Modeling charge transport in DNA using multi-scale methods

Physica Status Solidi (B) Basic Research

Volumn 250, Issue 11, 2013, Pages 2277-2287

  Kubař, Tomáš ^a   Gutiérrez, Rafael ^b   Kleinekathöfer, Ulrich ^c   Cuniberti, Gianaurelio ^b   Elstner, Marcus ^a  

^a KARLSRUHE INSTITUTE OF TECHNOLOGY   (Germany)

^b DRESDEN UNIVERSITY OF TECHNOLOGY   (Germany)

^c JACOBS UNIVERSITY BREMEN   (Germany)

Author keywords

Density functional theory; DNA; Electric conductivity; Green's functions; Landauer B ttiker approach; Non adiabatic dynamics

Indexed keywords

CARRIER TRANSPORT; CHARGE TRANSFER; CHEMICAL BONDS; DEGREES OF FREEDOM (MECHANICS); DNA; ELECTRIC CONDUCTIVITY; ELECTRONIC STRUCTURE; GREEN'S FUNCTION; MOLECULAR DYNAMICS; PERTURBATION TECHNIQUES;

CLASSICAL MOLECULAR DYNAMICS; ELECTRONIC STRUCTURE CALCULATIONS; LANDAUER; METAL-MOLECULE CONTACTS; METHODOLOGICAL APPROACH; MICROSCOPIC MECHANISMS; NON-ADIABATIC DYNAMICS; THEORETICAL INVESTIGATIONS;

DENSITY FUNCTIONAL THEORY;

EID: 84887239948     PISSN: 03701972     EISSN: 15213951     Source Type: Journal    
DOI: 10.1002/pssb.201349148     Document Type: Article

References (70)

1. G. Cuniberti, G. Fagas, and K. Richter (eds.), Introducing Molecular Electronics, Lecture Notes in Physics, Vol.680 (Springer, Berlin, 2005).
2. C. Joachim and M.A. Ratner, Proc. Natl. Acad. Sci. USA 102, 8801-8808 (2005).
3. M. Hazani, F. Hennrich, M. Kappes, R. Naaman, D. Peled, V. Sidorov, and D. Shvarts, Chem. Phys. Lett. 391, 389-392 (2004).
4. K. Keren, R.S. Berman, E. Buchstab, U. Sivan, and E. Braun, Science 302, 1380-1382 (2003).
5. E. Braun, Y. Eichen, U. Sivan, and G. Ben-Yoseph, Nature 391, 775-778 (1998).
6. Y. Zhang, R.H. Austin, J. Kraeft, E.C. Cox, and N.P. Ong, Phys. Rev. Lett. 89, 198102 (2002).
7. M. Mertig, R. Kirsch, W. Pompe, and H. Engelhardt, Eur. Phys. J. D 9, 45-48 (1999).
8. C.R. Treadway, M.G. Hill, and J.K. Barton, Chem. Phys. 281, 409 (2002).
9. C.J. Murphy, M.R. Arkin, Y. Jenkins, N.D. Ghatlia, S.H. Bossmann, N.J. Turro, and J.K. Barton, Science 262, 1025-1029 (1993).
10. E. Meggers, M.E. Michel-Beyerle, and B. Giese, J. Am. Chem. Soc. 120, 12950-12955 (1998).
11. F.C. Grozema, Y.A. Berlin, and L.D.A. Siebbeles, J. Am. Chem. Soc. 122, 10903-10909 (2000).
12. Y.A. Berlin, A.L. Burin, and M.A. Ratner, J. Am. Chem. Soc. 123, 260-268 (2001).
13. D. Porath, G. Cuniberti, and R. Di Felice, Top. Curr. Chem. 237, 183-227 (2004).
14. R.G. Endres, D.L. Cox, and R.R.P. Singh, Rev. Mod. Phys. 76, 195-214 (2004).
15. M.W. Shinwari, M.J. Deen, E.B. Starikov, and G. Cuniberti, Adv. Funct. Mater. 20, 1865-1883 (2010).
16. A.J. Storm, J. Van Noort, S. De Vries, and C. Dekker, Appl. Phys. Lett. 79, 3881-3883 (2001).
17. D. Porath, A. Bezryadin, S. De Vries, and C. Dekker, Nature 403, 635-638 (2000).
18. K.H. Yoo, D.H. Ha, J.O. Lee, J.W. Park, J. Kim, J.J. Kim, H.Y. Lee, T. Kawai, and H.Y. Choi, Phys. Rev. Lett. 87, 198102 (2001).
19. B. Xu, P. Zhang, X. Li, and N. Tao, Nano Lett. 4, 1105-1108 (2004).
20. H. Cohen, C. Nogues, R. Naaman, and D. Porath, Proc. Natl. Acad. Sci. USA 102, 11589-11593 (2005).
21. Y.A. Berlin, A.L. Burin, L.D.A. Siebbeles, and M.A. Ratner, J. Phys. Chem. A 105, 5666-5678 (2001).
22. K. Siriwong and A.A. Voityuk, WIREs: Comput. Mol. Sci. 2, 780-794 (2012).
23. F.C. Grozema and L.D.A. Siebbeles, Int. Rev. Phys. Chem. 27, 87-138 (2008).
24. H. Cao, J. Jiang, J. Ma, and Y. Luo, J. Am. Chem. Soc. 130, 6674-6675 (2008).
25. A. Troisi, D.L. Cheung, and D. Andrienko, Phys. Rev. Lett. 102, 116602 (2009).
26. A. Troisi and D.L. Cheung, J. Chem. Phys. 131, 014703 (2009).
27. R.G. Parr and W. Yang, Density-Functional Theory of Atoms and Molecules (Oxford University Press, New York, 1989).
28. T. Kuba ř and M. Elstner, J. Phys. Chem. B 114, 11221-11240 (2010).
29. F.C. Grozema, L.D.A. Siebbeles, Y.A. Berlin, and M.A. Ratner, ChemPhysChem 3, 536-539 (2002).
30. A. Troisi and G. Orlandi, Chem. Phys. Lett. 344, 509-518 (2001).
31. M. Elstner, D. Porezag, G. Jungnickel, J. Elsner, M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B 58, 7260-7268 (1998).
32. T. Kuba ř, P.B. Woiczikowski, G. Cuniberti, and M. Elstner, J. Phys. Chem. B 112, 7937-7947 (2008).
33. Q. Cui, M. Elstner, E. Kaxiras, T. Frauenheim, and M. Karplus, J. Phys. Chem. B 105, 569-585 (2001).
34. T. Kuba ř and M. Elstner, J. Phys. Chem. B 112, 8788-8798 (2008).
35. R. Landauer, IBM J. Res. Dev. 1, 223-231 (1957).
36. M. Büttiker and R. Landauer, Phys. Rev. Lett. 49, 1739-1742 (1982).
37. F.C. Grozema, S. Tonzani, Y.A. Berlin, G.C. Schatz, L.D.A. Siebbeles, and M.A. Ratner, J. Am. Chem. Soc. 130, 5157-5166 (2008).
38. F.C. Grozema, S. Tonzani, Y.A. Berlin, G.C. Schatz, L.D.A. Siebbeles, and M.A. Ratner, J. Am. Chem. Soc. 131, 14204-14205 (2009).
39. T. Kubař, U. Kleinekathöfer, and M. Elstner, J. Phys. Chem. B 113, 13107-13117 (2009).
40. T. Kubař and M. Elstner, Phys. Chem. Chem. Phys. 15, 5794-5813 (2013).
41. T. Takada, K. Kawai, X. Cai, A. Sugimoto, M. Fujitsuka, and T. Majima, J. Am. Chem. Soc. 126, 1125-1129 (2004).
42. G. King and A. Warshel, J. Chem. Phys. 93, 8682-8692 (1990).
43. K. Schulten and M. Tesch, Chem. Phys. 158, 421-446 (1991).
44. M. Marchi, J.N. Gehlen, D. Chandler, and M. Newton, J. Am. Chem. Soc. 115, 4178-4190 (1993).
45. M. Sulpizi, S. Raugei, J. VandeVondele, P. Carloni, and M. Sprik, J. Phys. Chem. B 111, 3969-3976 (2007).
46. J. Blumberger and G. Lamoureux, Mol. Phys. 106, 1597-1611 (2008).
47. M. Wanko, M. Hoffmann, J. Frähmcke, T. Frauenheim, and M. Elstner, J. Phys. Chem. B 112, 11468-11478 (2008).
48. P.B. Woiczikowski, T. Kuba ř, R. Gutiérrez, R.A. Caetano, G. Cuniberti, and M. Elstner, J. Chem. Phys. 130, 215104 (2009).
49. M.H. Lee, S. Avdoshenko, R. Gutiérrez, and G. Cuniberti Phys. Rev. B 82, 155455 (2010).
50. M.H. Lee, G. Brancolini, R. Gutiérrez, R. Di Felice, and G. Cuniberti J. Phys. Chem. B 116, 10977-10985 (2012).
51. P.B. Woiczikowski, T. Kubař, R. Gutiérrez, G. Cuniberti, and M. Elstner, J. Chem. Phys. 133, 035103 (2010).
52. R. Gutiérrez, R.A. Caetano, P.B. Woiczikowski, T. Kubař, M. Elstner, and G. Cuniberti Phys. Rev. Lett. 102, 208102 (2009).
53. R. Gutiérrez, R. Caetano, P.B. Woiczikowski, T. Kubař, M. Elstner, and G. Cuniberti New J. Phys. 12, 023022 (2010).
54. R. Gutiérrez, S. Mohapatra, H. Cohen, D. Porath, and G. Cuniberti Phys. Rev. B 74, 235105 (2006).
55. E. Shapir, H. Cohen, A. Calzolari, C. Cavazzoni, D.A. Ryndyk, G. Cuniberti, A. Kotlyar, R. Di Felice, and D. Porath, Nature Materials 7, 68-74 (2008).
56. D.A. Ryndyk, E. Shapir, D. Porath, A. Calzolari, R. Di Felice, and G. Cuniberti ACS Nano 3, 1651-1656 (2009).
57. N. Kang, A. Erbe, and E. Scheer, New J. Phys. 10, 023030 (2008).
58. A. Lebrun and R. Lavery, Nucleic Acids Res. 24, 2260-2267 (1996).
59. C.H. Albrecht, G. Neuert, R.A. Lugmaier, and H.E. Gaub, Biophys. J. 94, 4766-4774 (2008).
60. M. Wolter, P.B. Woiczikowski, M. Elstner, and T. Kubař, Phys. Rev. B 85, 075101 (2012).
61. M. Wolter, M. Elstner, and T. Kubař, paper submitted (2013).
62. M. Wolter, M. Elstner, and T. Kubař, J. Phys. Chem. A 115, 11238-11247 (2011).
63. A. Croy and U. Saalmann, Phys. Rev. B 80, 245311 (2009).
64. M. Aghtar, J. Liebers, J. Strümpfer, K. Schulten, and U. Kleinekathöfer, J. Chem. Phys. 136, 214101 (2012).
65. S. Welack, M. Schreiber, and U. Kleinekathöfer, J. Chem. Phys. 124, 044712 (2006).
66. Y. Tanimura, J. Phys. Soc. Jpn. 75, 082001 (2006).
67. U. Kleinekathöfer, G.Q. Li, S. Welack, and M. Schreiber, Europhys. Lett. 75, 139-145 (2006).
68. G.Q. Li, M. Schreiber, and U. Kleinekathöfer, Europhys. Lett. 79, 27006 (2007).
69. J.S. Jin, X. Zheng, and Y.J. Yan, J. Chem. Phys. 128, 234703 (2008).
70. B. Popescu, P.B. Woiczikowski, M. Elstner, and U. Kleinekathöfer, Phys. Rev. Lett. 109, 176802 (2012).