1
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Christofi E, Bačová P, Harmandaris VA. Physics-Informed Deep Learning Approach for Reintroducing Atomic Detail in Coarse-Grained Configurations of Multiple Poly(lactic acid) Stereoisomers. J Chem Inf Model 2024; 64:1853-1867. [PMID: 38427962 DOI: 10.1021/acs.jcim.3c01870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
Multiscale modeling of complex molecular systems, such as macromolecules, encompasses methods that combine information from fine and coarse representations of molecules to capture material properties over a wide range of spatiotemporal scales. Being able to exchange information between different levels of resolution is essential for the effective transfer of this information. The inverse problem of reintroducing atomistic degrees of freedom in coarse-grained (CG) molecular configurations is particularly challenging as, from a mathematical point of view, it is an ill-posed problem; the forward mapping from the atomistic to the CG description is typically defined via a deterministic operator ("one-to-one" problem), whereas the reversed mapping from the CG to the atomistic model refers to creating one representative configuration out of many possible ones ("one-to-many" problem). Most of the backmapping methods proposed so far balance accuracy, efficiency, and general applicability. This is particularly important for macromolecular systems with different types of isomers, i.e., molecules that have the same molecular formula and sequence of bonded atoms (constitution) but differ in the three-dimensional configurations of their atoms in space. Here, we introduce a versatile deep learning approach for backmapping multicomponent CG macromolecules with chiral centers, trained to learn structural correlations between polymer configurations at the atomistic level and their corresponding CG descriptions. This method is intended to be simple and flexible while presenting a generic solution for resolution transformation. In addition, the method is aimed to respect the structural features of the molecule, such as local packing, capturing therefore the physical properties of the material. As an illustrative example, we apply the model on linear poly(lactic acid) (PLA) in melt, which is one of the most popular biodegradable polymers. The framework is tested on a number of model systems starting from homopolymer stereoisomers of PLA to copolymers with randomly placed chiral centers. The results demonstrate the efficiency and efficacy of the new approach.
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Affiliation(s)
- Eleftherios Christofi
- Computation-based Science and Technology Research Center, The Cyprus Institute, Nicosia 2121, Cyprus
| | - Petra Bačová
- Departamento de Ciencia de los Materiales e Ingeniería Metalúrgica y Química Inorgánica, Facultad de Ciencias, IMEYMAT, Campus Universitario Río San Pedro s/n., Puerto Real, Cádiz 11510, Spain
| | - Vagelis A Harmandaris
- Computation-based Science and Technology Research Center, The Cyprus Institute, Nicosia 2121, Cyprus
- Department of Mathematics and Applied Mathematics, University of Crete, Heraklion GR-71110, Greece
- Institute of Applied and Computational Mathematics, Foundation for Research and Technology - Hellas, Heraklion GR-71110, Crete, Greece
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2
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Ricci E, Vergadou N. Integrating Machine Learning in the Coarse-Grained Molecular Simulation of Polymers. J Phys Chem B 2023; 127:2302-2322. [PMID: 36888553 DOI: 10.1021/acs.jpcb.2c06354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Machine learning (ML) is having an increasing impact on the physical sciences, engineering, and technology and its integration into molecular simulation frameworks holds great potential to expand their scope of applicability to complex materials and facilitate fundamental knowledge and reliable property predictions, contributing to the development of efficient materials design routes. The application of ML in materials informatics in general, and polymer informatics in particular, has led to interesting results, however great untapped potential lies in the integration of ML techniques into the multiscale molecular simulation methods for the study of macromolecular systems, specifically in the context of Coarse Grained (CG) simulations. In this Perspective, we aim at presenting the pioneering recent research efforts in this direction and discussing how these new ML-based techniques can contribute to critical aspects of the development of multiscale molecular simulation methods for bulk complex chemical systems, especially polymers. Prerequisites for the implementation of such ML-integrated methods and open challenges that need to be met toward the development of general systematic ML-based coarse graining schemes for polymers are discussed.
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Affiliation(s)
- Eleonora Ricci
- Institute of Nanoscience and Nanotechnology, National Center for Scientific Research "Demokritos", GR-15341 Agia Paraskevi, Athens, Greece
- Institute of Informatics and Telecommunications, National Center for Scientific Research "Demokritos", GR-15341 Agia Paraskevi, Athens, Greece
| | - Niki Vergadou
- Institute of Nanoscience and Nanotechnology, National Center for Scientific Research "Demokritos", GR-15341 Agia Paraskevi, Athens, Greece
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3
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Svaneborg C, Everaers R. Multiscale equilibration of highly entangled isotropic model polymer melts. J Chem Phys 2023; 158:054903. [PMID: 36754791 DOI: 10.1063/5.0123431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We present a computationally efficient multiscale method for preparing equilibrated, isotropic long-chain model polymer melts. As an application, we generate Kremer-Grest melts of 1000 chains with 200 entanglements and 25 000-2000 beads/chain, which cover the experimentally relevant bending rigidities up to and beyond the limit of the isotropic-nematic transition. In the first step, we employ Monte Carlo simulations of a lattice model to equilibrate the large-scale chain structure above the tube scale while ensuring a spatially homogeneous density distribution. We then use theoretical insight from a constrained mode tube model to introduce the bead degrees of freedom together with random walk conformational statistics all the way down to the Kuhn scale of the chains. This is followed by a sequence of simulations with carefully parameterized force-capped bead-spring models, which slowly introduce the local bead packing while reproducing the larger-scale chain statistics of the target Kremer-Grest system at all levels of force-capping. Finally, we can switch to the full Kremer-Grest model without perturbing the structure. The resulting chain statistics is in excellent agreement with literature results on all length scales accessible in brute-force simulations of shorter chains.
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Affiliation(s)
- Carsten Svaneborg
- University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Ralf Everaers
- ENSL, CNRS, Laboratoire de Physique and Centre Blaise Pascal de l'École Normale Supérieure de Lyon, F-69342 Lyon, France
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4
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Topological Catenation Enhances Elastic Modulus of Single Linear Polycatenane. CHINESE JOURNAL OF POLYMER SCIENCE 2023. [DOI: 10.1007/s10118-023-2902-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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5
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Cai X, Liu H, Zhang G. Control of the threading ratio of rings in a polypseudorotaxane: A computer simulation study. POLYMER 2023. [DOI: 10.1016/j.polymer.2023.125705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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6
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Shmilovich K, Stieffenhofer M, Charron NE, Hoffmann M. Temporally Coherent Backmapping of Molecular Trajectories From Coarse-Grained to Atomistic Resolution. J Phys Chem A 2022; 126:9124-9139. [PMID: 36417670 PMCID: PMC9743211 DOI: 10.1021/acs.jpca.2c07716] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Coarse-graining offers a means to extend the achievable time and length scales of molecular dynamics simulations beyond what is practically possible in the atomistic regime. Sampling molecular configurations of interest can be done efficiently using coarse-grained simulations, from which meaningful physicochemical information can be inferred if the corresponding all-atom configurations are reconstructed. However, this procedure of backmapping to reintroduce the lost atomistic detail into coarse-grain structures has proven a challenging task due to the many feasible atomistic configurations that can be associated with one coarse-grain structure. Existing backmapping methods are strictly frame-based, relying on either heuristics to replace coarse-grain particles with atomic fragments and subsequent relaxation or parametrized models to propose atomic coordinates separately and independently for each coarse-grain structure. These approaches neglect information from previous trajectory frames that is critical to ensuring temporal coherence of the backmapped trajectory, while also offering information potentially helpful to producing higher-fidelity atomic reconstructions. In this work, we present a deep learning-enabled data-driven approach for temporally coherent backmapping that explicitly incorporates information from preceding trajectory structures. Our method trains a conditional variational autoencoder to nondeterministically reconstruct atomistic detail conditioned on both the target coarse-grain configuration and the previously reconstructed atomistic configuration. We demonstrate our backmapping approach on two exemplar biomolecular systems: alanine dipeptide and the miniprotein chignolin. We show that our backmapped trajectories accurately recover the structural, thermodynamic, and kinetic properties of the atomistic trajectory data.
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Affiliation(s)
- Kirill Shmilovich
- Pritzker
School of Molecular Engineering, University
of Chicago, Chicago, Illinois60637, United States,E-mail:
| | | | - Nicholas E. Charron
- Weiss
School of Natural Sciences, Department of Physics and Astronomy, Rice University, Houston, Texas77005, United States,Department
of Physics, Freie Universität Berlin, Berlin14195, Germany
| | - Moritz Hoffmann
- Fachbereich
Mathematik und Informatik, Freie Universität
Berlin, Berlin14195, Germany
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7
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Schmid F. Understanding and Modeling Polymers: The Challenge of Multiple Scales. ACS POLYMERS AU 2022. [DOI: 10.1021/acspolymersau.2c00049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Friederike Schmid
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudingerweg 9, 55128Mainz, Germany
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8
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Christofi E, Chazirakis A, Chrysostomou C, Nicolaou MA, Li W, Doxastakis M, Harmandaris VA. Deep convolutional neural networks for generating atomistic configurations of multi-component macromolecules from coarse-grained models. J Chem Phys 2022; 157:184903. [DOI: 10.1063/5.0110322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Despite the modern advances in the available computational resources, the length and time scales of the physical systems that can be studied in full atomic detail, via molecular simulations, are still limited. To overcome such limitations, coarse-grained (CG) models have been developed to reduce the dimensionality of the physical system under study. However, to study such systems at the atomic level, it is necessary to re-introduce the atomistic details into the CG description. Such an ill-posed mathematical problem is typically treated via numerical algorithms, which need to balance accuracy, efficiency, and general applicability. Here, we introduce an efficient and versatile method for backmapping multi-component CG macromolecules of arbitrary microstructures. By utilizing deep learning algorithms, we train a convolutional neural network to learn structural correlations between polymer configurations at the atomistic and their corresponding CG descriptions, obtained from atomistic simulations. The trained model is then utilized to get predictions of atomistic structures from input CG configurations. As an illustrative example, we apply the convolutional neural network to polybutadiene copolymers of various microstructures, in which each monomer microstructure (i.e., cis-1,4, trans-1,4, and vinyl-1,2) is represented as a different CG particle type. The proposed methodology is transferable over molecular weight and various microstructures. Moreover, starting from a specific single CG configuration with a given microstructure, we show that by modifying its chemistry (i.e., CG particle types), we are able to obtain a set of well equilibrated polymer configurations of different microstructures (chemistry) than the one of the original CG configuration.
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Affiliation(s)
- Eleftherios Christofi
- Computation-based Science and Technology Research Center, The Cyprus Institute, Nicosia 2121, Cyprus
| | - Antonis Chazirakis
- Department of Mathematics and Applied Mathematics, University of Crete, Heraklion GR-71110, Greece
- Institute of Applied and Computational Mathematics, Foundation for Research and Technology–Hellas, GR-71110 Heraklion, Crete, Greece
| | - Charalambos Chrysostomou
- Computation-based Science and Technology Research Center, The Cyprus Institute, Nicosia 2121, Cyprus
| | - Mihalis A. Nicolaou
- Computation-based Science and Technology Research Center, The Cyprus Institute, Nicosia 2121, Cyprus
| | - Wei Li
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo 001-0021, Japan
| | - Manolis Doxastakis
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Vagelis A. Harmandaris
- Computation-based Science and Technology Research Center, The Cyprus Institute, Nicosia 2121, Cyprus
- Department of Mathematics and Applied Mathematics, University of Crete, Heraklion GR-71110, Greece
- Institute of Applied and Computational Mathematics, Foundation for Research and Technology–Hellas, GR-71110 Heraklion, Crete, Greece
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9
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Kim Y, Joo S, Kim WK, Jeon JH. Active Diffusion of Self-Propelled Particles in Flexible Polymer Networks. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Yeongjin Kim
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang37673, Republic of Korea
| | - Sungmin Joo
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang37673, Republic of Korea
| | - Won Kyu Kim
- School of Computational Sciences, Korea Institute for Advanced Study (KIAS), Seoul02455, Republic of Korea
| | - Jae-Hyung Jeon
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang37673, Republic of Korea
- Asia Pacific Center for Theoretical Physics (APCTP), Pohang37673, Republic of Korea
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10
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Conformation and structure of ring polymers in semidilute solutions: A molecular dynamics simulation study. POLYMER 2022. [DOI: 10.1016/j.polymer.2022.124953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Wang J, in ’t Veld PJ, Robbins MO, Ge T. Effects of Coarse-Graining on Molecular Simulation of Craze Formation in Polymer Glass. Macromolecules 2022. [DOI: 10.1021/acs.macromol.1c01969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jiuling Wang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | | | - Mark O. Robbins
- Department of Physics and Astronomy, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Ting Ge
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
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12
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Dietz JD, Hoy RS. Facile equilibration of well-entangled semiflexible bead-spring polymer melts. J Chem Phys 2022; 156:014103. [PMID: 34998323 DOI: 10.1063/5.0072386] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The widely used double-bridging hybrid (DBH) method for equilibrating simulated entangled polymer melts [Auhl et al., J. Chem. Phys. 119, 12718-12728 (2003)] loses its effectiveness as chain stiffness increases into the semiflexible regime because the energy barriers associated with double-bridging Monte Carlo moves become prohibitively high. Here we overcome this issue by combining DBH with the use of core-softened pair potentials. This reduces the energy barriers substantially, allowing us to equilibrate melts with N ≃ 40Ne and chain stiffnesses all the way up to the isotropic-nematic transition using simulations of no more than 100 × 106 time steps. For semiflexible chains, our method is several times faster than the standard DBH; we exploit this speedup to develop improved expressions for Kremer-Grest melts' chain-stiffness-dependent Kuhn length ℓK and entanglement length Ne.
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Affiliation(s)
- Joseph D Dietz
- Department of Physics, University of South Florida, Tampa, Florida 33620, USA
| | - Robert S Hoy
- Department of Physics, University of South Florida, Tampa, Florida 33620, USA
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13
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Simu-D: A Simulator-Descriptor Suite for Polymer-Based Systems under Extreme Conditions. Int J Mol Sci 2021; 22:ijms222212464. [PMID: 34830346 PMCID: PMC8621175 DOI: 10.3390/ijms222212464] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/03/2021] [Accepted: 11/12/2021] [Indexed: 11/21/2022] Open
Abstract
We present Simu-D, a software suite for the simulation and successive identification of local structures of atomistic systems, based on polymers, under extreme conditions, in the bulk, on surfaces, and at interfaces. The protocol is built around various types of Monte Carlo algorithms, which include localized, chain-connectivity-altering, identity-exchange, and cluster-based moves. The approach focuses on alleviating one of the main disadvantages of Monte Carlo algorithms, which is the general applicability under a wide range of conditions. Present applications include polymer-based nanocomposites with nanofillers in the form of cylinders and spheres of varied concentration and size, extremely confined and maximally packed assemblies in two and three dimensions, and terminally grafted macromolecules. The main simulator is accompanied by a descriptor that identifies the similarity of computer-generated configurations with respect to reference crystals in two or three dimensions. The Simu-D simulator-descriptor can be an especially useful tool in the modeling studies of the entropy- and energy-driven phase transition, adsorption, and self-organization of polymer-based systems under a variety of conditions.
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14
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Dhamankar S, Webb MA. Chemically specific coarse‐graining of polymers: Methods and prospects. JOURNAL OF POLYMER SCIENCE 2021. [DOI: 10.1002/pol.20210555] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Satyen Dhamankar
- Department of Chemical and Biological Engineering Princeton University Princeton New Jersey USA
| | - Michael A. Webb
- Department of Chemical and Biological Engineering Princeton University Princeton New Jersey USA
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15
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16
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Berressem F, Scherer C, Andrienko D, Nikoubashman A. Ultra-coarse-graining of homopolymers in inhomogeneous systems. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 33:254002. [PMID: 33845463 DOI: 10.1088/1361-648x/abf6e2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
We develop coarse-grained (CG) models for simulating homopolymers in inhomogeneous systems, focusing on polymer films and droplets. If the CG polymers interact solely through two-body potentials, then the films and droplets either dissolve or collapse into small aggregates, depending on whether the effective polymer-polymer interactions have been determined from reference simulations in the bulk or at infinite dilution. To address this shortcoming, we include higher order interactions either through an additional three-body potential or a local density-dependent potential (LDP). We parameterize the two- and three-body potentials via force matching, and the LDP through relative entropy minimization. While the CG models with three-body interactions fail at reproducing stable polymer films and droplets, CG simulations with an LDP are able to do so. Minor quantitative differences between the reference and the CG simulations, namely a slight broadening of interfaces accompanied by a smaller surface tension in the CG simulations, can be attributed to the deformation of polymers near the interfaces, which cannot be resolved in the CG representation, where the polymers are mapped to spherical beads.
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Affiliation(s)
- Fabian Berressem
- Institute of Physics, Johannes Gutenberg University Mainz, Staudingerweg 7, 55128 Mainz, Germany
| | - Christoph Scherer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Denis Andrienko
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Arash Nikoubashman
- Institute of Physics, Johannes Gutenberg University Mainz, Staudingerweg 7, 55128 Mainz, Germany
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17
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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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18
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Ge T, Wang J, Robbins MO. Effects of Coarse-Graining on Molecular Simulations of Mechanical Properties of Glassy Polymers. Macromolecules 2021. [DOI: 10.1021/acs.macromol.0c02467] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ting Ge
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Jiuling Wang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Mark O. Robbins
- Department of Physics and Astronomy, Johns Hopkins University, Baltimore, Maryland 21218, United States
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19
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Abstract
Four decades of molecular theory and computation have helped form the modern understanding of the physical chemistry of organic semiconductors. Whereas these efforts have historically centered around characterizations of electronic structure at the single-molecule or dimer scale, emerging trends in noncrystalline molecular and polymeric semiconductors are motivating the need for modeling techniques capable of morphological and electronic structure predictions at the mesoscale. Provided the challenges associated with these prediction tasks, the community has begun to evolve a computational toolkit for organic semiconductors incorporating techniques from the fields of soft matter, coarse-graining, and machine learning. Here, we highlight recent advances in coarse-grained methodologies aimed at the multiscale characterization of noncrystalline organic semiconductors. As organic semiconductor performance is dependent on the interplay of mesoscale morphology and molecular electronic structure, specific emphasis is placed on coarse-grained modeling approaches capable of both structural and electronic predictions without recourse to all-atom representations.
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Affiliation(s)
- Nicholas E Jackson
- Department of Chemistry, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801, United States
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20
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Zhang J, Meyer H, Virnau P, Daoulas KC. Can Soft Models Describe Polymer Knots? Macromolecules 2020; 53:10475-10486. [PMID: 33335339 PMCID: PMC7735749 DOI: 10.1021/acs.macromol.0c02079] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/02/2020] [Indexed: 11/30/2022]
Abstract
Similar to macroscopic ropes and cables, long polymers create knots. We address the fundamental question whether and under which conditions it is possible to describe these intriguing objects with crude models that capture only mesoscale polymer properties. We focus on melts of long polymers which we describe by a model typical for mesoscopic simulations. A worm-like chain model defines the polymer architecture. To describe nonbonded interactions, we deliberately choose a generic "soft" repulsive potential that leads to strongly overlapping monomers and coarse local liquid structure. The soft model is parametrized to accurately reproduce mesoscopic structure and conformations of reference polymer melts described by a microscopic model. The microscopically resolved samples retain all generic features affecting polymer topology and provide, therefore, reliable reference data on knots. We compare characteristic knotting properties in mesoscopic and microscopically resolved melts for different cases of chain stiffness. We conclude that mesoscopic models can reliably describe knots in those melts, where the length scale characterizing polymer stiffness is substantially larger than the size of monomer-monomer excluded volume. In this case, simplified local liquid structure influences knotting properties only marginally. In contrast, mesoscopic models perform poorly in melts with flexible chains. We qualitatively explain our findings through a free energy model of simple knots available in the literature.
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Affiliation(s)
- Jianrui Zhang
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Hendrik Meyer
- Institut
Charles Sadron, CNRS UPR 22, Université
de Strasbourg, 23 rue du Loess, 67034 Strasbourg, France
| | - Peter Virnau
- Institut
für Physik, Johannes Gutenberg-Universität Mainz, Staudingerweg 9, 55128 Mainz, Germany
- Graduate
School of Excellence Materials Science in Mainz, Staudingerweg 7, 55128 Mainz, Germany
| | - Kostas Ch. Daoulas
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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21
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Stieffenhofer M, Wand M, Bereau T. Adversarial reverse mapping of equilibrated condensed-phase molecular structures. MACHINE LEARNING-SCIENCE AND TECHNOLOGY 2020. [DOI: 10.1088/2632-2153/abb6d4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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22
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Thaler S, Praprotnik M, Zavadlav J. Back-mapping augmented adaptive resolution simulation. J Chem Phys 2020; 153:164118. [PMID: 33138420 DOI: 10.1063/5.0025728] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Concurrent multiscale techniques such as Adaptive Resolution Scheme (AdResS) can offer ample computational advantages over conventional atomistic (AT) molecular dynamics simulations. However, they typically rely on aphysical hybrid regions to maintain numerical stability when high-resolution degrees of freedom (DOFs) are randomly re-inserted at the resolution interface. We propose an Energy Minimized AT (DOF) Insertion (EMATI) method that uses an informed rather than random AT DOF insertion to tackle the root cause of the issue, i.e., overlapping AT potentials. EMATI enables us to directly couple AT and coarse-grained resolutions without any modifications of the interaction potentials. We exemplify AdResS-EMATI in a system of liquid butane and show that it yields improved structural and thermodynamic properties at the interface compared to competing AdResS approaches. Furthermore, our approach extends the applicability of the AdResS without a hybrid region to systems for which force capping is inadequate.
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Affiliation(s)
- S Thaler
- Professorship of Multiscale Modeling of Fluid Materials, Department of Mechanical Engineering, Technical University of Munich, Munich, Germany
| | - M Praprotnik
- Laboratory for Molecular Modeling, National Institute of Chemistry, SI-1001 Ljubljana, Slovenia
| | - J Zavadlav
- Professorship of Multiscale Modeling of Fluid Materials, Department of Mechanical Engineering, Technical University of Munich, Munich, Germany
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23
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Hsu HP, Kremer K. Efficient equilibration of confined and free-standing films of highly entangled polymer melts. J Chem Phys 2020; 153:144902. [PMID: 33086819 DOI: 10.1063/5.0022781] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Equilibration of polymer melts containing highly entangled long polymer chains in confinement or with free surfaces is a challenge for computer simulations. We approach this problem by first studying polymer melts based on the soft-sphere coarse-grained model confined between two walls with periodic boundary conditions in two directions parallel to the walls. Then, we insert the microscopic details of the underlying bead-spring model. Tuning the strength of the wall potential, the monomer density of confined polymer melts in equilibrium is kept at the bulk density even near the walls. In a weak confining regime, we observe the same conformational properties of chains as in the bulk melt showing that our confined polymer melts have reached their equilibrated state. Our methodology provides an efficient way of equilibrating large polymer films with different thicknesses and is not confined to a specific underlying microscopic model. Switching off the wall potential in the direction perpendicular to the walls enables to study free-standing highly entangled polymer films or polymer films with one supporting substrate.
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Affiliation(s)
- Hsiao-Ping Hsu
- Max-Planck-Institut für Polymerforschung, Ackermannweg 10, 55128 Mainz, Germany
| | - Kurt Kremer
- Max-Planck-Institut für Polymerforschung, Ackermannweg 10, 55128 Mainz, Germany
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24
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Li W, Burkhart C, Polińska P, Harmandaris V, Doxastakis M. Backmapping coarse-grained macromolecules: An efficient and versatile machine learning approach. J Chem Phys 2020; 153:041101. [DOI: 10.1063/5.0012320] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Wei Li
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Craig Burkhart
- The Goodyear Tire and Rubber Company, Akron, Ohio 44305, USA
| | - Patrycja Polińska
- Goodyear Innovation Center Luxembourg, Avenue Gordon Smith, L-7750 Colmar-Berg, Luxembourg
| | - Vagelis Harmandaris
- Department of Applied Mathematics, University of Crete, and IACM FORTH, GR-71110 Heraklion, Greece
- Computation-Based Science and Technology Research Center, The Cyprus Institute, Nicosia 2121, Cyprus
| | - Manolis Doxastakis
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, USA
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25
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Shahidi N, Chazirakis A, Harmandaris V, Doxastakis M. Coarse-graining of polyisoprene melts using inverse Monte Carlo and local density potentials. J Chem Phys 2020; 152:124902. [PMID: 32241142 DOI: 10.1063/1.5143245] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Bottom-up coarse-graining of polymers is commonly performed by matching structural order parameters such as distribution of bond lengths, bending and dihedral angles, and pair distribution functions. In this study, we introduce the distribution of nearest-neighbors as an additional order parameter in the concept of local density potentials. We describe how the inverse-Monte Carlo method provides a framework for forcefield development that is capable of overcoming challenges associated with the parameterization of interaction terms in polymer systems. The technique is applied on polyisoprene melts as a prototype system. We demonstrate that while different forcefields can be developed that perform equally in terms of matching target distributions, the inclusion of nearest-neighbors provides a straightforward route to match both thermodynamic and conformational properties. We find that several temperature state points can also be addressed, provided that the forcefield is refined accordingly. Finally, we examine both the single-particle and the collective dynamics of the coarse-grain models, demonstrating that all forcefields present a similar acceleration relative to the atomistic systems.
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Affiliation(s)
- Nobahar Shahidi
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Antonis Chazirakis
- Department of Mathematics and Applied Mathematics, University of Crete, Heraklion GR-71110, Greece
| | - Vagelis Harmandaris
- Department of Mathematics and Applied Mathematics, University of Crete, Heraklion GR-71110, Greece
| | - Manolis Doxastakis
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, USA
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26
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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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27
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Nowak C, Misra M, Escobedo FA. Framework for Inverse Mapping Chemistry-Agnostic Coarse-Grained Simulation Models into Chemistry-Specific Models. J Chem Inf Model 2019; 59:5045-5056. [DOI: 10.1021/acs.jcim.9b00232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Christian Nowak
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Mayank Misra
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Fernando A. Escobedo
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
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28
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Vergadou N, Theodorou DN. Molecular Modeling Investigations of Sorption and Diffusion of Small Molecules in Glassy Polymers. MEMBRANES 2019; 9:E98. [PMID: 31398889 PMCID: PMC6723301 DOI: 10.3390/membranes9080098] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 11/16/2022]
Abstract
With a wide range of applications, from energy and environmental engineering, such as in gas separations and water purification, to biomedical engineering and packaging, glassy polymeric materials remain in the core of novel membrane and state-of the art barrier technologies. This review focuses on molecular simulation methodologies implemented for the study of sorption and diffusion of small molecules in dense glassy polymeric systems. Basic concepts are introduced and systematic methods for the generation of realistic polymer configurations are briefly presented. Challenges related to the long length and time scale phenomena that govern the permeation process in the glassy polymer matrix are described and molecular simulation approaches developed to address the multiscale problem at hand are discussed.
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Affiliation(s)
- Niki Vergadou
- Molecular Thermodynamics and Modelling of Materials Laboratory, Institute of Nanoscience and Nanotechnology, National Center for Scientific Research Demokritos, Aghia Paraskevi Attikis, GR-15310 Athens, Greece.
| | - Doros N Theodorou
- School of Chemical Engineering, National Technical University of Athens, GR 15780 Athens, Greece
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29
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Hall KW, Sirk TW, Klein ML, Shinoda W. A coarse-grain model for entangled polyethylene melts and polyethylene crystallization. J Chem Phys 2019; 150:244901. [PMID: 31255065 DOI: 10.1063/1.5092229] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The Shinoda-DeVane-Klein (SDK) model is herein demonstrated to be a viable coarse-grain model for performing molecular simulations of polyethylene (PE), affording new opportunities to advance molecular-level, scientific understanding of PE materials and processes. Both structural and dynamical properties of entangled PE melts are captured by the SDK model, which also recovers important aspects of PE crystallization phenomenology. Importantly, the SDK model can be used to represent a variety of materials beyond PE and has a simple functional form, making it unique among coarse-grain PE models. This study expands the suite of tools for studying PE in silico and paves the way for future work probing PE and PE-based composites at the molecular level.
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Affiliation(s)
- Kyle Wm Hall
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Timothy W Sirk
- U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005, USA
| | - Michael L Klein
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Wataru Shinoda
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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