System dynamics revealed by recurrence quantification analysis: Application to molecular dynamics simulations

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 76, Issue 2, 2007, Pages

  Karakasidis, T E ^a   Fragkou, A ^a   Liakopoulos, A ^a  

^a UNIVERSITY OF THESSALY   (Greece)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL ANALYSIS; COMPUTER SIMULATION; LYAPUNOV FUNCTIONS; PROBLEM SOLVING; STATISTICAL MECHANICS; STATISTICAL METHODS;

LENNARD-JONES SYSTEM; MOLECULAR DYNAMICS SIMULATIONS; QUANTIFICATION ANALYSIS; RECURRENCE QUANTIFICATION ANALYSIS; STATISTICAL-MECHANICS-BASED SIMULATIONS; SYSTEM DYNAMICS;

MOLECULAR DYNAMICS;

EID: 35549008878     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.76.021120     Document Type: Article

References (33)

1. J. C. Sprott, Chaos and Time-Series Analysis (Oxford University Press, New York, 2003).
2. H. Kantz and T. Schreiber, Nonlinear Time Series Analysis, 2nd ed. (Cambridge University Press, Cambridge, U.K., 2004).
3. H. D. I. Abarbanel, Analysis of Observed Chaotic Data (Springer, Berlin, 1996).
4. J.-P. Eckmann, S. O. Kamphorst, and D. Ruelle, Europhys. Lett. EULEEJ 0295-5075 4, 973 (1987).
5. C. L. Webber, Jr. and J. P. Zbilut, J. Appl. Physiol. JAPHEV 8750-7587 76, 965 (1994).
6. D. C. Rapaport, The Art of Molecular Dynamics Simulation (Cambridge University Press, Cambridge, U.K., 1995).
7. M. P. Allen and T. J. Tildesley, Computer Simulation of Liquids (Clarendon Press, Oxford, 1987).
8. T. E. Karakasidis and A. B. Liakopoulos, Physica A PHYADX 0378-4371 10.1016/j.physa.2003.11.001 333, 225 (2004).
9. H. A. Posch and W. G. Hoover, Phys. Rev. A PLRAAN 1050-2947 10.1103/PhysRevA.38.473 38, 473 (1988).
10. H. A. Posch and W. G. Hoover, Phys. Rev. A PLRAAN 1050-2947 10.1103/PhysRevA.39.2175 39, 2175 (1989).
11. A. Giuliani and C. Manetti, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.53.6336 53, 6336 (1996).
12. C. Manetti, M.-A. Ceruso, A. Giuliani, C. L. Webber, Jr., and J. P. Zbilut, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.59.992 59, 992 (1999).
13. J. L. Lebowitz, J. K. Percus, and L. Verlet, Phys. Rev. PHRVAO 0031-899X 10.1103/PhysRev.153.250 153, 250 (1967).
14. B. L. Holian and D. J. Evans, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.445384 78, 5147 (1983).
15. L. Verlet, Phys. Rev. PHRVAO 0031-899X 10.1103/PhysRev.159.98 159, 98 (1967).
16. N. Marwan, M. C. Romano, M. Thiel, and J. Kurths, Phys. Rep. PRPLCM 0370-1573 10.1016/j.physrep.2006.11.001 438, 237 (2007).
17. C. L. Webber, Jr. and J. P. Zbilut, in Tutorials in Contemporary Nonlinear Methods for the Behavioral Sciences, edited by, M. A. Riley, and, G. Van Orden, (2005), Chap., pp. 26-94
18. http://www.nsf.gov/sbe/bcs/pac/nmbs/nmbs.pdf
19. J. S. Iwanski and E. Bradley, Chaos CHAOEH 1054-1500 10.1063/1.166372 8, 861 (1998).
20. N. Marwan, Ph.D. thesis, University of Potsdam, 2003 (unpublished).
21. N. Marwan, N. Wessel, U. Meyerfeldt, A. Schirdewan, and J. Kurths, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.66.026702 66, 026702 (2002).
22. J. P. Zbilut, A. Colosimo, F. Conti, M. Colafranceschi, C. Manetti, M. C. Valerio, C. L. Webber, Jr., and A. Giuliani, J. Proteome Research 3, 1243 (2004).
23. A. Giuliani, R. Benigni, J. P. Zbilut, C. L. Webber, Jr., P. Sirabella, and A. Colosimo, Chem. Rev. (Washington, D.C.) CHREAY 0009-2665 10.1021/cr0101499 102, 1471 (2002).
24. E. Cazares-Ibanez, G. A. Vazquez-Coutino, and E. Garcia-Ochoa, J. Electroanal. Chem. JECHES 0022-0728 10.1016/j.jelechem.2005.03.046 583, 17 (2005).
25. F. Strozzi, J.-M. Zaldiovar, and J. P. Zbilut, Physica A PHYADX 0378-4371 10.1016/S0378-4371(02)00846-4 312, 520 (2002).
26. A. Fabretti and M. Ausloos, Int. J. Mod. Phys. C IJMPEO 0129-1831 10.1142/S0129183105007492 16, 671 (2005).
27. N. Marwan and A. Meinke, Int. J. Bifurcation Chaos Appl. Sci. Eng. IJBEE4 0218-1274 10.1142/S0218127404009454 14, 761 (2004).
28. M. A. Riley, R. Balasubramaniam, and M. T. Turvey, Gait and Posture GAPOFK 0966-6362 10.1016/S0966-6362(98)00044-7 9, 65 (1999).
29. E. I. Vlahogianni, M. G. Karlaftis, and J. C. Golias, Transp. Res., Part C: Emerg. Technol. TRCEFH 0968-090X 10.1016/j.trc.2006.09.002 14, 351 (2006).
30. L. L. Trulla, A. Giuliani, J. Zbilut, and C. L. Webber, Jr., Phys. Lett. A PYLAAG 0375-9601 10.1016/S0375-9601(96)00741-4 223, 255 (1996).
31. E. Kononov, computer code VRA, http://home.netcom.com/~eugenek
32. D. A. McQuarrie, Statistical Mechanics (Harper Collins, New York, 1976).
33. K. Meier, A. Laesecke, and S. Kabelac, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1770695 121, 3671 (2004).