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

Scaling of Hamiltonian walks on fractal lattices

We investigate asymptotical behavior of numbers of long Hamiltonian walks (HWs), i.e. self-avoiding random walks that visit every site of a lattice, on various fractal lattices. By applying an exact recursive technique we obtain scaling forms for open HWs on 3-simplex lattice, Sierpinski gasket, and their generalizations: Given-Mandelbrot (GM), modified Sierpinski gasket (MSG) and n-simplex fractal families. For GM, MSG and n-simplex lattices with odd values of n, number of open HWs $Z_N$, for the lattice with $N\gg 1$ sites, varies as $\omega^N N^\gamma$. We explicitly calculate exponent $\gamma$ for several members of GM and MSG families, as well as for n-simplices with n=3,5, and 7. For n-simplex fractals with even n we find different scaling form: $Z_N\sim \omega^N \mu^{N^{1/d_f}}$, where $d_f$ is fractal dimension of the lattice, which also differs from the formula expected for homogeneous lattices. We discuss possible implications of our results on studies of real compact polymers.Comment: 19 pages, 13 figures, RevTex4; extended Introduction, several references added; one figure added in section II; corrected typos; version accepted for publication in Phys.Rev.

Force induced triple point for interacting polymers

We show the existence of a force induced triple point in an interacting polymer problem that allows two zero-force thermal phase transitions. The phase diagrams for three different models of mutually attracting but self avoiding polymers are presented. One of these models has an intermediate phase and it shows a triple point but not the others. A general phase diagram with multicritical points in an extended parameter space is also discussed.Comment: 4 pages, 8 figures, revtex

Universality of collapsing two-dimensional self-avoiding trails

Results of a numerically exact transfer matrix calculation for the model of Interacting Self-Avoiding Trails are presented. The results lead to the conclusion that, at the collapse transition, Self-Avoiding Trails are in the same universality class as the O(n=0) model of Blote and Nienhuis (or vertex-interacting self-avoiding walk), which has thermal exponent $\nu=12/23$, contrary to previous conjectures.Comment: Final version, accepted for publication in Journal of Physics A; 9 pages; 3 figure

Effects of Eye-phase in DNA unzipping

The onset of an "eye-phase" and its role during the DNA unzipping is studied when a force is applied to the interior of the chain. The directionality of the hydrogen bond introduced here shows oscillations in force-extension curve similar to a "saw-tooth" kind of oscillations seen in the protein unfolding experiments. The effects of intermediates (hairpins) and stacking energies on the melting profile have also been discussed.Comment: RevTeX v4, 9 pages with 7 eps figure

Force induced stretched state: Effects of temperature

A model of self avoiding walks with suitable constraint has been developed to study the effect of temperature on a single stranded DNA (ssDNA) in the constant force ensemble. Our exact calculations for small chains show that the extension (reaction co-ordinate) may increase or decrease with the temperature depending upon the applied force. The simple model developed here which incorporates semi-microscopic details of base direction provide an explanation of the force induced transitions in ssDNA as observed in experiments.Comment: 5 pages, 8 figures, RevTex

Theory of Boundary Effects in Invasion Percolation

We study the boundary effects in invasion percolation with and without trapping. We find that the presence of boundaries introduces a new set of surface critical exponents, as in the case of standard percolation. Numerical simulations show a fractal dimension, for the region of the percolating cluster near the boundary, remarkably different from the bulk one. We find a logarithmic cross-over from surface to bulk fractal properties, as one would expect from the finite-size theory of critical systems. The distribution of the quenched variables on the growing interface near the boundary self-organises into an asymptotic shape characterized by a discontinuity at a value $x_c=0.5$, which coincides with the bulk critical threshold. The exponent $\tau^{sur}$ of the boundary avalanche distribution for IP without trapping is $\tau^{sur}=1.56\pm0.05$; this value is very near to the bulk one. Then we conclude that only the geometrical properties (fractal dimension) of the model are affected by the presence of a boundary, while other statistical and dynamical properties are unchanged. Furthermore, we are able to present a theoretical computation of the relevant critical exponents near the boundary. This analysis combines two recently introduced theoretical tools, the Fixed Scale Transformation (FST) and the Run Time Statistics (RTS), which are particularly suited for the study of irreversible self-organised growth models with quenched disorder. Our theoretical results are in rather good agreement with numerical data.Comment: 11 pages, 13 figures, revte

Sequence randomness and polymer collapse transitions

Contrary to expectations based on Harris' criterion, chain disorder with frustration can modify the universality class of scaling at the theta transition of heteropolymers. This is shown for a model with random two-body potentials in 2D on the basis of exact enumeration and accurate Monte Carlo results. When frustration grows beyond a certain finite threshold, the temperature below which disorder becomes relevant coincides with the theta one and scaling exponents definitely start deviating from those valid for homopolymers.Comment: 4 pages, 4 eps figure

Effects of Molecular Crowding on stretching of polymers in poor solvent

We consider a linear polymer chain in a disordered environment modeled by percolation clusters on a square lattice. The disordered environment is meant to roughly represent molecular crowding as seen in cells. The model may be viewed as the simplest representation of biopolymers in a cell. We show the existence of intermediate states during stretching arising as a consequence of molecular crowding. In the constant distance ensemble the force-extension curves exhibit oscillations. We observe the emergence of two or more peaks in the probability distribution curves signaling the coexistence of different states and indicating that the transition is discontinuous unlike what is observed in the absence of molecular crowding.Comment: 14 pages, 6 figure