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.

Visualization of Biomolecular Radiation Damage at the Single-Particle Level Using Lanthanide-Sensitized DNA Origami.

Precise monitoring of biomolecular radiation damage is crucial for understanding X-ray-induced cell injury and improving the accuracy of clinical radiotherapy. We present the design and performance of lanthanide-DNA-origami nanodosimeters for directly visualizing radiation damage at the single-particle level. Lanthanide ions (Tb3+ or Eu3+) coordinated with DNA origami nanosensors enhance the sensitivity of X-ray irradiation. Atomic force microscopy (AFM) revealed morphological changes in Eu3+-sensitized DNA origami upon X-ray irradiation, indicating damage caused by ionization-generated electrons and free radicals. We further demonstrated the practical applicability of Eu3+-DNA-origami integrated chips in precisely monitoring radiation-mediated cancer radiotherapy. Quantitative results showed consistent trends with flow cytometry and histological examination under comparable X-ray irradiation doses, providing an affordable and user-friendly visualization tool for preclinical applications. These findings provide new insights into the impact of heavy metals on radiation-induced biomolecular damage and pave the way for future research in developing nanoscale radiation sensors for precise clinical radiography.

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.

A miniature X-ray diffraction setup on ID20 at the European Synchrotron Radiation Facility.

We describe an ultra-compact setup for in situ X-ray diffraction on the inelastic X-ray scattering beamline ID20 at the European Synchrotron Radiation Facility. The main motivation for the design and construction of this setup is the increasing demand for on-the-fly sample characterization, as well as ease of navigation through a sample's phase diagram, for example subjected to high-pressure and/or high-temperature conditions. We provide technical details and demonstrate the performance of the setup.

Electron Attachment to the Nucleobase Uracil in Diethylene Glycol: The Signature of a Doorway.

The cellular environment plays a significant role in low energy electron-mediated radiation damage to genetic materials. In this study, we have modeled the effect of the bulk medium on electron attachment to nucleobases in diethylene glycol (DEG) using uracil as a test case, in accordance with recent experimental work on the observation of dissociative quasi-free electron attachment to nucleoside via excited anion radical in solution (in DEG). Our EOM-CCSD-based quantum mechanical/molecular mechanical (QM/MM) simulations indicate that the electron scavenging by uracil in DEG is much slower than that observed in the aqueous medium due to its viscosity. This work also establishes that a doorway mechanism exists in uracil microsolvated and bulk solvated with DEG, with the dipole-bound state and solvent-bound state acting as doorway states, respectively.

Radiation and DNA Origami Nanotechnology: Probing Structural Integrity at the Nanoscale.

DNA nanotechnology has emerged as a groundbreaking field, using DNA as a scaffold to create nanostructures with customizable properties. These DNA nanostructures hold potential across various domains, from biomedicine to studying ionizing radiation-matter interactions at the nanoscale. This review explores how the various types of radiation, covering a spectrum from electrons and photons at sub-excitation energies to ion beams with high-linear energy transfer influence the structural integrity of DNA origami nanostructures. We discuss both direct effects and those mediated by secondary species like low-energy electrons (LEEs) and reactive oxygen species (ROS). Further we discuss the possibilities for applying radiation in modulating and controlling structural changes. Based on experimental insights, we identify current challenges in characterizing the responses of DNA nanostructures to radiation and outline further areas for investigation. This review not only clarifies the complex dynamics between ionizing radiation and DNA origami but also suggests new strategies for designing DNA nanostructures optimized for applications exposed to various qualities of ionizing radiation and their resulting byproducts.

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.

Quantum Simulations of Radiation Damage in a Molecular Polyethylene Analog.

An atomic-level understanding of radiation-induced damage in simple polymers like polyethylene is essential for determining how these chemical changes can alter the physical and mechanical properties of important technological materials such as plastics. Ensembles of quantum simulations of radiation damage in a polyethylene analog are performed using the Density Functional Tight Binding method to help bind its radiolysis and subsequent degradation as a function of radiation dose. Chemical degradation products are categorized with a graph theory approach, and occurrence rates of unsaturated carbon bond formation, crosslinking, cycle formation, chain scission reactions, and out-gassing products are computed. Statistical correlations between product pairs show significant correlations between chain scission reactions, unsaturated carbon bond formation, and out-gassing products, though these correlations decrease with increasing atom recoil energy. The results present relatively simple chemical descriptors as possible indications of network rearrangements in the middle range of excitation energies. Ultimately, the work provides a computational framework for determining the coupling between nonequilibrium chemistry in polymers and potential changes to macro-scale properties that can aid in the interpretation of future radiation damage experiments on plastic materials.

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 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.

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.

Study of Neutron-, Proton-, and Gamma-Irradiated Silicon Detectors Using the Two-Photon Absorption-Transient Current Technique.

The Two-Photon Absorption-Transient Current Technique (TPA-TCT) is a device characterisation technique that enables three-dimensional spatial resolution. Laser light in the quadratic absorption regime is employed to generate excess charge carriers only in a small volume around the focal spot. The drift of the excess charge carriers is studied to obtain information about the device under test. Neutron-, proton-, and gamma-irradiated p-type pad silicon detectors up to equivalent fluences of about 7 × 1015 neq/cm2 and a dose of 186 Mrad are investigated to study irradiation-induced effects on the TPA-TCT. Neutron and proton irradiation lead to additional linear absorption, which does not occur in gamma-irradiated detectors. The additional absorption is related to cluster damage, and the absorption scales according to the non-ionising energy loss. The influence of irradiation on the two-photon absorption coefficient is investigated, as well as potential laser beam depletion by the irradiation-induced linear absorption. Further, the electric field in neutron- and proton-irradiated pad detectors at an equivalent fluence of about 7 × 1015 neq/cm2 is investigated, where the space charge of the proton-irradiated devices appears inverted compared to the neutron-irradiated device.

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.

Local Strain Effects on Lattice Defect Dynamics and Interstitial Dislocation Loop Formation in Irradiated Tungsten-Molybdenum Alloys: A Molecular Dynamics Study.

In this study, molecular dynamics (MD) simulations were used to investigate how alloying tungsten (W) with molybdenum (Mo) and local strain affect the primary defect formation and interstitial dislocation loops (IDLs) in W-Mo alloys. While the number of Frenkel pairs (FPs) in the W-Mo alloy is similar to pure W, it is half that of pure Mo. The W-20% Mo alloy, chosen for further analysis, showed minimal FP variance after collision cascades induced by primary knock-on atoms (PKAs) at 10 to 80 keV. The research examined hydrostatic strains from -1.4% to 1.6%, finding that higher strains correlated with increased FP counts and cluster formation, including IDLs. The following two types of IDLs were identified: majority ½ <111> loops as well as <100> IDLs that formed within the initial picoseconds of the simulations under higher tensile strain (1.6%) and larger PKA energies (80 keV). The strain effects also correlated with changes in threshold displacement energy (TDE), with higher FP formation under tensile strain. This study highlights the impact of strain and alloying on radiation damage, particularly in low-temperature, high-energy environments.

TOPAS-Tissue: A Framework for the Simulation of the Biological Response to Ionizing Radiation at the Multi-Cellular Level.

This work aims to develop and validate a framework for the multiscale simulation of the biological response to ionizing radiation in a population of cells forming a tissue. We present TOPAS-Tissue, a framework to allow coupling two Monte Carlo (MC) codes: TOPAS with the TOPAS-nBio extension, capable of handling the track-structure simulation and subsequent chemistry, and CompuCell3D, an agent-based model simulator for biological and environmental behavior of a population of cells. We verified the implementation by simulating the experimental conditions for a clonogenic survival assay of a 2-D PC-3 cell culture model (10 cells in 10,000 µm2) irradiated by MV X-rays at several absorbed dose values from 0-8 Gy. The simulation considered cell growth and division, irradiation, DSB induction, DNA repair, and cellular response. The survival was obtained by counting the number of colonies, defined as a surviving primary (or seeded) cell with progeny, at 2.7 simulated days after irradiation. DNA repair was simulated with an MC implementation of the two-lesion kinetic model and the cell response with a p53 protein-pulse model. The simulated survival curve followed the theoretical linear-quadratic response with dose. The fitted coefficients α = 0.280 ± 0.025/Gy and ß = 0.042 ± 0.006/Gy2 agreed with published experimental data within two standard deviations. TOPAS-Tissue extends previous works by simulating in an end-to-end way the effects of radiation in a cell population, from irradiation and DNA damage leading to the cell fate. In conclusion, TOPAS-Tissue offers an extensible all-in-one simulation framework that successfully couples Compucell3D and TOPAS for multiscale simulation of the biological response to radiation.

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.