Methods and tools for the prediction of hydrodynamic coefficients and other solution properties of flexible macromolecules in solution. A tutorial minireview

Macromolecular Bioscience

Volumn 10, Issue 7, 2010, Pages 721-730

  De La Torre, José García ^a   Ortega, Álvaro ^a   Amorós, Diego ^a   Schmidt, Ricardo Rodríguez ^a   Cifre, José G Hernández ^a  

^a UNIVERSITY OF MURCIA   (Spain)

Author keywords

Brownian dynamics simulation; Computer modeling; DNA; Monte Carlo simulation; Ultracentrifugation

Indexed keywords

ANALYTICAL ULTRACENTRIFUGATION; BROWNIAN DYNAMICS; BROWNIAN DYNAMICS SIMULATIONS; COMPUTATIONAL TOOLS; COMPUTER MODELING; CONFORMATIONAL STATISTICS; DNA MOLECULES; HYDRODYNAMIC COEFFICIENTS; HYDRODYNAMIC TREATMENT; INTERNAL DYNAMICS; MONTE CARLO; MONTE CARLO SIMULATION; RIGID PARTICLES; SEDIMENTATION COEFFICIENTS; SIMULATION METHODS; SOLUTION PROPERTY; ULTRACENTRIFUGATION;

BROWNIAN MOVEMENT; CENTRIFUGATION; COMPUTER SOFTWARE; COSMIC RAY DETECTORS; DNA; FLUID DYNAMICS; GENES; HYDRODYNAMICS; MACROMOLECULES; MONTE CARLO METHODS; SAILING VESSELS; TRANSPORT PROPERTIES;

COMPUTER SIMULATION;

NANOPARTICLE;

CALCULATION; COMPUTER PROGRAM; HYDRODYNAMICS; MACROMOLECULE; MOLECULAR DYNAMICS; MOLECULAR WEIGHT; MONTE CARLO METHOD; NANOCHEMISTRY; PREDICTION; REVIEW;

COMPUTER SIMULATION; HYDRODYNAMICS; MACROMOLECULAR SUBSTANCES; PLIABILITY; SOLUTIONS; ULTRACENTRIFUGATION;

EID: 77954590918     PISSN: 16165187     EISSN: 16165195     Source Type: Journal    
DOI: 10.1002/mabi.200900464     Document Type: Review

References (65)

1. M. Daune, "Molecular Biophysics: Structures in Motion", Oxford Univ. Press, Oxford 1998.
2. nd edition, John Wiley and Sons, New Jersey 2004.
3. J. G. Kirkwood, J. Riseman, J. Chem. Phys. 1948, 16, 565.
4. B. H. Zimm, J. Chem. Phys. 1956, 24, 269.
5. V. A. Bloomfield, W. O. Dalton, K. E. Van Holde, Biopolymers 1967, 5, 135.
6. J. García de la Torre, V. A. Bloomfield, Biopolymers 1977, 16, 1747.
7. B. Carrasco, J. García de la Torre, Biophys. J. 1999, 76, 3044.
8. J. García de la Torre, M. L. Huertas, B. Carrasco, Biophys. J. 2000, 78, 719.
9. N. Rai, M. Nollmann, B. Spotorno, G. Tassara, O. Byron, M. Rocco, Structure 2005, 13, 723.
10. J. García de la Torre, G. Del Río Echenique, A. Ortega, J. Phys. Chem. B 2007, 111, 955.
11. O. Byron, Methods Cell Biol. 2008, 84, 327.
12. J. G. Kirkwood, J. Polym. Sci. 1954, 12, 1.
13. B. H. Zimm, Macromolecules 1980, 13, 592.
14. J. García de la Torre, M. C. López Martínez, M. M. Tirado, J. J. Freire, Macromolecules 1984, 17, 2715.
15. M. Fixman, J. Chem. Phys. 1983, 78, 1588.
16. J. J. Freire, A. Rey, Comput. Phys. Commun. 1990, 61, 297.
17. O. Kratky, G. Porod, Rec. Trav. Chim. 1949, 68, 1106.
18. V. A. Bloomfield" D. M. Crothers" I. Tinoco, Eds., "Nucleic Acids: Structure, Properties and Function", University Science Books, Sausalito 1999.
19. I. N. Serdyuk, N. R. Zaccai, J. Zaccai, "Methods in Molecular Biophysics. Structure, Dynamics, Function", Cambridge University Press, New York 2007.
20. H. Yamakawa, M. Fujii, J. Chem. Phys. 1973, 6, 408.
21. H. Yamakawa, M. Fujii, Macromolecules 1974, 7, 128.
22. J. A. Schellman, Biopolymers 1974, 13, 217.
23. P. Hagerman, B. H. Zimm, Biopolymers 1981, 20, 1481.
24. J. J. García Molina, M. C. López Martínez, J. García de la Torre, Biopolymers 1990, 29, 883.
25. A. Ortega, J. García de la Torre, Biomacromolecules 2007, 8, 2464.
26. J. García de la Torre, A. Ortega, H. E. Pérez Sánchez, J. G. Hernández Cifre, Biophys. Chem. 2005, 116, 121.
27. J. García de la Torre, J. G. Hernández Cifre, A. Ortega, R. Rodrígez Schmidt, M. X. Fernandes, H. E. Pérez Sánchez, R. Pamies, J. Chem. Theor. Comput. 2009, 5, 2606.
28. P. E. Rouse, J. Chem. Phys. 1953, 21, 1272.
29. H. R. Warner, Ind. Eng. Chem. Fundam. 1972, 11, 379.
30. J. García de la Torre, J. G. Hernández Cifre, M. C. López Martínez, R. Pamies, "Simulation of the non-Newtonian viscosity of dilute polymer solutions", in: Progress in Rheology of Biological and Synthetic Polymer Systems, A. C. Diogo, N. B. Alvarenga, J. Canada, S. Ferro, J. Dias, Eds., Beja, Portugal 2004, p. 193.
31. G. K. Fraenkel, J. Chem. Phys. 1952, 20, 642.
32. G. Del Río Echenique, R. Rodríguez Schmidt, J. J. Freire, J. G. Hernández Cifre, J. García de la Torre, J. Am. Chem. Soc. 2009, 131, 8548.
33. st edition, Clarendon, Oxford 1987.
34. F. G. Díaz, J. García de la Torre, J. Chem. Phys. 1988, 88, 7698.
35. R. Pamies, J. G. Hernández, J. Cifre, dela. Torre. García, J. Polym. Sci. Pol. Phys. 2007, 45, 1.
36. I. B. Bahar, R. Erman, R. L. Jernigan, A. R. Attilgan, D. G. Covell, J. Mol. Biol. 1999, 285, 1023.
37. B. Erman, Biophys. J. 2006, 91, 3580.
38. M. L. Huertas, S. Navarro, M. C. López Martínez, J. García de la Torre, Biophys. J. 1997, 73, 3142.
39. N. Metropolis, A. W. Metropolis, M. N. Rosenbluth, A. H. Teller, E. Teller, J. Chem. Phys. 1953, 21, 1087.
40. K. Binder, Ed., "Monte Carlo and Molecular Dynamics Simulations in Polymer Science", Oxford University Press, New York 1995.
41. M. Fixman, Macromolecules 1986, 19, 1195.
42. D. L. Ermak, J. A. McCammon, J. Chem. Phys. 1978, 69, 1352.
43. A. Iniesta, J. García de la Torre, J. Chem. Phys. 1990, 92, 2015.
44. G. Chirico, J. Langowski, Macromolecules 1992, 25, 769.
45. M. Fixman, Macromolecules 1986, 19, 1204.
46. I. Rubenstein, S. B. Leighton, Biophys. Chem. 1974, 1, 292.
47. B. H. Zimm, Biophys. Chem. 1974, 1, 279.
48. X. Schlagberger, R. R. Netz, Macromolecules 2008, 41, 1861.
49. T. T. Perkins, D. E. Smith, S. Chul, Science 1997, 276, 2016.
50. D. E. Smith, S. Chu, Science 1998, 281, 1335.
51. D. E. Smith, H. P. Babcock, S. Chu, Science 1999, 283, 1724.
52. P. G. De Gennes, Science 1997, 276, 1999.
53. P. Sunthar, J. R. Prakash, Macromolecules 2005, 38, 617.
54. R. G. Larson, H. Hu, D. E. Smith, S. Chu, J. Rheol. 1999, 43, 267.
55. J. S. Hur, E. S. G. Shaqfeh, R. G. Larson, J. Rheol. 2000, 44, 713.
56. C. M. Schroeder, E. S. G. Shaqfeh, S. Chu, Macromolecules 2004, 37, 9242.
57. R. B. Bird, H. H. Saab, P. J. Dotson, X. J. Fan, J. Chem. Phys. 1983, 79, 5729.
58. nd edition, John Wiley and Sons, New York 1987.
59. R. Pamies, M. C. López Martínez, J. G. Hernández Cifre, J. García de la Torre, Macromolecules 2005, 38, 1371.
60. J. A. Harpst, J. R. Dawson, Biophys. J. 1989, 55, 1237.
61. J. J. Freire, A. Rey, J. García de la Torre, Macromolecules 1986, 19, 457.
62. R. W. Clark, C. S. Lange, Biopolymers 1980, 19, 945.
63. B. H. Zimm, V. N. Schumaker, C. B. Zimm, Biophys. Chem. 1976, 5, 265.
64. E. J. Ralston, V. N. Schumaker, Biophys. Chem. 1979, 9, 375.
65. R. W. Clark, G. H. Wever, J. S. Wiberg, J. Virology 1980, 33, 438.