Russian version English version
About the Journal
Editorial Board
Instructions for Authors
Information for Readers and Authors
Current Issue
Archive
Contact Us
Search

Send manuscript
 


Volume 19   Issue 1   Year 2024
References

  1. Watson J.D., Crick F.H.C. A structure for deoxyribose nucleic acid. Nature. 1953;171:37–738. doi: 10.1038/171737a0
  2. Eley D.D., Spivey D.I. Semiconductivity of organic substances. Part9.–Nucleic acid in the dry state. Trans. Faraday Soc. 1962;58:411–415. doi: 10.1039/TF9625800411
  3. Dutreix J., Wambersie A., Tubiana M. Introduction to radiobiology. London: CRC Press, 1990. doi: 10.1111/j.1365-2184.1991.tb01162.x
  4. Frenkel K. Carcinogen-mediated oxidant formation and oxidative DNA damage. Pharmacol. Ther. 1992;53:127–166. doi: 10.1016/0163-7258(92)90047-4
  5. Demple B., Harrison L. Repair of oxidative damage to DNA: enzymology and biology. Annu. Rev. Biochem. 1994;63:915–948. doi: 10.1146/annurev.bi.63.070194.004411
  6. Hall D.B., Holmlin R.E., Barton J.K. Oxidative DNA damage through long-range electron transfer. Nature. 1996;382:731–735. doi: 10.1038/382731a0
  7. Lakhno V. D., Vinnikov A.V. DNA devices based on DNA. Nanobioelectronics. KIAM Preprint. 2018. ¹ 137. 26 p. doi: 10.20948/prepr-2018-137
  8. Skourtis S., Nitzan A. Effects of initial state preparation on the distance dependence of electron transfer through molecular bridges and wires. J. of Chem. Phys. 2003;119:6271–6276. doi: 10.1063/1.1601597
  9. Landa H., Misguich G. Nonlocal correlations in noisy multiqubit systems simulated using matrix product operators. SciPost Phys. Core. 2023;6. doi: 10.21468/SciPostPhysCore.6.2.037
  10. Landi A., Capobianco A., Peluso A. Coherent Effects in Charge Transport in Molecular Wires: Toward a Unifying Picture of Long-Range Hole Transfer in DNA. J. Phys. Chem. Lett. 2020;11:7769−7775. doi: 10.1021/acs.jpclett.0c01996
  11. Nardi A.N., D’Abramo M., Amadei A. Modeling Charge Transfer Reactions by Hopping between Electronic Ground State Minima: Application to Hole Transfer between DNA Bases. Molecules. 2022;27:7408. doi: 10.3390/molecules27217408
  12. Lima R.P.A., Malyshev A.V. Charge transfer mechanisms in DNA at finite temperatures: From quasiballistic to anomalous subdiffusive charge transfer. Phys. Rev. E. 2022;106:024414. doi: 10.1103/PhysRevE.106.024414
  13. Halliwell B., Gutteridge J.M.C. Free Radicals in Biology and Medicine. Oxford: Oxford University Press, 1999. doi: 10.1093/acprof:oso/9780198717478.001.0001
  14. Sies H., Schulz W.A., Steenken S. Adjacent Guanines as Preferred Sites for Strand Breaks in Plasmid DNA Irradiated with 193 nm and 248 nm UV laser light. Photochem. Photobiol. B. 1996;32:97–102. doi: 10.1016/1011-1344(95)07192-X
  15. Wolf P., Jones G.D.D., Candeias L.P., O’Neil P. Introduction of Strand Breaks in Polynucleotides and DNA by Sulfate Radical Anion: Role of Electron Loss Centres as Precursors of Strand Breakage. Int. J. Radiat. Biol. 1993;64:7–18. doi: 10.1080/09553009314551061
  16. Sugiyama H., Saito I. Theoretical Studies of GC-Specific Photocleavage of DNA via Electron Transfer: Significant Lowering of Ionization Potential and 5’-Localization of HOMO of Stacked G Bases in B-Form DNA. J. Am. Chem. Soc. 1996;118:7063–7068. doi: 10.1021/ja9609821
  17. Saito I., Nakamura T., Nakatani K., Yoshioka Y., Yamaguchi K., Sugiyama H. Mapping of the Hot Spots for DNA Damage by One-Electron Oxidation: Efficacy of GG Doublets and GGG Triplets as a Trap in Long-Range Hole Migration. J. Am. Chem. Soc. 1998;120:12686–12687. doi: 10.1021/ja981888i
  18. Brun A.M., Harriman A.J. Dynamics of electron transfer between intercalated polycyclic molecules: effect of interspersed bases. J. Am. Chem. Soc. 1992;114:3656–3660. doi: 10.1021/ja00036a013
  19. Mead T.J., Kayem J.F. Electron Transfer through DNA: Site‐ Specific Modification of Duplex DNA with Ruthenium Donors and Acceptors. Angew. Chem. Int. Ed. Engl. 1995;34:352–354. doi: 10.1002/anie.199503521
  20. Draganescu A., Tullius T.D. Targeting of nucleic acids by iron complexes. Metal Ions in Biological Systems. 1996;33:453–484.
  21. Murphy C.J., Arkin M.A., Jenkins Y., Ghatlia N.D., Bossmann S.H., Turro N.J., Barton J.K. Long-range photoinduced electron transfer through a DNA helix. Science. 1993;262:1025–1029. doi: 10.1126/science.7802858.
  22. Brun A.M., Harriman A. Energy- and electron-transfer processes involving palladium phorphyrins bound to DNA. J. Am. Chem. Soc. 1994;116:10383–10393. doi: 10.1021/ja00102a004
  23. Harriman A. Electron Tunneling in DNA. Angew. Chem. Int. Ed. 1999;38:945–949. doi: 10.1002/(SICI)1521-3773(19990401)38:7<945::AID-ANIE945>3.0.CO;2-S
  24. Boon E.M., Barton J.K. Charge transport in DNA. Curr. Opin. Stuct. Biol. 2002;12:320–329. doi: 10.1016/S0959-440X(02)00327-5
  25. Giese B., Amaudrut J., Köhler A.K., Spormann M., Wessely S. Direct observation of hole transfer through DNA by hopping between adenine bases and by tunneling. Nature. 2001;412:318–320. doi: 10.1038/35085542
  26. Giese B. Long-distance charge transport in DNA: the hopping mechanism. Acc. Chem. Res. 2000;33:631–636. doi: 10.1021/ar990040b
  27. Porath D., Bezryadin A., de Vries S., Dekker C. Direct measurement of electrical transport through DNA molecules. Nature. 2000;403:635–638. doi: 10.1038/35001029
  28. Shigematsu T., Shimotani K., Manabe C., Watanabe H., Shimizu M. Transport properties of carrier-injected DNA. J. Chem. Phys. 2003;118:4245–4252. doi: 10.1063/1.1541608
  29. Storm A.J., van Noort J., de Vries S., Dekker C. Insulating behavior for DNA molecules between nanoelectrodes at the 100 nm length scale. Appl. Phys. Lett. 2001;79:3881–3883. doi: 10.1063/1.1421086
  30. Yoo K.H., Ha D.H., Lee J.O., Park J.W., Kim J., Kim J.J., Lee H.-Y., Kawai T., Choi H.Y. Electrical conduction through poly(dA)-poly(dT) and poly(dG)-poly(dC) DNA molecules. Phys. Rev. Lett. 2001;87:198102. doi: 10.1103/PhysRevLett.87.198102
  31. Li C.-Z., Long Y.-T., Kraatz H.-B., Lee J.S. Electrochemical Investigations of M-DNA Self-Assembled Monolayers on Gold Electrodes. J. Phys. Chem. B. 2003;107:2291–2296. doi: 10.1021/jp026792w
  32. Wetting S.D., Wood D.O., Lee J.S. Thermodynamic investigation of M-DNA: a novel metal ion–DNA complex. Journal of Inorganic Biochemistry. 2003;94:94–99. doi: 10.1016/S0162-0134(02)00624-4
  33. Cuniberti G., Fagas G., Richter K. Introducing Molecular Electronics. In: Lecture Notes in Physics 680. Berlin, Heidelberg: Springer-Verlag, 2005. doi: 10.1007/3-540-31514-4_1
  34. Grozema F., Berlin Y., Siebbeles L. Mechanism of Charge Migration through DNA: Molecular Wire Behavior, Single-Step Tunneling or Hopping? J. Am. Chem. Soc. 2000;122(44):10903–10909. doi: 10.1021/ja001497f
  35. Wang X.F., Chakraborty T. Charge Transfer via a Two-Strand Superexchange Bridge in DNA. Phys. Rev. Lett. 2006;97:106602. doi: 10.1103/PhysRevLett.97.106602
  36. Segal D., Nitzan A., Davis W.B., Wasielewski M.R., Ratner M.A. Electron Transfer Rates in Bridged Molecular Systems 2. A Steady-State Analysis of Coherent Tunneling and Thermal Transitions. J. Phys. Chem. B. 2000;104:3817–3829. doi: 10.1021/jp993260f
  37. Alicki R., Lendi K. Quantum Dynamical Semigroups and Applications. Lect. Notes Phys. Berlin Heidelberg: Springer, 2007. 717 p. doi: 10.1007/3-540-70861-8
  38. Weiss E.A., Katz G., Goldsmith R.H., Wasielewski M.R., Ratner M.A. Electron transfer mechanism and the locality of the system-bath interaction: A comparison of local, semilocal, and pure dephasing models. J. Chem. Phys. 2006;124:074501. doi: 10.1063/1.2168457
  39. Lakhno V.D. Sequence Dependent Hole Evolution in DNA. J. Biol. Phys. 2004;30:123–138. doi: 10.1023/B:JOB:000035844.35839.60
  40. Fialko N.S., Lakhno V.D. Numerical Modeling of the Charge Transfer Along 1D Molecular Chain “Donor-Bridge-Acceptor” at T=300K. Lecture Notes in Computer Science. 2019;11386:225–232. doi: 10.1007/978-3-030-11539-5_24
  41. Fialko N. S., Lakhno V. D. Charge transfer in 1D chain “Donor-Bridge-Acceptor” at T=300 K. KIAM Preprint. 2018. ¹ 77. 17 p. doi: 10.20948/prepr-2018-77
  42. Datta S. Quantum Transport: Atom to Transistor. Cambridge University Press, 2005. 404 p. doi: 10.1017/CBO9781139164313
  43. Ryndyk D.A., Gutierrez R., Song B., Cuniberti G. Green function techniques in the treatement of quantum transport at the molecular scale. Energy Transfer Dynamics in Biomaterial Systems. Berlin Heidelberg: Springer-Verlag, 2009. (Springer Series in Chemical Physics 93). doi: 10.1007/978-3-642-02306-4_9
  44. Kilgour M., Segal D. Charge transport in molecular junctions: From tunneling to hopping with the probe technique. J. Chem. Phys. 2015;143:024111. doi: 10.1063/1.4926395
  45. Hawke L.G.D., Kalosakas G., Simserides C. Electronic parameters for charge transfer along DNA. Eur. Phys. J. E. 2010;32:291–305. doi: 10.1140/epje/i2010-10650-y
  46. Rengifo E., Murillo G., Arce J.C. Modeling the bandstructures of B-DNA base stacks. J. Appl. Phys. 2013;113:173703. doi: 10.1063/1.4803489
  47. Meggers E., Michel-Beyerle M.E., Giese B. Sequence Dependent Long Range Hole Transport in DNA. J. Am. Chem. Soc. 1998;120:12950–12955. doi: 10.1021/ja983092p
  48. Bixon M., Jortner J. Long-range and very long-range charge transport in DNA. Chemical Physics. 2002;281:393–408. doi: 10.1016/S0301-0104(02)00495-0
  49. Voityuk A., Rosch N., Bixon M., Jortner J. Electronic Coupling for Charge Transfer and Transport in DNA. J. Phys. Chem. B. 2000;104:9740–9745. doi: 10.1021/jp001109w
  50. Syurakshin A.V., Lakhno V. D., Yushankhai V.Y. Charge transfer in a DNA molecule within a simple model of an open quantum system. KIAM Preprint. 2021. ¹ 23. 26 p. doi: 10.20948/prepr-2021-23
  51. Petruccione F., Breuer H.-P. Teoriia otkrytykh kvantovykh sistem. Moscow Izhevsk, 2010. 824 p. (Translation of: Breuer H.-P., Petruccione F. The Theory of Open Quantum Systems. 2006. doi: 10.1093/acprof:oso/9780199213900.001.0001 ).
  52. May V., Kuhn O. Charge and Energy Transfer Dynamics in Molecular Systems. Wiley-VCH, 2004. ISBN: 978-3-527-40732-3.
  53. Chin A.W., Datta A., Caruso F., Huelga S.F., Plenio M.B. Noise-assisted energy transfer in quantum networks and light-harvesting complexes. New J. Phys. 2010;12:065002. doi: 10.1088/1367-2630/12/6/065002
  54. Lakhno V.D., Korshounova A.N. The modelling of selftrapped state formation in homogeneous polynucleotide chain. Nelin. Dinam. 2008;4(2):193–214. doi: 10.20537/nd0802007
  55. Menskii M.B. Decoherence and the theory of continuous quantum measurements. Phys. Usp. 1998;41:923–940. doi: 10.1070/PU1998v041n09ABEH000442
  56. Schlosshauer M., Quantum Decoherence. Physics Reports. 2019;831:1–57. doi: 10.1016/j.physrep.2019.10.001
  57. Zurek W.H. Pointer basis of quantum apparatus: Into what mixture does the wave packet collapse? Phys. Rev. D. 1981;24:1516–1525. doi: 10.1103/PhysRevD.24.1516
  58. Zurek W.H. Environment-induced superselection rules. Phys. Rev. D. 1982;26:1862–1880. doi: 10.1103/PhysRevD.26.1862
Table of Contents
Original Article
Syurakshin A.V., Lakhno V.D., Yushankhai V.Yu. Computer Simulation of Charge Transfer In a DNA Molecule within a Simple Model of an Open Quantum System. Ìàthematical biology and bioinformatics. 2024;19(1):212-231. doi: 10.17537/2024.19.212
(published in Russian)

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)
References

 
  Copyright IMPB RAS © 2005-2026