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Lauriello N, Lísal M, Boccardo G, Marchisio D, Buffo A. Modeling temperature-dependent transport properties in dissipative particle dynamics: A top-down coarse-graining toward realistic dynamics at the mesoscale. J Chem Phys 2024; 161:034112. [PMID: 39007396 DOI: 10.1063/5.0207530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 06/03/2024] [Indexed: 07/16/2024] Open
Abstract
Dissipative particle dynamics (DPD) is a widespread computational tool to simulate the behavior of soft matter and liquids in and out of equilibrium. Although there are many applications in which the effect of temperature is relevant, most of the DPD studies have been carried out at a fixed system temperature. Therefore, this work investigates how to incorporate the effect of system temperature variation within the DPD model to capture realistic temperature-dependent system properties. In particular, this work focuses on the relationship between temperature and transport properties, and therefore, an extended DPD model for transport properties prediction is employed. Transport properties, unlike the equilibrium properties, are often overlooked despite their significant influence on the flow dynamics of non-isothermal mesoscopic systems. Moreover, before simulating the response of the system induced by a temperature change, it is important to first estimate transport properties at a certain temperature. Thus here, the same fluid is simulated across different temperature conditions using isothermal DPD with the aim to identify a temperature-dependent parametrization methodology, capable of ensuring the correctness of both equilibrium and dynamical properties. Liquid water is used as a model system for these analyses. This work proposes a temperature-dependent form of the extended DPD model where both conservative and non-conservative interaction parameters incorporate the variation of the temperature. The predictions provided by our simulations are in excellent agreement with experimental data.
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Affiliation(s)
- N Lauriello
- DISAT-Institute of Chemical Engineering, Politecnico di Torino, C.so Duca degli Abruzzi 24, Torino 10129, Italy
| | - M Lísal
- Research Group of Molecular and Mesoscopic Modelling, The Czech Academy of Sciences, Institute of Chemical Process Fundamentals, Rozvojová 135/1, Prague, Czech Republic
- Department of Physics, Faculty of Science, Jan Evangelista Purkyně University in Ústí nad Labem, Pasteurova 3544/1, 40096 Ústí n. Lab, Czech Republic
| | - G Boccardo
- DISAT-Institute of Chemical Engineering, Politecnico di Torino, C.so Duca degli Abruzzi 24, Torino 10129, Italy
| | - D Marchisio
- DISAT-Institute of Chemical Engineering, Politecnico di Torino, C.so Duca degli Abruzzi 24, Torino 10129, Italy
| | - A Buffo
- DISAT-Institute of Chemical Engineering, Politecnico di Torino, C.so Duca degli Abruzzi 24, Torino 10129, Italy
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Malaspina DC, Lísal M, Larentzos JP, Brennan JK, Mackie AD, Avalos JB. Green-Kubo expressions for transport coefficients from dissipative particle dynamics simulations revisited. Phys Chem Chem Phys 2024; 26:1328-1339. [PMID: 38108233 DOI: 10.1039/d3cp03791f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
This article addresses the debate about the correct application of Green-Kubo expressions for transport coefficients from dissipative particle dynamics simulations. We demonstrate that the Green-Kubo expressions are valid provided that (i) the dynamic model conserves the physical property, whose transport is studied, and (ii) the fluctuations satisfy detailed balance. As a result, the traditional expressions used in molecular dynamics can also be applied to dissipative particle dynamics simulations. However, taking the calculation of the shear viscosity as a paradigmatic example, a random contribution, whose strength scales as 1/δt1/2, with δt the time-step, can cause difficulties if the stress tensor is not separated into the different contributions. We compare our expression to that of Ernst and Brito (M. H. Ernst and R. Brito, Europhys. Lett., 2006, 73, 183-189), which arises from a diametrically different perspective. We demonstrate that the two expressions are completely equivalent and find exactly the same result both analytically and numerically. We show that the differences are not due to the lack of time-reversibility but instead from a pre-averaging of the random contributions. Despite the overall validity of Green-Kubo expressions, we find that the Einstein-Helfand relations (D. C. Malaspina et al. Phys. Chem. Chem. Phys., 2023, 25, 12025-12040) do not suffer from the need to decompose the stress tensor and can readily be used with a high degree of accuracy. Consequently, Einstein-Helfand relations should be seen as the preferred method to calculate transport coefficients from dissipative particle dynamics simulations.
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Affiliation(s)
- D C Malaspina
- Departament d'Enginyeria Química, ETSEQ, Universitat Rovira i Virgili, Tarragona 43007, Spain.
| | - M Lísal
- Research Group of Molecular and Mesoscopic Modelling, The Czech Academy of Sciences, Institute of Chemical Process Fundamentals, Prague 16500, Czech Republic
- Department of Physics, Faculty of Science, Jan Evangelista Purkyně University in Ústí nad Labem, Ústí n. Lab. 40096, Czech Republic
| | - J P Larentzos
- U.S. Army Combat Capabilities Development Command (DEVCOM) Army Research Laboratory, Aberdeen Proving Ground, MD 21005, USA
| | - J K Brennan
- U.S. Army Combat Capabilities Development Command (DEVCOM) Army Research Laboratory, Aberdeen Proving Ground, MD 21005, USA
| | - A D Mackie
- Departament d'Enginyeria Química, ETSEQ, Universitat Rovira i Virgili, Tarragona 43007, Spain.
| | - J Bonet Avalos
- Departament d'Enginyeria Química, ETSEQ, Universitat Rovira i Virgili, Tarragona 43007, Spain.
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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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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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Yu X, Zhao J, Chen S, Huang D, Zhang K, Cao D. The calibration for many-body dissipative particle dynamics by using back-propagation neural networks. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2055755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Xin Yu
- School of Energy and Power Engineering, University of Shanghai for Science and Technology, Shanghai, People's Republic of China
| | - Jiayi Zhao
- School of Energy and Power Engineering, University of Shanghai for Science and Technology, Shanghai, People's Republic of China
| | - Shuo Chen
- School of Aerospace Engineering and Applied Mechanics, Tongji University, Shanghai, People's Republic of China
| | - Diangui Huang
- School of Energy and Power Engineering, University of Shanghai for Science and Technology, Shanghai, People's Republic of China
| | - Kaixuan Zhang
- Institute of Biomechanics and Medical Engineering, AML, Department of Engineering Mechanics, Tsinghua University, Beijing, People's Republic of China
| | - Damin Cao
- School of Air Transportation, Shanghai University of Engineering Science, Shanghai, People's Republic of China
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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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Santo KP, Neimark AV. Dissipative particle dynamics simulations in colloid and Interface science: a review. Adv Colloid Interface Sci 2021; 298:102545. [PMID: 34757286 DOI: 10.1016/j.cis.2021.102545] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 12/31/2022]
Abstract
Dissipative particle dynamics (DPD) is one of the most efficient mesoscale coarse-grained methodologies for modeling soft matter systems. Here, we comprehensively review the progress in theoretical formulations, parametrization strategies, and applications of DPD over the last two decades. DPD bridges the gap between the microscopic atomistic and macroscopic continuum length and time scales. Numerous efforts have been performed to improve the computational efficiency and to develop advanced versions and modifications of the original DPD framework. The progress in the parametrization techniques that can reproduce the engineering properties of experimental systems attracted a lot of interest from the industrial community longing to use DPD to characterize, help design and optimize the practical products. While there are still areas for improvements, DPD has been efficiently applied to numerous colloidal and interfacial phenomena involving phase separations, self-assembly, and transport in polymeric, surfactant, nanoparticle, and biomolecules systems.
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Affiliation(s)
- Kolattukudy P Santo
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States
| | - Alexander V Neimark
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States.
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