Energy transfer to the phonons of a macromolecule through light pumping

Faraji, Elham; Franzosi, Roberto; Mancini, Stefano; Pettini, Marco

doi:10.1038/s41598-021-85856-5

Cited by 5 publications

(4 citation statements)

References 27 publications

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“…Moreover, the sequence of probabilities of electron jumping from one site to the next one depends on the specific sequence of nucleotides. In so doing, a richer phenomenology is found with respect to a similar model recently investigated [ 20 ]. Instead of observing the propagation of a standard Davydov electro-soliton, depending on the initial excitation energy, we observed localized periodic motions of the electrons—giving rise to a narrow frequency spectrum of the electron current—or, depending on the initial excitation site, to more extended motions associated with a broad noisy frequency spectrum.…”

Section: Discussionmentioning

confidence: 89%

“…As shown in the following, the introduction of the site-dependent electron–phonon coupling constant

brings about a definitely richer phenomenology with respect to the site-independent case [ 20 ]. Here, we considered only a longitudinal sequence of nucleotides where

(

) is the electronic annihilation (creation) operator relative to the lattice sites

.…”

Section: Definition Of the Model And Its Solutionmentioning

confidence: 99%

“…As shown in the following, the introduction of the site-dependent electron-phonon coupling constant χ n brings about a definitely richer phenomenology with respect to the site-independent case [20]. Here, we considered only a longitudinal sequence of nucleotides whereB n (B † n ) is the electronic annihilation (creation) operator relative to the lattice sites n = 1, 2, ..., N. The term E 0B † nBn accounts for the initial "bare" electron energy distributed on several lattice sites according to initial shape of the electron wavefunction.…”

Section: Definition Of the Model And Its Solutionmentioning

confidence: 99%

“…Numerical simulations are performed by adopting dimensionless physical parameters in the dimensionless expressions of the Hamitonian (19) and of the dynamical Equation (20). These are found by rescaling time and lengths as t = ω −1 τ and β n = Lb n , respectively, where…”

Section: Physical Parametersmentioning

confidence: 99%

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Transition between Random and Periodic Electron Currents on a DNA Chain

Faraji

Franzosi

Mancini

et al. 2021

IJMS

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By resorting to a model inspired to the standard Davydov and Holstein-Fröhlich models, in the present paper we study the motion of an electron along a chain of heavy particles modeling a sequence of nucleotides proper to a DNA fragment. Starting with a model Hamiltonian written in second quantization, we use the Time Dependent Variational Principle to work out the dynamical equations of the system. It can be found that, under the action of an external source of energy transferred to the electron, and according to the excitation site, the electron current can display either a broad frequency spectrum or a sharply peaked frequency spectrum. This sequence-dependent charge transfer phenomenology is suggestive of a potentially rich variety of electrodynamic interactions of DNA molecules under the action of electron excitation. This could imply the activation of interactions between DNA and transcription factors, or between DNA and external electromagnetic fields.

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Section: Discussionmentioning

confidence: 89%

“…As shown in the following, the introduction of the site-dependent electron–phonon coupling constant

brings about a definitely richer phenomenology with respect to the site-independent case [ 20 ]. Here, we considered only a longitudinal sequence of nucleotides where

(

) is the electronic annihilation (creation) operator relative to the lattice sites

.…”

Section: Definition Of the Model And Its Solutionmentioning

confidence: 99%

Section: Definition Of the Model And Its Solutionmentioning

confidence: 99%

Section: Physical Parametersmentioning

confidence: 99%

See 2 more Smart Citations

Transition between Random and Periodic Electron Currents on a DNA Chain

Faraji

Franzosi

Mancini

et al. 2021

IJMS

Self Cite

View full text Add to dashboard Cite

show abstract

Optical van-der-Waals forces in molecules: from electronic Bethe-Salpeter calculations to the many-body dispersion model

et al. 2022

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Molecular forces induced by optical excitations are connected to a wide range of phenomena, from chemical bond dissociation to intricate biological processes that underpin vision. Commonly, the description of optical excitations requires the solution of computationally demanding electronic Bethe-Salpeter equation (BSE). However, when studying non-covalent interactions in large-scale systems, more efficient methods are desirable. Here we introduce an effective approach based on coupled quantum Drude oscillators (cQDO) as represented by the many-body dispersion model. We find that the cQDO Hamiltonian yields semi-quantitative agreement with BSE calculations and that both attractive and repulsive optical van der Waals (vdW) forces can be induced by light. These optical-vdW interactions dominate over vdW dispersion in the long-distance regime, showing a complexity that grows with system size. Evidence of highly non-local forces in the human formaldehyde dehydrogenase 1MC5 protein suggests the ability to selectively activate collective molecular vibrations by photoabsorption, in agreement with recent experiments.

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Examining the origins of observed terahertz modes from an optically pumped atomistic model protein in aqueous solution

et al. 2023

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The microscopic origins of terahertz (THz) vibrational modes in biological systems are an active and open area of current research. Recent experiments [Physical Review X 8, 031061 (2018)] have revealed the presence of a pronounced mode at ∼0.3 THz in fluorophore-decorated bovine serum albumin (BSA) protein in aqueous solution under nonequilibrium conditions induced by optical pumping. This result was heuristically interpreted as a collective elastic fluctuation originating from the activation of a low-frequency phonon mode. In this work, we show that the sub-THz spectroscopic response emerges in a statistically significant manner (> 2σ) from such collective behavior, illustrating how photoexcitation can alter specific THz vibrational modes. We revisit the theoretical analysis with proof-of-concept molecular dynamics that introduce optical excitations into the simulations. Using information theory techniques, we show that these excitations can give rise to a multiscale response involving two optically excited chromophores (tryptophans), other amino acids in the protein, ions, and water. Our results motivate new experiments and fully nonequilibrium simulations to probe these phenomena, as well as the refinement of atomistic models of Fröohlich condensates that are fundamentally determined by nonlinear interactions in biology.

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Energy transfer to the phonons of a macromolecule through light pumping

Cited by 5 publications

References 27 publications

Transition between Random and Periodic Electron Currents on a DNA Chain

Transition between Random and Periodic Electron Currents on a DNA Chain

Optical van-der-Waals forces in molecules: from electronic Bethe-Salpeter calculations to the many-body dispersion model

Examining the origins of observed terahertz modes from an optically pumped atomistic model protein in aqueous solution

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