Transition between Random and Periodic Electron Currents on a DNA Chain

Abstract

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.

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. − …”

In Silico Exploration of CD200 as a Therapeutic Target for COVID-19

“…Both steps represent “required and sufficient” conditions for efficient interaction between biological molecules. Notably, the selective long-distance attractive electromagnetic forces (up to 1000 Å) between biological molecules have recently been experimentally confirmed [ 20 ].…”

“…The physical and mathematical basis of ISM is described in detail elsewhere (for review, see refs. [ 19 , 20 , 21 , 22 ]), and here, the method will be presented only briefly. First, the primary structure of a protein is transformed into a numerical sequence by the representation of each amino acid by the corresponding value of the electron–ion interaction potential (EIIP) ( Table 1 ).…”