Bulletin of the American Physical Society
APS March Meeting 2019
Volume 64, Number 2
Monday–Friday, March 4–8, 2019; Boston, Massachusetts
Session S55: Polymers and Biopolymers in Very Strongly Confined Environments I: Structure and dynamics of packaged polymersFocus
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Sponsoring Units: DPOLY DBIO GSNP Chair: Zachary Dell, University of Massachusetts Amherst Room: BCEC 254B |
Thursday, March 7, 2019 11:15AM - 11:27AM |
S55.00001: Distribution of label spacings for genome mapping in nanochannels Daniel Odman, Erik Werner, Kevin Dorfman, Charles R Doering, Bernhard Mehlig In genome mapping experiments, long DNA molecules are stretched by confining them to very narrow channels, so that the locations of sequence-specific fluorescent labels along the channel axis provide large-scale genomic information. It is difficult, however, to make the channels narrow enough so that the DNA molecule is fully stretched. In practice its conformations may form hairpins that change the spacings between internal segments of the DNA molecule, and thus the label locations along the channel axis. Here we describe a theory for the distribution of label spacings that explains the heavy tails observed in distributions of label spacings in genome mapping experiments. This talk is based on the paper Ödman, E. Werner, K. D. Dorfman, C. R. Doering & B. Mehlig, arxiv:1803.11396. |
Thursday, March 7, 2019 11:27AM - 11:39AM |
S55.00002: Pathway-dependent nonequilibrium conformations of a polymer globule as a model for chromatin organization Seulki Kwon, Bong June Sung The spatial organization of chromatin in nucleus resembles a fractal globule, of which structure differs from an equilibrium polymer globule. Even though there have been efforts to develop a polymer model to describe nonequilibrium structure of tightly-packed chromatin, the dependence of a transition pathway toward a globule has been often ignored. Because biological systems are often in nonequilibrium states, the transition pathway the chromatin would take before it reaches the densely-packaged globule would be important. In this study, by using a simple polymer model and Langevin dynamics simulations, we investigate the conformational transition of a single polymer from swollen coil to compact globule in order to elucidate the effect of transition pathway on the final globular structure. We show that a fast collapse induces a nonequilibrium fractal-like structure, whose relaxation toward an equilibrium globule is extremely slow. Moreover, in strong confinement, polymer conformation never relaxes into equilibrium state, thus the structure of the globule becoming dependent on the transition pathway. |
Thursday, March 7, 2019 11:39AM - 11:51AM |
S55.00003: Organization and Dynamics of Multiple DNA Chains Confined in a Nanofluidic Compartment Zezhou Liu, Xavier Capaldi, Lili Zeng, Yuning Zhang, Thu Ha Dao, Walter Reisner The dynamics of multiple chains interacting in a confined environment is a fundamental problem in polymer physics and a model system for understanding confinement in biological systems. Here we present a nanofluidic device with compartments that can be opened and closed via pneumatic actuation of a thin membrane lid. The compartments are elliptical in shape with widths and lengths varying from hundreds of nm to microns. Differentially stained chains are trapped inside the cavities and the chain interactions assessed by monitoring the chain conformation and positioning in real-time via fluorescence video-microscopy. We observe a transition between different dynamical states as the confinement is varied from quasi-0D (cavity confinement) to quasi 1-D (nanochannel confinement). |
Thursday, March 7, 2019 11:51AM - 12:27PM |
S55.00004: Chromatin Rheology Tells a Story: From DNA Damage Loci to Cellular Monolayers Invited Speaker: Kris Dahl Over the past two decades here have been numerous intellectual intersections between polymer physics and modeling of intracellular environments including (i) soft glassy rheology as a description of the numerous relaxation states within the cell and (ii) athermal rheology from the contribution of cellular molecular motors. Within the nucleus we have also observed a powerlaw response of chromatin both by extracellular applied force and by particle tracking microrheology. Global condensation state of the chromatin greatly impacts its rheology, and both can be manipulated with epigenetic modifying drugs (trichostatin A) or growth factors. Locally, chromatin condensation can be manipulated with other methods such as tetracycline responsive elements (TRE) or is altered during transcription. We have developed methods to image changes in these regions using fluorescence lifetime imaging and particle tracking combined with multichannel registration and processing to determine the effects of DNA damage on heterochromatin and euchromatin. Measuring the impact of molecular motors within the cell show that actin-myosin forces produced in the cytoskeleton are transmitted into the nucleus where the athermal motions can be registered by nuclear particle tracking, thus allowing the dense chromatin to be used as a sensor for cellular force generation. This technique, which we refer to as SINK (Sensors from IntraNuclear Kinetics) has allowed us to determine strain variations within heterogeneous monolayers of cells. Mechanical defects in cell monolayers shows exponential propagation, which suggests that monolayers of cells may be better modeled as colloidal crystals than continuum sheets. The study of condensed chromatin inside of cells has provided interesting physical and biological insights into cells at length scales of tens of nanometers to hundreds of micrometers. |
Thursday, March 7, 2019 12:27PM - 12:39PM |
S55.00005: Conformation and Dynamics of Nonconcatenated Ring Polymers under Planar Confinement Tianren Zhang, Karen Winey, Robert Riggleman Understanding the segregation of nonconcatenated ring polymers in a restricted volume is important to the biological field, because ring polymers have been proven to be a good model to study DNA organization in the cell nucleus. From our previous study, linear polymers segregate under extreme cylindrically-confined systemsdue to the strong correlation hole effect that is enhanced by the confining surfaces. Unlike linear polymers, the correlation hole effect of ring polymers is much stronger under confined systems since there are no chain ends. In this study, we use MD simulation to investigate the chain conformations and dynamics of ring polymers under planar confinements with different thicknesses (H = 5, 7, 10, 14 and 20σ) that span from extreme confined case to bulk like case. Our results show that conformations of ring polymers are similar to the linear polymers under planar confinements, except that ring polymers are less compressed along the direction normal to the walls. On correlation hole effect analysis, we distinguish the segregation regime from the mixing regime based on self-density calculation for ring polymers. From the diffusion and local chain relaxation dynamics, we observe that chain dynamics are primarily affected by the friction from walls. |
Thursday, March 7, 2019 12:39PM - 12:51PM |
S55.00006: The Kinetoplast as a Model 2D Catenated Polymer Alexander Klotz, Beatrice Soh, Patrick Doyle Genomic length DNA molecules have served as a model system for studying the physics of single polymers, in part due to their large lengthscales, compatibility with fluorescence optical microscopy, excellent monodispersity, and the commercial availability of complete genomes of the lambda and T4 viruses. There has been theoretical interest in the physics of two dimensional polymers, but robust experimental systems have been lacking. Here, we extend the use of DNA as a model polymer into the second dimension by studying the physics of the kinetoplast in free solution. A kinetoplast is a complex genomic structure found in certain parasites that consists of thousands of topologically linked rings of DNA forming a two-dimensional network. Removed from the cell and viewed in fluorescence microscopy in good solvent conditions, it adopts a form akin to a jellyfish bell approximately 5 microns in diameter. We characterize the equilibrium conformation and dynamics of kinetoplasts and examine their response to flow, confinement, and varying solvent conditions. Due to the commercial availability of kinetoplasts and the possibility of controlling their size using topoisomerase reactions, this study will open the door to a new class of experiments on two-dimensional and catenated polymers. |
Thursday, March 7, 2019 12:51PM - 1:03PM |
S55.00007: Random Walks in Disordered Environments: Membrane-Induced Confinement of DNA Xavier Capaldi, Zezhou Liu, Yuning Zhang, Walter Reisner Understanding the conformation and dynamics of DNA in nanoslit structures is a topic of long-standing interest in the physics of nanoconfined polymers, yet introducing molecules into the most confined (sub 20 nm thick) structures is very challenging. Here we use a pneumatically-actuated membrane device to sandwich single DNA molecules between a flexible nitride flap and glass nanochannel floor, forcing the molecules into a degree of confinement limited only by the intrinsic roughness of the channel surfaces. In these environments the molecule undergoes a self-avoiding random walk in the disordered environment created by the surface roughness. We study single-molecule dynamics and conformation as a function of root-mean-square surface roughness and imposed confinement. |
Thursday, March 7, 2019 1:03PM - 1:15PM |
S55.00008: Molecular Confinement on Nanostructured Polymer Surfaces Sara Heedy, Albert Yee Polymers have characteristic dimensions of assembly which depend on processing, especially in nanofabrication. These dimensions may be important in properties such as electrical or thermal conductivity. These properties will be strongly affected when fabricated polymer nanostructures have dimensions comparable to the critical length scale of physical phenomena (mean free path of electrons, mass transport, etc.). Enhanced mechanical, optical, and electrical properties of nanostructures, including nanopillar arrays less than 1 µm tall, have been well documented. We fabricated nanostructures on poly(methyl methacrylate) surfaces with nanoimprint lithography. A consequence of such a process is confinement induced reordering of polymer chains which is affected by the mold geometry, surface properties, and imprinting variables. Using thermal imprinting, and the combined topographical and nanoscale chemical mapping of photoinduced force microscopy, we found that nanopillars (100-700 nm range) confine functional groups differently depending on the feature shape, height, and periodicity. These findings suggest that surface chemistry, as well as nanoscale phenomena, can be controlled for use in adhesion and bio-electronic interfaces. |
Thursday, March 7, 2019 1:15PM - 1:27PM |
S55.00009: Voltage-Driven Translocation through a Nanopore: How can we define a/the Capture Radius? Gary W. Slater, Le Qiao A typical translocation event includes the following three steps: (i) the diffusion, (ii) the capture, and finally (iii) the translocation of the analyte. The capture process remains rather ill-understood because it cannot easily be visualized or inferred from the blockage current measured across the nanopore. To estimate the size of the so-called capture zone, a capture radius Rc is generally defined as the radial distance from the pore where diffusion-dominated dynamics (at large distance) cross over to drift-dominated dynamics (near the pore). However, this definition is ambiguous and the models used are often over-simplified. We investigate several approaches to defining and estimating Rc for the simple case of a charged particle diffusing in a liquid and attracted to the nanopore by an applied electric field. We present a theoretical analysis of the flux and Péclet number methods as well as 2D Lattice Monte Carlo (LMC) simulations with different simulation protocols and boundary conditions, including particle evaporation from the pore under a reversed field conditions. We compare our results to experimental estimates and we stress the fact that the boundary conditions and finite experimental times both matter in the interpretation of Rc . |
Thursday, March 7, 2019 1:27PM - 1:39PM |
S55.00010: Exploring How the Capture Process Affects the Translocation of Polymers through Nanopores Hendrick W de Haan, Konstantinos Kastritis, Martin Magill The translocation of polymers across membranes through nanopores has received a great deal of attention in recent years. This work is motivated by applications such as sequencing DNA and also characterizing and sorting biopolymers by size. While the great majority of this work has focused on the translocation process itself (ie, when the polymer is in and passing through the pore), details such as the conformation of the polymer when it arrives at the pore are critical for real-world applications. In this talk I will present results from a simulation study of the capture of semiflexible polymers by nanopores and demonstrate how dynamics that yield non-equilibrium conformations affect the translocation process. The impact of these results will be demonstrated by presenting simulation and experimental results for nanofluidic devices that are designed to sort and count biopolymers. These will include having many nanopores in series connected by nano- or micro-channels and DNA passing through a nano-filtered nanopore device. |
Thursday, March 7, 2019 1:39PM - 1:51PM |
S55.00011: The effects of packaging on the ejection rate of a polymer from a nanopore Chung Bin Park, Bong June Sung DNA ejection and packaging are related in terms of DNA conformation. As the DNA becomes jammed, it cannot undergo dramatic conformational change in the capsid. That is, final conformation after packaging may be correlated with the conformation right before ejected. Then, a scientific question arises; whether a packaging process affects the ejection rate or not. In this work, we find three regimes of ejection processes: (1) knot dominant, (2) non-equilibrium dominant and (3) effective-ejection regime. We perform Langevin dynamics simulations of a semi-flexible single chain with 660 monomers. We package the chain with different packaging rates into a nanopore and eject the chain subsequently. If the chain is packaged slowly enough to be knotted, its ejection process becomes slow (~35%). Also, if the chain is packaged too fast to relax its conformation, its ejection rate decreases (~20%). Then, if a packaging rate is moderate (3), where DNA can relax but cannot be knotted, DNA ejects faster than other regimes. Our results show that ejection dynamics is determined by the history of packaging and suggest that there could be most effective packaging rate for ejection process in nature. |
Thursday, March 7, 2019 1:51PM - 2:03PM |
S55.00012: Capture and translocation of a stiff oligomer by a nanopore Le Qiao, Gary W. Slater Both the translational diffusion coefficient D and the electrophoretic mobility μ of an oligomer that is pulled towards a nanopore by an electric field depend on its orientation. Since a charged rod-like molecule tends to orient in the presence of an electric field gradient, D and μ will change as the molecule approaches the nanopore, and this will impact the capture radius (a somewhat ill-defined measure of the efficiency of the nanopore to attract analytes in its vicinity). We present a study of this problem using theoretical arguments and Langevin Dynamics simulations. In particular, we define an alignment radius which we compare to the capture radius, and we examine different physical limits. The hydrodynamic interactions with the wall are also investigated by coupling the Langevin MD oligomer to a Lattice-Boltzmann fluid. |
Thursday, March 7, 2019 2:03PM - 2:15PM |
S55.00013: Towards Single Molecule Protein Sequencing by Nanopore Mass Spectrometry Nicholas Drachman, Mathilde LePoitevin, Benjamin Wiener, hannah Szapary, Oliver G Isik, Derek Stein Here we describe an approach to sequencing single protein molecules that will combine the advantages of mass spectrometry with those of nanopores. The basic idea is to cleave the individual amino acids from a protein molecule as they transit a small hole in sequence, and then identify each one by determining its mass-to-charge ratio in a mass spectrometer. We present the results of studies of the transfer of single amino acid ions from liquid into vacuum from the nanoscale orifice of a charged needle. We also summarize the development of an instrument featuring a magnetic mass filter and an array of channeltron detectors, which will be able to photo-dissociate single proteins and then measure both the mass and the time of detection of the resulting fragments. |
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