The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013

The second round of the community-wide initiative Critical Assessment of automated Structure Determination of Proteins by NMR (CASD-NMR-2013) comprised ten blind target datasets, consisting of unprocessed spectral data, assigned chemical shift lists and unassigned NOESY peak and RDC lists, that were made available in both curated (i.e. manually refined) or un-curated (i.e. automatically generated) form. Ten structure calculation programs, using fully automated protocols only, generated a total of 164 three-dimensional structures (entries) for the ten targets, sometimes using both curated and un-curated lists to generate multiple entries for a single target. The accuracy of the entries could be established by comparing them to the corresponding manually solved structure of each target, which was not available at the time the data were provided. Across the entire data set, 71 % of all entries submitted achieved an accuracy relative to the reference NMR structure better than 1.5 Å. Methods based on NOESY peak lists achieved even better results with up to 100 % of the entries within the 1.5 Å threshold for some programs. However, some methods did not converge for some targets using un-curated NOESY peak lists. Over 90 % of the entries achieved an accuracy better than the more relaxed threshold of 2.5 Å that was used in the previous CASD-NMR-2010 round. Comparisons between entries generated with un-curated versus curated peaks show only marginal improvements for the latter in those cases where both calculations converged.

Supercontinuum Generation by Stimulated Raman Scattering and Parametric Four-Wave Mixing in Photonic Crystal Fibers

Supercontinuum generation is investigated experimentally and numerically in a highly nonlinear indexguiding photonic crystal optical fiber in a regime in which self-phase modulation of the pump wave makes a negligible contribution to spectral broadening. An ultrabroadband octave-spanning white-light continuum is generated with 60-ps pump pulses of subkilowatt peak power. The primary mechanism of spectral broadening is identified as the combined action of stimulated Raman scattering and parametric four-wave mixing. The observation of a strong anti-Stokes Raman component reveals the importance of the coupling between stimulated Raman scattering and parametric four-wave mixing in highly nonlinear photonic crystal fibers and also indicates that non-phase-matched processes contribute to the continuum. Additionally, the pump input polarization affects the generated continuum through the influence of polarization modulational instability. The experimental results are in good agreement with detailed numerical simulations. These findings demonstrate the importance of index-guiding photonic crystal fibers for the design of picosecond and nanosecond supercontinuum light sources. © 2002 Optical Society of America.

Supercontinuum generation in air-silica microstructured fibers with nanosecond and femtosecond pulse pumping

We study the generation of supercontinua in air-silica microstructured fibers by both nanosecond and femtosecond pulse excitation. In the nanosecond experiments, a 300-nm broadband visible continuum was generated in a 1.8-m length of fiber pumped at 532 nm by 0.8-ns pulses from a frequency-doubled passively Q-switched Nd:YAG microchip laser. At this wavelength, the dominant mode excited under the conditions of continuum generation is the LP 11 mode, and, with nanosecond pumping, self-phase modulation is negligible and the continuum generation is dominated by the interplay of Raman and parametric effects. The spectral extent of the continuum is well explained by calculations of the parametric gain curves for four-wave mixing about the zero-dispersion wavelength of the LP11 mode. In the femtosecond experiments, an 800-nm broad-band visible and near-infrared continuum has been generated in a 1-m length of fiber pumped at 780 nm by 100-fs pulses from a Kerr-lens model-locked Ti:sapphire laser. At this wavelength, excitation and continuum generation occur in the LP01 mode, and the spectral width of the observed continuum is shown to be consistent with the phase-matching bandwidth for parametric processes calculated for this fiber mode. In addition, numerical simulations based on an extended nonlinear Schrödinger equation were used to model supercontinuum generation in the femtosecond regime, with the simulation results reproducing the major features of the experimentally observed spectrum. © 2002 Optical Society of America.

Numerical Simulations and Coherence Properties of Supercontinuum Generation in Photonic Crystal and Tapered Optical Fibers

Numerical simulations have been used to study broad-band supercontinuum generation in optical fibers with dispersion and nonlinearity characteristics typical and photonic crystal or tapered fibers structures. The simulations include optical shock and Raman nonlinearity terms, with quantum noise taken into account phenomenologically by including in the input field a noise seed of one photon per mode with random phase. For input pulses of 150-fs duration injected in the anomalous dispersion regime, the effect of modulational instability is shown to lead to severe temporal jitter in the output, and associated fluctuations in the spectral amplitude and phase across the generated supercontinuum. The spectral phase fluctuations are quantified by performing multiple simulations and calculating both the standard deviation of the phase and, more rigorously, the degree of first-order coherence as a function of wavelength across the spectrum. By performing simulations over a range of input pulse durations and wavelengths, we can identify the conditions under which coherent supercontinua with a well-defined spectral phase are generated.