Related papers: Electronic parameters for the hole transfer in DNA…
Electronic decoherence processes in trans-polyacetylene oligomers are considered by explicitly computing the time dependent molecular polarization from the coupled dynamics of electronic and vibrational degrees of freedom in a mean-field…
The interaction between metal atoms and nucleobases has been a topic of high interest due to the wide scientific and technological implications. Combining density functional theory simulations with a literature overview, we achieved an…
The thermodynamic properties of DNA circular molecules are investigated by a new path integral computational method which treats in the real space the fundamental forces stabilizing the molecule. The base pair and stacking contributions to…
In this work we propose a model for DNA double helix within the tight-binding framework that incorporates the helicity of the molecules. We have studied localization properties of three DNAsequences,the periodic poly(dG)-poly(dC) and…
The phase diagram of a water solution of DNA and oppositely charged spherical macroions is studied. DNA winds around spheres to form beads-on-a-string complexes resembling the chromatin 10 nm fiber. At small enough concentration of spheres…
We study the electronic properties of DNA by way of a tight-binding model applied to four particular DNA sequences. The charge transfer properties are presented in terms of localisation lengths, crudely speaking the length over which…
Experiments have revealed correlation-driven behavior of DNA in charged solutions, including charge inversion and condensation. This paper presents calculations of a lattice-gas model of charge inversion for the adsorption of charged dimers…
Combining two-color infared pump-probe spectroscopy and anharmonic force field calculations we characterize the anharmonic coupling patterns between fingerprint modes and the hydrogen-bonded symmetric NH$_2$ stretching vibration in…
The binding of proteins onto DNA contributes to the shaping and packaging of genome as well as to the expression of specific genetic messages. With a view to understanding the interplay between the presence of proteins and the deformation…
Protonation of DNA basepairs is a reversible phenomenon which can be controlled by tuning the pH of the system. Under mild acidic conditions, the hydrogen bonding pattern of the DNA basepairs undergoes a change. We study the effect of…
Charge transfer in a DNA duplex chain is studied by constructing a system with virtual electrodes connected at the ends of each DNA strand. The systeym is described by the tight-binding model and its transport is analyzed by the transfer…
The collective behavior of the shortest DNA oligomers in high concentration aqueous solutions is an unexplored frontier of DNA science and technology. Here we broaden the realm of DNA nanoscience by demonstrating that single-component…
We performed an overview of the inner shell excitation phenomena in the study of electron recombination with multiply charged complex ions such as Au$^{q+}$ (q=49-52) and Pb$^{53+}$. It is found the the inner shell excitations play a…
From first principles calculations we determine the Coulomb interaction between two holes on oligo-acene and -thiophene molecules in a crystal, as a function of the oligomer length. The relaxation of the molecular geometry in the presence…
Concentrated solutions of short blunt-ended DNA duplexes, down to 6 base pairs, are known to order into the nematic liquid crystal phase. This self-assembly is due to the stacking interactions between the duplex terminals that promotes…
Optical antennas have been extensively employed to manipulate the photophysical properties of single photon emitters. Coupling between an emitter and a given resonant mode of an optical antenna depends mainly on three parameters: spectral…
We study electronic transport in long DNA chains using the tight-binding approach for a ladder-like model of DNA. We find insulating behavior with localizaton lengths xi ~ 25 in units of average base-pair seperation. Furthermore, we observe…
Accurate knowledge of the thermodynamic properties of nucleic acids is crucial to predicting their structure and stability. To date most measurements of base-pair free energies in DNA are obtained in thermal denaturation experiments, which…
In the past two decades, many research groups worldwide have tried to understand and categorize simple regimes in the charge transfer of such biological systems as DNA. Theoretically speaking, the lack of exact theories for electron-nuclear…
The interaction energies between the different types of bases of a single strand of DNA molecule have been calculated. Using these original values of energies the harmonic behavior of a number of base patterns of DNA has been studied. In…