Heat conductivity of the DNA double helix

Physical Review B - Condensed Matter and Materials Physics

Volumn 83, Issue 24, 2011, Pages

  Savin, Alexander V ^a   Mazo, Mikhail A ^a   Kikot, Irina P ^a   Manevitch, Leonid I ^a   Onufriev, Alexey V ^b  

^a SEMENOV INSTITUTE OF CHEMICAL PHYSICS   (Russian Federation)

^b VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 79961221884     PISSN: 10980121     EISSN: 1550235X     Source Type: Journal    
DOI: 10.1103/PhysRevB.83.245406     Document Type: Article

References (105)

1. A. A. Balandin, S. Ghosh, W. Bao, I. Calizo, D. Teweldebrhan, F. Miao, and C. N. Lau, Nano Lett. NALEFD 1530-6984 10.1021/nl0731872 8, 902 (2008).
2. S. Ghosh, I. Calizo, D. Teweldebrhan, E. P. Pokatilov, D. L. Nika, A. A. Balandin, W. Bao, F. Miao, and C. N. Lau, Appl. Pys. Lett. APPLAB 0003-6951 10.1063/1.2907977 92, 151911 (2008). (Pubitemid 351555695)
3. E. Pop, D. Mann, Q. Wang, K. Goodson, and H. Dai, Nano Lett. NALEFD 1530-6984 10.1021/nl052145f 6, 96 (2006). (Pubitemid 43166108)
4. C. W. Chang, D. Okawa, A. Majumdar, and A. Zettl, Science SCIEAS 0036-8075 10.1126/science.1132898 314, 1121 (2006). (Pubitemid 44789037)
5. N. Yang, G. Zhang, and B. Li, Appl. Phys. Lett. APPLAB 0003-6951 10.1063/1.3049603 93, 243111 (2008).
6. N. Yang, G. Zhang, and B. Li, Appl. Phys. Lett. APPLAB 0003-6951 10.1063/1.3183587 95, 033107 (2009).
7. G. Wu and B. Li, Phys. Rev. B PRBMDO 1098-0121 10.1103/PhysRevB.76.085424 76, 085424 (2007).
8. J. Hu, X. Ruan, and Y. P. Chen, Nano Lett. NALEFD 1530-6984 10.1021/nl901231s 9, 2730 (2009).
9. D. Li, Y. Wu, P. Kim, L. Shi, P. Yang, and A. Majumdar, Appl. Phys. Lett. APPLAB 0003-6951 10.1063/1.1616981 83, 2934 (2003).
10. C. W. Chang, D. Okawa, H. Garcia, A. Majumdar, and A. Zettl, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.101.075903 101, 075903 (2008).
11. S. Maruyama, Physica B PHYBE3 0921-4526 10.1016/S0921-4526(02)00898-0 323, 193 (2002). (Pubitemid 35019027)
12. G. Zhang and B. Li, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1949166 123, 014705 (2005). (Pubitemid 41037073)
13. A. V. Savin, B. Hu, and Y. S. Kivshar, Phys. Rev. B PRBMDO 1098-0121 10.1103/PhysRevB.80.195423 80, 195423 (2009).
14. M. Endo and H. Sugiyama, Chembiochem JCPSA6 1439-4227 10.1002/cbic.200900286 10, 2420 (2009).
15. R. K. Joshi, L. West, A. Kumar, N. Joshi, S. Alwarappan, and A. Kumar, Nanotechnology NNOTER 0957-4484 10.1088/0957-4484/21/18/185604 21, 185604 (2010).
16. T. Kodama, A. Jain, and K. E. Goodson, Nano Lett. NALEFD 1530-6984 10.1021/nl900272m 9, 2005 (2009).
17. S. Lepri, R. Livi, and A. Politi, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.78.1896 78, 1896 (1997).
18. S. Lepri, R. Livi, and A. Politi, Phys. Rep. PRPLCM 0370-1573 10.1016/S0370-1573(02)00558-6 377, 1 (2003). (Pubitemid 36288864)
19. W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz Jr. D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja00124a002 117, 5179 (1995).
20. N. Foloppe and A. D. MacKerell, J. Comput. Chem. JCCHDD 0192-8651 10.1002/(SICI)1096-987X(20000130)21:2<86::AID-JCC2>3.0.CO;2-G 21, 86 (2000).
21. A. D. MacKerell and N. K. Banavali, J. Comput. Chem. 0192-8651 10.1002/(SICI)1096-987X(20000130)21:2<105::AID-JCC3>3.0.CO;2-P 21, 105 (2000).
22. A. Perez, F. J. Luque, and M. Orozco, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja0753546 129, 14739 (2007). (Pubitemid 350207887)
23. A. Perez, I. Marchan, D. Svozil, J. Sponer, T. E. Cheatham II, C. A. Laughton, and M. Orozco, Biophys. J. BIOJAU 0006-3495 10.1529/biophysj.106. 097782 92, 3817 (2007). (Pubitemid 46910569)
24. A. Perez, F. Lankas, F. J. Luque, and M. Orozco, Nucleic Acids Res. NARHAD 0305-1048 10.1093/nar/gkn082 36, 2379 (2008). (Pubitemid 351567010)
25. I. Cozmuta and H. Mehrez, J. Comp. Theor. Nanoscien. 4, 349 (2007).
26. D. L. Beveridge, G. Barreiro, K. S. Byun, D. A. Case, T. E. Cheatham, S. B. Dixit, E. Giudice, F. Lankas, R. Lavery, J. H. Maddocks, Biophys. J. BIOJAU 0006-3495 10.1529/biophysj.104.045252 87, 3799 (2004). (Pubitemid 39602887)
27. V. Makarov, B. M. Pettitt, and M. Feig, Acc. Chem. Res. ACHRE4 0001-4842 10.1021/ar0100273 35, 376 (2002)
28. [http://www.hubmed.org/display.cgi?uids=12069622].
29. E. Giudice and R. Lavery, Acc. Chem. Res. ACHRE4 0001-4842 10.1021/ar010023y 35, 350 (2002).
30. T. E. Cheatham and P. A. Kollman, J. Mol. Biol. JMOBAK 0022-2836 10.1006/jmbi.1996.0330 259, 434 (1996). (Pubitemid 26179021)
31. M. Feig and B. M. Pettitt, J. Phys. Chem. B JPCBFK 1520-6106 10.1021/jp971180a 101, 7361 (1997).
32. M. Feig and B. M. Pettitt, Biopolymers BIPMAA 0006-3525 10.1002/(SICI)1097-0282(1998)48:4<199::AID-BIP2>3.0.CO;2-5 48, 199 (1998).
33. J. Norberg and L. Nilsson, J. Phys. Chem. JPCHAX 0022-3654 10.1021/j100040a043 99, 14876 (1995).
34. D. A. Case, T. E. Cheatham, T. Darden, H. Gohlke, R. Luo, K. M. Merz, A. Onufriev, C. Simmerling, B. Wang, and R. J. Woods, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.20290 26, 1668 (2005) (Pubitemid 43076180)
35. [http://www.hubmed.org/display.cgi?uids=16200636].
36. A. Pérez, J. Sponer, P. Jurecka, P. Hobza, F. J. Luque, and M. Orozco, Chemistry CEUJED 0947-6539 10.1002/chem.200500255 11, 5062 (2005) (Pubitemid 41251675)
37. [http://www.hubmed.org/display.cgi?uids=15977281].
38. J. Sponer, P. Jurecka, I. Marchan, F. J. Luque, M. Orozco, and P. Hobza, Chemistry CEUJED 0947-6539 10.1002/chem.200501239 12, 2854 (2006)
39. [http://www.hubmed.org/display.cgi?uids=16425171].
40. A. Onufriev, in Annual Reports in Computational Chemistry, edited by, R. Wheeler, and, D. Spellmeyer, (Elsevier, Amsterdam, The Netherlands, 2008), Vol. 4, pp. 125-137.
41. N. A. Baker, Curr. Opin. Struct. Biol. COSBEF 0959-440X 10.1016/j.sbi.2005.02.001 15, 137 (2005).
42. C. J. Cramer and D. G. Truhlar, Chem. Rev. CHREAY 0009-2665 10.1021/cr960149m 99, 2161 (1999).
43. M. K. Gilson, Curr. Opin. Struct. Biol. COSBEF 0959-440X 10.1016/0959-440X(95)80079-4 5, 216 (1995).
44. M. Scarsi, J. Apostolakis, and A. Caflisch, J. Phys. Chem. A JPCAFH 1089-5639 10.1021/jp9714227 101, 8098 (1997).
45. J. Z. Ruscio and A. Onufriev, Biophys. J. BIOJAU 0006-3495 10.1529/biophysj.106.082099 91, 4121 (2006). (Pubitemid 44887272)
46. D. F. N. Bruant, R. Lavery, and D. Genest, Biophys. J. BIOJAU 0006-3495 10.1016/S0006-3495(99)77074-8 77, 2366 (1999).
47. K. Drukker and G. C. Schatz, J. Phys. Chem. B JPCBFK 1520-6106 10.1021/jp000550j 104, 6108 (2000).
48. K. Drukker, G. Wu, and G. C. Schatz, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1329137 114, 579 (2001). (Pubitemid 32088417)
49. M. Orozco, A. Pérez, A. Noy, and F. J. Luque, Chem. Soc. Rev. JCPSA6 0306-0012 10.1039/b207226m 32, 350 (2003)
50. [http://www.hubmed.org/display.cgi?uids=14671790].
51. B. Mergell, M. R. Ejtehadi, and R. Everaers, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.68.021911 68, 021911 (2003).
52. S. O. Nielsen, C. F. Lopez, G. Srinivas, and M. L. Klein, J. Phys. Condens. Matter JCOMEL 0953-8984 10.1088/0953-8984/16/15/R03 16, R481 (2004).
53. Y.-L. Chen, M. D. Graham, J. J. de Pablo, K. Jo, and D. C. Schwartz, Macromol. MAMOBX 0024-9297 10.1021/ma050238d 38, 6680 (2005). (Pubitemid 41118727)
54. M. Sales-Pardo, R. Guimera, A. A. Moreira, J. Widom, and L. A. N. Amaral, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.71.051902 71, 051902 (2005). (Pubitemid 41480965)
55. H. L. Tepper and G. A. Voth, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1869417 122, 124906 (2005). (Pubitemid 40537498)
56. C. B. Hyeon and D. Thirumalai, Bioph. J. BIOJAU 0006-3495 10.1529/biophysj.105.078030 90, 3410 (2006).
57. J. Errami, M. Peyrard, and N. Theodorakopoulos, Eur. Phys. J. E EPJSFH 1292-8941 10.1140/epje/i2007-10200-x 23, 397 (2007). (Pubitemid 47404158)
58. T. A. Knotts IV, N. Rathore, D. C. Schwartz, and J. J. de Pablo, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2431804 126, 084901 (2007). (Pubitemid 46357459)
59. M. Cadoni, R. De Leo, and G. Gaeta, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.75.021919 75, 021919 (2007). (Pubitemid 46361440)
60. N. B. Becker and R. Everaers, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.76.021923 76, 021923 (2007). (Pubitemid 47311853)
61. M. McCullagh, T. Prytkova, S. Tonzani, N. D. Winter, and G. C. Schatz, J. Phys. Chem. B JPCBFK 1520-6106 10.1021/jp803192u 112, 10388 (2008).
62. L. Höfler and R. E. Gyurcsat'nyi, Electroanalysis ELANEU 1040-0397 10.1002/elan.200704058 20, 301 (2008).
63. A. K. Mazur, J. Phys. Chem. B JPCBFK 1520-6106 10.1021/jp711815x 112, 4975 (2008).
64. A. K. Mazur, J. Phys. Chem. B JPCBFK 1520-6106 10.1021/jp8098945 2113, 2077 (2009).
65. N. A. Kovaleva, L. I. Manevitch, A. I. Musienko, and A. V. Savin, Polymer Science Series A 0965-545X 10.1134/S0965545X09070104 51, 833 (2009).
66. A. Morriss-Andrews, J. Rottler, and S. S. Plotkin, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.3269994 132, 035105 (2010).
67. P. Yakovchuk, E. Protozanova, and M. D. Frank-Kamenetskii, Nucleic Acids Res. NARHAD 0305-1048 10.1093/nar/gkj454 34, 564 (2006). (Pubitemid 43240244)
68. T. Schlick, Molecular Modeling and Simulation (Springer, Berlin, 2002).
69. A. R. Leach, Molecular Modelling: Principles and Applications (Addison Wesley Longman, Essex, UK, 1996).
70. B. K. P. Horn, J. Opt. Soc. Am. A NARHAD 1084-7529 10.1364/JOSAA.4.000629 4, 629 (1987).
71. J. Chocholousova and M. Feig, J. Phys. Chem. B JPCBFK 1520-6106 10.1021/jp0627675 110, 17240 (2006). (Pubitemid 44412352)
72. V. Tsui and D. Case, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja9939385 122, 2489 (2000). (Pubitemid 30211961)
73. H. R. Drew, R. M. Wing, T. Takano, C. Broka, S. Tanaka, K. Itakura, and R. E. Dickerson, Proc. Natl. Acad. Sci. USA PNASA6 0027-8424 10.1073/pnas.78.4.2179 78, 2179 (1981).
74. X.-J. Lu and W. K. Olson, Nucleic Acids. Res. NARHAD 0305-1048 10.1093/nar/gkg680 31, 5108 (2003). (Pubitemid 37441878)
75. R. Dickerson, Nucleic Acids in International Tables for Crystallography (Kluwer Academic Publishers, Dordrecht, 2001), Vol. F of "Crystallography of Biological Macromolecules," pp. 588-622.
76. P. Cluzel, A. Lebrun, A. Heller, R. Lavery, J.-L. Viovy, D. Chatenay, and F. Caron, Science SCIEAS 0036-8075 10.1126/science.271.5250.792 271, 792 (1996).
77. S. B. Smith, Y. Cui, and C. Bustamante, Science SCIEAS 0036-8075 10.1126/science.271.5250.795 271, 795 (1996).
78. C. Bustamante, S. B. Smith, J. Liphardt, and D. Smith, Curr. Opin. Struct. Biol. COSBEF 0959-440X 10.1016/S0959-440X(00)00085-3 10, 279 (2000). (Pubitemid 30333096)
79. H. Clausen-Schaumann, M. Rief, C. Tolksdorf, and H. E. Gaub, Biophys. J. BIOJAU 0006-3495 10.1016/S0006-3495(00)76747-6 78, 1997 (2000).
80. A. Lebrun and R. Lavery, Nucleic Acids Res. NARHAD 0305-1048 10.1093/nar/24.12.2260 24, 2260 (1996). (Pubitemid 26193588)
81. Z. Bryant, M. D. Stone, J. Gore, and S. B. Smith, Nature (London) NATUAS 0028-0836 10.1038/nature01810 424, 338 (2003). (Pubitemid 36899378)
82. M. B. Hakim, S. M. Lindsay, and J. Powell, Biopolymers BIPMAA 0006-3525 10.1002/bip.360230704 23, 1185 (1984).
83. M. Krisch, A. Mermet, H. Grimm, V. T. Forsyth, and A. Rupprecht, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.7>3.061909 73, 061909 (2006).
84. S. Buyukdagli, A. V. Savin, and B. Hu, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.78.066702 78, 066702 (2008).
85. H. Dammak, Y. Chalopin, M. Laroche, M. Hayoun, and J.-J. Greffet, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.103.190601 103, 190601 (2009).
86. O. V. Gendelman and A. V. Savin, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.84.2381 84, 2381 (2000).
87. C. Giardina, R. Livi, A. Politi, and M. Vassalli, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.84.2144 84, 2144 (2000).
88. W. C. Still, A. Tempczyk, R. C. Hawley, and T. Hendrickson, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja00172a038 112, 6127 (1990).
89. D. Bashford and D. A. Case, Annu. Rev. Phys. Chem. ARPLAP 0066-426X 10.1146/annurev.physchem.51.1.129 51, 129 (2000).
90. C. Keslo and C. Simmerling, in Computational Studies of RNA and DNA, edited by, J. Sponer, and, F. Lankas, (Springer, Dordrecht, The Netherlands, 2006), Vol. 2 of "Challenges and Advances in Computational Chemistry and Physics," pp. 147-167.
91. M. Zacharias, in Computational Studies of RNA and DNA, edited by, J. Sponer, and, F. Lankas, (Springer, Dordrecht, The Netherlands, 2006), Vol. 2 of "Challenges and Advances in Computational Chemistry and Physics," pp. 95-119.
92. L. Wang, B. E. Hingerty, A. R. Srinivasan, W. K. Olson, and S. Broyde, Biophys. J. BIOJAU 0006-3495 10.1016/S0006-3495(02)75177-1 83, 382 (2002)
93. [http://www.hubmed.org/display.cgi?uids=12080128].
94. V. Tsui and D. Case, Biopolymers BIPMAA 0006-3525 10.1002/1097-0282(2000) 56:4<275::AID-BIP10024>3.0.CO;2-E 56, 275 (2001).
95. E. Sorin, Y. Rhee, B. Nakatani, and V. Pande, Biophys. J. BIOJAU 0006-3495 10.1016/S0006-3495(03)74520-2 85, 790 (2003)
96. [http://www.hubmed.org/display.cgi?uids=12885628].
97. A. Balaeff, M. E. Churchill, and K. Schulten, Proteins 18PLAF 0887-3585 10.1002/(SICI)1097-0134(19980201)30:2<113::AID-PROT2>3.0.CO;2-O 30, 113 (1998)
98. [http://www.hubmed.org/display.cgi?uids=9489920].
99. B. Jayaram, K. McConnell, S. B. Dixit, A. Das, and D. L. Beveridge, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.10009 23, 1 (2002) (Pubitemid 34063125)
100. [http://www.hubmed.org/display.cgi?uids=11913374].
101. L. F. De Castro and M. Zacharias, J. Mol. Recognit. JCCHDD 0952-3499 10.1002/jmr.581 15, 209 (2002) (Pubitemid 35249843)
102. [http://www.hubmed.org/display.cgi?uids=12382239].
103. H. Allawi, M. Kaiser, A. Onufriev, W. Ma, A. Brogaard, D. Case, B. Neri, and V. Lyamichev, J. Mol. Biol. JMOBAK 0022-2836 10.1016/S0022-2836(03)00351-6 328, 537 (2003). (Pubitemid 36438572)
104. A. Onufriev, D. A. Case, and D. Bashford, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.10126 23, 1297 (2002). (Pubitemid 35186231)
105. J. Srinivasan, M. Trevathan, P. Beroza, and D. Case, Theor. Chem. Acc. TCACFW 1432-881X 10.1007/s002140050460 101, 426 (1999).