding structure formation of polypeptide chains and synthetic polymers encapsulated in pores is important in biology and nanotechnology. The stability of ordered structures in confined spaces is determined by the interplay between hydration and confinement. Using replica exchange molecular dynamics simulations of a capped twenty three residue alanine peptide in open nanotubes (NTs) of varying diameters (D) and NT hydrophobicity we show that an alpha-helix forms only over a narrow range of diameters (D $\approx $ 13-15). Helix stability decreases sharply outside this range. Increasing the hydrophobicity of the NT leads to an enhancement in helix content for all diameters, which we show is due to an anti-correlation between water density inside the nanotube and structure formation. We find that helix formation is driven by a negative enthalpy and positive entropy at 300 K whereas the corresponding entropy of formation in bulk water is strongly negative resulting in helix destabilization. Our findings provide insights into alpha-helix formation within the folding zones of the ribosome tunnel, which has an average diameter remarkably close to that found for optimal helix formation in open NTs. [Preview Abstract] |
Tuesday, March 14, 2017 1:51PM - 2:03PM |
F6.00012: Phase separation and the formation of the pyrenoid, a carbon-fixing organelle Bin Xu, Elizabeth Freeman Rosenzweig, Luke Mackinder, Martin Jonikas, Ned S. Wingreen In the chloroplasts of most algae, the carbon-fixing enzyme Rubisco is concentrated in a non-membrane-bound structure called the pyrenoid, which enables more efficient carbon capture than that of most land plants. In contrast to the long-held assumptions of the field, the pyrenoid matrix is not a solid crystal, but behaves as a phase-separated, liquid-like organelle. In this system, the linker protein EPYC1 is thought to form multivalent specific bonds with Rubisco, and the formation of the pyrenoid occurs via the phase separation of these two associating proteins. Through analytical and numerical studies, we determine a phase diagram for this system. We also show how the length of the linker protein can affect the formation and dissolution of the pyrenoid in an unexpected manner. This new view of the pyrenoid matrix provides important insights into the structure, regulation, and inheritance of pyrenoid. More broadly, our findings give insights into fundamental principles of the architecture and inheritance of liquid-phase organelles. [Preview Abstract] |
Tuesday, March 14, 2017 2:03PM - 2:15PM |
F6.00013: Numerical modeling of reaction diffusion transport into a core-shell geometry Amelia A. Brown, Scott P. Beckman Cellular microencapsulation technology holds great promise for the treatment of several diseases including type one diabetes. The development of this technology requires an understanding of mass transport through semipermeable membranes and reactive materials. A non-dimensional Fickian diffusion model is developed that describes the transport of reagents into a core-shell structure similar to that of cells encapsulated in a protective polymer coating. The exterior is treated as an inert protective barrier and the interior is treated as a reactive, cellular, medium. The consumption of reagent is described using Michaelis-Menten kinetics. The model is solved numerically using the shooting method and the Runge-Kutta fourth order method. The resulting non-dimensional concentration curves show a competition between the diffusion and consumption of the diffusing species. The range within parameter phase space in which cellular life is maintained, is determined. [Preview Abstract] |
Follow Us |
Engage
Become an APS Member |
My APS
Renew Membership |
Information for |
About APSThe American Physical Society (APS) is a non-profit membership organization working to advance the knowledge of physics. |
© 2024 American Physical Society
| All rights reserved | Terms of Use
| Contact Us
Headquarters
1 Physics Ellipse, College Park, MD 20740-3844
(301) 209-3200
Editorial Office
100 Motor Pkwy, Suite 110, Hauppauge, NY 11788
(631) 591-4000
Office of Public Affairs
529 14th St NW, Suite 1050, Washington, D.C. 20045-2001
(202) 662-8700