Energy Transfer to the Phonons of A Macromolecule Through Light Pumping

Abstract

In the present paper we address the problem of the energy downconversion of the light absorbed by a protein into its internal vibrational modes. We consider the case in which the light receptors are fluorophores either naturally co-expressed with the protein or artificially covalently bound to some of its amino acids. In a recent work [Phys. Rev. X 8, 031061 (2018)], it has been experimentally found that by shining a laser light on the fluorophores attached to a protein the energy fed to it can be channeled into the normal mode of lowest frequency of vibration thus making the subunits of the protein coherently oscillate. Even if the phonon condensation phenomenon has been theoretically explained, the first step - the energy transfer from electronic excitation into phonon excitation - has been left open. The present work is aimed at filling this gap.

Transition between random and periodic electron currents on a DNA chain

“…Also 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 have 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.…”

“…As is 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 have considered only a longitudinal sequence of nucleotides where Bn ( B † n ) is the electronic annihilation (creation) operator relative to the lattice sites n = 1, 2, ..., N .…”

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

Ultraviolet Superradiance from Mega-Networks of Tryptophan in Biological Architectures

“…Significant disorder can effectively quench collective superradiance effects, even though our fluorescence QY measurements of Trp, TuD, and MTs in aqueous buffer solution suggest that even in thermal equilibrium, such effects survive. Certainly, more robust models are needed to account for exciton–phonon couplings in deformations of the protein scaffold, as well as for optical pumping of mechanical modes in nonequilibrium structural organization and assembly. − …”