Advertisement

Molecular Dynamics Models

  • Davide MichielettoEmail author
Chapter
  • 273 Downloads
Part of the Springer Theses book series (Springer Theses)

Abstract

Computer simulations, or “experiments” (Frenkel and Smit 2001), are important tools for studying complex systems. This Thesis itself largely relies on computational methods, in particular Molecular Dynamics (MD) simulations. For this reason, I devote this chapter to describing the essence of the MD simulations employed here and the computational details of the models described in the subsequent chapters.

Keywords

Persistence Length Torsional Stiffness Brownian Dynamics Verlet Algorithm Inertial Time 
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.

References

  1. Adams, C.C.: The knot book: an elementary introduction to the mathematical theory of knots. WH Freeman and Company, New York (1994)Google Scholar
  2. Åkerman, B.K.: Electrophoretic capture of circular DNA in gels, Electrophoresis and Cole, pp. 2549–2561. (2002)Google Scholar
  3. Alder, B.J., Wainwright, T.E.: Phase transition for a hard sphere system. J. Chem. Phys. 27(5), 1208 (1957)ADSCrossRefGoogle Scholar
  4. Alder, B.J., Wainwright, T.E.: Studies in molecular dynamics. I. general method. J. Chem. Phys. 31(2), 459 (1959)ADSMathSciNetCrossRefGoogle Scholar
  5. Arsuaga, J., Vázquez, M., Trigueros, S., Sumners, D., Roca, J.: Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids. Proc. Natl. Acad. Sci. USA 99(8), 5373 (2002)ADSCrossRefGoogle Scholar
  6. Bogle, M.G.V., Hearst, J.E., Jones, V.F.R., Stoilov, L.: Lissajous knots. J. Knot Theor. Ramif. 3(2), 121 (1994)MathSciNetCrossRefzbMATHGoogle Scholar
  7. Brackley, C.A., Morozov, A.N., Marenduzzo, D.: Models for twistable elastic polymers in Brownian dynamics, and their implementation for LAMMPS. J. Chem. Phys. 140(13), 135103 (2014)ADSCrossRefGoogle Scholar
  8. Broedersz, C.P., MacKintosh, F.C.: Modeling semiflexible polymer networks. Rev. Mod. Phys. 86(3), 995 (2014)ADSCrossRefGoogle Scholar
  9. Calladine, C.R., Collis, C.M., Drew, H.R., Mott, M.R.: A study of electrophoretic mobility of DNA in agarose and polyacrylamide gels. J. Mol. Biol. 221(3), 981 (1991)CrossRefGoogle Scholar
  10. Calladine, C.R., Drew, H., Luisi, F.B., Travers, A.A.: Understanding DNA: the molecule and how it works. Elsevier Academic Press, Cambridge (1997)Google Scholar
  11. Cole, K.D., Åkerman, B.: The influence of agarose concentration in gels on the electrophoretic trapping of circular DNA. Separ. Sci. Technol. 38(10), 2121 (2003)CrossRefGoogle Scholar
  12. Diao, Y., Dobay, A., Kusner, R.B., Millett, K., Stasiak, A.: The average crossing number of equilateral random polygons. J. Phys. A: Math. Gen. 36(46), 11561 (2003)ADSMathSciNetCrossRefzbMATHGoogle Scholar
  13. Doi, M., Edwards, S.: The theory of polymer dynamics. Oxford University Press, Oxford (1988)Google Scholar
  14. Frenkel, D., Smit, B.: Understanding molecular simulation: from algorithms to applications. Academic Press, Cambridge (2001)Google Scholar
  15. Guenet, J.M., Rochas, C.: Agarose sols and gels revisited. Macromol. Symp. 242, 65 (2006)CrossRefGoogle Scholar
  16. Karplus, M., Petsko, G.: Molecular dynamics simulations in biology. Nature 347 (1990)Google Scholar
  17. Katritch, V., Bednar, J., Michoud, D., Scharein, R., Dubochet, J., Stasiak, A.: Geometry and physics of knots. Nature 384, 142 (1996)ADSMathSciNetCrossRefGoogle Scholar
  18. Kolahi, K.S., Donjacour, A., Liu, X., Lin, W., Simbulan, R.K., Bloise, E., Maltepe, E., Rinaudo, P.: Effect of substrate stiffness on early mouse embryo development. PloS one 7(7), e41717 (2012)ADSCrossRefGoogle Scholar
  19. Kusner, R., Sullivan, J.: Möbius energies for knots and links, surfaces and submanifolds. Geometric Topology (Proceedings of the 1993 Georgia International Topology Conference) AMS/IP Studies in Adv. Math. pp. 570–604 (1994)Google Scholar
  20. Kusner, R., Sullivan, J.: Möbius-Invariant Knot Energies, In: Kauffman, L., Katritch, V., Stasiak, A. (eds.) Ideal Knots, pp. 315–352. World Scientific Press, London (1998)Google Scholar
  21. Maaloum, M., Pernodet, N., Tinland, B.: Agarose gel structure using atomic force microscopy: gel concentration and ionic strength effects. Electrophoresis 19, 1606 (1998)CrossRefGoogle Scholar
  22. MacKerell, A.D., Bashford, D., Bellott, M., Dunbrack, R.L., Evanseck, J.D., Field, M.J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F.T., Mattos, C., Michnick, S., Ngo, T., Nguyen, D.T., Prodhom, B., Reiher, W.E., Roux, B., Schlenkrich, M., Smith, J.C., Stote, R., Straub, J., Watanabe, M., Wiórkiewicz-Kuczera, J., Yin, D., Karplus, M.: All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 102(18), 3586 (1998)CrossRefGoogle Scholar
  23. Marko, J., Cocco, S.: The micromechanics of DNA. Phys. World. 37–41 (2003)Google Scholar
  24. McCammon, J., Gelin, B., Karplus, M.: Dynamics of folded proteins. Nature 267 (1977)Google Scholar
  25. Micheletti, C., Marenduzzo, D., Orlandini, E.: Polymers with spatial or topological constraints: theoretical and computational results. Phys. Rep. 504(1), 1 (2011)ADSMathSciNetCrossRefzbMATHGoogle Scholar
  26. Mickel, S., Arena, V., Bauer, W.: Physical properties and gel electrophoresis behavior of R12-derived plasmid DNAs. Nucleic Acids Res. 4(5), 1465 (1977)CrossRefGoogle Scholar
  27. Mogilner, A., Rubinstein, B.: The physics of filopodial protrusion. Biophys. J. 89(2), 782 (2005)Google Scholar
  28. Orlandini, E., Tesi, M.C., Whittington, S.G., Sumners, D.W., Rensburg, E.J.J.V.: The writhe of a self-avoiding walk. J. Phys. A: Math. Gen. 27, L333 (1994)ADSMathSciNetCrossRefzbMATHGoogle Scholar
  29. Orlandini, E., Whittington, S.G.: Statistical topology of closed curves: some applications in polymer physics. Rev. Mod. Phys. 79(2), 611 (2007)ADSMathSciNetCrossRefzbMATHGoogle Scholar
  30. Pernodet, N., Maaloum, M., Tinland, B.: Pore size of agarose gels by atomic force microscopy. Electrophoresis 18, 55 (1997)CrossRefGoogle Scholar
  31. Piili, J., Marenduzzo, D., Kaski, K., Linna, R.P.: Sedimentation of knotted polymers. Phys. Rev. E 87(1), 012728 (2013)ADSCrossRefGoogle Scholar
  32. Rahman, A.: Correlations in the motion of atoms in liquid argon. Phys. Rev. A 136(2), 405 (1964)ADSCrossRefGoogle Scholar
  33. Rahong, S., Yasui, T., Yanagida, T., Nagashima, K., Kanai, M., Klamchuen, A., Meng, G., He, Y., Zhuge, F., Kaji, N., Kawai, T., Baba, Y.: Ultrafast and wide range analysis of DNA molecules using rigid network structure of solid nanowires. Sci. Rep. 4, 5252 (2014)Google Scholar
  34. Ross, P.: Electrophoresis of DNA. I. On a relationship between electrophoresis and donnan equilibrium experiments on DNA. Biopolymers 2, 9 (1964)CrossRefGoogle Scholar
  35. Rybenkov, V., Cozzarelli, N., Vologodskii, A.: Probability of DNA knotting and the effective diameter of the DNA double helix. Proc. Natl. Acad. Sci. USA 90(June), 5307 (1993)ADSCrossRefGoogle Scholar
  36. Stasiak, A., Katritch, V., Bednar, J., Michoud, D., Dubochet, J.: Electrophoretic mobility of DNA knots. Nature 384, 122 (1996)ADSMathSciNetCrossRefGoogle Scholar
  37. Stellwagen, N.C.: Electrophoresis of DNA in agarose gels, polyacrylamide gels and in free solution. Electrophoresis 30(1), 1 (2009)CrossRefGoogle Scholar
  38. Stellwagen, N.C., Stellwagen, E.: Effect of the matrix on DNA electrophoretic mobility. J. Chromatogr. 1216(10), 1917 (2009)CrossRefGoogle Scholar
  39. Swope, W.C., Andersen, H., Berens, P., Wilson, K.: A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: Application to small water clusters. J. Chem. Phys. 76(1), 637 (1982)ADSCrossRefGoogle Scholar
  40. Trigueros, S., Arsuaga, J., Vazquez, M.E., Sumners, D., Roca, J.: Novel display of knotted DNA molecules by two-dimensional gel electrophoresis. Nucleic Acids Res. 29(13), E67 (2001)CrossRefGoogle Scholar
  41. Turmel, C., Brassard, E., Slater, G.W., Noolandi, J.: Molecular detrapping and band narrowing with high frequency modulation of pulsed field electrophoresis. Nucleic Acids Res. 18(3), 569 (1990)CrossRefGoogle Scholar
  42. Viovy, J.: Electrophoresis of DNA and other polyelectrolytes: physical mechanisms. Rev. Mod. Phys. 72(3), 813 (2000)ADSCrossRefGoogle Scholar
  43. Weber, C., Carlen, M., Dietler, G., Rawdon, E.J., Stasiak, A.: Sedimentation of macroscopic rigid knots and its relation to gel electrophoretic mobility of DNA knots. Sci. Rep. 3, 1091 (2013)Google Scholar
  44. Weber, C.: Stasiak, a., De Los Rios, P., Dietler, G.: Numerical simulation of gel electrophoresis of DNA knots in weak and strong electric fields. Biophys. J. 90(9), 3100 (2006)Google Scholar
  45. Weeks, J., Chandler, D., Andersen, H.: Role of repulsive forces in determining the equilibrium structure of simple liquids. J. Chem. Phys. 54(12), 5237 (1971)ADSCrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  1. 1.School of Physics and AstronomyUniversity of EdinburghEdinburghUK

Personalised recommendations