Development of a custom-made 2.8†T permanent-magnet dipole photon source for the ROCK beamline at SOLEIL.

In August 2021, the SOLEIL storage ring was restarted after the summer shutdown with a new bending magnet made entirely of permanent magnets. Producing a magnetic field of 2.8 T, it replaced one of the 32 electromagnetic dipoles (magnetic field of 1.7 T) of the ring to allow the ROCK beamline to exploit more intense photon fluxes in the hard X-ray range, thus improving the time resolution performances of the beamline for experiments carried out above 20 keV. The reduction of the new dipole magnetic gap required to produce the higher field has led to the construction and installation of a new vacuum vessel. The realization of the new dipole with permanent magnets was a technological feat due to the very strong magnetic forces. The permanent-magnet assembly required dedicated tools to be designed and constructed. Thanks to accurate magnetic measurements, a precise modelization of the new dipole was performed to identify its effects on the electron beam dynamics. The first measurements carried out on the ROCK beamline have highlighted the expected increase in photon flux, and the operation performances remain unchanged for the other beamlines. Here, the major developments and results of this innovative project are described in terms of technology, electron beam dynamics and photon beam performance on the ROCK beamline.

X-ray beam monitoring and wavelength calibration using four-beam diffraction.

Rigorous dynamical theory calculations show that four-beam diffraction (4BD) can be activated only by a unique photon energy and a unique incidence direction. Thus, 4BD may be used to precisely calibrate X-ray photon energies and beam positions. Based on the principles that the forbidden-reflection 4BD pattern, which is typically an X-shaped cross, can be generated by instant imaging using the divergent beam from a point source without rocking the crystal, a detailed real-time high-resolution beam (and source) position monitoring scheme is illustrated for monitoring two-dimensional beam positions and directions of modern synchrotron light sources, X-ray free-electron lasers and nano-focused X-ray sources.

Robotic sample changers for macromolecular X-ray crystallography and biological small-angle X-ray scattering at the National Synchrotron Light Source II. Corrigendum.

A correction in the paper by Lazo et al. [(2021). J. Synchrotron Rad. 28, 1649-1661] is made.

Commissioning and operation status of the MAX†IV 3†GeV storage ring vacuum system.

The 3 GeV electron storage ring of the MAX IV laboratory is the first storage-ring-based synchrotron radiation facility with the inner surface of almost all the vacuum chambers along its circumference coated with non-evaporable getter (NEG) thin film. The coating provides a low dynamic outgassing rate and pumping of active gases. As the NEG coating was applied on an unprecedented scale, there were doubts concerning the storage ring performance. Fast conditioning of the vacuum system and over five years of reliable accelerator operation have demonstrated that the chosen design proved to be good and does not impose limits on the operation. The vacuum system performance is comparable with or better than that of other similar facilities around the world, where conventional designs were implemented. Observed pressure levels are low, and the electron beam lifetime is long and not limited by residual gas density. A summary of the vacuum performance is presented.

Robotic sample changers for macromolecular X-ray crystallography and biological small-angle X-ray scattering at the National Synchrotron Light Source II.

Here we present two robotic sample changers integrated into the experimental stations for the macromolecular crystallography (MX) beamlines AMX and FMX, and the biological small-angle scattering (bioSAXS) beamline LiX. They enable fully automated unattended data collection and remote access to the beamlines. The system designs incorporate high-throughput, versatility, high-capacity, resource sharing and robustness. All systems are centered around a six-axis industrial robotic arm coupled with a force torque sensor and in-house end effectors (grippers). They have the same software architecture and the facility standard EPICS-based BEAST alarm system. The MX system is compatible with SPINE bases and Unipucks. It comprises a liquid nitrogen dewar holding 384 samples (24 Unipucks) and a stay-cold gripper, and utilizes machine vision software to track the sample during operations and to calculate the final mount position on the goniometer. The bioSAXS system has an in-house engineered sample storage unit that can hold up to 360 samples (20 sample holders) which keeps samples at a user-set temperature (277 K to 300 K). The MX systems were deployed in early 2017 and the bioSAXS system in early 2019.

Time-of-arrival detection for time-resolved scanning transmission X-ray microscopy imaging.

A setup for time-resolved scanning transmission X-ray microscopy imaging is presented, which allows for an increase in the temporal resolution without the requirement of operating the synchrotron light source with low-α optics through the measurement of the time-of-arrival of the X-ray photons. Measurements of two filling patterns in hybrid mode of the Swiss Light Source are presented as a first proof-of-principle and benchmark for the performances of this new setup. From these measurements, a temporal resolution on the order of 20-30 ps could be determined.

Light source based on a 100†mm-long monolithic undulator magnet with a very short 4†mm-period length.

A novel method to fabricate undulator magnets of a-few-millimetre-period length is being explored. Plate-type magnets, 100 mm-long with 4 mm-period length, have been successfully fabricated. They produce an undulator field of approximately 3 kG at a gap of 1.6 mm. Prototype undulators based on this technology have been constructed. Field measurements and characterization show that the quality of the undulator field of these plate magnets is sufficient for an undulator light source, and the calculated spectrum shows that the fundamental radiation emitted from this field is quite satisfactory. Test experiments for light generation using a real electron beam have been carried out at a test accelerator at the Research Center for Electron Photon Science (ELPH), Tohoku University, Japan, which is able to realize optics conditions to accept a very short gap of ∼1.6 mm. First observation and characterization of blue light was successfully accomplished.

Laser-slicing at a low-emittance storage ring.

Laser-slicing at a diffraction-limited storage ring light source in the soft X-ray region is investigated with theoretical and numerical modelling. It turns out that the slicing efficiency is favoured by the ultra-low beam emittance, and that slicing can be implemented without interference to the standard multi-bunch operation. Spatial and spectral separation of the sub-picosecond radiation pulse from a hundreds of picosecond-long background is achieved by virtue of 1:1 imaging of the radiation source. The spectral separation is enhanced when the radiator is a transverse gradient undulator. The proposed configuration applied to the Elettra 2.0 six-bend achromatic lattice envisages total slicing efficiency as high as 10-7, one order of magnitude larger than the demonstrated state-of-the-art, at the expense of pulse durations as long as 0.4 ps FWHM and average laser power as high as ∼40 W.

Commissioning and first-year operational results of the MAX†IV 3†GeV ring.

The MAX IV 3 GeV electron storage ring in Lund, Sweden, is the first of a new generation of light sources to make use of the multibend-achromat lattice (MBA) to achieve ultralow emitance and hence ultrahigh brightness and transverse coherence. The conceptual basis of the MAX IV 3 GeV ring project combines a robust lattice design with a number of innovative engineering choices: compact, multifunctional magnet blocks, narrow low-conductance NEG-coated copper vacuum chambers and a 100 MHz radio-frequency system with passively operated third-harmonic cavities for bunch lengthening. In this paper, commissioning and first-year operational results of the MAX IV 3 GeV ring are presented, highlighting those aspects that are believed to be most relevant for future MBA-based storage rings. The commissioning experience of the MAX IV 3 GeV ring offers in this way an opportunity for validation of concepts that are likely to be essential ingredients of future diffraction-limited light sources.

Refurbishment of a used in-vacuum undulator from the National Synchrotron Light Source for the National Synchrotron Light Source-II ring.

The National Synchrotron Light Source (NSLS) ceased operation in September 2014 and was succeeded by NSLS-II. There were four in-vacuum undulators (IVUs) in operation at NSLS. The most recently constructed IVU for NSLS was the mini-gap undulator (MGU-X25, to be renamed IVU18 for NSLS-II), which was constructed in 2006. This device was selected to be reused for the New York Structural Biology Consortium Microdiffraction beamline at NSLS-II. At the time of construction, IVU18 was a state-of-the-art undulator designed to be operated as a cryogenic permanent-magnet undulator. Due to the more stringent field quality and impedance requirements of the NSLS-II ring, the transition region was redesigned. The control system was also updated to NSLS-II specifications. This paper reports the details of the IVU18 refurbishment activities including additional magnetic measurement and tuning.

First multi-bend achromat lattice consideration.

By the beginning of 1990, three third-generation synchrotron light sources had been successfully commissioned in Grenoble, Berkeley and Trieste (ESRF, ALS and ELETTRA). Each of these new machines reached their target specifications without any significant problems. In parallel, already at that time discussions were underway regarding the next generation, the `diffraction-limited light source (DLSR)', which featured sub-nm rad electron beam emittance, photon beam brilliance exceeding 10(22) and the potential to emit coherent radiation. Also, at about that time, a first design for a 3 GeV DLSR was developed, based on a modified multiple-bend achromat (MBA) design leading to a lattice with normalized emittance of ℇx = 0.5 nm rad. The novel feature of the MBA lattice was the use of seven vertically focusing bend magnets with different bending angles throughout the achromat cell to keep the radiation integrals and resulting beam emittance low. The baseline design called for a 400 m ring circumference with 12 straight sections of 6 m length. The dynamic aperture behaviour of the DLSR lattice was estimated to produce > 5 h beam lifetime at 100 mA stored beam current.

The MAX†IV storage ring project.

The MAX IV facility, currently under construction in Lund, Sweden, features two electron storage rings operated at 3 GeV and 1.5 GeV and optimized for the hard X-ray and soft X-ray/VUV spectral ranges, respectively. A 3 GeV linear accelerator serves as a full-energy injector into both rings as well as a driver for a short-pulse facility, in which undulators produce X-ray pulses as short as 100 fs. The 3 GeV ring employs a multibend achromat (MBA) lattice to achieve, in a relatively short circumference of 528 m, a bare lattice emittance of 0.33 nm rad, which reduces to 0.2 nm rad as insertion devices are added. The engineering implementation of the MBA lattice raises several technological problems. The large number of strong magnets per achromat calls for a compact design featuring small-gap combined-function magnets grouped into cells and sharing a common iron yoke. The small apertures lead to a low-conductance vacuum chamber design that relies on the chamber itself as a distributed copper absorber for the heat deposited by synchrotron radiation, while non-evaporable getter (NEG) coating provides for reduced photodesorption yields and distributed pumping. Finally, a low main frequency (100 MHz) is chosen for the RF system yielding long bunches, which are further elongated by passively operated third-harmonic Landau cavities, thus alleviating collective effects, both coherent (e.g. resistive wall instabilities) and incoherent (intrabeam scattering). In this paper, we focus on the MAX IV 3 GeV ring and present the lattice design as well as the engineering solutions to the challenges inherent to such a design. As the first realisation of a light source based on the MBA concept, the MAX IV 3 GeV ring offers an opportunity for validation of concepts that are likely to be essential ingredients of future diffraction-limited light sources.

Fluorescent Proteins: Crystallization, Structural Determination, and Nonnatural Amino Acid Incorporation.

Fluorescent proteins have revolutionized cell biology and cell imaging through their use as genetically encoded tags. Structural biology has been pivotal in understanding how their unique fluorescent properties manifest through the formation of the chromophore and how the spectral properties are tuned through interaction networks. This knowledge has in turn led to the construction of novel variants with new and improved properties. Here we describe the process by which fluorescent protein structures are determined, starting from recombinant protein production to structure determination by molecular replacement. We also describe how to incorporate and determine the structures of proteins containing non-natural amino acids. Recent advances in protein engineering have led to reprogramming of the genetic code to allow incorporation of new chemistry at designed residue positions, with fluorescent proteins being at the forefront of structural studies in this area. The impact of such new chemistry on protein structure is still limited; the accumulation of more protein structures will undoubtedly improve our understanding and ability to engineer proteins with new chemical functionality.

Linking scientific instruments and computation: Patterns, technologies, and experiences.

Powerful detectors at modern experimental facilities routinely collect data at multiple GB/s. Online analysis methods are needed to enable the collection of only interesting subsets of such massive data streams, such as by explicitly discarding some data elements or by directing instruments to relevant areas of experimental space. Thus, methods are required for configuring and running distributed computing pipelines-what we call flows-that link instruments, computers (e.g., for analysis, simulation, artificial intelligence [AI] model training), edge computing (e.g., for analysis), data stores, metadata catalogs, and high-speed networks. We review common patterns associated with such flows and describe methods for instantiating these patterns. We present experiences with the application of these methods to the processing of data from five different scientific instruments, each of which engages powerful computers for data inversion,model training, or other purposes. We also discuss implications of such methods for operators and users of scientific facilities.

Imbalance of Mg Homeostasis as a Potential Biomarker in Colon Cancer.

BACKGROUND: Increasing evidences support a correlation between magnesium (Mg) homeostasis and colorectal cancer (CRC). Nevertheless, the role of Mg and its transporters as diagnostic markers in CRC is still a matter of debate. In this study we combined X-ray Fluorescence Microscopy and databases information to investigate the possible correlation between Mg imbalance and CRC. METHODS: CRC tissue samples and their non-tumoural counterpart from four patients were collected and analysed for total Mg level and distribution by X-Ray Fluorescence Microscopy. We also reviewed the scientific literature and the main tissue expression databases to collect data on Mg transporters expression in CRC. RESULTS: We found a significantly higher content of total Mg in CRC samples when compared to non-tumoural tissues. Mg distribution was also impaired in CRC. Conversely, we evidenced an uncertain correlation between Mg transporters expression and colon malignancies. DISCUSSION: Although further studies are necessary to determine the correlation between different cancer types and stages, this is the first report proposing the measurement of Mg tissue localisation as a marker in CRC. This study represents thus a proof-of-concept that paves the way for the design of a larger prospective investigation of Mg in CRC.

Crystal structures of the first condensation domain of CDA synthetase suggest conformational changes during the synthetic cycle of nonribosomal peptide synthetases.

Nonribosomal peptide synthetases (NRPSs) are large modular macromolecular machines that produce small peptide molecules with wide-ranging biological activities, such as antibiotics and green chemicals. The condensation (C) domain is responsible for amide bond formation, the central chemical step in nonribosomal peptide synthesis. Here we present two crystal structures of the first condensation domain of the calcium-dependent antibiotic (CDA) synthetase (CDA-C1) from Streptomyces coelicolor, determined at resolutions 1.8Å and 2.4Å. The conformations adopted by CDA-C1 are quite similar in these two structures yet distinct from those seen in other NRPS C domain structures. HPLC-based reaction assays show that this CDA-C1 construct is catalytically active, and small-angle X-ray scattering experiments suggest that the conformation observed in these crystal structures could faithfully represent the conformation in solution. We have performed targeted molecular dynamics simulations, normal mode analyses and energy-minimized linear interpolation to investigate the conformational changes required to transition between the observed structures. We discuss the implications of these conformational changes in the synthetic cycle and of the observation that the "latch" that covers the active site is consistently formed in all studied C domains.