Related papers: Anharmonic Vibrational Dynamics of DNA Oligomers
Charge transport through a short DNA oligomer (Dickerson dodecamer) in presence of structural fluctuations is investigated using a hybrid computational methodology based on a combination of quantum mechanical electronic structure…
Hydrogen and deuterium chemisorption on a single layer of graphene has been studied by path-integral molecular dynamics simulations. Finite-temperature properties of these point defects were analyzed in the range from 200 to 1500 K, by…
The macromolecules that encode and translate information in living systems, DNA and RNA, exhibit distinctive structural asymmetries, including homochirality or mirror image asymmetry and $3' - 5'$ directionality, that are invariant across…
The vibrational dynamics of a DNA molecule with counterions neutralizing the charged phosphate groups have been studied. With the help of elaborated model the conformational vibrations of the DNA double helix with alkaline metal ions have…
The low-frequency Raman spectra of Na-and Cs-DNA water solutions have been studied to determine the mode of counterion vibrations with respect to phosphate groups of the DNA double helix. The obtained spectra are characterized by the water…
We consider the regime in which the bands of the torsional acoustic (TA) and the hydrogen-bond-stretch (HBS) modes of the DNA interpenetrate each other. Within the framework of a model that accommodates the structure of the double helix, we…
Dynamics of the polymorphic A<->B transitions in DNA is compared for two polypurine sequences, poly(dA).poly(dT) and poly(dG).poly(dC), long known to exhibit contrasting properties in experiments. In free molecular dynamics simulations…
Hemoglobin (Hgb) forms tetramers (dimerized dimers), which enhance its globular stability and may also facilitate small gas molecule transport, as shown by recent all-atom Newtonian solvated simulations. Hydropathic bioinformatic scaling…
We investigate nonlinear dispersive mode coupling between the flexural in- and out-of-plane modes of two doubly clamped, nanomechanical silicon nitride string resonators. As the amplitude of one mode transitions from the linear response…
The ability to probe symmetry breaking transitions on their natural time scales is one of the key challenges in nonequilibrium physics. Stripe ordering represents an intriguing type of broken symmetry, where complex interactions result in…
We present in detail and validate an effective Monte Carlo approach for the calculation of the nuclear vibrational densities via integration of molecular eigenfunctions that we have preliminary employed to calculate the densities of the…
We study the effect of transcription on the kinetics of DNA supercoiling in 3D by means of Brownian dynamics simulations of a single nucleotide resolution coarse-grained model for double stranded DNA. By accounting for the action of a…
We propose a combined experimental (Atomic Force Microscopy) and theoretical study of the structural and dynamical properties of nucleosomes. In contrast to biochemical approaches, this method allows to determine simultaneously the DNA…
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
The control over DNA elongation in nanofluidic devices holds great potential for large-scale genomic analysis. So far, the manipulation of DNA in nanochannels has been mostly carried out with electrophoresis and seldom with hydrodynamics,…
Oligomers of the organic semiconductor PTCDA are studied by means of helium nanodroplet isolation (HENDI) spectroscopy. In contrast to the monomer absorption spectrum, which exhibits clearly separated, very sharp absorption lines, it is…
The conformational vibrations of Z-DNA with counterions are studied in framework of phenomenological model developed. The structure of left-handed double helix with counterions neutralizing the negatively charged phosphate groups of DNA is…
Understanding the properties of electronically interacting molecular chromophores, which involve internally coupled electronic-vibrational motions, is important to the spectroscopy of many biologically relevant systems. Here we apply linear…
The coupling of the electron system to lattice vibrations and their time-dependent control and detection provides unique insight into the non-equilibrium physics of semiconductors. Here, we investigate the ultrafast transient response of…
Detailed understanding of vibrational heat transfer mechanisms between solids is essential for the efficient thermal engineering and control of nanomaterials. We investigate the frequency dependence of anharmonic scattering and interfacial…