Related papers: Electronic parameters for the hole transfer in DNA…
The approach for the description of the DNA conformational transformations on the mesoscopic scales in the frame of the double helix is presented. Due to consideration of the joint motions of DNA structural elements along the conformational…
Molecular topology of polymers plays a key role in determining their physical properties. We studied herein the topological effects on the static and dynamic properties of a 2D catenated network of DNA rings called a kinetoplast.…
The dynamical properties of an extended Hubbard model, which is relevant to quarter-filled layered organic molecular crystals, are analyzed. We have computed the dynamical charge correlation function, spectral density, and optical…
We study DNA denaturation by integrating elasticity -- as described by the Gaussian network model -- with bond binding energies, distinguishing between different base-pair and stacking energies. We use exact calculation, within the model,…
Hydrogen bonding between nucleobases produces diverse DNA structural motifs, including canonical duplexes, guanine (G) quadruplexes and cytosine (C) i-motifs. Incorporating metal-mediated base pairs into nucleic acid structures can…
Hole doping in Nd${}_{2}$NiO${}_{4.00}$ can be either achieved by substituting the trivalent Nd atoms by bivalent alkaline earth metals or by oxygen doping, yielding Nd${}_{2}$NiO${}_{4+\delta}$. In this study, we investigated the interplay…
In this work, we report a novel strategy to construct molecular diodes with a record tunable rectification ratio of as high as 10^6 using oxidatively damaged DNA molecules. Being exposed to several endogenous and exogenous events, DNA…
The effect of secondary structure on DNA duplex formation is poorly understood. We use a coarse-grained model of DNA to show that specific 3- and 4-base pair hairpins reduce hybridization rates by factors of 2 and 10 respectively, in good…
The entropy loss due to the formation of one or multiple loops in circular and linear DNA chains is calculated from a scaling approach in the limit of long chain segments. The analytical results allow to obtain a fast estimate for the…
Ultrafast photoinduced dynamics of electronic excitation in molecular dimers is drastically affected by the dynamic reorganization of inter- and intra- molecular nuclear configuration modeled by a quantized nuclear degree of freedom [Cina…
We study electrostatic interaction between molecules of the DNA in which a number of phosphate groups of the sugar-phosphate backbone are exchanged for the pyrophosphate ones. We employ a model in which the DNA is considered as a…
The forming and melting of complementary base pairs in RNA duplexes are conformational transitions required to accomplish a plethora of biological functions. Yet the dynamic steps of these transitions have not been quantitatively…
We study the exchange coupling in small Wigner crystals confined to one-dimensional space. In particular we concentrate on the simplest nontrivial case of two electrons in a box potential and calculate analytically the energy splitting…
We showed in our previous studies that just $3\%$ cross-links, at special points along the contour of the bacterial DNA help the DNA-polymer to get organized at micron length scales \cite{jpcm,epl}. In this work, we investigate how does the…
Based on combined density functional theory and nonequilibrium Greens function quantum transport studies, we have demonstrated quantum interference effects on the transverse conductance of Hachimoji synthetic nucleic acids placed between…
The sequence-dependent elasticity of double-helical DNA on a nm length scale can be captured by the rigid base-pair model, whose strains are the relative position and orientation of adjacent base-pairs. Corresponding elastic potentials have…
Dynamics of resonant energy transfer of a single excitation in a molecular dimer system is studied in the simultaneous presence of diagonal and off-diagonal exciton-phonon coupling. It is found that the off-diagonal coupling plays an…
Unraveling the behavior of the electrons in the copper-oxygen planes of cuprate superconductors remains a challenge. Here we examine the electronic charge redistribution among planar copper and oxygen orbitals and the charge gap using the…
DNA capture with high fidelity is an essential part of nanopore translocation. We report several important aspects of the capture process and subsequent translocation of a model DNA polymer through a solid-state nanopore in presence of an…
Empirical evidence in heavy fermion, pnictide, and other systems suggests that unconventional superconductivity appears associated to some form of real-space electronic order. For the cuprates, despite several proposals, the emergence of…