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Karasawa N, Mitsutake A, Takano H. Intermediate scattering function for polymer molecules: An approach based on relaxation mode analysis. J Chem Phys 2024; 161:024902. [PMID: 38973764 DOI: 10.1063/5.0211504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 06/17/2024] [Indexed: 07/09/2024] Open
Abstract
The theory of polymer dynamics describes the intermediate scattering function for a polymer molecule in terms of relaxation modes defined by normal coordinates for the corresponding coarse-grained model. However, due to the difficulty of defining the normal coordinates for arbitrary polymer molecules, it is generally challenging to express the intermediate scattering function for a polymer molecule in terms of relaxation modes. To overcome this challenge, we propose a general method to calculate the intermediate scattering function for a polymer molecule on the basis of a relaxation mode analysis approach [Takano and Miyashita, J. Phys. Soc. Jpn. 64, 3688 (1995)]. In the proposed method, relaxation modes defined by eigenfunctions in a Markov process are evaluated on the basis of the simulation results for a polymer molecule and used to calculate the intermediate scattering function for that molecule. To demonstrate the effectiveness of the present method, we simulate the dynamics of a linear polymer molecule in a dilute solution and apply it to the calculation of the intermediate scattering function for the polymer molecule. The evaluation results regarding the relaxation modes reasonably describe the intermediate scattering function on the length scale of the radius of gyration of the polymer molecule. Accordingly, we examine the contributions of the pure relaxation and oscillatory relaxation processes to the entire intermediate scattering function.
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Affiliation(s)
- Naoyuki Karasawa
- Graduate School of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Ayori Mitsutake
- School of Science and Technology, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
| | - Hiroshi Takano
- Faculty of Science and Technology, Keio University, Minato-ku, Tokyo 108-8345, Japan
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Critical micelle concentration of SDS through DPD simulations using COSMO-RS–based interaction parameters, the thermal effects. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.128867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Wu Z, Müller-Plathe F. Slip-Spring Hybrid Particle-Field Molecular Dynamics for Coarse-Graining Branched Polymer Melts: Polystyrene Melts as an Example. J Chem Theory Comput 2022; 18:3814-3828. [PMID: 35617016 DOI: 10.1021/acs.jctc.2c00107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The topology of chains significantly modifies the dynamical properties of polymer melts. Here, we extend a recently developed efficient simulation method, namely the slip-spring hybrid particle-field (SS-hPF) model, to study the structural and dynamical properties of branched polymer melts over large spatial-temporal scales. In the coarse-grained SS-hPF simulation of polymers, the bonded potentials are derived by iterative Boltzmann inversion from the underlying fine-grained model. The nonbonded potentials are computed from a density functional field instead of pairwise interactions used in standard molecular dynamics simulations, which increases the computational efficiency by a factor of 10-20. The entangled dynamics is lost due to the soft-core nature of density functional field interactions. It is recovered by a multichain slip-spring model that is rigorously parametrized from existing experimental or simulation data. To quantitatively predict the relaxation and diffusion of branched polymers, which are dominated by arm retraction rather than chain reptation, the slip-spring algorithm is augmented to improve the polymer dynamics near the branch point. Multiple dynamical observables, e.g., diffusion coefficients, arm relaxations, and tube survival probabilities, are characterized in an example coarse-grained model of symmetric and asymmetric star-shaped polystyrene melts. Consistent dynamical behaviors are identified and compared with theoretical predictions. With a single rescaling factor, the prediction of diffusion coefficients agrees well with the available experimental measurements. In this work, an efficient approach is provided to build chemistry-specific coarse-grained models for predicting the dynamics of branched polymers.
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Affiliation(s)
- Zhenghao Wu
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Strasse 8, 64287 Darmstadt, Germany
| | - Florian Müller-Plathe
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Strasse 8, 64287 Darmstadt, Germany
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Hong W, Lin J, Tian X, Wang L. Linear and nonlinear viscoelasticity of self-associative hydrogen-bonded polymers. POLYMER 2021. [DOI: 10.1016/j.polymer.2021.124301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Paiva FL, Secchi AR, Calado V, Maia J, Khani S. Shear Flow and Relaxation Behaviors of Entangled Viscoelastic Nanorod-Stabilized Immiscible Polymer Blends. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c00030] [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)
- Felipe L. Paiva
- Department of Macromolecular Science and Engineering, Case Western Reserve University, 2100 Adelbert Road, Cleveland, Ohio 44106, United States
- School of Chemistry, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rua Horácio Macedo 2030, Rio de Janeiro, RJ 21941-909, Brazil
| | - Argimiro R. Secchi
- Chemical Engineering Graduate Program (COPPE), Universidade Federal do Rio de Janeiro, Cidade Universitária, Rua Horácio Macedo 2030, Rio de Janeiro, RJ 21941-909, Brazil
| | - Verônica Calado
- School of Chemistry, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rua Horácio Macedo 2030, Rio de Janeiro, RJ 21941-909, Brazil
| | - João Maia
- Department of Macromolecular Science and Engineering, Case Western Reserve University, 2100 Adelbert Road, Cleveland, Ohio 44106, United States
| | - Shaghayegh Khani
- Department of Macromolecular Science and Engineering, Case Western Reserve University, 2100 Adelbert Road, Cleveland, Ohio 44106, United States
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Effectiveness of coarse graining degree and speedup on the dynamic properties of homopolymer. J Mol Model 2021; 27:55. [PMID: 33511476 DOI: 10.1007/s00894-020-04661-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 12/20/2020] [Indexed: 10/22/2022]
Abstract
Evaluation of effective coarse graining (CG) degree and reasonable speedup relative to all-atomistic (AA) model was conducted to provide a basis for building appropriate larger-scale model. The reproducibility of atomistic conformation and temperature transferability both act as the analysis criteria to resolve the maximum acceptable CG degree. Taking short- and long time spans into account simultaneously in the estimation of computational speedup, a dynamic scaling factor is accessible in fitting mean squared displacement ratio of CG to AA as an exponential function. Computing loss in parallel running is an indispensable component in acceleration, which was also added in the evaluation. Subsequently, a quantified prediction of CG speedup arises as a multiplication of dynamic scaling factor, computing loss, time step, and the square of reduction in the number of degrees of freedom. Polyethylene oxide was adopted as a reference system to execute the direct Boltzmann inversion and iterative Boltzmann inversion. Bonded and non-bonded potentials were calculated in CG models with 1~4 monomers per bead. The effective CG degree was determined as two at the most with a speedup of four orders magnitude over AA in this study. Determination of effectiveness CG degree and the corresponding speedup prediction provide available tools in larger spatiotemporal-scale calculations.
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Goujon F, Martzel N, Dequidt A, Latour B, Garruchet S, Devémy J, Blaak R, Munch É, Malfreyt P. Backbone oriented anisotropic coarse grains for efficient simulations of polymers. J Chem Phys 2020; 153:214901. [PMID: 33291912 DOI: 10.1063/5.0019945] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Despite the fact that anisotropic particles have been introduced to describe molecular interactions for decades, they have been poorly used for polymers because of their computing time overhead and the absence of a relevant proof of their impact in this field. We first report a method using anisotropic beads for polymers, which solves the computing time issue by considering that beads keep their principal orientation alongside the mean local backbone vector of the polymer chain, avoiding the computation of torques during the dynamics. Applying this method to a polymer bulk, we study the effect of anisotropic interactions vs isotropic ones for various properties such as density, pressure, topology of the chain network, local structure, and orientational order. We show that for different classes of potentials traditionally used in molecular simulations, those backbone oriented anisotropic beads can solve numerous issues usually encountered with isotropic interactions. We conclude that the use of backbone oriented anisotropic beads is a promising approach for the development of realistic coarse-grained potentials for polymers.
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Affiliation(s)
- Florent Goujon
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Nicolas Martzel
- Manufacture Française des Pneumatiques Michelin, Site de Ladoux, 23 Place des Carmes Déchaux, France Cedex 9, 63040 Clermont-Ferrand, France
| | - Alain Dequidt
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Benoit Latour
- Manufacture Française des Pneumatiques Michelin, Site de Ladoux, 23 Place des Carmes Déchaux, France Cedex 9, 63040 Clermont-Ferrand, France
| | - Sébastien Garruchet
- Manufacture Française des Pneumatiques Michelin, Site de Ladoux, 23 Place des Carmes Déchaux, France Cedex 9, 63040 Clermont-Ferrand, France
| | - Julien Devémy
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Ronald Blaak
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Étienne Munch
- Manufacture Française des Pneumatiques Michelin, Site de Ladoux, 23 Place des Carmes Déchaux, France Cedex 9, 63040 Clermont-Ferrand, France
| | - Patrice Malfreyt
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
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Hagita K, Murashima T, Iwaoka N. Thinning Approximation for Calculating Two-Dimensional Scattering Patterns in Dissipative Particle Dynamics Simulations under Shear Flow. Polymers (Basel) 2018; 10:E1224. [PMID: 30961149 PMCID: PMC6290630 DOI: 10.3390/polym10111224] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 10/26/2018] [Accepted: 11/01/2018] [Indexed: 11/16/2022] Open
Abstract
Modifications to improve thinning approximation (TA) were considered in order to calculate two-dimensional scattering patterns (2DSPs) for dissipative particle dynamics (DPD) simulations of polymer melts under a shear flow. We proposed multipoint TA and adaptive TA because the bond lengths in DPD chains vary widely when compared to those in Kremer⁻Grest (KG) chains, and the effectiveness of these two types of TA for the two major DPD parameter sets were investigated. In this paper, we report our findings on the original DPD model with soft bonds and that with rigid bonds. Based on the behavior of the 2DSPs and the distribution of orientations of the bond vectors, two spot patterns originating from the oriented chain correlations were observed when distinct distributions of the highly oriented bond vectors in the shear direction were obtained. For multipoint TA, we concluded that at least two additional midpoints ( n mid ≥ 2 ) are required to clearly observe the two spot patterns. For adaptive TA, a dividing distance of l ATA ≤ 0.4 is sufficient for clear observation, which is consistent with the requirement of n mid ≥ 2 for multipoint TA.
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Affiliation(s)
- Katsumi Hagita
- Department of Applied Physics, National Defense Academy, Yokosuka 239-8686, Japan.
| | | | - Nobuyuki Iwaoka
- Department of Creative Engineering, Tsuruoka College, National Institute of Technology, Yamagata 997-8511, Japan.
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Hagita K, Shudo Y, Shibayama M. Two-dimensional scattering patterns and stress-strain relation of elongated clay nano composite gels: Molecular dynamics simulation analysis. POLYMER 2018. [DOI: 10.1016/j.polymer.2018.08.047] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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