Slow nucleic acid unzipping kinetics from sequence-defined barriers

Recent experiments on unzipping of RNA helix-loop structures by force have shown that about 40-base molecules can undergo kinetic transitions between two well-defined `open' and `closed' states, on a timescale = 1 sec [Liphardt et al., Science 297, 733-737 (2001)]. Using a simple dynamical model, we show that these phenomena result from the slow kinetics of crossing large free energy barriers which separate the open and closed conformations. The dependence of barriers on sequence along the helix, and on the size of the loop(s) is analyzed. Some DNAs and RNAs sequences that could show dynamics on different time scales, or three(or more)-state unzipping, are proposed.Comment: 8 pages Revtex, including 4 figure

Vector meson production at low x from gauge/gravity duality

We use gauge/gravity duality to study vector meson (J/?, ? 0 , ?, ?) production in electron-proton scattering, in the limit of high center of mass energy at fixed momentum transfer, corresponding to the limit of low Bjorken x, where the process is dominated by pomeron exchange. Our approach considers the pomeron at strong coupling, described by the graviton Regge trajectory in AdS space with a hard-wall to mimic confinement effects. Both the proton and vector mesons are described by simple holographic wave functions in AdS. This model agrees with HERA H1 data with a ? 2 per degree of freedom below one on total cross-sections, and below two on differential cross-sections, confirming the success of previous studies that model low x DIS and DVCS using gauge/gravity duality

A New Atom Trap: The Annular Shell Atom Trap (ASAT)

In the course of exploring some aspects of atom guiding in a hollow, optical fiber, a small negative potential energy well was found just in front of the repulsive or guiding barrier. This results from the optical dipole and the van der Waals potentials. The ground state for atoms bound in this negative potential well was determined by numerically solving the Schrodinger eq. and it was found that this negative well could serve as an atom trap. This trap is referred to as the Annular Shell Atom Trap or ASAT because of the geometry of the trapped atoms which are located in the locus of points defining a very thin annular shell just in front of the guiding barrier. A unique feature of the ASAT is the compression of the atoms from the entire volume to the volume of the annular shell resulting in a very high density of atoms in this trap. This trap may have applications to very low temperatures using evaporative cooling and possibly the formation of BEC. Finally, a scheme is discussed for taking advantage of the de Broglie wavelength to store atoms in a bottle trap based on the inability of long de Broglie wavelengths to escape through a selective de Broglie wavelength filter in the atom bottle trap.Comment: 13 pages total, 5 figure

Deeply Virtual Compton Scattering from Gauge/Gravity Duality

We use gauge/gravity duality to study deeply virtual Compton scattering (DVCS) in the limit of high center of mass energy at fixed momentum transfer, corresponding to the limit of low Bjorken x, where the process is dominated by the exchange of the pomeron. Using conformal Regge theory we review the form of the amplitude for pomeron exchange, both at strong and weak 't Hooft coupling. At strong coupling, the pomeron is described as the graviton Regge trajectory in AdS space, with a hard wall to mimic confinement effects. This model agrees with HERA data in a large kinematical range. The behavior of the DVCS cross section for very high energies, inside saturation, can be explained by a simple AdS black disk model. In a restricted kinematical window, this model agrees with HERA data as well.Comment: 48 pages, 10 figures; typos fixed, several clarifying remarks adde

Inflationary RSII Model with a Matter in the Bulk and Exponential Potential of Tachyon Field

In this paper we study a tachyon cosmological model based on dynamics of a 3-brane in the second Randall-Sundrum (RSII) model extended to include matter in the bulk. The presence of matter in the bulk changes warp factor which leads to modification of inflationary dynamics. The additional brane behaves effectively as a tachyon. We calculate numerically observation parameters of inflation: the scalar spectral index ($n_s$) and the tensor-to-scalar ratio ($r$) for the exponential potential of tachyon field.Comment: 9 pages, 1 figure, will be published in the Special Issue of Facta Universitatis, Series: Physics, Chemistry and Technology devoted to the SEENET-MTP Balkan Workshop BSW2018 (3-14 June 2018

Numerical Calculation of Hubble Hierarchy Parameters and Observational Parameters of Inflation

We present results obtained by a software we developed for computing observational cosmological inflation parameters: the scalar spectral index ($n_s$) and the tensor-to-scalar ratio ($r$) for a standard single field and tachyon inflation, as well as for a tachyon inflation in the second Randall-Sundrum model with an additional radion field. The calculated numerical values of observational parameters are compared with the latest results of observations obtained by the Planck Collaboration. The program is written in C/C++. The \textit{GNU Scientific Library} is used for some of the numerical computations and R language is used for data analysis and plots.Comment: 8 pages, 5 figures, based on talk presented at The 10th Jubilee Conference of the Balkan Physical Union (BPU10), 26-30 August 2018 (Sofia, Bulgaria