CEP-stable tunable THz-emission originating from laser-waveform-controlled sub-cycle plasma-electron bursts

We study THz-emission from a plasma driven by an incommensurate-frequency two-colour laser field. A semi-classical transient electron current model is derived from a fully quantum-mechanical description of the emission process in terms of sub-cycle field-ionization followed by continuum-continuum electron transitions. For the experiment, a CEP-locked laser and a near-degenerate optical parametric amplifier are used to produce two-colour pulses that consist of the fundamental and its near-half frequency. By choosing two incommensurate frequencies, the frequency of the CEP-stable THz-emission can be continuously tuned into the mid-IR range. This measured frequency dependence of the THz-emission is found to be consistent with the semi-classical transient electron current model, similar to the Brunel mechanism of harmonic generation.

Generation of high fidelity 62-fs, 7-nJ pulses at 1035 nm from a net normal-dispersion Yb-fiber laser with anomalous dispersion higher-order-mode fiber

Fiber oscillators operating in the normal dispersion regime allow generating high energy output pulses. The best stability of such oscillators is observed when the intracavity dispersion is close to zero. Intracavity dispersion compensation in such oscillators can be achieved using a higher-order mode fiber, which substantially reduces the higher order dispersion compared to all-normal dispersion oscillators or oscillators using intracavity gratings for dispersion compensation. Using this approach, we are able to obtain relatively high energy pulses, with high fidelity. Our modeling based on an analytic approach for oscillators operating in the normal dispersion regime predicts that at intermediate pulse energies an almost flat chirp can be obtained at the oscillator output enabling good pulse compression with a grating compressor close to Fourier limited duration. Here, we present a mode-locked ytterbium-doped fiber oscillator with a higher-order mode fiber operating in the net normal-dispersion regime, delivering 7.2 nJ pulses that can be dechirped down to 62 fs using a simple grating compressor.

Hollow-fiber compression of 6 mJ pulses from a continuous-wave diode-pumped single-stage Yb,Na:CaF2 chirped pulse amplifier

Here, 200 fs 6 mJ pulses from a cw diode-pumped Yb,Na:CaF(2) amplifier are spectrally broadened in an Ar- or Ne-filled hollow-core fiber and recompressed to 20 fs (Ar) and 35 fs (Ne) using a prism pair. The results of spectral broadening and phase measurement are in excellent agreement with numerical modeling based on the generalized nonlinear Schrödinger equation. The longer laser wavelength of 1030 nm permits favorable energy scaling for the hollow-fiber technique compared to ultrafast amplifiers operating at 800 nm.

Petabyte-scale innovations at the European Nucleotide Archive

Dramatic increases in the throughput of nucleotide sequencing machines, and the promise of ever greater performance, have thrust bioinformatics into the era of petabyte-scale data sets. Sequence repositories, which provide the feed for these data sets into the worldwide computational infrastructure, are challenged by the impact of these data volumes. The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/embl), comprising the EMBL Nucleotide Sequence Database and the Ensembl Trace Archive, has identified challenges in the storage, movement, analysis, interpretation and visualization of petabyte-scale data sets. We present here our new repository for next generation sequence data, a brief summary of contents of the ENA and provide details of major developments to submission pipelines, high-throughput rule-based validation infrastructure and data integration approaches.

Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database

The Ensembl Trace Archive (http://trace.ensembl.org/) and the EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl/), known together as the European Nucleotide Archive, continue to see growth in data volume and diversity. Selected major developments of 2007 are presented briefly, along with data submission and retrieval information. In the face of increasing requirements for nucleotide trace, sequence and annotation data archiving, data capture priority decisions have been taken at the European Nucleotide Archive. Priorities are discussed in terms of how reliably information can be captured, the long-term benefits of its capture and the ease with which it can be captured.

EMBL Nucleotide Sequence Database in 2006

The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl) at the EMBL European Bioinformatics Institute, UK, offers a large and freely accessible collection of nucleotide sequences and accompanying annotation. The database is maintained in collaboration with DDBJ and GenBank. Data are exchanged between the collaborating databases on a daily basis to achieve optimal synchrony. Webin is the preferred tool for individual submissions of nucleotide sequences, including Third Party Annotation, alignments and bulk data. Automated procedures are provided for submissions from large-scale sequencing projects and data from the European Patent Office. In 2006, the volume of data has continued to grow exponentially. Access to the data is provided via SRS, ftp and variety of other methods. Extensive external and internal cross-references enable users to search for related information across other databases and within the database. All available resources can be accessed via the EBI home page at http://www.ebi.ac.uk/. Changes over the past year include changes to the file format, further development of the EMBLCDS dataset and developments to the XML format.

Multimode anharmonic third-order harmonic generation in a photonic-crystal fiber

While the third harmonic of a monochromatic pump field with a frequency omega0 is generated exactly at the frequency 3omega0, frequency tripling of broadband ultrashort pump pulses in extended nonlinear media tends to generate isolated spectral peaks substantially shifted from 3omega0. We demonstrate this phenomenon by studying nonlinear spectral transformations of femtosecond Cr:forsterite laser pulses in multimode photonic-crystal fibers. Third-harmonic generation is shown to map adjacent guided modes of the third harmonic onto a manifold of spectral peaks within a 150-THz range around 3omega0. The spectral shifts and the widths of these peaks are controlled by the phase and group-velocity mismatch between the pump field and third-harmonic modes, as well as the length of nonlinear-optical interaction and broadening of the pump spectrum, allowing the spectral content of the third-harmonic signal to be engineered by tailoring the fiber dispersion.