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

Binary black hole mergers in gaseous disks: Simulations in general relativity

Simultaneous gravitational and electromagnetic wave observations of merging black hole binaries (BHBHs) can provide unique opportunities to study gravitation physics, accretion and cosmology. Here we perform fully general relativistic, hydrodynamic simulations of equal-mass, nonspinning BHBHs coalescing in a circumbinary disk. We evolve the metric using the Baumgarte-Shapiro-Shibata-Nakamura (BSSN) formulation of Einstein's field equations with standard moving puncture gauge conditions. We handle the hydrodynamics via a high-resolution shock-capturing (HRSC) scheme. We track the inspiral starting from a binary separation of 10M, where M is the total binary mass. We take the disks to have an inner radius at R_in~15M to account for the hollow created by the binary torques. Our disks extend to R=65M and have an initial scale height of H/R=0.03-0.11. The gas is governed by a Gamma-law EOS, with Gamma equal to 5/3, 4/3, and 1.1. Disks are allowed to relax in the "early inspiral" epoch to provide quasistationary realistic initial data. We then evolve the metric and matter during the "late inspiral and merger" epoch. The later simulations are designed to track BHBH inspiral following disk-binary decoupling, through merger and ringdown, terminating before viscosity has time to fill the hollow about the remnant. We compute the gas flow and accretion rate and estimate the electromagnetic luminosity due to bremsstrahlung and synchrotron emission as a perturbation for optically thin disks. The synchrotron component of the luminosity peaks in the infrared band and should be detectable by WFIRST and possibly the LSST for a 10^8 M_sun binary embedded in a disk with a density n~10^12/cm^3 at z=1, beginning with a maximum value of $L~10^46 n_12^2 M_8^3 erg/s at decoupling, and decreasing steadily over a timescale of ~100 M_8 hours to a value of L~10^45 n_12^2 M_8^3 erg/s at merger.Comment: accepted by PR

Tunable temperature induced magnetization jump in a GdVO3 single crystal

We report a novel feature of the temperature induced magnetization jump observed along the a-axis of the GdVO3 single crystal at temperature TM = 0.8 K. Below TM, the compound shows no coercivity and remanent magnetization indicating a homogenous antiferromagnetic structure. However, we will demonstrate that the magnetic state below TM is indeed history dependent and it shows up in different jumps in the magnetization only when warming the sample through TM. Such a magnetic memory effect is highly unusual and suggesting different domain arrangements in the supposedly homogenous antiferromagnetic phase of the compound.Comment: 17 pages, 8 Figure

The Parton Model and its Applications

This is a review of the program we started in 1968 to understand and generalize Bjorken scaling and Feynman's parton model in a canonical quantum field theory. It is shown that the parton model proposed for deep inelastic electron scatterings can be derived if a transverse momentum cutoff is imposed on all particles in the theory so that the impulse approximation holds. The deep inelastic electron-positron annihilation into a nucleon plus anything else is related by the crossing symmetry of quantum field theory to the deep inelastic electron-nucleon scattering. We have investigated the implication of crossing symmetry and found that the structure functions satisfy a scaling behavior analogous to the Bjorken limit for deep inelastic electron scattering. We then find that massive lepton pair production in collisions of two high energy hadrons can be treated by the parton model with an interesting scaling behavior for the differential cross sections. This turns out to be the first example of a class of hard processes involving two initial hadrons.Comment: Contribution to a book to be published by World Scientific for the occasion of 50 Years of Quarks. 17 pages, 4 figure

Uncertainties of predictions from parton distribution functions II: the Hessian method

We develop a general method to quantify the uncertainties of parton distribution functions and their physical predictions, with emphasis on incorporating all relevant experimental constraints. The method uses the Hessian formalism to study an effective chi-squared function that quantifies the fit between theory and experiment. Key ingredients are a recently developed iterative procedure to calculate the Hessian matrix in the difficult global analysis environment, and the use of parameters defined as components along appropriately normalized eigenvectors. The result is a set of 2d Eigenvector Basis parton distributions (where d=16 is the number of parton parameters) from which the uncertainty on any physical quantity due to the uncertainty in parton distributions can be calculated. We illustrate the method by applying it to calculate uncertainties of gluon and quark distribution functions, W boson rapidity distributions, and the correlation between W and Z production cross sections.Comment: 30 pages, Latex. Reference added. Normalization of Hessian matrix changed to HEP standar

Breaking an image encryption algorithm based on chaos

Recently, a chaos-based image encryption algorithm called MCKBA (Modified Chaotic-Key Based Algorithm) was proposed. This paper analyzes the security of MCKBA and finds that it can be broken with a differential attack, which requires only four chosen plain-images. Performance of the attack is verified by experimental results. In addition, some defects of MCKBA, including insensitivity with respect to changes of plain-image/secret key, are reported.Comment: 10 pages, 4 figure