Dynamics of unbinding of polymers in a random medium

We have studied the aging effect on the dynamics of unbinding of a double stranded directed polymer in a random medium. By using the Monte Carlo dynamics of a lattice model in two dimensions, for which disorder is known to be relevant, the unbinding dynamics is studied by allowing the bound polymer to relax in the random medium for a waiting time and then allowing the two strands to unbind. The subsequent dynamics is formulated in terms of the overlap of the two strands and also the overlap of each polymer with the configuration at the start of the unbinding process. The interrelations between the two and the nature of the dependence on the waiting time are studied.Comment: 7 pages, latex, 3 figures, To appear in J. Chem. Phy

Phase Transitions of Single Semi-stiff Polymer Chains

We study numerically a lattice model of semiflexible homopolymers with nearest neighbor attraction and energetic preference for straight joints between bonded monomers. For this we use a new algorithm, the "Pruned-Enriched Rosenbluth Method" (PERM). It is very efficient both for relatively open configurations at high temperatures and for compact and frozen-in low-T states. This allows us to study in detail the phase diagram as a function of nn-attraction epsilon and stiffness x. It shows a theta-collapse line with a transition from open coils to molten compact globules (large epsilon) and a freezing transition toward a state with orientational global order (large stiffness x). Qualitatively this is similar to a recently studied mean field theory (Doniach et al. (1996), J. Chem. Phys. 105, 1601), but there are important differences. In contrast to the mean field theory, the theta-temperature increases with stiffness x. The freezing temperature increases even faster, and reaches the theta-line at a finite value of x. For even stiffer chains, the freezing transition takes place directly without the formation of an intermediate globule state. Although being in contrast with mean filed theory, the latter has been conjectured already by Doniach et al. on the basis of low statistics Monte Carlo simulations. Finally, we discuss the relevance of the present model as a very crude model for protein folding.Comment: 11 pages, Latex, 8 figure

Structural insights into the nucleic acid remodeling mechanisms of the yeast THO-Sub2 complex

The yeast THO complex is recruited to active genes and interacts with the RNA-dependent ATPase Sub2 to facilitate the formation of mature export-competent messenger ribonucleoprotein particles and to prevent the co-transcriptional formation of RNA:DNA-hybrid-containing structures. How THO-containing complexes function at the mechanistic level is unclear. Here, we elucidated a 3.4 angstrom resolution structure of Saccharomyces cerevisiae THO-Sub2 by cryoelectron microscopy. THO subunits Tho2 and Hpr1 intertwine to form a platform that is bound by Mft1, Thp2, and Text. The resulting complex homodimerizes in an asymmetric fashion, with a Sub2 molecule attached to each protomer. The homodimerization interfaces serve as a fulcrum for a seesaw-like movement concomitant with conformational changes of the Sub2 ATPase. The overall structural architecture and topology suggest the molecular mechanisms of nucleic acid remodeling during mRNA biogenesis.We thank Daniel Bollschweiler and Tillman Schäfer at the MPIB cryo-EM facility..

Scaling of fluctuation for Directed polymers with random interaction

Using a finite size scaling form for reunion probability, we show numerically the existence of a binding-unbinding transition for Directed polymers with random interaction. The cases studied are (A1) two chains in 1+1 dimensions, (A2) two chains in 2+1 dimensions and (B) three chains in 1+1 dimensions. A similar finite size scaling form for fluctuation establishes a disorder induced transition with identical exponents for cases A2 and B. The length scale exponents in all the three cases are in agreement with previous exact renormalization group results.Comment: Revtex, 4 postscript figures available on request (email: [email protected]); To appear in J. Phys. A Letter