Related papers: Comment on `Nanoconfinement-enhanced conformationa…
We investigate the excluded volume effects in good solvents for the isolated comb polymers having $\nu_{0}=1/4$. In particular, we investigate the change of the size exponent, $\nu$, defined by $\langle s_{N}^{2}\rangle\propto N^{2\nu}$,…
We use molecular dynamics simulations to study a semidilute, unentangled polymer solution containing well dispersed, weakly attractive nanoparticles (NP) of size ($\sigma_N$) smaller than the polymer radius of gyration $R_g$. We find that…
I present a Hamiltonian model and a computational method suitable to evaluate structural and thermodynamic properties of helical molecules embedded in crowded environments which may confine the space available to the base pair fluctuations.…
The concentration dependence of the excluded volume effects in polymer solutions is investigated. Through thermodynamic arguments for the interpenetration of polymer segments and the free energy change, we show that the disappearance of the…
By exploring a recent model [Palmeri, J., M. Manghi, and N. Destainville. 2007. Phys. Rev. Lett. 99:088103] where DNA bending elasticity, described by the wormlike chain model, is coupled to base-pair denaturation, we demonstrate that small…
The dependence of DNA assemblies conductance on relative humidity is investigated theoretically. Following earlier suggestions, we consider the ionic conductivity through the layers of water adsorbed by DNA molecules. The increase in…
The problem of differentiating the informational content of coding (exons) and non-coding (introns) regions of a DNA sequence is one of the central problems of genomics. The introns are estimated to be nearly 95% of the DNA and since they…
Complex biological and physical transport processes are often described through systems of interacting particles. Excluded-volume effects on these transport processes are well studied, however the interplay between volume exclusion and…
Single-molecule experiments in which force is applied to DNA or RNA molecules have enabled important discoveries of nucleic acid properties and nucleic acid-enzyme interactions. These experiments rely on a model of the polymer…
The influence of decoherence and bonding on the linear conductance of single double-stranded DNA molecules is examined by fitting a phenomenological statistical model developed recently (EPJB {\bf 68}, 237 (2009)) to experimental results.…
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…
Nanochannels provide means for detailed experiments on the effect of confinement on biomacromolecules, such as DNA. We here introduce a model for the complete unfolding of DNA from the circular to linear configuration. Two main ingredients…
The permeability of certain polymer membranes with impenetrable nanoinclusions increases with the particle volume fraction (Merkel et al., Science, 296, 2002). This intriguing observation contradicts even qualitative expectations based on…
DNA stretching experiments are usually interpreted using the worm-like chain model; the persistence length A appearing in the model is then interpreted as the elastic stiffness of the double helix. In fact the persistence length obtained by…
The aim of the present paper is the study of the entropic elasticity of the dsDNA molecule, having a cristallographic length L of the order of 10 to 30 persistence lengths A, when it is subject to spatial obstructions. We have not tried to…
A theory is presented of the longitudinal dispersion of DNA under equilibrium confined in a nanochannel. Orientational fluctuations of the DNA chain build up to give rise to substantial fluctuations of the coil in the longitudinal direction…
The effect of a finite torque on semiflexible polymers in a confined environment is investigated. It is shown how a new lengthscale appears in the strongly confined limit. The influence of a torque on the extension of biopolymers in…
The effect of excluded volume interactions on the structure of a polymer in shear flow is investigated by Brownian Dynamics simulations for chains with size $30\leq N\leq 300$. The main results concern the structure factor $S({\bf q})$ of…
The effect of electrostatic interactions on the stretching of DNA is investigated using a simple worm like chain model. In the limit of small force there are large conformational fluctuations which are treated using a self-consistent…
A charged Yukawa liquid confined in a slit nanopore is studied in order to understand excluded volume effects in the interaction force between the pore walls. A previously developed self-consistent scheme (S. Buyukdagli el al., J. Stat.…