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Dissipative Particle Dynamics: A Method to Simulate Soft Matter Systems in Equilibrium and Under Flow

  • C. PastorinoEmail author
  • A. Gama Goicochea
Conference paper
Part of the Environmental Science and Engineering book series (ESE)

Abstract

We provide examples and a concise review of the method of Dissipative Particle Dynamics (DPD), as a simulation tool to study soft matter systems and simple liquids in equilibrium and under flow. DPD was initially thought as a simulation method, which in combination with soft potentials, could simulate “fluid particles” with suitable hydrodynamic correlations. Then DPD evolved to a generic “thermostat” to simulate systems in equilibrium and under flow, with arbitrary interaction potential among particles. We describe the application of the method with soft potentials and other coarse-grain models usually used in polymeric and other soft matter systems. We explain the advantages, common problems and limitations of DPD, in comparison with other thermostats widely used in simulations. The implementation of the DPD forces in a working Molecular Dynamics (MD) code is explained, which is a very convenient property of DPD. We present various examples of use, according to our research interests and experiences, and tricks of trade in different situations. The use of DPD in equilibrium simulations in the canonical ensemble, the grand canonical ensemble at constant chemical potential, and stationary Couette and Poiseuille flows is explained. It is also described in detail the use of different interaction models for molecules: soft and hard potentials, electrostatic interactions and bonding interactions to represent polymers. We end this contribution with our personal views and concluding remarks.

Keywords

Shear Rate Dissipative Particle Dynamics Polymer Brush Conservative Force Soft Potential 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

C.P. thanks Marcus Müller for the enjoyable and fruitful discussions since he started in this exciting topic of simulations of soft matter systems. Kurt Binder and Torsten Kreer are also gratefully acknowledged for the support and scientific discussions in the nice times of Mainz. AGG would like to thank F. Alarcón, M.A. Balderas Altamirano, C. Carmín, E. Mayoral, G. Pérez-Hernández, and E. Pérez for their help and collaborative efforts.

References

  1. Alarcón F, Pérez E, Gama Goicochea A (2013a) Dissipative particle dynamics simulations of weak polyelectrolyte adsorption on charged and neutral surfaces as a function of the degree of ionization. Soft Matter 9(3):777–3788. doi: 10.1039/C2SM27332B, http://dx.doi.org/10.1039/C2SM27332B
  2. Alarcón F, Pérez-Hernández G, Pérez E, Gama Goicochea A (2013b) Coarse-grained simulations of the salt dependence of the radius of gyration of polyelectrolytes as models for biomolecules in aqueous solution. Eur Biophys J 42(9):661–672Google Scholar
  3. Alexander S (1977) Adsorption of chain molecules with a polar head a scaling description. J Phys Fr 38(8):983–987CrossRefGoogle Scholar
  4. Allen MP, Tildesley DJ (1987) Computer simulations of liquids. Clarendom Press, OxfordGoogle Scholar
  5. Avalos JB, Mackie AD (1997) Dissipative particle dynamics with energy conservation. EPL (Europhys Lett) 40(2):141CrossRefGoogle Scholar
  6. Baschnagel J, Varnik F (2005) J Phys Condens Matter 17:R851CrossRefGoogle Scholar
  7. Binder K, Milchev A (2012) Polymer brushes on flat and curved surfaces: how computer simulations can help to test theories and to interpret experiments. J Polym Sci Part B: Polym Phys 50(22):1515–1555CrossRefGoogle Scholar
  8. Binder K, Kreer T, Milchev A (2011) Polymer brushes under flow and in other out-of-equilibrium conditions. Soft Matter 7:7159–7172CrossRefGoogle Scholar
  9. Brown WM, Kohlmeyer A, Plimpton SJ, Tharrington AN (2012) Implementing molecular dynamics on hybrid high performance computers-particle-particle particle-mesh. Comput Phys Commun 183(3):449–459CrossRefGoogle Scholar
  10. de Gennes PG (1980) Conformations of polymers attached to an interface. Macromolecules 13(5):1069–1075CrossRefGoogle Scholar
  11. Drechsler A, Synytska A, Uhlmann P, Elmahdy MM, Stamm M, Kremer F (2010) Interaction forces between microsized silica particles and weak polyelectrolyte brushes at varying ph and salt concentration. Langmuir 26(9):6400–6410CrossRefGoogle Scholar
  12. Dünweg B (2006) Mesoscopic simulations for problems with hydrodynamics, with emphasis on polymer dynamics. In: Ferrario M, Ciccotti G, Binder K (eds) Computer simulations in condensed matter systems: from materials to chemical biology vol 2, vol 704., Lecture Notes in PhysicsSpringer, Berlin, pp 309–340CrossRefGoogle Scholar
  13. Dünweg B, Kremer K (1993) J Chem Phys 99:6983CrossRefGoogle Scholar
  14. Español PE (1995) Hydrodynamics from dissipative particle dynamics. Phys Rev E 52:1734CrossRefGoogle Scholar
  15. Español P (1997) Dissipative particle dynamics with energy conservation. EPL (Europhys Lett) 40(6):631 http://stacks.iop.org/0295-5075/40/i=6/a=631
  16. Español P, Warren P (1995) Statistical mechanics of dissipative particle dynamics. Europhys Lett 30:191CrossRefGoogle Scholar
  17. Esumi K, Nakaie Y, Sakai K, Torigoe K (2001) Adsorption of poly(ethyleneglycol) and poly(amidoamine)dendrimer from their mixtures on alumina/water and silica/water interfaces. Colloids Surf A: Physicochem Eng Asp 194:7–12CrossRefGoogle Scholar
  18. Forrest BM, Suter UW (1995) Accelerated equilibration of polymer melts by time coarse graining. J Chem Phys 102(18):7256–7266CrossRefGoogle Scholar
  19. Frenkel D, Smit B (2002) Understanding molecular simulation: from algorithms to applications. Academic PressGoogle Scholar
  20. Galuschko A, Spirin L, Kreer T, Johner A, Pastorino C, Wittmer J, Baschnagel J (2010) Frictional forces between strongly compressed, nonentangled polymer brushes: molecular dynamics simulations and scaling theory. Langmuir 26(9):6418–6429CrossRefGoogle Scholar
  21. Gama Goicochea A (2007) Adsorption and disjoining pressure isotherms of confined polymers using dissipative particle dynamics. Langmuir 23(23):11656–11663Google Scholar
  22. Gama Goicochea A, Alarcón F (2011) Solvation force induced by short range, exact dissipative particle dynamics effective surfaces on a simple fluid and on polymer brushes. J Chem Phys 134(1):014703Google Scholar
  23. Gama Goicochea A, Romero-Bastida M, López-Rendón R (2007) Dependence of thermodynamic properties of model systems on some dissipative particle dynamics parameters. Mol Phys 105(17–18):2375–2381Google Scholar
  24. Gama Goicochea A, Mayoral E, Klapp J, Pastorino C (2014) Nanotribology of biopolymer brushes in aqueous solution using dissipative particle dynamics simulations: an application to peg covered liposomes in a theta solvent. Soft Matter 10:166–174Google Scholar
  25. Goujon F, Malfreyt P, Tildesley DJ (2004) Dissipative particle dynamics simulations in the grand canonical ensemble: applications to polymer brushes. ChemPhysChem 5(4):457–464CrossRefGoogle Scholar
  26. Grest G (1999) Adv Polym Sci 138:1CrossRefGoogle Scholar
  27. Grest GS, Kremer K (1986) Molecular dynamics simulations for polymers in the presence of a heat bath. Phys Rev A 33:3628CrossRefGoogle Scholar
  28. Groot RD, Warren PB (1997) Dissipative particle dynamics: bridging the gap between atomistic and mesoscopic simulation. J Chem Phys 107:4423–4435CrossRefGoogle Scholar
  29. Holmberg K (2003) Surfactants and polymers in aqueous solution. Wiley, ChichesterGoogle Scholar
  30. Hoogerbrugge PJ, Koelman JMV (1992) Simulating microscopic hydrodynamic phenomena with dissipative particle dynamics. Europhys Lett 19:155CrossRefGoogle Scholar
  31. Hsiao P-Y, Luijten E (2006) Salt-induced collapse and reexpansion of highly charged flexible polyelectrolytes. Phys Rev Lett 97:148301CrossRefGoogle Scholar
  32. Hünenberger P (2005) Thermostat algorithms for molecular simulations. Adv Polym Sci 173:105CrossRefGoogle Scholar
  33. Israelachvili J (2011) Intermolecular and surface forces. Academic Press, BurlingtonGoogle Scholar
  34. Kremer K, Grest GS (1990) Dynamics of entangled linear polymer melts: a molecular-dynamics simulation. J Chem Phys 92:5057CrossRefGoogle Scholar
  35. Kroger M (2004) Simple models for complex nonequilibrium fluids. Phys Rep-Rev Sect Phys Lett 390:453–551Google Scholar
  36. Léonforte F, Servantie J, Pastorino C, Müller M (2011) Molecular transport and flow past hard and soft surfaces: computer simulation of model systems. J Phys: Condens Matter 23(18):184105Google Scholar
  37. MacDowell L, Müller M, Vega C, Binder K (2000) Equation of state and critical behavior of polymer models: a quantitative comparison between wertheim’s thermodynamic perturbation theory and computer simulations. J Chem Phys 113:419–433CrossRefGoogle Scholar
  38. Macosko C (1994) Rheology principles, measurements, and applications. VCH, New YorkGoogle Scholar
  39. Mayoral E, Gama Goicochea A (2013) Modeling the temperature dependent interfacial tension between organic solvents and water using dissipative particle dynamics. J Chem Phys 138(9):094703Google Scholar
  40. Moeendarbary E, Ng TY, Zangeneh M (2010) Dissipative particle dynamics in soft matter and polymeric applications: a review. Int J Appl Mech 02(01):161–190CrossRefGoogle Scholar
  41. Müller M, MacDowell LG (2001) Wetting of a short chain liquid on a brush: First-order and critical wetting transitions. EPL (Europhys Lett) 55(2):221CrossRefGoogle Scholar
  42. Müller M, Pastorino C, Servantie J (2009) Hydrodynamic boundary condition of polymer melts at simple and complex surfaces. Comput Phys Commun 180(4):600–604CrossRefGoogle Scholar
  43. Murtola T, Bunker A, Vattulainen I, Deserno M, Karttunen M (2009) Multiscale modeling of emergent materials: biological and soft matter. Phys Chem Chem Phys 11:1869–1892CrossRefGoogle Scholar
  44. Pagonabarraga I, Frenkel D (2001) Dissipative particle dynamics for interacting systems. J Chem Phys 115(11):5015–5026CrossRefGoogle Scholar
  45. Pastorino C, Müller M (2014) Mixed brush of chemically and physically adsorbed polymers under shear: inverse transport of the physisorbed species. J Chem Phys 140(1):014901CrossRefGoogle Scholar
  46. Pastorino C, Binder K, Kreer T, Müller M (2006) Static and dynamic properties of the interface between a polymer brush and a melt of identical chains. J Chem Phys 124:064902CrossRefGoogle Scholar
  47. Pastorino C, Kreer T, Müller M, Binder K (2007) Comparison of dissipative particle dynamics and langevin thermostats for out-of-equilibrium simulations of polymeric systems. Phys Rev E 76:026706CrossRefGoogle Scholar
  48. Pastorino C, Binder K, Müller M (2009) Coarse-grained description of a brush-melt interface in equilibrium and under flow. Macromolecules 42(1):401–410CrossRefGoogle Scholar
  49. Plimpton S (1995) Fast parallel algorithms for short-range molecular dynamics. J Comp Phys 117:1–19CrossRefGoogle Scholar
  50. Rapaport D (2004) The art of molecular dynamics simulation, 2nd edn. Cambridge University Press, CambridgeCrossRefGoogle Scholar
  51. Servantie J, Müller M (2008) Statics and dynamics of a cylindrical droplet under an external body force. J Chem Phys 128:014709CrossRefGoogle Scholar
  52. Soddemann T, Dünweg B, Kremer K (2003) Dissipative particle dynamics: a useful thermostat for equilibrium and nonequilibrium molecular dynamics simulations. Phys Rev E 68:046702CrossRefGoogle Scholar
  53. Tretyakov N, Müller M (2013) Correlation between surface topography and slippage: a molecular dynamics study. Soft Matter 9:3613–3623CrossRefGoogle Scholar
  54. Tretyakov N, Müller M, Todorova D, Thiele U (2013) Parameter passing between molecular dynamics and continuum models for droplets on solid substrates: the static case. J Chem Phys 138(6):064905CrossRefGoogle Scholar
  55. Velázquez ME, Gama-Goicochea A, González-Melchor M, Neria M, Alejandre J (2006) Finite-size effects in dissipative particle dynamics simulations. J Chem Phys 124(8):084104CrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  1. 1.Departamento de Física de la Materia CondensadaCentro Atómico Constituyentes, CNEA and CONICETBuenos AiresArgentina
  2. 2.Instituto de FísicaUniversidad Autónoma de San Luis PotosíMexicoMexico

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