Random RNA under tension

The Laessig-Wiese (LW) field theory for the freezing transition of random RNA secondary structures is generalized to the situation of an external force. We find a second-order phase transition at a critical applied force f = f_c. For f f_c, the extension L as a function of pulling force f scales as (f-f_c)^(1/gamma-1). The exponent gamma is calculated in an epsilon-expansion: At 1-loop order gamma = epsilon/2 = 1/2, equivalent to the disorder-free case. 2-loop results yielding gamma = 0.6 are briefly mentioned. Using a locking argument, we speculate that this result extends to the strong-disorder phase.Comment: 6 pages, 10 figures. v2: corrected typos, discussion on locking argument improve

Microscopic Model versus Systematic Low-Energy Effective Field Theory for a Doped Quantum Ferromagnet

We consider a microscopic model for a doped quantum ferromagnet as a test case for the systematic low-energy effective field theory for magnons and holes, which is constructed in complete analogy to the case of quantum antiferromagnets. In contrast to antiferromagnets, for which the effective field theory approach can be tested only numerically, in the ferromagnetic case both the microscopic and the effective theory can be solved analytically. In this way the low-energy parameters of the effective theory are determined exactly by matching to the underlying microscopic model. The low-energy behavior at half-filling as well as in the single- and two-hole sectors is described exactly by the systematic low-energy effective field theory. In particular, for weakly bound two-hole states the effective field theory even works beyond perturbation theory. This lends strong support to the quantitative success of the systematic low-energy effective field theory method not only in the ferromagnetic but also in the physically most interesting antiferromagnetic case.Comment: 34 pages, 1 figur

Characterization of CoRoT target fields with BEST: Identification of periodic variable stars in the IR01 field

We report on observations of the CoRoT IR01 field with the Berlin Exoplanet Search Telescope (BEST). BEST is a small aperture telescope with a wide field of view (FOV). It is dedicated to search for variable stars within the target fields of the CoRoT space mission to aid in minimizing false-alarm rates and identify potential targets for additional science. CoRoT's observational programm started in February 2007 with the "initial run" field (IR01) observed for about two months. BEST observed this field for 12 nights spread over three months in winter 2006. From the total of 30426 stars observed in the IR01 field 3769 were marked as suspected variable stars and 54 from them showed clear periodicity. From these 19 periodic stars are within the part of the CoRoT FOV covered in our data set

Ebbie: automated analysis and storage of small RNA cloning data using a dynamic web server

BACKGROUND: DNA sequencing is used ubiquitously: from deciphering genomes[1] to determining the primary sequence of small RNAs (smRNAs) [2-5]. The cloning of smRNAs is currently the most conventional method to determine the actual sequence of these important regulators of gene expression. Typical smRNA cloning projects involve the sequencing of hundreds to thousands of smRNA clones that are delimited at their 5' and 3' ends by fixed sequence regions. These primers result from the biochemical protocol used to isolate and convert the smRNA into clonable PCR products. Recently we completed a smRNA cloning project involving tobacco plants, where analysis was required for ~700 smRNA sequences[6]. Finding no easily accessible research tool to enter and analyze smRNA sequences we developed Ebbie to assist us with our study. RESULTS: Ebbie is a semi-automated smRNA cloning data processing algorithm, which initially searches for any substring within a DNA sequencing text file, which is flanked by two constant strings. The substring, also termed smRNA or insert, is stored in a MySQL and BlastN database. These inserts are then compared using BlastN to locally installed databases allowing the rapid comparison of the insert to both the growing smRNA database and to other static sequence databases. Our laboratory used Ebbie to analyze scores of DNA sequencing data originating from an smRNA cloning project[6]. Through its built-in instant analysis of all inserts using BlastN, we were able to quickly identify 33 groups of smRNAs from ~700 database entries. This clustering allowed the easy identification of novel and highly expressed clusters of smRNAs. Ebbie is available under GNU GPL and currently implemented on CONCLUSION: Ebbie was designed for medium sized smRNA cloning projects with about 1,000 database entries [6-8].Ebbie can be used for any type of sequence analysis where two constant primer regions flank a sequence of interest. The reliable storage of inserts, and their annotation in a MySQL database, BlastN[9] comparison of new inserts to dynamic and static databases make it a powerful new tool in any laboratory using DNA sequencing. Ebbie also prevents manual mistakes during the excision process and speeds up annotation and data-entry. Once the server is installed locally, its access can be restricted to protect sensitive new DNA sequencing data. Ebbie was primarily designed for smRNA cloning projects, but can be applied to a variety of RNA and DNA cloning projects[2,3,10,11]

Systematic Low-Energy Effective Field Theory for Magnons and Holes in an Antiferromagnet on the Honeycomb Lattice

Based on a symmetry analysis of the microscopic Hubbard and t-J models, a systematic low-energy effective field theory is constructed for hole-doped antiferromagnets on the honeycomb lattice. In the antiferromagnetic phase, doped holes are massive due to the spontaneous breakdown of the $SU(2)_s$ symmetry, just as nucleons in QCD pick up their mass from spontaneous chiral symmetry breaking. In the broken phase the effective action contains a single-derivative term, similar to the Shraiman-Siggia term in the square lattice case. Interestingly, an accidental continuous spatial rotation symmetry arises at leading order. As an application of the effective field theory we consider one-magnon exchange between two holes and the formation of two-hole bound states. As an unambiguous prediction of the effective theory, the wave function for the ground state of two holes bound by magnon exchange exhibits $f$-wave symmetry.Comment: 33 pages, 6 figure

Scaling regimes and critical dimensions in the Kardar-Parisi-Zhang problem

We study the scaling regimes for the Kardar-Parisi-Zhang equation with noise correlator R(q) ~ (1 + w q^{-2 \rho}) in Fourier space, as a function of \rho and the spatial dimension d. By means of a stochastic Cole-Hopf transformation, the critical and correction-to-scaling exponents at the roughening transition are determined to all orders in a (d - d_c) expansion. We also argue that there is a intriguing possibility that the rough phases above and below the lower critical dimension d_c = 2 (1 + \rho) are genuinely different which could lead to a re-interpretation of results in the literature.Comment: Latex, 7 pages, eps files for two figures as well as Europhys. Lett. style files included; slightly expanded reincarnatio

Homogeneous versus Spiral Phases of Hole-doped Antiferromagnets: A Systematic Effective Field Theory Investigation

Using the low-energy effective field theory for magnons and holes -- the condensed matter analog of baryon chiral perturbation theory for pions and nucleons in QCD -- we study different phases of doped antiferromagnets. We systematically investigate configurations of the staggered magnetization that provide a constant background field for doped holes. The most general configuration of this type is either constant itself or it represents a spiral in the staggered magnetization. Depending on the values of the low-energy parameters, a homogeneous phase, a spiral phase, or an inhomogeneous phase is energetically favored. The reduction of the staggered magnetization upon doping is also investigated.Comment: 35 pages, 5 figure

Systematic Low-Energy Effective Field Theory for Electron-Doped Antiferromagnets

In contrast to hole-doped systems which have hole pockets centered at $(\pm \frac{\pi}{2a},\pm \frac{\pi}{2a})$, in lightly electron-doped antiferromagnets the charged quasiparticles reside in momentum space pockets centered at $(\frac{\pi}{a},0)$ or $(0,\frac{\pi}{a})$. This has important consequences for the corresponding low-energy effective field theory of magnons and electrons which is constructed in this paper. In particular, in contrast to the hole-doped case, the magnon-mediated forces between two electrons depend on the total momentum $\vec P$ of the pair. For $\vec P = 0$ the one-magnon exchange potential between two electrons at distance $r$ is proportional to $1/r^4$, while in the hole case it has a $1/r^2$ dependence. The effective theory predicts that spiral phases are absent in electron-doped antiferromagnets.Comment: 25 pages, 7 figure

Critical Exponents of the KPZ Equation via Multi-Surface Coding Numerical Simulations

We study the KPZ equation (in D = 2, 3 and 4 spatial dimensions) by using a RSOS discretization of the surface. We measure the critical exponents very precisely, and we show that the rational guess is not appropriate, and that 4D is not the upper critical dimension. We are also able to determine very precisely the exponent of the sub-leading scaling corrections, that turns out to be close to 1 in all cases. We introduce and use a {\em multi-surface coding} technique, that allow a gain of order 30 over usual numerical simulations.Comment: 10 pages, 8 eps figures (2 figures added). Published versio

Identification of Variable Stars in COROT's First Main Observing Field (LRc1)

The COROT space mission will monitor several target fields for up to 150 days to perform asteroseismology and to search for extrasolar planets by photometric transits. Variable stars in the target fields are important objects for additional scientific studies but can also disturb the search for planetary transits. A variability characterization of the target fields prior to COROT observations is therefore important for two reasons: to find interesting variable stars to monitor further and to make an analysis of the impact of the variable stars on detecting extrasolar planet transits with COROT. The Berlin Exoplanet Search Telescope (BEST) is a small wide-angle telescope dedicated to high-precision photometry. It has observed a 9 square degree field of view centered at (alpha, delta)=(19h00m00.0s, +00deg01'55.2") (J2000.0) over 98 nights to search for variable stars in the surroundings of the first long-run target field (LRc1) of the COROT space mission. In this data set we identified 92 periodic variable stars, 86 of which are new discoveries and 6 of which are known from the General Catalogue of Variable Stars (GCVS). For five of the GCVS stars, variability could not be confirmed. Forty-three of the 92 detected periodic variable stars are identified as eclipsing binaries. We have evaluated the completeness of our survey for eclipsing binaries by comparing it to the expected fraction of eclipsing binaries based on Hipparcos observations. From this evaluation we show that the BEST data set presented here has a completeness of 20%-30% for periods longer than 1 day and is complete relative to Hipparcos for short-period binaries