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Prasitnok O, Prasitnok K. A Temperature-Transferable Coarse-Grained Model for Poly(lactic Acid) Melts. J Phys Chem B 2024; 128:7280-7289. [PMID: 38988099 DOI: 10.1021/acs.jpcb.4c03534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
We present a temperature-transferable coarse-grained (CG) model for poly(lactic acid) (PLA), specifically designed to replicate its volumetric properties and solubility parameter in the molten state. The CG-bonded potentials were derived by using the iterative Boltzmann inversion (IBI) optimization method to match structural properties from detailed atomistic models. A parametrization workflow was employed to determine nonbonded interaction parameters with temperature-dependent corrections that provide agreement with the target properties across the melting temperature range. The CG model successfully replicates key features of the PLA melt. It satisfactory reproduces the density and solubility parameter, maintains the dependence of chain conformation on molecular weight, and captures the dynamic behavior through agreement in scaled mean squared displacement and diffusion coefficients with the atomistic model. Additionally, the CG model offers much faster equilibration compared with the atomistic model. The proposed model is expected to be particularly useful for investigating the miscibility characteristics of PLA in various blends and composites that remain challenging to explore using fully atomistic simulations or experiments.
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Affiliation(s)
- Orrasa Prasitnok
- Multidisciplinary Research Unit of Pure and Applied Chemistry, Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahasarakham University, Maha Sarakham 44150, Thailand
| | - Khongvit Prasitnok
- Multidisciplinary Research Unit of Pure and Applied Chemistry, Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahasarakham University, Maha Sarakham 44150, Thailand
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2
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Wu C. Temperature-Transferable Coarse-Grained Models for Volumetric Properties of Poly(lactic Acid). J Phys Chem B 2024; 128:358-370. [PMID: 38153413 DOI: 10.1021/acs.jpcb.3c07026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
A new coarse-grained (CG) model, for which each monomer is mapped as one bead at its center of mass, was developed for simulating the volumetric properties of the polylactide (PLA) bulk. The three bonded CG potentials are first parametrized against the strain energies of the dimer, trimer, and tetramer, and the nonbonded CG potentials are then optimized to match the melt densities of the decamer. With the derived CG potentials, molecular dynamics (MD) simulations are found to reproduce thermal expansion and glass transition. By rescaling the dihedral and nonbonded potentials with temperature-independent factors, the glass transition temperature (Tg) is also satisfactorily restored with little modifications on the volumetric expansive coefficients at both rubbery and glassy states. Therefore, the finally optimized CG potentials exhibit excellent temperature transferability, as rationalized by the Simha-Boyer relation. Furthermore, it is confirmed that the dihedral torsions and nonbonded interactions play key roles in glass transition. Also, the simulated bulk moduli and conformational properties in a wide temperature range compare well with the referenced data. The proposed multiscale scheme has great potential in simulating thermo-mechanical properties of PLA and other polymers.
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Affiliation(s)
- Chaofu Wu
- Hunan Provincial Key Laboratory of Fine Ceramics and Powder Materials, School of Materials and Environmental Engineering, Hunan University of Humanities, Science and Technology, Loudi 417000, Hunan, P. R. China
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3
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Jin J, Hwang J, Voth GA. Gaussian representation of coarse-grained interactions of liquids: Theory, parametrization, and transferability. J Chem Phys 2023; 159:184105. [PMID: 37942867 DOI: 10.1063/5.0160567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 10/06/2023] [Indexed: 11/10/2023] Open
Abstract
Coarse-grained (CG) interactions determined via bottom-up methodologies can faithfully reproduce the structural correlations observed in fine-grained (atomistic resolution) systems, yet they can suffer from limited extensibility due to complex many-body correlations. As part of an ongoing effort to understand and improve the applicability of bottom-up CG models, we propose an alternative approach to address both accuracy and transferability. Our main idea draws from classical perturbation theory to partition the hard sphere repulsive term from effective CG interactions. We then introduce Gaussian basis functions corresponding to the system's characteristic length by linking these Gaussian sub-interactions to the local particle densities at each coordination shell. The remaining perturbative long-range interaction can be treated as a collective solvation interaction, which we show exhibits a Gaussian form derived from integral equation theories. By applying this numerical parametrization protocol to CG liquid systems, our microscopic theory elucidates the emergence of Gaussian interactions in common phenomenological CG models. To facilitate transferability for these reduced descriptions, we further infer equations of state to determine the sub-interaction parameter as a function of the system variables. The reduced models exhibit excellent transferability across the thermodynamic state points. Furthermore, we propose a new strategy to design the cross-interactions between distinct CG sites in liquid mixtures. This involves combining each Gaussian in the proper radial domain, yielding accurate CG potentials of mean force and structural correlations for multi-component systems. Overall, our findings establish a solid foundation for constructing transferable bottom-up CG models of liquids with enhanced extensibility.
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Affiliation(s)
- Jaehyeok Jin
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 5735 S. Ellis Ave., Chicago, Illinois 60637, USA
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, USA
| | - Jisung Hwang
- Department of Statistics, The University of Chicago, 5747 S. Ellis Ave., Chicago, Illinois 60637, USA
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 5735 S. Ellis Ave., Chicago, Illinois 60637, USA
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4
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Wang Y, Li Z, Sun D, Jiang N, Niu K, Giuntoli A, Xia W. Understanding the thermomechanical behavior of graphene-reinforced conjugated polymer nanocomposites via coarse-grained modeling. NANOSCALE 2023; 15:17124-17137. [PMID: 37850476 DOI: 10.1039/d3nr03618a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
Graphene-reinforced conjugated polymer (CP) nanocomposites are attractive for flexible and electronic devices, but their mechanical properties have been less explored at a fundamental level. Here, we present a predictive multiscale modeling framework for graphene-reinforced poly(3-alkylthiophene) (P3AT) nanocomposites via atomistically informed coarse-grained molecular dynamics simulations to investigate temperature-dependent thermomechanical properties at a molecular level. Our results reveal reduced graphene dispersion with increasing graphene loading. Nanocomposites with shorter P3AT side chains, lower temperatures, and higher graphene content exhibit stronger mechanical responses, which correlates with polymer dynamics. The elastic modulus increases linearly with the graphene content, which slightly deviates from the "Halpin-Tsai" micromechanical model prediction. Local stiffness analysis shows that graphene possesses the highest stiffness, followed by the P3AT backbone and side chains. Deformation-induced stronger chain alignment of the P3AT backbone compared to graphene may further promote conductive behavior. Our findings provide insights into the dynamical heterogeneity of nanocomposites, paving the way for understanding and predicting their thermomechanical properties.
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Affiliation(s)
- Yang Wang
- School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, 9747AG, The Netherlands.
| | - Zhaofan Li
- Department of Aerospace Engineering, Iowa State University, Ames, IA 50011, USA.
| | - Dali Sun
- Department of Electrical & Computer Engineering, University of Denver, Denver, CO 80210, USA
| | - Naisheng Jiang
- School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
| | - Kangmin Niu
- School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
| | - Andrea Giuntoli
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, 9747AG, The Netherlands.
| | - Wenjie Xia
- Department of Aerospace Engineering, Iowa State University, Ames, IA 50011, USA.
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5
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Johnson LC, Phelan FR. Comparison of Friction Parametrization from Dynamics and Material Properties for a Coarse-Grained Polymer Melt. J Phys Chem B 2023; 127:7054-7069. [PMID: 37523783 PMCID: PMC10472480 DOI: 10.1021/acs.jpcb.3c03273] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
In this work, we extend an approach to coarse-grained (CG) modeling for polymer melts in which the conservative potential is parametrized using the iterative Boltzmann inversion (IBI) method and the accelerated dynamics inherent to IBI are corrected using the dissipative Langevin thermostat with a single tunable friction parameter (J. Chem. Phys. 2021, 154, 084114). Diffusive measures from picoseconds to nanoseconds are used to determine the Langevin friction factor to apply to the CG model to recover all-atom (AA) dynamics; the resulting friction factors are then compared for consistency. Here, we additionally parametrize the CG dynamics using a material property, the zero-shear viscosity, which we measure using the Green-Kubo (GK) method. Two materials are studied, squalane as a function of temperature and the same polystyrene oligomers previously studied as a function of chain length. For squalane, the friction derived from the long-time diffusive measures and the viscosity all strongly increase with decreasing temperature, showing an Arrhenius-like dependence, and remain consistent with each other over the entire temperature range. In contrast, the friction required for the picosecond diffusive measurement, the Debye-Waller factor, is somewhat lower than the friction from long-time measures and relatively insensitive to temperature. A time-dependent friction would be required to exactly reproduce the AA measurements during the caging transition connecting these two extremes over the entire timespan at this level of coarse-graining. For the polystyrene oligomers for which we previously characterized the diffusive friction, the viscosity-parametrized frictions are consistent with the diffusive measures for the smallest chain length. However, for the longer chains, we find different trends based on measurement method with friction derived from rotational diffusion remaining nearly constant, friction derived from translational diffusion showing a modestly increasing trend, and viscosity-derived friction showing a modest decreasing trend. This seems to indicate that there is some sensitivity of the friction measurement method for systems with increased relaxation times and that in particular, the unsteady dynamics of the individual parametrization schemes plays a role in this. Increased difficulty in applying the GK method with increasing relaxation time of the longer chain systems is also discussed. Overall, we find that when the material is in a high-temperature melt state and the viscosity measurement is reliable, the friction parametrization from the diffusive friction measures is consistent and the lower cost diffusive parametrization is a reliable means for modeling viscosity. Our data give insight into the time-dependent friction one might compute using a non-Markovian approach to enable the recovery of AA dynamics over a wider range of time scales than can be computed using a single friction.
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Affiliation(s)
- Lilian C Johnson
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Frederick R Phelan
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
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6
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Bag S, Meinel MK, Müller-Plathe F. Toward a Mobility-Preserving Coarse-Grained Model: A Data-Driven Approach. J Chem Theory Comput 2022; 18:7108-7120. [PMID: 36449362 DOI: 10.1021/acs.jctc.2c00898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Coarse-grained molecular dynamics (MD) simulation is a promising alternative to all-atom MD simulation for the fast calculation of system properties, which is imperative in designing materials with a specific target property. There have been several coarse-graining strategies developed over the past few years that provide accurate structural properties of the system. However, these coarse-grained models share a major drawback in that they introduce an artificial acceleration in molecular mobility. In this paper, we report a data-driven approach to generate coarse-grained models that preserve the all-atom molecular mobility. We designed a machine learning model in the form of an artificial neural network, which directly predicts the simulation-ready mobility-preserving coarse-grained potential as an output given the all-atom force field (FF) parameters as inputs. As a proof of principle, we took 2,3,4-trimethylpentane as a model system and described the development of machine learning models in detail. We quantify the artificial acceleration in molecular mobility by defining the acceleration factor as the ratio of the coarse-grained and the all-atom diffusion coefficient. The predicted coarse-grained potential generated by the best machine learning model can bring down the acceleration factor to a value of ∼2, which could be otherwise as large as 7 for a typical value of 3 × 10-9 m2 s-1 for the all-atom diffusion coefficient. We believe our method will be of interest in the community as a route to generating coarse-grained potentials with accurate dynamics.
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Affiliation(s)
- Saientan Bag
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 8, 64287Darmstadt, Germany
| | - Melissa K Meinel
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 8, 64287Darmstadt, Germany
| | - Florian Müller-Plathe
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 8, 64287Darmstadt, Germany
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7
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Shamaprasad P, Frame CO, Moore TC, Yang A, Iacovella CR, Bouwstra JA, Bunge AL, McCabe C. Using molecular simulation to understand the skin barrier. Prog Lipid Res 2022; 88:101184. [PMID: 35988796 PMCID: PMC10116345 DOI: 10.1016/j.plipres.2022.101184] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 11/15/2022]
Abstract
Skin's effectiveness as a barrier to permeation of water and other chemicals rests almost entirely in the outermost layer of the epidermis, the stratum corneum (SC), which consists of layers of corneocytes surrounded by highly organized lipid lamellae. As the only continuous path through the SC, transdermal permeation necessarily involves diffusion through these lipid layers. The role of the SC as a protective barrier is supported by its exceptional lipid composition consisting of ceramides (CERs), cholesterol (CHOL), and free fatty acids (FFAs) and the complete absence of phospholipids, which are present in most biological membranes. Molecular simulation, which provides molecular level detail of lipid configurations that can be connected with barrier function, has become a popular tool for studying SC lipid systems. We review this ever-increasing body of literature with the goals of (1) enabling the experimental skin community to understand, interpret and use the information generated from the simulations, (2) providing simulation experts with a solid background in the chemistry of SC lipids including the composition, structure and organization, and barrier function, and (3) presenting a state of the art picture of the field of SC lipid simulations, highlighting the difficulties and best practices for studying these systems, to encourage the generation of robust reproducible studies in the future. This review describes molecular simulation methodology and then critically examines results derived from simulations using atomistic and then coarse-grained models.
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Affiliation(s)
- Parashara Shamaprasad
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235-1604, United States of America; Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, TN 37235-1604, United States of America
| | - Chloe O Frame
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235-1604, United States of America; Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, TN 37235-1604, United States of America
| | - Timothy C Moore
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235-1604, United States of America; Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, TN 37235-1604, United States of America
| | - Alexander Yang
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235-1604, United States of America; Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, TN 37235-1604, United States of America
| | - Christopher R Iacovella
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235-1604, United States of America; Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, TN 37235-1604, United States of America
| | - Joke A Bouwstra
- Division of BioTherapeutics, LACDR, Leiden University, 2333 CC Leiden, the Netherlands
| | - Annette L Bunge
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, CO 80401, United States of America
| | - Clare McCabe
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235-1604, United States of America; Multiscale Modeling and Simulation (MuMS) Center, Vanderbilt University, Nashville, TN 37235-1604, United States of America; School of Engineering and Physical Science, Heriot-Watt University, Edinburgh, United Kingdom.
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8
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Multiscale modeling of thermomechanical properties of stereoregular polymers. J Mol Model 2022; 28:214. [PMID: 35802186 DOI: 10.1007/s00894-022-05214-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 07/01/2022] [Indexed: 10/17/2022]
Abstract
Multiscale coarse-grained (CG) models are expected to play the critical roles in molecular simulations of complex polymers. However, this poses a great challenge for accurately simulating their thermomechanical properties, for which excellent representability and transferability are required for the CG potentials. In this work, virtual sites and elastic network bonds are introduced to improve the structural and volumetric property-based CG models including explicit electrostatic interactions, which is exemplarily applied to the iso- and syndio-tactic poly(methyl methacrylate). A variety of thermomechanical properties of the two stereoregular polymer bulks are reasonably reproduced by the extensive molecular dynamics simulations with the so-parameterized CG potentials. In particular, the attractive nature of electrostatic interactions and tacticity effects on glass transition temperatures (Tg) are well captured. Furthermore, stronger electrostatic interactions lead to higher mass density and bulk modulus, and their effects on Young's modulus, Poisson's ratio, and shear modulus depend upon the chain tacticity. It is also demonstrated that all these elastic constants can be effectively modulated by imposing external electric field. The proposed multiscale scheme can be very valuable to molecular designs of polar polymer materials.
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9
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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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10
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Elahi A, Bidault X, Chaudhuri S. Temperature-Transferable Coarse-Grained Model for Poly(propylene oxide) to Study Thermo-Responsive Behavior of Triblock Copolymers. J Phys Chem B 2022; 126:292-307. [PMID: 34982567 DOI: 10.1021/acs.jpcb.1c06318] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Thermo-responsive behavior of ethylene oxide (EO)-propylene oxide (PO) copolymers makes them suitable for many potential applications. Reproducing the origins of the tunable properties of EO-PO copolymers using coarse-grained (CG) models such as the MARTINI force field is critically important for building a better understanding of their behavior. In the present work, we have investigated the effects of coarse-graining on the water-polymer interaction across a temperature range. We compared the performance of different all-atom force fields to find the most appropriate one for the purpose of PO block parameterization in the MARTINI platform. We parameterized a CG temperature-dependent PO model based on the reproduction of the atomistic free energy of transfer of propylene oxide trimer from octane to water over a range of temperatures (20-60 °C) and compared the atomistic bond and angle distributions. Then, we used the model to study the effects of EO/PO ratio, molecular weight, and concentration on the thermo-responsive behavior of EO-PO copolymers in water. The results show an excellent agreement with experiments in different areas. Our temperature-dependent model reproduces (1) micellar phase above critical micelle temperature (CMT) and unimer phase below CMT for different Pluronics (a class of EO-PO triblock copolymers) spanning many EO/PO ratios and molecular weights; (2) spherical-to-rodlike micellar shape transition for Pluronics with 60 wt % of PO content or more; (3) diffusion coefficients for Pluronics with high PO content (P104 Pluronic with a PO mass of 3500 g mol-1) across a broad range of temperatures; and (4) micelle core size and micelle diameter similar to experimental results. Overall, our model improves the temperature sensitivity of EO-PO copolymers of existing models significantly, particularly for copolymers that are dominated by PO agents.
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Affiliation(s)
- Arash Elahi
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Xavier Bidault
- Department of Civil, Materials, and Environmental Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Santanu Chaudhuri
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States.,Department of Civil, Materials, and Environmental Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
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11
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In‐noi O, Prasitnok K. A Coarse‐Grained Model for
cis
‐Polyisoprene: Thermal Expansion and Glass Transition Temperature. MACROMOL THEOR SIMUL 2022. [DOI: 10.1002/mats.202100083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Orrasa In‐noi
- Department of Chemistry Faculty of Science Mahasarakham University Mahasarakham 44150 Thailand
| | - Khongvit Prasitnok
- Department of Chemistry Faculty of Science Mahasarakham University Mahasarakham 44150 Thailand
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12
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Pretti E, Shell MS. A microcanonical approach to temperature-transferable coarse-grained models using the relative entropy. J Chem Phys 2021; 155:094102. [PMID: 34496595 DOI: 10.1063/5.0057104] [Citation(s) in RCA: 15] [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 methods provide systematic tools for creating simplified models of molecular systems. However, coarse-grained (CG) models produced with such methods frequently fail to accurately reproduce all thermodynamic properties of the reference atomistic systems they seek to model and, moreover, can fail in even more significant ways when used at thermodynamic state points different from the reference conditions. These related problems of representability and transferability limit the usefulness of CG models, especially those of strongly state-dependent systems. In this work, we present a new strategy for creating temperature-transferable CG models using a single reference system and temperature. The approach is based on two complementary concepts. First, we switch to a microcanonical basis for formulating CG models, focusing on effective entropy functions rather than energy functions. This allows CG models to naturally represent information about underlying atomistic energy fluctuations, which would otherwise be lost. Such information not only reproduces energy distributions of the reference model but also successfully predicts the correct temperature dependence of the CG interactions, enabling temperature transferability. Second, we show that relative entropy minimization provides a direct and systematic approach to parameterize such classes of temperature-transferable CG models. We calibrate the approach initially using idealized model systems and then demonstrate its ability to create temperature-transferable CG models for several complex molecular liquids.
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Affiliation(s)
- Evan Pretti
- Department of Chemical Engineering, Engineering II Building, University of California, Santa Barbara, Santa Barbara, California 93106-5080, USA
| | - M Scott Shell
- Department of Chemical Engineering, Engineering II Building, University of California, Santa Barbara, Santa Barbara, California 93106-5080, USA
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13
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Wu C, Li K, Ning X, Zhang L. An Enhanced Scheme for Multiscale Modeling of Thermomechanical Properties of Polymer Bulks. J Phys Chem B 2021; 125:8612-8626. [PMID: 34291641 DOI: 10.1021/acs.jpcb.1c02663] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While multiscale modeling significantly enhances the capability of molecular simulations of polymer systems, it is well realized that the systematically derived coarse-grained (CG) models generally underestimate the thermomechanical properties. In this work, a charge-based mapping scheme has been adopted to include explicit electrostatic interactions and benchmarked against two typical polymers, atactic poly(methyl methacrylate) (PMMA) and polystyrene (PS). The CG potentials are parameterized against the oligomer bulks of nine monomers per chain to match the essential structural features and the two basic pressure-volume-temperature (PVT) properties, which are obtained from the all-atomistic (AA) molecular dynamics (MD) simulations at a single elevated temperature. The so-parameterized CG potentials are extended with the MD method to simulate the two polymer bulks of one hundred monomers per chain over a wide temperature range. Without any scaling, all the simulated results, including mass densities and bulk moduli at room temperature, thermal expansion coefficients at rubbery and glassy states, and glass transition temperatures (Tg), compare well with the corresponding experimental data. The proposed scheme not only contributes to realistically simulating various thermomechanical properties of both apolar and polar polymers but also allows for directly simulating their electrical properties.
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Affiliation(s)
- Chaofu Wu
- Hunan Provincial Key Laboratory of Fine Ceramics and Powder Materials, School of Materials and Environmental Engineering, Hunan University of Humanities, Science and Technology, Loudi, Hunan 417000, P. R. China
| | - Kewen Li
- Hunan Provincial Key Laboratory of Fine Ceramics and Powder Materials, School of Materials and Environmental Engineering, Hunan University of Humanities, Science and Technology, Loudi, Hunan 417000, P. R. China
| | - Xutao Ning
- Hunan Provincial Key Laboratory of Fine Ceramics and Powder Materials, School of Materials and Environmental Engineering, Hunan University of Humanities, Science and Technology, Loudi, Hunan 417000, P. R. China
| | - Lei Zhang
- Hunan Provincial Key Laboratory of Fine Ceramics and Powder Materials, School of Materials and Environmental Engineering, Hunan University of Humanities, Science and Technology, Loudi, Hunan 417000, P. R. China
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14
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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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15
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Johnson LC, Phelan FR. Dynamically consistent coarse-grain simulation model of chemically specific polymer melts via friction parameterization. J Chem Phys 2021; 154:084114. [PMID: 33639746 PMCID: PMC10075510 DOI: 10.1063/5.0034910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Coarse-grained (CG) models of polymers involve grouping many atoms in an all-atom (AA) representation into single sites to reduce computational effort yet retain the hierarchy of length and time scales inherent to macromolecules. Parameterization of such models is often via "bottom-up" methods, which preserve chemical specificity but suffer from artificially accelerated dynamics with respect to the AA model from which they were derived. Here, we study the combination of a bottom-up CG model with a dissipative potential as a means to obtain a chemically specific and dynamically correct model. We generate the conservative part of the force-field using the iterative Boltzmann inversion (IBI) method, which seeks to recover the AA structure. This is augmented with the dissipative Langevin thermostat, which introduces a single parameterizable friction factor to correct the unphysically fast dynamics of the IBI-generated force-field. We study this approach for linear polystyrene oligomer melts for three separate systems with 11, 21, and 41 monomers per chain and a mapping of one monomer per CG site. To parameterize the friction factor, target values are extracted from the AA dynamics using translational monomer diffusion, translational chain diffusion, and rotational chain motion to test the consistency of the parameterization across different modes of motion. We find that the value of the friction parameter needed to bring the CG dynamics in line with AA target values varies based on the mode of parameterization with short-time monomer translational dynamics requiring the highest values, long-time chain translational dynamics requiring the lowest values, and rotational dynamics falling in between. The friction ranges most widely for the shortest chains, and the span narrows with increasing chain length. For longer chains, a practical working value of the friction parameter may be derived from the rotational dynamics, owing to the contribution of multiple relaxation modes to chain rotation and a lack of sensitivity of the translational dynamics at these intermediate levels of friction. A study of equilibrium chain structure reveals that all chains studied are non-Gaussian. However, longer chains better approximate ideal chain dimensions than more rod-like shorter chains and thus are most closely described by a single friction parameter. We also find that the separability of the conservative and dissipative potentials is preserved.
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Affiliation(s)
- Lilian C Johnson
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Frederick R Phelan
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
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Jin J, Han Y, Pak AJ, Voth GA. A new one-site coarse-grained model for water: Bottom-up many-body projected water (BUMPer). I. General theory and model. J Chem Phys 2021; 154:044104. [PMID: 33514116 PMCID: PMC7826168 DOI: 10.1063/5.0026651] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 12/14/2020] [Indexed: 12/26/2022] Open
Abstract
Water is undoubtedly one of the most important molecules for a variety of chemical and physical systems, and constructing precise yet effective coarse-grained (CG) water models has been a high priority for computer simulations. To recapitulate important local correlations in the CG water model, explicit higher-order interactions are often included. However, the advantages of coarse-graining may then be offset by the larger computational cost in the model parameterization and simulation execution. To leverage both the computational efficiency of the CG simulation and the inclusion of higher-order interactions, we propose a new statistical mechanical theory that effectively projects many-body interactions onto pairwise basis sets. The many-body projection theory presented in this work shares similar physics from liquid state theory, providing an efficient approach to account for higher-order interactions within the reduced model. We apply this theory to project the widely used Stillinger-Weber three-body interaction onto a pairwise (two-body) interaction for water. Based on the projected interaction with the correct long-range behavior, we denote the new CG water model as the Bottom-Up Many-Body Projected Water (BUMPer) model, where the resultant CG interaction corresponds to a prior model, the iteratively force-matched model. Unlike other pairwise CG models, BUMPer provides high-fidelity recapitulation of pair correlation functions and three-body distributions, as well as N-body correlation functions. BUMPer extensively improves upon the existing bottom-up CG water models by extending the accuracy and applicability of such models while maintaining a reduced computational cost.
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Affiliation(s)
- Jaehyeok Jin
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
| | - Yining Han
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
| | - Alexander J. Pak
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
| | - Gregory A. Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
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Jin J, Yu A, Voth GA. Temperature and Phase Transferable Bottom-up Coarse-Grained Models. J Chem Theory Comput 2020; 16:6823-6842. [PMID: 32975948 DOI: 10.1021/acs.jctc.0c00832] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Despite the high fidelity of bottom-up coarse-grained (CG) approaches to recapitulate the structural correlations in atomistic simulations, the general use of bottom-up CG methods is limited because of the nontransferable nature of these CG models under different thermodynamic conditions. Because bottom-up CG potentials usually correspond to configuration-dependent free energies of the system, recent studies have focused on adjusting enthalpic or entropic contributions to account for issues with transferability. However, these approaches can require a manual adjustment of the CG interaction a priori and are usually limited to constant volume ensembles. To overcome these limitations, we construct temperature and phase transferable CG models under constant pressure by developing the ultra-coarse-graining (UCG) methodology in the mean-field limit. In the mean-field ansatz, an embedded semi-global order parameter recapitulates global changes to the system by automatically adjusting the effective CG interactions, thus bridging free energy decompositions with UCG theory. The method presented is designed to faithfully capture structural correlations under different thermodynamic conditions, using a single UCG model. Specifically, we test the applicability of the developed theory in three distinct cases: (1) different temperatures at constant pressure in liquids, (2) different temperatures across thermodynamic phases, and (3) liquid/vapor interfaces. We demonstrate that the systematic construction of both temperature and phase transferable bottom-up CG models is possible using this generalized UCG theory. Based on our findings, this approach significantly extends the transferability and applicability of the bottom-up CG theory and method.
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Affiliation(s)
- Jaehyeok Jin
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 5735 S. Ellis Avenue, Chicago, Illinois 60637, United States
| | - Alvin Yu
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 5735 S. Ellis Avenue, Chicago, Illinois 60637, United States
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 5735 S. Ellis Avenue, Chicago, Illinois 60637, United States
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18
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Investigating nature of stresses in extension and compression of glassy polymers via stress relaxation. POLYMER 2020. [DOI: 10.1016/j.polymer.2020.122517] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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19
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Wu C. Molecular-weight dependence of simulated glass transition temperature for isolated poly(ethylene oxide) chain. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1763986] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Chaofu Wu
- Hunan Provincial Key Laboratory of Fine Ceramics and Powder Materials, School of Materials and Environmental Engineering, Hunan University of Humanities, Science and Technology, Loudi, People’s Republic of China
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20
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Wu C. Tacticity Effects on Polymer Glass Transition Revisited by Coarse‐Grained Simulations. MACROMOL THEOR SIMUL 2020. [DOI: 10.1002/mats.202000001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Chaofu Wu
- Hunan Provincial Key Laboratory of Fine Ceramics and Powder MaterialsSchool of Materials and Environmental EngineeringHunan University of Humanities Science and Technology Loudi Hunan 417000 China
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Walker CC, Genzer J, Santiso EE. Extending the fused-sphere SAFT-γ Mie force field parameterization approach to poly(vinyl butyral) copolymers. J Chem Phys 2020; 152:044903. [DOI: 10.1063/1.5126213] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Affiliation(s)
- Christopher C. Walker
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Jan Genzer
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Erik E. Santiso
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, USA
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Meinel MK, Müller-Plathe F. Loss of Molecular Roughness upon Coarse-Graining Predicts the Artificially Accelerated Mobility of Coarse-Grained Molecular Simulation Models. J Chem Theory Comput 2020; 16:1411-1419. [DOI: 10.1021/acs.jctc.9b00943] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Melissa K. Meinel
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Profile Area Thermofluids and Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Strasse 8, D-64287 Darmstadt, Germany
| | - Florian Müller-Plathe
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Profile Area Thermofluids and Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Strasse 8, D-64287 Darmstadt, Germany
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23
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Xu W, Xia W. Energy Renormalization for Coarse‐Graining Polymers with Different Fragilities: Predictions from the Generalized Entropy Theory. MACROMOL THEOR SIMUL 2020. [DOI: 10.1002/mats.201900051] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- 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
| | - Wenjie Xia
- Department of Civil & Environmental Engineering North Dakota State University Fargo ND 58108 USA
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Lebold KM, Noid WG. Dual-potential approach for coarse-grained implicit solvent models with accurate, internally consistent energetics and predictive transferability. J Chem Phys 2019; 151:164113. [PMID: 31675902 DOI: 10.1063/1.5125246] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The dual-potential approach promises coarse-grained (CG) models that accurately reproduce both structural and energetic properties, while simultaneously providing predictive estimates for the temperature-dependence of the effective CG potentials. In this work, we examine the dual-potential approach for implicit solvent CG models that reflect large entropic effects from the eliminated solvent. Specifically, we construct implicit solvent models at various resolutions, R, by retaining a fraction 0.10 ≤ R ≤ 0.95 of the molecules from a simple fluid of Lennard-Jones spheres. We consider the dual-potential approach in both the constant volume and constant pressure ensembles across a relatively wide range of temperatures. We approximate the many-body potential of mean force for the remaining solutes with pair and volume potentials, which we determine via multiscale coarse-graining and self-consistent pressure-matching, respectively. Interestingly, with increasing temperature, the pair potentials appear increasingly attractive, while the volume potentials become increasingly repulsive. The dual-potential approach not only reproduces the atomic energetics but also quite accurately predicts this temperature-dependence. We also derive an exact relationship between the thermodynamic specific heat of an atomic model and the energetic fluctuations that are observable at the CG resolution. With this generalized fluctuation relationship, the approximate CG models quite accurately reproduce the thermodynamic specific heat of the underlying atomic model.
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Affiliation(s)
- Kathryn M Lebold
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, USA
| | - W G Noid
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, USA
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25
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Hansoge NK, Keten S. Effect of Polymer Chemistry on Chain Conformations in Hairy Nanoparticle Assemblies. ACS Macro Lett 2019; 8:1209-1215. [PMID: 35651164 DOI: 10.1021/acsmacrolett.9b00526] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Matrix-free, polymer-grafted nanoparticles, called hairy nanoparticle assemblies (aHNPs), have proven advantageous over traditional nanocomposites, as good dispersion and structural order can be achieved. Recent studies have shown that conformational changes in the polymer structure can lead to significant enhancements in the mechanical properties of aHNPs. To quantify how polymer chemistry affects the chain conformations in aHNPs, here we present a comparative analysis based on coarse-grained molecular dynamics simulations. Specifically, we compare the chain conformations in an anisotropic cellulose nanoparticle grafted to four common polymers with distinct chemical groups, fragility, and segmental structures, that is, poly(methyl methacrylate) (PMMA), polystyrene (PS), polycarbonate (PC), and polybutadiene (PB). We observe that semiflexible glassy polymers such as PMMA and PS have a higher critical chain length (Ncr), the transition point where the polymer conformation changes from concentrated to semidilute brush regime. Flexible rubbery polymers (PB) can overcome the Ncr barrier at relatively lower molecular weights. We have used theoretical scaling laws based on Daoud-Cotton theory to uncover a direct correlation between empirical constants and physical parameters, such as persistence length and monomer excluded volume. Furthermore, we carried out a systematic study to understand the role of backbone rigidity and side-group size of polymer, and it revealed that the backbone rigidity significantly affects Ncr but the side-group size doesn't seem to have an appreciable effect on Ncr. We find that normalization of the monomer radial distribution curves using Ncr and other key molecular parameters collapses the curves for 110 distinct model aHNP systems studied. Our work paves the way for systematic quantification of these molecular design parameters to accelerate the design of polymer-grafted nanoparticle assemblies in combination with universal scaling relationships.
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Affiliation(s)
- Nitin K. Hansoge
- Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3109, United States
- Center for Hierarchical Materials Design, Northwestern University, 2205 Tech Drive, Evanston, Illinois 60208-3109, United States
| | - Sinan Keten
- Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3109, United States
- Center for Hierarchical Materials Design, Northwestern University, 2205 Tech Drive, Evanston, Illinois 60208-3109, United States
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3109, United States
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Tamir E, Sidess A, Srebnik S. Thermodynamic, structural, and mechanical properties of fluoropolymers from molecular dynamics simulation: Comparison of force fields. Chem Eng Sci 2019. [DOI: 10.1016/j.ces.2019.05.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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27
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Xia W, Lan T. Interfacial Dynamics Governs the Mechanical Properties of Glassy Polymer Thin Films. Macromolecules 2019. [DOI: 10.1021/acs.macromol.9b01235] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wenjie Xia
- Department of Civil & Environmental Engineering, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Tian Lan
- Formulation, Automation & Materials Science, Core R&D, The Dow Chemical Company, 400 Arcola Rd., Collegeville, Pennsylvania 19426, United States
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28
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Pervaje AK, Walker CC, Santiso EE. Molecular simulation of polymers with a SAFT-γ Mie approach. MOLECULAR SIMULATION 2019. [DOI: 10.1080/08927022.2019.1645331] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Amulya K. Pervaje
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Christopher C. Walker
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Erik E. Santiso
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
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29
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Griffiths MZ, Shinoda W. tSPICA: Temperature- and Pressure-Dependent Coarse-Grained Force Field for Organic Molecules. J Chem Inf Model 2019; 59:3829-3838. [DOI: 10.1021/acs.jcim.9b00480] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Mark Z. Griffiths
- Department of Materials Chemistry, Nagoya University, Furo-cho Chikusa-ku, Nagoya 464-8603, Japan
| | - Wataru Shinoda
- Department of Materials Chemistry, Nagoya University, Furo-cho Chikusa-ku, Nagoya 464-8603, Japan
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30
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Hu C, Lu T, Guo H. Developing a Transferable Coarse-Grained Model for the Prediction of Thermodynamic, Structural, and Mechanical Properties of Polyimides at Different Thermodynamic State Points. J Chem Inf Model 2019; 59:2009-2025. [DOI: 10.1021/acs.jcim.8b00887] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chenchen Hu
- Beijing National Laboratory for Molecular Sciences, Joint Laboratory of Polymer Sciences and Materials, State Key Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Teng Lu
- Beijing National Laboratory for Molecular Sciences, Joint Laboratory of Polymer Sciences and Materials, State Key Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Hongxia Guo
- Beijing National Laboratory for Molecular Sciences, Joint Laboratory of Polymer Sciences and Materials, State Key Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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31
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Aggregation Behavior of Model Asphaltenes Revealed from Large-Scale Coarse-Grained Molecular Simulations. J Phys Chem B 2019; 123:2380-2396. [PMID: 30735393 DOI: 10.1021/acs.jpcb.8b12295] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fully atomistic simulations of models of asphaltenes in simple solvents have allowed the study of trends in aggregation phenomena to understand the underlying role played by molecular structure. The detail included at this scale of molecular modeling is, however, at odds with the required spatial and temporal resolution needed to fully understand asphaltene aggregation. The computational cost required to explore the relevant scales can be reduced by employing coarse-grained (CG) models, which consist of lumping a few atoms into a single segment that is characterized by effective interactions. In this work, CG force fields developed via the statistical associating fluid theory (SAFT-γ) [ Müller , E. A. ; Jackson , G. Annu. Rev. Chem. Biomol. Eng. 5 , 2014 , 405 - 427 ] equation of state (EoS) provide a reliable pathway to link the molecular description with macroscopic thermophysical data. A recent modification of the SAFT-VR EoS [ Müller , E. A. ; Mejía , A. Langmuir 33 , 2017 , 11518 - 11529 ], which allows for the parameterization of homonuclear rings, is selected as the starting point to develop CG models for polycyclic aromatic hydrocarbons. The new aromatic-core models, along with others published for simpler organic molecules, are adopted for the construction of asphaltene models by combining different chemical moieties in a group-contribution fashion. We apply the procedure to two previously reported asphaltene models and perform molecular dynamics simulations to validate the coarse-grained representation against benchmark systems of 27 asphaltenes in a pure solvent (toluene or heptane) described in a fully atomistic fashion. An excellent match between both levels of description is observed for the cluster size, radii of gyration, and relative-shape-anisotropy-factor distributions. We exploit the advantages of the CG representation by simulating systems containing up to 2000 asphaltene molecules in an explicit solvent investigating the effect of asphaltene concentration, solvent composition, and temperature on aggregation. By studying large systems facilitated by the use of CG models, we observe stable continuous distributions of molecular aggregates at conditions away from the two-phase precipitation point. As a further example application, a widely accepted interpretation of cluster-size distributions in asphaltenic systems is challenged by performing system-size tests, reversibility checks, and a time-dependence analysis. The proposed coarse-graining procedure is seen to be general and predictive and, hence, can be applied to other asphaltenic molecular structures.
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Liu N, Becton M, Zhang L, Chen H, Zeng X, Pidaparti R, Wang X. A coarse-grained model for mechanical behavior of phosphorene sheets. Phys Chem Chem Phys 2019; 21:1884-1894. [PMID: 30632560 DOI: 10.1039/c8cp06918b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The popularity of phosphorene (known as monolayer black phosphorus) in electronic devices relies on not only its superior electrical properties, but also its mechanical stability beyond the nanoscale. However, the mechanical performance of phosphorene beyond the nanoscale remains poorly explored owing to the spatiotemporal limitation of experimental observations, first-principles calculations, and atomistic simulations. To overcome this limitation, here a coarse-grained molecular dynamics (CG-MD) model is developed via a strain energy conservation approach to offer a new computational tool for the investigation of the mechanical properties of phosphorene beyond the nanoscale. The mechanical properties of a single phosphorene sheet are first characterized by all-atom molecular dynamics (AA-MD) simulations, followed by a force-field parameter optimization of the CG-MD model by matching these mechanical properties from AA-MD simulations. The intrinsic out-of-plane puckered feature is conserved in our CG-MD model, rendering mechanical anisotropy and heterogeneity in both the in-plane and out-of-plane directions preserved. The results indicate that our coarse-grained model is able to accurately capture the anisotropic in-plane mechanical performance of phosphorene and quantitatively reproduce Young's modulus, ultimate strength, and fracture strain under various environmental temperatures. Our CG-MD model can also capture the anisotropic out-of-plane bending stiffness of phosphorene. We demonstrate the applicability of our model in capturing the fracture toughness of phosphorene in both the armchair and zigzag directions by comparison with the results from AA-MD simulations. This CG-MD model proposed here offers greater capability to perform mechanical mesoscale simulations for phosphorene-based systems, allowing for a deeper understanding of the mechanical properties of phosphorene beyond the nanoscale, and the potential transferability of the developed force-field can help design hybrid phosphorene devices and structures.
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Affiliation(s)
- Ning Liu
- College of Engineering, University of Georgia, Athens, GA 30602, USA.
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33
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Lebold KM, Noid WG. Systematic study of temperature and density variations in effective potentials for coarse-grained models of molecular liquids. J Chem Phys 2019; 150:014104. [DOI: 10.1063/1.5050509] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Affiliation(s)
- Kathryn M. Lebold
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, USA
| | - W. G. Noid
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, USA
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34
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A multiscale scheme for simulating polymer Tg. J Mol Model 2018; 24:335. [DOI: 10.1007/s00894-018-3867-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/18/2018] [Indexed: 10/27/2022]
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35
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Salerno KM, Bernstein N. Role of many-body interactions in the structure of coarse-grained polymers. Phys Rev E 2018; 98:023310. [PMID: 30253532 DOI: 10.1103/physreve.98.023310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Indexed: 11/07/2022]
Abstract
In developing coarse-grained (CG) polymer models it is important to reproduce both local and molecule-scale structure. We develop a procedure for fast calculation of the bond-orientation correlation and the internal squared distance 〈R^{2}(M)〉 through evaluation of the probability distribution functions that represent a CG model. Different CG models inherently contain or omit correlations between CG variables. Here, we construct CG models that contain specific correlations between CG variables. The importance of different correlations is tested on CG models of polyethylene, polytetrafluoroethylene, and poly-L-lactic acid. The chain stiffness and 〈R^{2}(M)〉 are calculated using both analytic evaluation and Monte Carlo sampling, and approximate model results are compared with exact results from all-atom simulations. For polymers with an exponential correlation decay, the bond-orientation correlation and 〈R^{2}(M)〉 indicate which CG variable correlations are most important to reproduce molecule-scale structure. Analysis of the bond-orientation correlation and internal-squared distance indicates that for poly-L-lactic acid the bond-orientation correlation requires qualitatively different additional terms in CG models and quantifies the error in neglecting this important behavior.
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Affiliation(s)
- K Michael Salerno
- NRC Research Associate, Resident at Center for Computational Materials Science, Naval Research Laboratory, Washington, DC 20375
| | - Noam Bernstein
- US Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, DC 20375
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Dinpajooh M, Guenza MG. Coarse-graining simulation approaches for polymer melts: the effect of potential range on computational efficiency. SOFT MATTER 2018; 14:7126-7144. [PMID: 30070292 DOI: 10.1039/c8sm00868j] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The integral equation coarse-graining (IECG) approach is a promising high-level coarse-graining (CG) method for polymer melts, with variable resolution from soft spheres to multi CG sites, which preserves the structural and thermodynamical consistencies with the related atomistic simulations. When compared to the atomistic description, the procedure of coarse-graining results in smoother free energy surfaces, longer-ranged potentials, a decrease in the number of interaction sites for a given polymer, and more. Because these changes have competing effects on the computational efficiency of the CG model, care needs to be taken when studying the effect of coarse-graining on the computational speed-up in CG molecular dynamics simulations. For instance, treatment of long-range CG interactions requires the selection of cutoff distances that include the attractive part of the effective CG potential and force. In particular, we show how the complex nature of the range and curvature of the effective CG potential, the selection of a suitable CG timestep, the choice of the cutoff distance, the molecular dynamics algorithms, and the smoothness of the CG free energy surface affect the efficiency of IECG simulations. By direct comparison with the atomistic simulations of relatively short chain polymer melts, we find that the overall computational efficiency is highest for the highest level of CG (soft spheres), with an overall improvement of the computational efficiency being about 106-108 for various CG levels/resolutions. Therefore, the IECG method can have important applications in molecular dynamics simulations of polymeric systems. Finally, making use of the standard spatial decomposition algorithm, the parallel scalability of the IECG simulations for various levels of CG is presented. Optimal parallel scaling is observed for a reasonably large number of processors. Although this study is performed using the IECG approach, its results on the relation between the level of CG and the computational efficiency are general and apply to any properly-constructed CG model.
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Affiliation(s)
- Mohammadhasan Dinpajooh
- Department of Chemistry and Biochemistry, and Institute of Theoretical Science, University of Oregon, Eugene, Oregon 97403, USA.
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Hansoge NK, Huang T, Sinko R, Xia W, Chen W, Keten S. Materials by Design for Stiff and Tough Hairy Nanoparticle Assemblies. ACS NANO 2018; 12:7946-7958. [PMID: 29975847 DOI: 10.1021/acsnano.8b02454] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Matrix-free polymer-grafted nanocrystals, called assembled hairy nanoparticles (aHNPs), can significantly enhance the thermomechanical performance of nanocomposites by overcoming nanoparticle dispersion challenges and achieving stronger interfacial interactions through grafted polymer chains. However, effective strategies to improve both the mechanical stiffness and toughness of aHNPs are lacking given the general conflicting nature of these two properties and the large number of molecular parameters involved in the design of aHNPs. Here, we propose a computational framework that combines multiresponse Gaussian process metamodeling and coarse-grained molecular dynamics simulations to establish design strategies for achieving optimal mechanical properties of aHNPs within a parametric space. Taking poly(methyl methacrylate) grafted to high-aspect-ratio cellulose nanocrystals as a model nanocomposite, our multiobjective design optimization framework reveals that the polymer chain length and grafting density are the main influencing factors governing the mechanical properties of aHNPs, in comparison to the nanoparticle size and the polymer-nanoparticle interfacial interactions. In particular, the Pareto frontier, that marks the upper bound of mechanical properties within the design parameter space, can be achieved when the weight percentage of nanoparticles is above around 60% and the grafted chains exceed the critical length scale governing transition into the semidilute brush regime. We show that theoretical scaling relationships derived from the Daoud-Cotton model capture the dependence of the critical length scale on graft density and nanoparticle size. Our established modeling framework provides valuable insights into the mechanical behavior of these hairy nanoparticle assemblies at the molecular level and allows us to establish guidelines for nanocomposite design.
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Affiliation(s)
- Nitin K Hansoge
- Department of Mechanical Engineering , Northwestern University , 2145 Sheridan Road , Evanston , Illinois 60208-3109 , United States
| | - Tianyu Huang
- Department of Mechanical Engineering , Northwestern University , 2145 Sheridan Road , Evanston , Illinois 60208-3109 , United States
| | - Robert Sinko
- Department of Mechanical Engineering , Northwestern University , 2145 Sheridan Road , Evanston , Illinois 60208-3109 , United States
- Department of Mechanical Engineering , Northern Illinois University , 590 Garden Road , DeKalb , Illinois 60115 , United States
| | - Wenjie Xia
- Department of Civil and Environmental Engineering , North Dakota State University , 1410 14th Avenue N , Fargo , North Dakota 58105 , United States
- Center for Hierarchical Materials Design , Northwestern University , 2205 Tech Drive , Evanston , Illinois 60208-3109 , United States
| | - Wei Chen
- Department of Mechanical Engineering , Northwestern University , 2145 Sheridan Road , Evanston , Illinois 60208-3109 , United States
- Center for Hierarchical Materials Design , Northwestern University , 2205 Tech Drive , Evanston , Illinois 60208-3109 , United States
| | - Sinan Keten
- Department of Mechanical Engineering , Northwestern University , 2145 Sheridan Road , Evanston , Illinois 60208-3109 , United States
- Center for Hierarchical Materials Design , Northwestern University , 2205 Tech Drive , Evanston , Illinois 60208-3109 , United States
- Department of Civil and Environmental Engineering , Northwestern University , 2145 Sheridan Road , Evanston , Illinois 60208-3109 , United States
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39
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Multiscale modeling of glass transition in polymeric films: Application to stereoregular poly(methyl methacrylate)s. POLYMER 2018. [DOI: 10.1016/j.polymer.2018.05.036] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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40
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Salerno KM, Bernstein N. Persistence Length, End-to-End Distance, and Structure of Coarse-Grained Polymers. J Chem Theory Comput 2018. [DOI: 10.1021/acs.jctc.7b01229] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- K. Michael Salerno
- NRC Research Associate, Resident at Center for Computational Materials Science, US Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Noam Bernstein
- US Naval Research Laboratory, 4555 Overlook Ave SW, Washington, D.C. 20375, United States
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41
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Xia W, Song J, Hansoge NK, Phelan FR, Keten S, Douglas JF. Energy Renormalization for Coarse-Graining the Dynamics of a Model Glass-Forming Liquid. J Phys Chem B 2018; 122:2040-2045. [PMID: 29400063 PMCID: PMC6217959 DOI: 10.1021/acs.jpcb.8b00321] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Coarse-grained modeling achieves the enhanced computational efficiency required to model glass-forming materials by integrating out "unessential" molecular degrees of freedom, but no effective temperature transferable coarse-graining method currently exists to capture dynamics. We address this fundamental problem through an energy-renormalization scheme, in conjunction with the localization model of relaxation relating the Debye-Waller factor ⟨u2⟩ to the structural relaxation time τ. Taking ortho-terphenyl as a model small-molecule glass-forming liquid, we show that preserving ⟨u2⟩ (at picosecond time scale) under coarse-graining by renormalizing the cohesive interaction strength allows for quantitative prediction of both short- and long-time dynamics covering the entire temperature range of glass formation. Our findings provide physical insights into the dynamics of cooled liquids and make progress for building temperature-transferable coarse-grained models that predict key properties of glass-forming materials.
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Affiliation(s)
- Wenjie Xia
- Materials Science & Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
- Center for Hierarchical Materials Design, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3109, United States
- Department of Civil & Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3109, United States
| | - Jake Song
- Department of Materials Science & Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3109, United States
| | - Nitin K. Hansoge
- Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3109, United States
| | - Frederick R. Phelan
- Materials Science & Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Sinan Keten
- Department of Civil & Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3109, United States
- Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3109, United States
| | - Jack F. Douglas
- Materials Science & Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
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42
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Song J, Hsu DD, Shull KR, Phelan FR, Douglas JF, Xia W, Keten S. Energy Renormalization Method for the Coarse-Graining of Polymer Viscoelasticity. Macromolecules 2018; 51:10.1021/acs.macromol.7b02560. [PMID: 30996476 PMCID: PMC6463302 DOI: 10.1021/acs.macromol.7b02560] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Developing temperature transferable coarse-grained (CG) models is essential for the computational prediction of polymeric glass-forming (GF) material behavior, but their dynamics are often greatly altered from those of all-atom (AA) models mainly because of the reduced fluid configurational entropy under coarse-graining. To address this issue, we have recently introduced an energy renormalization (ER) strategy that corrects the activation free energy of the CG polymer model by renormalizing the cohesive interaction strength ε as a function of temperature T, i.e., ε(T), thus semiempirically preserving the T-dependent dynamics of the AA model. Here we apply our ER method to consider-in addition to T-dependency-the frequency f-dependent polymer viscoelasticity. Through smallamplitude oscillatory shear molecular dynamics simulations, we show that changing the imposed oscillation f on the CG systems requires changes in ε values (i.e., ε(T, f)) to reproduce the AA viscoelasticity. By accounting for the dynamic fragility of polymers as a material parameter, we are able to predict ε(T, f) under coarse-graining in order to capture the AA viscoelasticity, and consequently the activation energy, across a wide range of T and f in the GF regime. Specifically, we showcase our achievements on two representative polymers of distinct fragilities, polybutadiene (PB) and polystyrene (PS), and show that our CG models are able to sample viscoelasticity up to the megahertz regime, which approaches state-of-the-art experimental resolutions, and capture results sampled via AA simulations and prior experiments.
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Affiliation(s)
- Jake Song
- Department of Materials Science & Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3109, United States
| | - David D. Hsu
- Department of Physics and Engineering, Wheaton College, 501 College Avenue, Wheaton, Illinois 60187, United States
| | - Kenneth R. Shull
- Department of Materials Science & Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3109, United States
| | - Frederick R. Phelan
- Materials Science & Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Jack F. Douglas
- Materials Science & Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Wenjie Xia
- Department of Civil & Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3109, United States
- Center for Hierarchical Materials Design, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3109, United States
- Materials Science & Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Sinan Keten
- Department of Civil & Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3109, United States
- Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3109, United States
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43
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Wu C. Multiscale Modeling Scheme for Simulating Polymeric Melts: Application to Poly(Ethylene Oxide). MACROMOL THEOR SIMUL 2017. [DOI: 10.1002/mats.201700066] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- C. Wu
- Hunan Provincial Key Laboratory of Fine Ceramics and Powder Materials; Hunan University of Humanities Science & Technology; Dixing Road 487, Louxing District Loudi 417000 Hunan Province P. R. China
- College of Materials and Environment Engineering; Hunan University of Humanities Science & Technology; Dixing Road 487, Louxing District Loudi 417000 Hunan Province P. R. China
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Dinpajooh M, Guenza MG. On the Density Dependence of the Integral Equation Coarse-Graining Effective Potential. J Phys Chem B 2017; 122:3426-3440. [DOI: 10.1021/acs.jpcb.7b10494] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mohammadhasan Dinpajooh
- Department of Chemistry and Biochemistry, and Institute of Theoretical Science, University of Oregon, Eugene, Oregon 97403, United States
| | - Marina G. Guenza
- Department of Chemistry and Biochemistry, and Institute of Theoretical Science, University of Oregon, Eugene, Oregon 97403, United States
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45
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Li B, Chen Q, Huang S, Liu H. Developing structure and thermodynamic properties-consistent coarse-grained model for random copolymer systems. POLYMER 2017. [DOI: 10.1016/j.polymer.2017.07.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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46
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Jiménez-Serratos G, Herdes C, Haslam AJ, Jackson G, Müller EA. Group Contribution Coarse-Grained Molecular Simulations of Polystyrene Melts and Polystyrene Solutions in Alkanes Using the SAFT-γ Force Field. Macromolecules 2017. [DOI: 10.1021/acs.macromol.6b02072] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Carmelo Herdes
- Department
of Chemical Engineering, University of Bath, Bath BA2 7AY, U.K
| | - Andrew J. Haslam
- Department
of Chemical Engineering, Imperial College London, London SW7 2AZ, U.K
| | - George Jackson
- Department
of Chemical Engineering, Imperial College London, London SW7 2AZ, U.K
| | - Erich A. Müller
- Department
of Chemical Engineering, Imperial College London, London SW7 2AZ, U.K
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47
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Patrone PN, Rosch TW, Phelan FR. Bayesian calibration of coarse-grained forces: Efficiently addressing transferability. J Chem Phys 2017; 144:154101. [PMID: 27389203 DOI: 10.1063/1.4945380] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Generating and calibrating forces that are transferable across a range of state-points remains a challenging task in coarse-grained (CG) molecular dynamics. In this work, we present a coarse-graining workflow, inspired by ideas from uncertainty quantification and numerical analysis, to address this problem. The key idea behind our approach is to introduce a Bayesian correction algorithm that uses functional derivatives of CG simulations to rapidly and inexpensively recalibrate initial estimates f0 of forces anchored by standard methods such as force-matching. Taking density-temperature relationships as a running example, we demonstrate that this algorithm, in concert with various interpolation schemes, can be used to efficiently compute physically reasonable force curves on a fine grid of state-points. Importantly, we show that our workflow is robust to several choices available to the modeler, including the interpolation schemes and tools used to construct f0. In a related vein, we also demonstrate that our approach can speed up coarse-graining by reducing the number of atomistic simulations needed as inputs to standard methods for generating CG forces.
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Affiliation(s)
- Paul N Patrone
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Thomas W Rosch
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Frederick R Phelan
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
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48
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Xia W, Song J, Jeong C, Hsu DD, Phelan FR, Douglas JF, Keten S. Energy-Renormalization for Achieving Temperature Transferable Coarse-Graining of Polymer Dynamics. Macromolecules 2017; 50:10.1021/acs.macromol.7b01717. [PMID: 30996475 PMCID: PMC6463524 DOI: 10.1021/acs.macromol.7b01717] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The bottom-up prediction of the properties of polymeric materials based on molecular dynamics simulation is a major challenge in soft matter physics. Coarse-grained (CG) models are often employed to access greater spatiotemporal scales required for many applications, but these models normally experience significantly altered thermodynamics and highly accelerated dynamics due to the reduced number of degrees of freedom upon coarse-graining. While CG models can be calibrated to meet certain properties at particular state points, there is unfortunately no temperature transferable and chemically specific coarse-graining method that allows for modeling of polymer dynamics over a wide temperature range. Here, we pragmatically address this problem by "correcting" for deviations in activation free energies that occur upon coarse-graining the dynamics of a model polymeric material (polystyrene). In particular, we propose a new strategy based on concepts drawn from the Adam-Gibbs (AG) theory of glass formation. Namely we renormalize the cohesive interaction strength and effective interaction length-scale parameters to modify the activation free energy. We show that this energy-renormalization method for CG modeling allows accurate prediction of atomistic dynamics over the Arrhenius regime, the non-Arrhenius regime of glass formation, and even the non-equilibrium glassy regime, thus allowing for the predictive modeling of dynamic properties of polymer over the entire range of glass formation. Our work provides a practical scheme for establishing temperature transferable coarse-grained models for predicting and designing the properties of polymeric materials.
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Affiliation(s)
- Wenjie Xia
- Materials Science & Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
- Department of Civil & Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3109, United States
- Center for Hierarchical Materials Design, Northwestern University, Evanston, Illinois 60208-3109, United States
| | - Jake Song
- Department of Materials Science & Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3109, United States
| | - Cheol Jeong
- Materials Science & Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - David D. Hsu
- Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3109, United States
| | - Frederick R. Phelan
- Materials Science & Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Jack F. Douglas
- Materials Science & Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Sinan Keten
- Department of Civil & Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3109, United States
- Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3109, United States
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49
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Xie Z, Chai D, Wang Y, Tan H. Directly Modifying the Nonbonded Potential Based on the Standard Iterative Boltzmann Inversion Method for Coarse-Grained Force Fields. J Phys Chem B 2016; 120:11834-11844. [PMID: 27766876 DOI: 10.1021/acs.jpcb.6b06457] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Effective potentials are of great importance for coarse-grained (CG) simulations, which can be obtained by the structure-based iterative Boltzmann inversion (IBI) method. However, the standard IBI method is incapable of maintaining the mechanical and thermodynamic properties of the CG model in agreement with those of the all-atom model. Unlike the existing techniques, such as introducing friction force as the dissipative force to reduce the superatom motion while keeping the conservative force arising from the CG potential intact, we directly modified the standard IBI nonbonded potential by adding an empirical function. According to an analysis of the dissipative particle dynamics, the additional function did compensate for the friction reduction of the standard IBI CG model. In this work, the thermal fluctuation information from the nonbonded radial distribution function was incorporated into the additional empirical function. As an illustration of the new CG force fields, we presented simulations of the stress-strain relation and thermodynamic properties in terms of cis-polyisoprene and compared the statistical structure information of the superatoms with those of the IBI CG model and the all-atom model. It should be emphasized that the additional empirical function contributed to compensating for the friction reduction, irrespective of the functional form it took. In this sense, the proposed method was easily operable.
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Affiliation(s)
- Zhimin Xie
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environment, Center for Composite Materials and Structures, Harbin Institute of Technology , Harbin 150001, People's Republic of China
| | - Dongliang Chai
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environment, Center for Composite Materials and Structures, Harbin Institute of Technology , Harbin 150001, People's Republic of China
| | - Youshan Wang
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environment, Center for Composite Materials and Structures, Harbin Institute of Technology , Harbin 150001, People's Republic of China
| | - Huifeng Tan
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environment, Center for Composite Materials and Structures, Harbin Institute of Technology , Harbin 150001, People's Republic of China
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50
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Agrawal V, Peralta P, Li Y, Oswald J. A pressure-transferable coarse-grained potential for modeling the shock Hugoniot of polyethylene. J Chem Phys 2016; 145:104903. [DOI: 10.1063/1.4962255] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Vipin Agrawal
- School for the Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, USA
| | - Pedro Peralta
- School for the Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, USA
| | - Yiyang Li
- School for the Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, USA
| | - Jay Oswald
- School for the Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, USA
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