Related papers: Structuring of counterions around dna double helix…

The study of configurational parameters of deformed DNA is a relevant problem in research of such important biological process as double helix compactization in cell. The deformations accompanied with local disruptions of the regular…

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…

Single molecule experiments on B-DNA stretching have revealed one or two structural transitions, when increasing the external force. They are characterized by a sudden increase of DNA contour length and a decrease of the bending rigidity.…

We investigate the dynamics of DNA translocation through a nanopore using 2D Langevin dynamics simulations, focusing on the dependence of the translocation dynamics on the details of DNA sequences. The DNA molecules studied in this work are…

Something about structure of the water shell of DNA and how it can help to design of novel biologically-active molecules and potential drugs with sequence-specific binding to nucleic acids.

As transistor features shrink beyond the 2 nm node, studying and designing for atomic scale effects become essential. Being able to combine conventional CMOS with new atomic scale fabrication routes capable of creating 2D patterns of highly…

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…

Novel approaches to DNA sequencing and detection require the measurement of electrical currents between metal probes immersed in ionic solution. Here, we experimentally demonstrate that these systems maintain large background currents with…

In order to detect the effect of the surface charge discreteness on the properties at the solid-liquid interface, molecular dynamics simulation model taking consideration of the vibration of wall atoms was used to investigate the ion and…

Explicit molecular dynamics simulations were applied to a pair of amorphous silica nanoparticles of diameter 3.2 nm immersed in a background electrolyte. Mean forces acting between the pair of silica nanoparticles were extracted at four…

Nanotechnology has revolutionized the fabrication of hybrid species with tailored functionalities. A milestone in this field is the DNA conjugation of nanoparticles, introduced almost 30 years ago, which typically exploits the affinity…

Dielectric spectroscopy is used to investigate fundamental length scales of 146 bp short-fragment (nucleosomal) dilute Na-DNA solutions. Two relaxation modes are detected: the high- and the low-frequency mode. Dependence of the…

A theory of condensation and resolubilization of a dilute DNA solution with growing concentration of multivalent cations, N is suggested. It is based on a new theory of screening of a macroion by multivalent cations, which shows that due to…

DNA condensation by multivalent cations plays a crucial role in genome packaging in viruses and sperm heads, and has been extensively studied using single-molecule experimental methods. In those experiments, the values of the critical…

Negatively charged DNA can be compacted by positively charged dendrimers and the degree of compaction is a delicate balance between the strength of the electrostatic interaction and the elasticity of DNA. We report various elastic…

The article presents a comprehensive study of counterion dynamics around a generic linear polyelectrolyte (PE) chain with the help of coarse-grained computer simulations. The ion-chain coupling is discussed in the form of binding time,…

The structural origin of the size of the 11 nm nucleosomal disc is addressed. On the nanometer length-scale the organization of DNA as chromatin in the chromosomes involves a coiling of DNA around the histone core of the nucleosome. We…

A mechanism of double strand breaking (DSB) in DNA due to the action of two electrons is considered. These are the electrons produced in the vicinity of DNA molecules due to ionization of water molecules with a consecutive emission of two…

The structure and stability of strongly charged complex fibers formed by complexation of a single long semi-flexible polyelectrolyte (PE) chain and many oppositely charged spherical macroions are investigated numerically at the ground-state…

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…