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Yamamoto T. Topology effects of cyclic polymers: Controlling the topology for innovative functionalities. REACT FUNCT POLYM 2018. [DOI: 10.1016/j.reactfunctpolym.2018.08.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Zhu L, Wang X, Li J, Wang Y. Radius of Gyration, Mean Span, and Geometric Shrinking Factors of Bridged Polycyclic Ring Polymers. MACROMOL THEOR SIMUL 2016. [DOI: 10.1002/mats.201600033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Lijuan Zhu
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; Department of Polymer Science and Engineering; College of Chemistry; Chemical Engineering and Materials Science; Soochow University; 199 Ren-ai Road Suzhou 215123 P. R. China
| | - Xiaoyan Wang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; Department of Polymer Science and Engineering; College of Chemistry; Chemical Engineering and Materials Science; Soochow University; 199 Ren-ai Road Suzhou 215123 P. R. China
| | - Jianfeng Li
- The State Key Laboratory of Molecular Engineering of Polymers; Department of Macromolecular Science; Fudan University; Shanghai 200433 P. R. China
| | - Yanwei Wang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; Department of Polymer Science and Engineering; College of Chemistry; Chemical Engineering and Materials Science; Soochow University; 199 Ren-ai Road Suzhou 215123 P. R. China
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Nikoofard N, Mashaghi A. Topology sorting and characterization of folded polymers using nano-pores. NANOSCALE 2016; 8:4643-4649. [PMID: 26853059 DOI: 10.1039/c5nr08828c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Here we report on the translocation of folded polymers through nano-pores using molecular dynamic simulations. Two cases are studied: one in which a folded molecule unfolds upon passage and one in which the folding remains intact as the molecule passes through the nano-pore. The topology of a folded polymer chain is defined as the arrangement of the intramolecular contacts, known as circuit topology. In the case where intramolecular contacts remain intact, we show that the dynamics of passage through a nano-pore varies for molecules with differing topologies: a phenomenon that can be exploited to enrich certain topologies in mixtures. We find that the nano-pore allows reading of the topology for short chains. Moreover, when the passage is coupled with unfolding, the nano-pore enables discrimination between pure states, i.e., states in which the majority of contacts are arranged identically. In this case, as we show here, it is also possible to read the positions of the contact sites along a chain. Our results demonstrate the applicability of nano-pore technology to characterize and sort molecules based on their topology.
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Affiliation(s)
- Narges Nikoofard
- Institute of Nanoscience and Nanotechnology, University of Kashan, Kashan 51167-87317, Iran
| | - Alireza Mashaghi
- Harvard Medical School, Harvard University, Boston, MA 02115, USA.
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Sun D, Cho J. Monte Carlo simulations on thermodynamic and conformational properties of catenated double-ring copolymers. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:062601. [PMID: 25615120 DOI: 10.1103/physreve.90.062601] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Indexed: 06/04/2023]
Abstract
The thermodynamic and conformational properties of catenated double-ring A-B copolymer melts are investigated through lattice Monte Carlo simulations. The topological constraint on the catenated copolymers is shown to suppress demixing of A and B monomers. This action results in their order-to-disorder transition (ODT) at an increased segregation level and the lamellae below ODT with reduced order, when compared to diblock copolymers of linear or single-ring topology. The A and B rings are pulled closer by catenation in the copolymer, which leads to its smaller gyration radius, lamellar domain spacing, and distance between mass centers of the two rings than for the diblock copolymers. With increasing segregation tendencies, the gyration radii of the A rings of the catenated copolymers stretch along the direction normal to lamellae, while the A-block conformations of the single-ring copolymers change their shapes from ellipsoid to sphere.
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Affiliation(s)
- Dachuan Sun
- Department of Polymer Science and Engineering, and Center for Photofunctional Energy Materials, Dankook University, 152 Jukjeon-ro, Suji-gu, Yongin, Gyeonggi-do 448-701, South Korea
| | - Junhan Cho
- Department of Polymer Science and Engineering, and Center for Photofunctional Energy Materials, Dankook University, 152 Jukjeon-ro, Suji-gu, Yongin, Gyeonggi-do 448-701, South Korea
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Yamamoto T, Tezuka Y. Topological polymer chemistry: a cyclic approach toward novel polymer properties and functions. Polym Chem 2011. [DOI: 10.1039/c1py00088h] [Citation(s) in RCA: 238] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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YAMAMOTO T. Emergence of Functionalities Originating from the Topology of Polymers. KOBUNSHI RONBUNSHU 2011. [DOI: 10.1295/koron.68.550] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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YAMAMOTO T, TEZUKA Y. Topological Polymer Chemistry: New Synthesis of Cyclic and Multicyclic Polymers and Topology Effects Thereby. KOBUNSHI RONBUNSHU 2011. [DOI: 10.1295/koron.68.782] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Takuya YAMAMOTO
- Department of Organic and Polymeric Materials, Tokyo Institute of Technology
| | - Yasuyuki TEZUKA
- Department of Organic and Polymeric Materials, Tokyo Institute of Technology
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Vakhrushev AV, Gorbunov AA, Tezuka Y, Tsuchitani A, Oike H. Liquid Chromatography of Theta-Shaped and Three-Armed Star Poly(tetrahydrofuran)s: Theory and Experimental Evidence of Topological Separation. Anal Chem 2008; 80:8153-62. [DOI: 10.1021/ac801229f] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrey V. Vakhrushev
- Institute for Highly Pure Biopreparations, 7 Pudozhskaya, 197110, St. Petersburg, Russia, and Department of Organic and Polymeric Materials, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Alexei A. Gorbunov
- Institute for Highly Pure Biopreparations, 7 Pudozhskaya, 197110, St. Petersburg, Russia, and Department of Organic and Polymeric Materials, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Yasuyuki Tezuka
- Institute for Highly Pure Biopreparations, 7 Pudozhskaya, 197110, St. Petersburg, Russia, and Department of Organic and Polymeric Materials, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Akiko Tsuchitani
- Institute for Highly Pure Biopreparations, 7 Pudozhskaya, 197110, St. Petersburg, Russia, and Department of Organic and Polymeric Materials, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Hideaki Oike
- Institute for Highly Pure Biopreparations, 7 Pudozhskaya, 197110, St. Petersburg, Russia, and Department of Organic and Polymeric Materials, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
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Hayashi S, Adachi K, Tezuka Y. ATRP-RCM Synthesis of 8-Shaped Poly(methyl acrylate) Using a 4-Armed Star Telechelics. Polym J 2008. [DOI: 10.1295/polymj.pj2008037] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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ADACHI K, TEZUKA Y. Topological Polymer Chemistry: Designing Unusual Macromolecular Architectures. KOBUNSHI RONBUNSHU 2007. [DOI: 10.1295/koron.64.709] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Martínez-Veracoechea FJ, Escobedo FA. Simulation of the gyroid phase in off-lattice models of pure diblock copolymer melts. J Chem Phys 2006; 125:104907. [PMID: 16999550 DOI: 10.1063/1.2345652] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Particle-based molecular simulations of pure diblock copolymer (DBC) systems were performed in continuum space via dissipative particle dynamics and Monte Carlo methods for a bead-spring chain model. This model consisted of chains of soft repulsive particles often used with dissipative particle dynamics. The gyroid phase was successfully simulated in DBC melts at selected conditions provided that the simulation box size was commensurate with the gyroid lattice spacing. Simulations were concentrated at conditions where the gyroid phase is expected to be stable which allowed us to outline approximate phase boundaries. When more than one phase was observed by varying simulation box size, thermodynamic stability was discerned by comparing the Helmholtz free energy of the competing phases. For this purpose, chemical potentials were efficiently simulated via an expanded ensemble that gradually inserts/deletes a target chain to/from the system. These simulations employed a novel combination of Bennett's [J. Comput. Phys. 22, 245 (1976)] acceptance-ratio method to estimate free-energy differences and a recently proposed method to get biasing weights that maximize the number of times that the target chain is regrown. The analysis of the gyroid nodes revealed clear evidence of packing frustration in the form of an (entropically) unfavorably overstretching of chains, a phenomenon that has been suggested to provide the structural basis for the limited region of stability of the gyroid phase in the DBC phase diagram. Finally, the G phase and nodal chain stretching were also found in simulations with a completely different DBC particle-based model.
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Ulas S, Diwekar UM. Efficient molecular simulations for environmentally benign processes. MOLECULAR SIMULATION 2006. [DOI: 10.1080/08927020600599113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Abstract
Non-Boltzmann sampling (NBS) methods have been extensively employed in recent years, mainly due to their ability to enhance ergodicity in simulations of complex systems. In addition, they make possible reliable computation of equilibrium properties (ensemble averages, free-energy differences, and potentials of mean force) over continuous ranges of thermodynamic conditions. In this work, we put forward a general and systematic framework for NBS methods that allows a single set of equations and procedures to be applied to diverse systems. Moreover, we show how to exploit simulation data most effectively by obtaining continuous profiles of any mechanical properties, including structural quantities not directly related to the ensemble parameters. Finally, we demonstrate the usefulness of the developed formulation by applying it to spin systems, Lennard-Jones fluids, and a model protein molecule (both in isolation and in the proximity of a flat wall).
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Affiliation(s)
- Charlles R A Abreu
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, USA
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