Related papers: dsDNA persistence length with divalent ions
The extension of DNA confined to nanochannels has been studied intensively and in detail. Yet quantitative comparisons between experiments and model calculations are difficult because most theoretical predictions involve undetermined…
DNA is a flexible molecule, but the degree of its flexibility is subject to debate. The commonly-accepted persistence length of $l_p \approx 500\,$\AA\ is inconsistent with recent studies on short-chain DNA that show much greater…
Single molecule DNA experiments often generate data from force versus extension measurements involving the tethering of a microsphere to one end of a single DNA molecule while the other is attached to a substrate. We show that the…
We applied the mean-field approach to a columnar bundle assembled by the parallel arrangement of stiff polyelectrolyte rods in a salt bath. The electrostatic potential can be divided into two regions: inside the bundle for condensed…
We determine the persistence length, $l_p$, for a bacterial group I ribozyme as a function of concentration of monovalent and divalent cations by fitting the distance distribution functions $P(r)$ obtained from small angle X-ray scattering…
At present, there have been suggested two types of physical mechanism that may facilitate preferential pairing between DNA molecules, with identical or similar base pair texts, without separation of base pairs. One solely relies on base…
Counterion distribution around an isolated flexible polyelectrolyte in the presence of a divalent salt is evaluated using the adsorption model [M. Muthukumar, J. Chem. Phys. {\bf 120}, 9343 (2004)] that considers Bjerrum length, salt…
The elusive presence of an anomalously increasing screening length at high ionic concentrations hampers a complete picture of interactions in electrolytes. Theories which extend the diluted Debye-Huckel framework to higher concentrations…
The closure of long equilibrated denaturation bubbles in DNA is studied using Brownian dynamics simulations. A minimal mesoscopic model is used where the double-helix is made of two interacting bead-spring freely rotating strands, with a…
We show that a mesoscale model, with a minimal number of parameters, can well describe the thermomechanical and mechanochemical behavior of homogeneous DNA at thermal equilibrium under tension and torque. We predict critical temperatures…
We present a computational method to evaluate the end-to-end and the contour length distribution functions of short DNA molecules described by a mesoscopic Hamiltonian. The method generates a large statistical ensemble of possible…
The problem of DNA$-$DNA interaction mediated by divalent counterions is studied using a generalized Grand-canonical Monte-Carlo simulation for a system of two salts. The effect of the divalent counterion size on the condensation behavior…
We study voltage driven translocation of a single stranded (ss) DNA through a membrane channel. Our model, based on a master equation (ME) approach, investigates the probability density function (pdf) of the translocation times, and shows…
We study the unexpected high flexibility of short dsDNA which recently has been reported by a number of experiments. Via the Langevin dynamics simulation of our Breathing DNA model, first we observe the formation of bubbles within the…
We study the electronic properties of DNA by way of a tight-binding model applied to four particular DNA sequences. The charge transfer properties are presented in terms of localisation lengths, crudely speaking the length over which…
In previous work, we constructed a statistical framework for estimating the rate of clustered ionization from charged particle radiation in DNA. This model is extended to include contributions from secondary electrons. Using a simple…
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…
We describe properties and constructions of constraint-based codes for DNA-based data storage which account for the maximum repetition length and AT/GC balance. We present algorithms for computing the number of sequences with maximum…
The thermal conductivity of double-stranded (ds) B-DNA was systematically investigated using classical molecular dynamics (MD) simulations. The effect of changing base-pairs on the thermal conductivity of dsDNA, needed investigation at a…
The swelling of the viscosity radius, $\alpha_\eta$, and the universal viscosity ratio, $U_{\eta R}$, have been determined experimentally for linear DNA molecules in dilute solutions with excess salt, and numerically by Brownian dynamics…