Related papers: Anharmonic Vibrational Dynamics of DNA Oligomers
We investigate the electron (hole) transport through short double-stranded DNA wires in which the electrons are strongly coupled to the specific vibrational modes (vibrons) of the DNA. We analyze the problem starting from a tight-binding…
The thermodynamical properties of heterogeneous DNA sequences are computed by path integral techniques applied to a nonlinear model Hamiltonian. The base pairs relative displacements are interpreted as time dependent paths whose amplitudes…
The temperature dependence of the phonon spectrum in the superconducting transition metal dichalcogenide 2H-NbS$_2$ is measured by diffuse and inelastic x-ray scattering. A deep, wide and strongly temperature dependent softening, of the two…
The probing of coherent lattice vibrations in solids has been conventionally carried out using time-resolved transient spectroscopy where only the relative oscillation amplitude can be obtained. Using time-resolved X-ray techniques,…
We investigate anharmonically coupled high- and low-frequency excitations in a planar lattice of adsorbed molecules interacting with phonons of a crystal. Dephasing of high-frequency local vibrations by low-frequency resonance modes is…
We investigate the effect of exciton coupling on the optical absorption spectrum of polymer molecules under conditions of strong inhomogeneous broadening. We demonstrate that the dependence of the maximum in the rescaled absorption spectrum…
We systematically examine all the tight-binding parameters pertinent to charge transfer along DNA. The $\pi$ molecular structure of the four DNA bases (adenine, thymine, cytosine, and guanine) is investigated by using the linear combination…
In living systems, DNA undergoes continuous and rhythmic mechanical remodeling through condensation, looping, and disentangling to regulate gene expression, segregate chromosomes, and guide morphogenesis. Here, we demonstrate a purely…
A U(2) algebraic model is presented to describe stretching vibrations of XY$_n$ (n=2, 3, and 4) systems, where anharmonic interactions between the bond modes are considered. This model in a limit corresponds to an anharmonically coupled…
We derive a Hierarchical Equations of Motion (HEOM) description of nonadiabatic Herzberg-Teller type coupling effects and of non-Condon effects in a system of electronic transitions interacting with intra- and inter-molecular vibrational…
A scheme for computing charge-transfer matrix elements with the linear combination of fragment molecular orbitals and the 'nonempirically tuned range-separated' density functional is presented. It takes account of the self-consistent…
The instantaneous normal modes corresponding to base pair vibrations (radial modes) and twist angle fluctuations (angular modes) of a DNA molecule model at ambient temperature are theoretically investigated. Due to thermal disorder, normal…
In the present work, we give an analytical non-perturbative treatment of mode-mode coupling and anharmonicity occurring in molecular vibrational systems analyzed by 2D-infrared spectroscopy. This analytical description allows a detailed…
Motivated by the wide ranging experimental results on the conductivity of DNA, we have investigated extraordinary configurations and chemical environments in which DNA might become a true molecular wire, perticularly from enhanced…
The scaling properties of DNA knots of different complexities were studied by atomic force microscope. Following two different protocols DNA knots are adsorbed onto a mica surface in regimes of (i) strong binding, that induces a kinetic…
A combination of the temporally and spatially resolved phonon spectroscopy has enabled calibration of hydrogen bond transition from the vibration mode of heavy water to the core/shelled nanodroplet and the subnanosized ionic hydration shell…
DNAs charge transfer and self-assembly characteristics have made it a hallmark of molecular electronics for the past two decades. A fast and efficient charge transfer mechanism with programmable properties using DNA nanostructures is…
Electric interactions have a strong impact on the structure and dynamics of biomolecules in their native water environment. Given the variety of water arrangements in hydration shells and the femto- to subnanosecond time range of structural…
We present a detailed study of the optical absorption spectra of DNA bases and base pairs, carried out by means of time dependent density functional theory. The spectra for the isolated bases are compared to available theoretical and…
In time-resolved pump-probe vibrational spectroscopy the internal stretch mode of polar molecules is utilized as a key observable to characterize the ultrafast dynamics of adsorbates on surfaces. The adsorbates non-adiabatic intermode…