1
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Paiva WA, Alakwe SD, Marfai J, Jennison-Henderson MV, Achong RA, Duche T, Weeks AA, Robertson-Anderson RM, Oldenhuis NJ. From Bioreactor to Bulk Rheology: Achieving Scalable Production of Highly Concentrated Circular DNA. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2405490. [PMID: 38935929 DOI: 10.1002/adma.202405490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/10/2024] [Indexed: 06/29/2024]
Abstract
DNA serves as a model system in polymer physics due to its ability to be obtained as a uniform polymer with controllable topology and nonequilibrium behavior. Currently, a major obstacle in the widespread adoption of DNA is obtaining it on a scale and cost basis that accommodates bulk rheology and high-throughput screening. To address this, recent advancements in bioreactor-based plasmid DNA production is coupled with anion exchange chromatography producing a unified approach to generating gram-scale quantities of monodisperse DNA. With this method, 1.1 grams of DNA is obtained per batch to generate solutions with concentrations up to 116 mg mL-1. This solution of uniform supercoiled and relaxed circular plasmid DNA, is roughly 69 times greater than the overlap concentration. The utility of this method is demonstrated by performing bulk rheology measurements at sample volumes up to 1 mL on DNA of different lengths, topologies, and concentrations. The measured elastic moduli are orders of magnitude larger than those previously reported for DNA and allowed for the construction of a time-concentration superposition curve that spans 12 decades of frequency. Ultimately, these results can provide important insights into the dynamics of ring polymers and the nature of highly condensed DNA dynamics.
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Affiliation(s)
- Wynter A Paiva
- Department of Chemistry, College of Engineering and Physical Science, University of New Hampshire, 23 Academic Way, Parsons Hall, Durham, NH 03824, USA
| | - Somkene D Alakwe
- Department of Chemistry, College of Engineering and Physical Science, University of New Hampshire, 23 Academic Way, Parsons Hall, Durham, NH 03824, USA
| | - Juexin Marfai
- Department of Physics and Biophysics, College of Arts and Sciences, University of San Diego, Shiley Center for Science and Technology, 5998 Alcala Park, San Diego, CA, 92110, USA
| | - Madigan V Jennison-Henderson
- Department of Chemistry, College of Engineering and Physical Science, University of New Hampshire, 23 Academic Way, Parsons Hall, Durham, NH 03824, USA
| | - Rachel A Achong
- Department of Chemistry, College of Engineering and Physical Science, University of New Hampshire, 23 Academic Way, Parsons Hall, Durham, NH 03824, USA
| | - Tinotenda Duche
- Department of Chemistry, College of Engineering and Physical Science, University of New Hampshire, 23 Academic Way, Parsons Hall, Durham, NH 03824, USA
| | - April A Weeks
- Department of Chemistry, College of Engineering and Physical Science, University of New Hampshire, 23 Academic Way, Parsons Hall, Durham, NH 03824, USA
| | - Rae M Robertson-Anderson
- Department of Physics and Biophysics, College of Arts and Sciences, University of San Diego, Shiley Center for Science and Technology, 5998 Alcala Park, San Diego, CA, 92110, USA
| | - Nathan J Oldenhuis
- Department of Chemistry, College of Engineering and Physical Science, University of New Hampshire, 23 Academic Way, Parsons Hall, Durham, NH 03824, USA
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2
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Funkenbusch WT, Silmore KS, Doyle PS. Dynamics of a self-interacting sheet in shear flow. SOFT MATTER 2024; 20:4474-4487. [PMID: 38787762 DOI: 10.1039/d4sm00197d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
Solution processing of 2D materials such as graphene is important for applications thereof, yet a complete fundamental understanding of how 2D materials behave dynamically in solution is lacking. Here, we extend previous work by Silmore et al., Soft Matter, 2021, 17(18), 4707-4718 by adding short-ranged Lennard-Jones interactions to 2D sheets in shear flow. We find that the addition of these interactions allows for a rich landscape of conformations which depend on the balance between shear strength, bending rigidity, and interaction strength as well as the initial configuration of the sheet. We explore this conformational space and classify sheets as flat, tumbling, 1D folded, or 2D folded based on their conformational properties. We use kinetic and energetic arguments to explain why sheets adopt certain conformations within the folded regime. Finally, we calculate the stresslet and find that, even in the absence of thermal fluctuations and multiple sheet interactions, shear-thinning followed by shear-thickening behavior can appear.
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Affiliation(s)
- William T Funkenbusch
- Massachusetts Institute of Technology Department of Chemical Engineering, 25 Ames St, Cambridge MA, 02139, USA.
| | - Kevin S Silmore
- Massachusetts Institute of Technology Department of Chemical Engineering, 25 Ames St, Cambridge MA, 02139, USA.
| | - Patrick S Doyle
- Massachusetts Institute of Technology Department of Chemical Engineering, 25 Ames St, Cambridge MA, 02139, USA.
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3
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Schneck C, Smrek J, Likos CN, Zöttl A. Supercoiled ring polymers under shear flow. NANOSCALE 2024. [PMID: 38639709 DOI: 10.1039/d3nr04258h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
We apply monomer-resolved computer simulations of supercoiled ring polymers under shear, taking full account of the hydrodynamic interactions, accompanied, in parallel, by simulations in which these are switched off. The combination of bending and torsional rigidities inherent in these polymers, in conjunction with hydrodynamics, has a profound impact on their flow properties. In contrast to their flexible counterparts, which dramatically deform and inflate under shear [Liebetreu et al., Commun. Mater. 2020, 1, 4], supercoiled rings undergo only weak changes in their overall shape and they display both a reduced propensity to tumbling (at fixed Weissenberg number) and a much stronger orientational resistance with respect to their flexible counterparts. In the presence of hydrodynamic interactions, the coupling of the polymer to solvent flow is capable of bringing about a topological transformation of writhe to twist at strong shear upon conservation of the overall linking number.
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Affiliation(s)
- Christoph Schneck
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria.
- Centro de Física de Materiales (CSIC, UPV/EHU) and Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
| | - Jan Smrek
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria.
| | - Christos N Likos
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria.
| | - Andreas Zöttl
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria.
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4
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Caraglio M, Micheletti C, Orlandini E. Unraveling the Influence of Topology and Spatial Confinement on Equilibrium and Relaxation Properties of Interlocked Ring Polymers. Macromolecules 2024; 57:3223-3233. [PMID: 38616813 PMCID: PMC11008367 DOI: 10.1021/acs.macromol.3c02203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 02/27/2024] [Accepted: 03/01/2024] [Indexed: 04/16/2024]
Abstract
We use Langevin dynamics simulations to study linked ring polymers in channel confinement. We address the in- and out-of-equilibrium behavior of the systems for varying degrees of confinement and increasing topological and geometrical complexity of the interlocking. The main findings are three. First, metric observables of different link topologies collapse onto the same master curve when plotted against the crossing number, revealing a universal response to confinement. Second, the relaxation process from initially stretched states is faster for more complex links. We ascribe these properties to the interplay of several effects, including the dependence of topological friction on the link complexity. Finally, we show that transient forms of geometrical entanglement purposely added to the initial stressed state can leave distinctive signatures in force-spectroscopy curves. The insight provided by the findings could be leveraged in single-molecule nanochannel experiments to identify geometric entanglement within topologically linked rings.
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Affiliation(s)
- Michele Caraglio
- Institut
für Theoretische Physik, Universität
Innsbruck, Technikerstraße 21A, Innsbruck A-6020, Austria
| | - Cristian Micheletti
- Scuola
Internazionale Superiore di Studi Avanzati—SISSA, Via Bonomea 265, Trieste 34136, Italy
| | - Enzo Orlandini
- Department
of Physics and Astronomy, University of
Padova, Via Marzolo 8, Padova I-35100, Italy
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5
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Farimani RA, Ahmadian Dehaghani Z, Likos CN, Ejtehadi MR. Effects of Linking Topology on the Shear Response of Connected Ring Polymers: Catenanes and Bonded Rings Flow Differently. PHYSICAL REVIEW LETTERS 2024; 132:148101. [PMID: 38640389 DOI: 10.1103/physrevlett.132.148101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/09/2023] [Accepted: 02/15/2024] [Indexed: 04/21/2024]
Abstract
We perform computer simulations of mechanically linked (poly[2]catenanes, PC) and chemically bonded (bonded rings, BR) pairs of self-avoiding ring polymers in steady shear. We find that BRs develop a novel motif, termed gradient tumbling, rotating around the gradient axis. For the PCs the rings are stretched and display another new pattern, termed slip tumbling. The dynamics of BRs is continuous and oscillatory, whereas that of PCs is intermittent between slip-tumbling attempts. Our findings demonstrate the interplay between topology and hydrodynamics in dilute solutions of connected polymers.
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Affiliation(s)
- Reyhaneh A Farimani
- Department of Physics, Sharif University of Technology, Tehran, Iran
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | | | - Christos N Likos
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
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6
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Becerra D, Klotz AR, Hall LM. Single-molecule analysis of solvent-responsive mechanically interlocked ring polymers and the effects of nanoconfinement from coarse-grained simulations. J Chem Phys 2024; 160:114906. [PMID: 38511659 DOI: 10.1063/5.0191295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/02/2024] [Indexed: 03/22/2024] Open
Abstract
In this study, we simulate mechanically interlocked semiflexible ring polymers inspired by the minicircles of kinetoplast DNA (kDNA) networks. Using coarse-grained molecular dynamics simulations, we investigate the impact of molecular topological linkage and nanoconfinement on the conformational properties of two- and three-ring polymer systems in varying solvent qualities. Under good-quality solvents, for two-ring systems, a higher number of crossing points lead to a more internally constrained structure, reducing their mean radius of gyration. In contrast, three-ring systems, which all had the same crossing number, exhibited more similar sizes. In unfavorable solvents, structures collapse, forming compact configurations with increased contacts. The morphological diversity of structures primarily arises from topological linkage rather than the number of rings. In three-ring systems with different topological conformations, structural uniformity varies based on link types. Extreme confinement induces isotropic and extended conformations for catenated polymers, aligning with experimental results for kDNA networks and influencing the crossing number and overall shape. Finally, the flat-to-collapse transition in extreme confinement occurs earlier (at relatively better solvent conditions) compared to non-confined systems. This study offers valuable insights into the conformational behavior of mechanically interlocked ring polymers, highlighting challenges in extrapolating single-molecule analyses to larger networks such as kDNA.
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Affiliation(s)
- Diego Becerra
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, USA
| | - Alexander R Klotz
- Department of Physics and Astronomy, California State University, Long Beach, California 90840, USA
| | - Lisa M Hall
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, USA
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7
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Staňo R, Smrek J, Likos CN. Cluster Formation in Solutions of Polyelectrolyte Rings. ACS NANO 2023; 17:21369-21382. [PMID: 37729077 PMCID: PMC10655244 DOI: 10.1021/acsnano.3c06083] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/13/2023] [Indexed: 09/22/2023]
Abstract
We use molecular dynamics simulations to explore concentrated solutions of semiflexible polyelectrolyte ring polymers, akin to the DNA mini-circles, with counterions of different valences. We find that the assembly of rings into nanoscopic cylindrical stacks is a generic feature of the systems, but the morphology and dynamics of such a cluster can be steered by the counterion conditions. In general, a small addition of trivalent ions can stabilize the emergence of clusters due to the counterion condensation, which mitigates the repulsion between the like-charged rings. Stoichiometric addition of trivalent ions can even lead to phase separation of the polyelectrolyte ring phase due to the ion-bridging effects promoting otherwise entropically driven clustering. On the other hand, monovalent counterions cause the formation of stacks to be re-entrant with density. The clusters are stable within a certain window of concentration, while above the window the polyelectrolytes undergo an osmotic collapse, disfavoring ordering. The cluster phase exhibits characteristic cluster glass dynamics with arrest of collective degrees of freedom but not the self-ones. On the other hand, the collapsed phase shows arrest on both the collective and single level, suggesting an incipient glass-to-glass transition, from a cluster glass of ring clusters to a simple glass of rings.
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Affiliation(s)
- Roman Staňo
- Faculty
of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
- Vienna
Doctoral School in Physics, University of
Vienna, Boltzmanngasse
5, 1090 Vienna, Austria
| | - Jan Smrek
- Faculty
of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Christos N. Likos
- Faculty
of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
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8
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Slongo F, Hauke P, Faccioli P, Micheletti C. Quantum-inspired encoding enhances stochastic sampling of soft matter systems. SCIENCE ADVANCES 2023; 9:eadi0204. [PMID: 37878707 PMCID: PMC10599611 DOI: 10.1126/sciadv.adi0204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 09/21/2023] [Indexed: 10/27/2023]
Abstract
Quantum advantage in solving physical problems is still hard to assess due to hardware limitations. However, algorithms designed for quantum computers may engender transformative frameworks for modeling and simulating paradigmatically hard systems. Here, we show that the quadratic unconstrained binary optimization encoding enables tackling classical many-body systems that are challenging for conventional Monte Carlo. Specifically, in self-assembled melts of rigid lattice ring polymers, the combination of high density, chain stiffness, and topological constraints results in divergent autocorrelation times for real-space Monte Carlo. Our quantum-inspired encoding overcomes this problem and enables sampling melts of lattice rings with fixed curvature and compactness, unveiling counterintuitive topological effects. Tackling the same problems with the D-Wave quantum annealer leads to substantial performance improvements and advantageous scaling of sampling computational cost with the size of the self-assembled ring melts.
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Affiliation(s)
- Francesco Slongo
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, I-34136 Trieste, Italy
| | - Philipp Hauke
- Pitaevskii BEC Center, Department of Physics, University of Trento, Via Sommarive 14, I-38123 Povo, Trento, Italy
- INFN-TIFPA, Via Sommarive 14, I-38123 Povo, Trento, Italy
| | - Pietro Faccioli
- Department of Physics and BiQuTe Center, University of Milano-Bicocca, Piazza della Scienza 3, I-20126 Milan, Italy
- Department of Physics, University of Trento, Via Sommarive 14, I-38123 Povo, Trento, Italy
| | - Cristian Micheletti
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, I-34136 Trieste, Italy
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9
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Staňo R, Likos CN, Egorov SA. Mixing Linear Polymers with Rings and Catenanes: Bulk and Interfacial Behavior. Macromolecules 2023; 56:8168-8182. [PMID: 37900098 PMCID: PMC10601540 DOI: 10.1021/acs.macromol.3c01267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/11/2023] [Indexed: 10/31/2023]
Abstract
We derive and parameterize effective interaction potentials between a multitude of different types of ring polymers and linear chains, varying the bending rigidity and solvent quality for the former species. We further develop and apply a density functional treatment for mixtures of both disconnected (chain-ring) and connected (chain-polycatenane) mixtures of the same, drawing coexistence binodals and exploring the ensuing response functions as well as the interface and wetting behavior of the mixtures. We show that worsening of the solvent quality for the rings brings about a stronger propensity for macroscopic phase separation in the linear-polycatenane mixtures, which is predominantly of the demixing type between phases of similar overall particle density. We formulate a simple criterion based on the effective interactions, allowing us to determine whether any specific linear-ring mixture will undergo a demixing phase separation.
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Affiliation(s)
- Roman Staňo
- Faculty
of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
- Vienna
Doctoral School in Physics, University of
Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Christos N. Likos
- Faculty
of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Sergei A. Egorov
- Department
of Chemistry, University of Virginia, Charlottesville, Virginia 22901, United States
- Erwin
Schrödinger International Institute for Mathematics and Physics, Boltzmanngasse 9, 1090 Vienna, Austria
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10
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Chiarantoni P, Micheletti C. Linear Catenanes in Channel Confinement. Macromolecules 2023. [DOI: 10.1021/acs.macromol.3c00249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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11
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Rheaume SN, Klotz AR. Nanopore translocation of topologically linked DNA catenanes. Phys Rev E 2023; 107:024504. [PMID: 36932513 DOI: 10.1103/physreve.107.024504] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
The electrical signal associated with a biopolymer translocating through a nanoscale pore depends on the size, topology, and configuration of each molecule. Building upon recent interest in using solid-state nanopores for studying the topology of knotted and supercoiled DNA, we present experimental observations of topologically linked catenanes translocating through a solid-state nanopore. Using restriction enzymes, linked circular molecules were isolated from the mitochondrial DNA of Crithidia fasciculata, a structure known as a kinetoplast that comprises thousands of topologically interlocked minicircles. Digested kinetoplasts produce a spectrum of catenane topologies, which are identified from their nanopore translocation signals by spikes in the blockade current associated with the topological linkages. We attribute the different patterns of the measured electrical signals to 2-catenanes, linear and triangular 3-catenanes, and several types of 4- and 5-catenanes as well as more complex structures. Measurements of the translocation time of signals consistent with 2- and 3-catenanes suggest that topological friction between the linkages and the pore slows the translocation time of these structures, as predicted in recent simulations.
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Affiliation(s)
- Sierra N Rheaume
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Alexander R Klotz
- Department of Physics and Astronomy, California State University, Long Beach, Long Beach, California 90815, USA
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12
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Staňo R, Likos CN, Smrek J. To thread or not to thread? Effective potentials and threading interactions between asymmetric ring polymers. SOFT MATTER 2022; 19:17-30. [PMID: 36477247 PMCID: PMC9768673 DOI: 10.1039/d2sm01177h] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
We use computer simulations to study a system of two unlinked ring polymers, whose length and bending stiffness are systematically varied. We derive the effective potentials between the rings, calculate the areas of minimal surfaces of the same, and characterize the threading between them. When the two rings are of the same kind, threading of a one ring through the surface of the other is immanent for small ring-ring separations. Flexible rings pierce the surface of the other ring several times but only shallowly, as compared to the stiff rings which pierce less frequently but deeply. Typically, the ring that is being threaded swells and flattens up into an oblate-like conformation, while the ring that is threading the other takes a shape of an elongated prolate. The roles of the threader and the threaded ring are being dynamically exchanged. If, on the other hand, the rings are of different kinds, the symmetry is broken and the rings tend to take up roles of the threader and the threaded ring with unequal probabilities. We propose a method how to predict these probabilities based on the parameters of the individual rings. Ultimately, our work captures the interactions between ring polymers in a coarse-grained fashion, opening the way to large-scale modelling of materials such as kinetoplasts, catenanes or topological brushes.
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Affiliation(s)
- Roman Staňo
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria.
- Vienna Doctoral School in Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Christos N Likos
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria.
| | - Jan Smrek
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria.
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13
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Tubiana L, Ferrari F, Orlandini E. Circular Polycatenanes: Supramolecular Structures with Topologically Tunable Properties. PHYSICAL REVIEW LETTERS 2022; 129:227801. [PMID: 36493458 DOI: 10.1103/physrevlett.129.227801] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 08/11/2022] [Accepted: 10/04/2022] [Indexed: 06/17/2023]
Abstract
Polycatenanes, macrochains of topologically interlocked rings with unique physical properties have recently gained considerable interest in supramolecular chemistry, biology, and soft matter. Most of the work has been, so far, focused on linear chains and on their variety of conformational properties compared to standard polymers. Here we go beyond the linear case and show that, by circularizing such macrochains, one can exploit the topology of the local interlockings to store twist in the system, significantly altering its metric and local properties. Moreover, by properly defining the twist (Tw) and writhe (Wr) of these macrorings we show the validity of a relation equivalent to the Călugăreanu-White-Fuller theorem Tw+Wr=const, originally proved for ribbonlike structures such as double stranded DNA. Our results suggest that circular polycatenanes with storable and tunable twist can form a new category of highly designable multiscale structures with potential applications in supramolecular chemistry and material science.
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Affiliation(s)
- L Tubiana
- Physics Department, University of Trento, via Sommarive, 14 I-38123 Trento, Italy; INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, I-38123 Trento, Italy and Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - F Ferrari
- CASA* and Institute of Physics, University of Szczecin, Wielkopolska 15, 70-451 Szczecin, Poland
| | - E Orlandini
- Department of Physics and Astronomy, University of Padova, Via Marzolo 8, I-35131 Padova, Italy and INFN, Sezione di Padova, Via Marzolo 8, I-35131 Padova, Italy
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14
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Abstract
Shuffling of genetic material via reconnection of proximal DNA segments is seen in meiosis and some cancers. In contrast with textbook pictures, reconnections are performed within an entangled environment and can result in knotting or linking, detrimental for cells. By performing Brownian dynamics simulations of reconnecting polymers under confinement, modeling the genome in vivo, we find a topological transition between a gas or liquid of unlinked rings and a gel-like structure with a large number of polydisperse linked rings. This transition can be triggered by increasing polymer stiffness or confinement. Our results suggest ways to design future topological materials, such as DNA-based gels involving recombinase proteins. DNA recombination is a ubiquitous process that ensures genetic diversity. Contrary to textbook pictures, DNA recombination, as well as generic DNA translocations, occurs in a confined and highly entangled environment. Inspired by this observation, here, we investigate a solution of semiflexible polymer rings undergoing generic cutting and reconnection operations under spherical confinement. Our setup may be realized using engineered DNA in the presence of recombinase proteins or by considering micelle-like components able to form living (or reversibly breakable) polymer rings. We find that in such systems, there is a topological gelation transition, which can be triggered by increasing either the stiffness or the concentration of the rings. Flexible or dilute polymers break into an ensemble of short, unlinked, and segregated rings, whereas sufficiently stiff or dense polymers self-assemble into a network of long, linked, and mixed loops, many of which are knotted. We predict that the two phases should behave qualitatively differently in elution experiments monitoring the escape dynamics from a permeabilized container. Besides shedding some light on the biophysics and topology of genomes undergoing DNA reconnection in vivo, our findings could be leveraged in vitro to design polymeric complex fluids—e.g., DNA-based complex fluids or living polymer networks—with desired topologies.
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15
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Sleiman JL, Burton RH, Caraglio M, Gutierrez Fosado YA, Michieletto D. Geometric Predictors of Knotted and Linked Arcs. ACS POLYMERS AU 2022; 2:341-350. [PMID: 36254317 PMCID: PMC9562465 DOI: 10.1021/acspolymersau.2c00021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Inspired by how certain proteins “sense”
knots and
entanglements in DNA molecules, here, we ask if local geometric features
that may be used as a readout of the underlying topology of generic
polymers exist. We perform molecular simulations of knotted and linked
semiflexible polymers and study four geometric measures to predict
topological entanglements: local curvature, local density, local 1D
writhe, and nonlocal 3D writhe. We discover that local curvature is
a poor predictor of entanglements. In contrast, segments with maximum
local density or writhe correlate as much as 90% of the time with
the shortest knotted and linked arcs. We find that this accuracy is
preserved across different knot types and also under significant spherical
confinement, which is known to delocalize essential crossings in knotted
polymers. We further discover that nonlocal 3D writhe is the best
geometric readout of the knot location. Finally, we discuss how these
geometric features may be used to computationally analyze entanglements
in generic polymer melts and gels.
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Affiliation(s)
- Joseph L. Sleiman
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Robin H. Burton
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Michele Caraglio
- Institut für Theoretische Physik, Universität Innsbruck, Technikerstraße 21A, A-6020 Innsbruck, Austria
| | - Yair Augusto Gutierrez Fosado
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Davide Michieletto
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
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16
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Liu G, Rauscher PM, Rawe BW, Tranquilli MM, Rowan SJ. Polycatenanes: synthesis, characterization, and physical understanding. Chem Soc Rev 2022; 51:4928-4948. [PMID: 35611843 DOI: 10.1039/d2cs00256f] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chemical composition and architecture are two key factors that control the physical and material properties of polymers. Some of the more unusual and intriguing polymer architectures are the polycatenanes, which are a class of polymers that contain mechanically interlocked rings. Since the development of high yielding synthetic routes to catenanes, there has been an interest in accessing their polymeric counterparts, primarily on account of the unique conformations and degrees of freedom offered by non-bonded interlocked rings. This has lead to the synthesis of a wide variety of polycatenane architectures and to studies aimed at developing structure-property relationships of these interesting materials. In this review, we provide an overview of the field of polycatenanes, exploring synthesis, architecture, properties, simulation, and modelling, with a specific focus on some of the more recent developments.
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Affiliation(s)
- Guancen Liu
- Department of Chemistry, University of Chicago, Chicago, IL, USA.
| | - Phillip M Rauscher
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Benjamin W Rawe
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | | | - Stuart J Rowan
- Department of Chemistry, University of Chicago, Chicago, IL, USA. .,Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA.,Chemical and Engineering Sciences, Argonne National Laboratory, Lemont, IL, USA
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17
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Chiarantoni P, Micheletti C. Effect of Ring Rigidity on the Statics and Dynamics of Linear Catenanes. Macromolecules 2022. [DOI: 10.1021/acs.macromol.1c02542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pietro Chiarantoni
- International School for Advanced Studies (SISSA), Via Bonomea 265, 34136 Trieste, Italy
| | - Cristian Micheletti
- International School for Advanced Studies (SISSA), Via Bonomea 265, 34136 Trieste, Italy
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18
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Silmore KS, Strano MS, Swan JW. Thermally fluctuating, semiflexible sheets in simple shear flow. SOFT MATTER 2022; 18:768-782. [PMID: 34985479 DOI: 10.1039/d1sm01510a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We perform Brownian dynamics simulations of semiflexible colloidal sheets with hydrodynamic interactions and thermal fluctuations in shear flow. As a function of the ratio of bending rigidity to shear energy (a dimensionless quantity we denote S) and the ratio of bending rigidity to thermal energy, we observe a dynamical transition from stochastic flipping to crumpling and continuous tumbling. This dynamical transition is broadened by thermal fluctuations, and the value of S at which it occurs is consistent with the onset of chaotic dynamics found for athermal sheets. The effects of different dynamical conformations on rheological properties such as viscosity and normal stress differences are also quantified. Namely, the viscosity in a dilute dispersion of sheets is found to decrease with increasing shear rate (shear-thinning) up until the dynamical crumpling transition, at which point it increases again (shear-thickening), and non-zero first normal stress differences are found that exhibit a local maximum with respect to temperature at large S (small shear rate). These results shed light on the dynamical behavior of fluctuating 2D materials dispersed in fluids and should greatly inform the design of associated solution processing methods.
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Affiliation(s)
- Kevin S Silmore
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Michael S Strano
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - James W Swan
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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19
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Amici G, Caraglio M, Orlandini E, Micheletti C. Topological Friction and Relaxation Dynamics of Spatially Confined Catenated Polymers. ACS Macro Lett 2022; 11:1-6. [PMID: 35574798 PMCID: PMC8772382 DOI: 10.1021/acsmacrolett.1c00594] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/03/2021] [Indexed: 11/30/2022]
Abstract
We study catenated ring polymers confined inside channels and slits with Langevin dynamics simulations and address how the contour position and size of the interlocked or physically linked region evolve with time. We show that the catenation constraints generate a drag, or topological friction, that couples the contour motion of the interlocked regions. Notably, the coupling strength decreases as the interlocking is made tighter, but also shorter, by confinement. Though the coupling strength differs for channel and slit confinement, the data outline a single universal curve when plotted against the size of the linked region. Finally, we study how the relaxation kinetics changes after one of the rings is cut open and conclude that considering interlocked circular polymers is key for isolating the manifestations of topological friction. The results ought to be relevant for linked biomolecules in experimental or biological confining conditions.
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Affiliation(s)
- Giulia Amici
- Scuola
Internazionale Superiore di Studi Avanzati - SISSA, via Bonomea 265, 34136 Trieste, Italy
| | - Michele Caraglio
- Institut
für Theoretische Physik, Universität
Innsbruck, Technikerstraße 21A, A-6020 Innsbruck, Austria
| | - Enzo Orlandini
- Department
of Physics and Astronomy, University of
Padova, Via Marzolo 8, I-35100 Padova, Italy
| | - Cristian Micheletti
- Scuola
Internazionale Superiore di Studi Avanzati - SISSA, via Bonomea 265, 34136 Trieste, Italy
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20
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Scholl D, Deniz AA. Conformational Freedom and Topological Confinement of Proteins in Biomolecular Condensates. J Mol Biol 2022; 434:167348. [PMID: 34767801 PMCID: PMC8748313 DOI: 10.1016/j.jmb.2021.167348] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 01/17/2023]
Abstract
The emergence of biomolecular condensation and liquid-liquid phase separation (LLPS) introduces a new layer of complexity into our understanding of cell and molecular biology. Evidence steadily grows indicating that condensates are not only implicated in physiology but also human disease. Macro- and mesoscale characterization of condensates as a whole have been instrumental in understanding their biological functions and dysfunctions. By contrast, the molecular level characterization of condensates and how condensates modify the properties of the molecules that constitute them thus far remain comparably scarce. In this minireview we summarize and discuss the findings of several recent studies that have focused on structure, dynamics, and interactions of proteins undergoing condensation. The mechanistic insights they provide help us identify the relevant properties nature and scientists can leverage to modulate the behavior of condensate systems. We also discuss the unique environment of the droplet surface and speculate on effects of topological constraints and physical exclusion on condensate properties.
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Affiliation(s)
- Daniel Scholl
- Department of Integrative and Computational Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, United States. https://twitter.com/@DanielScholl_be
| | - Ashok A Deniz
- Department of Integrative and Computational Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, United States.
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21
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Shankar S, Nelson DR. Thermalized buckling of isotropically compressed thin sheets. Phys Rev E 2021; 104:054141. [PMID: 34942813 DOI: 10.1103/physreve.104.054141] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 10/19/2021] [Indexed: 11/07/2022]
Abstract
The buckling of thin elastic sheets is a classic mechanical instability that occurs over a wide range of scales. In the extreme limit of atomically thin membranes like graphene, thermal fluctuations can dramatically modify such mechanical instabilities. We investigate here the delicate interplay of boundary conditions, nonlinear mechanics, and thermal fluctuations in controlling buckling of confined thin sheets under isotropic compression. We identify two inequivalent mechanical ensembles based on the boundaries at constant strain (isometric) or at constant stress (isotensional) conditions. Remarkably, in the isometric ensemble, boundary conditions induce a novel long-ranged nonlinear interaction between the local tilt of the surface at distant points. This interaction combined with a spontaneously generated thermal tension leads to a renormalization group description of two distinct universality classes for thermalized buckling, realizing a mechanical variant of Fisher-renormalized critical exponents. We formulate a complete scaling theory of buckling as an unusual phase transition with a size-dependent critical point, and we discuss experimental ramifications for the mechanical manipulation of ultrathin nanomaterials.
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Affiliation(s)
- Suraj Shankar
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
| | - David R Nelson
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Molecular and Cellular Biology and School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
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22
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Ubertini MA, Rosa A. Computer simulations of melts of ring polymers with nonconserved topology: A dynamic Monte Carlo lattice model. Phys Rev E 2021; 104:054503. [PMID: 34942724 DOI: 10.1103/physreve.104.054503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/26/2021] [Indexed: 11/07/2022]
Abstract
We present computer simulations of a dynamic Monte Carlo algorithm for polymer chains on a fcc lattice which explicitly takes into account the possibility to overcome topological constraints by controlling the rate at which nearby polymer strands may cross through each other. By applying the method to systems of interacting ring polymers at melt conditions, we characterize their structure and dynamics by measuring, in particular, the amounts of knots and links which are formed during the relaxation process. In comparison with standard melts of unknotted and unconcatenated rings, our simulations demonstrate that the mechanism of strand crossing makes polymer dynamics faster provided the characteristic timescale of the process is smaller than the typical timescale for chain relaxation in the unperturbed state, in agreement with recent experiments employing solutions of DNA rings in the presence of the type II topoisomerase enzyme. In the opposite case of slow rates the melt is shown to become slower, and this prediction may be easily validated experimentally.
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Affiliation(s)
- Mattia Alberto Ubertini
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy
| | - Angelo Rosa
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy
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23
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Polson JM, Garcia EJ, Klotz AR. Flatness and intrinsic curvature of linked-ring membranes. SOFT MATTER 2021; 17:10505-10515. [PMID: 34755161 DOI: 10.1039/d1sm01307f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Recent experiments have elucidated the physical properties of kinetoplasts, which are chain-mail-like structures found in the mitochondria of trypanosome parasites formed from catenated DNA rings. Inspired by these studies, we use Monte Carlo simulations to examine the behavior of two-dimensional networks ("membranes") of linked rings. For simplicity, we consider only identical rings that are circular and rigid and that form networks with a regular linking structure. We find that the scaling of the eigenvalues of the shape tensor with membrane size are consistent with the behavior of the flat phase observed in self-avoiding covalent membranes. Increasing ring thickness tends to swell the membrane. Remarkably, unlike covalent membranes, the linked-ring membranes tend to form concave structures with an intrinsic curvature of entropic origin associated with local excluded-volume interactions. The degree of concavity increases with increasing ring thickness and is also affected by the type of linking network. The relevance of the properties of linked-ring model membranes to those observed in kinetoplasts is discussed.
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Affiliation(s)
- James M Polson
- Department of Physics, University of Prince Edward Island, Charlottetown, Prince Edward Island, C1A 4P3, Canada.
| | - Edgar J Garcia
- Department of Physics and Astronomy, California State University, Long Beach, California, 90840, USA
| | - Alexander R Klotz
- Department of Physics and Astronomy, California State University, Long Beach, California, 90840, USA
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24
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Yadav I, Al Sulaiman D, Soh BW, Doyle PS. Phase Transition of Catenated DNA Networks in Poly(ethylene glycol) Solutions. ACS Macro Lett 2021; 10:1429-1435. [PMID: 35549007 DOI: 10.1021/acsmacrolett.1c00463] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Conformational phase transitions of macromolecules are an important class of problems in fundamental polymer physics. While the conformational phase transitions of linear DNA have been extensively studied, this feature of topologically complex DNA remains unexplored. We report herein the polymer-and-salt-induced (Ψ) phase transition of 2D catenated DNA networks, called kinetoplasts, using single-molecule fluorescence microscopy. We observe that kinetoplasts can undergo a reversible transition from the flat phase to the collapsed phase in the presence of NaCl as a function of the crowding agent poly(ethylene glycol). The nature of this phase transition is tunable through varying ionic strengths. For linear DNA, the coexistence of coil and globule phases was attributed to a first order phase transition associated with a double well potential in the transition regime. Kinetoplasts, however, navigate from the flat to the collapsed phase by passing through an intermediate regime, characterized by the coexistence of a multipopulation with varying shapes and sizes. Conformations of individual molecules in the multipopulation are long-lived, which suggests a rugged energy landscape.
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Affiliation(s)
- Indresh Yadav
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Dana Al Sulaiman
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Beatrice W. Soh
- Institute of Materials Research and Engineering, 2 Fusionopolis Way, Singapore 138634, Singapore
| | - Patrick S. Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Harvard Medical School Initiative for RNA Medicine, Boston, Massachusetts 02215, United States
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25
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Orlandini E, Micheletti C. Topological and physical links in soft matter systems. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 34:013002. [PMID: 34547745 DOI: 10.1088/1361-648x/ac28bf] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
Linking, or multicomponent topological entanglement, is ubiquitous in soft matter systems, from mixtures of polymers and DNA filaments packedin vivoto interlocked line defects in liquid crystals and intertwined synthetic molecules. Yet, it is only relatively recently that theoretical and experimental advancements have made it possible to probe such entanglements and elucidate their impact on the physical properties of the systems. Here, we review the state-of-the-art of this rapidly expanding subject and organize it as follows. First, we present the main concepts and notions, from topological linking to physical linking and then consider the salient manifestations of molecular linking, from synthetic to biological ones. We next cover the main physical models addressing mutual entanglements in mixtures of polymers, both linear and circular. Finally, we consider liquid crystals, fluids and other non-filamentous systems where topological or physical entanglements are observed in defect or flux lines. We conclude with a perspective on open challenges.
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Affiliation(s)
- Enzo Orlandini
- Department of Physics and Astronomy, University of Padova and Sezione INFN, Via Marzolo 8, Padova, Italy
| | - Cristian Micheletti
- SISSA, International School for Advanced Studies, via Bonomea 265, Trieste, Italy
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26
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Soh BW, Doyle PS. Equilibrium Conformation of Catenated DNA Networks in Slitlike Confinement. ACS Macro Lett 2021; 10:880-885. [PMID: 35549205 DOI: 10.1021/acsmacrolett.1c00299] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A kinetoplast is a planar network of catenated DNA rings with topology that resembles that of chain mail armor. In this work, we use single-molecule experiments to probe the conformation of kinetoplasts confined to slits. We find that the in-plane size of kinetoplasts increases with degree of confinement, akin to the slitlike confinement of linear DNA. The change in kinetoplast size with channel height is consistent with the scaling prediction from a Flory-type approach for a 2D polymer. With an increase in extent of confinement, the kinetoplasts appear to unfold and take on more uniform circular shapes, in contrast to the broad range of conformations observed for kinetoplasts in bulk.
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Affiliation(s)
- Beatrice W. Soh
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Patrick S. Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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27
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Silmore KS, Strano MS, Swan JW. Buckling, crumpling, and tumbling of semiflexible sheets in simple shear flow. SOFT MATTER 2021; 17:4707-4718. [PMID: 33978658 DOI: 10.1039/d0sm02184a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
As 2D materials such as graphene, transition metal dichalcogenides, and 2D polymers become more prevalent, solution processing and colloidal-state properties are being exploited to create advanced and functional materials. However, our understanding of the fundamental behavior of 2D sheets and membranes in fluid flow is still lacking. In this work, we perform numerical simulations of athermal semiflexible sheets with hydrodynamic interactions in shear flow. For sheets initially oriented near the flow-vorticity plane, we find buckling instabilities of different mode numbers that vary with bending stiffness and can be understood with a quasi-static model of elasticity. For different initial orientations, chaotic tumbling trajectories are observed. Notably, we find that sheets fold or crumple before tumbling but do not stretch again upon applying greater shear.
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Affiliation(s)
- Kevin S Silmore
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Michael S Strano
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - James W Swan
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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28
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Locatelli E, Bianco V, Malgaretti P. Activity-Induced Collapse and Arrest of Active Polymer Rings. PHYSICAL REVIEW LETTERS 2021; 126:097801. [PMID: 33750170 DOI: 10.1103/physrevlett.126.097801] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 01/24/2021] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
We investigate, using numerical simulations, the conformations of isolated active ring polymers. We find that their behavior depends crucially on their size: Short rings (N≲100) swell, whereas longer rings (N≳200) collapse, at sufficiently high activity. By investigating the nonequilibrium process leading to the steady state, we find a universal route driving both outcomes; we highlight the central role of steric interactions, at variance with linear chains, and of topology conservation. We further show that the collapsed rings are arrested by looking at different observables, all underlining the presence of an extremely long timescales at the steady state, associated with the internal dynamics of the collapsed section. Finally, we found that in some circumstances the collapsed state spins about its axis.
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Affiliation(s)
| | - Valentino Bianco
- Faculty of Chemistry, Chemical Physics Department, Complutense University of Madrid, Plaza de las Ciencias, Ciudad Universitaria, Madrid 28040, Spain
| | - Paolo Malgaretti
- Max Planck Institute for Intelligent Systems, Heisenbergstrasse 3, 70569 Stuttgart, Germany
- IV Institute for Theoretical Physics, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Helmholtz Institut Erlangen-Nürnberg for Renewable Energy (IEK-11), Forschungszentrum Jülich, Fürther Strasse 248, 90429 Nürnberg, Germany
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29
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Moghimi E, Chubak I, Founta D, Ntetsikas K, Polymeropoulos G, Hadjichristidis N, Likos CN, Vlassopoulos D. The influence of arm composition on the self-assembly of low-functionality telechelic star polymers in dilute solutions. Colloid Polym Sci 2021. [DOI: 10.1007/s00396-020-04742-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AbstractWe combine synthesis, physical experiments, and computer simulations to investigate self-assembly patterns of low-functionality telechelic star polymers (TSPs) in dilute solutions. In particular, in this work, we focus on the effect of the arm composition and length on the static and dynamic properties of TSPs, whose terminal blocks are subject to worsening solvent quality upon reducing the temperature. We find two populations, single stars and clusters, that emerge upon worsening the solvent quality of the outer block. For both types of populations, their spatial extent decreases with temperature, with the specific details (such as temperature at which the minimal size is reached) depending on the coupling between inter- and intra-molecular associations as well as their strength. The experimental results are in very good qualitative agreement with coarse-grained simulations, which offer insights into the mechanism of thermoresponsive behavior of this class of materials.
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30
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Parisi D, Costanzo S, Jeong Y, Ahn J, Chang T, Vlassopoulos D, Halverson JD, Kremer K, Ge T, Rubinstein M, Grest GS, Srinin W, Grosberg AY. Nonlinear Shear Rheology of Entangled Polymer Rings. Macromolecules 2021. [DOI: 10.1021/acs.macromol.0c02839] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Daniele Parisi
- FORTH and University of Crete, Heraklion 71110, Greece
- Penn State University, State College, Pennsylvania 16801, United States
| | - Salvatore Costanzo
- FORTH and University of Crete, Heraklion 71110, Greece
- University of Naples Federico II, Naples 80125, Italy
| | - Youncheol Jeong
- Pohang University of Science and Technology, Pohang 790-784, South Korea
| | - Junyoung Ahn
- Pohang University of Science and Technology, Pohang 790-784, South Korea
| | - Taihyun Chang
- Pohang University of Science and Technology, Pohang 790-784, South Korea
| | | | | | - Kurt Kremer
- Max Planck Institute for Polymer Research, Mainz 55021, Germany
| | - Ting Ge
- University of South Carolina, Columbia, South Carolina 29208-0001, United States
| | - Michael Rubinstein
- Duke University, Durham, North Carolina 27708-9976, United States
- Hokkaido University, Sapporo, Hokkaido 060-0808, Japan
| | - Gary S. Grest
- Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Watee Srinin
- Naresuan University, Mueang Phitsanulok, Phitsanulok 65000, Thailand
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31
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Abstract
Cellular liquid-liquid phase separation (LLPS) plays a key role in the dynamics and function of RNA-protein condensates like stress granules. In this issue of Cell, Yang et al., Guillén-Boixet et al., and Sanders et al. use a combination of experiment and modeling to provide an exciting mechanistic insight into the relationship between stress granules and LLPS, for example, in the context of protein disorder, switchable interactions, graph theory, and multiple interacting dense phases.
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32
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Plummer A, Nelson DR. Buckling and metastability in membranes with dilation arrays. Phys Rev E 2020; 102:033002. [PMID: 33075876 DOI: 10.1103/physreve.102.033002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/07/2020] [Indexed: 11/07/2022]
Abstract
We study periodic arrays of impurities that create localized regions of expansion, embedded in two-dimensional crystalline membranes. These arrays provide a simple elastic model of shape memory. As the size of each dilational impurity increases (or the relative cost of bending to stretching decreases), it becomes energetically favorable for each of the M impurities to buckle up or down into the third dimension, thus allowing for of order 2^{M} metastable surface configurations corresponding to different impurity "spin" configurations. With both discrete simulations and the nonlinear continuum theory of elastic plates, we explore the buckling of both isolated dilations and dilation arrays at zero temperature, guided by analogies with Ising antiferromagnets. We conjecture ground states for systems with triangular and square impurity superlattices, and comment briefly on the possible behaviors at finite temperatures.
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Affiliation(s)
- Abigail Plummer
- Department of Physics, Harvard University, 17 Oxford Street, Cambridge, Massachusetts 02138, USA
| | - David R Nelson
- Department of Physics, Harvard University, 17 Oxford Street, Cambridge, Massachusetts 02138, USA
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33
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Rauscher PM, Rowan SJ, de Pablo JJ. Hydrodynamic interactions in topologically linked ring polymers. Phys Rev E 2020; 102:032502. [PMID: 33076028 DOI: 10.1103/physreve.102.032502] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 08/21/2020] [Indexed: 11/07/2022]
Abstract
Despite decades of interdisciplinary research on topologically linked ring polymers, their dynamics remain largely unstudied. These systems represent a major scientific challenge as they are often subject to both topological and hydrodynamic interactions (HI), which render dynamical solutions either mathematically intractable or computationally prohibitive. Here we circumvent these limitations by preaveraging the HI of linked rings. We show that the symmetry of ring polymers leads to a hydrodynamic decoupling of ring dynamics. This decoupling is valid even for nonideal polymers and nonequilibrium conditions. Physically, our findings suggest that the effects of topology and HI are nearly independent and do not act cooperatively to influence polymer dynamics. We use this result to develop highly efficient Brownian dynamics algorithms that offer enormous performance improvements over conventional methods and apply these algorithms to simulate catenated ring polymers at equilibrium, confirming the independence of topological effects and HI. The methods developed here can be used to study and simulate large systems of linked rings with HI, including kinetoplast DNA, Olympic gels, and poly[n]catenanes.
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Affiliation(s)
- Phillip M Rauscher
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Stuart J Rowan
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA.,Department of Chemistry, University of Chicago, Chicago, Illinois 60637, USA.,Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, USA.,Center for Molecular Engineering, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Juan J de Pablo
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA.,Center for Molecular Engineering, Argonne National Laboratory, Lemont, Illinois 60439, USA.,Materials Science Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
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34
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Soh BW, Khorshid A, Al Sulaiman D, Doyle PS. Ionic Effects on the Equilibrium Conformation of Catenated DNA Networks. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c01706] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Beatrice W. Soh
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ahmed Khorshid
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Dana Al Sulaiman
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Patrick S. Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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35
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Liebetreu M, Likos CN. Cluster prevalence in concentrated ring-chain mixtures under shear. SOFT MATTER 2020; 16:8710-8719. [PMID: 32996544 DOI: 10.1039/d0sm01309a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Semiflexible ring polymers are known to exhibit clustering behavior and form stacks in concentrated solutions. Recently, weak shear was suggested to re-orient these stacks with flow, a phenomenon more easily visible in more concentrated solutions [Liebetreu et al., ACS Appl. Polym. Mater., 2020, 2(8), 3505-3517, DOI: 10.1021/acsapm.0c00522]. In this work, we investigate the impact of mixing linear chains and rings in a similar system under shear, studying clustering in the presence of semiflexible, rod-like chains. We present a correlation between chain monomer fraction and clustering behavior as linear chains take up less space, thus decreasing the system's effective density and, subsequently, clustering. However, we suggest mixtures with a low chain concentration to maintain or potentially enhance clustering at equilibrium while this effect is destroyed under shear. The mixing of chains and rings may therefore be used to create more strongly organized structures susceptible to reorientation via weak shear.
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Affiliation(s)
- Maximilian Liebetreu
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria.
| | - Christos N Likos
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria.
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Soh BW, Doyle PS. Deformation Response of Catenated DNA Networks in a Planar Elongational Field. ACS Macro Lett 2020; 9:944-949. [PMID: 35648605 DOI: 10.1021/acsmacrolett.0c00360] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
A kinetoplast is a complex catenated DNA network that bears resemblance to a two-dimensional polymeric system. In this work, we use single-molecule experiments to study the transient and steady-state deformation of kinetoplasts in a planar elongational field. We demonstrate that kinetoplasts deform in a stagewise manner and undergo transient deformation at large strains, due to conformational rearrangements from an intermediate metastable state. Kinetoplasts in an elongational field achieve a steady-state deformation that depends on strain rate, akin to the deformation of linear polymers. We do not observe an abrupt transition between the nondeformed and deformed states of a kinetoplast, in contrast to the coil-stretch transition for a linear polymer.
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Affiliation(s)
- Beatrice W. Soh
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Patrick S. Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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Grosberg AY. Human bloodsucking parasite in service of materials science. Proc Natl Acad Sci U S A 2020; 117:18-20. [PMID: 31879357 PMCID: PMC6955344 DOI: 10.1073/pnas.1920496117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Alexander Y Grosberg
- Department of Physics, New York University, New York, NY 10003;
- Center for Soft Matter Research, New York University, New York, NY 10003
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Klotz AR, Soh BW, Doyle PS. Equilibrium structure and deformation response of 2D kinetoplast sheets. Proc Natl Acad Sci U S A 2020; 117:121-127. [PMID: 31811027 PMCID: PMC6955370 DOI: 10.1073/pnas.1911088116] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The considerable interest in two-dimensional (2D) materials and complex molecular topologies calls for a robust experimental system for single-molecule studies. In this work, we study the equilibrium properties and deformation response of a complex DNA structure called a kinetoplast, a 2D network of thousands of linked rings akin to molecular chainmail. Examined in good solvent conditions, kinetoplasts appear as a wrinkled hemispherical sheet. The conformation of each kinetoplast is dictated by its network topology, giving it a unique shape, which undergoes small-amplitude thermal fluctuations at subsecond timescales, with a wide separation between fluctuation and diffusion timescales. They deform elastically when weakly confined and swell to their equilibrium dimensions when the confinement is released. We hope that, in the same way that linear DNA became a canonical model system on the first investigations of its polymer-like behavior, kinetoplasts can serve that role for 2D and catenated polymer systems.
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Affiliation(s)
- Alexander R Klotz
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142
- Department of Physics and Astronomy, California State University, Long Beach, CA 90840
| | - Beatrice W Soh
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Patrick S Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142;
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