The IMG/M data management and analysis system v.7: content updates and new features.

The Integrated Microbial Genomes & Microbiomes system (IMG/M: https://img.jgi.doe.gov/m/) at the Department of Energy (DOE) Joint Genome Institute (JGI) continues to provide support for users to perform comparative analysis of isolate and single cell genomes, metagenomes, and metatranscriptomes. In addition to datasets produced by the JGI, IMG v.7 also includes datasets imported from public sources such as NCBI Genbank, SRA, and the DOE National Microbiome Data Collaborative (NMDC), or submitted by external users. In the past couple years, we have continued our effort to help the user community by improving the annotation pipeline, upgrading the contents with new reference database versions, and adding new analysis functionalities such as advanced scaffold search, Average Nucleotide Identity (ANI) for high-quality metagenome bins, new cassette search, improved gene neighborhood display, and improvements to metatranscriptome data display and analysis. We also extended the collaboration and integration efforts with other DOE-funded projects such as NMDC and DOE Biology Knowledgebase (KBase).

IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata.

Viruses are widely recognized as critical members of all microbiomes. Metagenomics enables large-scale exploration of the global virosphere, progressively revealing the extensive genomic diversity of viruses on Earth and highlighting the myriad of ways by which viruses impact biological processes. IMG/VR provides access to the largest collection of viral sequences obtained from (meta)genomes, along with functional annotation and rich metadata. A web interface enables users to efficiently browse and search viruses based on genome features and/or sequence similarity. Here, we present the fourth version of IMG/VR, composed of >15 million virus genomes and genome fragments, a ≈6-fold increase in size compared to the previous version. These clustered into 8.7 million viral operational taxonomic units, including 231 408 with at least one high-quality representative. Viral sequences in IMG/VR are now systematically identified from genomes, metagenomes, and metatranscriptomes using a new detection approach (geNomad), and IMG standard annotation are complemented with genome quality estimation using CheckV, taxonomic classification reflecting the latest taxonomic standards, and microbial host taxonomy prediction. IMG/VR v4 is available at https://img.jgi.doe.gov/vr, and the underlying data are available to download at https://genome.jgi.doe.gov/portal/IMG_VR.

The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities.

The Integrated Microbial Genomes & Microbiomes system (IMG/M: https://img.jgi.doe.gov/m/) contains annotated isolate genome and metagenome datasets sequenced at the DOE's Joint Genome Institute (JGI), submitted by external users, or imported from public sources such as NCBI. IMG v 6.0 includes advanced search functions and a new tool for statistical analysis of mixed sets of genomes and metagenome bins. The new IMG web user interface also has a new Help page with additional documentation and webinar tutorials to help users better understand how to use various IMG functions and tools for their research. New datasets have been processed with the prokaryotic annotation pipeline v.5, which includes extended protein family assignments.

A photon-photon quantum gate based on a single atom in an optical resonator.

That two photons pass each other undisturbed in free space is ideal for the faithful transmission of information, but prohibits an interaction between the photons. Such an interaction is, however, required for a plethora of applications in optical quantum information processing. The long-standing challenge here is to realize a deterministic photon-photon gate, that is, a mutually controlled logic operation on the quantum states of the photons. This requires an interaction so strong that each of the two photons can shift the other's phase by π radians. For polarization qubits, this amounts to the conditional flipping of one photon's polarization to an orthogonal state. So far, only probabilistic gates based on linear optics and photon detectors have been realized, because "no known or foreseen material has an optical nonlinearity strong enough to implement this conditional phase shift''. Meanwhile, tremendous progress in the development of quantum-nonlinear systems has opened up new possibilities for single-photon experiments. Platforms range from Rydberg blockade in atomic ensembles to single-atom cavity quantum electrodynamics. Applications such as single-photon switches and transistors, two-photon gateways, nondestructive photon detectors, photon routers and nonlinear phase shifters have been demonstrated, but none of them with the ideal information carriers: optical qubits in discriminable modes. Here we use the strong light-matter coupling provided by a single atom in a high-finesse optical resonator to realize the Duan-Kimble protocol of a universal controlled phase flip (π phase shift) photon-photon quantum gate. We achieve an average gate fidelity of (76.2 ± 3.6) per cent and specifically demonstrate the capability of conditional polarization flipping as well as entanglement generation between independent input photons. This photon-photon quantum gate is a universal quantum logic element, and therefore could perform most existing two-photon operations. The demonstrated feasibility of deterministic protocols for the optical processing of quantum information could lead to new applications in which photons are essential, especially long-distance quantum communication and scalable quantum computing.

A quantum gate between a flying optical photon and a single trapped atom.

The steady increase in control over individual quantum systems supports the promotion of a quantum technology that could provide functionalities beyond those of any classical device. Two particularly promising applications have been explored during the past decade: photon-based quantum communication, which guarantees unbreakable encryption but which still has to be scaled to high rates over large distances, and quantum computation, which will fundamentally enhance computability if it can be scaled to a large number of quantum bits (qubits). It was realized early on that a hybrid system of light qubits and matter qubits could solve the scalability problem of each field--that of communication by use of quantum repeaters, and that of computation by use of an optical interconnect between smaller quantum processors. To this end, the development of a robust two-qubit gate that allows the linking of distant computational nodes is "a pressing challenge". Here we demonstrate such a quantum gate between the spin state of a single trapped atom and the polarization state of an optical photon contained in a faint laser pulse. The gate mechanism presented is deterministic and robust, and is expected to be applicable to almost any matter qubit. It is based on reflection of the photonic qubit from a cavity that provides strong light-matter coupling. To demonstrate its versatility, we use the quantum gate to create atom-photon, atom-photon-photon and photon-photon entangled states from separable input states. We expect our experiment to enable various applications, including the generation of atomic and photonic cluster states and Schrödinger-cat states, deterministic photonic Bell-state measurements, scalable quantum computation and quantum communication using a redundant quantum parity code.

An elementary quantum network of single atoms in optical cavities.

Quantum networks are distributed quantum many-body systems with tailored topology and controlled information exchange. They are the backbone of distributed quantum computing architectures and quantum communication. Here we present a prototype of such a quantum network based on single atoms embedded in optical cavities. We show that atom-cavity systems form universal nodes capable of sending, receiving, storing and releasing photonic quantum information. Quantum connectivity between nodes is achieved in the conceptually most fundamental way-by the coherent exchange of a single photon. We demonstrate the faithful transfer of an atomic quantum state and the creation of entanglement between two identical nodes in separate laboratories. The non-local state that is created is manipulated by local quantum bit (qubit) rotation. This efficient cavity-based approach to quantum networking is particularly promising because it offers a clear perspective for scalability, thus paving the way towards large-scale quantum networks and their applications.

Cavity Carving of Atomic Bell States.

We demonstrate entanglement generation of two neutral atoms trapped inside an optical cavity. Entanglement is created from initially separable two-atom states through carving with weak photon pulses reflected from the cavity. A polarization rotation of the photons heralds the entanglement. We show the successful implementation of two different protocols and the generation of all four Bell states with a maximum fidelity of (90±2)%. The protocol works for any distance between cavity-coupled atoms, and no individual addressing is required. Our result constitutes an important step towards applications in quantum networks, e.g., for entanglement swapping in a quantum repeater.

A single-atom quantum memory.

The faithful storage of a quantum bit (qubit) of light is essential for long-distance quantum communication, quantum networking and distributed quantum computing. The required optical quantum memory must be able to receive and recreate the photonic qubit; additionally, it must store an unknown quantum state of light better than any classical device. So far, these two requirements have been met only by ensembles of material particles that store the information in collective excitations. Recent developments, however, have paved the way for an approach in which the information exchange occurs between single quanta of light and matter. This single-particle approach allows the material qubit to be addressed, which has fundamental advantages for realistic implementations. First, it enables a heralding mechanism that signals the successful storage of a photon by means of state detection; this can be used to combat inevitable losses and finite efficiencies. Second, it allows for individual qubit manipulations, opening up avenues for in situ processing of the stored quantum information. Here we demonstrate the most fundamental implementation of such a quantum memory, by mapping arbitrary polarization states of light into and out of a single atom trapped inside an optical cavity. The memory performance is tested with weak coherent pulses and analysed using full quantum process tomography. The average fidelity is measured to be 93%, and low decoherence rates result in qubit coherence times exceeding 180 microseconds. This makes our system a versatile quantum node with excellent prospects for applications in optical quantum gates and quantum repeaters.

Electromagnetically induced transparency with single atoms in a cavity.

Optical nonlinearities offer unique possibilities for the control of light with light. A prominent example is electromagnetically induced transparency (EIT), where the transmission of a probe beam through an optically dense medium is manipulated by means of a control beam. Scaling such experiments into the quantum domain with one (or just a few) particles of light and matter will allow for the implementation of quantum computing protocols with atoms and photons, or the realization of strongly interacting photon gases exhibiting quantum phase transitions of light. Reaching these aims is challenging and requires an enhanced matter-light interaction, as provided by cavity quantum electrodynamics. Here we demonstrate EIT with a single atom quasi-permanently trapped inside a high-finesse optical cavity. The atom acts as a quantum-optical transistor with the ability to coherently control the transmission of light through the cavity. We investigate the scaling of EIT when the atom number is increased one-by-one. The measured spectra are in excellent agreement with a theoretical model. Merging EIT with cavity quantum electrodynamics and single quanta of matter is likely to become the cornerstone for novel applications, such as dynamic control of the photon statistics of propagating light fields or the engineering of Fock state superpositions of flying light pulses.

Heralded Storage of a Photonic Quantum Bit in a Single Atom.

Combining techniques of cavity quantum electrodynamics, quantum measurement, and quantum feedback, we have realized the heralded transfer of a polarization qubit from a photon onto a single atom with 39% efficiency and 86% fidelity. The reverse process, namely, qubit transfer from the atom onto a given photon, is demonstrated with 88% fidelity and an estimated efficiency of up to 69%. In contrast to previous work based on two-photon interference, our scheme is robust against photon arrival-time jitter and achieves much higher efficiencies. Thus, it constitutes a key step toward the implementation of a long-distance quantum network.

Ground-state cooling of a single atom at the center of an optical cavity.

A single neutral atom is trapped in a three-dimensional optical lattice at the center of a high-finesse optical resonator. Using fluorescence imaging and a shiftable standing-wave trap, the atom is deterministically loaded into the maximum of the intracavity field where the atom-cavity coupling is strong. After 5 ms of Raman sideband cooling, the three-dimensional motional ground state is populated with a probability of (89±2)%. Our system is the first to simultaneously achieve quantum control over all degrees of freedom of a single atom: its position and momentum, its internal state, and its coupling to light.

Efficient teleportation between remote single-atom quantum memories.

We demonstrate teleportation of quantum bits between two single atoms in distant laboratories. Using a time-resolved photonic Bell-state measurement, we achieve a teleportation fidelity of (88.0 ± 1.5)%, largely determined by our entanglement fidelity. The low photon collection efficiency in free space is overcome by trapping each atom in an optical cavity. The resulting success probability of 0.1% is almost 5 orders of magnitude larger than in previous experiments with remote material qubits. It is mainly limited by photon propagation and detection losses and can be enhanced with a cavity-based deterministic Bell-state measurement.

Cavity QED with a Bose-Einstein condensate.

Cavity quantum electrodynamics (cavity QED) describes the coherent interaction between matter and an electromagnetic field confined within a resonator structure, and is providing a useful platform for developing concepts in quantum information processing. By using high-quality resonators, a strong coupling regime can be reached experimentally in which atoms coherently exchange a photon with a single light-field mode many times before dissipation sets in. This has led to fundamental studies with both microwave and optical resonators. To meet the challenges posed by quantum state engineering and quantum information processing, recent experiments have focused on laser cooling and trapping of atoms inside an optical cavity. However, the tremendous degree of control over atomic gases achieved with Bose-Einstein condensation has so far not been used for cavity QED. Here we achieve the strong coupling of a Bose-Einstein condensate to the quantized field of an ultrahigh-finesse optical cavity and present a measurement of its eigenenergy spectrum. This is a conceptually new regime of cavity QED, in which all atoms occupy a single mode of a matter-wave field and couple identically to the light field, sharing a single excitation. This opens possibilities ranging from quantum communication to a wealth of new phenomena that can be expected in the many-body physics of quantum gases with cavity-mediated interactions.

Draft Genome Sequence of Yokenella regensburgei Strain WCD67, Isolated from the Boxelder Bug.

We report here the draft genome sequence of Yokenella regensburgei strain WCD67, isolated from the boxelder bug (Boisea trivittata). The genome is 5,277,883 bp in size, has a GC content of 54.12%, and has 5,416 genes. A total of 17 mobile elements were discovered, 6 of which were predicted to be phages.

Heterogeneity of Z-band structure within a single muscle sarcomere: implications for sarcomere assembly.

The vertebrate striated muscle Z-band connects actin filaments of opposite polarity from adjacent sarcomeres and allows tension to be transmitted along a myofibril during contraction. Z-bands in different muscles have a modular structure formed by layers of alpha-actinin molecules cross-linking actin filaments. Successive layers occur at 19 nm intervals and have 90 degrees rotations between them. 3D reconstruction from electron micrographs show a two-layer "simple" Z-band in fish body fast muscle, a three-layer Z-band in fish fin fast muscle, and a six-layer Z-band in mammalian slow muscle. Related to the number of these layers, longitudinal sections of the Z-band show a number of zigzag connections between the oppositely oriented actin filaments. The number of layers also determines the axial width of the Z-band, which is a useful indicator of fibre type; fast fibres have narrow (approximately 30-50 nm) Z-bands; slow and cardiac fibres have wide (approximately 100-140 nm) Z-bands. Here, we report the first observation of two different Z-band widths within a single sarcomere. By comparison with previous studies, the narrower Z-band comprises three layers. Since the increase in width of the wider Z-band is about 19 nm, we conclude that it comprises four layers. This finding is consistent with a Z-band assembly model involving molecular control mechanisms that can add additional layers of 19 nm periodicity. These multiple Z-band structures suggest that different isoforms of nebulin and titin with a variable number of Z-repeats could be present within a single sarcomere.

Nondestructive detection of an optical photon.

All optical detectors to date annihilate photons upon detection, thus excluding repeated measurements. Here, we demonstrate a robust photon detection scheme that does not rely on absorption. Instead, an incoming photon is reflected from an optical resonator containing a single atom prepared in a superposition of two states. The reflection toggles the superposition phase, which is then measured to trace the photon. Characterizing the device with faint laser pulses, a single-photon detection efficiency of 74% and a survival probability of 66% are achieved. The efficiency can be further increased by observing the photon repeatedly. The large single-photon nonlinearity of the experiment should enable the development of photonic quantum gates and the preparation of exotic quantum states of light.

Cavity optomechanics with a Bose-Einstein condensate.

Cavity optomechanics studies the coupling between a mechanical oscillator and the electromagnetic field in a cavity. We report on a cavity optomechanical system in which a collective density excitation of a Bose-Einstein condensate serves as the mechanical oscillator coupled to the cavity field. A few photons inside the ultrahigh-finesse cavity trigger strongly driven back-action dynamics, in quantitative agreement with a cavity optomechanical model. We approach the strong coupling regime of cavity optomechanics, where a single excitation of the mechanical oscillator substantially influences the cavity field. The results open up new directions for investigating mechanical oscillators in the quantum regime and the border between classical and quantum physics.

Observing the formation of long-range order during Bose-Einstein condensation.

We have experimentally investigated the formation of off-diagonal long-range order in a gas of ultracold atoms. A magnetically trapped atomic cloud prepared in a highly nonequilibrium state thermalizes and thereby crosses the Bose-Einstein condensation phase transition. The evolution of phase coherence between different regions of the sample is constantly monitored and information on the spatial first-order correlation function is obtained. We observe the growth of the spatial coherence and the formation of long-range order in real time and compare it to the growth of the atomic density. Moreover, we study the evolution of the momentum distribution during the nonequilibrium formation of the condensate.

Correlations and counting statistics of an atom laser.

We demonstrate time-resolved counting of single atoms extracted from a weakly interacting Bose-Einstein condensate of 87Rb atoms. The atoms are detected with a high-finesse optical cavity and single atom transits are identified. An atom laser beam is formed by continuously output coupling atoms from the Bose-Einstein condensate. We investigate the full counting statistics of this beam and measure its second order correlation function g((2))(tau) in a Hanbury Brown-Twiss type experiment. For the monoenergetic atom laser we observe a constant correlation function g((2))(tau)=1.00 +/- 0.01 and an atom number distribution close to a Poissonian statistics. A pseudothermal atomic beam shows a bunching behavior and a Bose distributed counting statistics.