Related papers: Anharmonic Vibrational Dynamics of DNA Oligomers
We investigate the electronic structure of the 2H and 3R polytypes of NbS$_2$. The Fermi surfaces measured by angle-resolved photoemission spectroscopy show a remarkable difference in size, reflecting a significantly increased band filling…
X-ray Transient Absorption Spectroscopy near the carbon K-edge (1s, $\sim$ 285 eV) and chlorine L$_{2,3}$ edges (2p, $\sim$ 200 eV) is used to study the nuclear dynamics of CCl$_4$ vibrationally activated by impulsive stimulated Raman…
Current simulations of ultraviolet-visible absorption lineshapes, and dynamics of condensed phase systems, largely adopt a harmonic description to model vibrations. Often, this involves a model of displaced harmonic oscillators that have…
Inelastic neutron scattering measurements on silver oxide (Ag$_2$O) with the cuprite structure were performed at temperatures from 40 to 400\,K, and Fourier transform far-infrared spectra were measured from 100 to 300\,K. The measured…
Vibrational energy transfer of the amide I mode of N-methylacetamide (NMA) is studied theoretically using the vibrational configuration interaction method. A quartic force field of NMA is constructed at the B3LYP/6-31G+(d) level of theory…
The high linear charge density of 20-base-pair oligomers of DNA is shown to lead to a striking non-monotonic dependence of the long-time self-diffusion on the concentration of the DNA in low-salt conditions. This generic non-monotonic…
Recent low-temperature scanning-tunneling microscopy experiments [T. Kumagai et al., Phys. Rev. B 79, 035423 (2009)] observed the vibrationally induced flip motion of a hydroxyl dimer (OD)2 on Cu(110). We propose a model to describe…
In order to interpret recent experimental studies of the dependence of conductance of ds-DNA as the DNA is pulled from the 3'end1-3'end2 ends, which find a sharp conductance jump for a very short (4.5 %) stretching length, we carried out…
Vibrational coupling is relevant not only for dissipation of excess energy after chemical reactions but also for elucidating molecular structure and dynamics. It is particularly important for OH stretch vibrational spectra of water, for…
We present an O(N) algorithm to study the vibrational properties of amorphous silicon within the framework of tight-binding approach. The dynamical matrix elements have been evaluated numerically in the harmonic approximation exploiting the…
Infrared spectra of the CO2-N2 dimer are observed in the carbon dioxide nu3 asymmetric stretch region (~2350 cm-1) using a tunable infrared optical parametric oscillator to probe a pulsed slit jet supersonic expansion. Previous results for…
The thermodynamical stability of DNA minicircles is investigated by means of path integral techniques. Hydrogen bonds between base pairs on complementary strands can be broken by thermal fluctuations and temporary fluctuational openings…
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…
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 bring forth a consistent theory for the electron-mediated vibrational intermode coupling that clarifies the microscopic mechanism behind the vibrational relaxation of adsorbates on metal surfaces. Our analysis points out the inability of…
The electrodynamic response of DNA in the millimeter wave range is investigated. By performing measurements under a wide range of humidity conditions and comparing the response of single strand DNA and double strand DNA, we show that the…
Vibronic coupling plays a crucial role in X-ray photoelectron spectra (XPS) of molecules. In a series of three papers, we present a comprehensive exploration of the N-heterocycles family, known for their diverse structures, to summarize the…
A model of self-avoiding walk with suitable constraints on self-attraction is developed to describe the conformational behavior of a short RNA or a single stranded DNA molecule that forms hairpin structure and calculate the properties…
By equilibrating condensed DNA arrays against reservoirs of known osmotic stress and examining them with several structural probes, it has been possible to achieve a detailed thermodynamic and structural characterization of the change…
We investigate the charge transfer characteristics of one and two excess charges in a DNA base-pair dimer using a model Hamiltonian approach. The electron part comprises diagonal and off-diagonal Coulomb matrix elements such a correlated…