Related papers: Anharmonic Vibrational Dynamics of DNA Oligomers
DNA stretching experiments are usually interpreted using the worm-like chain model; the persistence length A appearing in the model is then interpreted as the elastic stiffness of the double helix. In fact the persistence length obtained by…
To study the elastic properties of rod-like DNA nanostructures, we perform long simulations of these structure using the oxDNA coarse-grained model. By analysing the fluctuations in these trajectories we obtain estimates of the bend and…
A systematic study of electron or hole transfer along DNA dimers, trimers and polymers is presented with a tight-binding approach at the base-pair level, using the relevant on-site energies of the base-pairs and the hopping parameters…
By exploring a recent model [Palmeri, J., M. Manghi, and N. Destainville. 2007. Phys. Rev. Lett. 99:088103] where DNA bending elasticity, described by the wormlike chain model, is coupled to base-pair denaturation, we demonstrate that small…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
We devise an efficient scheme to determine vibrational properties from Path Integral Molecular Dynamics (PIMD) simulations. The method is based on zero-time Kubo-transformed correlation functions and captures the anharmonicity of the…
We employ Real-Time Time-Dependent Density Functional Theory to study hole oscillations within a B-DNA monomer (one base pair) or dimer (two base pairs). Placing the hole initially at any of the bases which make up a base pair, results in…
Vibrational spectroscopy has been widely employed to unravel physical-chemical properties of biological systems. Due to its high sensitivity to monitor real time "in situ" changes, Raman spectroscopy has been successfully employed, e.g., in…
Time-resolved Raman spectroscopy has been applied to probe the anharmonic coupling and electron-phonon interaction of optical phonons in graphite. From the decay of the transient anti-Stokes scattering of the G-mode following ultrafast…
For an understanding of DNA elasticity at high mechanical loads (F > 30 pN), its helical nature needs to be taken into account, in the form of coupling between the twist and stretch degrees of freedom. The prevailing model for DNA…
We are presenting the electronic photo fragment spectra of the protonated pyrimidine DNA bases homo-dimers. Only the thymine dimer exhibits a well structured vibrational progression, while protonated monomer shows broad vibrational bands.…
We present imaging and force spectroscopy measurements of DNA molecules adsorbed on functionalized mica. By means of Non-Contact mode AFM (NC-AFM) in Ultra High Vacuum (UHV), the frequency shift (\Delta f) versus separation (z) curves were…
We explore a prototype of an oscillatory neural network (ONN) based on vanadium dioxide switching devices. The model system under study represents two oscillators based on thermally coupled VO2 switches. Numerical simulation shows that the…
We call {\it monomer} a B-DNA base-pair and examine, analytically and numerically, electron or hole oscillations in monomer- and dimer-polymers, i.e., periodic sequences with repetition unit made of one or two monomers. We employ a…
Attraction between the polycyclic aromatic surface elements of carbon nanotubes (CNT) and the aromatic nucleotides of deoxyribonucleic acid (DNA) leads to reversible adsorption (physisorption) between the two, a phenomenon related to…
The denaturation of the double helix is a template for fundamental biological functions such as replication and transcription involving the formation of local fluctuational openings. The denaturation transition is studied for heterogeneous…
We have investigated the simultaneous absorption of near-infrared photons by pairs of neighboring molecules in liquid methanol. Simultaneous absorption by two OH-stretching modes is found to occur at an energy higher than the sum of the two…
We study a class of micromanipulation experiments, exemplified by the pulling apart of the two strands of double-stranded DNA (dsDNA). When the pulling force is increased to a critical value, an ``unzipping'' transition occurs. For random…
A systematic Raman study in the visible carried out on the YBa2Cu316,18Ox (x=6-7) compounds, with isotopic substitution of 18O for 16O, has detected a doping dependent deviation from harmonic behavior for the frequency shift of the in-phase…
Biomolecules couple to their aqueous environment through a variety of noncovalent interactions. Local structures at the surface of DNA and RNA are frequently determined by hydrogen bonds with water molecules, complemented by non-specific…