Diffusion-limited loop formation of semiflexible polymers: Kramers theory and the intertwined time scales of chain relaxation and closing

We show that Kramers rate theory gives a straightforward, accurate estimate of the closing time $\tau_c$ of a semiflexible polymer that is valid in cases of physical interest. The calculation also reveals how the time scales of chain relaxation and closing are intertwined, illuminating an apparent conflict between two ways of calculating $\tau_c$ in the flexible limit.Comment: Europhys. Lett., 2003 (in press). 8 pages, 3 figures. See also, physics/0101087 for physicist's approach to and the importance of semiflexible polymer looping, in DNA replicatio

Probing protein-protein interactions by dynamic force correlated spectroscopy (FCS)

We develop a formalism for single molecule dynamic force spectroscopy to map the energy landscape of protein-protein complex ($P_1$$P_2$). The joint distribution $P(\tau_1,\tau_2)$ of unbinding lifetimes $\tau_1$ and $\tau_2$ measurable in a compression-tension cycle, which accounts for the internal relaxation dynamics of the proteins under tension, shows that the histogram of $\tau_1$ is not Poissonian. The theory is applied to the forced unbinding of protein $P_1$, modeled as a wormlike chain, from $P_1$$P_2$. We propose a new class of experiments which can resolve the effect of internal protein dynamics on the unbinding lifetimes.Comment: 12 pages, 3 figures, accepted to Phys. Rev. Let