Related papers: Electrostatic effects in DNA stretching
We had combined the Neukirch-Marko model that describes the extension, torque and supercoiling in single, stretched and twisted DNA of infinite contour length, with a form of the free energy suggested by Sinha and Samuels to describe short…
Taking into account the nonequivalence of fixed-force and fixed-length ensembles in the weak-force regime, equations of state are derived that describe the equilibrium extension or compression of an ideal Gaussian polymer chain in response…
We extend our previous study [J. Chem. Phys. 138, 204907 (2013)] to quantify the screening properties of four mesoscale smoothed charge models used in dissipative particle dynamics. Using a combination of the hypernetted chain integral…
The high linear charge density of 20-base-pair oligomers of DNA is shown to lead to a striking non-monotonic dependence of the long-time self-diffusion on the concentration of the DNA in low-salt conditions. This generic non-monotonic…
While analyzing the persistence length of DNA atomistic simulations Wu et al. [J. Chem. Phys. 142, 125103 (2015)] introduced an empirical formula to account for the observed length-dependence. In particular they found that the persistence…
We analyze the nonequilibrium dynamics of single inextensible semiflexible biopolymers as stretching forces are applied at the ends. Based on different (contradicting) heuristic arguments, various scaling laws have been proposed for the…
We present an exact many-body framework for electrostatic interactions among $N$ arbitrarily charged spheres in an electrolyte, modeled by the linearized Poisson--Boltzmann equation. Building on a spectral analysis of nonstandard…
We study the dynamical response of a single semiflexible polymer chain based on the theory developed by Hallatschek et al. for the wormlike-chain model. The linear viscoelastic response under oscillatory forces acting at the two chain ends…
The folding transition of biopolymers from the coil to compact structures has attracted wide research interest in the past and is well studied in polymer physics. Recent seminal works on DNA in confined devices have shown that these long…
We study the compression and extension dynamics of a DNA-like polymer interacting with non-DNA binding and DNA-binding proteins, by means of computer simulations. The geometry we consider is inspired by recent experiments probing the…
We propose a model for the photo-deactivation mechanism for DNA based upon accurate quantum chemical and molecular dynamical evaluations of model Watson/Crick nucleoside pairs and stacked pairs. Our results corroborate recent ultrafast…
Although the stretching of polymers and biomolecules is important in numerous settings, their response when confined to two-dimensions is relatively poorly-studied. In this paper, we derive closed-form analytical expressions for the…
We theoretically study the polarizability and the interactions of neutral complexes consisting of a semi-flexible polyelectrolyte adsorbed onto an oppositely charged spherical colloid. In the systems we studied, the bending energy of the…
The electrostatic screening length predicted by Debye-H\"uckel theory decreases with increasing ionic strength, but recent experiments have found that the screening length can instead increase in concentrated electrolytes. This phenomenon,…
Motivated by the wide ranging experimental results on the conductivity of DNA, we have investigated extraordinary configurations and chemical environments in which DNA might become a true molecular wire, perticularly from enhanced…
DNA bending is biologically important for genome regulation and is relevant to a range of nanotechnological systems. Recent results suggest that sharp bending is much easier than implied by the widely-used worm-like chain model; many of…
Large-scale DNA deformation is ubiquitous in transcriptional regulation in prokaryotes and eukaryotes alike. Though much is known about how transcription factors and constellations of binding sites dictate where and how gene regulation will…
We investigate the properties of a system of semi-diluted polymers in the presence of charged groups and counter-ions, by means of self-consistent field theory. We study a system of polyelectrolyte chains grafted to a similarly, as well as…
A scaling analysis is presented of the statistics of long DNA confined in nanochannels and nanoslits. It is argued that there are several regimes in between the de Gennes and Odijk limits introduced long ago. The DNA chain folds back on…
The effective interaction between two parallel strands of helical bio-molecules, such as deoxyribose nucleic acids (DNA), is calculated using computer simulations of the "primitive" model of electrolytes. In particular we study a simple…