PDBe: Protein Data Bank in Europe.

The Protein Data Bank in Europe (PDBe) (http://www.ebi.ac.uk/pdbe/) is actively working with its Worldwide Protein Data Bank partners to enhance the quality and consistency of the international archive of bio-macromolecular structure data, the Protein Data Bank (PDB). PDBe also works closely with its collaborators at the European Bioinformatics Institute and the scientific community around the world to enhance its databases and services by adding curated and actively maintained derived data to the existing structural data in the PDB. We have developed a new database infrastructure based on the remediated PDB archive data and a specially designed database for storing information on interactions between proteins and bound molecules. The group has developed new services that allow users to carry out simple textual queries or more complex 3D structure-based queries. The newly designed 'PDBeView Atlas pages' provide an overview of an individual PDB entry in a user-friendly layout and serve as a starting point to further explore the information available in the PDBe database. PDBe's active involvement with the X-ray crystallography, Nuclear Magnetic Resonance spectroscopy and cryo-Electron Microscopy communities have resulted in improved tools for structure deposition and analysis.

Noise figure and photon statistics in coherent anti-Stokes Raman scattering.

Coherent anti-Stokes Raman scattering (CARS) is a well-known Raman scattering process that occurs when Stokes, anti-Stokes and pump waves are properly phase-matched. Using a quantum-field approach with Langevin noise sources, we calculate the noise figure for wavelength conversion between the Stokes and anti-Stokes waves in CARS and show its dependence on phase mismatch. Under phase matched conditions, the minimum noise figure is approximately 3 dB, with a correction that depends on the pump frequency, Stokes shift, refractive indices, and nonlinear susceptibilities. We calculate the photon statistics of CARS and show that the photon number distribution is non-Gaussian. Our findings may be significant for currently pursued applications of CARS including wavelength conversion in data transmission and spectroscopic detection of dilute biochemical species.

E-MSD: an integrated data resource for bioinformatics.

The Macromolecular Structure Database (MSD) group (http://www.ebi.ac.uk/msd/) continues to enhance the quality and consistency of macromolecular structure data in the Protein Data Bank (PDB) and to work towards the integration of various bioinformatics data resources. We have implemented a simple form-based interface that allows users to query the MSD directly. The MSD 'atlas pages' show all of the information in the MSD for a particular PDB entry. The group has designed new search interfaces aimed at specific areas of interest, such as the environment of ligands and the secondary structures of proteins. We have also implemented a novel search interface that begins to integrate separate MSD search services in a single graphical tool. We have worked closely with collaborators to build a new visualization tool that can present both structure and sequence data in a unified interface, and this data viewer is now used throughout the MSD services for the visualization and presentation of search results. Examples showcasing the functionality and power of these tools are available from tutorial webpages (http://www. ebi.ac.uk/msd-srv/docs/roadshow_tutorial/).

E-MSD: the European Bioinformatics Institute Macromolecular Structure Database.

The E-MSD macromolecular structure relational database (http://www.ebi.ac.uk/msd) is designed to be a single access point for protein and nucleic acid structures and related information. The database is derived from Protein Data Bank (PDB) entries. Relational database technologies are used in a comprehensive cleaning procedure to ensure data uniformity across the whole archive. The search database contains an extensive set of derived properties, goodness-of-fit indicators, and links to other EBI databases including InterPro, GO, and SWISS-PROT, together with links to SCOP, CATH, PFAM and PROSITE. A generic search interface is available, coupled with a fast secondary structure domain search tool.

Anti-Stokes Raman conversion in silicon waveguides.

The first observation of parametric down-conversion in silicon is reported. Conversion from 1542.3nm to 1328.8nm is achieved using a CW pump laser at 1427 nm. The conversion occurs via Coherent Anti-Stokes Raman Scattering (CARS) in which two pump photons and one Stokes photon couple through a zone-center optical phonon to an anti-Stokes photon. The maximum measured Stokes/anti-Stokes power conversion efficiency is 1x10-5. The value depends on the effective pump power, the Stimulated Raman Scattering (SRS) coefficient of bulk silicon, and waveguide dispersion. It is shown that the power conversion efficiency is a strong function of phase mismatch inside the waveguide.

Influence of nonlinear absorption on Raman amplification in Silicon waveguides.

We model the TPA-induced free carrier absorption effect in silicon Raman amplifiers and quantify the conditions under which net gain may be obtained. The achievable Raman gain strongly depends on the free carrier lifetime, propagation loss, and on the effective Raman gain coefficient, through pump-induced broadening.

Observation of stimulated Raman amplification in silicon waveguides.

We report the first observation of Stimulated Raman Scattering (SRS) in silicon waveguides. Amplification of the Stokes signal, at 1542.3 nm, of up to 0.25 dB has been observed in Silicon-on-Insulator (SOI) waveguides, using a 1427 nm pump laser with a CW power of 1.6 W, measured before the waveguide. Two-Photon-Absorption (TPA) measurements on these waveguides are also reported, and found to be negligible at the pump power where SRS was observed.

Coupled-mode theory of the Raman effect in silicon-on-insulator waveguides.

Coupled-mode theory is used to calculate Raman gain and spontaneous efficiency in silicon waveguides with cross-sectional areas ranging from 0.16 to 16 microm2. We find a monotonic increase in the Raman gain as the waveguide cross section decreases for the range of dimensions considered. It is also found that mode coupling between the Stokes modes is insignificant, and thus polarization multiplexing is possible. The results also demonstrate that for submicrometer waveguide dimensions the Einstein relation between spontaneous efficiency and stimulated gain no longer holds.