Related papers: Anharmonic Vibrational Dynamics of DNA Oligomers
Several living systems have been examined for their apparent optimization of structure and function for quantum behavior at biological length scales. Orthodox type II endonucleases, the largest class of restriction enzymes, recognize…
The structure of DNA in the nucleosome core particle is studied using an elastic model that incorporates anisotropy in the bending energetics and twist-bend coupling. Using the experimentally determined structure of nucleosomal DNA [T.J.…
Coherent energy exchange between plasmons and excitons is a phenomenon that arises in the strong coupling regime resulting in distinct hybrid states. The DNA-origami technique provides an ideal framework to custom-tune plasmon-exciton…
Anomalous non-exponential relaxation in hydrated biomolecules is commonly attributed to the complexity of the free-energy landscapes, similarly to polymers and glasses. It was found recently that the hydrogen-bond breathing of terminal DNA…
We call \textit{monomer} a B-DNA base pair and study, analytically and numerically, electron or hole oscillations in \textit{monomers}, \textit{dimers} and \textit{trimers}. We employ two Tight Binding (TB) approaches: (I) at the base-pair…
We present a simple and efficient method to incorporate anharmonic effects in the vibrational \textcolor{black}{analyses} of molecules within density functional theory (DFT) calculations. This approach is closely related to the traditional…
The response of a short DNA segment to bending is studied, taking into account the anisotropy in the bending rigidities caused by the double-helical structure. It is shown that the anisotropy introduces an effective nonlinear twist-bend…
The statistical physics of homogeneous DNA is investigated by the imaginary time path integral formalism. The base pair stretchings are described by an ensemble of paths selected through a macroscopic constraint, the fulfillement of the…
DNA adsorption on solid or liquid surfaces is a topic of broad fundamental and applied interest. Here we study by x-ray reflectivity the adsorption of monodisperse double-stranded DNA molecules a positively-charged surface, obtained through…
By combining analytical theory and Molecular Dynamics simulations we study the relaxation dynamics of DNA circular plasmids that initially undergo a local twist perturbation. We identify three distinctive time scales; (I) a rapid relaxation…
The influence of the orientation of gold nanorods in different assemblies has been investigated using the Finite Difference Time Domain (FDTD) simulation method. To understand the relative orientation, we vary the size and angle in dimer…
A promising new method for measuring intramolecular distances in solution uses small-angle X-ray scattering interference between gold nanocrystal labels (Mathew-Fenn et al, Science, 322, 446 (2008)). When applied to double stranded DNA, it…
We calculate the spectrum of torsional vibrations of a double-stranded structure that models the double helix of the DNA. We come to the conclusion that within the framework of the model elementary excitations may display an asymmetry as…
Double-stranded DNA `overstretches' at a pulling force of about 65 pN, increasing in length by a factor of 1.7. The nature of the overstretched state is unknown, despite its considerable importance for DNA's biological function and…
Transition metal dichalcogenides (TMDs) are layered materials which show excellent potential for nanoelectronic and optoelectronic applications. However, as many of the exciting features of these materials are controlled by the anharmonic…
By means of computer simulations of a coarse-grained DNA model we show that the DNA hairpin zippering dynamics is anomalous, i.e. the characteristic time T scales non-linearly with N, the hairpin length: T ~ N^a with a>1. This is in sharp…
In this work, we develop an extended dissipaton theory that generalizes the environmental couplings beyond the conventional linear and quadratic forms, enabling the treatment of arbitrary order of bath couplings. Applying this theoretical…
The approach for calculation of the mode intensities of DNA conformational vibrations in the Raman spectra is developed. It is based on the valence-optic theory and the model for description of conformational vibrations of DNA with…
The infrared absorption spectrum of the protonated water dimer (H5O2+) is simulated in full dimensionality (15D) in the spectral range 0-4000 cm-1. The calculations are performed using the Multiconfiguration Time-Dependent Hartree (MCTDH)…
We investigate quantum transport characteristics of a ladder model, which effectively mimics the topology of a double-stranded DNA molecule. We consider the interaction of tunneling charges with a selected internal vibrational degree of…