A rapid method for assessing the RNA-binding potential of a protein

In recent years, evidence has emerged for the existence of many diverse types of RNA, which play roles in a wide range of biological processes in all kingdoms of life. These molecules generally do not, however, act in isolation, and identifying which proteins partner with RNA is a major challenge. Many methods, in vivo and in vitro, have been used to address this question, including combinatorial or high-throughput approaches, such as systematic evolution of ligands, cross-linking and immunoprecipitation and RNA immunoprecipitation combined with deep sequencing. However, most of these methods are not trivial to pursue and often require substantial optimization before results can be achieved. Here, we demonstrate a simple technique that allows one to screen proteins for RNA-binding properties in a gel-shift experiment and can be easily implemented in any laboratory. This assay should be a useful first-pass tool for assessing whether a protein has RNA- or DNA-binding properties, prior to committing resources to more complex procedure

Heavy Quark Fragmentation Functions for D-wave Quarkonium and Charmed Beauty Mesons

At the large transverse momentum region, the production of heavy-heavy bound-states such as charmonium, bottomonium, and $\bar bc$ mesons in high energy $e^+e^-$ and hadronic collisions is dominated by parton fragmentation. We calculate the heavy quark fragmentation functions into the D-wave quarkonium and $\bar bc$ mesons to leading order in the strong coupling constant and in the non-relativistic expansion. In the $\bar b c$ meson case, one set of its D-wave states is expected to lie below the open flavor threshold. The total fragmentation probability for a $\bar b$ antiquark to split into the D-wave $\bar b c$ mesons is about $2 \times 10^{-5}$, which implies that only 2\% of the total pseudo-scalar ground state $B_c$ comes from the cascades of these orbitally excited states.Comment: 26 pages in RevteX and 3 figures in postscript. Also available at http://www.ph.utexas.edu/~cheung/paper.htm

Conductance and persistent current of a quantum ring coupled to a quantum wire under external fields

The electronic transport of a noninteracting quantum ring side-coupled to a quantum wire is studied via a single-band tunneling tight-binding Hamiltonian. We found that the system develops an oscillating band with antiresonances and resonances arising from the hybridization of the quasibound levels of the ring and the coupling to the quantum wire. The positions of the antiresonances correspond exactly to the electronic spectrum of the isolated ring. Moreover, for a uniform quantum ring the conductance and the persistent current density were found to exhibit a particular odd-even parity related with the ring-order. The effects of an in-plane electric field was also studied. This field shifts the electronic spectrum and damps the amplitude of the persistent current density. These features may be used to control externally the energy spectra and the amplitude of the persistent current.Comment: Revised version, 7 pages and 9 figures. To appear in Phys. Rev.

Critical fields on the M5-brane and noncommutative open strings

The M5-brane is investigated near critical field-strength. We show that this limit on the M5-brane reduces to the noncommutative open string limit on the D4-brane. The reduction on a two-torus leads to both the noncommutative open string limit and the noncommutative Yang-Mills limit on the D3-brane. The decoupled noncommutative five-brane is identified with the strong coupling limit of the noncommutative open string theory on the D4-brane and S-duality on the noncommutative D3-brane is identified with a modular transformation on the five-brane. We argue that the open membrane metric defines a finite length scale on the worldvolume of the M5-brane in the decoupling limit. This length scale can be associated to the effective length scale of an open membrane.Comment: RevTex 16 pages, one figure,typos corrected and reference adde

A parton picture of de Sitter space during slow-roll inflation

It is well-known that expectation values in de Sitter space are afflicted by infra-red divergences. Long ago, Starobinsky proposed that infra-red effects in de Sitter space could be accommodated by evolving the long-wavelength part of the field according to the classical field equations plus a stochastic source term. I argue that--when quantum-mechanical loop corrections are taken into account--the separate-universe picture of superhorizon evolution in de Sitter space is equivalent, in a certain leading-logarithm approximation, to Starobinsky's stochastic approach. In particular, the time evolution of a box of de Sitter space can be understood in exact analogy with the DGLAP evolution of partons within a hadron, which describes a slow logarithmic evolution in the distribution of the hadron's constituent partons with the energy scale at which they are probed.Comment: 36 pages; uses iopart.cls and feynmp.sty. v2: Minor typos corrected. Matches version published in JCA

Features of heavy physics in the CMB power spectrum

The computation of the primordial power spectrum in multi-field inflation models requires us to correctly account for all relevant interactions between adiabatic and non-adiabatic modes around and after horizon crossing. One specific complication arises from derivative interactions induced by the curvilinear trajectory of the inflaton in a multi-dimensional field space. In this work we compute the power spectrum in general multi-field models and show that certain inflaton trajectories may lead to observationally significant imprints of `heavy' physics in the primordial power spectrum if the inflaton trajectory turns, that is, traverses a bend, sufficiently fast (without interrupting slow roll), even in cases where the normal modes have masses approaching the cutoff of our theory. We emphasise that turning is defined with respect to the geodesics of the sigma model metric, irrespective of whether this is canonical or non-trivial. The imprints generically take the form of damped superimposed oscillations on the power spectrum. In the particular case of two-field models, if one of the fields is sufficiently massive compared to the scale of inflation, we are able to compute an effective low energy theory for the adiabatic mode encapsulating certain relevant operators of the full multi-field dynamics. As expected, a particular characteristic of this effective theory is a modified speed of sound for the adiabatic mode which is a functional of the background inflaton trajectory and the turns traversed during inflation. Hence in addition, we expect non-Gaussian signatures directly related to the features imprinted in the power spectrum.Comment: 41 pages, 6 figures, references updated, minor modifications. Version to appear in JCAP. v4: Equations (4.28) and (4.30) and Figures 5 and 6 correcte