Skip to main content
SpringerLink
Log in

Speeding up Monte Carlo simulation of patchy hard cylinders

  • Regular Article
  • Published:
The European Physical Journal E Aims and scope Submit manuscript

Abstract.

The hard cylinder model decorated with attractive patches proved to be very useful recently in studying physical properties of several colloidal systems. Phase diagram, elastic constants and cholesteric properties obtained from computer simulations based on a simple hard cylinder model have been all successfully and quantitatively compared to experimental results. Key to these simulations is an efficient algorithm to check the overlap between hard cylinders. Here, we propose two algorithms to check the hard cylinder overlap and we assess their efficiency through a comparison with an existing method available in the literature and with the well-established algorithm for simulating hard spherocylinders. In addition, we discuss a couple of optimizations for performing computer simulations of patchy anisotropic particles and we estimate the speed-up which they can provide in the case of patchy hard cylinders.

Graphical abstract

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. P. Teixeira, J. Tavares, Curr. Opin. Colloid Interface Sci. 30, 16 (2017)

    Article  Google Scholar 

  2. F. Sciortino, E. Zaccarelli, Curr. Opin. Colloid Interface Sci. 30, 90 (2017)

    Article  Google Scholar 

  3. F. Sciortino, Collect. Czech. Chem. Commun. 75, 349 (2010)

    Article  Google Scholar 

  4. G.R. Yi, D.J. Pine, S. Sacanna, J. Phys: Condens. Matter 25, 193101 (2013)

    ADS  Google Scholar 

  5. J.P.K. Doye, A.A. Louis, I.C. Lin, L.R. Allen, E.G. Noya, A.W. Wilber, H.C. Kok, R. Lyus, Phys. Chem. Chem. Phys. 9, 2197 (2007)

    Article  Google Scholar 

  6. B.J. Alder, T.E. Wainwright, J. Chem. Phys. 27, 1208 (1957)

    Article  ADS  Google Scholar 

  7. L. Onsager, Ann. N.Y. Acad. Sci. 51, 627 (1949)

    Article  ADS  Google Scholar 

  8. D. Frenkel, B.M. Mulder, J.P. McTague, Phys. Rev. Lett. 52, 287 (1984)

    Article  ADS  Google Scholar 

  9. A. Khan, Curr. Opin. Colloid Interface Sci. 1, 614 (1996)

    Article  Google Scholar 

  10. P. van der Schoot, M. Cates, Langmuir 10, 670 (1994)

    Article  Google Scholar 

  11. D.M. Kuntz, L.M. Walker, Soft Matter 4, 286 (2008)

    Article  ADS  Google Scholar 

  12. J.M. Jung, R. Mezzenga, Langmuir 26, 504 (2010)

    Article  Google Scholar 

  13. C.F. Lee, Phys. Rev. E 80, 031902 (2009)

    Article  ADS  Google Scholar 

  14. A. Ciferri, Liq. Cryst. 34, 693 (2007)

    Article  Google Scholar 

  15. A. Aggeli, M. Bell, L.M. Carrick, C.W.G. Fishwick, R. Harding, P.J. Mawer, S.E. Radford, A.E. Strong, N. Boden, J. Am. Chem. Soc. 125, 9619 (2003)

    Article  Google Scholar 

  16. M. Nakata, G. Zanchetta, B.D. Chapman, C.D. Jones, J.O. Cross, R. Pindak, T. Bellini, N.A. Clark, Science 318, 1276 (2007)

    Article  ADS  Google Scholar 

  17. G. Zanchetta, M. Nakata, M. Buscaglia, N.A. Clark, T. Bellini, J. Phys.: Condens. Matter 20, 494214 (2008)

    Google Scholar 

  18. G. Zanchetta, F. Giavazzi, M. Nakata, M. Buscaglia, R. Cerbino, N.A. Clark, T. Bellini, Proc. Natl. Acad. Sci. U.S.A. 107, 17497 (2010)

    Article  ADS  Google Scholar 

  19. C. Robinson, Tetrahedron 13, 219 (1961)

    Article  Google Scholar 

  20. F. Livolant, A.M. Levelut, J. Doucet, J.P. Benoit, Nature 339, 724 (1989)

    Article  ADS  Google Scholar 

  21. K. Merchant, R.L. Rill, Biophys. J. 73, 3154 (1997)

    Article  Google Scholar 

  22. F. Tombolato, A. Ferrarini, J. Chem. Phys. 122, 054908 (2005)

    Article  ADS  Google Scholar 

  23. M. Salamonczyk, J. Zhang, G. Portale, C. Zhu, E. Kentzinger, J.T. Gleeson, A. Jakli, C. De Michele, J.K.G. Dhont, S. Sprunt et al., Nat. Commun. 7, 13358 EP (2016)

    Article  ADS  Google Scholar 

  24. F. Tombolato, A. Ferrarini, E. Grelet, Phys. Rev. Lett. 96, 258302 (2006)

    Article  ADS  Google Scholar 

  25. E. Barry, D. Beller, Z. Dogic, Soft Matter 5, 2563 (2009)

    Google Scholar 

  26. E. Grelet, S. Fraden, Phys. Rev. Lett. 90, 198302 (2003)

    Article  ADS  Google Scholar 

  27. S. Tomar, M.M. Green, L.A. Day, J. Am. Chem. Soc. 129, 3367 (2007)

    Article  Google Scholar 

  28. J. Lydon, J. Mater. Chem. 20, 10071 (2010)

    Article  Google Scholar 

  29. K. Liu, Z. Nie, N. Zhao, W. Li, M. Rubinstein, E. Kumacheva, Science 329, 197 (2010)

    Article  ADS  Google Scholar 

  30. C. De Michele, T. Bellini, F. Sciortino, Macromolecules 45, 1090 (2012)

    Article  ADS  Google Scholar 

  31. C. De Michele, L. Rovigatti, T. Bellini, F. Sciortino, Soft Matter 8, 8388 (2012)

    Article  ADS  Google Scholar 

  32. K.T. Nguyen, F. Sciortino, C. De Michele, Langmuir 30, 4814 (2014)

    Article  Google Scholar 

  33. T. Kouriabova, M. Betterton, M. Glaser, J. Mater. Chem. 20, 10366 (2010)

    Article  Google Scholar 

  34. X. Lü, J. Kindt, J. Chem. Phys. 120, 10328 (2004)

    Article  Google Scholar 

  35. N. Ibarra-Avalos, A. Gil-Villegas, A. Martinez Richa, Mol. Simul. 33, 505 (2007)

    Article  Google Scholar 

  36. R. Blaak, D. Frenkel, B.M. Mulder, J. Chem. Phys. 110, 11652 (1999)

    Article  ADS  Google Scholar 

  37. H.E. Salzer, Math. Comput. 14, 279 (1960)

    Article  MathSciNet  Google Scholar 

  38. M. Abramowitz, I.A. Stegun, Handbook of Mathematical Functions, 10th edition (National Bureau of Standards, 1964)

  39. W.H. Press, S.A. Teukolsky, W.T. Vetterling, B.P. Flannery, Numerical Recipes - The Art of Scientific Computing, 3rd edition (Cambridge University Press, 2007)

  40. N. Flocke, ACM Trans. Math. Softw. 41, 30 (2015)

    Article  MathSciNet  Google Scholar 

  41. P. Strobach, internal technical report (AST-Consulting Inc., 2015) https://doi.org/10.13140/2.1.3955.7440

  42. P. Strobach, J. Comput. Appl. Math. 234, 3007 (2010)

    Article  MathSciNet  Google Scholar 

  43. M.P. Allen, D.J. Tildesley, Computer Simulation of Liquids, 3rd edition (Clarendon Press, Oxford, 1991)

  44. D. Frenkel, B. Smit, Understanding Molecular Simulation, 1st edition (Academic Press, 2002)

  45. C. De Michele, Comput. Phys. Commun. 182, 1846 (2011)

    Article  ADS  Google Scholar 

  46. C. De Michele, J. Comput. Phys. 229, 3276 (2010)

    Article  ADS  MathSciNet  Google Scholar 

  47. M.G. Coutinho, Dynamic Simulations of Multibody Systems, 1st edition (Springer-Verlag New York, 2001)

  48. S.C. McGrother, D.C. Williamson, G. Jackson, J. Chem. Phys. 104, 6755 (1996)

    Article  ADS  Google Scholar 

  49. P. Bolhuis, D. Frenkel, J. Chem. Phys. 106, 666 (1997)

    Article  ADS  Google Scholar 

  50. J.A.C. Veerman, D. Frenkel, Phys. Rev. A 43, 4334 (1991)

    Article  ADS  Google Scholar 

  51. M.P. Allen, G.T. Evans, D. Frenkel, B.M. Mulder, Hard Convex Body Fluids (John Wiley & Sons, Inc., 1993) pp. 1--166

  52. C. Vega, S. Lago, Comput. Chem. 18, 55 (1994)

    Article  Google Scholar 

  53. S. Zhou, Y.A. Nastishin, M.M. Omelchenko, L. Tortora, V.G. Nazarenko, O.P. Boiko, T. Ostapenko, T. Hu, C.C. Almasan, S.N. Sprunt et al., Phys. Rev. Lett. 109, 037801 (2012)

    Article  ADS  Google Scholar 

  54. S. Zhou, K. Neupane, Y.A. Nastishin, A.R. Baldwin, S.V. Shiyanovskii, O.D. Lavrentovich, S. Sprunt, Soft Matter 10, 6571 (2014)

    Article  ADS  Google Scholar 

  55. S. Zhou, A.J. Cervenka, O.D. Lavrentovich, Phys. Rev. E 90, 042505 (2014)

    Article  ADS  Google Scholar 

  56. V.R. Horowitz, L.A. Janowitz, A.L. Modic, P.A. Heiney, P.J. Collings, Phys. Rev. E 72, 041710 (2005)

    Article  ADS  Google Scholar 

  57. Y.A. Nastishin, H. Liu, T. Schneider, V. Nazarenko, R. Vasyuta, S.V. Shiyanovskii, O.D. Lavrentovich, Phys. Rev. E 72, 041711 (2005)

    Article  ADS  Google Scholar 

  58. D.J. Edwards, J.W. Jones, O. Lozman, A.P. Ormerod, M. Sintyureva, G.J.T. Tiddy, J. Phys. Chem. B 112, 14628 (2008)

    Article  Google Scholar 

  59. F. Chami, M.R. Wilson, J. Am. Chem. Soc. 132, 7794 (2010)

    Article  Google Scholar 

  60. H.S. Park, S.W. Kang, L. Tortora, Y. Nastishin, D. Finotello, S. Kumar, O.D. Lavrentovich, J. Phys. Chem. B 112, 16307 (2008)

    Article  Google Scholar 

  61. M.P. Renshaw, I.J. Day, J. Phys. Chem. B 114, 10032 (2010)

    Article  Google Scholar 

  62. L. Joshi, S.W. Kang, D.M. Agra-Kooijman, S. Kumar, Phys. Rev. E 80, 041703 (2009)

    Article  ADS  Google Scholar 

  63. H. Docherty, A. Galindo, Mol. Phys. 104, 3551 (2006)

    Article  ADS  Google Scholar 

  64. G. Jiménez, S. Santillán, C. Avendaño, M. Castro, A. Gil-Villegas, Oil Gas Sci. Technol. -- Rev. IFP Energ. Nouv. 63, 329 (2008)

    Article  Google Scholar 

  65. E.G. Gilbert, D.W. Johnson, S.S. Keerthi, IEEE J. Robot. Autom. 4, 193 (1988)

    Article  Google Scholar 

  66. M. Montanari, N. Petrinic, E. Barbieri, ACM Trans. Graph. 36, 30 (2017)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Dipartimento di Fisica, “Sapienza” Università di Roma, P.le A. Moro 2, 00185, Roma, Italy

    Alberto Giacomo Orellana, Emanuele Romani & Cristiano De Michele

Authors
  1. Alberto Giacomo Orellana
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Emanuele Romani
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Cristiano De Michele
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Cristiano De Michele.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Orellana, A.G., Romani, E. & De Michele, C. Speeding up Monte Carlo simulation of patchy hard cylinders. Eur. Phys. J. E 41, 51 (2018). https://doi.org/10.1140/epje/i2018-11657-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1140/epje/i2018-11657-0

Keywords

Search

Navigation