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Zhu C, Wei N, Zhao J. Coarse-Grained Potentials of Poly(vinyl alcohol)/Graphene Oxide Interfaces. Macromolecules 2022. [DOI: 10.1021/acs.macromol.1c02117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chunhua Zhu
- Jiangsu Key Laboratory of Advanced Food Manufacturing Equipment and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Ning Wei
- Jiangsu Key Laboratory of Advanced Food Manufacturing Equipment and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Junhua Zhao
- Jiangsu Key Laboratory of Advanced Food Manufacturing Equipment and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Institute of Mechanics and Advanced Materials, School of Mechanical Engineering, Jiangnan University, Wuxi 214122, P. R. China
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2
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Szukalo RJ, Noid WG. Investigating the energetic and entropic components of effective potentials across a glass transition. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 33:154004. [PMID: 33498016 DOI: 10.1088/1361-648x/abdff8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/26/2021] [Indexed: 06/12/2023]
Abstract
By eliminating unnecessary details, coarse-grained (CG) models provide the necessary efficiency for simulating scales that are inaccessible to higher resolution models. However, because they average over atomic details, the effective potentials governing CG degrees of freedom necessarily incorporate significant entropic contributions, which limit their transferability and complicate the treatment of thermodynamic properties. This work employs a dual-potential approach to consider the energetic and entropic contributions to effective interaction potentials for CG models. Specifically, we consider one- and three-site CG models for ortho-terphenyl (OTP) both above and below its glass transition. We employ the multiscale coarse-graining (MS-CG) variational principle to determine interaction potentials that accurately reproduce the structural properties of an all-atom (AA) model for OTP at each state point. We employ an energy-matching variational principle to determine an energy operator that accurately reproduces the intra- and inter-molecular energy of the AA model. While the MS-CG pair potentials are almost purely repulsive, the corresponding pair energy functions feature a pronounced minima that corresponds to contacting benzene rings. These energetic functions then determine an estimate for the entropic component of the MS-CG interaction potentials. These entropic functions accurately predict the MS-CG pair potentials across a wide range of liquid state points at constant density. Moreover, the entropic functions also predict pair potentials that quite accurately model the AA pair structure below the glass transition. Thus, the dual-potential approach appears a promising approach for modeling AA energetics, as well as for predicting the temperature-dependence of CG effective potentials.
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Affiliation(s)
- Ryan J Szukalo
- Department of Chemistry, Penn State University, University Park, PA 16802 United States of America
| | - W G Noid
- Department of Chemistry, Penn State University, University Park, PA 16802 United States of America
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3
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Li Q, Guo Y, Tong J, He H, Zhang X, Huo F. Development of a coarse-grained force field model of polymeric 1-vinyl-3-ethylimidazolium tetrafluoroborate ionic liquids. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137656] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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4
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Alesadi A, Xia W. Understanding the Role of Cohesive Interaction in Mechanical Behavior of a Glassy Polymer. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c00067] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Amirhadi Alesadi
- Department of Civil & Environmental Engineering, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Wenjie Xia
- Department of Civil & Environmental Engineering, North Dakota State University, Fargo, North Dakota 58108, United States
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5
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Kubo A, Albina JM, Umeno Y. Construction of master yield stress curves for polycarbonate: A coarse-grained molecular dynamics study. POLYMER 2019. [DOI: 10.1016/j.polymer.2019.05.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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6
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Xia W, Hansoge NK, Xu WS, Phelan FR, Keten S, Douglas JF. Energy renormalization for coarse-graining polymers having different segmental structures. SCIENCE ADVANCES 2019; 5:eaav4683. [PMID: 31016241 PMCID: PMC6474771 DOI: 10.1126/sciadv.aav4683] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 03/05/2019] [Indexed: 05/23/2023]
Abstract
Multiscale coarse-grained (CG) modeling of soft materials, such as polymers, is currently an art form because CG models normally have significantly altered dynamics and thermodynamic properties compared to their atomistic counterparts. We address this problem by exploiting concepts derived from the generalized entropy theory (GET), emphasizing the central role of configurational entropy s c in the dynamics of complex fluids. Our energy renormalization (ER) method involves varying the cohesive interaction strength in the CG models in such a way that dynamic properties related to s c are preserved. We test this ER method by applying it to coarse-graining polymer melts (i.e., polybutadiene, polystyrene, and polycarbonate), representing polymer materials having a relatively low, intermediate, and high degree of glass "fragility". We find that the ER method allows the dynamics of the atomistic polymer models to be faithfully described to a good approximation by CG models over a wide temperature range.
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Affiliation(s)
- Wenjie Xia
- Department of Civil and Environmental Engineering, North Dakota State University, Fargo, ND 58108, USA
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Nitin K. Hansoge
- Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Wen-Sheng Xu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
| | - Frederick R. Phelan
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Sinan Keten
- Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Jack F. Douglas
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
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Jacinto-Méndez D, Villada-Balbuena M, Cruz y Cruz SG, Carbajal-Tinoco MD. Static structure of sodium polystyrene sulfonate solutions obtained through a coarse-grained model. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1471225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Damián Jacinto-Méndez
- Instituto Politécnico Nacional, UPIITA, Cd. de México, Mexico
- Departamento de Física, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Cd. de México, Mexico
| | - Mario Villada-Balbuena
- Departamento de Física, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Cd. de México, Mexico
| | | | - Mauricio D. Carbajal-Tinoco
- Departamento de Física, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Cd. de México, Mexico
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Villada-Balbuena M, Carbajal-Tinoco MD. One-bead coarse-grained model for RNA dynamics. J Chem Phys 2018; 146:045101. [PMID: 28147510 DOI: 10.1063/1.4974899] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We present a revised version of a coarse-grained model for RNA dynamics. In such approach, the description of nucleotides is reduced to single points that interact between them through a series of effective pair potentials that were obtained from an improved analysis of RNA structures from the Protein Data Bank. These interaction potentials are the main constituents of a Brownian dynamics simulation algorithm that allows to perform a variety of tasks by taking advantage of the reduced number of variables. Such tasks include the prediction of the three-dimensional configuration of a series of test molecules. Moreover, the model permits the inclusion of effective magnesium ions and the ends of the RNA chains can be pulled with an external force to study the process of unfolding. In spite of the simplicity of the model, we obtain a good agreement with the experimental results.
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Affiliation(s)
- Mario Villada-Balbuena
- Departamento de Física, Centro de Investigación y de Estudios Avanzados del IPN, Av. Instituto Politécnico Nacional No. 2508, Colonia San Pedro Zacatenco, CP 07360 Ciudad de México, Mexico
| | - Mauricio D Carbajal-Tinoco
- Departamento de Física, Centro de Investigación y de Estudios Avanzados del IPN, Av. Instituto Politécnico Nacional No. 2508, Colonia San Pedro Zacatenco, CP 07360 Ciudad de México, Mexico
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Banerjee P, Roy S, Nair N. Coarse-Grained Molecular Dynamics Force-Field for Polyacrylamide in Infinite Dilution Derived from Iterative Boltzmann Inversion and MARTINI Force-Field. J Phys Chem B 2018; 122:1516-1524. [PMID: 29278334 DOI: 10.1021/acs.jpcb.7b09019] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a mesoscale model of aqueous polyacrylamide in the infinitely dilute concentration regime, by combining an extant coarse-grained (CG) force-field, MARTINI, and the Iterative Boltzmann Inversion protocol (IBI). MARTINI force-field was used to retain the thermodynamics of solvation of the polymer in water, whereas the structural properties and intrapolymer interactions were optimized by IBI. Atomistic molecular dynamics simulations of polymer in water were performed to benchmark the mesoscale simulations. Our results from the CG model show excellent agreement in structure with the atomistic system. We also studied the dynamical behavior of our CG system by computing the shear viscosity and compared it with the standard IBI model. The viscosity trends of our model were similar to the atomistic system, whereas the standard IBI model was highly dissimilar as expected. In summary, our hybrid CG model sufficiently mimics an infinitely dilute system, and is superior to both MARTINI and IBI in representing the structure and thermodynamics of the atomistic system, respectively. Our hybrid coarse-graining strategy promises applicability in large-scale simulations of polymeric/biological systems where the structure needs to be replicated accurately while preserving the thermodynamics of a smoother surrounding.
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Affiliation(s)
- Pallavi Banerjee
- Shell Technology Center , Bande Kodigehalli, Bengaluru, Karnataka 562149, India.,Department of Chemistry, Indian Institute of Science Education and Research , Pune, 411008 Maharashtra, India
| | - Sudip Roy
- Shell Technology Center , Bande Kodigehalli, Bengaluru, Karnataka 562149, India
| | - Nitish Nair
- Shell Technology Center , Bande Kodigehalli, Bengaluru, Karnataka 562149, India
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Di Pasquale N, Carbone P. Local and global dynamics of multi-resolved polymer chains: Effects of the interactions atoms-beads on the dynamic of the chains. J Chem Phys 2017; 146:084905. [PMID: 28249431 DOI: 10.1063/1.4976645] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- N. Di Pasquale
- School of Chemistry, The University of Manchester, Manchester M13 9PL, United Kingdom
| | - P. Carbone
- School of Chemical Engineering and Analytical Science, The University of Manchester, Manchester M13 9PL, United Kingdom
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