Related papers: DNA-based tunable THz oscillator
A theory is presented of the longitudinal dispersion of DNA under equilibrium confined in a nanochannel. Orientational fluctuations of the DNA chain build up to give rise to substantial fluctuations of the coil in the longitudinal direction…
Gel electrophoresis allows to separate knotted DNA (nicked circular) of equal length according to the knot type. At low electric fields, complex knots being more compact, drift faster than simpler knots. Recent experiments have shown that…
The interplay between bending of the molecule axis and appearance of disruptions in circular DNA molecules, with $\sim 100$ base pairs, is addressed. Three minicircles with different radii and almost equal content of AT and GC pairs are…
We model unzipping of DNA/RNA molecules subject to an external force by a spin-oscillator system. The system comprises a macroscopic degree of freedom, represented by a one-dimensional oscillator, and internal degrees of freedom,…
The theoretical study of deformability of special sequence of DNA double helix TATA-box is presentated. The paper elaborates on the mechanisms of abnormal deformation of DNA TATA-box double helix that cannot be explained using the standard…
Nucleic acids are highly deformable helical molecules constantly stretched, twisted and bent in their biological functioning. Single molecule experiments have shown that double stranded (ds)-RNA and standard ds-DNA have opposite…
This paper introduces an oscillator scheme based on the oscillations of magnetic domain walls due to spin-polarized currents, where the current is injected perpendicular to the sample plane in a localized part of a nanowire. Depending on…
Within a simple elastic theory, we study the elongation versus force characteristics of a supercoiled DNA molecule at thermal equilibrium in the regime of small supercoiling. The partition function is mapped to the path integral…
Most living systems rely on double-stranded DNA (dsDNA) to store their genetic information and perpetuate themselves. This biological information has been considered the main target of evolution. However, here we show that symmetries and…
Previous theoretical studies have shown that measuring the transverse current across DNA strands while they translocate through a nanopore or channel may provide a statistically distinguishable signature of the DNA bases, and may thus allow…
We study the oscillatory behaviour of a gene regulatory network with interlinked positive and negative feedback loop. Frequency and amplitude are two important properties of oscillation. Studied network produces two different modes of…
Due to its polyionic character the DNA double helix is stable and biologically active only in salty aqueous media where its charge is compensated by solvent counterions. Monovalent metal ions are ubiquitous in DNA environment and they are…
DNA nanostructures are made using synthetic DNA strands, the sequences of which are designed such that they will self-assemble into the desired form by hybridization of complementary domains. Various structures and devices have been…
We study electric dipole spin resonance caused by sub-terahertz (THz) radiation in a multilevel finite-size quantum dot formed in a nanowire focusing on the range of driving electric fields amplitudes where a strong interplay between the…
The formation of DNA loops by proteins and protein complexes is ubiquitous to many fundamental cellular processes, including transcription, recombination, and replication. Here we review recent advances in understanding the properties of…
The formation of bubbles in nucleic acids (NAs) are fundamental in many biological processes such as DNA replication, recombination, telomeres formation, nucleotide excision repair, as well as RNA transcription and splicing. These precesses…
We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special…
We theoretically study domain wall oscillations upon the injection of a dc current through a geometrically constrained wire with perpendicular magnetic anisotropy. The oscillation frequency spectrum can be tuned by the injected current…
The unzipping of a double stranded DNA whose ends are subjected to a time dependent periodic force with frequency $\omega$ and amplitude $G$ is studied using Monte Carlo simulations. We obtain the dynamical order parameter, $Q$, defined as…
Based on a structure consisting of a single graphene layer situated on a periodic dielectric grating, we show theoretically that intense terahertz (THz) radiations can be generated by an electron bunch moving atop the graphene layer. The…