1
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Ye BB, Chen S, Wang ZG. GCMe: Efficient Implementation of the Gaussian Core Model with Smeared Electrostatic Interactions for Molecular Dynamics Simulations of Soft Matter Systems. J Chem Theory Comput 2024; 20:6870-6880. [PMID: 39013595 PMCID: PMC11325544 DOI: 10.1021/acs.jctc.4c00603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
In recent years, molecular dynamics (MD) simulations have emerged as an essential tool for understanding the structure, dynamics, and phase behavior of charged soft matter systems. To explore phenomena across greater length and time scales in MD simulations, molecules are often coarse-grained for better computational performance. However, commonly used force fields represent particles as hard-core interaction centers with point charges, which often overemphasizes the packing effect and short-range electrostatics, especially in systems with bulky deformable organic molecules and systems with strong coarse-graining. This underscores the need for an efficient soft-core model to physically capture the effective interactions between coarse-grained particles. To this end, we implement a soft-core model uniting the Gaussian core model with smeared electrostatic interactions that is phenomenologically equivalent to recent theoretical models. We first parametrize it generically using water as the model solvent. Then, we benchmark its performance in the OpenMM toolkit for different boundary conditions to highlight a computational speedup of up to 34 × compared to commonly used force fields and existing implementations. Finally, we demonstrate its utility by investigating how boundary polarizability affects the adsorption behavior of a polyelectrolyte solution on perfectly conducting and nonmetal boundaries.
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Affiliation(s)
- Benjamin Bobin Ye
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Shensheng Chen
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Zhen-Gang Wang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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2
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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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3
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Zhang D, Wang Y, Safaripour M, Bellido-Aguilar DA, Van Donselaar KR, Webster DC, Croll AB, Xia W. Energy renormalization for temperature transferable coarse-graining of silicone polymer. Phys Chem Chem Phys 2024; 26:4541-4554. [PMID: 38241021 DOI: 10.1039/d3cp05969c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
The bottom-up prediction of thermodynamic and mechanical behaviors of polymeric materials based on molecular dynamics (MD) simulation is of critical importance in polymer physics. Although the atomistically informed coarse-grained (CG) model can access greater spatiotemporal scales and retain essential chemical specificity, the temperature-transferable CG model is still a big challenge and hinders widespread application of this technique. Herein, we use a silicone polymer, i.e., polydimethylsiloxane (PDMS), having an incredibly low chain rigidity as a model system, combined with an energy-renormalization (ER) approach, to systematically develop a temperature-transferable CG model. Specifically, by introducing temperature-dependent ER factors to renormalize the effective distance and cohesive energy parameters, the developed CG model faithfully preserved the dynamics, mechanical and conformational behaviors compared with the target all-atomistic (AA) model from glassy to melt regimes, which was further validated by experimental data. With the developed CG model featuring tremendously improved computational efficiency, we systematically explored the influences of cohesive interaction strength and temperature on the dynamical heterogeneity and mechanical response of polymers, where we observed consistent trends with other linear polymers with varying chain rigidity and monomeric structures. This study serves as an extension of our proposed ER approach of developing temperature transferable CG models with diverse segmental structures, highlighting the critical role of cohesive interaction strength on CG modeling of polymer dynamics and thermomechanical behaviors.
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Affiliation(s)
- Dawei Zhang
- Department of Civil, Construction, and Environmental Engineering, North Dakota State University, Fargo, ND 58108, USA
| | - Yang Wang
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Maryam Safaripour
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, ND 58108, USA
| | - Daniel A Bellido-Aguilar
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, ND 58108, USA
| | | | - Dean C Webster
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, ND 58108, USA
| | - Andrew B Croll
- Department of Physics, North Dakota State University, Fargo, ND 58108, USA
| | - Wenjie Xia
- Department of Aerospace Engineering, Iowa State University, Ames, IA 50011, USA.
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4
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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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5
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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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6
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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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7
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Jin J, Pak AJ, Durumeric AEP, Loose TD, Voth GA. Bottom-up Coarse-Graining: Principles and Perspectives. J Chem Theory Comput 2022; 18:5759-5791. [PMID: 36070494 PMCID: PMC9558379 DOI: 10.1021/acs.jctc.2c00643] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Indexed: 01/14/2023]
Abstract
Large-scale computational molecular models provide scientists a means to investigate the effect of microscopic details on emergent mesoscopic behavior. Elucidating the relationship between variations on the molecular scale and macroscopic observable properties facilitates an understanding of the molecular interactions driving the properties of real world materials and complex systems (e.g., those found in biology, chemistry, and materials science). As a result, discovering an explicit, systematic connection between microscopic nature and emergent mesoscopic behavior is a fundamental goal for this type of investigation. The molecular forces critical to driving the behavior of complex heterogeneous systems are often unclear. More problematically, simulations of representative model systems are often prohibitively expensive from both spatial and temporal perspectives, impeding straightforward investigations over possible hypotheses characterizing molecular behavior. While the reduction in resolution of a study, such as moving from an atomistic simulation to that of the resolution of large coarse-grained (CG) groups of atoms, can partially ameliorate the cost of individual simulations, the relationship between the proposed microscopic details and this intermediate resolution is nontrivial and presents new obstacles to study. Small portions of these complex systems can be realistically simulated. Alone, these smaller simulations likely do not provide insight into collectively emergent behavior. However, by proposing that the driving forces in both smaller and larger systems (containing many related copies of the smaller system) have an explicit connection, systematic bottom-up CG techniques can be used to transfer CG hypotheses discovered using a smaller scale system to a larger system of primary interest. The proposed connection between different CG systems is prescribed by (i) the CG representation (mapping) and (ii) the functional form and parameters used to represent the CG energetics, which approximate potentials of mean force (PMFs). As a result, the design of CG methods that facilitate a variety of physically relevant representations, approximations, and force fields is critical to moving the frontier of systematic CG forward. Crucially, the proposed connection between the system used for parametrization and the system of interest is orthogonal to the optimization used to approximate the potential of mean force present in all systematic CG methods. The empirical efficacy of machine learning techniques on a variety of tasks provides strong motivation to consider these approaches for approximating the PMF and analyzing these approximations.
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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, United States
| | - Alexander J. Pak
- Department of Chemistry,
Chicago Center for Theoretical Chemistry, Institute for Biophysical
Dynamics, and James Franck Institute, The
University of Chicago, Chicago, Illinois 60637, United States
| | - Aleksander E. P. Durumeric
- Department of Chemistry,
Chicago Center for Theoretical Chemistry, Institute for Biophysical
Dynamics, and James Franck Institute, The
University of Chicago, Chicago, Illinois 60637, United States
| | - Timothy D. Loose
- Department of Chemistry,
Chicago Center for Theoretical Chemistry, Institute for Biophysical
Dynamics, and James Franck Institute, The
University of Chicago, Chicago, Illinois 60637, United States
| | - 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, United States
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8
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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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9
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Dhamankar S, Webb MA. Chemically specific coarse‐graining of polymers: Methods and prospects. JOURNAL OF POLYMER SCIENCE 2021. [DOI: 10.1002/pol.20210555] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Satyen Dhamankar
- Department of Chemical and Biological Engineering Princeton University Princeton New Jersey USA
| | - Michael A. Webb
- Department of Chemical and Biological Engineering Princeton University Princeton New Jersey USA
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10
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Peters BL, Salerno KM, Ge T, Perahia D, Grest GS. Viscoelastic Response of Dispersed Entangled Polymer Melts. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c01403] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Brandon L. Peters
- Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - K. Michael Salerno
- U. S. Army Research Laboratory, Aberdeen Proving Grounds, Aberdeen, Maryland 21005, United States
| | - Ting Ge
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Dvora Perahia
- Department of Chemistry and Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, United States
| | - Gary S. Grest
- Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
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11
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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
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12
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Rondina GG, Böhm MC, Müller-Plathe F. Predicting the Mobility Increase of Coarse-Grained Polymer Models from Excess Entropy Differences. J Chem Theory Comput 2020; 16:1431-1447. [DOI: 10.1021/acs.jctc.9b01088] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gustavo G. Rondina
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 8, 64287 Darmstadt, Germany
| | - Michael C. Böhm
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 8, 64287 Darmstadt, Germany
| | - Florian Müller-Plathe
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 8, 64287 Darmstadt, Germany
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13
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Meinel MK, Müller-Plathe F. Loss of Molecular Roughness upon Coarse-Graining Predicts the Artificially Accelerated Mobility of Coarse-Grained Molecular Simulation Models. J Chem Theory Comput 2020; 16:1411-1419. [DOI: 10.1021/acs.jctc.9b00943] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Melissa K. Meinel
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Profile Area Thermofluids and Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Strasse 8, D-64287 Darmstadt, Germany
| | - Florian Müller-Plathe
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Profile Area Thermofluids and Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Strasse 8, D-64287 Darmstadt, Germany
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14
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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.
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15
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Dinpajooh M, Guenza MG. Coarse-graining simulation approaches for polymer melts: the effect of potential range on computational efficiency. SOFT MATTER 2018; 14:7126-7144. [PMID: 30070292 DOI: 10.1039/c8sm00868j] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The integral equation coarse-graining (IECG) approach is a promising high-level coarse-graining (CG) method for polymer melts, with variable resolution from soft spheres to multi CG sites, which preserves the structural and thermodynamical consistencies with the related atomistic simulations. When compared to the atomistic description, the procedure of coarse-graining results in smoother free energy surfaces, longer-ranged potentials, a decrease in the number of interaction sites for a given polymer, and more. Because these changes have competing effects on the computational efficiency of the CG model, care needs to be taken when studying the effect of coarse-graining on the computational speed-up in CG molecular dynamics simulations. For instance, treatment of long-range CG interactions requires the selection of cutoff distances that include the attractive part of the effective CG potential and force. In particular, we show how the complex nature of the range and curvature of the effective CG potential, the selection of a suitable CG timestep, the choice of the cutoff distance, the molecular dynamics algorithms, and the smoothness of the CG free energy surface affect the efficiency of IECG simulations. By direct comparison with the atomistic simulations of relatively short chain polymer melts, we find that the overall computational efficiency is highest for the highest level of CG (soft spheres), with an overall improvement of the computational efficiency being about 106-108 for various CG levels/resolutions. Therefore, the IECG method can have important applications in molecular dynamics simulations of polymeric systems. Finally, making use of the standard spatial decomposition algorithm, the parallel scalability of the IECG simulations for various levels of CG is presented. Optimal parallel scaling is observed for a reasonably large number of processors. Although this study is performed using the IECG approach, its results on the relation between the level of CG and the computational efficiency are general and apply to any properly-constructed CG model.
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Affiliation(s)
- Mohammadhasan Dinpajooh
- Department of Chemistry and Biochemistry, and Institute of Theoretical Science, University of Oregon, Eugene, Oregon 97403, USA.
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16
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Guenza MG, Dinpajooh M, McCarty J, Lyubimov IY. Accuracy, Transferability, and Efficiency of Coarse-Grained Models of Molecular Liquids. J Phys Chem B 2018; 122:10257-10278. [DOI: 10.1021/acs.jpcb.8b06687] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M. G. Guenza
- Department of Chemistry and Biochemistry and Institute of Theoretical Science, University of Oregon, Eugene, Oregon 97403, United States
| | - M. Dinpajooh
- Department of Chemistry and Biochemistry and Institute of Theoretical Science, University of Oregon, Eugene, Oregon 97403, United States
| | - J. McCarty
- Department of Chemistry and Biochemistry and Institute of Theoretical Science, University of Oregon, Eugene, Oregon 97403, United States
| | - I. Y. Lyubimov
- Department of Chemistry and Biochemistry and Institute of Theoretical Science, University of Oregon, Eugene, Oregon 97403, United States
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17
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Peters BL, Salerno KM, Ge T, Perahia D, Grest GS. Effect of Chain Length Dispersity on the Mobility of Entangled Polymers. PHYSICAL REVIEW LETTERS 2018; 121:057802. [PMID: 30118305 DOI: 10.1103/physrevlett.121.057802] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Indexed: 06/08/2023]
Abstract
While nearly all theoretical and computational studies of entangled polymer melts have focused on uniform samples, polymer synthesis routes always result in some dispersity, albeit narrow, of distribution of molecular weights (Đ_{M}=M_{w}/M_{n}∼1.02-1.04). Here, the effects of dispersity on chain mobility are studied for entangled, disperse melts using a coarse-grained model for polyethylene. Polymer melts with chain lengths set to follow a Schulz-Zimm distribution for the same average M_{w}=36 kg/mol with Đ_{M}=1.0 to 1.16, were studied for times of 600-800 μs using molecular dynamics simulations. This time frame is longer than the time required to reach the diffusive regime. We find that dispersity in this range does not affect the entanglement time or tube diameter. However, while there is negligible difference in the average mobility of chains for the uniform distribution Đ_{M}=1.0 and Đ_{M}=1.02, the shortest chains move significantly faster than the longest ones offering a constraint release pathway for the melts for larger Đ_{M}.
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Affiliation(s)
- Brandon L Peters
- Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | | | - Ting Ge
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA
| | - Dvora Perahia
- Department of Chemistry and Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, USA
| | - Gary S Grest
- Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
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18
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Xia W, Song J, Hansoge NK, Phelan FR, Keten S, Douglas JF. Energy Renormalization for Coarse-Graining the Dynamics of a Model Glass-Forming Liquid. J Phys Chem B 2018; 122:2040-2045. [PMID: 29400063 PMCID: PMC6217959 DOI: 10.1021/acs.jpcb.8b00321] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Coarse-grained modeling achieves the enhanced computational efficiency required to model glass-forming materials by integrating out "unessential" molecular degrees of freedom, but no effective temperature transferable coarse-graining method currently exists to capture dynamics. We address this fundamental problem through an energy-renormalization scheme, in conjunction with the localization model of relaxation relating the Debye-Waller factor ⟨u2⟩ to the structural relaxation time τ. Taking ortho-terphenyl as a model small-molecule glass-forming liquid, we show that preserving ⟨u2⟩ (at picosecond time scale) under coarse-graining by renormalizing the cohesive interaction strength allows for quantitative prediction of both short- and long-time dynamics covering the entire temperature range of glass formation. Our findings provide physical insights into the dynamics of cooled liquids and make progress for building temperature-transferable coarse-grained models that predict key properties of glass-forming materials.
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Affiliation(s)
- Wenjie Xia
- Materials Science & Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
- Center for Hierarchical Materials Design, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3109, United States
- Department of Civil & Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3109, United States
| | - Jake Song
- Department of Materials Science & Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3109, United States
| | - Nitin K. Hansoge
- Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3109, United States
| | - Frederick R. Phelan
- Materials Science & Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Sinan Keten
- Department of Civil & Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3109, United States
- Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3109, United States
| | - Jack F. Douglas
- Materials Science & Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
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Song J, Hsu DD, Shull KR, Phelan FR, Douglas JF, Xia W, Keten S. Energy Renormalization Method for the Coarse-Graining of Polymer Viscoelasticity. Macromolecules 2018; 51:10.1021/acs.macromol.7b02560. [PMID: 30996476 PMCID: PMC6463302 DOI: 10.1021/acs.macromol.7b02560] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Developing temperature transferable coarse-grained (CG) models is essential for the computational prediction of polymeric glass-forming (GF) material behavior, but their dynamics are often greatly altered from those of all-atom (AA) models mainly because of the reduced fluid configurational entropy under coarse-graining. To address this issue, we have recently introduced an energy renormalization (ER) strategy that corrects the activation free energy of the CG polymer model by renormalizing the cohesive interaction strength ε as a function of temperature T, i.e., ε(T), thus semiempirically preserving the T-dependent dynamics of the AA model. Here we apply our ER method to consider-in addition to T-dependency-the frequency f-dependent polymer viscoelasticity. Through smallamplitude oscillatory shear molecular dynamics simulations, we show that changing the imposed oscillation f on the CG systems requires changes in ε values (i.e., ε(T, f)) to reproduce the AA viscoelasticity. By accounting for the dynamic fragility of polymers as a material parameter, we are able to predict ε(T, f) under coarse-graining in order to capture the AA viscoelasticity, and consequently the activation energy, across a wide range of T and f in the GF regime. Specifically, we showcase our achievements on two representative polymers of distinct fragilities, polybutadiene (PB) and polystyrene (PS), and show that our CG models are able to sample viscoelasticity up to the megahertz regime, which approaches state-of-the-art experimental resolutions, and capture results sampled via AA simulations and prior experiments.
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Affiliation(s)
- Jake Song
- Department of Materials Science & Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3109, United States
| | - David D. Hsu
- Department of Physics and Engineering, Wheaton College, 501 College Avenue, Wheaton, Illinois 60187, United States
| | - Kenneth R. Shull
- Department of Materials Science & Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3109, United States
| | - Frederick R. Phelan
- Materials Science & Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Jack F. Douglas
- Materials Science & Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Wenjie Xia
- Department of Civil & Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3109, United States
- Center for Hierarchical Materials Design, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3109, United States
- Materials Science & Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Sinan Keten
- Department of Civil & Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3109, United States
- Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3109, United States
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Peters BL, Salerno KM, Agrawal A, Perahia D, Grest GS. Coarse-Grained Modeling of Polyethylene Melts: Effect on Dynamics. J Chem Theory Comput 2017; 13:2890-2896. [PMID: 28535348 DOI: 10.1021/acs.jctc.7b00241] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The distinctive viscoelastic behavior of polymers results from a coupled interplay of motion on multiple length and time scales. Capturing the broad time and length scales of polymer motion remains a challenge. Using polyethylene (PE) as a model macromolecule, we construct coarse-grained (CG) models of PE with three to six methyl groups per CG bead and probe two critical aspects of the technique: pressure corrections required after iterative Boltzmann inversion (IBI) to generate CG potentials that match the pressure of reference fully atomistic melt simulations and the transferability of CG potentials across temperatures. While IBI produces nonbonded pair potentials that give excellent agreement between the atomistic and CG pair correlation functions, the resulting pressure for the CG models is large compared with the pressure of the atomistic system. We find that correcting the potential to match the reference pressure leads to nonbonded interactions with much deeper minima and slightly smaller effective bead diameter. However, simulations with potentials generated by IBI and pressure-corrected IBI result in similar mean-square displacements (MSDs) and stress autocorrelation functions G(t) for PE melts. While the time rescaling factor required to match CG and atomistic models is the same for pressure- and non-pressure-corrected CG models, it strongly depends on temperature. Transferability was investigated by comparing the MSDs and stress autocorrelation functions for potentials developed at different temperatures.
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Affiliation(s)
- Brandon L Peters
- Sandia National Laboratories , Albuquerque, New Mexico 87185, United States
| | - K Michael Salerno
- U.S. Naval Research Laboratory , Washington, D.C. 20375, United States
| | - Anupriya Agrawal
- Department of Mechanical Engineering and Materials Science, Washington University in St. Louis , St. Louis, Missouri 63130, United States
| | - Dvora Perahia
- Department of Chemistry, Clemson University , Clemson, South Carolina 29634, United States
| | - Gary S Grest
- Sandia National Laboratories , Albuquerque, New Mexico 87185, United States
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Gooneie A, Schuschnigg S, Holzer C. A Review of Multiscale Computational Methods in Polymeric Materials. Polymers (Basel) 2017; 9:E16. [PMID: 30970697 PMCID: PMC6432151 DOI: 10.3390/polym9010016] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 12/07/2016] [Accepted: 12/22/2016] [Indexed: 11/17/2022] Open
Abstract
Polymeric materials display distinguished characteristics which stem from the interplay of phenomena at various length and time scales. Further development of polymer systems critically relies on a comprehensive understanding of the fundamentals of their hierarchical structure and behaviors. As such, the inherent multiscale nature of polymer systems is only reflected by a multiscale analysis which accounts for all important mechanisms. Since multiscale modelling is a rapidly growing multidisciplinary field, the emerging possibilities and challenges can be of a truly diverse nature. The present review attempts to provide a rather comprehensive overview of the recent developments in the field of multiscale modelling and simulation of polymeric materials. In order to understand the characteristics of the building blocks of multiscale methods, first a brief review of some significant computational methods at individual length and time scales is provided. These methods cover quantum mechanical scale, atomistic domain (Monte Carlo and molecular dynamics), mesoscopic scale (Brownian dynamics, dissipative particle dynamics, and lattice Boltzmann method), and finally macroscopic realm (finite element and volume methods). Afterwards, different prescriptions to envelope these methods in a multiscale strategy are discussed in details. Sequential, concurrent, and adaptive resolution schemes are presented along with the latest updates and ongoing challenges in research. In sequential methods, various systematic coarse-graining and backmapping approaches are addressed. For the concurrent strategy, we aimed to introduce the fundamentals and significant methods including the handshaking concept, energy-based, and force-based coupling approaches. Although such methods are very popular in metals and carbon nanomaterials, their use in polymeric materials is still limited. We have illustrated their applications in polymer science by several examples hoping for raising attention towards the existing possibilities. The relatively new adaptive resolution schemes are then covered including their advantages and shortcomings. Finally, some novel ideas in order to extend the reaches of atomistic techniques are reviewed. We conclude the review by outlining the existing challenges and possibilities for future research.
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Affiliation(s)
- Ali Gooneie
- Chair of Polymer Processing, Montanuniversitaet Leoben, Otto Gloeckel-Strasse 2, 8700 Leoben, Austria.
| | - Stephan Schuschnigg
- Chair of Polymer Processing, Montanuniversitaet Leoben, Otto Gloeckel-Strasse 2, 8700 Leoben, Austria.
| | - Clemens Holzer
- Chair of Polymer Processing, Montanuniversitaet Leoben, Otto Gloeckel-Strasse 2, 8700 Leoben, Austria.
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Salerno KM, Agrawal A, Perahia D, Grest GS. Resolving Dynamic Properties of Polymers through Coarse-Grained Computational Studies. PHYSICAL REVIEW LETTERS 2016; 116:058302. [PMID: 26894738 DOI: 10.1103/physrevlett.116.058302] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Indexed: 06/05/2023]
Abstract
Coupled length and time scales determine the dynamic behavior of polymers and underlie their unique viscoelastic properties. To resolve the long-time dynamics it is imperative to determine which time and length scales must be correctly modeled. Here we probe the degree of coarse graining required to simultaneously retain significant atomistic details and access large length and time scales. The degree of coarse graining in turn sets the minimum length scale instrumental in defining polymer properties and dynamics. Using linear polyethylene as a model system, we probe how the coarse-graining scale affects the measured dynamics. Iterative Boltzmann inversion is used to derive coarse-grained potentials with 2-6 methylene groups per coarse-grained bead from a fully atomistic melt simulation. We show that atomistic detail is critical to capturing large-scale dynamics. Using these models we simulate polyethylene melts for times over 500 μs to study the viscoelastic properties of well-entangled polymer melts.
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Affiliation(s)
| | - Anupriya Agrawal
- Department of Mechanical Engineering and Materials Science, Washington University, St. Louis, Missouri 63130, USA
- Department of Chemistry, Clemson University, Clemson, South Carolina 29634, USA
| | - Dvora Perahia
- Department of Chemistry, Clemson University, Clemson, South Carolina 29634, USA
| | - Gary S Grest
- Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
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Guenza MG. Structural and thermodynamic consistency in coarse-grained models of macromolecules. ACTA ACUST UNITED AC 2015. [DOI: 10.1088/1742-6596/640/1/012009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Pandey YN, Brayton A, Burkhart C, Papakonstantopoulos GJ, Doxastakis M. Multiscale modeling of polyisoprene on graphite. J Chem Phys 2014; 140:054908. [DOI: 10.1063/1.4863918] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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Clark AJ, McCarty J, Guenza MG. Effective potentials for representing polymers in melts as chains of interacting soft particles. J Chem Phys 2013; 139:124906. [DOI: 10.1063/1.4821818] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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