π-π orbital resonance in twisting duplex DNA: Dynamical phyllotaxis and electronic structure effects

Physical Review B - Condensed Matter and Materials Physics

Volumn 80, Issue 12, 2009, Pages

  Maciá, Enrique ^a  

^a UNIVERSIDAD COMPLUTENSE DE MADRID   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 70350646966     PISSN: 10980121     EISSN: 1550235X     Source Type: Journal    
DOI: 10.1103/PhysRevB.80.125102     Document Type: Article

References (68)

1. D. Beeker, A. Adhikary, and M. D. Sevilla, in Charge Migration in DNA. Perspectives from Physics, Chemistry and Biology, edited by, T. Chakraborty, (Springer, Berlin, 2007), p. 139.
2. E. Braun, Y. Eichen, U. Sivan, and G. Ben-Yoseph, Nature (London) 391, 775 (1998). 10.1038/35826
3. C. R. Treadway, M. G. Hill, and J. K. Barton, Chem. Phys. 281, 409 (2002). 10.1016/S0301-0104(02)00447-0
4. R. G. Endres, D. L. Cox, and R. R. P. Singh, Rev. Mod. Phys. 76, 195 (2004). 10.1103/RevModPhys.76.195
5. A. A. Voityuk, J. Chem. Phys. 128, 045104 (2008). 10.1063/1.2823015
6. A. A. Voityuk, K. Siriwong, and N. Rösch, Phys. Chem. Chem. Phys. 3, 5421 (2001). 10.1039/b105432p
7. Y. A. Berlin, F. C. Grozema, L. D. A. Siebbeles, and M. A. Ratner, J. Phys. Chem. C 112, 10988 (2008). 10.1021/jp801646g
8. Y. A. Berlin, I. V. Kurnikov, D. Beratan, M. A. Ratner, and A. L. Burin, in DNA Electron Transfer Processes: Some Theoretical Notions, edited by, G. B. Schuster, (Springer, Berlin, 2004), p. 1.
9. A. Troisi and G. Orlandi, J. Phys. Chem. B 106, 2093 (2002). 10.1021/jp0133182
10. A. A. Voityuk, J. Chem. Phys. 128, 115101 (2008). 10.1063/1.2841421
11. A. A. Voityuk, J. Jortner, M. Bixon, and N. Rösch, J. Chem. Phys. 114, 5614 (2001) 10.1063/1.1352035
12. A. A. Voityuk, Chem. Phys. Lett. 439, 162 (2007). 10.1016/j.cplett.2007. 03.066
13. P. J. de Pablo, F. Moreno-Herrero, J. Colchero, J. Gomez Herrero, P. Herrero, A. M. Baro, P. Ordejón, J. M. Soler, and E. Artacho, Phys. Rev. Lett. 85, 4992 (2000). 10.1103/PhysRevLett.85.4992
14. R. Di Felice, A. Calzolari, E. Molinari, and A. Garbesi, Phys. Rev. B 65, 045104 (2001). 10.1103/PhysRevB.65.045104
15. H. Wang, J. P. Lewis, and O. F. Sankey, Phys. Rev. Lett. 93, 016401 (2004). 10.1103/PhysRevLett.93.016401
16. Y. A. Berlin, M. L. Burin, and M. A. Ratner, Superlattices Microstruct. 28, 241 (2000). 10.1006/spmi.2000.0915
17. E. Artacho, M. Machado, D. Sánchez-Portal, P. Ordejón, and J. M. Soler, Mol. Phys. 101, 1587 (2003). 10.1080/0026897031000068587
18. H. Sugiyama and I. Saito, J. Am. Chem. Soc. 118, 7063 (1996). 10.1021/ja9609821
19. E. B. Starikov, Philos. Mag. 85, 3435 (2005). 10.1080/14786430500157110
20. K. Senthilkumar, F. C. Grozema, C. Fonseca Guerra, F. M. Bickelhaupt, F. D. Lewis, Y. A. Berlin, M. A. Ratner, and L. D. A. Siebbeles, J. Am. Chem. Soc. 127, 14894 (2005). 10.1021/ja054257e
21. F. C. Grozema and L. D. A. Siebbeles, in Charge Migration in DNA. Perspectives from Physics, Chemistry and Biology (Ref.), p. 21.
22. T. Kubar and M. Elstner, J. Phys. Chem. B 112, 8788 (2008). 10.1021/jp803661f
23. C. Wan, T. Fiebig, S. O. Kelley, C. R. Treadway, J. K. Barton, and A. H. Zewail, Proc. Natl. Acad. Sci. U.S.A. 96, 6014 (1999). 10.1073/pnas.96.11.6014
24. C. Wan, T. Fiebig, O. Schiemann, J. K. Barton, and A. H. Zewail, Proc. Natl. Acad. Sci. U.S.A. 97, 14052 (2000). 10.1073/pnas.250483297
25. Y. Duan, P. Wilkosz, M. Crowley, and J. Rosenberg, J. Mol. Biol. 272, 553 (1997). 10.1006/jmbi.1997.1247
26. S. Roche, Phys. Rev. Lett. 91, 108101 (2003). 10.1103/PhysRevLett.91. 108101
27. Y. Zhu, C. C. Kaun, and H. Guo, Phys. Rev. B 69, 245112 (2004). 10.1103/PhysRevB.69.245112
28. W. Ren, J. Wang, Z. Ma, and H. Guo, Phys. Rev. B 72, 035456 (2005) 10.1103/PhysRevB.72.035456
29. W. Ren, J. Wang, Z. Ma, and H. Guo, J. Chem. Phys. 125, 164704 (2006). 10.1063/1.2359447
30. A.-M. Guo and H. Xu, Physica B 391, 292 (2007). 10.1016/j.physb.2006.10. 008
31. R. Gutiérrez, S. Mandal, and G. Cuniberti, Phys. Rev. B 71, 235116 (2005). 10.1103/PhysRevB.71.235116
32. R. Gutiérrez, S. Mohapatra, H. Cohen, D. Porath, and G. Cuniberti, Phys. Rev. B 74, 235105 (2006). 10.1103/PhysRevB.74.235105
33. G. Cuniberti, E. Maciá, A. Rodríguez and R. A. Römer, in Charge Migration in DNA. Perspectives from Physics, Chemistry and Biology (Ref.), p. 1.
34. E. Maciá, Phys. Rev. B 76, 245123 (2007). 10.1103/PhysRevB.76. 245123
35. J. P. Lewis, Th. E. Cheatham III, E. B. Starikov, H. Wang, and O. F. Sankey, J. Phys. Chem. B 107, 2581 (2003). 10.1021/jp026772u
36. C. J. Paez and P. A. Shulz, Microelectron. J. 39, 1222 (2008). 10.1016/j.mejo.2008.01.007
37. Phyllotaxis refers to the geometrical ordering of certain botanical elements, like leaves or flowers, on the stem of a plant. The interested reader is referred to the classical works: I. Adler, J. Theor. Biol. 45, 1 (1974) 10.1016/0022-5193(74)90043-5
38. I. Adler, J. Theor. Biol. 53, 435 (1975) 10.1016/S0022-5193(75)80014-2
39. I. Adler, J. Theor. Biol. 65, 29 (1977) 10.1016/0022-5193(77)90077-7
40. G. J. Mitchison, Science 196, 270 (1977) 10.1126/science.196.4287.270
41. R. V. Jean, Phyllotaxis: A Systemic Study in Plant Morphogenesis (Cambridge University Press, Cambridge, 1994).
42. N. Rivier, R. Occelli, J. Pantaloni, and A. J. Lissowski, J. Phys. (France) 45, 49 (1984).
43. L. S. Levitov, Phys. Rev. Lett. 66, 224 (1991) 10.1103/PhysRevLett.66.224
44. L. S. Levitov, EPL 14, 533 (1991). 10.1209/0295-5075/14/6/006
45. S. Douady and Y. Couder, Phys. Rev. Lett. 68, 2098 (1992). 10.1103/PhysRevLett.68.2098
46. E. Maciá, Z. Kristallogr. 224, 91 (2009). 10.1524/zkri.2009.1123
47. E. Maciá, Rep. Prog. Phys. 69, 397 (2006). 10.1088/0034-4885/69/2/ R03
48. E. Maciá, Aperiodic Structures in Condensed Matter: Fundamentals and Applications (CRC Press, Boca Raton, FL, 2009).
49. E. Maciá and S. Roche, Nanotechnology 17, 3002 (2006). 10.1088/0957-4484/17/12/031
50. E. Maciá, Phys. Rev. B 74, 245105 (2006) 10.1103/PhysRevB.74. 245105
51. E. Maciá, Phys. Rev. B 75, 035130 (2007). 10.1103/PhysRevB.75. 035130
52. Z. G. Yu and X. Song, Phys. Rev. Lett. 86, 6018 (2001). 10.1103/PhysRevLett.86.6018
53. W. Zhang, A. O. Govorov, and S. E. Ulloa, Phys. Rev. B 66, 060303 (R) (2002). 10.1103/PhysRevB.66.060303
54. S. Cocco and R. Monasson, Phys. Rev. Lett. 83, 5178 (1999) 10.1103/PhysRevLett.83.5178
55. S. Cocco and R. Monasson, J. Chem. Phys. 112, 10017 (2000). 10.1063/1.481646
56. R. Endres, D. Cox, and R. Singh, arXiv:cond-mat/0201404 (unpublished).
57. Note that the adopted μ value coincides with the averaged mass of the four nucleotides, i.e., μ□ (mG + mC + mA + mT) /4.
58. A similar effect, involving dipolar magnetic interactions among magnets arranged in a helicoidal manner has been recently reported by C. Nisoli, N. M. Gabor, P. E. Lammert, J. D. Maynard, and V. H. Crespi, Phys. Rev. Lett. 102, 186103 (2009). 10.1103/PhysRevLett.102.186103
59. This interesting issue will be addressed elsewhere.
60. J. Ladik, A. Bende, and F. Bogár, J. Chem. Phys. 128, 105101 (2008) 10.1063/1.2832860
61. J. Ladik, A. Bende, and F. Bogár, J. Chem. Phys. 127, 055102 (2007). 10.1063/1.2752806
62. T. J. Richmond and C. A. Davey, Nature (London) 423, 145 (2003) 10.1038/nature01595
63. K. Luger, A. W. Mäder, R. K. Richmond, D. F. Sargent, and T. J. Richmond, Nature (London) 389, 251 (1997). 10.1038/38444
64. A. Hübsch, R. G. Endres, D. L. Cox, and R. R. P. Singh, Phys. Rev. Lett. 94, 178102 (2005). 10.1103/PhysRevLett.94.178102
65. A. Omerzu, D. Mihailovic, B. Anzelak, and I. Turel, Phys. Rev. B 75, 121103 (R) (2007). 10.1103/PhysRevB.75.121103
66. P. B. Woiczikowski, T. Kubar, R. Gutiérrez, R. A. Caetano, G. Cuniberti, and M. Elstner, J. Chem. Phys. 130, 215104 (2009). 10.1063/1.3146905
67. P. Thomen, U. Bockelmann, and F. Heslot, Phys. Rev. Lett. 88, 248102 (2002). 10.1103/PhysRevLett.88.248102
68. S. Roche, D. Bicout, E. Maciá, and E. Kats, Phys. Rev. Lett. 91, 228101 (2003). 10.1103/PhysRevLett.91.228101