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Izvekov S, Kroonblawd MP, Larentzos JP, Brennan JK, Rice BM. Maximum Entropy Theory of Multiscale Coarse-Graining via Matching Thermodynamic Forces: Application to a Molecular Crystal (TATB). J Phys Chem B 2024. [PMID: 38489758 DOI: 10.1021/acs.jpcb.3c07078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
The MSCG/FM (multiscale coarse-graining via force-matching) approach is an efficient supervised machine learning method to develop microscopically informed coarse-grained (CG) models. We present a theory based on the principle of maximum entropy (PME) enveloping the existing MSCG/FM approaches. This theory views the MSCG/FM method as a special case of matching the thermodynamic forces from the extended ensemble described by the set of thermodynamic (relevant) system coordinates. This set may include CG coordinates, the stress tensor, applied external fields, and so forth, and may be characterized by nonequilibrium conditions. Following the presentation of the theory, we discuss the consistent matching of both bonded and nonbonded interactions. The proposed PME formulation is used as a starting point to extend the MSCG/FM method to the constant strain ensemble, which together with the explicit matching of the bonded forces is better suited for coarse-graining anisotropic media at a submolecular resolution. The theory is demonstrated by performing the fine coarse-graining of crystalline 1,3,5-triamino-2,4,6-trinitrobenzene (TATB), a well-known insensitive molecular energetic material, which exhibits highly anisotropic mechanical properties.
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Affiliation(s)
- Sergei Izvekov
- U.S. Army DEVCOM Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005, United States
| | - Matthew P Kroonblawd
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - James P Larentzos
- U.S. Army DEVCOM Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005, United States
| | - John K Brennan
- U.S. Army DEVCOM Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005, United States
| | - Betsy M Rice
- U.S. Army DEVCOM Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005, United States
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2
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Lesniewski MC, Noid WG. Insight into the Density-Dependence of Pair Potentials for Predictive Coarse-Grained Models. J Phys Chem B 2024; 128:1298-1316. [PMID: 38271676 DOI: 10.1021/acs.jpcb.3c06890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
We investigate the temperature- and density-dependence of effective pair potentials for 1-site coarse-grained (CG) models of two industrial solvents, 1,4-dioxane and tetrahydrofuran. We observe that the calculated pair potentials are much more sensitive to density than to temperature. The generalized-Yvon-Born-Green framework reveals that this striking density-dependence reflects corresponding variations in the many-body correlations that determine the environment-mediated indirect contribution to the pair mean force. Moreover, we demonstrate, perhaps surprisingly, that this density-dependence is not important for accurately modeling the intermolecular structure. Accordingly, we adopt a density-independent interaction potential and transfer the density-dependence of the calculated pair potentials into a configuration-independent volume potential. Furthermore, we develop a single global potential that accurately models the intermolecular structure and pressure-volume equation of state across a very wide range of liquid state points. Consequently, this work provides fundamental insight into the density-dependence of effective pair potentials and also provides a significant step toward developing predictive CG models for efficiently modeling industrial solvents.
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Affiliation(s)
- Maria C Lesniewski
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - W G Noid
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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3
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Jin J, Hwang J, Voth GA. Gaussian representation of coarse-grained interactions of liquids: Theory, parametrization, and transferability. J Chem Phys 2023; 159:184105. [PMID: 37942867 DOI: 10.1063/5.0160567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 10/06/2023] [Indexed: 11/10/2023] Open
Abstract
Coarse-grained (CG) interactions determined via bottom-up methodologies can faithfully reproduce the structural correlations observed in fine-grained (atomistic resolution) systems, yet they can suffer from limited extensibility due to complex many-body correlations. As part of an ongoing effort to understand and improve the applicability of bottom-up CG models, we propose an alternative approach to address both accuracy and transferability. Our main idea draws from classical perturbation theory to partition the hard sphere repulsive term from effective CG interactions. We then introduce Gaussian basis functions corresponding to the system's characteristic length by linking these Gaussian sub-interactions to the local particle densities at each coordination shell. The remaining perturbative long-range interaction can be treated as a collective solvation interaction, which we show exhibits a Gaussian form derived from integral equation theories. By applying this numerical parametrization protocol to CG liquid systems, our microscopic theory elucidates the emergence of Gaussian interactions in common phenomenological CG models. To facilitate transferability for these reduced descriptions, we further infer equations of state to determine the sub-interaction parameter as a function of the system variables. The reduced models exhibit excellent transferability across the thermodynamic state points. Furthermore, we propose a new strategy to design the cross-interactions between distinct CG sites in liquid mixtures. This involves combining each Gaussian in the proper radial domain, yielding accurate CG potentials of mean force and structural correlations for multi-component systems. Overall, our findings establish a solid foundation for constructing transferable bottom-up CG models of liquids with enhanced extensibility.
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Affiliation(s)
- Jaehyeok Jin
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 5735 S. Ellis Ave., Chicago, Illinois 60637, USA
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, USA
| | - Jisung Hwang
- Department of Statistics, The University of Chicago, 5747 S. Ellis Ave., Chicago, Illinois 60637, USA
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 5735 S. Ellis Ave., Chicago, Illinois 60637, USA
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4
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Izvekov S, Rice BM. Hierarchical Machine Learning of Low-Resolution Coarse-Grained Free Energy Potentials. J Chem Theory Comput 2023. [PMID: 37256918 DOI: 10.1021/acs.jctc.3c00128] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A force-matching-based method for supervised machine learning (ML) of coarse-grained (CG) free energy (FE) potentials─known as multiscale coarse-graining via force-matching (MSCG/FM)─is an efficient method to develop microscopically informed CG models that are thermodynamically and statistically equivalent to the reference microscopic models. For low-resolution models, when the coarse-graining is at supramolecular scales, objective-oriented clustering of nonbonded particles is required and the reduced description becomes a function of the clustering algorithm. In the present work, we explore the dependence of the ML of the CG Helmholtz FE potential on the clustering algorithm. We consider coarse-graining based on partitional (k-means, leading to Voronoi diagram) and hierarchical agglomerative (bottom-up) clustering algorithms common in unsupervised ML and develop theory connecting the MSCG/FM learned CG Helmholtz potential and the clustering statistics. By combining the agglomerative clustering and the MSCG/FM learning in a recursive manner, we propose an efficient ML methodology to develop the fine-to-low resolution hierarchies of the CG models. The methodology does not suffer from degrading accuracy or increased computational cost to construct larger hierarchies and as such does not impose an upper size limitation of the CG particles resulting from the extended hierarchies. The utility of the methodology is demonstrated by obtaining the bottom-up agglomerative hierarchy for liquid nitromethane from all-atom molecular dynamics (MD) simulations. For agglomerative hierarchies, we prove the existence of renormalization group transformations that indicate self-similarity and allow for learning the low-resolution MSCG/FM potentials at low computational cost by rescaling and renormalizing the certain finer-resolution members of the hierarchy. The hierarchies of the CG models can be used to carry out simulations under constant-pressure conditions.
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Affiliation(s)
- Sergei Izvekov
- U.S. Army DEVCOM Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005, United States
| | - Betsy M Rice
- U.S. Army DEVCOM Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005, United States
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5
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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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6
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Wu Z, Müller-Plathe F. Slip-Spring Hybrid Particle-Field Molecular Dynamics for Coarse-Graining Branched Polymer Melts: Polystyrene Melts as an Example. J Chem Theory Comput 2022; 18:3814-3828. [PMID: 35617016 DOI: 10.1021/acs.jctc.2c00107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The topology of chains significantly modifies the dynamical properties of polymer melts. Here, we extend a recently developed efficient simulation method, namely the slip-spring hybrid particle-field (SS-hPF) model, to study the structural and dynamical properties of branched polymer melts over large spatial-temporal scales. In the coarse-grained SS-hPF simulation of polymers, the bonded potentials are derived by iterative Boltzmann inversion from the underlying fine-grained model. The nonbonded potentials are computed from a density functional field instead of pairwise interactions used in standard molecular dynamics simulations, which increases the computational efficiency by a factor of 10-20. The entangled dynamics is lost due to the soft-core nature of density functional field interactions. It is recovered by a multichain slip-spring model that is rigorously parametrized from existing experimental or simulation data. To quantitatively predict the relaxation and diffusion of branched polymers, which are dominated by arm retraction rather than chain reptation, the slip-spring algorithm is augmented to improve the polymer dynamics near the branch point. Multiple dynamical observables, e.g., diffusion coefficients, arm relaxations, and tube survival probabilities, are characterized in an example coarse-grained model of symmetric and asymmetric star-shaped polystyrene melts. Consistent dynamical behaviors are identified and compared with theoretical predictions. With a single rescaling factor, the prediction of diffusion coefficients agrees well with the available experimental measurements. In this work, an efficient approach is provided to build chemistry-specific coarse-grained models for predicting the dynamics of branched polymers.
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Affiliation(s)
- Zhenghao Wu
- 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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7
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Izvekov S, Rice BM. Bottom-up coarse-grain modeling of plasticity and nanoscale shear bands in α-RDX. J Chem Phys 2021; 155:064503. [PMID: 34391357 DOI: 10.1063/5.0057223] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Computationally inexpensive particle-based coarse-grained (CG) models are essential for use in molecular dynamics (MD) simulations of mesoscopically slow cooperative phenomena, such as plastic deformations in solids. Molecular crystals possessing complex symmetry present enormous practical challenges for particle-based coarse-graining at molecularly resolved scales, when each molecule is in a single-site representation, and beyond. Presently, there is no published pairwise non-bonded single-site CG potential that is able to predict the space group and structure of a molecular crystal. In this paper, we present a successful coarse-graining at a molecular level from first principles of an energetic crystal, hexahydro-1,3,5-trinitro-s-triazine (RDX) in the alpha phase, using the force-matching-based multiscale coarse-graining (MSCG/FM) approach. The new MSCG/FM model, which implements an optimal pair decomposition of the crystal Helmholtz free energy potential in molecular center-of-mass coordinates, was obtained by force-matching atomistic MD simulations of liquid, amorphous, and crystalline states and in a wide range of pressures (up to 20 GPa). The MSCG/FM potentials for different pressures underwent top-down optimization to fine-tune the mechanical and thermodynamic properties, followed by consolidation into a transferable density-dependent model referred to as RDX-TC-DD (RDX True-Crystal Density-Dependent). The RDX-TC-DD model predicts accurately the crystal structure of α-RDX at room conditions and reproduces the atomistic reference system under isothermal (300 K) hydrostatic compression up to 20 GPa, in particular, the Pbca symmetry of α-RDX in the elastic regime. The RDX-TC-DD model was then used to simulate the plastic response of uniaxially ([100]) compressed α-RDX resulting in nanoscale shear banding, a key mechanism for plastic deformation and defect-free detonation initiation proposed for many molecular crystalline explosives. Additionally, a comparative analysis of the effect of core-softening of the RDX-TC-DD potential and the degree of molecular rigidity in the all-atom treatment suggests a stress-induced short-range softening of the effective intermolecular interaction as a fundamental cause of plastic instability in α-RDX. The reported RDX-TC-DD model and overall workflow to develop it open up possibilities to perform high quality simulation studies of molecular energetic materials under thermal and mechanical stimuli, including extreme conditions.
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Affiliation(s)
- Sergei Izvekov
- Weapons and Materials Research Directorate, U.S. Army DEVCOM Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005, USA
| | - Betsy M Rice
- Weapons and Materials Research Directorate, U.S. Army DEVCOM Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005, USA
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8
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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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9
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DeLyser M, Noid WG. Bottom-up coarse-grained models for external fields and interfaces. J Chem Phys 2020; 153:224103. [PMID: 33317310 DOI: 10.1063/5.0030103] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Bottom-up coarse-grained (CG) models accurately describe the structure of homogeneous systems but sometimes provide limited transferability and a poor description of thermodynamic properties. Consequently, inhomogeneous systems present a severe challenge for bottom-up models. In this work, we examine bottom-up CG models for interfaces and inhomogeneous systems. We first analyze the effect of external fields upon the many-body potential of mean force. We also demonstrate that the multiscale CG (MS-CG) variational principle for modeling the external field corresponds to a generalization of the first Yvon-Born-Green equation. This provides an important connection with liquid state theory, as well as physical insight into the structure of interfaces and the resulting MS-CG models. We then develop and assess MS-CG models for a film of liquid methanol that is adsorbed on an attractive wall and in coexistence with its vapor phase. While pair-additive potentials provide unsatisfactory accuracy and transferability, the inclusion of local-density (LD) potentials dramatically improves the accuracy and transferability of the MS-CG model. The MS-CG model with LD potentials quite accurately describes the wall-liquid interface, the bulk liquid density, and the liquid-vapor interface while simultaneously providing a much improved description of the vapor phase. This model also provides an excellent description of the pair structure and pressure-density equation of state for the bulk liquid. Thus, LD potentials hold considerable promise for transferable bottom-up models that accurately describe the structure and thermodynamic properties of both bulk and interfacial systems.
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Affiliation(s)
- Michael 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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10
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Shahidi N, Chazirakis A, Harmandaris V, Doxastakis M. Coarse-graining of polyisoprene melts using inverse Monte Carlo and local density potentials. J Chem Phys 2020; 152:124902. [PMID: 32241142 DOI: 10.1063/1.5143245] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Bottom-up coarse-graining of polymers is commonly performed by matching structural order parameters such as distribution of bond lengths, bending and dihedral angles, and pair distribution functions. In this study, we introduce the distribution of nearest-neighbors as an additional order parameter in the concept of local density potentials. We describe how the inverse-Monte Carlo method provides a framework for forcefield development that is capable of overcoming challenges associated with the parameterization of interaction terms in polymer systems. The technique is applied on polyisoprene melts as a prototype system. We demonstrate that while different forcefields can be developed that perform equally in terms of matching target distributions, the inclusion of nearest-neighbors provides a straightforward route to match both thermodynamic and conformational properties. We find that several temperature state points can also be addressed, provided that the forcefield is refined accordingly. Finally, we examine both the single-particle and the collective dynamics of the coarse-grain models, demonstrating that all forcefields present a similar acceleration relative to the atomistic systems.
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Affiliation(s)
- Nobahar Shahidi
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Antonis Chazirakis
- Department of Mathematics and Applied Mathematics, University of Crete, Heraklion GR-71110, Greece
| | - Vagelis Harmandaris
- Department of Mathematics and Applied Mathematics, University of Crete, Heraklion GR-71110, Greece
| | - Manolis Doxastakis
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, USA
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11
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Barnes BC, Leiter KW, Larentzos JP, Brennan JK. Forging of Hierarchical Multiscale Capabilities for Simulation of Energetic Materials. PROPELLANTS EXPLOSIVES PYROTECHNICS 2019. [DOI: 10.1002/prep.201900187] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Brian C. Barnes
- Energetic Materials Science Branch, FCDD-RLW-LB U.S. Army Research Laboratory Aberdeen Proving Ground MD 21005-5066
| | - Kenneth W. Leiter
- Simulation Sciences Branch, FCDD-RLC-NB U.S. Army Research Laboratory Aberdeen Proving Ground MD 21005-5066
| | - James P. Larentzos
- Energetic Materials Science Branch, FCDD-RLW-LB U.S. Army Research Laboratory Aberdeen Proving Ground MD 21005-5066
| | - John K. Brennan
- Energetic Materials Science Branch, FCDD-RLW-LB U.S. Army Research Laboratory Aberdeen Proving Ground MD 21005-5066
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12
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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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13
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Avalos JB, Lísal M, Larentzos JP, Mackie AD, Brennan JK. Generalised dissipative particle dynamics with energy conservation: density- and temperature-dependent potentials. Phys Chem Chem Phys 2019; 21:24891-24911. [PMID: 31690923 DOI: 10.1039/c9cp04404c] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a generalised, energy-conserving dissipative particle dynamics (DPDE) method appropriate for the non-isothermal simulation of particle interaction force fields that are both density- and temperature-dependent. A detailed derivation is formulated in a bottom-up manner by considering the thermodynamics of small systems with the appropriate consideration of the fluctuations. Connected to the local volume is a local density and corresponding local pressure, which is determined from an equation-of-state based force field that depends also on a particle temperature. Compared to the original DPDE method, the formulation of the generalised DPDE method requires a change in the independent variable from the particle internal energy to the particle entropy. As part of the re-formulation, the terms dressed particle entropy and the corresponding dressed particle temperature are introduced, which depict the many-body contributions in the local volume. The generalised DPDE method has similarities to the energy form of the smoothed dissipative particle dynamics method, yet fundamental differences exist, which are described in the manuscript. The basic dynamic equations are presented along with practical considerations for implementing the generalised DPDE method, including a numerical integration scheme based on the Shardlow-like splitting algorithm. Demonstrations and validation tests are performed using analytical equation-of-states for the van der Waals and Lennard-Jones fluids. Particle probability distributions are analysed, where excellent agreement with theoretical estimates is demonstrated. As further validation of the generalised DPDE method, both equilibrium and non-equilibrium simulation scenarios are considered, including adiabatic flash heating response and vapour-liquid phase separation.
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Affiliation(s)
- Josep Bonet Avalos
- Department d'Enginyeria Qumica, ETSEQ, Universitat Rovira i Virgili, Tarragona, Spain
| | - Martin Lísal
- Department of Molecular and Mesoscopic Modelling, Institute of Chemical Process Fundamentals of the CAS, Prague, Czech Republic and Department of Physics, Faculty of Science, J. E. Purkinje University, Úst n. Lab., Czech Republic
| | - James P Larentzos
- Weapons and Materials Research Directorate, U.S. Army Combat Capabilities Development Command Army Research Laboratory, Aberdeen Proving Ground, MD, USA.
| | - Allan D Mackie
- Department d'Enginyeria Qumica, ETSEQ, Universitat Rovira i Virgili, Tarragona, Spain
| | - John K Brennan
- Weapons and Materials Research Directorate, U.S. Army Combat Capabilities Development Command Army Research Laboratory, Aberdeen Proving Ground, MD, USA.
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14
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Lísal M, Larentzos JP, Sellers MS, Schweigert IV, Brennan JK. Dissipative particle dynamics with reactions: Application to RDX decomposition. J Chem Phys 2019; 151:114112. [DOI: 10.1063/1.5117904] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Martin Lísal
- Department of Molecular and Mesoscopic Modelling, Institute of Chemical Process Fundamentals of the CAS, Prague, Czech Republic
- Department of Physics, Faculty of Science, J. E. Purkinje University, Ústí n. Lab., Czech Republic
| | - James P. Larentzos
- Weapons and Materials Research Directorate, U.S. Army Combat Capabilities Development Command Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005-5066, USA
| | - Michael S. Sellers
- Weapons and Materials Research Directorate, U.S. Army Combat Capabilities Development Command Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005-5066, USA
| | - Igor V. Schweigert
- Code 6189, Theoretical Chemistry Section, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - John K. Brennan
- Weapons and Materials Research Directorate, U.S. Army Combat Capabilities Development Command Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005-5066, 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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Wagner JW, Dannenhoffer-Lafage T, Jin J, Voth GA. Extending the range and physical accuracy of coarse-grained models: Order parameter dependent interactions. J Chem Phys 2018; 147:044113. [PMID: 28764380 DOI: 10.1063/1.4995946] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Order parameters (i.e., collective variables) are often used to describe the behavior of systems as they capture different features of the free energy surface. Yet, most coarse-grained (CG) models only employ two- or three-body non-bonded interactions between the CG particles. In situations where these interactions are insufficient for the CG model to reproduce the structural distributions of the underlying fine-grained (FG) model, additional interactions must be included. In this paper, we introduce an approach to expand the basis sets available in the multiscale coarse-graining (MS-CG) methodology by including order parameters. Then, we investigate the ability of an additive local order parameter (e.g., density) and an additive global order parameter (i.e., distance from a hard wall) to improve the description of CG models in interfacial systems. Specifically, we study methanol liquid-vapor coexistence, acetonitrile liquid-vapor coexistence, and acetonitrile liquid confined by hard-wall plates, all using single site CG models. We find that the use of order parameters dramatically improves the reproduction of structural properties of interfacial CG systems relative to the FG reference as compared with pairwise CG interactions alone.
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Affiliation(s)
- Jacob W Wagner
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Thomas Dannenhoffer-Lafage
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Jaehyeok Jin
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Gregory A Voth
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
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17
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Larentzos JP, Mansell JM, Lísal M, Brennan JK. Coarse-grain modelling using an equation-of-state many-body potential: application to fluid mixtures at high temperature and high pressure. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1459920] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- James P. Larentzos
- U.S. Army Research Laboratory, Weapons and Materials Research Directorate , Aberdeen Proving Ground, MD, USA
| | - J. Matthew Mansell
- Department of Chemical and Biomolecular Engineering, North Carolina State University , Raleigh, NC, USA
| | - Martin Lísal
- Department of Molecular and Mesoscopic Modelling, Institute of Chemical Process Fundamentals of the CAS, v. v. i. , Prague, Czech Republic
- Department of Physics, Faculty of Science, J. E. Purkinje University , Ústí n. Lab., Czech Republic
| | - John K. Brennan
- U.S. Army Research Laboratory, Weapons and Materials Research Directorate , Aberdeen Proving Ground, MD, USA
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18
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Langenberg M, Jackson NE, de Pablo JJ, Müller M. Role of translational entropy in spatially inhomogeneous, coarse-grained models. J Chem Phys 2018. [DOI: 10.1063/1.5018178] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Marcel Langenberg
- Institut für Theoretische Physik, Universität Göttingen, 37077 Göttingen, Germany
| | - Nicholas E. Jackson
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60615, USA
- Argonne National Laboratory, Lemont, Illinois 06349, USA
| | - Juan J. de Pablo
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60615, USA
- Argonne National Laboratory, Lemont, Illinois 06349, USA
| | - Marcus Müller
- Institut für Theoretische Physik, Universität Göttingen, 37077 Göttingen, Germany
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19
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Sanyal T, Shell MS. Transferable Coarse-Grained Models of Liquid-Liquid Equilibrium Using Local Density Potentials Optimized with the Relative Entropy. J Phys Chem B 2018; 122:5678-5693. [PMID: 29466859 DOI: 10.1021/acs.jpcb.7b12446] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bottom-up coarse-grained (CG) models are now regularly pursued to enable large length and time scale molecular simulations of complex, often macromolecular systems. However, predicting fluid phase equilibria using such models remains fundamentally challenging. A major problem stems from the typically low transferability of CG models beyond the densities and/or compositions at which they are parametrized, which is necessary if they are to describe distinct structural and thermodynamic properties unique to each phase. CG model transferability is compounded by the representation of the inherently multibody coarse interactions using pair potentials that neglect higher order effects. Here, we propose to construct transferable single site CG models of liquid mixtures by supplementing traditional CG pair interactions with local density potentials, which constitute a computationally inexpensive mean-field approach to describe many-body effects, in that site energies are modulated by the local solution environment. To illustrate the approach, we use intra- and interspecies local density potentials to develop CG models of benzene-water solutions that show impressive transferability in structural metrics (pair correlation functions, density profiles) throughout composition space, in contrast to pair-only CG representations. While further refinement may be necessary to represent more complex thermodynamic properties, like the liquid-liquid interfacial tension, the generality and improvement offered by the local density approach are highly encouraging for enabling complex phase equilibrium modeling using CG models.
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Affiliation(s)
- Tanmoy Sanyal
- Department of Chemical Engineering , University of California, Santa Barbara , Santa Barbara , California , United States
| | - M Scott Shell
- Department of Chemical Engineering , University of California, Santa Barbara , Santa Barbara , California , United States
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20
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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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21
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Kuo AT, Okazaki S, Shinoda W. Transferable coarse-grained model for perfluorosulfonic acid polymer membranes. J Chem Phys 2017; 147:094904. [DOI: 10.1063/1.4986287] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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22
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Sanyal T, Shell MS. Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation. J Chem Phys 2017; 145:034109. [PMID: 27448876 DOI: 10.1063/1.4958629] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Bottom-up multiscale techniques are frequently used to develop coarse-grained (CG) models for simulations at extended length and time scales but are often limited by a compromise between computational efficiency and accuracy. The conventional approach to CG nonbonded interactions uses pair potentials which, while computationally efficient, can neglect the inherently multibody contributions of the local environment of a site to its energy, due to degrees of freedom that were coarse-grained out. This effect often causes the CG potential to depend strongly on the overall system density, composition, or other properties, which limits its transferability to states other than the one at which it was parameterized. Here, we propose to incorporate multibody effects into CG potentials through additional nonbonded terms, beyond pair interactions, that depend in a mean-field manner on local densities of different atomic species. This approach is analogous to embedded atom and bond-order models that seek to capture multibody electronic effects in metallic systems. We show that the relative entropy coarse-graining framework offers a systematic route to parameterizing such local density potentials. We then characterize this approach in the development of implicit solvation strategies for interactions between model hydrophobes in an aqueous environment.
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Affiliation(s)
- Tanmoy Sanyal
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - M Scott Shell
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, USA
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23
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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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24
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Liu J, Zeng Q, Zhang Y, Zhang C. A Limited Sample Coarse-Grained Strategy and Its Applications to Molecular Crystals: Elastic Property Prediction and Nanoindentation Simulations of 1,3,5-Trinitro-1,3,5-Triazinane. J Phys Chem B 2016. [DOI: 10.1021/acs.jpcb.6b04256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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25
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Lee K, Joshi K, Chaudhuri S, Stewart DS. Mirrored continuum and molecular scale simulations of the ignition of high-pressure phases of RDX. J Chem Phys 2016; 144:184111. [DOI: 10.1063/1.4948548] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
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26
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Moore JD, Barnes BC, Izvekov S, Lísal M, Sellers MS, Taylor DE, Brennan JK. A coarse-grain force field for RDX: Density dependent and energy conserving. J Chem Phys 2016; 144:104501. [DOI: 10.1063/1.4942520] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Joshua D. Moore
- Energetic Materials Science Branch, RDRL-WML-B, US Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005-5066, USA
| | - Brian C. Barnes
- Energetic Materials Science Branch, RDRL-WML-B, US Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005-5066, USA
| | - Sergei Izvekov
- Energetic Materials Science Branch, RDRL-WML-B, US Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005-5066, USA
| | - Martin Lísal
- Laboratory of Aerosols Chemistry and Physics, Institute of Chemical Process Fundamentals of the Czech Academy of Sciences, v. v. i., 165 02 Prague 6-Suchdol, Czech Republic
- Department of Physics, Institute of Science, J. E. Purkinje University, 400 96 Ústí n. Lab., Czech Republic
| | - Michael S. Sellers
- Energetic Materials Science Branch, RDRL-WML-B, US Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005-5066, USA
| | - DeCarlos E. Taylor
- Energetic Materials Science Branch, RDRL-WML-B, US Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005-5066, USA
| | - John K. Brennan
- Energetic Materials Science Branch, RDRL-WML-B, US Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005-5066, USA
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27
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Kroonblawd MP, Sewell TD, Maillet JB. Characteristics of energy exchange between inter- and intramolecular degrees of freedom in crystalline 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) with implications for coarse-grained simulations of shock waves in polyatomic molecular crystals. J Chem Phys 2016; 144:064501. [DOI: 10.1063/1.4941332] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Matthew P. Kroonblawd
- Department of Chemistry, University of Missouri-Columbia, Columbia, Missouri 65211-7600, USA
| | - Thomas D. Sewell
- Department of Chemistry, University of Missouri-Columbia, Columbia, Missouri 65211-7600, USA
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28
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Xiao Q, Guo H. Transferability of a coarse-grained atactic polystyrene model: the non-bonded potential effect. Phys Chem Chem Phys 2016; 18:29808-29824. [DOI: 10.1039/c6cp03753d] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper, we construct an efficient and simple coarse grained (CG) model for atactic polystyrene (PS) by using a 1 : 1 mapping scheme at 463 K and 1 atm pressure and derive the corresponding bonded and non-bonded potentials in the CG force field (FF) via a direct Boltzmann inversion approach and a combined structure-based and thermodynamic quantities-based CG method, respectively.
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Affiliation(s)
- Qiang Xiao
- Beijing National Laboratory for Molecular Sciences
- Joint Laboratory of Polymer Sciences and Materials
- State Key Laboratory of Polymer Physics and Chemistry
- Institute of Chemistry
- Chinese Academy of Sciences
| | - Hongxia Guo
- Beijing National Laboratory for Molecular Sciences
- Joint Laboratory of Polymer Sciences and Materials
- State Key Laboratory of Polymer Physics and Chemistry
- Institute of Chemistry
- Chinese Academy of Sciences
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29
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Gao P, Guo H. Transferability of the coarse-grained potentials for trans-1,4-polybutadiene. Phys Chem Chem Phys 2015; 17:31693-706. [DOI: 10.1039/c5cp05017k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The CG torsion potential has a dual effect on the reproduction of crystallization of trans-1,4-polybutadiene in CG simulation.
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Affiliation(s)
- Peiyuan Gao
- Beijing National Laboratory for Molecular Sciences
- State Key Laboratory of Polymer Physics and Chemistry
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
| | - Hongxia Guo
- Beijing National Laboratory for Molecular Sciences
- State Key Laboratory of Polymer Physics and Chemistry
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
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30
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Izvekov S, Rice BM. On the importance of shear dissipative forces in coarse-grained dynamics of molecular liquids. Phys Chem Chem Phys 2015; 17:10795-804. [DOI: 10.1039/c4cp06116k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work we demonstrate from first principles that the shear frictions describing dissipative forces in the direction normal to the vector connecting the coarse-grained (CG) particles in dissipative particle dynamics (DPD) could be dominant for certain real molecular liquids at high-resolution coarse-graining.
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Affiliation(s)
- Sergei Izvekov
- Weapons and Materials Research Directorate
- U.S. Army Research Laboratory
- Aberdeen Proving Ground
- USA
| | - Betsy M. Rice
- Weapons and Materials Research Directorate
- U.S. Army Research Laboratory
- Aberdeen Proving Ground
- USA
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31
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Brennan JK, Lísal M, Moore JD, Izvekov S, Schweigert IV, Larentzos JP. Coarse-Grain Model Simulations of Nonequilibrium Dynamics in Heterogeneous Materials. J Phys Chem Lett 2014; 5:2144-2149. [PMID: 26270506 DOI: 10.1021/jz500756s] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A suite of computational tools is described for particle-based mesoscale simulations of the nonequilibrium dynamics of energetic solids, including mechanical deformation, phase transitions, and chemical reactivity triggered by shock or thermal loading. The method builds upon our recent advances both in generating coarse-grain models under high strains and in developing a variant of dissipative particle dynamics (DPD) that includes chemical reactions. To describe chemical reactivity, a coarse-grain particle equation-of-state was introduced into the constant-energy DPD variant that rigorously treats complex chemical reactions and the associated chemical energy release. As illustration of these developments, we present simulations of shock compression of an RDX crystal and its thermal decomposition under high temperatures. We also discuss our current efforts toward a highly scalable domain-decomposition implementation that extends applicability to micrometer-size simulations. With appropriate parametrization, the method is applicable to other materials whose dynamic response is driven by microstructural heterogeneities.
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Affiliation(s)
- John K Brennan
- †Weapons and Materials Research Directorate, U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005-5425, United States
| | - Martin Lísal
- ‡Laboratory of Chemistry and Physics of Aerosols, Institute of Chemical Process Fundamentals of the ASCR, v. v. i., 165 02 Prague, Czech Republic
- §Department of Physics, Faculty of Science, J. E. Purkinje University, České Mládeže 8, 400 96 Ústí n. Lab., Czech Republic
| | - Joshua D Moore
- †Weapons and Materials Research Directorate, U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005-5425, United States
| | - Sergei Izvekov
- †Weapons and Materials Research Directorate, U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005-5425, United States
| | - Igor V Schweigert
- ∥Code 6189, Theoretical Chemistry Section, U.S. Naval Research Laboratory, Washington, District of Columbia 20375, United States
| | - James P Larentzos
- ⊥Engility Corporation, High Performance Technologies Group at the U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005-5425, United States
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32
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Faure G, Maillet JB, Stoltz G. Local density dependent potential for compressible mesoparticles. J Chem Phys 2014; 140:114105. [DOI: 10.1063/1.4868547] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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33
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Izvekov S, Rice BM. Multi-scale coarse-graining of non-conservative interactions in molecular liquids. J Chem Phys 2014; 140:104104. [DOI: 10.1063/1.4866142] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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34
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Taylor DE, Rice BM. Quantum-Informed Multiscale M&S for Energetic Materials. ADVANCES IN QUANTUM CHEMISTRY 2014. [DOI: 10.1016/b978-0-12-800345-9.00005-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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35
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Cai Y, Zhao FP, An Q, Wu HA, Goddard WA, Luo SN. Shock response of single crystal and nanocrystalline pentaerythritol tetranitrate: Implications to hotspot formation in energetic materials. J Chem Phys 2013; 139:164704. [DOI: 10.1063/1.4825400] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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36
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Larini L, Shea JE. Double Resolution Model for Studying TMAO/Water Effective Interactions. J Phys Chem B 2013; 117:13268-77. [DOI: 10.1021/jp403635g] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Luca Larini
- Department of Chemistry
and Biochemistry
and of Physics, University of California, Santa Barbara, Santa Barbara, California 93106, United
States
| | - Joan-Emma Shea
- Department of Chemistry
and Biochemistry
and of Physics, University of California, Santa Barbara, Santa Barbara, California 93106, United
States
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37
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Rosch TW, Brennan JK, Izvekov S, Andzelm JW. Exploring the ability of a multiscale coarse-grained potential to describe the stress-strain response of glassy polystyrene. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 87:042606. [PMID: 23679442 DOI: 10.1103/physreve.87.042606] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 03/01/2013] [Indexed: 06/02/2023]
Abstract
A new particle-based bottom-up method to develop coarse-grained models of polymers is presented and applied to polystyrene. The multiscale coarse-graining (MS-CG) technique of Izvekov et al. [J. Chem. Phys. 120, 10896 (2004)] is applied to a polymer system to calculate nonbonded interactions. The inverse Boltzmann inversion method was used to parametrize the bonded and bond-angle bending interactions. Molecular dynamics simulations were performed, and the CG model exhibited a significantly lower modulus compared to the atomistic model at low temperature and high strain rate. In an attempt to improve the CG model performance, several other parametrization schemes were used to build other models from this base model. The first of these models included standard frictional forces through use of the constant-temperature dissipative particle dynamics method that improved the modulus, yet was not transferrable to higher temperatures and lower strain rates. Other models were built by increasing the attraction between CG beads through direct manipulation of the nonbonded potential, where an improvement of the stress response was found. For these models, two parametrization protocols that shifted the force to more attractive values were explored. The first protocol involved a uniform shift, while the other protocol shifted the force in a more localized region. The uniformly shifted potential greatly affected the structure of the equilibrium model as compared to the locally shifted potential, yet was more transferrable to different temperatures and strain rates. Further improvements in the coarse-graining protocol to generate models that more satisfactorily capture mechanical properties are suggested.
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Affiliation(s)
- Thomas W Rosch
- U.S. Army Research Laboratory, Weapons and Materials Research Directorate, Aberdeen Proving Ground, Maryland 21005-5066, USA
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38
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Izvekov S, Rice BM. Free-energy based pair-additive potentials for bulk Ni-Al systems: Application to study Ni-Al reactive alloying. J Chem Phys 2012; 137:094704. [DOI: 10.1063/1.4747546] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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39
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Mukherjee B, Delle Site L, Kremer K, Peter C. Derivation of Coarse Grained Models for Multiscale Simulation of Liquid Crystalline Phase Transitions. J Phys Chem B 2012; 116:8474-84. [DOI: 10.1021/jp212300d] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Biswaroop Mukherjee
- Max-Planck-Institut für Polymerforschung, Ackermannweg 10, 55128
Mainz, Germany
| | - Luigi Delle Site
- Institute for Mathematics, Freie Universität Berlin, Arnimallee
6, D-14195 Berlin, Germany
| | - Kurt Kremer
- Max-Planck-Institut für Polymerforschung, Ackermannweg 10, 55128
Mainz, Germany
| | - Christine Peter
- Max-Planck-Institut für Polymerforschung, Ackermannweg 10, 55128
Mainz, Germany
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