Bulletin of the American Physical Society
APS March Meeting 2018
Volume 63, Number 1
Monday–Friday, March 5–9, 2018; Los Angeles, California
Session R28: Polymer Physics in Very Strongly Confined Environments II : Nanoslits and NanochannelsFocus
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Sponsoring Units: DPOLY GSNP Chair: Yeng-Long Chen, Inst of Physics Academia Sinica Room: LACC 405 |
Thursday, March 8, 2018 8:00AM - 8:12AM |
R28.00001: Effect of chain stiffness for semiflexible macromolecules in array of cylindrical nanoposts Peter Cifra, Zuzana Benkova, Lucia Rispanova Equilibrium conformation of a semiflexible macromolecule in an array of nanoposts exhibits a non-monotonic behavior both at variation of the chain stiffness or increased crowding imposed by nanoposts. This is a result of the competition between the axial chain extension in channel-like interstitial volumes between nanoposts and the chain partitioning among these volumes. The approximation of a nanopost array as a combination of a quasi-channel and a quasi-slit like geometry semi-qualitatively explains the behavior of a chain in the array. In this approximation, the interstitial spaces are viewed as being of the channel geometry while the passages between two adjacent posts are viewed as being of the slit geometry. Interestingly, the stiffer chains tend to penetrate more readily through the passage apertures, in the direction perpendicular to the post axes, and thus to occupy more interstitial volumes. This is consistent with the prediction of the free-energy penalty that is lower for a stiffer chain at strong slit like confinement. These findings can find applications in the control of macromolecular conformations in recent nanotechnological techniques with biomacromolecules such as a DNA. |
Thursday, March 8, 2018 8:12AM - 8:24AM |
R28.00002: Compression of Nanoslit Confined Polymer Solutions Lili Zeng, Yue Qi, Ahmed Khorshid, Reghan Hill, Walter Reisner Many systems of biophysical and technological interest consist of multiple interpenetrating chains in a confined volume, i.e. a confined polymer solution. Using nanofluidic approaches developed originally for the study of single chains in confined geometries, we develop an assay to create confined polymer solutions on-chip, and then probe the solution response to applied compressive forcing. In our approach, multiple chains are introduced into a nanoslit via hydrodynamic flow, and are then concentrated against a barrier that is permeable only to solvent. For sufficiently high concentration, the compressed solution profile can be described by a mean-field polymer model based on Doi’s two-fluid approach, with the chain free energy described by a Ginzburg type free energy functional. This theory furnishes a partial differential equation based description of the concentration profile in terms of a nonlinear Schrödinger type equation, providing a general theoretical framework for modelling confined polymer solution dynamics. |
Thursday, March 8, 2018 8:24AM - 8:36AM |
R28.00003: Free Energy of a Folded Semiflexible Polymer Confined to a Nanochannel James Polson Monte Carlo simulations are used to study the conformational properties of a folded semiflexible polymer confined to a long channel. We measure the variation in the conformational free energy with respect to the end-to-end distance of the polymer, and from these functions we extract the free energy of the hairpin fold, as well as the entropic force arising from interactions between overlapping portions of the polymer. We consider the scaling of the free energy with respect to varying the persistence and contour lengths of the polymer, as well as the channel dimensions, for confinement in cylindrical, rectangular and triangular channels. We focus on polymer behaviour in both the classic Odijk and backfolded Odijk regimes. We find the scaling of the entropic force to be close to that predicted from a scaling argument that treats interactions between deflection segments at the second virial level. In addition, the measured hairpin fold free energy is consistent with that obtained directly from a recent theoretical calculation for cylindrical channels. It is also consistent with values determined from measurements of the global persistence length of a polymer in the backfolded Odijk regime in recent simulation studies. |
Thursday, March 8, 2018 8:36AM - 9:12AM |
R28.00004: Where is the Odijk back-folding regime when a self-excluding wormlike polymer is confined by a cylindrical tube? Invited Speaker: Jeff Chen When a semiflexible chain is confined in a cylindrical tube, it forms hairpin loops back and forth inside the confining tube. The multi-threads of polymer segments in the narrow tube crosssection impose the excluded-volume interactions among the folded chain segments. Recent theories and Monte Carlo simulations have explored the scaling properties of the chain extension and confinement free energy caused by both confinement and excluded-volume effects. In particular, an Odijk scaling regime, distinguished from the extended de Gennes regime, is expected when the tube diameter is smaller than the persistence length. Here, the excluded-volume effects are added to |
Thursday, March 8, 2018 9:12AM - 9:24AM |
R28.00005: Telegraph model of DNA confinement in a nanochannel Kevin Dorfman, Erik Werner, Guo Kang Cheong, Damini Gupta, Bernhard Mehlig The classical models of a wormlike chain in channel confinement correspond to either (i) a chain of Odijk deflection segments (when the channel size is much smaller than the persistence length) or (ii) a chain of de Gennes blobs (when the channel size exceeds the thermal blob size). Unfortunately, the vast majority of the experimental data for DNA confinement in a nanochannel, which is a very convenient experimental system, lie between these two limiting cases. We have developed a new model, based on a correlated telegraph model, that describes the regime between Odijk and de Gennes behavior. The model naturally leads to a new scaling parameter alpha that reflects the typical number of overlaps per hairpin turn in the channel, and we have developed scaling laws for both the chain extension and variance in terms of alpha. The extension and variance produced by detailed simulations of confined wormlike chains collapse onto a single master curve in terms of alpha, and that these simulations are in exact agreement with simulations of the telegraph model. We also find that the theory provides good collapse of the experimental data for approximately square nanochannels. |
Thursday, March 8, 2018 9:24AM - 9:36AM |
R28.00006: Dynamical transition from diffusion to frustrated localization of polyelectrolyte in charged gels Di Jia, Murugappan Muthukumar Using Dynamic Light Scattering (DLS), we have investigated the dynamics of polyelectrolyte chains embedded in a polyelectrolyte gel matrix. The matrix is polyacrylamide-co-polyacrylate hydrogel with controllable crosslink density and charge density. The embedded polyelectrolyte is sodium polystyrene sulfonate (PSS) of molecular weight M and concentration C. For the gel alone, DLS exhibits essentially one diffusive mode representing the elasticity of the gel. When PSS is embedded inside the gel, DLS exhibits three modes at lower values of M and C: one gel mode, one PSS diffusive mode, and one PSS non-diffusive stretched exponential mode. At sufficiently higher values of C and M, there is only one PSS non-diffusive stretched exponential behavior, in addition to the elastic gel mode. Our results reveal a novel dynamical transition from chain diffusion to frustrated localization as the ratio of radius of gyration of PSS to the mesh size of the gel, as well as C, are increased. |
Thursday, March 8, 2018 9:36AM - 9:48AM |
R28.00007: The Self-assembly of Disk-coil Block Copolymers within 2D Cylinder Confinement with Asymmetric Pair Interactions. Ji Ho Ryu, Won Bo Lee, YongJoo Kim Chlorosomes, the most efficient light-harvesting antenna system in nature, have multi-layered tubular architecture of bacteriochlorophyll molecules with specific molecular arrangement covered by lipid layer. In order to investigate the self-assembly of bacteriochlorophyll molecules on the novel architecture of chlorosomes, self-assembly of a disk-coil block copolymer modeled from porphyrin attached to single alkyl chain of bacteriochlorophyll molecule was investigated. To mimic the self-assembly nature of bacteriochlorophyll molecules covered by lipid layer, disk-coil block copolymers confined in cylinder are systematically studied using molecular dynamics simulation as functions of radius of cylinders, length of coil-like chain and asymmetric pair interaction between disks. Our study is differentiated from the self-assembly behavior of linear block copolymers within cylindrical confinement due to the specific packing structure arising from asymmetric pair interaction between disk part of our modeled molecules. We believe that our study provides physical principles of self-assembled behavior of bacteriochlorophyll molecules to design next generation photoelectronic devices. |
Thursday, March 8, 2018 9:48AM - 10:00AM |
R28.00008: Diffusion of polymers through periodic networks of lipid-based nanochannels Reza Ghanbari, Salvatore Assenza, Abhijit Saha, Raffaele Mezzenga We present an experimental investigation on the diffusion of unfolded polymers in the triply-periodic water-channel network of inverse bicontinuous cubic phases. Depending on the chain size, our results indicate the presence of two different dynamical regimes corresponding to Zimm and Rouse diffusion. We support our findings by scaling arguments based on a combination of blob and effective-medium theories, and suggest the presence of a third regime where dynamics is driven by reptation. Our experimental results also show an increasing behavior of the partition coefficient as a function of polymer molecular weight, indicative of a reduction of the conformational degrees of freedom induced by the confinement. |
Thursday, March 8, 2018 10:00AM - 10:12AM |
R28.00009: Polymer Confinement via Crowding: Influence of Solvent Quality on Conformations Wyatt Davis, Alan Denton The structure and function of polymers in confined environments, e.g., biopolymers in the cytoplasm of a cell, are affected by macromolecular crowding. To explore the influence of solvent quality on conformations of crowded polymers, we model polymers as penetrable ellipsoids, whose shapes are governed by the statistics of self-avoiding walks. Within this coarse-grained model, we perform Monte Carlo simulations of mixtures of polymers and hard nanosphere crowders, including trial changes in polymer size and shape. Penetration of polymers by nanospheres is incorporated via a free energy cost predicted by polymer field theory. To analyze the impact of crowding on polymer conformations, we compute average polymer shape distributions, radius of gyration, and asphericity over ranges of crowder size and volume fraction. We compare simulation results with predictions of free-volume theory for polymers in good and theta solvents. Our results indicate that excluded-volume interactions significantly affect crowding, especially in the limit of small crowders. Our approach may help to motivate future experimental studies of polymers in crowded environments, with relevance for drug delivery and gene therapy. |
Thursday, March 8, 2018 10:12AM - 10:24AM |
R28.00010: Curvature effect on the surface-patterning of end-tethered polymers under nanoconfinement Kai Huang, Igal Szleifer Surface-patterning of end-tethered polymers is of fundamental importance in polymer physics. Understanding the effect of nanoconfinement on such patterning is crucial for the functionalization of nanochannels/pores for a wide range of applications from biosensing to molecular filtering. On the other hand, the confinement also imposes a great challenge for in-vivo experimental analysis of the polymer behavior. Here we use a molecular theory to study the molecular organization of polymeric materials grafted to the inner surface of solid-state nanochannels/pores. Our theory shows that nanoconfined end-tethered polymers can microphase-separate into rich morphologies in bad solvent. These morphologies and their broken symmetries depend on many factors including the solvent quality, the grafting density of the polymer, the shape of the channel and so on. By investigating the nanoconfinement effect in a larger geometrical context covering flat, convex and concave topologies, we reveal a generic curvature effect on the thermodynamics of the surface-patterning. Furthermore, our theory predicts a strong coupling between such curvature-dependent morphology and external stimuli such as an in-channel flow. Our insights can be used to guide the rational design of smart nanochannels. |
Thursday, March 8, 2018 10:24AM - 10:36AM |
R28.00011: Probing Organization of Multiple Chains in Nanofluidic Cavities Zezhou Liu, Xavier Capaldi, Yuning Zhang, Carlos Vargas, Rodrigo Reyes-Lamothe, Walter Reisner How do multiple interacting polymers behave in confined environments? This is a fundamental problem in confined polymer physics with important implications in a range of biological systems, from chromosomal segregation and plasmid distribution in dividing bacteria to chromatin organization. Here we use nanofluidics to trap multiple chains in cavity structures. Differential staining of the chains is used to independently assess the conformation of each chain, determine the degree of partitioning/mixing and assess coupled diffusion of the chain center-of-mass positions. Measurements are performed as a function of cavity dimension, salt concentration and polymer topology. In addition, we use varying chain size ratio to assess the degree to which small chains can interpenetrate large chains, a toy model of the phenomena of “nucleoid occlusion.” |
Thursday, March 8, 2018 10:36AM - 10:48AM |
R28.00012: Membrane-induced Confinement of DNA in Pneumatically-actuated Nanofluidic Device Xavier Capaldi, Zezhou Liu, Carlos Ruiz-Vargas, Yuning Zhang, Walter Reisner We present a pneumatically-actuated nanofluidic platform that has the capability of dynamically controlling the confinement environment of biomolecules in solution. Our approach, based on flexible nanoscale nitride membranes, provides a facile and economical means of actuated confinement using standard microfabrication techniques. DNA is loaded into nanofluidic slits and hydrodynamic flow is used to drive the molecules over embedded features such as cavities and concentric rings. The device is bonded with a membrane lid that can be deflected pneumatically to dynamically confine passing DNA. By carefully calibrating the pressure applied to the membrane, we can control membrane deflection to tune the deflection rate and degree of confinement. Using this approach, we study the trapping rate of DNA in embedded features as a function of deflection rate and feature geometry to obtain loading conditions that optimize molecular trapping. We also study the effect of non-equilibrium forcing, arising from confinement variation, on dynamical and conformational behavior of confined molecules. |
Thursday, March 8, 2018 10:48AM - 11:00AM |
R28.00013: Nematic to smectic transition and dynamics for semiflexible polymers in very strong slit-like confinement Supriyo Roy, Dmytro Luzhbin, Yeng-Long Chen We performed GPU-accelerated Langevin dynamics simulations to investigate the density induced nematic to smectic phase transition for semiflexible polymers in slits comparable and smaller than the chain persistence length. The smectic transition occurs with chains with different bending rigiditites, with the persistence length P to slit height H ratios 1.25, 2.5, 3.75, 5 and 25. For all cases, smectic C is found with the polymer director tilted with respect to lateral alignment. The transition density systematically shifts higher for more flexible polymers. |
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