On the Calculations of the Exciton-Phonon Coupling Parameters in the Theory of Davydov Solitons

Kuprievich, V. A.

doi:10.1007/978-1-4757-9948-4_15

Cited by 8 publications

(7 citation statements)

References 5 publications

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“…which leads to stronger coupling of the amide I exciton (C = O group) to the hydrogen bond on the right (−C = O · · · H) as compared to the hydrogen bond on the left (O · · · H − N − C = O), namely, χ r > χ l [55], could effectively enhance the stability of solitons bouncing off massive barriers as created by the presence of external protein clamps acting on the protein α-helix. The dependence of the soliton stability on the direction of barrier impact, also shows that protein α-helices with anisotropic exciton-lattice coupling (ξ < 1) may then have a preferential direction for transmission of energy inside proteins.…”

Section: Effect Of Anisotropy Of the Exciton-lattice Coupling On Solimentioning

confidence: 99%

Quantum tunneling of Davydov solitons through massive barriers

Georgiev

Glazebrook

2019

Chaos, Solitons & Fractals

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Protein clamps provide the cell with effective mechanisms for sensing of environmental changes and triggering adaptations that maintain homeostasis. The general physical mechanism behind protein clamping action, however, is poorly understood. Here, we explore the Davydov model for quantum transport of amide I energy, which is self-trapped in soliton states that propagate along the protein α-helix spines and preserve their shape upon reflection from the α-helix ends. We study computationally whether the Davydov solitons are able to reflect from massive barriers that model the presence of external protein clamps acting on a portion of the α-helix, and characterize the range of barrier conditions for which the Davydov solitons are capable of tunneling through the barrier. The simulations showed that the variability of amino acid masses in proteins has a negligible effect on Davydov soliton dynamics, but a massive barrier that is a hundred times the mass of a single amino acid presents an obstacle for the soliton propagation. The greater width of Davydov solitons stabilizes the soliton upon reflection from such a massive barrier and increases the probability of tunneling through it, whereas the greater isotropy of the exciton-lattice coupling suppresses the tunneling efficiency by increasing the interaction time between the Davydov soliton and the barrier, thereby prolonging the tunneling time through the barrier and enhancing the probability for reflection from the latter. The results as presented, demonstrate the feasibility of Davydov solitons reflecting from or tunneling through massive barriers, and suggest a general physical mechanism underlying the action of protein clamps through local enhancement of an effective protein α-helix mass.

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Section: Effect Of Anisotropy Of the Exciton-lattice Coupling On Solimentioning

confidence: 99%

Quantum tunneling of Davydov solitons through massive barriers

Georgiev

Glazebrook

2019

Chaos, Solitons & Fractals

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“…According to these estimations, the value of this constant in hydrogen bonded macromolecular chains ranges between 30 pN and 60 pN [16,20]. However, there are such estimations of that parameter, performed by the ab initio calculations for the formamide dimmer, which suggests that its value is significantly lower [21,22,23]. This fact became by the motivation for some authors to define criteria to discriminate between the weak and the strong vibron-phonon coupling limits [11,24].…”

Section: Introductionmentioning

confidence: 99%

“…[16,20] However, there are such estimations of that parameter, performed by the ab initio calculations for the formamide dimmer, which suggest that its value is significantly lower. [21][22][23] This fact has become the motivation for some authors to define criteria to discriminate between the weak and the strong vibron-phonon coupling limits. [11,24] According to Ref.…”

Section: Introductionmentioning

confidence: 99%

The vibron dressing in α-helicoidal macromolecular chains

Čevizović¹,

Galović²,

Reshetnyak³

et al. 2013

Chinese Phys. B

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We present a study of the physical properties of the vibrational excitation in α-helicoidal macromolecular chains, caused by the interaction with acoustical and optical phonon modes. The influence of the temperature and the basic system parameters on the vibron dressing has been analyzed by employing the simple mean-field approach based on the variational extension of the Lang-Firsov unitary transformation. Applied approach predicts a region in system parameter space where one takes place an abrupt transition from partially dressed (light and mobile) to fully dressed (immobile) vibron states. We found that the boundary of this region depends on system temperature and type of bond among structural elements in the macromolecular chain.The authors are grateful to I. Bondarev, for valuable comments and discussion on possibility of coexistence two vibron states, mobile and immobile ones.

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“…As a matter of fact, they are not determined directly by measurement, but indirectly through a proposed theoretical model. Consequently, the corresponding estimation of their numerical values can vary from those that correspond to the conditions of weak interaction of excitons with the phonon subsystem, up to those that belong to strong coupling interaction limit [94][95][96][97][98]! In addition, MCs in living cells do not have the forms of pure 1D chains, but also they are neither classical two-dimensional (2D) nor threedimensional (3D) structures.…”

Section: : 200774mentioning

confidence: 99%

“…Similarly, in the case of the α-helix protein macromolecules, electron bandwidth is approximately a few eV, while the maximal energy of the acoustic phonons is approximately 17 meV [ 100 , 101 ]. As was mentioned above, the soliton formation can occur mainly due to the process of the self-trapping of an excess charge (photogenerated electron, or such charge that was created upon doping mechanism, for example), and the creation of polaron quasi-particles, which then can perform the role of charge carriers in the structure [ 94 , 95 ]. The soliton model can also be applied to the study of dynamics of electrons in macromolecular chains, in the presence of an external electric field [ 102 ].…”

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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On the Calculations of the Exciton-Phonon Coupling Parameters in the Theory of Davydov Solitons

Cited by 8 publications

References 5 publications

Quantum tunneling of Davydov solitons through massive barriers

Quantum tunneling of Davydov solitons through massive barriers

The vibron dressing in α-helicoidal macromolecular chains

A review on nonlinear DNA physics

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