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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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Ge P, Zhang L, Lei H. Machine learning assisted coarse-grained molecular dynamics modeling of meso-scale interfacial fluids. J Chem Phys 2023; 158:064104. [PMID: 36792498 DOI: 10.1063/5.0131567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
A hallmark of meso-scale interfacial fluids is the multi-faceted, scale-dependent interfacial energy, which often manifests different characteristics across the molecular and continuum scale. The multi-scale nature imposes a challenge to construct reliable coarse-grained (CG) models, where the CG potential function needs to faithfully encode the many-body interactions arising from the unresolved atomistic interactions and account for the heterogeneous density distributions across the interface. We construct the CG models of both single- and two-component polymeric fluid systems based on the recently developed deep coarse-grained potential [Zhang et al., J. Chem. Phys. 149, 034101 (2018)] scheme, where each polymer molecule is modeled as a CG particle. By only using the training samples of the instantaneous force under the thermal equilibrium state, the constructed CG models can accurately reproduce both the probability density function of the void formation in bulk and the spectrum of the capillary wave across the fluid interface. More importantly, the CG models accurately predict the volume-to-area scaling transition for the apolar solvation energy, illustrating the effectiveness to probe the meso-scale collective behaviors encoded with molecular-level fidelity.
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Affiliation(s)
- Pei Ge
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, Michigan 48824, USA
| | | | - Huan Lei
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, Michigan 48824, USA
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4
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Lee BH, Sakano MN, Larentzos JP, Brennan JK, Strachan A. A coarse-grain reactive model of RDX: Molecular resolution at the μm scale. J Chem Phys 2023; 158:024702. [PMID: 36641383 DOI: 10.1063/5.0122940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Predictive models for the thermal, chemical, and mechanical response of high explosives at extreme conditions are important for investigating their performance and safety. We introduce a particle-based, reactive model of 1,3,5-trinitro-1,3,5-triazinane (RDX) with molecular resolution utilizing generalized energy-conserving dissipative particle dynamics with reactions. The model is parameterized with respect to the data from atomistic molecular dynamics simulations as well as from quantum mechanical calculations, thus bridging atomic processes to the mesoscales, including microstructures and defects. It accurately captures the response of RDX under a range of thermal loading conditions compared to atomistic simulations. In addition, the Hugoniot response of the CG model in the overdriven regime reasonably matches atomistic simulations and experiments. Exploiting the model's high computational efficiency, we investigate mesoscale systems involving millions of molecules and characterize size-dependent criticality of hotspots in RDX. The combination of accuracy and computational efficiency of our reactive model provides a tool for investigation of mesoscale phenomena, such as the role of microstructures and defects in the shock-to-deflagration transition, through particle-based simulation.
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Affiliation(s)
- Brian H Lee
- School of Materials Engineering and Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana 47907, USA
| | - Michael N Sakano
- School of Materials Engineering and Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana 47907, USA
| | - James P Larentzos
- U.S. Army Combat Capabilities Development Command (DEVCOM) Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005, USA
| | - John K Brennan
- U.S. Army Combat Capabilities Development Command (DEVCOM) Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005, USA
| | - Alejandro Strachan
- School of Materials Engineering and Birck Nanotechnology Center, Purdue University, West Lafayette, Indiana 47907, USA
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5
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Avalos JB, Lísal M, Larentzos JP, Mackie AD, Brennan JK. Generalized Energy-Conserving Dissipative Particle Dynamics with Mass Transfer. Part 1: Theoretical Foundation and Algorithm. J Chem Theory Comput 2022; 18:7639-7652. [PMID: 36306139 DOI: 10.1021/acs.jctc.2c00452] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
An extension of the generalized energy-conserving dissipative particle dynamics method (GenDPDE) that allows mass transfer between mesoparticles via a diffusion process is presented. By considering the concept of the mesoparticles as property carriers, the complexity and flexibility of the GenDPDE framework were enhanced to allow for interparticle mass transfer under isoenergetic conditions, notated here as GenDPDE-M. In the formulation, diffusion is described via the theory of mesoscale irreversible processes based on linear relationships between the fluxes and thermodynamic forces, where their fluctuations are described by Langevin-like equations. The mass exchange between mesoparticles is such that the mass of the mesoparticle remains unchanged after the transfer process and requires additional considerations regarding the coupling with other system properties such as the particle internal energy. The proof-of-concept work presented in this article is the first part of a two-part article series. In Part 1, the development of the GenDPDE-M theoretical framework and the derivation of the algorithm are presented in detail. Part 2 of this article series is targeted for practitioners, where applications, demonstrations, and practical considerations for implementing the GenDPDE-M method are presented and discussed.
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Affiliation(s)
- Josep Bonet Avalos
- Department d'Enginyeria Química, ETSEQ, Universitat Rovira i Virgili, Tarragona 43007 Spain
| | - Martin Lísal
- Department of Molecular and Mesoscopic Modeling, The Czech Academy of Sciences, Institute of Chemical Process Fundamentals, Prague 165 01 Czech Republic.,Department of Physics, Faculty of Science, J. E. Purkyně University, Ústí nad Labem, 40096 Czech Republic
| | - James P Larentzos
- U.S. Army Combat Capabilities Development Command (DEVCOM) Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005 United States
| | - Allan D Mackie
- Department d'Enginyeria Química, ETSEQ, Universitat Rovira i Virgili, Tarragona 43007 Spain
| | - John K Brennan
- U.S. Army Combat Capabilities Development Command (DEVCOM) Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005 United States
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6
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Lísal M, Avalos JB, Larentzos JP, Mackie AD, Brennan JK. Generalized Energy-Conserving Dissipative Particle Dynamics with Mass Transfer. Part 2: Applications and Demonstrations. J Chem Theory Comput 2022; 18:7653-7670. [PMID: 36399703 DOI: 10.1021/acs.jctc.2c00453] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We present the second part of a two-part paper series intended to address a gap in computational capability for coarse-grain particle modeling and simulation, namely, the simulation of phenomena in which diffusion via mass transfer is a contributing mechanism. In part 1, we presented a formulation of a dissipative particle dynamics method to simulate interparticle mass transfer, termed generalized energy-conserving dissipative particle dynamics with mass transfer (GenDPDE-M). In the GenDPDE-M method, the mass of each mesoparticle remains constant following the interparticle mass exchange. In part 2 of this series, further verification and demonstrations of the GenDPDE-M method are presented for mesoparticles with embedded binary mixtures using the ideal gas (IG) and van der Waals (vdW) equation-of-state (EoS). The targeted readership of part 2 is toward practitioners, where applications and practical considerations for implementing the GenDPDE-M method are presented and discussed, including a numerical discretisztion algorithm for the equations-of-motion. The GenDPDE-M method is verified by reproducing the particle distributions predicted by Monte Carlo simulations for the IG and vdW fluids, along with several demonstrations under both equilibrium and non-equilibrium conditions. GenDPDE-M can be generally applied to multi-component mixtures and to other fundamental EoS, such as the Lennard-Jones or Exponential-6 models, as well as to more advanced EoS models such as Statistical Associating Fluid Theory.
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Affiliation(s)
- Martin Lísal
- Department of Molecular and Mesoscopic Modelling, The Czech Academy of Sciences, Institute of Chemical Process Fundamentals, Prague 165 01, Czech Republic.,Department of Physics, Faculty of Science, J. E. Purkyně University, Ústí nad Labem 400 96, Czech Republic
| | - Josep Bonet Avalos
- Department d'Enginyeria Química, ETSEQ, Universitat Rovira i Virgili, Tarragona 43007 Spain
| | - James P Larentzos
- U.S. Army Combat Capabilities Development Command (DEVCOM) Army Research Laboratory, Aberdeen Proving Ground, Maryland, 21005 United States
| | - Allan D Mackie
- Department d'Enginyeria Química, ETSEQ, Universitat Rovira i Virgili, Tarragona 43007 Spain
| | - John K Brennan
- U.S. Army Combat Capabilities Development Command (DEVCOM) Army Research Laboratory, Aberdeen Proving Ground, Maryland, 21005 United States
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7
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Schmid F. Understanding and Modeling Polymers: The Challenge of Multiple Scales. ACS POLYMERS AU 2022. [DOI: 10.1021/acspolymersau.2c00049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Friederike Schmid
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudingerweg 9, 55128Mainz, Germany
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8
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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: 72] [Impact Index Per Article: 36.0] [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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9
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Particle shape characterizations for energetic materials by computational geometry and stereology method. SN APPLIED SCIENCES 2022. [DOI: 10.1007/s42452-022-05031-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
AbstractParticle shapes significantly affect viscosity and flow behavior of energetic materials, and therefore affect their packability and processability. This study presents a computational geometry framework for automatically quantifying two-dimensional (2D) and three-dimensional (3D) particle shapes of energetic materials. A specimen by mixing three typical energetic materials including HMX (octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine), RDX (1,3,5-Trinitroperhydro-1,3,5-triazine) and AP (Ammonium Perchlorate) particles is used in this study. This specimen is scanned by high-resolution X-ray computed tomography (X-ray CT), yielding a volumetric image. An improved watershed analysis algorithm is used to process the volumetric image to identify individual 3D particles. The stereology sampling method is used to obtain 2D projections of 3D particles. Computational geometry techniques are developed by this study to analyze 2D particle projections and 3D particle geometries to compute seven commonly used shape descriptors, including convexity, circularity, intercept sphericity, area sphericity, diameter sphericity, circle ratio sphericity, and surface area sphericity. Results show that those different shape descriptors of energetic materials can be divided into three groups based on their numerical ranges. This study also evaluates the effectiveness and accuracy of 2D shape descriptors for quantifying the true 3D shapes. The inconsistent characterization results between 2D and 3D shape descriptors suggest that researchers should be cautious when using 2D images to characterize 3D particle shapes of energetic materials. The computational geometry framework and particle shape analysis results presented in this study can be potentially useful in numerical modeling, experimental analysis, and theoretical investigation for energetic materials.
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10
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Lísal M, Larentzos JP, Avalos JB, Mackie AD, Brennan JK. Generalized Energy-Conserving Dissipative Particle Dynamics with Reactions. J Chem Theory Comput 2022; 18:2503-2512. [PMID: 35294175 DOI: 10.1021/acs.jctc.1c01294] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present an extension of the generalized energy-conserving dissipative particle dynamics method (J. Bonet Avalos, et al., Phys Chem Chem Phys, 2019, 21, 24891-24911) to include chemical reactivity, denoted GenDPDE-RX. GenDPDE-RX provides a means of simulating chemical reactivity at the micro- and mesoscales, while exploiting the attributes of density- and temperature-dependent many-body force fields, which include improved transferability and scalability compared to two-body pairwise models. The GenDPDE-RX formulation considers intra-particle reactivity via a coarse-grain reactor construct. Extent-of-reaction variables assigned to each coarse-grain particle monitor the temporal evolution of the prescribed reaction mechanisms and kinetics assumed to occur within the particle. Descriptions of the algorithm, equations of motion, and numerical discretization are presented, followed by verification of the GenDPDE-RX method through comparison with reaction kinetics theoretical model predictions. Demonstrations of the GenDPDE-RX method are performed using constant-volume adiabatic heating simulations of three different reaction models, including both reversible and irreversible reactions, as well as multistep reaction mechanisms. The selection of the demonstrations is intended to illustrate the flexibility and generality of the method but is inspired by real material systems that span from fluids to solids. Many-body force fields using analytical forms of the ideal gas, Lennard-Jones, and exponential-6 equations of state are used for demonstration, although application to other forms of equation of states is possible. Finally, the flexibility of the GenDPDE-RX framework is addressed with a brief discussion of other possible adaptations and extensions of the method.
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Affiliation(s)
- Martin Lísal
- Department of Molecular and Mesoscopic Modelling, The Czech Academy of Sciences, Institute of Chemical Process Fundamentals, Prague 165 01, Czech Republic.,Department of Physics, Faculty of Science, Jan Evangelista Purkyně University in Ústí nad Labem, Ústí n. Lab. 400 96, Czech Republic
| | - James P Larentzos
- U.S. Army Combat Capabilities Development Command (DEVCOM) Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005, United States
| | - Josep Bonet Avalos
- Departament d'Enginyeria Química, ETSEQ, Universitat Rovira i Virgili, Tarragona 43007, Spain
| | - Allan D Mackie
- Departament d'Enginyeria Química, ETSEQ, Universitat Rovira i Virgili, Tarragona 43007, Spain
| | - John K Brennan
- U.S. Army Combat Capabilities Development Command (DEVCOM) Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005, United States
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11
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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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12
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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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13
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Bonet Avalos J, Lísal M, Larentzos JP, Mackie AD, Brennan JK. Generalized energy-conserving dissipative particle dynamics revisited: Insight from the thermodynamics of the mesoparticle leading to an alternative heat flow model. Phys Rev E 2021; 103:062128. [PMID: 34271720 DOI: 10.1103/physreve.103.062128] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/21/2021] [Indexed: 11/07/2022]
Abstract
Recently we introduced the generalized energy-conserving dissipative particle dynamics method (GenDPDE) [J. Bonet Avalos, M. Lísal, J. P. Larentzos, A. D. Mackie, and J. K. Brennan, Phys. Chem. Chem. Phys. 21, 24891 (2019)]PPCPFQ1463-907610.1039/C9CP04404C, which has been formulated for an emerging class of density- and temperature-dependent coarse-grain models. In the original work, GenDPDE was formulated to ensure a fundamental link is maintained with the underlying physical system at the higher resolution scale. In this paper, we revisit the formulation of the GenDPDE method, and rederive the particle thermodynamics to ensure consistency at the opposing scale extreme, i.e., between the local thermodynamics in the mesoscopic systems and the corresponding macroscopic properties. We demonstrate this consistency by introducing unambiguous, physically meaningful definitions of the heat and work, which lead to the formulation of an alternative heat flow model that is analogous to Fourier's law of heat conduction. We present further analysis of the internal, unresolved degrees-of-freedom of the mesoparticles by considering the thermodynamics of an individual mesoparticle within the GenDPDE framework. Several key outcomes of the analysis include: (i) demonstration that the choice of the independent variables alters the particle thermodynamic description; (ii) demonstration that the mesoscopic thermodynamic transformations introduce additional terms of the order of the size of the local fluctuations, which prevent an unambiguous definition of both the heat and work; (iii) an emphasis on the importance of the choice of the proper estimators of the thermodynamic properties that are embedded in the chosen thermodynamic description; and (iv) a clearly defined path for determining any thermodynamic quantity dressed by the fluctuations. The further insight provided by this deeper analysis is useful for both readers interested in the GenDPDE theoretical framework, as well as readers interested in the practical ramifications of the analysis, namely, the alternative heat flow model.
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Affiliation(s)
- Josep Bonet Avalos
- Department d'Enginyeria Química, ETSEQ, Universitat Rovira i Virgili, Tarragona 43007, Spain
| | - Martin Lísal
- Department of Molecular and Mesoscopic Modelling, The Czech Academy of Sciences, Institute of Chemical Process Fundamentals, Prague 165 01, Czech Republic.,Department of Physics, Faculty of Science, J. E. Purkinje University, Ústí n. Lab. 400 96, Czech Republic
| | - James P Larentzos
- Weapons and Materials Research Directorate, U.S. Army CCDC Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005, USA
| | - Allan D Mackie
- Department d'Enginyeria Química, ETSEQ, Universitat Rovira i Virgili, Tarragona 43007, Spain
| | - John K Brennan
- Weapons and Materials Research Directorate, U.S. Army CCDC Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005, USA
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14
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Jin J, Han Y, Pak AJ, Voth GA. A new one-site coarse-grained model for water: Bottom-up many-body projected water (BUMPer). I. General theory and model. J Chem Phys 2021; 154:044104. [PMID: 33514116 PMCID: PMC7826168 DOI: 10.1063/5.0026651] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 12/14/2020] [Indexed: 12/26/2022] Open
Abstract
Water is undoubtedly one of the most important molecules for a variety of chemical and physical systems, and constructing precise yet effective coarse-grained (CG) water models has been a high priority for computer simulations. To recapitulate important local correlations in the CG water model, explicit higher-order interactions are often included. However, the advantages of coarse-graining may then be offset by the larger computational cost in the model parameterization and simulation execution. To leverage both the computational efficiency of the CG simulation and the inclusion of higher-order interactions, we propose a new statistical mechanical theory that effectively projects many-body interactions onto pairwise basis sets. The many-body projection theory presented in this work shares similar physics from liquid state theory, providing an efficient approach to account for higher-order interactions within the reduced model. We apply this theory to project the widely used Stillinger-Weber three-body interaction onto a pairwise (two-body) interaction for water. Based on the projected interaction with the correct long-range behavior, we denote the new CG water model as the Bottom-Up Many-Body Projected Water (BUMPer) model, where the resultant CG interaction corresponds to a prior model, the iteratively force-matched model. Unlike other pairwise CG models, BUMPer provides high-fidelity recapitulation of pair correlation functions and three-body distributions, as well as N-body correlation functions. BUMPer extensively improves upon the existing bottom-up CG water models by extending the accuracy and applicability of such models while maintaining a reduced computational cost.
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Affiliation(s)
- Jaehyeok Jin
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
| | - Yining Han
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
| | - 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, USA
| | - Gregory A. Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
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15
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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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16
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17
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Hong Z, Xiao N, Li L, Xie X. Investigation of nanoemulsion interfacial properties: A mesoscopic simulation. J FOOD ENG 2020. [DOI: 10.1016/j.jfoodeng.2019.109877] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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18
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Dočkal J, Lísal M, Moučka F. Molecular Force Field Development for Aqueous Electrolytes: 2. Polarizable Models Incorporating Crystalline Chemical Potential and Their Accurate Simulations of Halite, Hydrohalite, Aqueous Solutions of NaCl, and Solubility. J Chem Theory Comput 2020; 16:3677-3688. [DOI: 10.1021/acs.jctc.0c00161] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jan Dočkal
- Department of Physics, Faculty of Science, J. E. Purkyně University, 400 96 Ústí n. Lab., Czech Republic
| | - Martin Lísal
- Department of Physics, Faculty of Science, J. E. Purkyně University, 400 96 Ústí n. Lab., Czech Republic
- Department of Molecular and Mesoscopic Modelling, Institute of Chemical Process Fundamentals of the CAS, v. v. i., 165 02 Prague 6-Suchdol, Czech Republic
| | - Filip Moučka
- Department of Physics, Faculty of Science, J. E. Purkyně University, 400 96 Ústí n. Lab., Czech Republic
- Department of Molecular and Mesoscopic Modelling, Institute of Chemical Process Fundamentals of the CAS, v. v. i., 165 02 Prague 6-Suchdol, Czech Republic
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19
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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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20
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Abstract
Low resolution coarse-grained (CG) models are widely adopted for investigating phenomena that cannot be effectively simulated with all-atom (AA) models. Since the development of the many-body dissipative particle dynamics method, CG models have increasingly supplemented conventional pair potentials with one-body potentials of the local density (LD) around each site. These LD potentials appear to significantly extend the transferability of CG models, while also enabling more accurate descriptions of thermodynamic properties, interfacial phenomena, and many-body correlations. In this work, we systematically examine the properties of LD potentials. We first derive and numerically demonstrate a nontrivial transformation of pair and LD potentials that leaves the total forces and equilibrium distribution invariant. Consequently, the pair and LD potentials determined via bottom-up methods are not unique. We then investigate the sensitivity of CG models for glycerol to the weighting function employed for defining the local density. We employ the multiscale coarse-graining (MS-CG) method to simultaneously parameterize both pair and LD potentials. When employing a short-ranged Lucy function that defines the local density from the first solvation shell, the MS-CG model accurately reproduces the pair structure, pressure-density equation of state, and liquid-vapor interfacial profile of the AA model. The accuracy of the model generally decreases as the range of the Lucy function increases further. The MS-CG model provides similar accuracy when a smoothed Heaviside function is employed to define the local density from the first solvation shell. However, the model performs less well when this function acts on either longer or shorter length scales.
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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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21
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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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22
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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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23
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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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24
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Brian D, Bruno J, Zhen L, Tau-Mu Y, Linda P. A hybrid smoothed dissipative particle dynamics (SDPD) spatial stochastic simulation algorithm (sSSA) for advection-diffusion-reaction problems. JOURNAL OF COMPUTATIONAL PHYSICS 2019; 378:1-17. [PMID: 31031417 PMCID: PMC6481948 DOI: 10.1016/j.jcp.2018.10.043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We have developed a new algorithm which merges discrete stochastic simulation, using the spatial stochastic simulation algorithm (sSSA), with the particle based fluid dynamics simulation framework of smoothed dissipative particle dynamics (SDPD). This hybrid algorithm enables discrete stochastic simulation of spatially resolved chemically reacting systems on a mesh-free dynamic domain with a Lagrangian frame of reference. SDPD combines two popular mesoscopic techniques: smoothed particle hydrodynamics and dissipative particle dynamics (DPD), linking the macroscopic and mesoscopic hydrodynamics effects of these two methods. We have implemented discrete stochastic simulation using the reaction-diffusion master equations (RDME) formalism, and deterministic reaction-diffusion equations based on the SDPD method. We validate the new method by comparing our results to four canonical models, and demonstrate the versatility of our method by simulating a flow containing a chemical gradient past a yeast cell in a microfluidics chamber.
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Affiliation(s)
- Drawert Brian
- Department of Computer Science, University of North Carolina at Asheville, Asheville, North Carolina, 28804, USA
| | - Jacob Bruno
- Department of Mechanical Engineering, University of California-Santa Barbara, Santa Barbara, California, 93106, USA
| | - Li Zhen
- Division of Applied Mathematics, Brown University, Providence, Rhode Island 02912, USA
| | - Yi Tau-Mu
- Department of Molecular, Cellular, and Developmental Biology, University of California-Santa Barbara, Santa Barbara, California 93106, USA
| | - Petzold Linda
- Department of Mechanical Engineering, University of California-Santa Barbara, Santa Barbara, California, 93106, USA
- Department of Computer Science, University of California-Santa Barbara, Santa Barbara, California, 93106, USA
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25
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Deichmann G, van der Vegt NFA. Conditional Reversible Work Coarse-Grained Models with Explicit Electrostatics—An Application to Butylmethylimidazolium Ionic Liquids. J Chem Theory Comput 2019; 15:1187-1198. [DOI: 10.1021/acs.jctc.8b00881] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Gregor Deichmann
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287 Darmstadt, Germany
| | - Nico F. A. van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287 Darmstadt, Germany
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26
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Zhang L, Han J, Wang H, Car R, E W. DeePCG: Constructing coarse-grained models via deep neural networks. J Chem Phys 2018; 149:034101. [PMID: 30037247 DOI: 10.1063/1.5027645] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We introduce a general framework for constructing coarse-grained potential models without ad hoc approximations such as limiting the potential to two- and/or three-body contributions. The scheme, called the Deep Coarse-Grained Potential (abbreviated DeePCG), exploits a carefully crafted neural network to construct a many-body coarse-grained potential. The network is trained with full atomistic data in a way that preserves the natural symmetries of the system. The resulting model is very accurate and can be used to sample the configurations of the coarse-grained variables in a much faster way than with the original atomistic model. As an application, we consider liquid water and use the oxygen coordinates as the coarse-grained variables, starting from a full atomistic simulation of this system at the ab initio molecular dynamics level. We find that the two-body, three-body, and higher-order oxygen correlation functions produced by the coarse-grained and full atomistic models agree very well with each other, illustrating the effectiveness of the DeePCG model on a rather challenging task.
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Affiliation(s)
- Linfeng Zhang
- Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08544, USA
| | - Jiequn Han
- Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08544, USA
| | - Han Wang
- Institute of Applied Physics and Computational Mathematics, Fenghao East Road 2, Beijing 100094, People's Republic of China and CAEP Software Center for High Performance Numerical Simulation, Huayuan Road 6, Beijing 100088, People's Republic of China
| | - Roberto Car
- Department of Chemistry, Department of Physics, Program in Applied and Computational Mathematics, Princeton Institute for the Science and Technology of Materials, Princeton University, Princeton, New Jersey 08544, USA
| | - Weinan E
- Department of Mathematics and Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08544, USA and Beijing Institute of Big Data Research, Beijing 100871, People's Republic of China
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27
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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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28
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Mattox TI, Larentzos JP, Moore SG, Stone CP, Ibanez DA, Thompson AP, Lísal M, Brennan JK, Plimpton SJ. Highly scalable discrete-particle simulations with novel coarse-graining: accessing the microscale. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1471532] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Timothy I. Mattox
- Engility Corporation, DoD High Performance Computing Modernization Program (HPCMP) PETTT Group, U.S. Army Research Laboratory, Aberdeen Proving Ground, MD, USA
| | - James P. Larentzos
- Weapons and Materials Research Directorate, U.S. Army Research Laboratory, Aberdeen Proving Ground, MD, USA
| | - Stan G. Moore
- Multiscale Science Department, Sandia National Laboratories, Albuquerque, NM, USA
| | - Christopher P. Stone
- Computational Science and Engineering, LLC, DoD High Performance Computing Modernization Program (HPCMP) PETTT Group, U.S. Air Force Research Laboratory, Dayton, OH, USA
| | - Daniel A. Ibanez
- Computational Multiphysics Department, Sandia National Laboratories, Albuquerque, NM, USA
| | - Aidan P. Thompson
- Multiscale Science Department, Sandia National Laboratories, Albuquerque, NM, 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
- Weapons and Materials Research Directorate, U.S. Army Research Laboratory, Aberdeen Proving Ground, MD, USA
| | - Steven J. Plimpton
- Multiscale Science Department, Sandia National Laboratories, Albuquerque, NM, USA
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29
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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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30
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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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31
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Lafond PG, Izvekov S. Multiscale Coarse-Graining with Effective Polarizabilities: A Fully Bottom-Up Approach. J Chem Theory Comput 2018; 14:1873-1886. [DOI: 10.1021/acs.jctc.7b00917] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Patrick G. Lafond
- Weapons and Materials Research Directorate, U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005, United States
| | - Sergei Izvekov
- Weapons and Materials Research Directorate, U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005, United States
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32
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Dunn NJH, Lebold KM, DeLyser MR, Rudzinski JF, Noid W. BOCS: Bottom-up Open-source Coarse-graining Software. J Phys Chem B 2017; 122:3363-3377. [DOI: 10.1021/acs.jpcb.7b09993] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Nicholas J. H. Dunn
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Kathryn M. Lebold
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Michael R. DeLyser
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Joseph F. Rudzinski
- 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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33
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John ST, Csányi G. Many-Body Coarse-Grained Interactions Using Gaussian Approximation Potentials. J Phys Chem B 2017; 121:10934-10949. [PMID: 29117675 DOI: 10.1021/acs.jpcb.7b09636] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We introduce a computational framework that is able to describe general many-body coarse-grained (CG) interactions of molecules and use it to model the free energy surface of molecular liquids as a cluster expansion in terms of monomer, dimer, and trimer terms. The contributions to the free energy due to these terms are inferred from all-atom molecular dynamics (MD) data using Gaussian Approximation Potentials, a type of machine-learning model that employs Gaussian process regression. The resulting CG model is much more accurate than those possible using pair potentials. Though slower than the latter, our model can still be faster than all-atom simulations for solvent-free CG models commonly used in biomolecular simulations.
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Affiliation(s)
- S T John
- Department of Physics, Cavendish Laboratory, University of Cambridge , Cambridge CB3 0HE, United Kingdom.,PROWLER.io , 66-68 Hills Road, Cambridge CB2 1LA, United Kingdom
| | - Gábor Csányi
- Department of Engineering, University of Cambridge , Cambridge CB2 1PZ, United Kingdom
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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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Faure G, Delgado-Buscalioni R, Español P. The entropy of a complex molecule. J Chem Phys 2017; 146:224106. [PMID: 29166055 PMCID: PMC5468121 DOI: 10.1063/1.4984965] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 05/22/2017] [Indexed: 01/02/2023] Open
Abstract
Entropy is a central concept in the theory of coarse-graining. Through Einstein's formula, it provides the equilibrium probability distribution of the coarse-grained variables used to describe the system of interest. We study with molecular dynamics simulations the equilibrium probability distribution of thermal blobs representing at a coarse-grained level star polymer molecules in melt. Thermal blobs are characterized by the positions and momenta of the centers of mass, and internal energies of the molecules. We show that the entropy of the level of description of thermal blobs can be very well approximated as the sum of the thermodynamic entropy of each single molecule considered as isolated thermodynamic systems. The entropy of a single molecule depends on the intrinsic energy, involving only contributions from the atoms that make the molecule and not from the interactions with atoms of other molecules.
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Affiliation(s)
| | - Rafael Delgado-Buscalioni
- Departamento de Física Teórica de la Materia Condensada Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Pep Español
- Departamento de Física Fundamental, Universidad Nacional de Educación a Distancia, Apartado 60141, E-28080 Madrid, Spain
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Affiliation(s)
- Pep Español
- Dept. Física Fundamental, Universidad Nacional de Educación a Distancia, Aptdo. 60141, E-28080 Madrid, Spain
| | - Patrick B. Warren
- Unilever R&D Port Sunlight, Quarry Road East, Bebington, Wirral CH63 3JW, United Kingdom
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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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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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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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