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Dinpajooh M, Millis J, Donley JP, Guenza MG. Chemical Potential of a Flexible Polymer Liquid in a Coarse-Grained Representation. J Phys Chem B 2024; 128:1275-1288. [PMID: 38109172 DOI: 10.1021/acs.jpcb.3c06795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
While the excess chemical potential is the key quantity in determining phase diagrams, its direct computation for high-density liquids of long polymer chains has posed a significant challenge. Computationally, the excess chemical potential is calculated using the Widom insertion method, which involves monitoring the change in internal energy as one incrementally introduces individual molecules into the liquid. However, when dealing with dense polymer liquids, inserting long chains requires generating trial configurations with a bias that favors those at low energy on a unit-by-unit basis: a procedure that becomes more challenging as the number of units increases. Thus, calculating the excess chemical potential of dense polymer liquids using this method becomes computationally intractable as the chain length exceeds N ≥ 30. Here, we adopt a coarse-grained model derived from the integral equation theory for which inserting long polymer chains becomes feasible. The integral equation theory of coarse graining (IECG) represents a polymer as a sphere or a collection of blobs interacting through a soft potential. We employ the IECG approach to compute the excess chemical potential using Widom's method for polymer chains of increasing lengths, extending up to N = 720 monomers, and at densities reaching up to ρ = 0.767 g/cm3. From a fundamental perspective, we demonstrate that the excess chemical potentials remain nearly constant across various levels of coarse graining, offering valuable insights into the consistency of this type of procedure. Ultimately, we argue that current Monte Carlo algorithms, originally designed for atomistic simulations, such as configurational bias Monte Carlo (CBMC) methods, can significantly benefit from the integration of the IECG approach, thereby enhancing their performance in the study of phase diagrams of polymer liquids.
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Affiliation(s)
- M Dinpajooh
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403, United States
| | - J Millis
- Department of Physics, University of Oregon, Eugene, Oregon 97403, United States
| | - J P Donley
- Material Science Institute, University of Oregon, Eugene, Oregon 97403, United States
| | - M G Guenza
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403, United States
- Department of Physics, University of Oregon, Eugene, Oregon 97403, United States
- Material Science Institute, University of Oregon, Eugene, Oregon 97403, United States
- Institute for Fundamental Science, University of Oregon, Eugene, Oregon 97403, United States
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2
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Abstract
Coarse-grained models have proven helpful for simulating complex systems over long time scales to provide molecular insights into various processes. Methodologies for systematic parametrization of the underlying energy function or force field that describes the interactions among different components of the system are of great interest for ensuring simulation accuracy. We present a new method, potential contrasting, to enable efficient learning of force fields that can accurately reproduce the conformational distribution produced with all-atom simulations. Potential contrasting generalizes the noise contrastive estimation method with umbrella sampling to better learn the complex energy landscape of molecular systems. When applied to the Trp-cage protein, we found that the technique produces force fields that thoroughly capture the thermodynamics of the folding process despite the use of only α-carbons in the coarse-grained model. We further showed that potential contrasting could be applied over large data sets that combine the conformational ensembles of many proteins to improve force field transferability. We anticipate potential contrasting as a powerful tool for building general-purpose coarse-grained force fields.
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Affiliation(s)
- Xinqiang Ding
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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3
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Stieffenhofer M, Scherer C, May F, Bereau T, Andrienko D. Benchmarking coarse-grained models of organic semiconductors via deep backmapping. Front Chem 2022; 10:982757. [PMID: 36157043 PMCID: PMC9500322 DOI: 10.3389/fchem.2022.982757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 07/22/2022] [Indexed: 11/13/2022] Open
Abstract
The potential of mean force is an effective coarse-grained potential, which is often approximated by pairwise potentials. While the approximated potential reproduces certain distributions of the reference all-atom model with remarkable accuracy, important cross-correlations are typically not captured. In general, the quality of coarse-grained models is evaluated at the coarse-grained resolution, hindering the detection of important discrepancies between the all-atom and coarse-grained ensembles. In this work, the quality of different coarse-grained models is assessed at the atomistic resolution deploying reverse-mapping strategies. In particular, coarse-grained structures for Tris-Meta-Biphenyl-Triazine are reverse-mapped from two different sources: 1) All-atom configurations projected onto the coarse-grained resolution and 2) snapshots obtained by molecular dynamics simulations based on the coarse-grained force fields. To assess the quality of the coarse-grained models, reverse-mapped structures of both sources are compared revealing significant discrepancies between the all-atom and the coarse-grained ensembles. Specifically, the reintroduced details enable force computations based on the all-atom force field that yield a clear ranking for the quality of the different coarse-grained models.
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Affiliation(s)
| | | | | | - Tristan Bereau
- Van ‘t Hoff Institute for Molecular Sciences and Informatics Institute, University of Amsterdam, Amsterdam, Netherlands
| | - Denis Andrienko
- Max Planck Institute for Polymer Research, Mainz, Germany
- *Correspondence: Denis Andrienko,
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4
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DeLyser MR, Noid WG. Coarse-grained models for local density gradients. J Chem Phys 2022; 156:034106. [DOI: 10.1063/5.0075291] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- Michael R. DeLyser
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, USA
| | - W. G. Noid
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, USA
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5
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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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6
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Sherck N, Shen K, Nguyen M, Yoo B, Köhler S, Speros JC, Delaney KT, Shell MS, Fredrickson GH. Molecularly Informed Field Theories from Bottom-up Coarse-Graining. ACS Macro Lett 2021; 10:576-583. [PMID: 35570772 DOI: 10.1021/acsmacrolett.1c00013] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Polymer formulations possessing mesostructures or phase coexistence are challenging to simulate using atomistic particle-explicit approaches due to the disparate time and length scales, while the predictive capability of field-based simulations is hampered by the need to specify interactions at a coarser scale (e.g., χ-parameters). To overcome the weaknesses of both, we introduce a bottom-up coarse-graining methodology that leverages all-atom molecular dynamics to molecularly inform coarser field-theoretic models. Specifically, we use relative-entropy coarse-graining to parametrize particle models that are directly and analytically transformable into statistical field theories. We demonstrate the predictive capability of this approach by reproducing experimental aqueous poly(ethylene oxide) (PEO) cloud-point curves with no parameters fit to experimental data. This synergistic approach to multiscale polymer simulations opens the door to de novo exploration of phase behavior across a wide variety of polymer solutions and melt formulations.
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Affiliation(s)
- Nicholas Sherck
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Kevin Shen
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
- Materials Research Laboratory, University of California, Santa Barbara, California 93106, United States
| | - My Nguyen
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Brian Yoo
- BASF Corporation, Tarrytown, New York 10591, United States
| | | | - Joshua C. Speros
- California Research Alliance (CARA) by BASF, Berkeley, California 94720, United States
| | - Kris T. Delaney
- Materials Research Laboratory, University of California, Santa Barbara, California 93106, United States
| | - M. Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Glenn H. Fredrickson
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
- Materials Research Laboratory, University of California, Santa Barbara, California 93106, United States
- Department of Materials, University of California, Santa Barbara, California 93106, United States
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7
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Szukalo RJ, Noid WG. Investigating the energetic and entropic components of effective potentials across a glass transition. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 33:154004. [PMID: 33498016 DOI: 10.1088/1361-648x/abdff8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/26/2021] [Indexed: 06/12/2023]
Abstract
By eliminating unnecessary details, coarse-grained (CG) models provide the necessary efficiency for simulating scales that are inaccessible to higher resolution models. However, because they average over atomic details, the effective potentials governing CG degrees of freedom necessarily incorporate significant entropic contributions, which limit their transferability and complicate the treatment of thermodynamic properties. This work employs a dual-potential approach to consider the energetic and entropic contributions to effective interaction potentials for CG models. Specifically, we consider one- and three-site CG models for ortho-terphenyl (OTP) both above and below its glass transition. We employ the multiscale coarse-graining (MS-CG) variational principle to determine interaction potentials that accurately reproduce the structural properties of an all-atom (AA) model for OTP at each state point. We employ an energy-matching variational principle to determine an energy operator that accurately reproduces the intra- and inter-molecular energy of the AA model. While the MS-CG pair potentials are almost purely repulsive, the corresponding pair energy functions feature a pronounced minima that corresponds to contacting benzene rings. These energetic functions then determine an estimate for the entropic component of the MS-CG interaction potentials. These entropic functions accurately predict the MS-CG pair potentials across a wide range of liquid state points at constant density. Moreover, the entropic functions also predict pair potentials that quite accurately model the AA pair structure below the glass transition. Thus, the dual-potential approach appears a promising approach for modeling AA energetics, as well as for predicting the temperature-dependence of CG effective potentials.
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Affiliation(s)
- Ryan J Szukalo
- Department of Chemistry, Penn State University, University Park, PA 16802 United States of America
| | - W G Noid
- Department of Chemistry, Penn State University, University Park, PA 16802 United States of America
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8
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Wu Z, Milano G, Müller-Plathe F. Combination of Hybrid Particle-Field Molecular Dynamics and Slip-Springs for the Efficient Simulation of Coarse-Grained Polymer Models: Static and Dynamic Properties of Polystyrene Melts. J Chem Theory Comput 2020; 17:474-487. [PMID: 33275441 DOI: 10.1021/acs.jctc.0c00954] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A quantitative prediction of polymer-entangled dynamics based on molecular simulation is a grand challenge in contemporary computational material science. The drastic increase of relaxation time and viscosity in high-molecular-weight polymeric fluids essentially limits the usage of classic molecular dynamics simulation. Here, we demonstrate a systematic coarse-graining approach for modeling entangled polymers under the slip-spring particle-field scheme. Specifically, a frequency-controlled slip-spring model, a hybrid particle-field model, and a coarse-grained model of polystyrene melts are combined into a hybrid simulation technique. Via a rigorous parameterization strategy to determine the parameters in slip-springs from existing experimental or simulation data, we show that the reptation behavior is clearly observed in multiple characteristics of polymer dynamics, mean-square displacements, diffusion coefficients, reorientational relaxation, and Rouse mode analysis, consistent with the predictions of the tube theory. All dynamical properties of the slip-spring particle-field models are in good agreement with classic molecular dynamics models. Our work provides an efficient and practical approach to establish chemical-specific coarse-grained models for predicting polymer-entangled dynamics.
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Affiliation(s)
- Zhenghao Wu
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 8, 64287 Darmstadt, Germany
| | - Giuseppe Milano
- Department of Organic Materials Science, Yamagata University, 4-3-16 Jonan, Yonezawa, 992-8510 Yamagata-ken, Japan
| | - Florian Müller-Plathe
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 8, 64287 Darmstadt, Germany
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9
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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
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10
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Lebold KM, Noid WG. Dual-potential approach for coarse-grained implicit solvent models with accurate, internally consistent energetics and predictive transferability. J Chem Phys 2019; 151:164113. [PMID: 31675902 DOI: 10.1063/1.5125246] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The dual-potential approach promises coarse-grained (CG) models that accurately reproduce both structural and energetic properties, while simultaneously providing predictive estimates for the temperature-dependence of the effective CG potentials. In this work, we examine the dual-potential approach for implicit solvent CG models that reflect large entropic effects from the eliminated solvent. Specifically, we construct implicit solvent models at various resolutions, R, by retaining a fraction 0.10 ≤ R ≤ 0.95 of the molecules from a simple fluid of Lennard-Jones spheres. We consider the dual-potential approach in both the constant volume and constant pressure ensembles across a relatively wide range of temperatures. We approximate the many-body potential of mean force for the remaining solutes with pair and volume potentials, which we determine via multiscale coarse-graining and self-consistent pressure-matching, respectively. Interestingly, with increasing temperature, the pair potentials appear increasingly attractive, while the volume potentials become increasingly repulsive. The dual-potential approach not only reproduces the atomic energetics but also quite accurately predicts this temperature-dependence. We also derive an exact relationship between the thermodynamic specific heat of an atomic model and the energetic fluctuations that are observable at the CG resolution. With this generalized fluctuation relationship, the approximate CG models quite accurately reproduce the thermodynamic specific heat of the underlying atomic model.
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Affiliation(s)
- Kathryn M Lebold
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, USA
| | - W G Noid
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, USA
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11
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Dannenhoffer-Lafage T, Wagner JW, Durumeric AEP, Voth GA. Compatible observable decompositions for coarse-grained representations of real molecular systems. J Chem Phys 2019; 151:134115. [PMID: 31594316 DOI: 10.1063/1.5116027] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Coarse-grained (CG) observable expressions, such as pressure or potential energy, are generally different than their fine-grained (FG, e.g., atomistic) counterparts. Recently, we analyzed this so-called "representability problem" in Wagner et al. [J. Chem. Phys. 145, 044108 (2016)]. While the issue of representability was clearly and mathematically stated in that work, it was not made clear how to actually determine CG observable expressions from the underlying FG systems that can only be simulated numerically. In this work, we propose minimization targets for the CG observables of such systems. These CG observables are compatible with each other and with structural observables. Also, these CG observables are systematically improvable since they are variationally minimized. Our methods are local and data efficient because we decompose the observable contributions. Hence, our approaches are called the multiscale compatible observable decomposition (MS-CODE) and the relative entropy compatible observable decomposition (RE-CODE), which reflect two main approaches to the "bottom-up" coarse-graining of real FG systems. The parameterization of these CG observable expressions requires the introduction of new, symmetric basis sets and one-body terms. We apply MS-CODE and RE-CODE to 1-site and 2-site CG models of methanol for the case of pressure, as well as to 1-site methanol and acetonitrile models for potential energy.
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Affiliation(s)
- Thomas Dannenhoffer-Lafage
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, USA
| | - Jacob W Wagner
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, USA
| | - Aleksander E P Durumeric
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, USA
| | - Gregory A Voth
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, USA
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12
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Oprzeska-Zingrebe EA, Smiatek J. Some Notes on the Thermodynamic Accuracy of Coarse-Grained Models. Front Mol Biosci 2019; 6:87. [PMID: 31552269 PMCID: PMC6746972 DOI: 10.3389/fmolb.2019.00087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 08/27/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Ewa Anna Oprzeska-Zingrebe
- Institute for Computational Physics, Theoretical Chemical Physics, University of Stuttgart, Stuttgart, Germany
| | - Jens Smiatek
- Institute for Computational Physics, Theoretical Chemical Physics, University of Stuttgart, Stuttgart, Germany
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13
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Dinpajooh M, Guenza MG. Can pure polymer liquids be represented at two different resolutions simultaneously? J Chem Phys 2019. [DOI: 10.1063/1.5115791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Affiliation(s)
- M. Dinpajooh
- Department of Chemistry and Biochemistry, and Institute of Theoretical Science, University of Oregon, Eugene, Oregon 97403, USA
| | - M. G. Guenza
- Department of Chemistry and Biochemistry, and Institute of Theoretical Science, University of Oregon, Eugene, Oregon 97403, USA
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14
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Lebold KM, Noid WG. Dual approach for effective potentials that accurately model structure and energetics. J Chem Phys 2019; 150:234107. [PMID: 31228924 DOI: 10.1063/1.5094330] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Because they eliminate unnecessary degrees of freedom, coarse-grained (CG) models enable studies of phenomena that are intractable with more detailed models. For the same reason, the effective potentials that govern CG degrees of freedom incorporate entropic contributions from the eliminated degrees of freedom. Consequently, these effective potentials demonstrate limited transferability and provide a poor estimate of atomic energetics. Here, we propose a simple dual-potential approach that combines "structure-based" and "energy-based" variational principles to determine effective potentials that model free energies and potential energies, respectively, as a function of the CG configuration. We demonstrate this approach for 1-site CG models of water and methanol. We accurately sample configuration space by performing simulations with the structure-based potential. We accurately estimate average atomic energies by postprocessing the sampled configurations with the energy-based potential. Finally, the difference between the two potentials predicts a qualitatively accurate estimate for the temperature dependence of the structure-based potential.
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Affiliation(s)
- Kathryn M Lebold
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, USA
| | - W G Noid
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, USA
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15
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Lebold KM, Noid WG. Systematic study of temperature and density variations in effective potentials for coarse-grained models of molecular liquids. J Chem Phys 2019; 150:014104. [DOI: 10.1063/1.5050509] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Affiliation(s)
- Kathryn M. Lebold
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, USA
| | - W. G. Noid
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, USA
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16
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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.
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Affiliation(s)
- Guojie Zhang
- Institute for Systems Rheology, Advanced Institute of Engineering Science for Intelligent Manufacturing, Guangzhou University, 510006 Guangzhou, China.
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17
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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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18
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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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19
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Dinpajooh M, Guenza MG. On the Density Dependence of the Integral Equation Coarse-Graining Effective Potential. J Phys Chem B 2017; 122:3426-3440. [DOI: 10.1021/acs.jpcb.7b10494] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mohammadhasan Dinpajooh
- Department of Chemistry and Biochemistry, and Institute of Theoretical Science, University of Oregon, Eugene, Oregon 97403, United States
| | - Marina G. Guenza
- Department of Chemistry and Biochemistry, and Institute of Theoretical Science, University of Oregon, Eugene, Oregon 97403, United States
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20
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Affiliation(s)
- Zhen-Gang Wang
- Division of Chemistry and
Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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21
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DeLyser MR, Noid WG. Extending pressure-matching to inhomogeneous systems via local-density potentials. J Chem Phys 2017; 147:134111. [DOI: 10.1063/1.4999633] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Michael R. DeLyser
- Department of Chemistry, Penn State University, University
Park, Pennsylvania 16802, USA
| | - William G. Noid
- Department of Chemistry, Penn State University, University
Park, Pennsylvania 16802, USA
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22
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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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23
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Systematic and simulation-free coarse graining of multi-component polymeric systems: Structure-based coarse graining of binary polymer blends. POLYMER 2017. [DOI: 10.1016/j.polymer.2017.04.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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24
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25
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The recent structure-based coarse graining of polymer melts using PRISM theory does not give thermodynamic consistency. POLYMER 2017. [DOI: 10.1016/j.polymer.2017.01.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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26
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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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27
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Chao H, Koski J, Riggleman RA. Solvent vapor annealing in block copolymer nanocomposite films: a dynamic mean field approach. SOFT MATTER 2016; 13:239-249. [PMID: 27320693 DOI: 10.1039/c6sm00770h] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Polymer nanocomposites are an important class of materials due to the nanoparticles' ability to impart functionality not commonly found in a polymer matrix, such as electrical conductivity or tunable optical properties. While the equilibrium properties of polymer nanocomposites can be treated using numerous theoretical and simulation approaches, in experiments the effects of processing and kinetic traps are significant and thus critical for understanding the structure and the functionality of polymer nanocomposites. However, simulation methods that can efficiently predict kinetically trapped and metastable structures of polymer nanocomposites are currently not common. This is particularly important in inhomogeneous polymers such as block copolymers, where techniques such as solvent vapor annealing are commonly employed to improve the long-range order. In this work, we introduce a dynamic mean field theory that is capable of predicting the result of processing the structure of polymer nanocomposites, and we demonstrate that our method accurately predicts the equilibrium properties of a model system more efficiently than a particle-based model. We subsequently use our method to predict the structure of block copolymer thin films with grafted nanoparticles after solvent annealing, where we find that the final distribution of the grafted nanoparticles can be controlled by varying the solvent evaporation rate. The extent to which the solvent evaporation rate can affect the final nanoparticle distribution in the film depends on the grafting density and the length of the grafted chains. Furthermore, the effects of the solvent evaporation rate can be anticipated from the equilibrium nanoparticle distribution in the swollen and dry states.
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Affiliation(s)
- Huikuan Chao
- Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Jason Koski
- Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Robert A Riggleman
- Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA.
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28
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Dunn NJH, Foley TT, Noid WG. Van der Waals Perspective on Coarse-Graining: Progress toward Solving Representability and Transferability Problems. Acc Chem Res 2016; 49:2832-2840. [PMID: 27993007 DOI: 10.1021/acs.accounts.6b00498] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Low-resolution coarse-grained (CG) models provide the necessary efficiency for simulating phenomena that are inaccessible to more detailed models. However, in order to realize their considerable promise, CG models must accurately describe the relevant physical forces and provide useful predictions. By formally integrating out the unnecessary details from an all-atom (AA) model, "bottom-up" approaches can, at least in principle, quantitatively reproduce the structural and thermodynamic properties of the AA model that are observable at the CG resolution. In practice, though, bottom-up approaches only approximate this "exact coarse-graining" procedure. The resulting models typically reproduce the intermolecular structure of AA models at a single thermodynamic state point but often describe other state points less accurately and, moreover, tend to provide a poor description of thermodynamic properties. These two limitations have been coined the "transferability" and "representability" problems, respectively. Perhaps, the simplest and most commonly discussed manifestation of the representability problem regards the tendency of structure-based CG models to dramatically overestimate the pressure. Furthermore, when these models are adjusted to reproduce the pressure, they provide a poor description of the compressibility. More generally, it is sometimes suggested that CG models are fundamentally incapable of reproducing both structural and thermodynamic properties. After all, there is no such thing as a "free lunch"; any significant gain in computational efficiency should come at the cost of significant model limitations. At least in the case of structural and thermodynamic properties, though, we optimistically propose that this may be a false dichotomy. Accordingly, we have recently re-examined the "exact coarse-graining" procedure and investigated the intrinsic consequences of representing an AA model in reduced resolution. These studies clarify the origin and inter-relationship of representability and transferability problems. Both arise as consequences of transferring thermodynamic information from the high resolution configuration space and encoding this information into the many-body potential of mean force (PMF), that is, the potential that emerges from an exact coarse-graining procedure. At least in principle, both representability and transferability problems can be resolved by properly addressing this thermodynamic information. In particular, we have demonstrated that "pressure-matching" provides a practical and rigorous means for addressing the density dependence of the PMF. The resulting bottom-up models accurately reproduce the structure, equilibrium density, compressibility, and pressure equation of state for AA models of molecular liquids. Additionally, we have extended this approach to develop transferable potentials that provide similar accuracy for heptane-toluene mixtures. Moreover, these potentials provide predictive accuracy for modeling concentrations that were not considered in their parametrization. More generally, this work suggests a "van der Waals" perspective on coarse-graining, in which conventional structure-based methods accurately describe the configuration dependence of the PMF, while independent variational principles infer the thermodynamic information that is necessary to resolve representability and transferability problems.
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Affiliation(s)
- Nicholas J. H. Dunn
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Thomas T. Foley
- Department
of Physics, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - William G. Noid
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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29
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Fraaije JGEM, van Male J, Becherer P, Serral Gracià R. Coarse-Grained Models for Automated Fragmentation and Parametrization of Molecular Databases. J Chem Inf Model 2016; 56:2361-2377. [DOI: 10.1021/acs.jcim.6b00003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Johannes G. E. M. Fraaije
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
- Culgi BV, Galileiweg 8, 2333 BD Leiden, The Netherlands
| | - Jan van Male
- Culgi BV, Galileiweg 8, 2333 BD Leiden, The Netherlands
| | - Paul Becherer
- Culgi BV, Galileiweg 8, 2333 BD Leiden, The Netherlands
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30
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Agrawal V, Peralta P, Li Y, Oswald J. A pressure-transferable coarse-grained potential for modeling the shock Hugoniot of polyethylene. J Chem Phys 2016; 145:104903. [DOI: 10.1063/1.4962255] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Vipin Agrawal
- School for the Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, USA
| | - Pedro Peralta
- School for the Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, USA
| | - Yiyang Li
- School for the Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, USA
| | - Jay Oswald
- School for the Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, USA
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31
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D’Adamo G, Pelissetto A, Pierleoni C. Phase Diagram and Structure of Mixtures of Large Colloids and Linear Polymers under Good-Solvent Conditions. Macromolecules 2016. [DOI: 10.1021/acs.macromol.6b00600] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Andrea Pelissetto
- Dipartimento di Fisica, Sapienza Università di Roma and INFN, Sezione di Roma I, P.le Aldo Moro
2, I-00185 Rome, Italy
| | - Carlo Pierleoni
- Dipartimento di Scienze Fisiche
e Chimiche, Università dell’Aquila, V. Vetoio 10, Loc. Coppito, I-67100 L’Aquila, Italy
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32
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Dunn NJH, Noid WG. Bottom-up coarse-grained models with predictive accuracy and transferability for both structural and thermodynamic properties of heptane-toluene mixtures. J Chem Phys 2016; 144:204124. [DOI: 10.1063/1.4952422] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Nicholas J. H. Dunn
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - W. G. Noid
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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33
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Dunn NJH, Noid WG. Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids. J Chem Phys 2015; 143:243148. [DOI: 10.1063/1.4937383] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- Nicholas J. H. Dunn
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - W. G. Noid
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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34
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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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35
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Yang D, Wang Q. Systematic and simulation-free coarse graining of homopolymer melts: a relative-entropy-based study. SOFT MATTER 2015; 11:7109-7118. [PMID: 26252719 DOI: 10.1039/c5sm01142f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We applied the systematic and simulation-free strategy proposed in our previous work (D. Yang and Q. Wang, J. Chem. Phys., 2015, 142, 054905) to the relative-entropy-based (RE-based) coarse graining of homopolymer melts. RE-based coarse graining provides a quantitative measure of the coarse-graining performance and can be used to select the appropriate analytic functional forms of the pair potentials between coarse-grained (CG) segments, which are more convenient to use than the tabulated (numerical) CG potentials obtained from structure-based coarse graining. In our general coarse-graining strategy for homopolymer melts using the RE framework proposed here, the bonding and non-bonded CG potentials are coupled and need to be solved simultaneously. Taking the hard-core Gaussian thread model (K. S. Schweizer and J. G. Curro, Chem. Phys., 1990, 149, 105) as the original system, we performed RE-based coarse graining using the polymer reference interaction site model theory under the assumption that the intrachain segment pair correlation functions of CG systems are the same as those in the original system, which de-couples the bonding and non-bonded CG potentials and simplifies our calculations (that is, we only calculated the latter). We compared the performance of various analytic functional forms of non-bonded CG pair potential and closures for CG systems in RE-based coarse graining, as well as the structural and thermodynamic properties of original and CG systems at various coarse-graining levels. Our results obtained from RE-based coarse graining are also compared with those from structure-based coarse graining.
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Affiliation(s)
- Delian Yang
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523-1370, USA.
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36
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Clark AJ, McCarty J, Guenza MG. Comment on “Systematic and simulation-free coarse graining of homopolymer melts: A structure-based study” [J. Chem. Phys. 142, 054905 (2015)]. J Chem Phys 2015; 143:067101. [DOI: 10.1063/1.4928457] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- A. J. Clark
- Department of Chemistry and Biochemistry, and Institute of Theoretical Science, University of Oregon, Eugene, Oregon 97403, USA
| | - J. McCarty
- Department of Chemistry and Biochemistry, and Institute of Theoretical Science, University of Oregon, Eugene, Oregon 97403, USA
| | - M. G. Guenza
- Department of Chemistry and Biochemistry, and Institute of Theoretical Science, University of Oregon, Eugene, Oregon 97403, USA
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37
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Yang D, Wang Q. Systematic and simulation-free coarse graining of homopolymer melts: A structure-based study. J Chem Phys 2015; 142:054905. [DOI: 10.1063/1.4906493] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Delian Yang
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, Colorado 80523-1370, USA
| | - Qiang Wang
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, Colorado 80523-1370, USA
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38
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D’Adamo G, Pelissetto A, Pierleoni C. Accurate coarse-grained models for mixtures of colloids and linear polymers under good-solvent conditions. J Chem Phys 2014; 141:244905. [DOI: 10.1063/1.4904392] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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39
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Li Z, Bian X, Caswell B, Karniadakis GE. Construction of dissipative particle dynamics models for complex fluids via the Mori-Zwanzig formulation. SOFT MATTER 2014; 10:8659-8672. [PMID: 25252001 DOI: 10.1039/c4sm01387e] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We present a bottom-up coarse-graining procedure to construct mesoscopic force fields directly from microscopic dynamics. By grouping many bonded atoms in the molecular dynamics (MD) system into a single cluster, we compute both the conservative and non-conservative interactions between neighboring clusters. In particular, we perform MD simulations of polymer melts to provide microscopic trajectories for evaluating coarse-grained (CG) interactions. Subsequently, dissipative particle dynamics (DPD) is considered as the effective dynamics resulting from the Mori-Zwanzig (MZ) projection of the underlying atomistic dynamics. The forces between finite-size clusters have, in general, both radial and transverse components and hence we employ four different DPD models to account differently for such interactions. Quantitative comparisons between these DPD models indicate that the DPD models with MZ-guided force fields yield much better static and dynamics properties, which are consistent with the underlying MD system, compared to standard DPD with empirical formulae. When the rotational motion of the particle is properly taken into account, the entire velocity autocorrelation function of the MD system as well as the pair correlation function can be accurately reproduced by the MD-informed DPD model. Since this coarse-graining procedure is performed on an unconstrained MD system, our framework is general and can be used in other soft matter systems in which the clusters can be faithfully defined as CG particles.
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Affiliation(s)
- Zhen Li
- Division of Applied Mathematics, Brown University, Providence, RI 02912, USA.
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40
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McCarty J, Clark AJ, Copperman J, Guenza MG. An analytical coarse-graining method which preserves the free energy, structural correlations, and thermodynamic state of polymer melts from the atomistic to the mesoscale. J Chem Phys 2014; 140:204913. [DOI: 10.1063/1.4875923] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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41
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Guenza MG. Localization of chain dynamics in entangled polymer melts. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:052603. [PMID: 25353822 DOI: 10.1103/physreve.89.052603] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Indexed: 06/04/2023]
Abstract
The dynamics of polymer melts in both the unentangled and entangled regimes is described by a Langevin equation for the correlated motion of a group of chains, interacting through both intra- and inter-molecular potentials. Entanglements are represented by an intermolecular monomer-monomer confining potential that has no effect on short chains, while interpolymer interactions, responsible for correlated motion and subdiffusive center-of-mass dynamics, are represented by an intermolecular center-of-mass potential derived from the Ornstein-Zernike equation. This potential ensures that the liquid of phantom chains reproduces the compressibility and free energy of the real samples. For polyethylene melts the calculated dynamic structure factor is found to be in quantitative agreement with neutron spin echo experiments of polyethylene melts with chain lengths that span both the unentangled and the entangled regimes. The theory shows a progressive localization of the cooperative chain dynamics at the crossover from the unentangled to the entangled regime, in the spirit of the reptation model.
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Affiliation(s)
- M G Guenza
- Department of Chemistry and Biochemistry, and Institute of Theoretical Science, University of Oregon, Eugene, Oregon 97403, USA
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42
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Abstract
By focusing on essential features, while averaging over less important details, coarse-grained (CG) models provide significant computational and conceptual advantages with respect to more detailed models. Consequently, despite dramatic advances in computational methodologies and resources, CG models enjoy surging popularity and are becoming increasingly equal partners to atomically detailed models. This perspective surveys the rapidly developing landscape of CG models for biomolecular systems. In particular, this review seeks to provide a balanced, coherent, and unified presentation of several distinct approaches for developing CG models, including top-down, network-based, native-centric, knowledge-based, and bottom-up modeling strategies. The review summarizes their basic philosophies, theoretical foundations, typical applications, and recent developments. Additionally, the review identifies fundamental inter-relationships among the diverse approaches and discusses outstanding challenges in the field. When carefully applied and assessed, current CG models provide highly efficient means for investigating the biological consequences of basic physicochemical principles. Moreover, rigorous bottom-up approaches hold great promise for further improving the accuracy and scope of CG models for biomolecular systems.
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Affiliation(s)
- W G Noid
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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43
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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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44
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D'Adamo G, Pelissetto A, Pierleoni C. Consistent coarse-graining strategy for polymer solutions in the thermal crossover from good to θ solvent. J Chem Phys 2013; 139:034901. [DOI: 10.1063/1.4812691] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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45
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D'Adamo G, Pelissetto A, Pierleoni C. Predicting the thermodynamics by using state-dependent interactions. J Chem Phys 2013; 138:234107. [DOI: 10.1063/1.4810881] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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46
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47
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Lyubimov IY, Guenza MG. Theoretical reconstruction of realistic dynamics of highly coarse-grained cis-1,4-polybutadiene melts. J Chem Phys 2013; 138:12A546. [DOI: 10.1063/1.4792367] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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