Comparison of Brownian dynamics algorithms with hydrodynamic interaction

Journal of Chemical Physics

Volumn 135, Issue 8, 2011, Pages

  Schmidt, Ricardo Rodríguez ^a   Cifre, José G Hernández ^a   De La Torre, José García ^a  

^a UNIVERSITY OF MURCIA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BEAD-AND-SPRING; BROWNIAN DYNAMICS; BROWNIAN DYNAMICS SIMULATIONS; CHAIN MODELS; CHEBYSHEV POLYNOMIAL EXPANSION; CHOLESKY DECOMPOSITION; DILUTE SOLUTION; HYDRODYNAMIC INTERACTION; MATHEMATICAL APPROACH;

ALGORITHMS; HYDRODYNAMICS;

BROWNIAN MOVEMENT;

EID: 80052395891     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3626868     Document Type: Article

References (28)

1. H. C. ttinger, Stochastic Processes in Polymer Fluids (Springer-Verlag, Berlin, 1996).
2. J. G. Hernández Cifre and J. Garca de la Torre, J. Rheol. 43, 339 (1999). 10.1122/1.550987
3. D. Petera and M. Muthukumar, J. Chem. Phys. 111, 7614 (1999). 10.1063/1.480087
4. C.-C. Hsieh, L. Li, and R. G. Larson, J. Non-Newtonian Fluid Mech. 113, 147 (2003). 10.1016/S0377-0257(03)00107-1
5. C. M. Schroeder, E. S. G. Shaqfeh, and S. Chu, Macromolecules 37, 9242 (2004). 10.1021/ma049461l
6. G. Chirico and J. Langowski, Macromolecules 25, 769 (1992). 10.1021/ma00028a041
7. H. Jian, T. Schlick, and A. Vologodskii, J. Mol. Biol. 284, 287 (1998). 10.1006/jmbi.1998.2170
8. T. Frembgen-Kesner and A. H. Elcock, J. Chem. Theory Comput. 5, 242 (2009). 10.1021/ct800499p
9. D. L. Ermak and J. A. McCammon, J. Chem. Phys. 69, 1352 (1978). 10.1063/1.436761
10. A. Iniesta and J. Garca de la Torre, J. Chem. Phys. 92, 2015 (1990). 10.1063/1.458034
11. M. Fixman, Macromolecules 19, 1195 (1986). 10.1021/ma00158a042
12. M. Krger, A. Alba Pérez, M. Laso, and H. C. ttinger, J. Chem. Phys. 113, 4767 (2000). 10.1063/1.1288803
13. R. M. Jendrejack, M. D. Graham, and J. J. de Pablo, J. Chem. Phys. 113, 2894 (2009). 10.1063/1.1305884
14. T. Geyer and U. Winter, J. Chem. Phys. 130, 1149051 (2009). 10.1063/1.3089668
15. R. Rzehak, W. Kromen, T. Kawakatsu, and W. Zimmermann, Eur. Phys. J. E 2, 3 (2000). 10.1007/s101890050036
16. J. Huang and T. Schlick, J. Chem. Phys. 117, 8573 (2002). 10.1063/1.1511506
17. D. M. Heyes, J. Phys.: Condens. Matter 7, 8857 (1995). 10.1088/0953-8984/7/47/006
18. A. J. Banchio and J. F. Brady, J. Chem. Phys. 118, 103231 (2003). 10.1063/1.1571819
19. T. Geyer, BMC Biophys. 4, 7 (2011). 10.1186/2046-1682-4-7
20. M. Dlugosz, P. Zieliski, and J. Trylska, J. Comput. Chem. 32, 2734 (2011). 10.1002/jcc.21847
21. J. Rotne and S. Prager, J. Chem. Phys. 50, 4831 (1969). 10.1063/1.1670977
22. J. Garca de la Torre and V. A. Bloomfield, Biopolymers 16, 1747 (1977). 10.1002/bip.1977.360160811
23. M. L. Huertas, S. Navarro, M. C. Lpez Martnez, and J. Garca de la Torre, Biophys. J. 73, 3142 (1997). 10.1016/S0006-3495(97)78340-1
24. W. H. Press, B. P. Flannery, S. A. Teukolsky, and M. T. Vetterling, Numerical Recipes: The Art of Scientific Computing (Cambridge University Press, Cambridge, England, 1986).
25. J. J. Freire, J. Pla, A. Rey, and R. Prats, Macromolecules 19, 452 (1986). 10.1021/ma00156a037
26. H. Yamakawa, Modern Theory of Polymer Solutions (Harper and Row, New York, 1971).
27. S. A. Allison and J. A. McCammon, Biopolymers 23, 167 (1984). 10.1002/bip.360230113
28. B. Liu and B. Dnweg, J. Chem. Phys. 118, 8061 (2003). 10.1063/1.1564047