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Том 14   Выпуск 1   Год 2019
Никитюк А.С.1, Корзникова Е.А.2, Дмитриев С.В.2,3, Наймарк О.Б.1

Бризеры в молекуле ДНК и динамика клетки

Математическая биология и биоинформатика. 2019;14(1):137-149.

doi: 10.17537/2019.14.137.

Список литературы

 

  1. Yakushevich L.V. Nonlinear physics of DNA. Weinheim: WILEY-VCH Verlag GmbH & Co. KGaA.; 2004. 205 p. doi: 10.1002/3527603700
  2. Naimark O.B. Structural-scaling transitions and localized distortion modes in the DNA double helix. Phys. Mesomech. 2007;10(1–2):33–45. doi: 10.1016/j.physme.2007.06.004
  3. Dauxois T., Peyrard M., Bishop A.R. Entropy-driven DNA denaturation. Phys. Rev. E. 1993;47(1):44–47. doi: 10.1103/PhysRevE.47.R44
  4. Campa A. Bubble propagation in a helicoidal molecular chain. Phys. Rev. E. 2001;63(2):021901. doi: 10.1103/PhysRevE.63.021901
  5. Alvarez A., Romero F.R., Archilla J.F.R., Cuevas J., Larsen P.V. Breather tapping and breather transmission in a DNA model with an interface. Eur. Phys. J. B. 2006;51(1):119–130. doi: 10.1140/epjb/e2006-00191-0
  6. Yakushevich L.V., Grinevich A.A., Ryasik A.A. Simulation of a kink movement in homogeneous and heterogeneous DNA sequences taking into account the dissipation. Russ. J. Numer. Anal. Math. Modelling. 2014;29(3):197–204. doi: 10.1515/rnam-2014-0015
  7. Zdravkovic S., Sataric M., Tuszynskic J. Biophysical Implications of the Peyrard–Bishop–Dauxois Model of DNA Dynamics. J. Comput. Theor. Nanosci. 2004;1(2):169–179. doi: 10.1166/jctn.2004.013
  8. Lakhno V.D. DNA nanobioelectronics. International Journal of Quantum Chemistry. 2008;108(11):1970–1981. doi: 10.1002/qua.21717
  9. Lakhno V.D. Soliton-like solutions and electron transfer in DNA. Journal of Biological Physics. 2000;26(2):133–147. doi: 10.1023/A:1005275211233
  10. Lakhno V.D., Fialko N.S. Hole mobility in a homogeneous nucleotide chain. JETP Letters. 2003;78(5):336–338. doi: 10.1134/1.1625737
  11. Chetverikov A.P., Sergeev K.S., Lakhno V.D. Trapping and transport of charges in DNA by mobile discrete breathers. Mathematical Biology and Bioinformatics. 2018;13(1):1–12. doi: 10.17537/2018.13.1
  12. Lakhno V.D., Chetverikov A.P. Excitation of bubbles and breathers in DNA and their interaction with the charge carriers. Mathematical Biology and Bioinformatics. 2014;9(1):4–19. doi: 10.17537/2014.9.4
  13. Chetverikov A.P., Sergeev K.S., Lakhno V.D. The excitation of mobile discrete breathers in DNA by initial disturbance of displacements or velocities of a few of adjacent nucleotide pairs. Mathematical Biology and Bioinformatics. 2017;12(2):375–384. doi: 10.17537/2017.12.375
  14. Shigaev A.S., Ponomarev O.A., Lakhno V.D. Theoretical and experimental investigations of DNA open states. Mathematical Biology and Bioinformatics. 2018;13(Suppl.):t162–t267. doi: 10.17537/2018.13.t162
  15. Velarde M.G., Chetverikov A.P., Ebeling W., Dmitriev S.V., Lakhno V.D. From solitons to discrete breathers. European Physical Journal B. 2016;89(10):233. doi: 10.1140/epjb/e2016-70489-3
  16. Velarde M.G., Chetverikov A.P., Ebeling W., Dmitriev S.V., Lakhno V.D. Wave motions along lattices with nonlinear on-site and inter-site potentials. Cooperation and/or competition leading to lattice Solitons and/or discrete breathers. Proceedings of the Estonian Academy of Sciences. 2015;64(3):396–404. doi: 10.3176/proc.2015.3S.10
  17. Dmitriev S.V., Korznikova E.A., Baimova Y.A., Velarde M.G. Discrete breathers in crystals. Physics-Uspekhi. 2016;59(5):446–461. doi: 10.3367/UFNe.2016.02.037729
  18. Sulaiman A., Zen F.P., Alatas H., Handoko L.T. Dynamics of DNA breathing in the Peyrard–Bishop model with damping and external force. Physica D. 2012;241:1640–1647. doi: 10.1016/j.physd.2012.06.011
  19. Ikot A.N., Akpabio L.E., Akpan I.O., Umo M.I., Ituen E.E. Quantum damped mechanical oscillator. International Journal of Optics. 2010;1(5–6):1–6. doi: 10.1155/2010/275910
  20. Peyrard M. Nonlinear dynamics and statistical physics of DNA. Nonlinearity. 2004;17(2):1–40. doi: 10.1088/0951-7715/17/2/R01
  21. Barbi M., Cocco S., Peyrard M. Helicoidal model for DNA opening. Physics Letters A. 1999;253:358–369. doi: 10.1016/S0375-9601(99)00059-6
  22. Barbi M., Lepri S., Peyrard M., Theodorakopoulos N. Thermal denaturation of a helicoidal DNA model. Physical Review E. 2003;68(6):061909. doi: 10.1103/PhysRevE.68.061909
  23. Argwal J., Henning D. Breather solutions of a nonlinear DNA model including a longitudinal degree of freedom. Physica A. 2003;323:519–533. doi: 10.1016/S0378-4371(02)02028-9
  24. Klevecz R.R., Bolen J., Forrest G., Murray D.B. A genomewide oscillation in transcription gates DNA replication and cell cycle. Proc. Natl. Acad. Sci. 2004;101(5):1200–1205. doi: 10.1073/pnas.0306490101
  25. Yoshikawa K. Field hypothesis on the self-regulation of gene expression. J. Biol. Phys. 2002;28(4):701–712. doi: 10.1023/A:1021251125101
  26. Huang S., Eishier G., Bar-Yam Y., Ingber D.E. Cell Fates as High-Dimensional Attractor States of a Complex Gene Regulatory Network. Phys. Rev. Lett. 2005;94:128701–128705. doi: 10.1103/PhysRevLett.94.128701
  27. Goldberg A., Allis C.D., Bernstein E. Epigenetics: A Landscape Takes Shape. Cell. 2007;128(4):635–638. doi: 10.1016/j.cell.2007.02.006
  28. Tsuchiya M., Giuliani A., Hashimoto M., Erenpreisa J., Yoshikawa K. Emergent Self-Organized Criticality in gene expression dynamics: Temporal development of global phase transition revealed in a cancer cell line. PLOS ONE. 2015;11:1–33. doi: 10.1371/journal.pone.0128565
  29. Tsuchiya M., Hashimoto M., Takenaka Y., Motoike I.N., Yoshikawa K. Global genetic response in a cancer cell: Self-organized coherent expression dynamics. PLOS ONE. 2014;9:1–33. doi: 10.1371/journal.pone.0097411
  30. Tychinsky V. P., Kretushev A.V., Klemyashov I.V., Vyshenskaya T.V., Shtil A.A., Zatsepina O.V. Coherent phase microscopy, a novel approach to study the physiological state of the nucleolus. Doklady Biochemistry and Biophysics. 2005;405:432–436. doi: 10.1007/s10628-005-0133-4
  31. Lyapunova E., Nikituk A., Bayandin Y., Naimark O., Rianna C., Radmacher M. Passive microrheology of normal and cancer cells after ML7 treatment by atomic force microscopy. In: AIP Conference Proceedings “International Conference on Physics of Cancer: Interdisciplinary Problems and Clinical Applications (PC’16)”. 2016;1760(1):020046. doi: 10.1063/1.4960265
  32. Popescu G. Quantitative Phase Imaging of Cells and Tissues. McGraw-Hill biophotonics: McGraw-Hill; 2011. 362 p.
  33. Martinez-Torres C., Berguiga L., Streppa L., Boyer-Provera E., Schaeffer L., Elezgaray J., Arneodo A., Argoul F. Diffraction phase microscopy: retrieving phase contours on living cells with a wavelet-based space-scale analysis. Journal of Biomedical Optics. 2014;19(3):8–19. doi: 10.1117/1.JBO.19.3.036007
  34. Gerasimova E., Audit B., Roux S.-G., Khalil A., Argoul F., Naimark O., Arneodo A. Multifractal analysis of dynamic infrared imaging of breast cancer. Europhysics Letters. 2013;104:64001. doi: 10.1209/0295-5075/104/68001
  35. Gerasimova E., Audit B., Roux S.-G., Khalil A., Gileva O., Argoul F., Naimark O., Arneodo A. Wavelet-based multifractal analysis of dynamic infrared thermograms to assist in early breast cancer diagnosis. Frontiers in Physiology. 2014;5:176. doi: 10.3389/fphys.2014.00176
Содержание
Оригинальная статья
Мат. биол. и биоинф.
2019;14(1):137-149
doi: 10.17537/2019.14.137
опубликована на англ. яз.

Аннотация (англ.)
Аннотация (рус.)
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