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Tubiana L, Kobayashi H, Potestio R, Dünweg B, Kremer K, Virnau P, Daoulas K. Comparing equilibration schemes of high-molecular-weight polymer melts with topological indicators. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 33:204003. [PMID: 33765663 DOI: 10.1088/1361-648x/abf20c] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/25/2021] [Indexed: 06/12/2023]
Abstract
Recent theoretical studies have demonstrated that the behaviour of molecular knots is a sensitive indicator of polymer structure. Here, we use knots to verify the ability of two state-of-the-art algorithms-configuration assembly and hierarchical backmapping-to equilibrate high-molecular-weight (MW) polymer melts. Specifically, we consider melts with MWs equivalent to several tens of entanglement lengths and various chain flexibilities, generated with both strategies. We compare their unknotting probability, unknotting length, knot spectra, and knot length distributions. The excellent agreement between the two independent methods with respect to knotting properties provides an additional strong validation of their ability to equilibrate dense high-MW polymeric liquids. By demonstrating this consistency of knotting behaviour, our study opens the way for studying topological properties of polymer melts beyond time and length scales accessible to brute-force molecular dynamics simulations.
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Affiliation(s)
- Luca 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
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Hideki Kobayashi
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Raffaello Potestio
- 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
| | - Burkhard Dünweg
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Department of Chemical Engineering, Monash University, Clayton, Victoria 3800, Australia
| | - Kurt Kremer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Peter Virnau
- Institute of Physics, Johannes Gutenberg University, Staudingerweg 9, 55128 Mainz, Germany
| | - Kostas Daoulas
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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Nieto Simavilla D, Sgouros AP, Vogiatzis GG, Tzoumanekas C, Georgilas V, Verbeeten WMH, Theodorou DN. Molecular Dynamics Test of the Stress-Thermal Rule in Polyethylene and Polystyrene Entangled Melts. Macromolecules 2020. [DOI: 10.1021/acs.macromol.9b02088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- David Nieto Simavilla
- Universidad de Burgos, Burgos 09006, Spain
- Basque Center for Applied Mathematics, Bilbao 48009, Spain
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Vogiatzis GG, Theodorou DN. Multiscale Molecular Simulations of Polymer-Matrix Nanocomposites: or What Molecular Simulations Have Taught us About the Fascinating Nanoworld. ARCHIVES OF COMPUTATIONAL METHODS IN ENGINEERING : STATE OF THE ART REVIEWS 2017; 25:591-645. [PMID: 29962833 PMCID: PMC6003436 DOI: 10.1007/s11831-016-9207-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 12/20/2016] [Indexed: 06/08/2023]
Abstract
Following the substantial progress in molecular simulations of polymer-matrix nanocomposites, now is the time to reconsider this topic from a critical point of view. A comprehensive survey is reported herein providing an overview of classical molecular simulations, reviewing their major achievements in modeling polymer matrix nanocomposites, and identifying several open challenges. Molecular simulations at multiple length and time scales, working hand-in-hand with sensitive experiments, have enhanced our understanding of how nanofillers alter the structure, dynamics, thermodynamics, rheology and mechanical properties of the surrounding polymer matrices.
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Affiliation(s)
- Georgios G. Vogiatzis
- School of Chemical Engineering, National Technical University of Athens, 9 Heroon Polytechniou Street, Zografou Campus, 15780 Athens, Greece
- Present Address: Department of Mechanical Engineering, Eindhoven University of Technology, PO Box 513, 5600MB Eindhoven, The Netherlands
| | - Doros N. Theodorou
- School of Chemical Engineering, National Technical University of Athens, 9 Heroon Polytechniou Street, Zografou Campus, 15780 Athens, Greece
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Lachet V, Teuler JM, Rousseau B. Classical force field for hydrofluorocarbon molecular simulations. Application to the study of gas solubility in poly(vinylidene fluoride). J Phys Chem A 2014; 119:140-51. [PMID: 25479370 DOI: 10.1021/jp506895p] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A classical all-atoms force field for molecular simulations of hydrofluorocarbons (HFCs) has been developed. Lennard-Jones force centers plus point charges are used to represent dispersion-repulsion and electrostatic interactions. Parametrization of this force field has been performed iteratively using three target properties of pentafluorobutane: the quantum energy of an isolated molecule, the dielectric constant in the liquid phase, and the compressed liquid density. The accuracy and transferability of this new force field has been demonstrated through the simulation of different thermophysical properties of several fluorinated compounds, showing significant improvements compared to existing models. This new force field has been applied to study solubilities of several gases in poly(vinylidene fluoride) (PVDF) above the melting temperature of this polymer. The solubility of CH4, CO2, H2S, H2, N2, O2, and H2O at infinite dilution has been computed using test particle insertions in the course of a NpT hybrid Monte Carlo simulation. For CH4, CO2, and their mixtures, some calculations beyond the Henry regime have also been performed using hybrid Monte Carlo simulations in the osmotic ensemble, allowing both swelling and solubility determination. An ideal mixing behavior is observed, with identical solubility coefficients in the mixtures and in pure gas systems.
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Affiliation(s)
- V Lachet
- IFP Energies nouvelles, 1-4 Avenue de Bois-Préau, 92852 Rueil-Malmaison, France
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Theodorou DN, Vogiatzis GG, Kritikos G. Self-Consistent-Field Study of Adsorption and Desorption Kinetics of Polyethylene Melts on Graphite and Comparison with Atomistic Simulations. Macromolecules 2014. [DOI: 10.1021/ma501454t] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Doros N. Theodorou
- School of Chemical Engineering, National Technical University of Athens, 9 Heroon Polytechniou Street, Zografou
Campus, GR-15780 Athens, Greece
| | - Georgios G. Vogiatzis
- School of Chemical Engineering, National Technical University of Athens, 9 Heroon Polytechniou Street, Zografou
Campus, GR-15780 Athens, Greece
| | - Georgios Kritikos
- School of Chemical Engineering, National Technical University of Athens, 9 Heroon Polytechniou Street, Zografou
Campus, GR-15780 Athens, Greece
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6
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Alexandris S, Sakellariou G, Steinhart M, Floudas G. Dynamics of Unentangled cis-1,4-Polyisoprene Confined to Nanoporous Alumina. Macromolecules 2014. [DOI: 10.1021/ma5006638] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - Martin Steinhart
- Institut
für Chemie neuer Materialien, Universität Osnabrück, D-49069 Osnabrück, Germany
| | - George Floudas
- Department
of Physics, University of Ioannina, 45110 Ioannina, Greece
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Yiannourakou M, Ungerer P, Leblanc B, Ferrando N, Teuler JM. Overview of MedeA®-GIBBS capabilities for thermodynamic property calculation and VLE behaviour description of pure compounds and mixtures: application to polar compounds generated from ligno-cellulosic biomass. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2013.830182] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Memari P, Lachet V, Klopffer MH, Flaconnèche B, Rousseau B. Gas mixture solubilities in polyethylene below its melting temperature: Experimental and molecular simulation studies. J Memb Sci 2012. [DOI: 10.1016/j.memsci.2011.11.035] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Hanson B, Pryamitsyn V, Ganesan V. Computer Simulations of Gas Diffusion in Polystyrene–C60 Fullerene Nanocomposites Using Trajectory Extending Kinetic Monte Carlo Method. J Phys Chem B 2011; 116:95-103. [DOI: 10.1021/jp209294t] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Ben Hanson
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Victor Pryamitsyn
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Venkat Ganesan
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
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Scoring function based on weighted residue network. Int J Mol Sci 2011; 12:8773-86. [PMID: 22272103 PMCID: PMC3257100 DOI: 10.3390/ijms12128773] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 11/04/2011] [Accepted: 11/28/2011] [Indexed: 11/17/2022] Open
Abstract
Molecular docking is an important method for the research of protein-protein interaction and recognition. A protein can be considered as a network when the residues are treated as its nodes. With the contact energy between residues as link weight, a weighted residue network is constructed in this paper. Two weighted parameters (strength and weighted average nearest neighbors' degree) are introduced into this model at the same time. The stability of a protein is characterized by its strength. The global topological properties of the protein-protein complex are reflected by the weighted average nearest neighbors' degree. Based on this weighted network model and these two parameters, a new docking scoring function is proposed in this paper. The scoring and ranking for 42 systems' bound and unbounded docking results are performed with this new scoring function. Comparing the results obtained from this new scoring function with that from the pair potentials scoring function, we found that this new scoring function has a similar performance to the pair potentials on some items, and this new scoring function can get a better success rate. The calculation of this new scoring function is easy, and the result of its scoring and ranking is acceptable. This work can help us better understand the mechanisms of protein-protein interactions and recognition.
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Metatla N, Soldera A. Effect of the Molar Volume on the Elastic Properties of Vinylic Polymers: A Static Molecular Modeling Approach. MACROMOL THEOR SIMUL 2011. [DOI: 10.1002/mats.201000088] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Abroshan H, Akbarzadeh H, Taherkhani F, Parsafar G. Effect of water–methanol content on the structure of Nafion in the sandwich model and solvent dynamics in nano-channels; a molecular dynamics study. Mol Phys 2011. [DOI: 10.1080/00268976.2010.549846] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Long M, Rogers SH, Thornthwaite DW, Livens FR, Rannard SP. Monitoring Atom Transfer Radical Polymerisation using14C-radiolabelled initiators. Polym Chem 2011. [DOI: 10.1039/c0py00275e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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14
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Abroshan H, Akbarzadeh H, Taherkhani F, Parsafar G. Effect of a monomeric sequence on the structure of hydrated Nafion in the sandwich model and solvent dynamics in nano-channels: a molecular dynamic study. Mol Phys 2010. [DOI: 10.1080/00268976.2010.511635] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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15
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Memari P, Lachet V, Rousseau B. Molecular simulations of the solubility of gases in polyethylene below its melting temperature. POLYMER 2010. [DOI: 10.1016/j.polymer.2010.08.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Majumder MK, S R, Mahajan DK, Basu S. Coarse-graining scheme for simulating uniaxial stress-strain response of glassy polymers through molecular dynamics. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 81:011803. [PMID: 20365391 DOI: 10.1103/physreve.81.011803] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Indexed: 05/29/2023]
Abstract
Simulation of the deformation of polymers below their glass transition through molecular dynamics provides an useful route to correlate their molecular architecture to deformation behavior. However, present computational capabilities severely restrict the time and length scales that can be simulated when detailed models of these macromolecules are used. Coarse-graining techniques for macromolecular structures intend to make bigger and longer simulations possible by grouping atoms into superatoms and devising ways of determining reasonable force fields for the superatoms in a manner that retains essential macromolecular features relevant to the process under study but jettisons unnecessary details. In this work we systematically develop a coarse-graining scheme aimed at simulating uniaxial stress-strain behavior of polymers below their glass transition. The scheme involves a two step process of obtaining the coarse grained force field parameters above glass transition. This seems to be enough to obtain "faithful" stress-strain responses after quenching to below the glass transition temperature. We apply the scheme developed to a commercially important polymer polystyrene, derive its complete force field parameters and thus demonstrate the effectiveness of the technique.
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Affiliation(s)
- Manoj K Majumder
- Department of Mechanical Engineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
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Karayiannis NC, Kröger M. Combined molecular algorithms for the generation, equilibration and topological analysis of entangled polymers: methodology and performance. Int J Mol Sci 2009; 10:5054-5089. [PMID: 20087477 PMCID: PMC2808023 DOI: 10.3390/ijms10115054] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2009] [Revised: 11/17/2009] [Accepted: 11/20/2009] [Indexed: 12/02/2022] Open
Abstract
We review the methodology, algorithmic implementation and performance characteristics of a hierarchical modeling scheme for the generation, equilibration and topological analysis of polymer systems at various levels of molecular description: from atomistic polyethylene samples to random packings of freely-jointed chains of tangent hard spheres of uniform size. Our analysis focuses on hitherto less discussed algorithmic details of the implementation of both, the Monte Carlo (MC) procedure for the system generation and equilibration, and a postprocessing step, where we identify the underlying topological structure of the simulated systems in the form of primitive paths. In order to demonstrate our arguments, we study how molecular length and packing density (volume fraction) affect the performance of the MC scheme built around chain-connectivity altering moves. In parallel, we quantify the effect of finite system size, of polydispersity, and of the definition of the number of entanglements (and related entanglement molecular weight) on the results about the primitive path network. Along these lines we approve main concepts which had been previously proposed in the literature.
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Affiliation(s)
- Nikos Ch. Karayiannis
- Institute for Optoelectronics and Microsystems (ISOM) and ETSII, Universidad Politécnica de Madrid (UPM), José Gutiérrez Abascal 2, E-28006 Madrid, Spain
| | - Martin Kröger
- Polymer Physics, Swiss Federal Institute of Technology, ETH Zurich, Wolfgang-Pauli-Strasse 10, 8049 Zurich, Switzerland
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Steinhauser MO, Schneider J, Blumen A. Simulating dynamic crossover behavior of semiflexible linear polymers in solution and in the melt. J Chem Phys 2009; 130:164902. [DOI: 10.1063/1.3111038] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Alemán C, Karayiannis NC, Curcó D, Foteinopoulou K, Laso M. Computer simulations of amorphous polymers: From quantum mechanical calculations to mesoscopic models. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2008.07.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Ramos J, Peristeras LD, Theodorou DN. Monte Carlo Simulation of Short Chain Branched Polyolefins in the Molten State. Macromolecules 2007. [DOI: 10.1021/ma071615k] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Javier Ramos
- Department of Materials Science and Engineering, School of Chemical Engineering, National Technical University of Athens, 9 Heroon Polytechniou Street, Zografou Campus, 15780 Athens, Greece and Department of Macromolecular Physics, Instituto de Estructura de la Materia, CSIC, Serrano 113 bis, 28006 Madrid, Spain
| | - Loukas D. Peristeras
- Department of Materials Science and Engineering, School of Chemical Engineering, National Technical University of Athens, 9 Heroon Polytechniou Street, Zografou Campus, 15780 Athens, Greece and Department of Macromolecular Physics, Instituto de Estructura de la Materia, CSIC, Serrano 113 bis, 28006 Madrid, Spain
| | - Doros N. Theodorou
- Department of Materials Science and Engineering, School of Chemical Engineering, National Technical University of Athens, 9 Heroon Polytechniou Street, Zografou Campus, 15780 Athens, Greece and Department of Macromolecular Physics, Instituto de Estructura de la Materia, CSIC, Serrano 113 bis, 28006 Madrid, Spain
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22
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Molecular simulation of the thermophysical properties of fluids: From understanding toward quantitative predictions. J Mol Liq 2007. [DOI: 10.1016/j.molliq.2006.12.019] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Advanced Monte Carlo Methods for the atomistic simulation of polymers with a linear or a non-linear molecular architecture. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/s1570-7946(06)80004-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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