Related papers: Excluded Volume Effects in Gene Stretching
A double stranded DNA molecule when pulled with a force acting on one end of the molecule can become either partially or completely unzipped depending on the magnitude of the force F. For a random DNA sequence, the number M of unzipped base…
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…
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 $\langle s_{N}^{2}\rangle\propto N^{2\nu}$,…
In the present Comment we show that, contrary to the recent findings of Reisner et al. [Phys. Rev. Lett. 99, 058302 (2007)], the excluded volume effect does not play an important role in determining DNA behavior in nanochannels at low ionic…
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 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 force-extension relation for a semi-flexible polymer such as DNA confined in a nanoslit is investigated and it is found that both the effective persistence length and the form of the force-extension relation change as the chain goes…
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 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…
The chiral nature of DNA plays a crucial role in cellular processes. Here we use magnetic tweezers to explore one of the signatures of this chirality, the coupling between stretch and twist deformations. We show that the extension of a…
Semiflexible macromolecules in dilute solution under very good solvent conditions are modeled by self-avoiding walks on the simple cubic lattice ($d=3$ dimensions) and square lattice ($d=2$ dimensions), varying chain stiffness by an energy…
Two-dimensional semiflexible polymer rings are studied both by imaging circular DNA adsorbed on a mica surface and by Monte Carlo simulations of phantom polymers as well as of polymers with finite thickness. Comparison of size and shape of…
The nature and the universal properties of DNA thermal denaturation are investigated by Monte Carlo simulations. For suitable lattice models we determine the exponent c describing the decay of the probability distribution of denaturated…
Mathew-Fenn et al. (Science (2008) 322, 446-9) measured end-to-end distances of short DNA and concluded that stretching fluctuations in several consecutive turns of the double helix should be strongly correlated. I argue that this…
Excluded volume effects are incorporated in the quark meson coupling model to take into account in a phenomenological way the hard core repulsion of the nuclear force. The formalism employed is thermodynamically consistent and does not…
By resorting to the thick-chain model we discuss how the stretching response of a polymer is influenced by the self-avoidance entailed by its finite thickness. The characterization of the force versus extension curve for a thick chain is…
A variety of viruses tightly pack their genetic material into protein capsids that are barely large enough to enclose the genome. In particular, in bacteriophages, forces as high as 60 pN are encountered during packaging and ejection,…
The tethered-particle method is a single-molecule technique that has been used to explore the dynamics of a variety of macromolecules of biological interest. We give a theoretical analysis of the particle motions in such experiments. Our…
Theoretical results for the extension of a polymer confined to a channel are usually derived in the limit of infinite contour length. But experimental studies and simulations of DNA molecules confined to nanochannels are not necessarily in…
We discuss the extension of the empirical equation: $\left\langle s_{N}^{2}\right\rangle_{0}\propto g\,l^{2}$, where the subscript 0 denotes the ideal value with no excluded volume and $g$ the generation number from the root to the youngest…