Trapping and transport of charges in DNA by mobile discrete breathers

Chetverikov, A. P.; Sergeev, K. S.; Лахно, В. Д.

doi:10.17537/2018.13.t59

Cited by 8 publications

(4 citation statements)

References 30 publications

(48 reference statements)

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“…Мы используем стандартную модель ПБДХ, в которой эволюция возмущений в цепочке нуклеотидных пар описывается классическими уравнениями движения под действием всех учитываемых в рассматриваемой задаче сил, важных для данного механизма транспорта, но динамика электрона рассматривается как эволюция волновой функции частицы, связанной с цепочкой нуклеотидов [13][14][15][16][17]. Уравнения модели выглядят следующим образом:…”

Section: математическая модель пейрарда-бишопа-доксуа-холстейна (пбдхunclassified

“…Исследования фокусируются на выявлении особенностей механизмов взаимодействия электронов с молекулой ДНК [6][7][8], расчетах вольтамперных характеристик [9][10], выяснении возможностей управления процессом переноса зарядов [11], анализе различных перспективных схем организации транспорта заряженных частиц [12]. Одним из возможных механизмов транспорта заряженной частицы (электрона) вдоль молекулы ДНК является захват заряженной частицы в потенциальную яму сформированного тем или иным способом мобильного дискретного бризера [1][2][3][4][5][6][7][8][9][10][11][12][13][14]…”

Section: Introductionunclassified

See 1 more Smart Citation

Evolution of electron energy under trapping by mobile discrete breathers in DNA with fixed ends

Лахно¹,

Sergeev²,

Chetverikov³

2018

Proceedings of the International Conference "Mathematical Biology and Bioinformatics"

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Section: математическая модель пейрарда-бишопа-доксуа-холстейна (пбдхunclassified

Section: Introductionunclassified

Evolution of electron energy under trapping by mobile discrete breathers in DNA with fixed ends

Лахно¹,

Sergeev²,

Chetverikov³

2018

Proceedings of the International Conference "Mathematical Biology and Bioinformatics"

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“…Using ab initio simulations, the presence of DBs in strained graphene and graphane has been confirmed [36,37]. With the help of molecular dynamics method DBs have been studied in the ionic crystals [38][39][40], lattices with pair-wise potentials [41,42], crystals with covalent bonding [43,44], metals [45][46][47][48][49][50][51], intermetallic compounds [52][53][54][55], carbon and hydrocarbon nanomaterials [56][57][58][59][60][61][62][63][64][65][66][67][68], h-BN [69], and DNA [70][71][72][73].…”

Section: Introductionmentioning

confidence: 97%

Effect of discrete breathers on macroscopic properties of the Fermi-Pasta-Ulam chain

Korznikova,

Morkina,

Singh

et al. 2019

Preprint

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For a number of crystals the existence of spatially localized nonlinear vibrational modes, called discrete breathers (DBs), has been demonstrated using molecular dynamics and in a few cases the first-principle simulations. High-resolution imaging of DBs is a challenging task due to their relatively short lifetime ranging typically from 10 to 10 3 atomic oscillation periods (1 to 100 ps). Another way to prove that DBs exist consists in evaluation of their effect on macroscopic properties of crystals. In this paper, we study the effect of DBs on macroscopic properties of the Fermi-Pasta-Ulam chain with symmetric and asymmetric potentials. The specific heat, thermal expansion (stress), and Young's modulus are monitored during the development of modulational instability of the zone boundary mode. The instability results in the formation of chaotic DBs followed by the transition to thermal equilibrium when DBs disappear due to energy radiation in the form of small-amplitude phonons. Time evolution of the macroscopic properties during this transition is monitored. It is found that DBs reduce the specific heat for all the considered chain parameters. They increase the thermal expansion when the potential is asymmetric and, as expected, thermal expansion is not observed in the case of symmetric potential. The Young's modulus in the presence of DBs is smaller than in thermal equilibrium for the symmetric potential and for the potential with a small asymmetry, but it is larger than in thermal equilibrium for the potential with greater asymmetry.

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“…[39,40]. Using molecular dynamics, DBs have been found in monoatomic Morse crystals [41,42], covalent crystals Si, Ge and diamond [43,44], pure metals [45][46][47][48][49][50], ordered alloys [51][52][53][54], carbon and hydrocarbon nanomaterials [55][56][57][58][59][60][61][62][63][64][65][66][67], boron nitride [68], and proteins [69][70][71][72]. Essential limitation of any MD model is the choice of the interatomic potentials which largely determine the reliability of the obtained results [66].…”

Section: Introductionmentioning

confidence: 99%

Effect of discrete breathers on the specific heat of a nonlinear chain

Singh,

Morkina,

Korznikova

et al. 2019

Preprint

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Defect-free crystal lattices can accommodate spatially localized, high amplitude atomic vibrations called either discrete breathers (DBs) or intrinsic localized modes (ILMs). This has been explored by a number of molecular dynamics studies and, in few cases, by the first-principles calculations. A number of experimental measurements of crystal vibrational spectra was performed aiming to prove the existence of DBs in thermal equilibrium at elevated temperature. However, the interpretation of these experimental results is still debated. Direct high-resolution imaging of DBs in crystals is hardly possible due to their nanometer size and short lifetime. An alternative way to substantiate the existence of DBs is to evaluate their impact on the measurable macroscopic properties of crystals and validate such prediction. One of such properties is specific heat. In fact, the measurements of heat capacity was done for alpha-uranium by Manley and co-workers in conditions where the presence of DBs was expected. In the present study, employing a one-dimensional nonlinear lattice with an on-site potential, we analyze the effect of DBs on its specific heat. In the most transparent way, this can be done by monitoring the chain temperature in a non-equilibrium process, at the emergence of modulational instability, with total energy of the chain being conserved. For the onsite potential of hard-type (soft-type) anharmonicity, the instability of q = π mode (q = 0 mode) results in the appearance of long-living DBs that gradually dissipate their energy and eventually the system approaches thermal equilibrium with spatially uniform and temporally constant temperature. The variation of specific heat at constant volume is evaluated during this relaxation process. It is concluded that DBs affect specific heat of the nonlinear chain and for the case of hard-type (softtype) anharmonicity they reduce (increase) the specific heat.

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Trapping and transport of charges in DNA by mobile discrete breathers

Cited by 8 publications

References 30 publications

Evolution of electron energy under trapping by mobile discrete breathers in DNA with fixed ends

Evolution of electron energy under trapping by mobile discrete breathers in DNA with fixed ends

Effect of discrete breathers on macroscopic properties of the Fermi-Pasta-Ulam chain

Effect of discrete breathers on the specific heat of a nonlinear chain

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