Список литературы
- Vinogradov G.A., Lakhno V.D. On The Thermalization of One-Dimensional Lattices. I. Microcanonical Ensemble. Mathematical Biology and Bioinformatics. 2024;19(1):248-260. doi: 10.17537/2024.19.248
- Andersen H.C. Molecular dynamics simulations at constant pressure and/or temperature. J. Chem. Phys. 1980;72(4):2384-2393. doi: 10.1063/1.439486
- Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F., DiNola A., Haak J.R. Molecular-Dynamics with Coupling to an External Bath. J. Chem. Phys. 1984;81(8):3684-3690. doi: 10.1063/1.448118
- Bussi G., Donadio D., Parrinello M. Canonical sampling through velocity rescaling. J. Chem. Phys. 2007;126(1). Article No. 014101. doi: 10.1063/1.2408420
- Nose S . A unified formulation of the constant temperature molecular-dynamics methods. J. Chem. Phys. 1984;81(1):511-519. doi: 10.1063/1.447334
- Hoover W.G. Canonical dynamics: Equilibrium phase-space distributions. Phys. Rev. A. 1985;31(3):1695-1697. doi: 10.1103/PhysRevA.31.1695
- Hoover W.G., Holian B.L. Kinetic moments method for the canonical ensemble distribution. Phys. Lett. A. 1996;211(5):253-257. doi: 10.1016/0375-9601(95)00973-6
- Martyna G.J., Klein M.L., Tuckerman M. Nose-Hoover chains: The canonical ensemble via continuous dynamics. J. Chem. Phys. 1992;97(4):2635-2643. doi: 10.1063/1.463940
- Rapaport D.C. The Art of Molecular Dynamics Simulation. Cambridge University Press, 2011. doi: 10.1017/CBO9780511816581
- Hunenberger P.H. Thermostat Algorithms for Molecular Dynamics Simulations. Adv. Polym. Sci. 2005;173:105-149. doi: 10.1007/b99427
- Klages R. Microscopic chaos and transport in thermostated dynamical systems. arXiv:nlin/0309069v1. doi: 10.48550/arXiv.nlin/0309069
- Lemak A.S., Balabaev N.K. A comparison between collisional dynamics and brownian dynamics. Mol. Simul. 1995;15:223-231. doi: 10.1080/08927029508022336
- Lemak A.S., Balabaev N.K. Molecular dynamics simulation of a polymer chain in solution by collisional dynamics method. J. Comput. Chem. 1996;17(15):1685-1695. doi: 10.1002/(SICI)1096-987X(19961130)17:15<1685::AID-JCC1>3.0.CO;2-L
- Helfand E. Numerical Integration of Stochastic Differential Equations. The Bell System Technical Journal 1979;58(10):2289-2299. doi: 10.1002/j.1538-7305.1979.tb02967.x
- Greenside H.S., Helfand E. Numerical Integration of Stochastic Differential Equations - II. The Bell System Technical Journal 1981;60:1927-1940. doi: 10.1002/j.1538-7305.1981.tb00303.x
- 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. Article No. 024414. doi: 10.1103/PhysRevE.106.024414
- Livi R., Pettini M., Ruffo S., Sparpaglione M., Vulpiani A. Equipartition threshold in nonlinear large Hamiltonian systems: The Fermi-Pasta-Ulam model. Phys. Rev. A. 1985;31(2):1039-1045. doi: 10.1103/PhysRevA.31.1039
- Ganapa S., Apte A., Dhar A. Thermalization of local observables in the α-FPUT chain. J. Stat. Phys. 2020;180:1010-1030. doi: 10.1007/s10955-020-02576-2
- Schmid H., Succi S., Ruffo S. Nonlinearity accelerates the thermalization of the quartic FPUT model with stochastic baths. J. Stat. Mech. 2021;2021(5). Article No. 053205. doi: 10.1088/1742-5468/abfcbc
- Dauxois T., Peyrard M., Bishop A.R. Entropy-driven DNA denaturation. Phys. Rev. E. 1993;47:R44-R47. doi: 10.1103/PhysRevE.47.R44
- Campa A., Giansanti A. Experimental tests of the Peyrard-Bishop model applied to the melting of very short DNA chains. Phys. Rev. E. 1998;58:3585-3588. doi: 10.1103/PhysRevE.58.3585
- Campa A., Giansanti A. Melting of DNA oligomers: dynamical models and comparison with experimental results. J. Biol. Phys. 1999;24:141-155. doi: 10.1023/A:1005166612156
- Cule D., Hwa T. Denaturation of Heterogeneous DNA. Phys. Rev. Lett. 1997;79:2375-2378. doi: 10.1103/PhysRevLett.79.2375
- Peyrard M., Bishop A.R. Statistical mechanics of a nonlinear model for DNA denaturation. Phys. Rev. Lett. 1989;62:2755-2758. doi: 10.1103/PhysRevLett.62.2755
- Peyrard M. Using DNA to probe nonlinear localized excitations? EPL. 1998;44:271. doi: 10.1209/epl/i1998-00469-9
- Maniadis P., Alexandrov B.S., Bishop A.R., Rasmussen K.Ø. Feigenbaum cascade of discrete breathers in a model of DNA. Phys. Rev. E. 2011;83. Article No. 011904. doi: 10.1103/PhysRevE.83.011904
- Ambjornsson T., Banik S.K., Krichevsky O., Metzler R. Breathing dynamics in heteropolymer DNA. Biophys. J. 2007;92:2674-2684. doi: 10.1529/biophysj.106.095935
- Diaz E., Lima R.P.A., Dominguez-Adame F. Bloch-like oscillations in the Peyrard-Bishop-Holstein model. Phys. Rev. B. 2008;78. Article No. 134303. doi: 10.1103/PhysRevB.78.134303
- Komineas S., Kalosakas G., Bishop A.R. Effects of intrinsic base-pair fluctuations on charge transport in DNA. Phys. Rev. E. 2002;65. Article No. 061905. doi: 10.1103/PhysRevE.65.061905
- Landau L.D. Lifshits E.M. Mechanics . Butterworth-Heinemann, 1976. (Course of Theoretical Physics, V. 1).
- Mondal S., Mukherjee S., Bagchi B. Melting and Bubble Formation in a Double-Stranded DNA: Microscopic Aspects of Early Base-Pair Opening Events and the Role of Water. J. Phys. Chem. B. 2024;128(9):2076-2086. doi: 10.1021/acs.jpcb.3c06519
- Dammak H., Chalopin Y., Laroche M., Hayoun M., Greffet J.-J. Quantum Thermal Bath for Molecular Dynamics Simulation. Phys. Rev. Lett. 2009;103. Article No. 190601. doi: 10.1103/PhysRevLett.103.190601
- Tsyan' Syue-Sen'. Fizicheskaya mekhanika . Moscow: Mir, 1965. P. 67-68.
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