Probing the elastic limit of DNA bending

Many structures inside the cell such as nucleosomes and protein-mediated DNA loops contain sharply bent double-stranded (ds) DNA. Therefore, the energetics of strong dsDNA bending constitutes an essential part of cellular thermodynamics. Although the thermomechanical behavior of long dsDNA is well described by the worm-like chain (WLC) model, the length limit of such elastic behavior remains controversial. To investigate the energetics of strong dsDNA bending, we measured the opening rate of small dsDNA loops with contour lengths of 40-200 bp using Fluorescence Resonance Energy Transfer (FRET). From the measured relationship of loop stability to loop size, we observed a transition between two separate bending regimes at a critical loop size below 100 bp. Above this loop size, the loop lifetime decreased with decreasing loop size in a manner consistent with an elastic bending stress. Below the critical loop size, however, the loop lifetime became less sensitive to loop size, indicative of softening of the double helix. The critical loop size was measured to be ~60 bp with sodium only and ~100 bp with 5 mM magnesium, which suggests that magnesium facilitates the softening transition. We show that our results are in quantitative agreement with the kinkable worm-like chain model. Furthermore, the model parameters constrained by our data can reproduce previously measured J factors between 50 and 200 bp. Our work provides powerful means to study dsDNA bending in the strong bending regime

Entropy of the Randall-Sundrum brane world with the generalized uncertainty principle

By introducing the generalized uncertainty principle, we calculate the entropy of the bulk scalar field on the Randall-Sundrum brane background without any cutoff. We obtain the entropy of the massive scalar field proportional to the horizon area. Here, we observe that the mass contribution to the entropy exists in contrast to all previous results, which is independent of the mass of the scalar field, of the usual black hole cases with the generalized uncertainty principle.Comment: 12 pages. The improved version published in Phys. Rev.

Observation of inhomogeneous domain nucleation in epitaxial Pb(Zr,Ti)O3 capacitors

We investigated domain nucleation process in epitaxial Pb(Zr,Ti)O3 capacitors under a modified piezoresponse force microscope. We obtained domain evolution images during polarization switching process and observed that domain nucleation occurs at particular sites. This inhomogeneous nucleation process should play an important role in an early stage of switching and under a high electric field. We found that the number of nuclei is linearly proportional to log(switching time), suggesting a broad distribution of activation energies for nucleation. The nucleation sites for a positive bias differ from those for a negative bias, indicating that most nucleation sites are located at ferroelectric/electrode interfaces

Lattice Calculation of Quarkonium Decay Matrix Elements

We calculate the NRQCD matrix elements for the decays of the lowest-lying S- and P-wave states of charmonium and bottomonium in quenched lattice QCD. We also compute the one-loop relations between the lattice and continuum matrix elements.Comment: 10 pages, LaTeX. Talk presented at the Quarkonium Physics Workshop, University of Illinois, Chicago, June 13-15, 199