Related papers: Excluded Volume Effects in Gene Stretching
Recent measurements of the force versus extension curves in stretched single stranded DNA, under conditions where the hydrogen bonding between complementary bases is inhibited, provide a new handle for the study of self-avoiding effects in…
Using Langevin Dynamic simulations, we study effects of the shear force on the rupture of a double stranded DNA molecule. The model studied here contains two single diblock copolymers interacting with each other. The elastic constants of…
We study numerically the effect of sequence heterogeneity on the thermodynamic properties of a Poland-Scheraga model for DNA denaturation taking into account self-avoidance, i.e. with exponent c_p=2.15 for the loop length probability…
We consider a hydrogen atom confined in a thick brane embedded in a higher-dimensional space. Due to effects of the extra dimensions, the gravitational potential is amplified in distances smaller than the size of the supplementary space, in…
Dimensional reduction occurs when the critical behavior of one system can be related to that of another system in a lower dimension. We show that this occurs for directed branched polymers (DBP) by giving an exact relationship between DBP…
We report extensive simulations of the relaxation dynamics of a self-avoiding polymer confined inside a cylindrical pore. In particular, we concentrate on examining how confinement influences the scaling behavior of the global relaxation…
We study the effects of the sequence on the propagation of nonlinear excitations in simple models of DNA, and how those effects are modified by noise. Starting from previous results on soliton dynamics on lattices defined by aperiodic…
We present an extension of the Edwards model for conformations of individual chain molecules in solvents in terms of fractional Brownian motion, and discuss the excluded volume effect on the end-to-end length of such trajectories or…
The size of a zero thickness (no excluded volume) polymer ring is shown to scale with chain length $N$ in the same way as the size of the excluded volume (self-avoiding) linear polymer, as $N^{\nu}$, where $\nu \approx 0.588$. The…
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…
The expansion factor, $\alpha^{2}=\langle s_{N}^{2}\rangle/\langle s_{N}^{2}\rangle_{0}$, of branched molecules in the melt state is estimated. The equilibrium expansion factor is determined as the point in which all the inhomogeneity terms…
Force-induced deformations of a self-avoiding chain confined inside a cylindrical cavity, with diameter $D$, are probed using molecular dynamics simulations, scaling analysis, and analytical calculations. We obtain and confirm a simple…
The recently proposed compressed backbone theory suggested that the intrinsic curvature in DNA can result from a geometric mismatch between the specific backbone length and optimal base stacking orientations. It predicted that the curvature…
DNA is structurally and mechanically altered by the binding of intercalator molecules. Intercalation strongly affects the force-extension behavior of DNA, in particular the overstretching transition. We present a statistical model that…
The symmetries of the DNA double helix require a new term in its linear response to stress: the coupling between twist and stretch. Recent experiments with torsionally-constrained single molecules give the first direct measurement of this…
The work addresses the analogy between trivial knotting and excluded volume in looped polymer chains of moderate length, $N<N_0$, where the effects of knotting are small. A simple expression for the swelling seen in trivially knotted loops…
Effects of Kaluza-Klein excitations associated with extra dimensions with large radius compactifications on the Fermi constant are explored. It is shown that the current precision determinations of the Fermi constant, of the fine structure…
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…
A double stranded DNA molecule under the stress of a pulling force acting on the strand terminals exhibits a partially denatured structure or can be completely unzipped depending the magnitude of the pulling force. A scaling argument for…
Stretched exponential probability density functions (pdf), having the form of the exponential of minus a fractional power of the argument, are commonly found in turbulence and other areas. They can arise because of an underlying random…