X-Ray Free-Electron Lasers for the Structure and Dynamics of Macromolecules.

X-ray free-electron lasers provide femtosecond-duration pulses of hard X-rays with a peak brightness approximately one billion times greater than is available at synchrotron radiation facilities. One motivation for the development of such X-ray sources was the proposal to obtain structures of macromolecules, macromolecular complexes, and virus particles, without the need for crystallization, through diffraction measurements of single noncrystalline objects. Initial explorations of this idea and of outrunning radiation damage with femtosecond pulses led to the development of serial crystallography and the ability to obtain high-resolution structures of small crystals without the need for cryogenic cooling. This technique allows the understanding of conformational dynamics and enzymatics and the resolution of intermediate states in reactions over timescales of 100 fs to minutes. The promise of more photons per atom recorded in a diffraction pattern than electrons per atom contributing to an electron micrograph may enable diffraction measurements of single molecules, although challenges remain.

Location of S-nitrosylated cysteines in protein three-dimensional structures.

Although S-nitrosylation of cysteines is a common protein posttranslational modification, little is known about its three-dimensional structural features. This paper describes a systematic survey of the data available in the Protein Data Bank. Several interesting observations could be made. (1) As a result of radiation damage, S-nitrosylated cysteines (Snc) are frequently reduced, at least partially. (2) S-nitrosylation may be a protection against irreversible thiol oxidation; because the NO group of Snc is relatively accessible to the solvent, it may act as a cork to protect the sulfur atoms of cysteines from oxidation by molecular oxygen to sulfenic, sulfinic, and sulfonic acid; moreover, Snc are frequently found at the start or end of helices and strands and this might shield secondary structural elements from unfolding.

Effects of gamma-ray irradiation on material and electrical properties of AlN gate dielectric on 4H-SiC.

This article investigates the radiation effects on as-deposited and annealed AlN films on 4H-SiC substrates under gamma-rays. The AlN films are prepared using plasma-enhanced-atomic-layer-deposition on an n-type 4H-SiC substrate. The AlN/4H-SiC MIS structure is subjected to gamma-ray irradiation with total doses of 0, 300, and 600 krad(Si). Physical, chemical, and electrical methods were employed to study the variations in surface morphology, charge transport, and interfacial trapping characteristics induced by irradiation. After 300 krad(Si) irradiation, the as-deposited and annealed samples exhibit their highest root mean square values of 0.917 nm and 1.190 nm, respectively, which is attributed to N vacancy defects induced by irradiation. Under irradiation, the flatband voltage (Vfb) of the as-deposited sample shifts from 2.24 to 0.78 V, while the annealed sample shifts from 1.18 to 2.16 V. X-ray photoelectron spectrum analysis reveals the decomposition of O-related defects in the as-deposited AlN and the formation of Al(NOx)ycompounds in the annealed sample. Furthermore, the space-charge-limits-conduction (SCLC) in the as-deposited sample is enhanced after radiation, while the barrier height of the annealed sample decreases from 1.12 to 0.84 eV, accompanied by the occurrence of the SCLC. The physical mechanism of the degradation of electrical performance in irradiated devices is the introduction of defects like N vacancies and O-related defects like Al(NOx)y. These findings provide valuable insights for SiC power devices in space applications.

Radiation Damage Mechanisms and Research Status of Radiation-Resistant Optical Fibers: A Review.

In recent years, optical fibers have found extensive use in special environments, including high-energy radiation scenarios like nuclear explosion diagnostics and reactor monitoring. However, radiation exposure, such as X-rays, gamma rays, and neutrons, can compromise fiber safety and reliability. Consequently, researchers worldwide are focusing on radiation-resistant fiber optic technology. This paper examines optical fiber radiation damage mechanisms, encompassing ionization damage, displacement damage, and defect centers. It also surveys the current research on radiation-resistant fiber optic design, including doping and manufacturing process improvements. Ultimately, it summarizes the effectiveness of various approaches and forecasts the future of radiation-resistant optical fibers.

Determination of Self-Heating in Silicon Photomultipliers.

The main consequence of radiation damage on a silicon photomultiplier (SiPM) is a significant increase in the dark current. If the SiPM is not adequately cooled, the power dissipation causes it to heat up, which alters its performance parameters. To investigate this heating effect, a measurement cycle was developed and performed with a KETEK SiPM glued to an Al2O3 substrate and with HPK SiPMs glued to either an Al2O3 substrate or a flexible PCB. The assemblies were connected either directly to a temperature-controlled chuck on a probe station, or through layers of materials with defined thermal resistance. An LED operated in DC mode was used to illuminate the SiPM and to tune the power dissipated in a measurement cycle. The SiPM current was used to determine the steady-state temperature reached by the SiPM via a calibration curve. The increase in SiPM temperature due to self-heating is analyzed as a function of the power dissipation in the SiPM and the thermal resistance. This information can be used to adjust the operating voltage of the SiPMs, taking into account the effects of self-heating. Similarly, this approach can be applied to investigate the unknown thermal contact of packaged SiPMs.

A Lightweight Algorithm to Model Radiation Damage Effects in Monte Carlo Events for High-Luminosity Large Hadron Collider Experiments.

Radiation damage significantly impacts the performance of silicon tracking detectors in Large Hadron Collider (LHC) experiments such as ATLAS and CMS, with signal reduction being the most critical effect; adjusting sensor bias voltage and detection thresholds can help mitigate these effects, generating simulated data that accurately mirror the performance evolution with the accumulation of luminosity, hence fluence, is crucial. The ATLAS and CMS collaborations have developed and implemented algorithms to correct simulated Monte Carlo (MC) events for radiation damage effects, achieving impressive agreement between collision data and simulated events. In preparation for the high-luminosity phase (HL-LHC), the demand for a faster ATLAS MC production algorithm becomes imperative due to escalating collision, events, tracks, and particle hit rates, imposing stringent constraints on available computing resources. This article outlines the philosophy behind the new algorithm, its implementation strategy, and the essential components involved. The results from closure tests indicate that the events simulated using the new algorithm agree with fully simulated events at the level of few %. The first tests on computing performance show that the new algorithm is as fast as it is when no radiation damage corrections are applied.

Radiation Damage on Silicon Photomultipliers from Ionizing and Non-Ionizing Radiation of Low-Earth Orbit Operations.

Silicon Photomultipliers (SiPMs) are single photon detectors that gained increasing interest in many applications as an alternative to photomultiplier tubes. In the field of space experiments, where volume, weight and power consumption are a major constraint, their advantages like compactness, ruggedness, and their potential to achieve high quantum efficiency from UV to NIR makes them ideal candidates for spaceborne, low photon flux detectors. During space missions however, SiPMs are usually exposed to high levels of radiation, both ionizing and non-ionizing, which can deteriorate the performance of these detectors over time. The goal of this work is to compare process and layout variation of SiPMs in terms of their radiation damage effects to identify the features that helps reduce the deterioration of the performance and develop the next generation of more radiation-tolerant detectors. To do this, we used protons and X-rays to irradiate several Near Ultraviolet High-Density (NUV-HD) SiPMs with small areas (single microcell, 0.2 × 0.2 mm2 and 1 × 1 mm2) produced at Fondazione Bruno Kessler (FBK), Italy. We performed online current-voltage measurements right after each irradiation step, and a complete functional characterization before and after irradiation. We observed that the main contribution to performance degradation in space applications comes from proton damage in the form of an increase in primary dark count rate (DCR) proportional to the proton fluence and a reduction in activation energy. In this context, small active area devices show a lower DCR before and after irradiation, and we propose light or charge-focusing mechanisms as future developments for high-sensitivity radiation-tolerant detectors.

Direct Observation of Grain-Boundary-Migration-Assisted Radiation Damage Healing in Ultrafine Grained Gold under Mechanical Stress.

Nanostructured metals are a promising class of radiation-tolerant materials. A large volume fraction of grain boundaries (GBs) can provide plenty of sinks for radiation damage, and understanding the underlying healing mechanisms is key to developing more effective radiation tolerant materials. Here, we observe radiation damage absorption by stress-assisted GB migration in ultrafine-grained Au thin films using a quantitative in situ transmission electron microscopy nanomechanical testing technique. We show that the GB migration rate is significantly higher in the unirradiated specimens. This behavior is attributed to the presence of smaller grains in the unirradiated specimens that are nearly absent in the irradiated specimens. Our experimental results also suggest that the GB mobility is decreased as a result of irradiation. This work implies that the deleterious effects of irradiation can be reduced by an evolving network of migrating GBs under stress.

Beam-induced redox chemistry in iron oxide nanoparticle dispersions at ESRF-EBS.

The storage ring upgrade of the European Synchrotron Radiation Facility makes ESRF-EBS the most brilliant high-energy fourth-generation light source, enabling in situ studies with unprecedented time resolution. While radiation damage is commonly associated with degradation of organic matter such as ionic liquids or polymers in the synchrotron beam, this study clearly shows that highly brilliant X-ray beams readily induce structural changes and beam damage in inorganic matter, too. Here, the reduction of Fe3+ to Fe2+ in iron oxide nanoparticles by radicals in the brilliant ESRF-EBS beam, not observed before the upgrade, is reported. Radicals are created due to radiolysis of an EtOH-H2O mixture with low EtOH concentration (∼6 vol%). In light of extended irradiation times during insitu experiments in, for example, battery and catalysis research, beam-induced redox chemistry needs to be understood for proper interpretation of insitu data.

Gene Therapeutic Delivery to the Salivary Glands.

The salivary glands, exocrine glands in our body producing saliva, can be easily damaged by various factors. Radiation therapy and Sjogren's syndrome (a systemic autoimmune disease) are the two main causes of salivary gland damage, leading to a severe reduction in patients' quality of life. Gene transfer to the salivary glands has been considered a promising approach to treating the dysfunction. Gene therapy has long been applied to cure multiple diseases, including cancers, and hereditary and infectious diseases, which are proven to be safe and effective for the well-being of patients. The application of this treatment on salivary gland injuries has been studied for decades, yet its clinical progress is delayed. This chapter provides a coup d'oeil into gene transfer methods and various gene/vector types for salivary glands to help the new scientists and update established scientists on the progress that has been made during the past decades for the treatment of salivary gland disorders.

Radiation damage and dose limits in serial synchrotron crystallography at cryo- and room temperatures.

Radiation damage limits the accuracy of macromolecular structures in X-ray crystallography. Cryogenic (cryo-) cooling reduces the global radiation damage rate and, therefore, became the method of choice over the past decades. The recent advent of serial crystallography, which spreads the absorbed energy over many crystals, thereby reducing damage, has rendered room temperature (RT) data collection more practical and also extendable to microcrystals, both enabling and requiring the study of specific and global radiation damage at RT. Here, we performed sequential serial raster-scanning crystallography using a microfocused synchrotron beam that allowed for the collection of two series of 40 and 90 full datasets at 2- and 1.9-Å resolution at a dose rate of 40.3 MGy/s on hen egg white lysozyme (HEWL) crystals at RT and cryotemperature, respectively. The diffraction intensity halved its initial value at average doses (D1/2) of 0.57 and 15.3 MGy at RT and 100 K, respectively. Specific radiation damage at RT was observed at disulfide bonds but not at acidic residues, increasing and then apparently reversing, a peculiar behavior that can be modeled by accounting for differential diffraction intensity decay due to the nonuniform illumination by the X-ray beam. Specific damage to disulfide bonds is evident early on at RT and proceeds at a fivefold higher rate than global damage. The decay modeling suggests it is advisable not to exceed a dose of 0.38 MGy per dataset in static and time-resolved synchrotron crystallography experiments at RT. This rough yardstick might change for proteins other than HEWL and at resolutions other than 2 Å.

Surface Passivation by Quantum Exclusion: On the Quantum Efficiency and Stability of Delta-Doped CCDs and CMOS Image Sensors in Space.

Radiation-induced damage and instabilities in back-illuminated silicon detectors have proved to be challenging in multiple NASA and commercial applications. In this paper, we develop a model of detector quantum efficiency (QE) as a function of Si-SiO2 interface and oxide trap densities to analyze the performance of silicon detectors and explore the requirements for stable, radiation-hardened surface passivation. By analyzing QE data acquired before, during, and after, exposure to damaging UV radiation, we explore the physical and chemical mechanisms underlying UV-induced surface damage, variable surface charge, QE, and stability in ion-implanted and delta-doped detectors. Delta-doped CCD and CMOS image sensors are shown to be uniquely hardened against surface damage caused by ionizing radiation, enabling the stability and photometric accuracy required by NASA for exoplanet science and time domain astronomy.

Atomic-Scale Dynamics at Solid-Liquid Nanointerfaces Induced by Electron-Beam Irradiation.

We report electron-beam induced dynamics at PbS-Pb solid-liquid interfaces. We fabricated PbS-Pb solid-liquid nanointerfaces by heating PbS nanocrystals under vacuum to observe the entire process of structural evolution at the atomic scale. We investigated the dynamics using time-resolved high-angle annular dark-field imaging. Electron-beam irradiation caused layer-by-layer dissolution of PbS at the interface, resulting in the formation of the Pb nanodroplet. Ordered liquid layers were observed adjacent to the interface even under continuous electron-beam irradiation and followed the movement of the interface. Instantaneous epitaxial growth of PbS was observed as a reverse process of the dissolution. The resultant Pb nanodroplet provides indisputable evidence for selective sputtering of sulfur atoms via electron-beam irradiation. This paper demonstrates atomic resolution in situ observations of selective and complete sputtering. The observed dynamics can be explained by the intermittent phase transition via nonequilibrium states of the solid-liquid nanointerface triggered by selective sputtering.

Atomistic Study for the Tantalum and Tantalum-Tungsten Alloy Threshold Displacement Energy under Local Strain.

The threshold displacement energy (TDE) is an important measure of the extent of a material's radiation damage. In this study, we investigate the influence of hydrostatic strains on the TDE of pure tantalum (Ta) and Ta-tungsten (W) alloy with a W content ranging from 5% to 30% in 5% intervals. Ta-W alloy is commonly used in high-temperature nuclear applications. We found that the TDE decreased under tensile strain and increased under compressive strain. When Ta was alloyed with 20 at% W, the TDE increased by approximately 15 eV compared to pure Ta. The directional-strained TDE (Ed,i) appears to be more influenced by complex ⟨i j k⟩ directions rather than soft directions, and this effect is more prominent in the alloyed structure than in the pure one. Our results suggest that radiation defect formation is enhanced by tensile strain and suppressed by compressive strain, in addition to the effects of alloying.

Delayed Reaction of Radiation on the Central Nervous System and Bone System in C57BL/6J Mice.

The aim of this study was to provide a suitable mouse model of radiation-induced delayed reaction and identify potential targets for drug development related to the prevention and treatment of radiation injury. C57BL/6J mice were subjected to singular (109 cGy/min, 5 Gy*1) and fractional (109 cGy/min, 5 Gy*2) total body irradiation. The behavior and activity of mice were assessed 60 days after ionizing radiation (IR) exposure. After that, the pathological changes and mechanism of the mouse brain and femoral tissues were observed by HE, Nissl, Trap staining micro-CT scanning and RNA sequencing (RNA-Seq), and Western blot. The results show that singular or fractional IR exposure led to a decrease in spatial memory ability and activity in mice, and the cognitive and motor functions gradually recovered after singular 5 Gy IR in a time-dependent manner, while the fractional 10 Gy IR group could not recover. The decrease in bone density due to the increase in osteoclast number may be relative to the down-regulation of RUNX2, sclerostin, and beta-catenin. Meanwhile, the brain injury caused by IR exposure is mainly linked to the down-regulation of BNDF and Tau. IR exposure leads to memory impairment, reduced activity, and self-recovery, which are associated with time and dose. The mechanism of cognitive and activity damage was mainly related to oxidative stress and apoptosis induced by DNA damage. The damage caused by fractional 10 Gy TBI is relatively stable and can be used as a stable multi-organ injury model for radiation mechanism research and anti-radiation medicine screening.

Electron Scattering from 1-Methyl-5-Nitroimidazole: Cross-Sections for Modeling Electron Transport through Potential Radiosensitizers.

In this study, we present a complete set of electron scattering cross-sections from 1-Methyl-5-Nitroimidazole (1M5NI) molecules for impact energies ranging from 0.1 to 1000 eV. This information is relevant to evaluate the potential role of 1M5NI as a molecular radiosensitizers. The total electron scattering cross-sections (TCS) that we previously measured with a magnetically confined electron transmission apparatus were considered as the reference values for the present analysis. Elastic scattering cross-sections were calculated by means of two different schemes: The Schwinger multichannel (SMC) method for the lower energies (below 15 eV) and the independent atom model-based screening-corrected additivity rule with interferences (IAM-SCARI) for higher energies (above 15 eV). The latter was also applied to calculate the total ionization cross-sections, which were complemented with experimental values of the induced cationic fragmentation by electron impact. Double differential ionization cross-sections were measured with a reaction microscope multi-particle coincidence spectrometer. Using a momentum imaging spectrometer, direct measurements of the anion fragment yields and kinetic energies by the dissociative electron attachment are also presented. Cross-sections for the other inelastic channels were derived with a self-consistent procedure by sampling their values at a given energy to ensure that the sum of the cross-sections of all the scattering processes available at that energy coincides with the corresponding TCS. This cross-section data set is ready to be used for modelling electron-induced radiation damage at the molecular level to biologically relevant media containing 1M5NI as a potential radiosensitizer. Nonetheless, a proper evaluation of its radiosensitizing effects would require further radiobiological experiments.

Unintended consequences: Assessing thermo-mechanical changes in vinyl nitrile foam due to micro-computed X-ray tomographic imaging.

Micro-computed X-ray tomography (µCT) is a volumetric imaging tool used to quantify the internal structure of materials. µCT imaging with mechanical testing (in situ µCT) helps visualize strain-induced structural changes and develop structure-property relationships. However, the effects on thermophysical properties of radiation exposure during in situ µCT imaging are seldom addressed, despite potential radiation sensitivity in elastomers. This work quantifies the radiation dosage effect on thermo-, chemical-, and mechanical-properties for a vinyl nitrile-based foam. Material properties were measured after (0, 1, 2, and 3) days at (8.1 ± 0.9) kGy/d. Morphological characteristics were investigated via scanning electron microscopy. Thermal transitions were assessed using differential scanning calorimetry. Viscoelasticity was measured with dynamic mechanical analysis over a range from -30 °C to 60 °C. Higher dose lead to stiffening and increased dissipation. Chemical structure was assessed with Fourier transform infrared spectroscopy and energy-dispersive X-ray spectroscopy. Soxhlet extraction was used to measure gel content. In summary, substantial changes occur in thermophysical properties, which may confound structure-property measurements. However, this also provides a modification pathway. Quantitation and calibration of the properties changes informed a finite element user material for material designers to explore tunablity and design optimization for impact protection engineers.

PCNA from Thermococcus gammatolerans: A protein involved in chromosomal DNA metabolism intrinsically resistant at high levels of ionizing radiation.

Proliferating cell nuclear antigen (PCNA) is an essential protein for cell viability in archaea and eukarya, since it is involved in DNA replication and repair. In order to obtain insights regarding the characteristics that confer radioresistance, the structural study of the PCNA from Thermococcus gammatolerans (PCNATg ) in a gradient of ionizing radiation by X-ray crystallography was carried out, together with a bioinformatic analysis of homotrimeric PCNA structures, their sequences, and their molecular interactions. The results obtained from the datasets and the accumulated radiation dose for the last collection from three crystals revealed moderate and localized damage, since even with the loss of resolution, the electron density map corresponding to the last collection allowed to build the whole structure. Attempting to understand this behavior, multiple sequence alignments, and structural superpositions were performed, revealing that PCNA is a protein with a poorly conserved sequence, but with a highly conserved structure. The PCNATg presented the highest percentage of charged residues, mostly negatively charged, with a proportion of glutamate more than double aspartate, lack of cysteines and tryptophan, besides a high number of salt bridges. The structural study by X-ray crystallography reveals that the PCNATg has the intrinsic ability to resist high levels of ionizing radiation, and the bioinformatic analysis suggests that molecular evolution selected a particular composition of amino acid residues, and their consequent network of synergistic interactions for extreme conditions, as a collateral effect, conferring radioresistance to a protein involved in the chromosomal DNA metabolism of a radioresistant microorganism.

Guidelines for de novo phasing using multiple small-wedge data collection. Corrigendum.

A figure in the article by Baba et al. [(2021), J. Synchrotron Rad. 28, 1284-1295] is corrected.

Electron-beam induced damage process for Ca2Na2Nb5O16nanosheets.

Dielectric two-dimensional oxide nanosheets are attractive because of their thermal stability and high-k property. However, their atomic structure characterization has been limited since they are easily degraded by electron-beams. This study aimed to investigate the electron-beam induced damage mechanisms for exfoliated Ca2Na2Nb5O16(CNNO) nanosheets. Knock-on damage dominantly occurred at high voltages, leaving short-range order in the final amorphous structure. On the other hand, a series of chemical reactions predominantly occurred at low voltages, resulting in random elemental loss and a fully disordered amorphous structure. This radiolysis was facilitated by insulated CNNO nanosheets that contained a large number of dangling bonds after the chemical solution process. The radiolysis damage kinetics was faster than knock-on damage and induced more elemental loss. Based on our understanding of the electron beam-induced degradation, atomic-scale imaging of the CNNO nanosheets was successfully performed using Cs-corrected scanning transmission electron microscopy at 300 keV with a decreased beam current. This result is of particular significance because understanding of electron-beam damage in exfoliated and insulating 2D oxide sheets could improve identification of their atomic structure using electron microscopy techniques and lead to a practical guide for further extensive characterization of doped elements and layered structures to improve their properties.