A beginner’s guide to radiation damage

Radiation damage considerations affecting data collection by more than a factor of two are summarized and damage avoidance strategies are suggested

Towards the spatial resolution of metalloprotein charge states by detailed modeling of XFEL crystallographic diffraction.

Oxidation states of individual metal atoms within a metalloprotein can be assigned by examining X-ray absorption edges, which shift to higher energy for progressively more positive valence numbers. Indeed, X-ray crystallography is well suited for such a measurement, owing to its ability to spatially resolve the scattering contributions of individual metal atoms that have distinct electronic environments contributing to protein function. However, as the magnitude of the shift is quite small, about +2 eV per valence state for iron, it has only been possible to measure the effect when performed with monochromated X-ray sources at synchrotron facilities with energy resolutions in the range 2-3 × 10-4 (ΔE/E). This paper tests whether X-ray free-electron laser (XFEL) pulses, which have a broader bandpass (ΔE/E = 3 × 10-3) when used without a monochromator, might also be useful for such studies. The program nanoBragg is used to simulate serial femtosecond crystallography (SFX) diffraction images with sufficient granularity to model the XFEL spectrum, the crystal mosaicity and the wavelength-dependent anomalous scattering factors contributed by two differently charged iron centers in the 110-amino-acid protein, ferredoxin. Bayesian methods are then used to deduce, from the simulated data, the most likely X-ray absorption curves for each metal atom in the protein, which agree well with the curves chosen for the simulation. The data analysis relies critically on the ability to measure the incident spectrum for each pulse, and also on the nanoBragg simulator to predict the size, shape and intensity profile of Bragg spots based on an underlying physical model that includes the absorption curves, which are then modified to produce the best agreement with the simulated data. This inference methodology potentially enables the use of SFX diffraction for the study of metalloenzyme mechanisms and, in general, offers a more detailed approach to Bragg spot data reduction

A Model Study of Zonal Forcing in the Equatorial Stratosphere by Convectively Induced Gravity Waves

A two-dimensional cloud-resolving model is used to examine the possible role of gravity waves generated by a simulated tropical squall line in forcing the quasi-biennial oscillation (QBO) of the zonal winds in the equatorial stratosphere. A simulation with constant background stratospheric winds is compared to simulations with background winds characteristic of the westerly and easterly QBO phases, respectively. In all three cases a broad spectrum of both eastward and westward propagating gravity waves is excited. In the constant background wind case the vertical momentum flux is nearly constant with height in the stratosphere, after correction for waves leaving the model domain. In the easterly and westerly shear cases, however, westward and eastward propagating waves, respectively, are strongly damped as they approach their critical levels, owing to the strongly scale-dependent vertical diffusion in the model. The profiles of zonal forcing induced by this wave damping are similar to profiles given by critical level absorption, but displaced slightly downward. The magnitude of the zonal forcing is of order 5 m/s/day. It is estimated that if 2% of the area of the Tropics were occupied by storms of similar magnitude, mesoscale gravity waves could provide nearly 1/4 of the zonal forcing required for the QBO

Wave Dynamics and Transport in the Stratosphere

The report discusses: (1) Gravity waves generated by tropical convection: A study in which a two-dimensional cloud-resolving model was used to examine the possible role of gravity waves generated by a simulated tropical squall line in forcing the quasi-biennial oscillation was completed. (2) Gravity wave ray tracing studies:It was developed a linear ray tracing model of gravity wave propagation to extend the nonlinear storm model results into the mesosphere and thermosphere. (3) tracer filamentation: Vertical soundings of stratospheric ozone often exhibit laminated tracer structures characterized by strong vertical tracer gradients. (4) Mesospheric gravity wave modeling studies: Although our emphasis in numerical simulation of gravity waves generated by convection has shifted from simulation of idealized two-dimensional squall lines to the most realistic (and complex) study of wave generation by three-dimensional storms. (5) Gravity wave climatology studies: Mr. Alexander applied a linear gravity wave propagation model together with observations of the background wind and stability fields to compute climatologies of gravity wave activity for comparison to observations. (6) Convective forcing of gravity waves: Theoretical study of gravity wave forcing by convective heat sources has completed. (7) Gravity waves observation from UARS: The objective of this work is to apply ray tracing, and other model technique, in order to determine to what extend the horizontal and vertical variation in satellite observed distribution of small-scale temperature variance can be attributed to gravity waves from particular sources. (8) The annual and interannual variations in temperature and mass flux near the tropical tropopause. and (9) Three dimensional cloud model

Structural Insight into KCNQ (Kv7) Channel Assembly and Channelopathy

SummaryKv7.x (KCNQ) voltage-gated potassium channels form the cardiac and auditory IKs current and the neuronal M-current. The five Kv7 subtypes have distinct assembly preferences encoded by a C-terminal cytoplasmic assembly domain, the A-domain Tail. Here, we present the high-resolution structure of the Kv7.4 A-domain Tail together with biochemical experiments that show that the domain is a self-assembling, parallel, four-stranded coiled coil. Structural analysis and biochemical studies indicate conservation of the coiled coil in all Kv7 subtypes and that a limited set of interactions encode assembly specificity determinants. Kv7 mutations have prominent roles in arrhythmias, deafness, and epilepsy. The structure together with biochemical data indicate that A-domain Tail arrhythmia mutations cluster on the solvent-accessible surface of the subunit interface at a likely site of action for modulatory proteins. Together, the data provide a framework for understanding Kv7 assembly specificity and the molecular basis of a distinct set of Kv7 channelopathies

Determination of X-ray flux using silicon pin diodes

Accurate measurement of photon flux from an X-ray source is a parameter required to calculate the dose absorbed by a sample. The development of a model for determining the photon flux incident on pin diodes, and experiments to test this model, are described for incident energies between 4 and 18 keV used in macromolecular crystallography

Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source.

The SIBYLS beamline (12.3.1) of the Advanced Light Source at Lawrence Berkeley National Laboratory, supported by the US Department of Energy and the National Institutes of Health, is optimized for both small-angle X-ray scattering (SAXS) and macromolecular crystallography (MX), making it unique among the world's mostly SAXS or MX dedicated beamlines. Since SIBYLS was commissioned, assessments of the limitations and advantages of a combined SAXS and MX beamline have suggested new strategies for integration and optimal data collection methods and have led to additional hardware and software enhancements. Features described include a dual mode monochromator [containing both Si(111) crystals and Mo/B(4)C multilayer elements], rapid beamline optics conversion between SAXS and MX modes, active beam stabilization, sample-loading robotics, and mail-in and remote data collection. These features allow users to gain valuable insights from both dynamic solution scattering and high-resolution atomic diffraction experiments performed at a single synchrotron beamline. Key practical issues considered for data collection and analysis include radiation damage, structural ensembles, alternative conformers and flexibility. SIBYLS develops and applies efficient combined MX and SAXS methods that deliver high-impact results by providing robust cost-effective routes to connect structures to biology and by performing experiments that aid beamline designs for next generation light sources

A Method of Specifying the Gravity Wave Spectrum above Convection Based on Latent Heating Properties and Background Wind

The spectrum of convectively generated gravity waves is currently not resolved in general circulation models and must be parameterized. Due to the lack of understanding of the connection between convection properties and gravity waves, such parameterizations assume a source spectrum of gravity waves that is not linked to the forcing region. This paper introduces a method of specifying the gravity wave spectrum above convection based on the latent heating properties and background wind in the convective region that can be implemented in general circulation models. This method is based on linear calculations of momentum flux generated by a multifrequency thermal forcing and incorporates the effects of tropospheric mean wind in the convective environment. In the analysis, gravity waves that are generated by both the steady and the oscillatory component of the heating are included. It is shown that an accurate spectrum of convectively generated gravity waves can be deduced from the knowledge of approximate horizontal and vertical scales of the latent heating region, the heating rate, and tropospheric wind profile. 1