Two-polaron energy diffusion in a 1D lattice of hydrogen bonded peptide units

Pouthier, Vincent

doi:10.1016/j.physd.2007.08.007

Cited by 7 publications

(5 citation statements)

References 33 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Then, a generalization of the present work will be presented to characterize the vibrational energy flow when two vibrons are excited. In that case, the intramolecular anharmonicity of each amide-I mode acts as a nonlinear source and it favors the occurrence of specific states called two-vibron bound states [4,42]. These states exhibit an experimental signature within nonlinear pump-probe spectroscopy [43] and they are expected to play a key role for energy storage in proteins due to their formal resemblance to classical breathers.…”

Section: Discussionmentioning

confidence: 99%

“…In a recent series of papers, a small polaron approach has been used to describe how narrow band excitons may promote vibrational energy flow in a lattice of H-bonded peptide units [1][2][3][4][5]. These works were based on the seminal model introduced by Davydov and Kisluka [6], and later by Scott [7], to describe bioenergy transport in α-helices in terms of a soliton mechanism.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Narrow band exciton coupled with acoustical anharmonic phonons: application to the vibrational energy flow in a lattice of H-bonded peptide units

Pouthier

2009

J. Phys.: Condens. Matter

Self Cite

View full text Add to dashboard Cite

A time-convolutionless master equation is established for describing the transport properties of amide-I vibrons coupled with acoustic phonons in a lattice of H-bonded peptide units. Within the non-adiabatic weak coupling limit, it is shown that the vibron dynamics strongly depends on the nature of the phonons and two distinct mechanisms have been identified. Harmonic phonons, which support spatial correlations over an infinite length scale, induce a fast dephasing-rephasing mechanism in the short time limit. Consequently, the vibron keeps its wavelike nature and a coherent vibrational energy flow takes place whatever the temperature. By contrast, anharmonic phonons carry spatial correlations over a finite length scale, only. As a result, the rephasing process no longer compensates the dephasing mechanism so that dephasing-limited band motion occurs. It gives rise to the incoherent diffusion of the vibron characterized by a diffusion coefficient whose temperature dependence scales as 1/T(α). In the weak anharmonicity limit, the exponent α is about 2. It becomes smaller than unity in the strong anharmonicity limit, indicating that the diffusion coefficient behaves as a slowly decaying function of the temperature.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Narrow band exciton coupled with acoustical anharmonic phonons: application to the vibrational energy flow in a lattice of H-bonded peptide units

Pouthier

2009

J. Phys.: Condens. Matter

Self Cite

View full text Add to dashboard Cite

show abstract

“…These localized non-linear oscillating breather solutions play an important role in the transport properties of hydrogen-bonded chains [36][37][38][39][40][41][42][43]. The computational tools for studying DB properties are confined to the case of a finite lattice size.…”

Section: Localization Of Energymentioning

confidence: 99%

“…Zolotaryuk et al reported that a diatomic chain of heavy ions coupled by hydrogen bonds admits discrete breather solutions in the anticontinuous limit [36]. Since the study of breather-type excitations is important for the theory of protonic conductivity based on soliton phenomenology [37][38][39][40][41][42][43], in this paper we investigate the localization of the charge transfer in one-dimensional hydrogen-bonded (HB) chains with the nearest neighbor interactions of protons. The paper is organized as follows: In Section 2, we describe the model and derive the discrete non-linear equation of motion with the aid of the Holstein-Primakoff transformation combined with Glauber's coherent state representation.…”

Section: Introductionmentioning

confidence: 99%

Nano breathers and molecular dynamics simulations in hydrogen-bonded chains

Kavitha¹,

Muniyappan²,

Prabhu³

et al. 2012

J Biol Phys

View full text Add to dashboard Cite

Non-linear localization phenomena in biological lattices have attracted a steadily growing interest and their existence has been predicted in a wide range of physical settings. We investigate the non-linear proton dynamics of a hydrogen-bonded chain in a semiclassical limit using the coherent state method combined with a Holstein-Primakoff bosonic representation. We demonstrate that even a weak inherent discreteness in the hydrogenbonded (HB) chain may drastically modify the dynamics of the non-linear system, leading to instabilities that have no analog in the continuum limit. We suggest a possible localization mechanism of polarization oscillations of protons in a hydrogen-bonded chain through modulational instability analysis. This mechanism arises due to the neighboring protonproton interaction and coherent tunneling of protons along hydrogen bonds and/or around heavy atoms. We present a detailed analysis of modulational instability, and highlight the role of the interaction strength of neighboring protons in the process of bioenergy localization. We perform molecular dynamics simulations and demonstrate the existence of nanoscale discrete breather (DB) modes in the hydrogen-bonded chain. These highly

show abstract

“…In a series of publications [53,[62][63][64][65][66][67][68], V. Pouthier et al have studied the bio-energy transport in a lattice of H-bonded peptide units using the framework of Davydov soliton mechanism. The idea is that the energy is transferred through phonon dressed vibrational excitons known as vibrons.…”

Section: Introductionmentioning

confidence: 99%

Bio-energy Transport as a Phonon Dressed Vibrational Exciton in Protein Molecules

De Silva,

Bolt

2019

Preprint

View full text Add to dashboard Cite

Following the ideas of Davydov's soliton theory, we study the bio-energy transport in protein molecules. By using a quantum Brownian motion model for a phonon dressed vibrational exciton, we calculate the time-dependence on the mean square distance, diffusion coefficient, and energy of the vibrational exciton. We find the time-dependence by solving the quantum Langevin equation and find oscillatory behaviors due to the super-diffusive non-ohmic dissipation. We find that the vibrational exciton gains an overall energy due to the coupling to the phonon bath; it also dissipates its energy to the environment as it propagates. The amount of energy gain and the oscillatory features depend on both temperature and the phonon-vibron coupling.

show abstract

Two-polaron energy diffusion in a 1D lattice of hydrogen bonded peptide units

Cited by 7 publications

References 33 publications

Narrow band exciton coupled with acoustical anharmonic phonons: application to the vibrational energy flow in a lattice of H-bonded peptide units

Narrow band exciton coupled with acoustical anharmonic phonons: application to the vibrational energy flow in a lattice of H-bonded peptide units

Nano breathers and molecular dynamics simulations in hydrogen-bonded chains

Bio-energy Transport as a Phonon Dressed Vibrational Exciton in Protein Molecules

Contact Info

Product

Resources

About