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An Introduction to Dissipative Particle Dynamics

  • Zhong-Yuan LuEmail author
  • Yong-Lei Wang
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 924)

Abstract

Dissipative particle dynamics (DPD) is a particle-based mesoscopic simulation method, which facilitates the studies of thermodynamic and dynamic properties of soft matter systems at physically interesting length and time scales. In this method, molecule groups are clustered into the dissipative beads, and this coarse-graining procedure is a very important aspect of DPD as it allows significant computational speed-up. In this chapter, we introduce the DPD methodology, including its theoretical foundation and its parameterization. With this simulation technique, we can study complex behaviors of biological systems, such as the formation of vesicles and their fusion and fission processes, and the phase behavior of lipid membranes.

Key words

Dissipative particle dynamics Parameterization Biomacromolecules Vesicle Lipid membrane 

References

  1. 1.
    Hoogerbrugge PJ, Koelman JMVA (1992) Simulation microscopic hydrodynamic phenomena with dissipative particle dynamics. Europhys Lett 19:155–160CrossRefGoogle Scholar
  2. 2.
    Koelman JMVA, Hoogerbrugge PJ (1993) Dynamic simulation of hard-sphere suspensions under steady shear. Europhys Lett 21:363–368CrossRefGoogle Scholar
  3. 3.
    Español P, Warren PB (1995) Statistical mechanics of dissipative particle dynamics. Europhys Lett 30:191–196CrossRefGoogle Scholar
  4. 4.
    Groot RD, Warren PB (1997) Dissipative particle dynamics: bridging the gap between atomistic and mesoscopic simulation. J Chem Phys 107:4423–4435CrossRefGoogle Scholar
  5. 5.
    Maiti A, McGrother S (2004) Bead-bead interaction parameters in dissipative particle dynamics: relation to bead-size, solubility parameter, and surface tension. J Chem Phys 120:1594–1601PubMedCrossRefGoogle Scholar
  6. 6.
    Flekkøy EG, Coveney PV (1999) From molecular dynamics to dissipative particle dynamics. Phys Rev Lett 83:1775–1778CrossRefGoogle Scholar
  7. 7.
    Flekkøy EG, Coveney PV, Fabritiis GD (2000) Foundation of dissipative particle dynamics. Phys Rev E 62:2140–2157CrossRefGoogle Scholar
  8. 8.
    Lowe CP (1999) An alternative approach to dissipative particle dynamics. Europhys Lett 47:145–151CrossRefGoogle Scholar
  9. 9.
    Chen LJ, Lu ZY, Qian HJ et al (2005) The effect of Lowe-Andersen temperature controlling method on the polymer properties in mesoscopic simulation. J Chem Phys 122:104907PubMedCrossRefGoogle Scholar
  10. 10.
    Koopman EA, Lowe CP (2006) Advantages of a Lowe-Andersen thermostat in molecular dynamics simulations. J Chem Phys 124:204103PubMedCrossRefGoogle Scholar
  11. 11.
    Novik KE, Coveney PV (1998) Finite-difference methods for simulation models incorporating nonconservative forces. J Chem Phys 109:7667–7677CrossRefGoogle Scholar
  12. 12.
    Pagonabarrage I, Hagen MHJ, Frenkel D (1998) Self-consistent dissipative particle dynamics algorithm. Europhys Lett 42:377–382CrossRefGoogle Scholar
  13. 13.
    Besold G, Vattulainen I, Karttunen M et al (2000) Towards better integrators for dissipative particle dynamics simulations. Phys Rev E 62:R7611–R7614CrossRefGoogle Scholar
  14. 14.
    Vattulainen I, Karttunen M, Besold G et al (2002) Integration schemes for dissipative particle dynamics simulation: from softly interacting systems towards hybrid models. J Chem Phys 116:3967–3979CrossRefGoogle Scholar
  15. 15.
    Nikunen P, Karttunen M, Vattulainen I (2003) How would you integrate the equations of motion in dissipative particle dynamics simulations. Comput Phys Commun 153:407–423CrossRefGoogle Scholar
  16. 16.
    Symeonidis V, Karniadakis GE (2006) A family of time-staggered schemes for integrating hybrid DPD models for polymers: algorithms and applications. J Comput Phys 218:82–101CrossRefGoogle Scholar
  17. 17.
    Den Otter WK, Clarke JHR (2001) A new algorithm for dissipative particle dynamics. Europhys Lett 53:426–431CrossRefGoogle Scholar
  18. 18.
    Marsh CA, Yeomans JM (1997) Dissipative particle dynamics: the equilibrium for finite time steps. Europhys Lett 37:511–516CrossRefGoogle Scholar
  19. 19.
    Jakobsen AF, Mouritsen OG, Besold G (2005) Artifacts in dynamical simulations of coarse-grained model lipid bilayers. J Chem Phys 122:204901PubMedCrossRefGoogle Scholar
  20. 20.
    Allen MP (2006) Configurational temperature in membrane simulations using dissipative particle dynamics. J Phys Chem B 110:3823–3830PubMedCrossRefGoogle Scholar
  21. 21.
    Groot RD, Rabone KL (2001) Mesoscopic simulation of cell membrane damage, morphology changes and rupture by nonionic surfactant. Biophys J 81:725–736PubMedCrossRefGoogle Scholar
  22. 22.
    Kranenburg M, Nicolas JP, Smit B (2004) Comparision of mesoscopic phospholipids-water models. Phys Chem Chem Phys 6:4142–4151CrossRefGoogle Scholar
  23. 23.
    Kranenburg M, Laforge C, Smit B (2004) Mesoscopic simulations of phase transitions in lipid bilayers. Phys Chem Chem Phys 6:4531–4534CrossRefGoogle Scholar
  24. 24.
    Kranenburg M, Smit B (2005) Phase behavior of model lipid bilayers. J Phys Chem B 109:6553–6563PubMedCrossRefGoogle Scholar
  25. 25.
    Kranenburg M, Vlaar M, Smit B (2004) Simulating induced integration in membranes. Biophys J 87:1596–1605PubMedCrossRefGoogle Scholar
  26. 26.
    Patra M, Salonen E, Terama E et al (2006) Under the influence of alcohol: the effect of ethanol and methanol on lipid bilayers. Biophys J 90:1121–1135PubMedCrossRefGoogle Scholar
  27. 27.
    De Meyer F, Smit B (2009) Effect of cholesterol on the structure of a phospholipids bilayer. Proc Natl Acad Sci USA 106:3654–3658PubMedCrossRefGoogle Scholar
  28. 28.
    Shillcock JC, Lipowsky R (2002) Equilibrium structure and lateral stress distribution of amphiphilic bilayers from dissipative particle dynamics simulations. J Chem Phys 117:5048–5061CrossRefGoogle Scholar
  29. 29.
    Gao LH, Shillcock JC, Lipowsky R (2007) Improved dissipative particle dynamics simulations of lipid bilayers. J Chem Phys 126:015101PubMedCrossRefGoogle Scholar
  30. 30.
    Shillcock JC, Lipowsky R (2005) Tension-induced fusion of bilayer membranes and vesicles. Mater 4:225–228PubMedCrossRefGoogle Scholar
  31. 31.
    Grafmüller A, Shillcock JC, Lipowsky R (2007) Pathway of membrane fusion with two tension-dependent energy barriers. Phys Rev Lett 98:218101PubMedCrossRefGoogle Scholar
  32. 32.
    Gao LH, Lipowsky R, Shillcock JC (2008) Tension-induced vesicle fusion: pathway and pore dynamics. Soft Matter 4:1208–1214CrossRefGoogle Scholar
  33. 33.
    Grafmüller A, Shillcock JC, Lipowsky R (2009) The fusion of membranes and vesicles: pathway and energy barriers from dissipative particle dynamics. Biophys J 96:2658–2675PubMedCrossRefGoogle Scholar
  34. 34.
    Shillcock JC, Lipowsky R (2006) The computational route from bilayer membranes to vesicle fusion. J Phys Condens Matter 18:S1191–S1219PubMedCrossRefGoogle Scholar
  35. 35.
    Lyubartsev AP, Karttunen M, Vattulainen I et al (2003) On coarse-graining by the inverse Monte Carlo method: dissipative particle dynamics simulations made to a precise tool in soft matter modeling. Soft Mater 1:121–137CrossRefGoogle Scholar
  36. 36.
    Chen LJ, Qian HJ, Lu ZY et al (2006) An automatic coarse-graining and fine-graining simulation method: application on polyethylene. J Phys Chem B 110:24093–24100PubMedCrossRefGoogle Scholar
  37. 37.
    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
  38. 38.
    Junghans C, Praprotnik M, Kremer K (2008) Transport properties controlled by a thermostat: an extended dissipative particle dynamics thermostat. Soft Matter 4:156–161CrossRefGoogle Scholar
  39. 39.
    Eriksson A, Jacobi MN, Nystrom J et al (2008) Effective thermostat induced by coarse-graining of simple point charge water. J Chem Phys 129:024106PubMedCrossRefGoogle Scholar
  40. 40.
    Qian HJ, Liew CC, Müller-Plathe F (2009) Effective control of the transport coefficients of a coarse-grained liquid and polymer models using the dissipative particle dynamics and Lowe-Andersen equations of motion. Phys Chem Chem Phys 11:1962–1969PubMedCrossRefGoogle Scholar
  41. 41.
    Wu SG, Guo HX (2009) Simulation study of protein-mediated vesicle fusion. J Phys Chem B 113:589–591PubMedCrossRefGoogle Scholar
  42. 42.
    Yamamoto S, Hyodo S (2003) Budding and fission dynamics of two-component vesicles. J Chem Phys 118:7937–7943CrossRefGoogle Scholar
  43. 43.
    Hong BB, Qiu F, Zhang HD et al (2007) Budding dynamics of individual domains in multicomponent membranes simulated by N-varied dissipative particle dynamics. J Phys Chem B 111:5837–5849PubMedCrossRefGoogle Scholar
  44. 44.
    Liu YT, Zhao Y, Liu H et al (2009) Spontaneous fusion between the vesicle formed by A2n(B2)n type comb-like block copolymers with a semiflexible hydrophobic backbone. J Phys Chem B 113:15256–15262PubMedCrossRefGoogle Scholar
  45. 45.
    Yang K, Shao X, Ma YQ (2009) Shape deformation and fission route of the lipid domain in a multicomponent vesicle. Phys Rev E 79:051924CrossRefGoogle Scholar
  46. 46.
    Pivkin IV, Karniadakis GE (2008) Accurate coarse-grained modeling of red blood cells. Phys Rev Lett 101:118105PubMedCrossRefGoogle Scholar
  47. 47.
    Smith KA, Uspal WE (2007) Shear-driven release of a bud from a multicomponent vesicle. J Chem Phys 126:075102PubMedCrossRefGoogle Scholar
  48. 48.
    Avalos JB, Mackie AD (1997) Dissipative particle dynamics with energy conservation. Europhys Lett 40:141–146CrossRefGoogle Scholar
  49. 49.
    Español P (1997) Dissipative particle dynamics with energy conservation. Europhys Lett 40:631–636CrossRefGoogle Scholar
  50. 50.
    Mackie AD, Avalos JB, Navas V (1999) Dissipative particle dynamics with energy conservation: modeling of heat flow. Phys Chem Chem Phys 1:2039–2049CrossRefGoogle Scholar
  51. 51.
    Español P, Revenga M (2003) Smoothed dissipative particle dynamics. Phys Rev E 67:026705CrossRefGoogle Scholar
  52. 52.
    Pagonabarraga I, Frenkel D (2001) Dissipative particle dynamics for interacting systems. J Chem Phys 115:5015–5026CrossRefGoogle Scholar
  53. 53.
    Trofimov SY, Nies ELF, Michels MAJ (2002) Thermodynamics consistency in dissipative particle dynamics simulations of strongly nonideal liquids and liquid mixtures. J Chem Phys 117:9383–9394CrossRefGoogle Scholar
  54. 54.
    Trofimov SY, Nies ELF, Michels MAJ (2005) Constant-pressure simulations with dissipative particle dynamics. J Chem Phys 123:144102PubMedCrossRefGoogle Scholar
  55. 55.
    Warren PB (2003) Vapor-liquid coexistence in many-body dissipative particle dynamics. Phys Rev E 68:066702CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  1. 1.State Key Laboratory of Theoretical and Computational ChemistryInstitute of Theoretical Chemistry, Jilin UniversityChangchunChina

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