Related papers: Concerted motion of protons in hydrogen bonds of D…
We study the nonlinear dynamics of a protein-DNA molecular system by treating DNA as a set of two coupled linear chains and protein in the form of a single linear chain sliding along the DNA at the physiological temperature in a viscous…
The hydrogen bond is usually described within the clamped nucleus approximation in which electronic and vibrational motions are considered separately. This approach leads to a double-well potential which facilitates proton tunnelling. In…
The formation of polaron and its migration in a DNA chain are studied within a semiclassical Peyrard-Biship-Holstein polaron model. Comparing the energetics of the polaron system found from the quantum chemical and semiclassical…
Novel experimental and computational studies have uncovered the proton momentum distribution in hydrogen bonded systems. In this work, we utilize recently developed open path integral Car-Parrinello molecular dynamics methodology in order…
The subject of this report is the dynamics of elastic system in conjunction with hydrogen bonds of the DNA. We draw attention to the draw-back of the familiar rod model of the DNA, and make a case of constructing models that could…
Hydrogen bonds play a pivotal role in chemistry, biology, and condensed-matter physics, where quantum tunnelling can strongly influence structure and dynamics. Isotope substitution (H $\rightarrow$ D) provides a sensitive probe of such…
We study the tautomeric transitions in base pairs of DNA considering elastic properties of DNA as classical and tunneling of protons as quantum, and show that the dynamics of the transitions admits of soliton like solutions whose shape and…
We study nonlinear dynamics of a periodic inhomogeneous DNA double helical chain under dynamic plane-base rotator model by considering angular rotation of bases in a plane normal to the helical axis. The dynamics is governed by a perturbed…
A solution of the two-dimensional Schr\"odinger equation with Pauli-Fierz Hamiltonian and trigonometric double-well potential is obtained within the framework of the first-order of adiabatic approximation. The case of vibrational strong…
We study a model for polaron-like charge transport mechanism along DNA molecules with emphasis on the impact of parametrical and structural disorder. Our model Hamiltonian takes into account the coupling of the charge carrier to two…
In hydrogen bonded systems, nuclear quantum effects such as zero-point motion and tunneling can significantly affect their material properties through underlying physical and chemical processes. Presently, direct observation of the…
The ability of double-stranded DNA or RNA to locally melt and form kinks leads to strong non-linear elasticity effects that qualitatively affect their packing in confined spaces. Using analytical theory and numerical simulation we show that…
We suggest that the DNA molecules could form the cholesteric phase owing to an interaction mediated by the network of the hydrogen bonds (H-network) in the solvent. The model admits of the dependence of the optical activity of the solution…
In this work we propose a model for DNA double helix within the tight-binding framework that incorporates the helicity of the molecules. We have studied localization properties of three DNAsequences,the periodic poly(dG)-poly(dC) and…
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…
We propose a dynamical model depicting the interactions between DNA and a specific binding protein involving long range transmissions. The dynamics rely on the coupling between Hydrogen bonds formed between DNA and protein and between the…
The process of protons transport in molecular water chains is of fundamental interest for many biological systems. Although many features of such systems can be analyzed using large-scale computational modeling, other features are better…
Dynamics of topological solitons describing open states in the DNA double helix are studied in the frameworks of the model which takes into account asymmetry of the helix. It is shown that three types of topological solitons can occur in…
In our report we consider two weakly coupled Schr\"odinger equations as a model of the interchain energy transport in the DNA double-helix. We use the reduction of the Yakushevich-type model considering the torsional dynamics of the DNA. In…
The effect of sequence heterogeneity on polynucleotide translocation across a pore and on simple models of molecular motors such as helicases, DNA polymerase/exonuclease and RNA polymerase is studied in detail. Pore translocation of RNA or…