Geometry and topology of knotted ring polymers in an array of obstacles

We study knotted polymers in equilibrium with an array of obstacles which models confinement in a gel or immersion in a melt. We find a crossover in both the geometrical and the topological behavior of the polymer. When the polymers' radius of gyration, $R_G$, and that of the region containing the knot, $R_{G,k}$, are small compared to the distance b between the obstacles, the knot is weakly localised and $R_G$ scales as in a good solvent with an amplitude that depends on knot type. In an intermediate regime where $R_G > b > R_{G,k}$, the geometry of the polymer becomes branched. When $R_{G,k}$ exceeds b, the knot delocalises and becomes also branched. In this regime, $R_G$ is independent of knot type. We discuss the implications of this behavior for gel electrophoresis experiments on knotted DNA in weak fields.Comment: 4 pages, 6 figure

Unbinding of mutually avoiding random walks and two dimensional quantum gravity

We analyze the unbinding transition for a two dimensional lattice polymer in which the constituent strands are mutually avoiding random walks. At low temperatures the strands are bound and form a single self-avoiding walk. We show that unbinding in this model is a strong first order transition. The entropic exponents associated to denaturated loops and end-segments distributions show sharp differences at the transition point and in the high temperature phase. Their values can be deduced from some exact arguments relying on a conformal mapping of copolymer networks into a fluctuating geometry, i.e. in the presence of quantum gravity. An excellent agreement between analytical and numerical estimates is observed for all cases analized.Comment: 9 pages, 11 figures, revtex

Fractional Brownian motion and the critical dynamics of zipping polymers

We consider two complementary polymer strands of length $L$ attached by a common end monomer. The two strands bind through complementary monomers and at low temperatures form a double stranded conformation (zipping), while at high temperature they dissociate (unzipping). This is a simple model of DNA (or RNA) hairpin formation. Here we investigate the dynamics of the strands at the equilibrium critical temperature $T=T_c$ using Monte Carlo Rouse dynamics. We find that the dynamics is anomalous, with a characteristic time scaling as $\tau \sim L^{2.26(2)}$, exceeding the Rouse time $\sim L^{2.18}$. We investigate the probability distribution function, the velocity autocorrelation function, the survival probability and boundary behaviour of the underlying stochastic process. These quantities scale as expected from a fractional Brownian motion with a Hurst exponent $H=0.44(1)$. We discuss similarities and differences with unbiased polymer translocation.Comment: 7 pages, 8 figure

Stiffness dependence of critical exponents of semiflexible polymer chains situated on two-dimensional compact fractals

We present an exact and Monte Carlo renormalization group (MCRG) study of semiflexible polymer chains on an infinite family of the plane-filling (PF) fractals. The fractals are compact, that is, their fractal dimension $d_f$ is equal to 2 for all members of the fractal family enumerated by the odd integer $b$ ($3\le b< \infty$). For various values of stiffness parameter $s$ of the chain, on the PF fractals (for $3\le b\le 9$) we calculate exactly the critical exponents $\nu$ (associated with the mean squared end-to-end distances of polymer chain) and $\gamma$ (associated with the total number of different polymer chains). In addition, we calculate $\nu$ and $\gamma$ through the MCRG approach for $b$ up to 201. Our results show that, for each particular $b$, critical exponents are stiffness dependent functions, in such a way that the stiffer polymer chains (with smaller values of $s$) display enlarged values of $\nu$, and diminished values of $\gamma$. On the other hand, for any specific $s$, the critical exponent $\nu$ monotonically decreases, whereas the critical exponent $\gamma$ monotonically increases, with the scaling parameter $b$. We reflect on a possible relevance of the criticality of semiflexible polymer chains on the PF family of fractals to the same problem on the regular Euclidean lattices.Comment: 22 pages, 6 figure

Stretching of a single-stranded DNA: Evidence for structural transition

Recent experiments have shown that the force-extension (F-x) curve for single-stranded DNA (ssDNA) consisting only of adenine [poly(dA)] is significantly different from thymine [poly(dT)]. Here, we show that the base stacking interaction is not sufficient to describe the F-x curves as seen in the experiments. A reduction in the reaction co-ordinate arising from the formation of helix at low forces and an increase in the distance between consecutive phosphates of unstacked bases in the stretched state at high force in the proposed model, qualitatively reproduces the experimentally observed features. The multi-step plateau in the F-x curve is a signature of structural change in ssDNA.Comment: 10 pages, 4 figure

Does changing the pulling direction give better insight into biomolecules?

Single molecule manipulation techniques reveal that the mechanical resistance of a protein depends on the direction of the applied force. Using a lattice model of polymers, we show that changing the pulling direction leads to different phase diagrams. The simple model proposed here indicates that in one case the system undergoes a transition akin to the unzipping of a $\beta$ sheet, while in the other case the transition is of a shearing (slippage) nature. Our results are qualitatively similar to experimental results. This demonstrates the importance of varying the pulling direction since this may yield enhanced insights into the molecular interactions responsible for the stability of biomolecules.Comment: RevTeX v4, 10 pages with 6 eps figure