Charge transport properties of a twisted DNA molecule: A renormalization approach

Almeida, M.L. de; Ourique, G.S.; Fulco, U. L.; Albuquerque, E.L.; Moura, F. A. B. F. de; Lyra, M. L.

doi:10.1016/j.chemphys.2016.05.020

Cited by 9 publications

(7 citation statements)

References 45 publications

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“…The DNA molecules can be modelled as a double-strand ladder of coarse grains, which has been transformed into a single string of base pairs with dangling backbones, known as the fishbone model, and in turn, it was reduced to a single chain after a two-step renormalization at each base pair [132]. This chain has been used for the study of electronic transport in Fibonacci [133,134] and asymmetric [135] DNA molecules, helical structures [136][137][138], thermoelectric devices [139], diluted random base-pair segments [140], and Hubbard systems [141]. An additional renormalization process can be carried out along organic molecular wires to calculate the density of states [142,143], Lyapunov coefficient [144,145], transmittance [142][143][144][145], and magnetoconductance [146].…”

Section: Multidimensional Aperiodic Latticesmentioning

confidence: 99%

Real Space Theory for Electron and Phonon Transport in Aperiodic Lattices via Renormalization

Sánchez

Wang

2020

Symmetry

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Structural defects are inherent in solids at a finite temperature, because they diminish free energies by growing entropy. The arrangement of these defects may display long-range orders, as occurring in quasicrystals, whose hidden structural symmetry could greatly modify the transport of excitations. Moreover, the presence of such defects breaks the translational symmetry and collapses the reciprocal lattice, which has been a standard technique in solid-state physics. An alternative to address such a structural disorder is the real space theory. Nonetheless, solving 1023 coupled Schrödinger equations requires unavailable yottabytes (YB) of memory just for recording the atomic positions. In contrast, the real-space renormalization method (RSRM) uses an iterative procedure with a small number of effective sites in each step, and exponentially lessens the degrees of freedom, but keeps their participation in the final results. In this article, we review aperiodic atomic arrangements with hierarchical symmetry investigated by means of RSRM, as well as their consequences in measurable physical properties, such as electrical and thermal conductivities.

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Section: Multidimensional Aperiodic Latticesmentioning

confidence: 99%

Real Space Theory for Electron and Phonon Transport in Aperiodic Lattices via Renormalization

Sánchez

Wang

2020

Symmetry

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“…In the fist step, the Watson–Crick bps present in the triplet codon shown in Figure 3 a are renormalized to obtain the tight-binding model depicted in Figure 3 b. The renormalized on-site energies and transfer integrals are respectively given by [ 36 , 37 ]:

, which describes the charge carrier hopping from one base to its complementary base within the same bp [ 38 ], and:

are the effective transfer integrals between the bps and the sugar-phosphate groups, where

is the glycosidic bond transfer integral, E is the charge carrier energy,

measure the sugar-phosphate groups’ on-site energies, and

are the on-site energies of the corresponding nucleobases. In general,

will depend on the nature of the neighboring base, as well as the presence of water molecules and/or counterions attached to the backbone.…”

Section: Dna Model Hamiltonianmentioning

confidence: 99%

Base-Pairs’ Correlated Oscillation Effects on the Charge Transfer in Double-Helix B-DNA Molecules

Maciá

2020

Materials

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By introducing a suitable renormalization process, the charge carrier and phonon dynamics of a double-stranded helical DNA molecule are expressed in terms of an effective Hamiltonian describing a linear chain, where the renormalized transfer integrals explicitly depend on the relative orientations of the Watson–Crick base pairs, and the renormalized on-site energies are related to the electronic parameters of consecutive base pairs along the helix axis, as well as to the low-frequency phonons’ dispersion relation. The existence of synchronized collective oscillations enhancing the π-π orbital overlapping among different base pairs is disclosed from the study of the obtained analytical dynamical equations. The role of these phonon-correlated, long-range oscillation effects on the charge transfer properties of double-stranded DNA homopolymers is discussed in terms of the resulting band structure.

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“…Отметим, что теоретические и экспериментальные исследования различных модификаций ДНК, направленные на изучение свойств транспорта зарядов, развиваются в последнее время очень активно. Изучаются детали механизмов взаимодействия электронов с возмущениями цепочки нуклеотидов [23][24][25], рассчитываются вольт-амперные характеристики молекулы ДНК [26,27], анализируются способы управления характеристиками транспорта зарядов [28,29], исследуется влияние внешней среды [30], рассматриваются как перспективные сложные модификации, включающие ДНК [31][32][33][34][35][36], описываются различные прикладные возможности [37]. В настоящей же работе изучается взаимодействие электрона с мобильным бризером, возбужденным в небольшой группе смежных нуклеотидных пар у одного из закрепленных концов молекулы за счет начальных смещений нуклеотидов или возмущений их скорости.…”

Section: Introductionunclassified

Trapping and transport of charges in DNA by mobile discrete breathers

Chetverikov¹,

Sergeev²,

Лахно³

2018

Math.Biol.Bioinf.

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Аннотация. С использованием модели Пейрарда-Бишопа-Доксуа-Холстейна проведено численное моделирование захвата и транспорта заряда (электрона или дырки) в молекуле ДНК мобильными дискретными бризерами, возбуждаемыми начальными возмущениями скоростей или координат смежных нуклеотидных пар, дислоцированных около закрепленного конца молекулы. Показано, что эффективное образование стабильной квазичастицы «мобильный дискретный бризер + электрон» достигается при возмущении нескольких нуклеотидных пар, расположенных на конце молекулы. Бризеры могут быть возбуждены при возмущениях координат и скорости частиц как направленных к оси, так и от оси молекулы. Волновая функция электрона должна быть вначале локализована в области возмущения молекулы. Установлено, что метастабильная квазичастица может перемещаться на дистанцию до 200 межпарных расстояний. Описанный механизм транспорта заряженной частицы не требует наложения внешнего электрического поля и может рассматриваться как альтернативный поляронному механизму.

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Charge transport properties of a twisted DNA molecule: A renormalization approach

Cited by 9 publications

References 45 publications

Real Space Theory for Electron and Phonon Transport in Aperiodic Lattices via Renormalization

Real Space Theory for Electron and Phonon Transport in Aperiodic Lattices via Renormalization

Base-Pairs’ Correlated Oscillation Effects on the Charge Transfer in Double-Helix B-DNA Molecules

Trapping and transport of charges in DNA by mobile discrete breathers

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