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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: 25] [Impact Index Per Article: 8.3] [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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2
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Zohravi E, Shirani E, Pishevar A, Karimpour H. Dissipative particle dynamics study of velocity autocorrelation function and self-diffusion coefficient in terms of interaction potential strength. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1441463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Elnaz Zohravi
- Department of Mechanical Engineering, Isfahan University of Technology, Isfahan, Iran
| | - Ebrahim Shirani
- Faculty of Engineering, Foolad Institute of Technology – Fooladshahr, Isfahan, Iran
| | - Ahmadreza Pishevar
- Department of Mechanical Engineering, Isfahan University of Technology, Isfahan, Iran
| | - Hossein Karimpour
- Department of Mechanical Engineering, Faculty of Engineering, University of Isfahan, Isfahan, Iran
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3
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Hansen JS, Greenfield ML, Dyre JC. Hydrodynamic relaxations in dissipative particle dynamics. J Chem Phys 2018; 148:034503. [DOI: 10.1063/1.4986569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- J. S. Hansen
- “Glass and Time,” IMFUFA, Department of Science and Environment, Roskilde University, Postbox 260, DK-4000 Roskilde, Denmark
| | - Michael L. Greenfield
- Department of Chemical Engineering, University of Rhode Island, Kingston, Rhode Island 02881, USA
| | - Jeppe C. Dyre
- “Glass and Time,” IMFUFA, Department of Science and Environment, Roskilde University, Postbox 260, DK-4000 Roskilde, Denmark
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4
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Zohravi E, Shirani E, Pishevar A. Influence of the conservative force on transport coefficients in the DPD method. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1373193] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Elnaz Zohravi
- Department of Mechanical Engineering, Isfahan University of Technology, Isfahan, Iran
| | | | - Ahmadreza Pishevar
- Department of Mechanical Engineering, Isfahan University of Technology, Isfahan, Iran
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5
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Azarnykh D, Litvinov S, Bian X, Adams NA. Determination of macroscopic transport coefficients of a dissipative particle dynamics solvent. Phys Rev E 2016; 93:013302. [PMID: 26871186 DOI: 10.1103/physreve.93.013302] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Indexed: 11/07/2022]
Abstract
We present an approach to determine macroscopic transport coefficients of a dissipative particle dynamics (DPD) solvent. Shear viscosity, isothermal speed of sound, and bulk viscosity result from DPD-model input parameters and can be determined only a posteriori. For this reason approximate predictions of these quantities are desirable in order to set appropriate DPD input parameters. For the purpose of deriving an improved approximate prediction we analyze the autocorrelation of shear and longitudinal modes in Fourier space of a DPD solvent for Kolmogorov flow. We propose a fitting function with nonexponential properties which gives a good approximation to these autocorrelation functions. Given this fitting function we improve significantly the capability of a priori determination of macroscopic solvent transport coefficients in comparison to previously used exponential fitting functions.
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Affiliation(s)
- Dmitrii Azarnykh
- Institute of Aerodynamics and Fluid Mechanics, Technische Universität München, Garching, Germany
| | - Sergey Litvinov
- Chair for Computational Science, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Xin Bian
- Division of Applied Mathematics, Brown University, Providence, Rhode Island 02912, USA
| | - Nikolaus A Adams
- Institute of Aerodynamics and Fluid Mechanics, Technische Universität München, Garching, Germany
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Kojic M, Filipovic N, Tsuda A. A mesoscopic bridging scale method for fluids and coupling dissipative particle dynamics with continuum finite element method. COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING 2013; 197:821-833. [PMID: 23814322 PMCID: PMC3693461 DOI: 10.1016/j.cma.2007.09.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
A multiscale procedure to couple a mesoscale discrete particle model and a macroscale continuum model of incompressible fluid flow is proposed in this study. We call this procedure the mesoscopic bridging scale (MBS) method since it is developed on the basis of the bridging scale method for coupling molecular dynamics and finite element models [G.J. Wagner, W.K. Liu, Coupling of atomistic and continuum simulations using a bridging scale decomposition, J. Comput. Phys. 190 (2003) 249-274]. We derive the governing equations of the MBS method and show that the differential equations of motion of the mesoscale discrete particle model and finite element (FE) model are only coupled through the force terms. Based on this coupling, we express the finite element equations which rely on the Navier-Stokes and continuity equations, in a way that the internal nodal FE forces are evaluated using viscous stresses from the mesoscale model. The dissipative particle dynamics (DPD) method for the discrete particle mesoscale model is employed. The entire fluid domain is divided into a local domain and a global domain. Fluid flow in the local domain is modeled with both DPD and FE method, while fluid flow in the global domain is modeled by the FE method only. The MBS method is suitable for modeling complex (colloidal) fluid flows, where continuum methods are sufficiently accurate only in the large fluid domain, while small, local regions of particular interest require detailed modeling by mesoscopic discrete particles. Solved examples - simple Poiseuille and driven cavity flows illustrate the applicability of the proposed MBS method.
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Affiliation(s)
- Milos Kojic
- Harvard School of Public Health, 665 Huntington Avenue, Boston, MA 02115, USA
- University of Kragujevac, 34000 Kragujevac, Serbia
| | - Nenad Filipovic
- Harvard School of Public Health, 665 Huntington Avenue, Boston, MA 02115, USA
- University of Kragujevac, 34000 Kragujevac, Serbia
| | - Akira Tsuda
- Harvard School of Public Health, 665 Huntington Avenue, Boston, MA 02115, USA
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Chaudhri A, Lukes JR. Velocity and stress autocorrelation decay in isothermal dissipative particle dynamics. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 81:026707. [PMID: 20365675 DOI: 10.1103/physreve.81.026707] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2008] [Revised: 11/02/2009] [Indexed: 05/29/2023]
Abstract
The velocity and stress autocorrelation decay in a dissipative particle dynamics ideal fluid model is analyzed in this paper. The autocorrelation functions are calculated at three different friction parameters and three different time steps using the well-known Groot/Warren algorithm and newer algorithms including self-consistent leap-frog, self-consistent velocity Verlet and Shardlow first and second order integrators. At low friction values, the velocity autocorrelation function decays exponentially at short times, shows slower-than exponential decay at intermediate times, and approaches zero at long times for all five integrators. As friction value increases, the deviation from exponential behavior occurs earlier and is more pronounced. At small time steps, all the integrators give identical decay profiles. As time step increases, there are qualitative and quantitative differences between the integrators. The stress correlation behavior is markedly different for the algorithms. The self-consistent velocity Verlet and the Shardlow algorithms show very similar stress autocorrelation decay with change in friction parameter, whereas the Groot/Warren and leap-frog schemes show variations at higher friction factors. Diffusion coefficients and shear viscosities are calculated using Green-Kubo integration of the velocity and stress autocorrelation functions. The diffusion coefficients match well-known theoretical results at low friction limits. Although the stress autocorrelation function is different for each integrator, fluctuates rapidly, and gives poor statistics for most of the cases, the calculated shear viscosities still fall within range of theoretical predictions and nonequilibrium studies.
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Affiliation(s)
- Anuj Chaudhri
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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Füchslin RM, Fellermann H, Eriksson A, Ziock HJ. Coarse graining and scaling in dissipative particle dynamics. J Chem Phys 2009; 130:214102. [DOI: 10.1063/1.3143976] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Vázquez-Quesada A, Ellero M, Español P. Smoothed particle hydrodynamic model for viscoelastic fluids with thermal fluctuations. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009; 79:056707. [PMID: 19518593 DOI: 10.1103/physreve.79.056707] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2008] [Indexed: 05/27/2023]
Abstract
We present a fluid-particle model for a polymer solution in nonisothermal situations. The state of the fluid particles is characterized by the thermodynamic variables and a configuration tensor that describes the underlying molecular orientation of the polymer molecules. The specification of very simple physical mechanisms inspired by the dynamics of single polymer molecules allows one, with the help of the general equation for nonequilibrium reversible-irreversible coupling (GENERIC) formalism, to derive the equations of motion for a set of fluid particles carrying polymer molecules in suspension. In the simplest case of Hookean dumbbells we recover a fluid-particle version of the Oldroyd-B model in which thermal fluctuations are included consistently. Generalization to more complex viscoelastic models, such as finitely extensible nonlinear elastic Peterlin (FENE-P) model, with the proper introduction of thermal fluctuations is straightforward.
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Dissipative particle dynamics simulation of on-chip hydrodynamic chromatography. J Chromatogr A 2008; 1198-1199:140-7. [DOI: 10.1016/j.chroma.2008.05.055] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2007] [Revised: 04/11/2008] [Accepted: 05/20/2008] [Indexed: 11/15/2022]
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Lahmar F, Rousseau B. Influence of the adjustable parameters of the DPD on the global and local dynamics of a polymer melt. POLYMER 2007. [DOI: 10.1016/j.polymer.2007.04.018] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Dzwinel W, Yuen DA, Boryczko K. Bridging diverse physical scales with the discrete-particle paradigm in modeling colloidal dynamics with mesoscopic features. Chem Eng Sci 2006. [DOI: 10.1016/j.ces.2004.01.075] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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13
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Cubero D, Yaliraki SN. Formal derivation of dissipative particle dynamics from first principles. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2005; 72:032101. [PMID: 16241496 DOI: 10.1103/physreve.72.032101] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2005] [Revised: 05/20/2005] [Indexed: 05/05/2023]
Abstract
We show that the Markovian approximation assumed in current particle-based coarse-grained techniques, like dissipative particle dynamics, is unreliable in situations in which sound plays an important role. As an example we solve analytically and numerically the dynamics of coarse-grained harmonic systems by using first principle methods, showing the presence of long-lived memory kernels. This effect raises questions about the connection of these approaches at their current form to molecular dynamics.
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Affiliation(s)
- David Cubero
- Department of Chemistry, South Kensington Campus, Imperial College London, London SW7 2AZ, United Kingdom
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Ripoll M, Ernst MH. Power law tails of time correlations in a mesoscopic fluid model. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2005; 72:011101. [PMID: 16089931 DOI: 10.1103/physreve.72.011101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2005] [Indexed: 05/03/2023]
Abstract
In a quenched mesoscopic fluid, modeling transport processes at high densities, we perform computer simulations of the single particle energy autocorrelation function C(e) (t) , which is essentially a return probability. This is done to test the predictions for power law tails, obtained from mode coupling theory. We study both off and on-lattice systems in one- and two-dimensions. The predicted long time tail approximately t(-d/2) is in excellent agreement with the results of computer simulations. We also account for finite size effects, such that smaller systems are fully covered by the present theory as well.
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Affiliation(s)
- M Ripoll
- Institut für Festkörperforschung, Forschungszentrum Jülich, Germany
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15
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Chatterji A, Horbach J. Combining molecular dynamics with Lattice Boltzmann: A hybrid method for the simulation of (charged) colloidal systems. J Chem Phys 2005; 122:184903. [PMID: 15918761 DOI: 10.1063/1.1890905] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a hybrid method for the simulation of colloidal systems that combines molecular dynamics (MD) with the Lattice Boltzmann (LB) scheme. The LB method is used as a model for the solvent in order to take into account the hydrodynamic mass and momentum transport through the solvent. The colloidal particles are propagated via MD and they are coupled to the LB fluid by viscous forces. With respect to the LB fluid, the colloids are represented by uniformly distributed points on a sphere. Each such point [with a velocity V(r) at any off-lattice position r] is interacting with the neighboring eight LB nodes by a frictional force F = xi0(V(r)-u(r)), with xi0 being a friction coefficient and u(r) being the velocity of the fluid at the position r. Thermal fluctuations are introduced in the framework of fluctuating hydrodynamics. This coupling scheme has been proposed recently for polymer systems by Ahlrichs and Dunweg [J. Chem. Phys. 111, 8225 (1999)]. We investigate several properties of a single colloidal particle in a LB fluid, namely, the effective Stokes friction and long-time tails in the autocorrelation functions for the translational and rotational velocity. Moreover, a charged colloidal system is considered consisting of a macroion, counterions, and coions that are coupled to a LB fluid. We study the behavior of the ions in a constant electric field. In particular, an estimate of the effective charge of the macroion is yielded from the number of counterions that move with the macroion in the direction of the electric field.
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Affiliation(s)
- Apratim Chatterji
- Institut für Physik, Johannes Gutenberg-Universität Mainz, D-55099 Mainz, Germany
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Boryczko K, Dzwinel W, Yuen DA. Dynamical clustering of red blood cells in capillary vessels. J Mol Model 2003; 9:16-33. [PMID: 12638008 DOI: 10.1007/s00894-002-0105-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2002] [Accepted: 10/16/2002] [Indexed: 11/24/2022]
Abstract
We have modeled the dynamics of a 3-D system consisting of red blood cells (RBCs), plasma and capillary walls using a discrete-particle approach. The blood cells and capillary walls are composed of a mesh of particles interacting with harmonic forces between nearest neighbors. We employ classical mechanics to mimic the elastic properties of RBCs with a biconcave disk composed of a mesh of spring-like particles. The fluid particle method allows for modeling the plasma as a particle ensemble, where each particle represents a collective unit of fluid, which is defined by its mass, moment of inertia, translational and angular momenta. Realistic behavior of blood cells is modeled by considering RBCs and plasma flowing through capillaries of various shapes. Three types of vessels are employed: a pipe with a choking point, a curved vessel and bifurcating capillaries. There is a strong tendency to produce RBC clusters in capillaries. The choking points and other irregularities in geometry influence both the flow and RBC shapes, considerably increasing the clotting effect. We also discuss other clotting factors coming from the physical properties of blood, such as the viscosity of the plasma and the elasticity of the RBCs. Modeling has been carried out with adequate resolution by using 1 to 10 million particles. Discrete particle simulations open a new pathway for modeling the dynamics of complex, viscoelastic fluids at the microscale, where both liquid and solid phases are treated with discrete particles. Figure A snapshot from fluid particle simulation of RBCs flowing along a curved capillary. The red color corresponds to the highest velocity. We can observe aggregation of RBCs at places with the most stagnant plasma flow.
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Affiliation(s)
- Krzysztof Boryczko
- AGH Institute of Computer Science, al. Mickiewicza 30, 30-059, Kraków, Poland
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Vattulainen I, Karttunen M, Besold G, Polson JM. Integration schemes for dissipative particle dynamics simulations: From softly interacting systems towards hybrid models. J Chem Phys 2002. [DOI: 10.1063/1.1450554] [Citation(s) in RCA: 152] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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18
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Ripoll M, Ernst MH, Español P. Large scale and mesoscopic hydrodynamics for dissipative particle dynamics. J Chem Phys 2001. [DOI: 10.1063/1.1402989] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Pagonabarraga I, Frenkel D. Dissipative particle dynamics for interacting systems. J Chem Phys 2001. [DOI: 10.1063/1.1396848] [Citation(s) in RCA: 253] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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