1
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Jin J, Voth GA. Understanding dynamics in coarse-grained models. IV. Connection of fine-grained and coarse-grained dynamics with the Stokes-Einstein and Stokes-Einstein-Debye relations. J Chem Phys 2024; 161:034114. [PMID: 39012809 DOI: 10.1063/5.0212973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 06/28/2024] [Indexed: 07/18/2024] Open
Abstract
Applying an excess entropy scaling formalism to the coarse-grained (CG) dynamics of liquids, we discovered that missing rotational motions during the CG process are responsible for artificially accelerated CG dynamics. In the context of the dynamic representability between the fine-grained (FG) and CG dynamics, this work introduces the well-known Stokes-Einstein and Stokes-Einstein-Debye relations to unravel the rotational dynamics underlying FG trajectories, thereby allowing for an indirect evaluation of the effective rotations based only on the translational information at the reduced CG resolution. Since the representability issue in CG modeling limits a direct evaluation of the shear stress appearing in the Stokes-Einstein and Stokes-Einstein-Debye relations, we introduce a translational relaxation time as a proxy to employ these relations, and we demonstrate that these relations hold for the ambient conditions studied in our series of work. Additional theoretical links to our previous work are also established. First, we demonstrate that the effective hard sphere radius determined by the classical perturbation theory can approximate the complex hydrodynamic radius value reasonably well. Furthermore, we present a simple derivation of an excess entropy scaling relationship for viscosity by estimating the elliptical integral of molecules. In turn, since the translational and rotational motions at the FG level are correlated to each other, we conclude that the "entropy-free" CG diffusion only depends on the shape of the reference molecule. Our results and analyses impart an alternative way of recovering the FG diffusion from the CG description by coupling the translational and rotational motions at the hydrodynamic level.
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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
- Department of Chemistry, Columbia University, New York, New York 10027, 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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2
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Bag S, Meinel MK, Müller-Plathe F. Synthetic Force-Field Database for Training Machine Learning Models to Predict Mobility-Preserving Coarse-Grained Molecular-Simulation Potentials. J Chem Theory Comput 2024; 20:3046-3060. [PMID: 38593205 DOI: 10.1021/acs.jctc.4c00242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Balancing accuracy and efficiency is a common problem in molecular simulation. This tradeoff is evident in coarse-grained molecular dynamics simulation, which prioritizes efficiency, and all-atom molecular simulation, which prioritizes accuracy. Despite continuous efforts, creating a coarse-grained model that accurately captures both the system's structure and dynamics remains elusive. In this article, we present a data-driven approach for constructing coarse-grained models that aim to describe both the structure and dynamics of the system equally well. While the development of machine learning models is well-received in the scientific community, the significance of dataset creation for these models is often overlooked. However, data-driven approaches cannot progress without a robust dataset. To address this, we construct a database of synthetic coarse-grained potentials generated from unphysical all-atom models. A neural network is trained with the generated database to predict the coarse-grained potentials of real liquids. We evaluate their quality by calculating the combined loss of structural and dynamical accuracy upon coarse-graining. When we compare our machine learning-based coarse-grained potential with the one from iterative Boltzmann inversion, the machine learning prediction turns out better for all eight hydrocarbon liquids we studied. As all-atom surfaces turn more nonspherical, both ways of coarse-graining degrade. Still, the neural network outperforms iterative Boltzmann inversion in constructing good quality coarse-grained models for such cases. The synthetic database and the developed machine learning models are freely available to the community, and we believe that our approach will generate interest in efficiently deriving accurate coarse-grained models for liquids.
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Affiliation(s)
- Saientan Bag
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Peter-Grünberg-Str. 8, 64287 Darmstadt, Germany
| | - Melissa K Meinel
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Peter-Grünberg-Str. 8, 64287 Darmstadt, Germany
| | - Florian Müller-Plathe
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Peter-Grünberg-Str. 8, 64287 Darmstadt, Germany
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3
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Wu Z, Zhou T. Structural Coarse-Graining via Multiobjective Optimization with Differentiable Simulation. J Chem Theory Comput 2024; 20:2605-2617. [PMID: 38483262 DOI: 10.1021/acs.jctc.3c01348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
In the realm of multiscale molecular simulations, structure-based coarse-graining is a prominent approach for creating efficient coarse-grained (CG) representations of soft matter systems, such as polymers. This involves optimizing CG interactions by matching static correlation functions of the corresponding degrees of freedom in all-atom (AA) models. Here, we present a versatile method, namely, differentiable coarse-graining (DiffCG), which combines multiobjective optimization and differentiable simulation. The DiffCG approach is capable of constructing robust CG models by iteratively optimizing the effective potentials to simultaneously match multiple target properties. We demonstrate our approach by concurrently optimizing bonded and nonbonded potentials of a CG model of polystyrene (PS) melts. The resulting CG-PS model effectively reproduces both the structural characteristics, such as the equilibrium probability distribution of microscopic degrees of freedom and the thermodynamic pressure of the AA counterpart. More importantly, leveraging the multiobjective optimization capability, we develop a precise and efficient CG model for PS melts that is transferable across a wide range of temperatures, i.e., from 400 to 600 K. It is achieved via optimizing a pairwise potential with nonlinear temperature dependence in the CG model to simultaneously match target data from AA-MD simulations at multiple thermodynamic states. The temperature transferable CG-PS model demonstrates its ability to accurately predict the radial distribution functions and density at different temperatures, including those that are not included in the target thermodynamic states. Our work opens up a promising route for developing accurate and transferable CG models of complex soft-matter systems through multiobjective optimization with differentiable simulation.
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Affiliation(s)
- Zhenghao Wu
- Department of Chemistry, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, P. R. China
| | - Tianhang Zhou
- College of Carbon Neutrality Future Technology, State Key Laboratory of Heavy Oil Processing, China University of Petroleum (Beijing), Beijing 102249, P. R. China
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4
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Zhang XZ, Shi R, Lu ZY, Qian HJ. Chemically Specific Systematic Coarse-Grained Polymer Model with Both Consistently Structural and Dynamical Properties. JACS AU 2024; 4:1018-1030. [PMID: 38559727 PMCID: PMC10976574 DOI: 10.1021/jacsau.3c00756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 04/04/2024]
Abstract
The coarse-grained (CG) model serves as a powerful tool for the simulation of polymer systems; its reliability depends on the accurate representation of both structural and dynamical properties. However, strong correlations between structural and dynamical properties on different scales and also a strong memory effect, enforced by chain connectivity between monomers in polymer systems, render developing a chemically specific systematic CG model a formidable task. In this study, we report a systematic CG approach that combines the iterative Boltzmann inversion (IBI) method and the generalized Langevin equation (GLE) dynamics. Structural properties are ensured by using conservative CG potentials derived from the IBI method. To retrieve the correct dynamical properties in the system, we demonstrate that using a combination of a Rouse-type delta function and a time-dependent short-time kernel in the GLE simulation is practically efficient. The former can be used to adjust the long-time diffusion dynamics, and the latter can be reconstructed from an iterative procedure according to the velocity autocorrelation function (ACF) from all-atomistic (AA) simulations. Taking the polystyrene as an example, we show that not only structural properties of radial distribution function, intramolecular bond, and angle distributions can be reproduced but also dynamical properties of mean-square displacement, velocity ACF, and force ACF resulted from our CG model have quantitative agreement with the reference AA model. In addition, reasonable agreements are observed in other collective properties between our GLE-CG model and the AA simulations as well.
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Affiliation(s)
| | | | - Zhong-Yuan Lu
- State Key Laboratory of Supramolecular
Structure and Materials, Institute of Theoretical Chemistry, College
of Chemistry, Jilin University, Changchun 130021, China
| | - Hu-Jun Qian
- State Key Laboratory of Supramolecular
Structure and Materials, Institute of Theoretical Chemistry, College
of Chemistry, Jilin University, Changchun 130021, China
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5
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Nie Y, Zheng Z, Li C, Zhan H, Kou L, Gu Y, Lü C. Resolving the dynamic properties of entangled linear polymers in non-equilibrium coarse grain simulation with a priori scaling factors. NANOSCALE 2024. [PMID: 38494916 DOI: 10.1039/d3nr06185j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The molecular weight of polymers can influence the material properties, but the molecular weight at the experiment level sometimes can be a huge burden for property prediction with full-atomic simulations. The traditional bottom-up coarse grain (CG) simulation can reduce the computation cost. However, the dynamic properties predicted by the CG simulation can deviate from the full-atomic simulation result. Usually, in CG simulations, the diffusion is faster and the viscosity and modulus are much lower. The fast dynamics in CG are usually solved by a posteriori scaling on time, temperature, or potential modifications, which usually have poor transferability to other non-fitted physical properties because of a lack of fundamental physics. In this work, a priori scaling factors were calculated by the loss of degrees of freedom and implemented in the iterative Boltzmann inversion. According to the simulation results on 3 different CG levels at different temperatures and loading rates, such a priori scaling factors can help in reproducing some dynamic properties of polycaprolactone in CG simulation more accurately, such as heat capacity, Young's modulus, and viscosity, while maintaining the accuracy in the structural distribution prediction. The transferability of entropy-enthalpy compensation and a dissipative particle dynamics thermostat is also presented for comparison. The proposed method reveals the huge potential for developing customized CG thermostats and offers a simple way to rebuild multiphysics CG models for polymers with good transferability.
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Affiliation(s)
- Yihan Nie
- College of Civil Engineering and Architecture, Zhejiang University, Hangzhou 310058, China
| | - Zhuoqun Zheng
- School of Astronautics, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Chengkai Li
- School of Materials Science and Engineering, Taiyuan University of Science and Technology, Taiyuan 030024, China
| | - Haifei Zhan
- College of Civil Engineering and Architecture, Zhejiang University, Hangzhou 310058, China
- School of Mechanical, Medical and Process Engineering, Queensland University of Technology (QUT), Brisbane QLD 4001, Australia
- Center for Materials Science, Queensland University of Technology (QUT), Brisbane QLD 4001, Australia
| | - Liangzhi Kou
- School of Mechanical, Medical and Process Engineering, Queensland University of Technology (QUT), Brisbane QLD 4001, Australia
- Center for Materials Science, Queensland University of Technology (QUT), Brisbane QLD 4001, Australia
| | - Yuantong Gu
- School of Mechanical, Medical and Process Engineering, Queensland University of Technology (QUT), Brisbane QLD 4001, Australia
- Center for Materials Science, Queensland University of Technology (QUT), Brisbane QLD 4001, Australia
| | - Chaofeng Lü
- Faculty of Mechanical Engineering & Mechanics, Ningbo University, Ningbo 315211, China
- College of Civil Engineering and Architecture, Zhejiang University, Hangzhou 310058, China
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6
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Lesniewski MC, Noid WG. Insight into the Density-Dependence of Pair Potentials for Predictive Coarse-Grained Models. J Phys Chem B 2024; 128:1298-1316. [PMID: 38271676 DOI: 10.1021/acs.jpcb.3c06890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
We investigate the temperature- and density-dependence of effective pair potentials for 1-site coarse-grained (CG) models of two industrial solvents, 1,4-dioxane and tetrahydrofuran. We observe that the calculated pair potentials are much more sensitive to density than to temperature. The generalized-Yvon-Born-Green framework reveals that this striking density-dependence reflects corresponding variations in the many-body correlations that determine the environment-mediated indirect contribution to the pair mean force. Moreover, we demonstrate, perhaps surprisingly, that this density-dependence is not important for accurately modeling the intermolecular structure. Accordingly, we adopt a density-independent interaction potential and transfer the density-dependence of the calculated pair potentials into a configuration-independent volume potential. Furthermore, we develop a single global potential that accurately models the intermolecular structure and pressure-volume equation of state across a very wide range of liquid state points. Consequently, this work provides fundamental insight into the density-dependence of effective pair potentials and also provides a significant step toward developing predictive CG models for efficiently modeling industrial solvents.
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Affiliation(s)
- Maria C Lesniewski
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - W G Noid
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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7
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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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8
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Jawed A, Khan MN, Khan NA, Hakeem MA, Khan P. Thermodynamic Insights into Variation in Thermomechanical and Physical Properties of Isotactic Polypropylene: Effect of Shear and Cooling Rates. ACS OMEGA 2023; 8:36775-36788. [PMID: 37841128 PMCID: PMC10569009 DOI: 10.1021/acsomega.3c03378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 08/24/2023] [Indexed: 10/17/2023]
Abstract
In order to elucidate the effect of shear and cooling process on structural, thermomechanical, and physical properties of polymer melt, excess entropy, a thermodynamic quantity is calculated from radial distribution function generated from equilibrated parts of the molecular simulation trajectories. The structural properties are calculated, which includes the density of polypropylene melt, end to end distance, radius of gyration of the polypropylene polymer chain, and monomer-monomer radial distribution function. Non-equilibrium molecular dynamics simulation was employed to investigate the role of the applied shear rate on the properties of polypropylene. Furthermore, a range of cooling rates were employed to cool the melt. Thermomechanical properties, such as Young's modulus, and physical properties, such as glass transition temperature, were determined for different cases. Results showed that slow cooling and high shear substantially improved the Young's modulus and glass transition temperature of the i-PP. Furthermore, a two-body contribution to the excess entropy was used to elucidate the structure-property relationships in the polymer melt as well as the glassy state and the dependence of shear and cooling rate on these properties. We have used the Rosenfeld excess entropy-viscosity relationship to calculate the viscous behavior of the polymer under a steady shear condition.
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Affiliation(s)
- Ahmad
S. Jawed
- Department of Chemical Engineering, Aligarh Muslim University, Aligarh 202002, India
| | - Mohd Nasir Khan
- Department of Chemical Engineering, Aligarh Muslim University, Aligarh 202002, India
| | - Naseem A. Khan
- Department of Chemical Engineering, Aligarh Muslim University, Aligarh 202002, India
| | - Mohammed A. Hakeem
- Department of Chemical Engineering, Aligarh Muslim University, Aligarh 202002, India
| | - Parvez Khan
- Department of Chemical Engineering, Aligarh Muslim University, Aligarh 202002, India
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9
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Jin J, Schweizer KS, Voth GA. Understanding dynamics in coarse-grained models. II. Coarse-grained diffusion modeled using hard sphere theory. J Chem Phys 2023; 158:034104. [PMID: 36681632 DOI: 10.1063/5.0116300] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The first paper of this series [J. Chem. Phys. 158, 034103 (2023)] demonstrated that excess entropy scaling holds for both fine-grained and corresponding coarse-grained (CG) systems. Despite its universality, a more exact determination of the scaling relationship was not possible due to the semi-empirical nature. In this second paper, an analytical excess entropy scaling relation is derived for bottom-up CG systems. At the single-site CG resolution, effective hard sphere systems are constructed that yield near-identical dynamical properties as the target CG systems by taking advantage of how hard sphere dynamics and excess entropy can be analytically expressed in terms of the liquid packing fraction. Inspired by classical equilibrium perturbation theories and recent advances in constructing hard sphere models for predicting activated dynamics of supercooled liquids, we propose a new approach for understanding the diffusion of molecular liquids in the normal regime using hard sphere reference fluids. The proposed "fluctuation matching" is designed to have the same amplitude of long wavelength density fluctuations (dimensionless compressibility) as the CG system. Utilizing the Enskog theory to derive an expression for hard sphere diffusion coefficients, a bridge between the CG dynamics and excess entropy is then established. The CG diffusion coefficient can be roughly estimated using various equations of the state, and an accurate prediction of accelerated CG dynamics at different temperatures is also possible in advance of running any CG simulation. By introducing another layer of coarsening, these findings provide a more rigorous method to assess excess entropy scaling and understand the accelerated CG dynamics of molecular fluids.
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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
| | - Kenneth S Schweizer
- Department of Material Science, Department of Chemistry, Department of Chemical and Biomolecular Engineering, and Materials Research Laboratory, University of Illinois, Urbana, Illinois 61801, 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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10
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Jin J, Schweizer KS, Voth GA. Understanding dynamics in coarse-grained models. I. Universal excess entropy scaling relationship. J Chem Phys 2023; 158:034103. [PMID: 36681649 DOI: 10.1063/5.0116299] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Coarse-grained (CG) models facilitate an efficient exploration of complex systems by reducing the unnecessary degrees of freedom of the fine-grained (FG) system while recapitulating major structural correlations. Unlike structural properties, assessing dynamic properties in CG modeling is often unfeasible due to the accelerated dynamics of the CG models, which allows for more efficient structural sampling. Therefore, the ultimate goal of the present series of articles is to establish a better correspondence between the FG and CG dynamics. To assess and compare dynamical properties in the FG and the corresponding CG models, we utilize the excess entropy scaling relationship. For Paper I of this series, we provide evidence that the FG and the corresponding CG counterpart follow the same universal scaling relationship. By carefully reviewing and examining the literature, we develop a new theory to calculate excess entropies for the FG and CG systems while accounting for entropy representability. We demonstrate that the excess entropy scaling idea can be readily applied to liquid water and methanol systems at both the FG and CG resolutions. For both liquids, we reveal that the scaling exponents remain unchanged from the coarse-graining process, indicating that the scaling behavior is universal for the same underlying molecular systems. Combining this finding with the concept of mapping entropy in CG models, we show that the missing entropy plays an important role in accelerating the CG dynamics.
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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
| | - Kenneth S Schweizer
- Department of Material Science, Department of Chemistry, Department of Chemical and Biomolecular Engineering, and Materials Research Laboratory, University of Illinois, Urbana, Illinois 61801, 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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11
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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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12
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Schmid F. Understanding and Modeling Polymers: The Challenge of Multiple Scales. ACS POLYMERS AU 2022. [DOI: 10.1021/acspolymersau.2c00049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Friederike Schmid
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudingerweg 9, 55128Mainz, Germany
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13
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Oliveira MP, Gonçalves YMH, Ol Gheta SK, Rieder SR, Horta BAC, Hünenberger PH. Comparison of the United- and All-Atom Representations of (Halo)alkanes Based on Two Condensed-Phase Force Fields Optimized against the Same Experimental Data Set. J Chem Theory Comput 2022; 18:6757-6778. [PMID: 36190354 DOI: 10.1021/acs.jctc.2c00524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The level of accuracy that can be achieved by a force field is influenced by choices made in the interaction-function representation and in the relevant simulation parameters. These choices, referred to here as functional-form variants (FFVs), include for example the model resolution, the charge-derivation procedure, the van der Waals combination rules, the cutoff distance, and the treatment of the long-range interactions. Ideally, assessing the effect of a given FFV on the intrinsic accuracy of the force-field representation requires that only the specific FFV is changed and that this change is performed at an optimal level of parametrization, a requirement that may prove extremely challenging to achieve in practice. Here, we present a first attempt at such a comparison for one specific FFV, namely the choice of a united-atom (UA) versus an all-atom (AA) resolution in a force field for saturated acyclic (halo)alkanes. Two force-field versions (UA vs AA) are optimized in an automated way using the CombiFF approach against 961 experimental values for the pure-liquid densities ρliq and vaporization enthalpies ΔHvap of 591 compounds. For the AA force field, the torsional and third-neighbor Lennard-Jones parameters are also refined based on quantum-mechanical rotational-energy profiles. The comparison between the UA and AA resolutions is also extended to properties that have not been included as parameterization targets, namely the surface-tension coefficient γ, the isothermal compressibility κT, the isobaric thermal-expansion coefficient αP, the isobaric heat capacity cP, the static relative dielectric permittivity ϵ, the self-diffusion coefficient D, the shear viscosity η, the hydration free energy ΔGwat, and the free energy of solvation ΔGche in cyclohexane. For the target properties ρliq and ΔHvap, the UA and AA resolutions reach very similar levels of accuracy after optimization. For the nine other properties, the AA representation leads to more accurate results in terms of η; comparably accurate results in terms of γ, κT, αP, ϵ, D, and ΔGche; and less accurate results in terms of cP and ΔGwat. This work also represents a first step toward the calibration of a GROMOS-compatible force field at the AA resolution.
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Affiliation(s)
- Marina P Oliveira
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Yan M H Gonçalves
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - S Kashef Ol Gheta
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Salomé R Rieder
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Bruno A C Horta
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Philippe H Hünenberger
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
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14
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Meinel MK, Müller-Plathe F. Roughness Volumes: An Improved RoughMob Concept for Predicting the Increase of Molecular Mobility upon Coarse-Graining. J Phys Chem B 2022; 126:3737-3747. [PMID: 35559647 DOI: 10.1021/acs.jpcb.2c00944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The reduced number of degrees of freedom in a coarse-grained molecular model compared to its parent atomistic model not only makes it possible to simulate larger systems for longer time scales but also results in an artificial mobility increase. The RoughMob method [Meinel, M. K. and Müller-Plathe, F. J. Chem. Theory Comput. 2020, 16, 1411.] linked the acceleration factor of the dynamics to the loss of geometric information upon coarse-graining. Our hypothesis is that coarse-graining a multiatom molecule or group into a single spherical bead smooths the molecular surface and, thus, leads to reduced intermolecular friction. A key parameter is the molecular roughness difference, which is calculated via a numerical comparison of the molecular surfaces of both the atomistic and coarse-grained models. Augmenting the RoughMob method, we add the concept of the region where the roughness acts. This information is contained in four so-called roughness volumes. For 17 systems of homogeneous hydrocarbon fluids, simple one-bead coarse-grained models are derived by the structure-based iterative Boltzmann inversion. They include 13 different homogeneous aliphatic and aromatic molecules and two different mapping schemes. We present a simple way to correlate the roughness volumes to the acceleration factor. The resulting relation is able to a priori predict the acceleration factors for an extended size and shape range of hydrocarbon molecules, with different mapping schemes and different densities.
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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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15
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Nguyen HTL, Huang DM. Systematic bottom-up molecular coarse-graining via force and torque matching using anisotropic particles. J Chem Phys 2022; 156:184118. [DOI: 10.1063/5.0085006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We derive a systematic and general method for parametrizing coarse-grained molecular models consisting of anisotropic particles from fine-grained (e.g. all-atom) models for condensed-phase molecular dynamics simulations. The method, which we call anisotropic force-matching coarse-graining (AFM-CG), is based on rigorous statistical mechanical principles, enforcing consistency between the coarse-grained and fine-grained phase-space distributions to derive equations for the coarse-grained forces, torques, masses, and moments of inertia in terms of properties of a condensed-phase fine-grained system. We verify the accuracy and efficiency of the method by coarse-graining liquid-state systems of two different anisotropic organic molecules, benzene and perylene, and show that the parametrized coarse-grained models more accurately describe properties of these systems than previous anisotropic coarse-grained models parametrized using other methods that do not account for finite-temperature and many-body effects on the condensed-phase coarse-grained interactions. The AFM-CG method will be useful for developing accurate and efficient dynamical simulation models of condensed-phase systems of molecules consisting of large, rigid, anisotropic fragments, such as liquid crystals, organic semiconductors, and nucleic acids.
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16
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Zheng T, Li T, Shi J, Wu T, Zhuang Z, Xu J, Guo B. Molecular Insight into the Toughness of Polyureas: A Hybrid All-Atom/Coarse-Grained Molecular Dynamics Study. Macromolecules 2022. [DOI: 10.1021/acs.macromol.1c02453] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tianze Zheng
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Ting Li
- Aerospace Research Institute of Materials and Processing Technology, Beijing 100076, China
| | - Jiaxin Shi
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Tianyu Wu
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Zhuo Zhuang
- School of Aerospace Engineering, Tsinghua University, Beijing 100084, China
| | - Jun Xu
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Baohua Guo
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
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17
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Kubincová A, Riniker S, Hünenberger PH. Solvent-scaling as an alternative to coarse-graining in adaptive-resolution simulations: The adaptive solvent-scaling (AdSoS) scheme. J Chem Phys 2021; 155:094107. [PMID: 34496576 DOI: 10.1063/5.0057384] [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
A new approach termed Adaptive Solvent-Scaling (AdSoS) is introduced for performing simulations of a solute embedded in a fine-grained (FG) solvent region itself surrounded by a coarse-grained (CG) solvent region, with a continuous FG ↔ CG switching of the solvent resolution across a buffer layer. Instead of relying on a distinct CG solvent model, the AdSoS scheme is based on CG models defined by a dimensional scaling of the FG solvent by a factor s, accompanied by an s-dependent modulation of the atomic masses and interaction parameters. The latter changes are designed to achieve an isomorphism between the dynamics of the FG and CG models, and to preserve the dispersive and dielectric solvation properties of the solvent with respect to a solute at FG resolution. This scaling approach offers a number of advantages compared to traditional coarse-graining: (i) the CG parameters are immediately related to those of the FG model (no need to parameterize a distinct CG model); (ii) nearly ideal mixing is expected for CG variants with similar s-values (ideal mixing holding in the limit of identical s-values); (iii) the solvent relaxation timescales should be preserved (no dynamical acceleration typical for coarse-graining); (iv) the graining level NG (number of FG molecules represented by one CG molecule) can be chosen arbitrarily (in particular, NG = s3 is not necessarily an integer); and (v) in an adaptive-resolution scheme, this level can be varied continuously as a function of the position (without requiring a bundling mechanism), and this variation occurs at a constant number of particles per molecule (no occurrence of fractional degrees of freedom in the buffer layer). By construction, the AdSoS scheme minimizes the thermodynamic mismatch between the different regions of the adaptive-resolution system, leading to a nearly homogeneous scaled solvent density s3ρ. Residual density artifacts in and at the surface of the boundary layer can easily be corrected by means of a grid-based biasing potential constructed in a preliminary pure-solvent simulation. This article introduces the AdSoS scheme and provides an initial application to pure atomic liquids (no solute) with Lennard-Jones plus Coulomb interactions in a slab geometry.
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Affiliation(s)
- Alžbeta Kubincová
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Sereina Riniker
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Philippe H Hünenberger
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir Prelog-Weg 2, CH-8093 Zürich, Switzerland
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Takase N, Koyanagi J, Mori K, Sakai T. Molecular Dynamics Simulation for Evaluating Fracture Entropy of a Polymer Material under Various Combined Stress States. MATERIALS 2021; 14:ma14081884. [PMID: 33920091 PMCID: PMC8070208 DOI: 10.3390/ma14081884] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 11/28/2022]
Abstract
Herein, the stress-state dependence of fracture entropy for a polyamide 6 material is investigated through molecular dynamics simulations. Although previous research suggests that a constant entropy increase can be universally applied for the definition of material fracture, the dependence of stress triaxiality has not yet been discussed. In this study, entropy values are evaluated by molecular dynamics simulations with varied combined stress states. The calculation is implemented using the 570,000 all-atom model. Similar entropy values are obtained independently of stress triaxiality. This study also reveals the relationship between material damage, which is correlated with void size, and the entropy value.
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Affiliation(s)
- Naohiro Takase
- Department of Materials Science and Technology, Graduate School of Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan;
| | - Jun Koyanagi
- Department of Materials Science and Technology, University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
- Correspondence: ; Tel.: +81-35-876-1411
| | - Kazuki Mori
- Itochu Techno-Solutions Corporation, Art Village Osaki Central Tower, 1-2-2, Osaki, Shinagawa-ku, Tokyo 141-8522, Japan;
| | - Takenobu Sakai
- Department of Mechanical Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan;
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Goujon F, Martzel N, Dequidt A, Latour B, Garruchet S, Devémy J, Blaak R, Munch É, Malfreyt P. Backbone oriented anisotropic coarse grains for efficient simulations of polymers. J Chem Phys 2020; 153:214901. [PMID: 33291912 DOI: 10.1063/5.0019945] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Despite the fact that anisotropic particles have been introduced to describe molecular interactions for decades, they have been poorly used for polymers because of their computing time overhead and the absence of a relevant proof of their impact in this field. We first report a method using anisotropic beads for polymers, which solves the computing time issue by considering that beads keep their principal orientation alongside the mean local backbone vector of the polymer chain, avoiding the computation of torques during the dynamics. Applying this method to a polymer bulk, we study the effect of anisotropic interactions vs isotropic ones for various properties such as density, pressure, topology of the chain network, local structure, and orientational order. We show that for different classes of potentials traditionally used in molecular simulations, those backbone oriented anisotropic beads can solve numerous issues usually encountered with isotropic interactions. We conclude that the use of backbone oriented anisotropic beads is a promising approach for the development of realistic coarse-grained potentials for polymers.
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Affiliation(s)
- Florent Goujon
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Nicolas Martzel
- Manufacture Française des Pneumatiques Michelin, Site de Ladoux, 23 Place des Carmes Déchaux, France Cedex 9, 63040 Clermont-Ferrand, France
| | - Alain Dequidt
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Benoit Latour
- Manufacture Française des Pneumatiques Michelin, Site de Ladoux, 23 Place des Carmes Déchaux, France Cedex 9, 63040 Clermont-Ferrand, France
| | - Sébastien Garruchet
- Manufacture Française des Pneumatiques Michelin, Site de Ladoux, 23 Place des Carmes Déchaux, France Cedex 9, 63040 Clermont-Ferrand, France
| | - Julien Devémy
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Ronald Blaak
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Étienne Munch
- Manufacture Française des Pneumatiques Michelin, Site de Ladoux, 23 Place des Carmes Déchaux, France Cedex 9, 63040 Clermont-Ferrand, France
| | - Patrice Malfreyt
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
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20
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Wu Z, Milano G, Müller-Plathe F. Combination of Hybrid Particle-Field Molecular Dynamics and Slip-Springs for the Efficient Simulation of Coarse-Grained Polymer Models: Static and Dynamic Properties of Polystyrene Melts. J Chem Theory Comput 2020; 17:474-487. [PMID: 33275441 DOI: 10.1021/acs.jctc.0c00954] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A quantitative prediction of polymer-entangled dynamics based on molecular simulation is a grand challenge in contemporary computational material science. The drastic increase of relaxation time and viscosity in high-molecular-weight polymeric fluids essentially limits the usage of classic molecular dynamics simulation. Here, we demonstrate a systematic coarse-graining approach for modeling entangled polymers under the slip-spring particle-field scheme. Specifically, a frequency-controlled slip-spring model, a hybrid particle-field model, and a coarse-grained model of polystyrene melts are combined into a hybrid simulation technique. Via a rigorous parameterization strategy to determine the parameters in slip-springs from existing experimental or simulation data, we show that the reptation behavior is clearly observed in multiple characteristics of polymer dynamics, mean-square displacements, diffusion coefficients, reorientational relaxation, and Rouse mode analysis, consistent with the predictions of the tube theory. All dynamical properties of the slip-spring particle-field models are in good agreement with classic molecular dynamics models. Our work provides an efficient and practical approach to establish chemical-specific coarse-grained models for predicting polymer-entangled dynamics.
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Affiliation(s)
- Zhenghao Wu
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 8, 64287 Darmstadt, Germany
| | - Giuseppe Milano
- Department of Organic Materials Science, Yamagata University, 4-3-16 Jonan, Yonezawa, 992-8510 Yamagata-ken, Japan
| | - Florian Müller-Plathe
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 8, 64287 Darmstadt, Germany
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21
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Kapoor U, Kulshreshtha A, Jayaraman A. Development of Coarse-Grained Models for Poly(4-vinylphenol) and Poly(2-vinylpyridine): Polymer Chemistries with Hydrogen Bonding. Polymers (Basel) 2020; 12:E2764. [PMID: 33238611 PMCID: PMC7709027 DOI: 10.3390/polym12112764] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 11/16/2022] Open
Abstract
In this paper, we identify the modifications needed in a recently developed generic coarse-grained (CG) model that captured directional interactions in polymers to specifically represent two exemplary hydrogen bonding polymer chemistries-poly(4-vinylphenol) and poly(2-vinylpyridine). We use atomistically observed monomer-level structures (e.g., bond, angle and torsion distribution) and chain structures (e.g., end-to-end distance distribution and persistence length) of poly(4-vinylphenol) and poly(2-vinylpyridine) in an explicitly represented good solvent (tetrahydrofuran) to identify the appropriate modifications in the generic CG model in implicit solvent. For both chemistries, the modified CG model is developed based on atomistic simulations of a single 24-mer chain. This modified CG model is then used to simulate longer (36-mer) and shorter (18-mer and 12-mer) chain lengths and compared against the corresponding atomistic simulation results. We find that with one to two simple modifications (e.g., incorporating intra-chain attraction, torsional constraint) to the generic CG model, we are able to reproduce atomistically observed bond, angle and torsion distributions, persistence length, and end-to-end distance distribution for chain lengths ranging from 12 to 36 monomers. We also show that this modified CG model, meant to reproduce atomistic structure, does not reproduce atomistically observed chain relaxation and hydrogen bond dynamics, as expected. Simulations with the modified CG model have significantly faster chain relaxation than atomistic simulations and slower decorrelation of formed hydrogen bonds than in atomistic simulations, with no apparent dependence on chain length.
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Affiliation(s)
- Utkarsh Kapoor
- Department of Chemical and Biomolecular Engineering, Colburn Laboratory, University of Delaware, 150 Academy Street, Newark, DE 19716, USA; (U.K.); (A.K.)
| | - Arjita Kulshreshtha
- Department of Chemical and Biomolecular Engineering, Colburn Laboratory, University of Delaware, 150 Academy Street, Newark, DE 19716, USA; (U.K.); (A.K.)
| | - Arthi Jayaraman
- Department of Chemical and Biomolecular Engineering, Colburn Laboratory, University of Delaware, 150 Academy Street, Newark, DE 19716, USA; (U.K.); (A.K.)
- Department of Materials Science and Engineering, University of Delaware, Newark, DE 19716, USA
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22
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Heinemann T, Jung Y. Coarse-graining strategy for modeling effective, highly diffusive fluids with reduced polydispersity: A dynamical study. J Chem Phys 2020; 153:104509. [PMID: 32933276 DOI: 10.1063/5.0009156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
We present a coarse-graining strategy for reducing the number of particle species in mixtures to achieve a simpler system with higher diffusion while preserving the total particle number and characteristic dynamic features. As a system of application, we chose the bidisperse Lennard-Jones-like mixture, discovered by Kob and Andersen [Phys. Rev. Lett. 73, 1376 (1994)], possessing a slow dynamics due to the fluid's multi-component character with its apparently unconventional choice for the pair potential of the type-A-type-B arrangement. We further established in a so-formed coarse-grained and temperature-independent monodisperse system an equilibrium structure with a radial distribution function resembling its mixture counterpart. This one-component system further possesses similar dynamic features such as glass transition temperature and critical exponents while subjected to Newtonian mechanics. This strategy may finally lead to the manufacturing of new nanoparticle/colloidal fluids by experimentally modeling only the outcoming effective pair potential(s) and no other macroscopic quantity.
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Affiliation(s)
- Thomas Heinemann
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
| | - YounJoon Jung
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
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23
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Martzel N, Dequidt A, Devémy J, Blaak R, Garruchet S, Latour B, Goujon F, Munch E, Malfreyt P. Grain Shape Dynamics for Molecular Simulations at the Mesoscale. ADVANCED THEORY AND SIMULATIONS 2020. [DOI: 10.1002/adts.202000124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Nicolas Martzel
- Manufacture Française des Pneumatiques Michelin Site de Ladoux, 23 Place des Carmes Déchaux, France Cedex 9 Clermont‐Ferrand 63040 France
| | - Alain Dequidt
- Université Clermont Auvergne, CNRS, SIGMA Clermont Institut de Chimie de Clermont‐Ferrand Clermont‐Ferrand F‐63000 France
| | - Julien Devémy
- Université Clermont Auvergne, CNRS, SIGMA Clermont Institut de Chimie de Clermont‐Ferrand Clermont‐Ferrand F‐63000 France
| | - Ronald Blaak
- Université Clermont Auvergne, CNRS, SIGMA Clermont Institut de Chimie de Clermont‐Ferrand Clermont‐Ferrand F‐63000 France
| | - Sebastien Garruchet
- Manufacture Française des Pneumatiques Michelin Site de Ladoux, 23 Place des Carmes Déchaux, France Cedex 9 Clermont‐Ferrand 63040 France
| | - Benoit Latour
- Manufacture Française des Pneumatiques Michelin Site de Ladoux, 23 Place des Carmes Déchaux, France Cedex 9 Clermont‐Ferrand 63040 France
| | - Florent Goujon
- Université Clermont Auvergne, CNRS, SIGMA Clermont Institut de Chimie de Clermont‐Ferrand Clermont‐Ferrand F‐63000 France
| | - Etienne Munch
- Manufacture Française des Pneumatiques Michelin Site de Ladoux, 23 Place des Carmes Déchaux, France Cedex 9 Clermont‐Ferrand 63040 France
| | - Patrice Malfreyt
- Université Clermont Auvergne, CNRS, SIGMA Clermont Institut de Chimie de Clermont‐Ferrand Clermont‐Ferrand F‐63000 France
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