Interchain coupling effects on large acoustic polaron in two parallel molecular chains

Čevizović, Dalibor; Ivić, Zoran; Pržulj, Željko; Tekić, Jasmina; Kapor, D.

doi:10.1016/j.chemphys.2013.09.005

Cited by 11 publications

(30 citation statements)

References 54 publications

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“…However, the most interesting aspect of these features is the superposition of planar charge oscillations with longitudinal complex wave patterns, as the latter cannot simultaneously appear with open states. Likewise, two regimes for charge spreading are apparent in our system, as strong and slight charge‐lattice couplings have been shown to display different behaviors for efficient polaron delocalization in single‐ and double‐stranded nonlinear chains . This otherwise proves the strong effect of charges that spread in DNA on its structural dynamics, as we remember that only the electronic part has initially been excited.…”

Section: Numerical Analysismentioning

confidence: 55%

“…Furthermore, the condition under which these polarons may be shared among coupled chains have been investigated in Ref. , and their robustness in such systems was proven. Importantly, quasiperiodic nonlinear trains of waves are obtained for the bending dynamics.…”

Section: Numerical Analysismentioning

confidence: 99%

“…Likewise, two regimes for charge spreading are apparent in our system, as strong and slight charge-lattice couplings have been shown to display different behaviors for efficient polaron delocalization in single-and double-stranded nonlinear chains. [28] This otherwise proves the strong effect of charges that spread in DNA on its structural dynamics, as we remember that only the electronic part has initially been excited. This also calls for new directions and proper biological implications for charge spreading in DNA, as key phenomena like DNA damage-repair as well as drug intercalation are still to be comprehended.…”

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confidence: 95%

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Discrete charge patterns in a Holstein‐SSH DNA lattice

Dang

Tabi

Fouda

et al. 2014

Int J of Quantum Chemistry

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DNA nonlinear charge transport is addressed in a combined Holstein-Su-Schrieffer-Heeger (HSSH) model. In the adiabatic approximation the dynamics of the system is shown to be governed by a modified discrete nonlinear Schr€ odinger (MDNLS) equation, where charge-lattice coupling parameters are obvious. Attention is paid to the effective coupling parameter, m 0 , between charge and internal molecular vibrations, which importantly influences the stability/instability features of the plane wave, solution to the MDNLS equation. Region of instability are remarkably reduced, therefore predicting that increasing m 0 could progressively quench charge transport. This is confirmed by numerical simulations on the generic HSSH model, where only the charge density is excited and drives the dynamics of the global system. Polarons, as well as longitudinal and transversal nonlinear waves, are obtained and the dependence of charge transport on DNA conformation is discussed. Accordingly, the longtime evolution of the found polarons is studied and we observe a progressive extinction of its temporal evolution as m 0 increases.

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Section: Numerical Analysismentioning

confidence: 55%

Section: Numerical Analysismentioning

confidence: 99%

mentioning

confidence: 95%

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Discrete charge patterns in a Holstein‐SSH DNA lattice

Dang

Tabi

Fouda

et al. 2014

Int J of Quantum Chemistry

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“…Apart from the solitons, certain aspects of the stable migration of electrons along biomolecules, some other mechanisms, can be found in the literature. Such are, for example, models based on continuous super-exchange theory that can provide a good basis for further research on electron migration on shorter segments of DNA [ 106 ].…”

Section: Long-distance Electron Transport Along Dna Macromolecular Chmentioning

confidence: 99%

A review on nonlinear DNA physics

et al. 2020

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The study and the investigation of structural and dynamical properties of complex systems have attracted considerable interest among scientists in general and physicists and biologists in particular. The present review paper represents a broad overview of the research performed over the nonlinear dynamics of DNA, devoted to some different aspects of DNA physics and including analytical, quantum and computational tools to understand nonlinear DNA physics. We review in detail the semi-discrete approximation within helicoidal Peyrard–Bishop model and show that localized modulated solitary waves, usually called breathers, can emerge and move along the DNA. Since living processes occur at submolecular level, we then discuss a quantum treatment to address the problem of how charge and energy are transported on DNA and how they may play an important role for the functioning of living cells. While this problem has attracted the attention of researchers for a long time, it is still poorly understood how charge and energy transport can occur at distances comparable to the size of macromolecules. Here, we review a theory based on the mechanism of ‘self-trapping’ of electrons due to their interaction with mechanical (thermal) oscillation of the DNA structure. We also describe recent computational models that have been developed to capture nonlinear mechanics of DNA in vitro and in vivo , possibly under topological constraints. Finally, we provide some conjectures on potential future directions for this field.

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“…In effect, amino acid inhomogeneity [2, 3], discreteness [4, 5], finite length of the α-spiral section [6], and other factors [7–10] are inherent in general to the structures containing carbon [11–13]. Particularly, average-electron structure and average-nuclear structure of the protein molecule were analysed in detail in article [14].…”

Section: Introductionmentioning

confidence: 99%

Current in the Protein Nanowires: Quantum Calculations of the Base States

Suprun¹,

Shmeleva²

2016

Nanoscale Res Lett

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It is known that synthesis of adenosine triphosphoric acid in mitochondrions may be only completed on the condition of transport of the electron pairs, which were created due to oxidation processes, to mitochondrions. As of today, many efforts were already taken in order to understand those processes that occur in the course of donor-acceptor electron transport between cellular organelles (that is, between various proteins and protein structures). However, the problem concerning the mechanisms of electron transport over these organelles still remains understudied. This paper is dedicated to the investigation of these same issues.It has been shown that regardless of the amino acid inhomogeneity of the primary structure, it is possible to apply a representation of the second quantization in respect of the protein molecule (hereinafter “numbers of filling representation”). Based on this representation, it has been established that the primary structure of the protein molecule is actually a semiconductor nanowire. In addition, at the same time, its conduction band, into which an electron is injected as the result of donor-acceptor processes, consists of five sub-bands. Three of these sub-bands have normal dispersion laws, while the rest two sub-bands have abnormal dispersion laws (reverse laws). Test calculation of the current density was made under the conditions of the complete absence of the factors, which may be interpreted as external fields. It has been shown that under such conditions, current density is exactly equal to zero. This is the evidence of correctness of the predictive model of the conductivity band of the primary structure of the protein molecule (protein nanowire). At the same time, it makes it possible to apply the obtained results in respect of the actual situation, where factors, which may be interpreted as external fields, exist.

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Interchain coupling effects on large acoustic polaron in two parallel molecular chains

Cited by 11 publications

References 54 publications

Discrete charge patterns in a Holstein‐SSH DNA lattice

Discrete charge patterns in a Holstein‐SSH DNA lattice

A review on nonlinear DNA physics

Current in the Protein Nanowires: Quantum Calculations of the Base States

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