To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation.

For strong interactions, we find evidence for an emergent incompressible Mott insulating phase.

Transport properties are among the defining characteristics of many important phases in condensed matter physics. In the presence of strong correlations they are difficult to predict even for model systems like the Hubbard model. In real materials they are in general obscured by additional complications including impurities, lattice defects or multi-band effects. Ultracold atoms in contrast offer the possibility to study transport and out-of-equilibrium phenomena in a clean and well-controlled environment and can therefore act as a quantum simulator for condensed matter systems. Here we studied the expansion of an initially confined fermionic quantum gas in the lowest band of a homogeneous optical lattice. While we observe ballistic transport for non-interacting atoms, even small interactions render the expansion almost bimodal with a dramatically reduced expansion velocity. The dynamics is independent of the sign of the interaction, revealing a novel, dynamic symmetry of the Hubbard model.In solid state physics, transport properties are among the key observables, the most prominent example being the electrical conductivity, which e.g. allows to distinguish normal conductors from insulators or superconductors. Furthermore, many of today's most intriguing solid state phenomena manifest themselves in transport properties, examples including high-temperature superconductivity, giant magnetoresistance, quantum hall physics, topological insulators and disorder phenomena. Especially in strongly correlated systems, where the interactions between the conductance electrons are important, transport properties are difficult to calculate beyond the linear response regime. In general, predicting out-of-equilibrium fermionic dynamics represents an even harder problem than the prediction of static properties like the nature of the ground state. In real solids further complications arise due to the effects of e.g. impurities, lattice defects and phonons. These complications render an experimental investigation in a clean and well controlled ultracold atom system highly desirable. While the last years have seen dramatic progress in the control of quantum gases in optical lattices [1-3], a thorough understanding of the dynamics in these systems is still lacking. Genuine dynamical experiments can not only uncover new dynamic phenomena but are also essential to gain insight into the timescales needed to achieve equilibrium in the lattice [4,5] or to adiabatically load into the lattice [6,7].Using both bosonic and fermionic [8-10] atoms, it has become possible to simulate models of strongly interacting quantum particles, for which the Hubbard model [11] * ulrich.schneider@lmu.de is probably the most important example. A major advantage of these systems compared to real solids is the possibility to change all relevant parameters in real-time by e.g. varying laser intensities or magnetic fields. While first studies of dynamical properties of both bosonic and fermionic quantum gases [12][13][14] have already been performed, a remaining...

We report on the creation of an ultracold dipolar gas of fermionic 23 Na 40 K molecules in their absolute rovibrational and hyperfine ground state. Starting from weakly bound Feshbach molecules, we demonstrate hyperfine resolved two-photon transfer into the singlet X 1 Σ þ jv ¼ 0; J ¼ 0i ground state, coherently bridging a binding energy difference of 0.65 eV via stimulated rapid adiabatic passage. The spin-polarized, nearly quantum degenerate molecular gas displays a lifetime longer than 2.5 s, highlighting NaK's stability against two-body chemical reactions. A homogeneous electric field is applied to induce a dipole moment of up to 0.8 D. With these advances, the exploration of many-body physics with strongly dipolar Fermi gases of 23 Na 40 K molecules is within experimental reach. DOI: 10.1103/PhysRevLett.114.205302 PACS numbers: 67.85.−d, 03.75.Ss, 33.20.−t, 37.10.Mn Quantum gases of dipolar molecules promise to become a platform for precision measurements, quantum information processing, high-speed quantum simulation, and the creation of novel many-body systems [1][2][3]. The long-range, anisotropic nature of electric dipolar interactions between molecules is expected to yield novel types of order, such as topological superfluidity with fermionic molecules [4][5][6], interlayer pairing between two-dimensional systems [7,8], and the formation of dipolar quantum crystals [9]. The necessary prerequisite is the full control over the molecules' translational, electronic, vibrational, rotational, and nuclear spin degrees of freedom [10]. In pioneering work on 40 K 87 Rb and nondipolar 133 Cs 2 , weakly bound molecules were associated from ultracold atoms via Feshbach resonances and were subsequently coherently transferred into the absolute rovibrational ground state via a two-photon stimulated rapid adiabatic passage (STIRAP) [11][12][13][14][15]. Hyperfine control of the KRb molecules was demonstrated using microwave radiation [16]. Ground state KRb molecules are chemically unstable against two-body collisions, as the reaction KRb þ KRb → K 2 þ Rb 2 is energetically allowed. This enabled studies of quantum-state controlled chemical reactions [17,18], but it also led to loss and heating of the trapped molecules. Loading of KRb molecules into optical lattice potentials efficiently suppressed the reactions and enhanced the lifetime of molecular samples [19][20][21].For the study of collisionally dense molecular gases in the quantum regime, molecules that are stable against two-body collisions are of great interest. Possible choices among the alkali-metal dimers were summarized in Ref. [ 2 =ð4πϵ 0 ℏ 2 Þ (m NaK denotes the molecular mass) reaches 0.6 μm, comparable to the interparticle spacing of 1.6 μm for the realized peak densities of n 0 ¼ 2.5 × 10 11 cm −3 . The corresponding dipolar interaction energy E d ¼ d 2 n 0 =ð4πϵ 0 Þ approaches 5% of the local Fermi energy and should therefore dominate the many-body physics of the gas.Our starting point is a gas of about 7 × 10 3 Feshbach molecules of 23 Na 40 K, tr...

Background: The prediction of a consensus structure for a set of related RNAs is an important first step for subsequent analyses. RNAalifold, which computes the minimum energy structure that is simultaneously formed by a set of aligned sequences, is one of the oldest and most widely used tools for this task. In recent years, several alternative approaches have been advocated, pointing to several shortcomings of the original RNAalifold approach.

The RFAM database defines families of ncRNAs by means of sequence similarities that are sufficient to establish homology. In some cases, such as microRNAs and box H/ACA snoRNAs, functional commonalities define classes of RNAs that are characterized by structural similarities, and typically consist of multiple RNA families. Recent advances in high-throughput transcriptomics and comparative genomics have produced very large sets of putative noncoding RNAs and regulatory RNA signals. For many of them, evidence for stabilizing selection acting on their secondary structures has been derived, and at least approximate models of their structures have been computed. The overwhelming majority of these hypothetical RNAs cannot be assigned to established families or classes. We present here a structure-based clustering approach that is capable of extracting putative RNA classes from genome-wide surveys for structured RNAs. The LocARNA (local alignment of RNA) tool implements a novel variant of the Sankoff algorithm that is sufficiently fast to deal with several thousand candidate sequences. The method is also robust against false positive predictions, i.e., a contamination of the input data with unstructured or nonconserved sequences. We have successfully tested the LocARNA-based clustering approach on the sequences of the RFAM-seed alignments. Furthermore, we have applied it to a previously published set of 3,332 predicted structured elements in the Ciona intestinalis genome (Missal K, Rose D, Stadler PF (2005) Noncoding RNAs in Ciona intestinalis. Bioinformatics 21 (Supplement 2): i77–i78). In addition to recovering, e.g., tRNAs as a structure-based class, the method identifies several RNA families, including microRNA and snoRNA candidates, and suggests several novel classes of ncRNAs for which to date no representative has been experimentally characterized.

Interactions lie at the heart of correlated many-body quantum phases. Typically, the interactions between microscopic particles are described as two-body interactions. However, it has been shown that higher-order multi-body interactions could give rise to novel quantum phases with intriguing properties. So far, multi-body interactions have been observed as inelastic loss resonances in three- and four-body recombinations of atom-atom and atom-molecule collisions. Here we demonstrate the presence of effective multi-body interactions in a system of ultracold bosonic atoms in a three-dimensional optical lattice, emerging through virtual transitions of particles from the lowest energy band to higher energy bands. We observe such interactions up to the six-body case in time-resolved traces of quantum phase revivals, using an atom interferometric technique that allows us to precisely measure the absolute energies of atom number states at a lattice site. In addition, we show that the spectral content of these time traces can reveal the atom number statistics at a lattice site, similar to foundational experiments in cavity quantum electrodynamics that yield the statistics of a cavity photon field. Our precision measurement of multi-body interaction energies provides crucial input for the comparison of optical-lattice quantum simulators with many-body quantum theory.

We measure the relative phase of two Bose-Einstein condensates confined in a radio frequency induced double-well potential on an atom chip. We observe phase coherence between the separated condensates for times up to approximately 200 ms after splitting, a factor of 10 longer than the phase diffusion time expected for a coherent state for our experimental conditions. The enhanced coherence time is attributed to number squeezing of the initial state by a factor of 10. In addition, we demonstrate a rotationally sensitive (Sagnac) geometry for a guided atom interferometer by propagating the split condensates.