1
|
Klippenstein V, Wolf N, van der Vegt NFA. A Gauss-Newton method for iterative optimization of memory kernels for generalized Langevin thermostats in coarse-grained molecular dynamics simulations. J Chem Phys 2024; 160:204115. [PMID: 38804493 DOI: 10.1063/5.0203832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/08/2024] [Indexed: 05/29/2024] Open
Abstract
In molecular dynamics simulations, dynamically consistent coarse-grained (CG) models commonly use stochastic thermostats to model friction and fluctuations that are lost in a CG description. While Markovian, i.e., time-local, formulations of such thermostats allow for an accurate representation of diffusivities/long-time dynamics, a correct description of the dynamics on all time scales generally requires non-Markovian, i.e., non-time-local, thermostats. These thermostats typically take the form of a Generalized Langevin Equation (GLE) determined by a memory kernel. In this work, we use a Markovian embedded formulation of a position-independent GLE thermostat acting independently on each CG degree of freedom. Extracting the memory kernel of this CG model from atomistic reference data requires several approximations. Therefore, this task is best understood as an inverse problem. While our recently proposed approximate Newton scheme allows for the iterative optimization of memory kernels (IOMK), Markovian embedding remained potentially error-prone and computationally expensive. In this work, we present an IOMK-Gauss-Newton scheme (IOMK-GN) based on IOMK that allows for the direct parameterization of a Markovian embedded model.
Collapse
Affiliation(s)
- Viktor Klippenstein
- Department of Chemistry, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Niklas Wolf
- Department of Chemistry, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Nico F A van der Vegt
- Department of Chemistry, Technical University of Darmstadt, 64287 Darmstadt, Germany
| |
Collapse
|
2
|
Zhu Q, Wu Y, Luo R. Understanding and fine tuning the propensity of ATP-driven liquid-liquid phase separation with oligolysine. Phys Chem Chem Phys 2024; 26:10568-10578. [PMID: 38512104 PMCID: PMC11056285 DOI: 10.1039/d4cp00761a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Liquid-liquid phase separation (LLPS) plays a pivotal role in the organization and functionality of living cells. It is imperative to understand the underlying driving forces behind LLPS and to control its occurrence. In this study, we employed coarse-grained (CG) simulations as a research tool to investigate systems comprising oligolysine and adenosine triphosphate (ATP) under conditions of various ionic concentrations and oligolysine lengths. Consistent with experimental observations, our CG simulations captured the formation of LLPS upon the addition of ATP and tendency of dissociating under high ionic concentration. The electrostatic interaction between oligolysine and ATP is of great importance in forming LLPS. An in-depth analysis on the structural properties of LLPS was conducted, where the oligolysine structure remained unchanged with increased ionic concentration and the addition of ATP led to a more pronounced curvature, aligning with the observed enhancement of α-helical secondary structure in experiments. In terms of the dynamic properties, the introduction of ATP led to a significant reduction in translational and vibrational degrees of freedom but not rotational degrees of freedom. Through keeping the total number of charged residues constant and varying their entropic effects, we constructed two systems of similar biochemical significance and further validated the entropy effects on the LLPS formation. These findings provide a deeper understanding of LLPS formation and shed lights on the development of novel bioreactor and primitive artificial cells for synthesizing key chemicals for certain diseases.
Collapse
Affiliation(s)
- Qiang Zhu
- Department of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, California 92697, USA.
| | - Yongxian Wu
- Department of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, California 92697, USA.
| | - Ray Luo
- Department of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, California 92697, USA.
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Khot A, Lindsey RK, Lewicki JP, Maiti A, Goldman N, Kroonblawd MP. United atom and coarse grained models for crosslinked polydimethylsiloxane with applications to the rheology of silicone fluids. Phys Chem Chem Phys 2023; 25:9669-9684. [PMID: 36943730 DOI: 10.1039/d2cp04920a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Siloxane systems consisting primarily of polydimethylsiloxane (PDMS) are versatile, multifaceted materials that play a key role in diverse applications. However, open questions exist regarding the correlation between their varied atomic-level properties and observed macroscale features. To this effect, we have created a systematic workflow to determine coarse-grained simulation models for crosslinked PDMS in order to further elucidate the effects of network changes on the system's rheological properties below the gel point. Our approach leverages a fine-grained united atom model for linear PDMS, which we extend to include crosslinking terms, and applies iterative Boltzmann inversion to obtain a coarse-grain "bead-spring-type" model. We then perform extensive molecular dynamics simulations to explore the effect of crosslinking on the rheology of silicone fluids, where we compute systematic increases in both density and shear viscosity that compare favorably to experiments that we conduct here. The kinematic viscosity of partially crosslinked fluids follows an empirical linear relationship that is surprisingly consistent with Rouse theory, which was originally derived for systems comprised of a uniform distribution of linear chains. The models developed here serve to enable quantitative bottom-up predictions for curing- and age-induced effects on macroscale rheological properties, allowing for accurate prediction of material properties based on fundamental chemical data.
Collapse
Affiliation(s)
- Aditi Khot
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.
- Department of Chemical Engineering, Purdue University, West Lafayette, Indiana 47907, USA
| | - Rebecca K Lindsey
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - James P Lewicki
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.
| | - Amitesh Maiti
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.
| | - Nir Goldman
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.
- Department of Chemical Engineering, University of California, Davis, California 95616, USA
| | - Matthew P Kroonblawd
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.
| |
Collapse
|
5
|
Klippenstein V, van der Vegt NFA. Bottom-Up Informed and Iteratively Optimized Coarse-Grained Non-Markovian Water Models with Accurate Dynamics. J Chem Theory Comput 2023; 19:1099-1110. [PMID: 36745567 PMCID: PMC9979609 DOI: 10.1021/acs.jctc.2c00871] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Molecular dynamics (MD) simulations based on coarse-grained (CG) particle models of molecular liquids generally predict accelerated dynamics and misrepresent the time scales for molecular vibrations and diffusive motions. The parametrization of Generalized Langevin Equation (GLE) thermostats based on the microscopic dynamics of the fine-grained model provides a promising route to address this issue, in conjunction with the conservative interactions of the CG model obtained with standard coarse graining methods, such as iterative Boltzmann inversion, force matching, or relative entropy minimization. We report the application of a recently introduced bottom-up dynamic coarse graining method, based on the Mori-Zwanzig formalism, which provides accurate estimates of isotropic GLE memory kernels for several CG models of liquid water. We demonstrate that, with an additional iterative optimization of the memory kernels (IOMK) for the CG water models based on a practical iterative optimization technique, the velocity autocorrelation function of liquid water can be represented very accurately within a few iterations. By considering the distinct Van Hove function, we demonstrate that, with the presented methods, an accurate representation of structural relaxation can be achieved. We consider several distinct CG potentials to study how the choice of the CG potential affects the performance of bottom-up informed and iteratively optimized models.
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Weber F, Ries M, Bauer C, Wick C, Pfaller S. On equilibrating non-periodic molecular dynamics samples for coupled particle-continuum simulations of amorphous polymers. FORCES IN MECHANICS 2022. [DOI: 10.1016/j.finmec.2022.100159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
8
|
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
| |
Collapse
|
9
|
Nkepsu Mbitou RL, Goujon F, Dequidt A, Latour B, Devémy J, Blaak R, Martzel N, Emeriau-Viard C, Tchoufag J, Garruchet S, Munch E, Hauret P, Malfreyt P. Consistent and Transferable Force Fields for Statistical Copolymer Systems at the Mesoscale. J Chem Theory Comput 2022; 18:6940-6951. [PMID: 36205431 DOI: 10.1021/acs.jctc.2c00945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The statistical trajectory matching (STM) method was applied successfully to derive coarse grain (CG) models for bulk properties of homopolymers. The extension of the methodology for building CG models for statistical copolymer systems is much more challenging. We present here the strategy for developing CG models for styrene-butadiene-rubber, and we compare the quality of the resulting CG force fields on the structure and thermodynamics at different chemical compositions. The CG models are used through the use of a genuine mesoscopic method called the dissipative particle dynamics method and compared to high-resolution molecular dynamics simulations. We conclude that the STM method is able to produce coarse-grained potentials that are transferable in composition by using only a few reference systems. Additionally, this methodology can be applied on any copolymer system.
Collapse
Affiliation(s)
- R L Nkepsu Mbitou
- Université Clermont Auvergne, CNRS, Clermont Auvergne INP, Institut de Chimie de Clermont-Ferrand, F-63000Clermont-Ferrand, France.,Manufacture Française des Pneumatiques Michelin, 23, Place des Carmes, 63040Clermont-Ferrand, France
| | - F Goujon
- Université Clermont Auvergne, CNRS, Clermont Auvergne INP, Institut de Chimie de Clermont-Ferrand, F-63000Clermont-Ferrand, France
| | - A Dequidt
- Université Clermont Auvergne, CNRS, Clermont Auvergne INP, Institut de Chimie de Clermont-Ferrand, F-63000Clermont-Ferrand, France
| | - B Latour
- Manufacture Française des Pneumatiques Michelin, 23, Place des Carmes, 63040Clermont-Ferrand, France
| | - J Devémy
- Université Clermont Auvergne, CNRS, Clermont Auvergne INP, Institut de Chimie de Clermont-Ferrand, F-63000Clermont-Ferrand, France
| | - R Blaak
- Université Clermont Auvergne, CNRS, Clermont Auvergne INP, Institut de Chimie de Clermont-Ferrand, F-63000Clermont-Ferrand, France
| | - N Martzel
- Manufacture Française des Pneumatiques Michelin, 23, Place des Carmes, 63040Clermont-Ferrand, France
| | - C Emeriau-Viard
- Manufacture Française des Pneumatiques Michelin, 23, Place des Carmes, 63040Clermont-Ferrand, France
| | - J Tchoufag
- Manufacture Française des Pneumatiques Michelin, 23, Place des Carmes, 63040Clermont-Ferrand, France
| | - S Garruchet
- Manufacture Française des Pneumatiques Michelin, 23, Place des Carmes, 63040Clermont-Ferrand, France
| | - E Munch
- Manufacture Française des Pneumatiques Michelin, 23, Place des Carmes, 63040Clermont-Ferrand, France
| | - P Hauret
- Manufacture Française des Pneumatiques Michelin, 23, Place des Carmes, 63040Clermont-Ferrand, France
| | - P Malfreyt
- Université Clermont Auvergne, CNRS, Clermont Auvergne INP, Institut de Chimie de Clermont-Ferrand, F-63000Clermont-Ferrand, France
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Rissanou A, Chazirakis A, Polinska P, Burkhart C, Doxastakis M, Harmandaris V. Polybutadiene Copolymers via Atomistic and Systematic Coarse-Grained Simulations. Macromolecules 2022. [DOI: 10.1021/acs.macromol.1c01939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anastassia Rissanou
- Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas, (FORTH), IACM/FORTH, GR-71110 Heraklion, Greece
- Department of Mathematics and Applied Mathematics, University of Crete, GR-71409 Heraklion, Crete, Greece
| | - Antonis Chazirakis
- Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas, (FORTH), IACM/FORTH, GR-71110 Heraklion, Greece
- Department of Mathematics and Applied Mathematics, University of Crete, GR-71409 Heraklion, Crete, Greece
| | | | - Craig Burkhart
- The Goodyear Tire and Rubber Company, 142 Goodyear Blvd., 44305 Akron, Ohio, United States
| | - Manolis Doxastakis
- Department of Chemical and Biomolecular Engineering, University of Tennessee, 37996 Knoxville, Tennessee, United States
| | - Vagelis Harmandaris
- Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas, (FORTH), IACM/FORTH, GR-71110 Heraklion, Greece
- Department of Mathematics and Applied Mathematics, University of Crete, GR-71409 Heraklion, Crete, Greece
- Computation-Based Science and Technology Research Center, The Cyprus Institute, 2121 Nicosia, Cyprus
| |
Collapse
|
12
|
Klippenstein V, van der Vegt NFA. Cross-correlation corrected friction in (generalized) Langevin models. J Chem Phys 2021; 154:191102. [PMID: 34240903 DOI: 10.1063/5.0049324] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We propose a route for parameterizing isotropic (generalized) Langevin [(G)LE] thermostats with the aim to correct the dynamics of coarse-grained (CG) models with pairwise conservative interactions. The approach is based on the Mori-Zwanzig formalism and derives the memory kernels from Q-projected time correlation functions. Bottom-up informed (GLE and LE) thermostats for a CG star-polymer melt are investigated, and it is demonstrated that the inclusion of memory in the CG simulation leads to predictions of polymer diffusion in quantitative agreement with fine-grained simulations. Interestingly, memory effects are observed in the diffusive regime. We demonstrate that previously neglected cross-correlations between the "irrelevant" and the CG degree of freedom are important and lie at the origin of shortcomings in previous CG simulations.
Collapse
Affiliation(s)
- Viktor Klippenstein
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Nico F A van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| |
Collapse
|
13
|
Klippenstein V, Tripathy M, Jung G, Schmid F, van der Vegt NFA. Introducing Memory in Coarse-Grained Molecular Simulations. J Phys Chem B 2021; 125:4931-4954. [PMID: 33982567 PMCID: PMC8154603 DOI: 10.1021/acs.jpcb.1c01120] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Preserving the correct dynamics at the coarse-grained (CG) level is a pressing problem in the development of systematic CG models in soft matter simulation. Starting from the seminal idea of simple time-scale mapping, there have been many efforts over the years toward establishing a meticulous connection between the CG and fine-grained (FG) dynamics based on fundamental statistical mechanics approaches. One of the most successful attempts in this context has been the development of CG models based on the Mori-Zwanzig (MZ) theory, where the resulting equation of motion has the form of a generalized Langevin equation (GLE) and closely preserves the underlying FG dynamics. In this Review, we describe some of the recent studies in this regard. We focus on the construction and simulation of dynamically consistent systematic CG models based on the GLE, both in the simple Markovian limit and the non-Markovian case. Some recent studies of physical effects of memory are also discussed. The Review is aimed at summarizing recent developments in the field while highlighting the major challenges and possible future directions.
Collapse
Affiliation(s)
- Viktor Klippenstein
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Madhusmita Tripathy
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Gerhard Jung
- Institut für Theoretische Physik, Universität Innsbruck, Technikerstraße 21 A, A-6020 Innsbruck, Austria
| | - Friederike Schmid
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudingerweg 9, 55128 Mainz, Germany
| | - Nico F A van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| |
Collapse
|
14
|
Clavier G, Blaak R, Dequidt A, Goujon F, Devémy J, Latour B, Garruchet S, Martzel N, Munch É, Malfreyt P. Assessing the derivation of time parameters from branched polymer coarse-grain model. J Chem Phys 2021; 154:124901. [PMID: 33810686 DOI: 10.1063/5.0039843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The parameterization of rheological models for polymers is often obtained from experiments via the top-down approach. This procedure allows us to determine good fitting parameters for homogeneous materials but is less effective for polymer mixtures. From a molecular simulation point of view, the timescales needed to derive those parameters are often accessed through the use of coarse-grain potentials. However, these potentials are often derived from linear model systems and the transferability to a more complex structure is not straightforward. Here, we verify the transferability of a potential computed from linear polymer simulations to more complex molecular shapes and present a type of analysis, which was recently formulated in the framework of a tube theory, to a coarse-grain molecular approach in order to derive the input parameters for a rheological model. We describe the different behaviors arising from the local topological structure of molecular sub-units. Coarse-grain models and mean-field based tube theory for polymers form a powerful combination with potentially important applications.
Collapse
Affiliation(s)
- Germain Clavier
- 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
| | - Alain Dequidt
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Florent Goujon
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Julien Devémy
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Benoit Latour
- Manufacture Française des Pneumatiques Michelin, 23, Place des Carmes, 63040 Clermont-Ferrand, France
| | - Sébastien Garruchet
- Manufacture Française des Pneumatiques Michelin, 23, Place des Carmes, 63040 Clermont-Ferrand, France
| | - Nicolas Martzel
- Manufacture Française des Pneumatiques Michelin, 23, Place des Carmes, 63040 Clermont-Ferrand, France
| | - Étienne Munch
- Manufacture Française des Pneumatiques Michelin, 23, Place des Carmes, 63040 Clermont-Ferrand, France
| | - Patrice Malfreyt
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| |
Collapse
|
15
|
Tanis I, Rousseau B, Soulard L, Lemarchand CA. Assessment of an anisotropic coarse-grained model for cis-1,4-polybutadiene: a bottom-up approach. SOFT MATTER 2021; 17:621-636. [PMID: 33206108 DOI: 10.1039/d0sm01572e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The spherical representation usually utilized for the coarse-grained particles of soft matter systems is an assumption and pertinent studies have shown that both structural and dynamical properties can depend on anisotropic effects. On these grounds, we develop coarse-grained equations of motion which take into account explicitly the anisotropy of the beads. As a first step, this model incorporates only conservative terms. Inclusion of the dissipative and random terms is in principle possible but is beyond the scope of this study. The translational dynamics of the beads is tracked using the position and momentum of their center of mass, while their rotational dynamics is modeled by representing their orientation through the use of quaternions, similarly to the case of rigid bodies. The associated force and torque controlling the motion are derived from atomistic molecular dynamics (MD) simulations via a bottom-up approach and define a coarse-grained potential. The assumptions of the model are clearly stated and checked for a reference system of a cis-1,4-polybutadiene melt. In particular, the choice of the angular velocity as a slow variable is justified by comparing its dynamics to atomic vibrations. The accuracy of this approach to reproduce static structural features of the polymer melt is assessed.
Collapse
Affiliation(s)
| | - Bernard Rousseau
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR 8000, 91405 Orsay, France
| | - Laurent Soulard
- CEA, DAM, DIF, 91297 Arpajon Cedex, France. and Université Paris-Saclay, CEA, Laboratoire Matière sous Conditions Extrêmes, 91680, Bruyères-le-Châtel, France
| | - Claire A Lemarchand
- CEA, DAM, DIF, 91297 Arpajon Cedex, France. and Université Paris-Saclay, CEA, Laboratoire Matière sous Conditions Extrêmes, 91680, Bruyères-le-Châtel, France
| |
Collapse
|
16
|
Lecoutre G, Lemarchand CA, Soulard L, Pineau N. Hugoniostat and Direct Shock Simulations in cis‐1,4‐Polybutadiene Melts. MACROMOL THEOR SIMUL 2020. [DOI: 10.1002/mats.202000068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Claire A. Lemarchand
- CEA, DAM, DIF Arpajon Cedex 91297 France
- Université Paris Saclay, CEA Laboratoire Matière en Conditions Extrêmes Bruyères‐le‐Châtel 91680 France
| | - Laurent Soulard
- CEA, DAM, DIF Arpajon Cedex 91297 France
- Université Paris Saclay, CEA Laboratoire Matière en Conditions Extrêmes Bruyères‐le‐Châtel 91680 France
| | - Nicolas Pineau
- CEA, DAM, DIF Arpajon Cedex 91297 France
- Université Paris Saclay, CEA Laboratoire Matière en Conditions Extrêmes Bruyères‐le‐Châtel 91680 France
| |
Collapse
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
Joshi SY, Deshmukh SA. A review of advancements in coarse-grained molecular dynamics simulations. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1828583] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Soumil Y. Joshi
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA
| | | |
Collapse
|
19
|
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
| |
Collapse
|
20
|
Li W, Burkhart C, Polińska P, Harmandaris V, Doxastakis M. Backmapping coarse-grained macromolecules: An efficient and versatile machine learning approach. J Chem Phys 2020; 153:041101. [DOI: 10.1063/5.0012320] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Wei Li
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Craig Burkhart
- The Goodyear Tire and Rubber Company, Akron, Ohio 44305, USA
| | - Patrycja Polińska
- Goodyear Innovation Center Luxembourg, Avenue Gordon Smith, L-7750 Colmar-Berg, Luxembourg
| | - Vagelis Harmandaris
- Department of Applied Mathematics, University of Crete, and IACM FORTH, GR-71110 Heraklion, Greece
- Computation-Based Science and Technology Research Center, The Cyprus Institute, Nicosia 2121, Cyprus
| | - Manolis Doxastakis
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, USA
| |
Collapse
|
21
|
Greenfield ML. Representing polymer molecular structure using molecular simulations for the study of liquid sorption and diffusion. Curr Opin Chem Eng 2020. [DOI: 10.1016/j.coche.2020.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
22
|
Kempfer K, Devémy J, Dequidt A, Couty M, Malfreyt P. Multi-scale modeling of the polymer-filler interaction. SOFT MATTER 2020; 16:1538-1547. [PMID: 31939976 DOI: 10.1039/c9sm01959f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We report mesoscopic simulations of the interaction between a silica nanoparticle and cis-1,4-polybutadiene chains with realistic coarse-(CG) grained models. The CG models are obtained with a bottom-up Bayesian method based on trajectory matching of atomistic configurations of the system. We then investigate the structural properties of the interfacial region as a function of the grafting density and polymer chain length. We take advantage of the realistic CG models to explore the dynamics of the nanoparticle over a period of 10 microseconds. We show that the dynamics of the nanoparticle is affected by the grafting density and the polymer chain length of the grafted chains.
Collapse
Affiliation(s)
- Kevin Kempfer
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France.
| | | | | | | | | |
Collapse
|
23
|
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
| |
Collapse
|
24
|
Recent Progress towards Chemically-Specific Coarse-Grained Simulation Models with Consistent Dynamical Properties. COMPUTATION 2019. [DOI: 10.3390/computation7030042] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Coarse-grained (CG) models can provide computationally efficient and conceptually simple characterizations of soft matter systems. While generic models probe the underlying physics governing an entire family of free-energy landscapes, bottom-up CG models are systematically constructed from a higher-resolution model to retain a high level of chemical specificity. The removal of degrees of freedom from the system modifies the relationship between the relative time scales of distinct dynamical processes through both a loss of friction and a “smoothing” of the free-energy landscape. While these effects typically result in faster dynamics, decreasing the computational expense of the model, they also obscure the connection to the true dynamics of the system. The lack of consistent dynamics is a serious limitation for CG models, which not only prevents quantitatively accurate predictions of dynamical observables but can also lead to qualitatively incorrect descriptions of the characteristic dynamical processes. With many methods available for optimizing the structural and thermodynamic properties of chemically-specific CG models, recent years have seen a stark increase in investigations addressing the accurate description of dynamical properties generated from CG simulations. In this review, we present an overview of these efforts, ranging from bottom-up parameterizations of generalized Langevin equations to refinements of the CG force field based on a Markov state modeling framework. We aim to make connections between seemingly disparate approaches, while laying out some of the major challenges as well as potential directions for future efforts.
Collapse
|
25
|
Solano Canchaya JG, Dequidt A, Garruchet S, Latour B, Martzel N, Devémy J, Goujon F, Blaak R, Schnell B, Munch E, Seeboth N, Malfreyt P. Development of a coarse-grain model for the description of the metal oxide-polymer interface from a bottom-up approach. J Chem Phys 2019. [DOI: 10.1063/1.5115148] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- José G. Solano Canchaya
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Alain Dequidt
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Sebastien Garruchet
- Manufacture Française des Pneumatiques Michelin, 23, Place des Carmes, 63040 Clermont-Ferrand, France
| | - Benoit Latour
- Manufacture Française des Pneumatiques Michelin, 23, Place des Carmes, 63040 Clermont-Ferrand, France
| | - Nicolas Martzel
- Manufacture Française des Pneumatiques Michelin, 23, Place des Carmes, 63040 Clermont-Ferrand, France
| | - Julien Devémy
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Florent Goujon
- 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
| | - Benoit Schnell
- Manufacture Française des Pneumatiques Michelin, 23, Place des Carmes, 63040 Clermont-Ferrand, France
| | - Etienne Munch
- Manufacture Française des Pneumatiques Michelin, 23, Place des Carmes, 63040 Clermont-Ferrand, France
| | - Nicolas Seeboth
- Manufacture Française des Pneumatiques Michelin, 23, Place des Carmes, 63040 Clermont-Ferrand, France
| | - Patrice Malfreyt
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| |
Collapse
|
26
|
Kempfer K, Devémy J, Dequidt A, Couty M, Malfreyt P. Development of Coarse-Grained Models for Polymers by Trajectory Matching. ACS OMEGA 2019; 4:5955-5967. [PMID: 31459746 PMCID: PMC6648800 DOI: 10.1021/acsomega.9b00144] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 03/18/2019] [Indexed: 05/21/2023]
Abstract
Coarse-grained (CG) models allow for simulating the necessary time and length scales relevant to polymers. However, developing realistic force fields at the CG level is still a challenge because there is no guarantee that the CG model reproduces all the properties of the atomistic model. A recent promising method was proposed for small molecules using statistical trajectory matching. Here, we extend this method to the case of polymeric systems. As the quality of the final model crucially depends on the model design, we study and discuss the effect of the modeling choices on the structure and dynamics of bulk polymers before a quantitative comparison is made between CG methods on different properties and polymers.
Collapse
Affiliation(s)
- Kévin Kempfer
- Université
Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
- Manufacture
Française des Pneumatiques Michelin, 23, Place des Carmes, 63040 Clermont-Ferrand, France
| | - Julien Devémy
- Université
Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Alain Dequidt
- Université
Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
- E-mail: (A.D.)
| | - Marc Couty
- Manufacture
Française des Pneumatiques Michelin, 23, Place des Carmes, 63040 Clermont-Ferrand, France
| | - Patrice Malfreyt
- Université
Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
- E-mail: (P.M.)
| |
Collapse
|
27
|
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
| |
Collapse
|
28
|
Kempfer K, Devémy J, Dequidt A, Couty M, Malfreyt P. Realistic Coarse-Grain Model of cis-1,4-Polybutadiene: From Chemistry to Rheology. Macromolecules 2019. [DOI: 10.1021/acs.macromol.8b02750] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- K. Kempfer
- CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
- Manufacture Française des Pneumatiques Michelin, 23, Place des Carmes, 63040 Clermont-Ferrand, France
| | - J. Devémy
- CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| | - A. Dequidt
- CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| | - M. Couty
- Manufacture Française des Pneumatiques Michelin, 23, Place des Carmes, 63040 Clermont-Ferrand, France
| | - P. Malfreyt
- CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| |
Collapse
|
29
|
Deichmann G, van der Vegt NFA. Bottom-up approach to represent dynamic properties in coarse-grained molecular simulations. J Chem Phys 2019; 149:244114. [PMID: 30599732 DOI: 10.1063/1.5064369] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Several molecular coarse-graining methods have been proposed in recent years to derive chemical- and state-point transferable force fields. While these force fields describe structural and thermodynamic properties in good agreement with fine-grained models and experiments, dynamic properties are usually overestimated. Herein, we examine if the long-time dynamic properties of molecular coarse-grained (CG) systems can be correctly represented by employing a dissipative particle dynamics (DPD) thermostat, which is "bottom-up informed" by means of a variant of the Markovian Mori-Zwanzig (MZ) DPD coarse-graining method. We report single-site and multiple-site CG models for a monomer, dimer, and 24mer based on 2,2-dimethyl propane as a chemical repeat unit and report data obtained from MZ-DPD simulations of liquids, polymer solutions, and polymer melts. We find that despite incomplete time scale separation of the molecular CG model, MZ-DPD achieves quantitative accuracy in predicting diffusive dynamics in single-component liquids and polymer solutions (24mers in a dimer solvent). We also find that MZ-DPD simulations of molecular penetrant diffusion in polymer networks do not reach quantitative agreement with the fine-grained model. Modeling diffusion governed by the activated barrier crossing of small molecular penetrants in these dense systems requires an accurate description of energy barriers, presumably combined with the treatment of memory effects. The use of a MZ-DPD thermostat extends the scope and applicability of molecular CG models for multicomponent systems where a correct description of the relative diffusion rates of the different components is important.
Collapse
Affiliation(s)
- Gregor Deichmann
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287 Darmstadt, Germany
| | - Nico F A van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287 Darmstadt, Germany
| |
Collapse
|
30
|
Zhang G, Chazirakis A, Harmandaris VA, Stuehn T, Daoulas KC, Kremer K. Hierarchical modelling of polystyrene melts: from soft blobs to atomistic resolution. SOFT MATTER 2019; 15:289-302. [PMID: 30543257 DOI: 10.1039/c8sm01830h] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We demonstrate that hierarchical backmapping strategies incorporating generic blob-based models can equilibrate melts of high-molecular-weight polymers, described with chemically specific, atomistic models. The central idea is first to represent polymers by chains of large soft blobs (spheres) and efficiently equilibrate the melt on large scales. Then, the degrees of freedom of more detailed models are reinserted step by step. The procedure terminates when the atomistic description is reached. Reinsertions are feasible computationally because the fine-grained melt must be re-equilibrated only locally. We consider polystyrene (PS) which is sufficiently complex to serve method development because of stereo-chemistry and bulky side groups. Our backmapping strategy bridges mesoscopic and atomistic scales by incorporating a blob-based, a moderately coarse-grained (CG), and a united-atom model of PS. We demonstrate that the generic blob-based model can be parameterised to reproduce the mesoscale properties of a specific polymer - here PS. The moderately CG model captures stereo-chemistry. To perform backmapping we improve and adjust several fine-graining techniques. We prove equilibration of backmapped PS melts by comparing their structural and conformational properties with reference data from smaller systems, equilibrated with less efficient methods.
Collapse
Affiliation(s)
- Guojie Zhang
- Institute for Systems Rheology, Advanced Institute of Engineering Science for Intelligent Manufacturing, Guangzhou University, 510006 Guangzhou, China.
| | | | | | | | | | | |
Collapse
|