Related papers: Elastic Correlations in Nucleosomal DNA Structure
The chromatin fiber is a complex of DNA and specific proteins called histones forming the first structural level of organization of eukaryotic chromosomes. In tightly organized chromatin fibers, the short segments of naked DNA linking the…
By combining analytical results and simulations of various coarse-grained models we investigate the minimal energy shape of DNA minicircles which are torsionally constrained by an imposed over or undertwist. We show that twist-bend…
The flexibility of short DNA chains is investigated via computation of the average correlation function between dimers which defines the persistence length. Path integration techniques have been applied to confine the phase space available…
Sophisticated high-energy and large momentum-transfer scattering experiments combined with ab-initio calculations can reveal the short-distance behavior of nucleon pairs in nuclei. On an opposite energy and resolution scale, elastic…
Twisting DNA under a constant applied force reveals a thermally activated transition into a state with a supercoiled structure known as a plectoneme. Using transition state theory, we predict the rate of this plectoneme nucleation to be of…
We study DNA self-assembly and DNA computation using a coarse-grained DNA model within the directional dynamic bonding framework {[}C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012){]}. In our model, a single nucleotide or domain is…
Normal mode analysis offers an efficient way of modeling the conformational flexibility of protein structures. Simple models defined by contact topology, known as elastic network models, have been used to model a variety of systems, but the…
A phenomenological model based on the three-dimensional theory of nonlinear elasticity is developed to describe the phenomenon of overstretching in the force-extension curve for dsDNA. By using the concept of a material with multiple…
We study the elastic response of a worm-like polymer chain with reversible kink-like structural defects. This is a generic model for (a) the double-stranded DNA with sharp bends induced by binding of certain proteins, and (b) effects of…
In analogy with classic rigidity problems of networks and frames, the elastic properties of hydrogels made of DNA nanostars (DNAns) are expected to strongly depend on the precise geometry of their building blocks. However, it is currently…
A chemical kinetic model of the elongation dynamics of RNA polymerase along a DNA sequence is introduced. The proposed model governs the discrete movement of the RNA polymerase along a DNA template, with no consideration given to elastic…
In order to interpret recent experimental studies of the dependence of conductance of ds-DNA as the DNA is pulled from the 3'end1-3'end2 ends, which find a sharp conductance jump for a very short (4.5 %) stretching length, we carried out…
Entangled ring polymers, along with blends of ring and linear polymers, continue to be a topic of great interest and debate due to the conflicting experimental results in the literature as well as the difficulty of producing entangled…
Advances in DNA nanotechnology have stimulated the search for simple motifs that can be used to control the properties of DNA nanostructures. One such motif, which has been used extensively in structures such as polyhedral cages,…
We present in this paper an original approach to compute the electrophoretic mobility of rigid nucleo-protein complexes like nucleosomes. This model allows to address theoretically the influence of complex position along DNA, as well as…
We have studied the effect of amino acids on electron attachment properties of DNA nucleobases, taking cytosine as a model system. The equation of motion coupled cluster theory with an extended basis set has been used to simulate the…
Macroscopic elastic core-shell systems can be generated as toy models to be deformed and haptically studied by hand. On the mesoscale, colloidal core-shell particles and microgels are fabricated and investigated by different types of…
Dielectric spectroscopy of a twist bend nematic phase of an achiral bent core liquid crystalline compound under DC bias is used to investigate its response to electric field. Two collective relaxation processes are revealed, these are…
We report a structural polymorphism of the S-DNA when a canonical B-DNA is stretched under different pulling protocols and provide a fundamental molecular understanding of the DNA stretching mechanism. Extensive all atom molecular dynamics…
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…