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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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Han Y, Jin J, Voth GA. Constructing many-body dissipative particle dynamics models of fluids from bottom-up coarse-graining. J Chem Phys 2021; 154:084122. [PMID: 33639745 DOI: 10.1063/5.0035184] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Since their emergence in the 1990s, mesoscopic models of fluids have been widely used to study complex organization and transport phenomena beyond the molecular scale. Even though these models are designed based on results from physics at the meso- and macroscale, such as fluid mechanics and statistical field theory, the underlying microscopic foundation of these models is not as well defined. This paper aims to build such a systematic connection using bottom-up coarse-graining methods. From the recently developed dynamic coarse-graining scheme, we introduce a statistical inference framework of explicit many-body conservative interaction that quantitatively recapitulates the mesoscopic structure of the underlying fluid. To further consider the dissipative and fluctuation forces, we design a novel algorithm that parameterizes these forces. By utilizing this algorithm, we derive pairwise decomposable friction kernels under both non-Markovian and Markovian limits where both short- and long-time features of the coarse-grained dynamics are reproduced. Finally, through these new developments, the many-body dissipative particle dynamics type of equations of motion are successfully derived. The methodologies developed in this work thus open a new avenue for the construction of direct bottom-up mesoscopic models that naturally bridge the meso- and macroscopic physics.
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Affiliation(s)
- Yining Han
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Jaehyeok Jin
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 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, Chicago, Illinois 60637, USA
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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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Barrett JC. Random phase approximation for the non-uniform Yukawa fluid. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:155002. [PMID: 30665210 DOI: 10.1088/1361-648x/ab0037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Mean-field density functional theory can be used to estimate the free energy of non-uniform fluids. The second functional derivative with respect to density of the free energy is related to the direct correlation function of the fluid and, in principle, this can be inverted to find an improved approximation for the pair correlation function and hence the free energy, the so-called 'random phase approximation'. If the repulsive molecular interaction is approximated by the local density approximation and the attractive interaction is assumed to be of the Yukawa form, the problem reduces to that of finding the eigenvalues of Schrödinger-like equations, which, for certain models (such as the 'Φ4 model'), can be done analytically in the planar case. The relationship between this approach and field theoretical treatment of the vapour-liquid interface is discussed. The ultraviolet divergence of the expression can be eliminated by separating the first term in the expansion, although quantitative results still depend on the behaviour of the attractive potential in the repulsive core. In the case of a spherical droplet of radius R, correction terms to the free energy involving lnR appear due to (i) cluster translational invariance, (ii) the unstable mode corresponding to droplet growth, and (iii) capillary waves. The net effect of these terms is to modify the classical expression for the nucleation rate by a factor proportional to R 4/3.
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Affiliation(s)
- Jonathan C Barrett
- Nuclear Department, Defence Academy, HMS Sultan, Military Road, Gosport PO12 3BY, United Kingdom
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Abe K, Sumi T, Koga K. Mean-Field Approximation to the Hydrophobic Hydration in the Liquid–Vapor Interface of Water. J Phys Chem B 2015; 120:2012-9. [DOI: 10.1021/acs.jpcb.5b10169] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kiharu Abe
- Department
of Chemistry,
Faculty of Science, Okayama University, Okayama 700-8530, Japan
| | - Tomonari Sumi
- Department
of Chemistry,
Faculty of Science, Okayama University, Okayama 700-8530, Japan
| | - Kenichiro Koga
- Department
of Chemistry,
Faculty of Science, Okayama University, Okayama 700-8530, Japan
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Ghobadi AF, Elliott JR. Adapting SAFT-γ perturbation theory to site-based molecular dynamics simulation. II. Confined fluids and vapor-liquid interfaces. J Chem Phys 2014; 141:024708. [DOI: 10.1063/1.4886398] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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Dalton BA, Glavatskiy KS, Daivis PJ, Todd BD, Snook IK. Linear and nonlinear density response functions for a simple atomic fluid. J Chem Phys 2013; 139:044510. [DOI: 10.1063/1.4816514] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Das S, Chakraborty S, Mitra SK. Contribution of interfacial electrostriction in surface tension. J Colloid Interface Sci 2013; 400:130-4. [DOI: 10.1016/j.jcis.2013.02.043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Accepted: 02/26/2013] [Indexed: 11/29/2022]
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Ghosh S, Ghosh SK. Density functional theory of size-dependent surface tension of Lennard-Jones fluid droplets using a double well type Helmholtz free energy functional. J Chem Phys 2011; 135:124710. [DOI: 10.1063/1.3633475] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Lutsko JF. Density functional theory of inhomogeneous liquids. IV. Squared-gradient approximation and classical nucleation theory. J Chem Phys 2011; 134:164501. [DOI: 10.1063/1.3582901] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Lutsko JF. Recent Developments in Classical Density Functional Theory. ADVANCES IN CHEMICAL PHYSICS 2010. [DOI: 10.1002/9780470564318.ch1] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Yamamoto T, Ohnishi S. Nano bubbles in liquid of a noble-gas mixture. Phys Chem Chem Phys 2010; 12:1033-7. [DOI: 10.1039/b918541k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Lutsko JF. Density functional theory of inhomogeneous liquids. II. A fundamental measure approach. J Chem Phys 2008; 128:184711. [DOI: 10.1063/1.2916694] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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