Repeated γ irradiation and thermal annealing via built-in thermo-electric coolers of Si avalanche photodiodes.

When operating in space, on-board Silicon Geiger-Mode Avalanche Photodiodes (GM-APDs) are exposed to radiation damage that result in an increase in dark count rates. Thermal annealing has been found to mitigate the damage, although prior studies have largely focused on annealing following a single session of proton irradiation. This work reports that thermal annealing can be performed simply with the built-in thermo-electric coolers of the GM-APDs. Annealing was also done in 10 min intervals for a clearer view of the recovery curve. Mitigation of damage from repeated γ radiation was observed from the: (1) halving of the increase in dark count rates on average and (2) outperformance of room temperature annealing ( 25 ∘ C) by 33 % . Additionally, we show that heavy doses of γ radiation (21 krad) have a probability of causing Random Telegraph Signals in GM-APDs that can be suppressed by lowering the operating temperature.

Spectroscopic insights on defects in self-irradiated natural Zircon: A natural analogue for slag host matrix for Zr-metallic wasteform.

Zircon is a proposed slag host matrix associated with the metallic wasteform route developed for Zr-hull management. This study de-alienates the nature of radiation damage in Zr- and Si- sublattice in self-irradiated zircon matrices under long term of geological times using a natural analogue approach. To address this, self-irradiated reddish-brown zircon from Tamil Nadu, India was characterized using spectroscopic techniques such as X-ray Photoelectron Spectroscopy (XPS), Raman spectroscopy and Photoluminescence (PL) combined with Monte Carlo Based SRIM calculations. The observations revealed that the "as-received" zircon showed significant radiation damage primarily in the Si-sublattice (Si-O-Si linkages) while retaining its crystallinity, indicating a high degree of radiation resistance. The accumulated alpha-dose and displacements per atom (dpa) were evaluated to be 0.59 × 1018 decays/g and 0.019, respectively using RAMAN and SRIM calculations. Photoluminescence studies reveal that after annealing at 1673 K for 96 h, there was a partial recovery of radiation defects and a decrease in Si-O-Si bonds, although defects from dopant atoms remained unchanged. The damage observed is correlated with the nature of atomic bonding in Si-O and Zr-O bonds. The conclusions drawn suggest that zircon demonstrates considerable durability and selective recovery from radiation damage, making it a promising candidate for radioactive waste management.

A novel sample pre-screening methodology for accurate in situ U-Pb dating of zircon crystals.

Internal inhomogeneity of the zircon crystals makes it difficult to date succedent geological processes. To overcome this limitation, a four-step pre-examination method is suggested before LA-ICP-MS based in situ U-Pb age determination of zircon crystals: 1. determination of morphology types of zircon, 2. description of internal textural patterns of zircon, 3. identification of mineral inclusions in zircon, 4. characterization of the structural state and chemical composition of zircon zones/areas. The novel four-step pre-examination protocol integrates established and partially established methods into comprehensive analytical techniques approach that enhances U-Pb dating. The paper demonstrates the effectiveness of this method using examples of zircons derived from granitoid rocks of the Variscan collision zone from the Mórágy Complex in southern Hungary and the Rastenberg Pluton in northern Austria. The study revealed that the areas of the primary textures within zircon crystals (growth zoning ± xenocrystic core, sector zoning) represent the effect of the primary magmatic event from both locations. The xenocrystic core suggests antecedent crustal origin. The secondary texture (convolute zoning) of zircon crystals reflects the post-magmatic event. It causes an overprinting of age data, highlighting the importance of a four-step pre-examination methodology in clarifying and separating nearly coeval geological processes. For age dating, 80 % of the core, 90 % of growth, sector zoning, and 100 % of convolute zoning of studied zircon crystals were appropriate. The suggested method can also be applied to U-Pb age dating of other mineral phases (allanite, apatite, titanite, rutile, xenotime, monazite) separated from igneous and sedimentary or metamorphic rocks.

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.

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.

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.

Radiation effects in head and neck and role of hyperbaric oxygen therapy: An adjunct to management.

Background: Radiotherapy is considered an essential treatment modality in cancers, especially head and neck cancers. Radiotherapy can be given as a definitive, supportive, or adjuvant therapy for various cancers. Radiation damage is an avoidable complication in many patients, after or during radiotherapy. It may be either dose-related, duration-related, or frequency-related. The effects of radiation damage are mainly caused by ischemic necrosis, and once settled it is difficult to manage due to the low vascularity of the affected area. Aim: To find out the effectiveness of hyperbaric oxygen therapy (HBOT) in the management of radiation damage in the head and neck region. Materials and Methods: Retrospective data of patients attending the HBOT clinic for postradiotherapy changes were recorded in an Excel sheet and analyzed in this study. Statistical analysis was done. Result: Our study showed that HBOT is effective in postradiation trismus, xerostomia, discharge, foul smell, discharging sinus, etc., However, it was not found to be significant in the closure of fistula with exposed bone. Conclusion: HBOT is an effective adjunct modality for the management of postradiation changes in the head and neck region.

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.

A Comparative Study on Force-Fields for Interstitial Diffusion in α-Zr and Zr Alloys.

Interstitial diffusion is important for radiation defect evolution in zirconium alloys. This study employed molecular dynamics simulations to investigate interstitial diffusion in α-Zr and its alloys with 1.0 at.% Nb and 1.0 at.% Sn using a variety of interatomic potentials. Pronounced differences in diffusion anisotropy were observed in pure Zr among the employed potentials. This was attributed to the considerable differences in migration barriers among the various interstitial configurations. The introduction of small concentrations of Nb and Sn solute atoms was found to significantly influence diffusion anisotropy by either directly participating in the diffusion process or altering the chemical environment around the diffusing species. Based on the moderate agreement of interstitial energetics in pure Zr, accurately describing interstitial diffusion in Zr alloys is expected to be more complex. This work underscores the importance of the careful validation and selection of interatomic potentials and highlights the need to understand the effects of solute atoms on interstitial diffusion.

Dataset of simulated vibrational density of states and X-ray diffraction profiles of mechanically deformed and disordered atomic structures in Gold, Iron, Magnesium, and Silicon.

This dataset is comprised of a library of atomistic structure files and corresponding X-ray diffraction (XRD) profiles and vibrational density of states (VDoS) profiles for bulk single crystal silicon (Si), gold (Au), magnesium (Mg), and iron (Fe) with and without disorder introduced into the atomic structure and with and without mechanical loading. Included with the atomistic structure files are descriptor files that measure the stress state, phase fractions, and dislocation content of the microstructures. All data was generated via molecular dynamics or molecular statics simulations using the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) code. This dataset can inform the understanding of how local or global changes to a materials microstructure can alter their spectroscopic and diffraction behavior across a variety of initial structure types (cubic diamond, face-centered cubic (FCC), hexagonal close-packed (HCP), and body-centered cubic (BCC) for Si, Au, Mg, and Fe, respectively) and overlapping changes to the microstructure (i.e., both disorder insertion and mechanical loading).

Solvent organization in the ultrahigh-resolution crystal structure of crambin at room temperature.

Ultrahigh-resolution structures provide unprecedented details about protein dynamics, hydrogen bonding and solvent networks. The reported 0.70 Å, room-temperature crystal structure of crambin is the highest-resolution ambient-temperature structure of a protein achieved to date. Sufficient data were collected to enable unrestrained refinement of the protein and associated solvent networks using SHELXL. Dynamic solvent networks resulting from alternative side-chain conformations and shifts in water positions are revealed, demonstrating that polypeptide flexibility and formation of clathrate-type structures at hydrophobic surfaces are the key features endowing crambin crystals with extraordinary diffraction power.

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.

The myth of high-resolution liquid phase biological electron microscopy.

Cryo-electron microscopy (cryo-EM) has transformed structural biology over the past 12 years, with it now being routine rather than exceptional to reach a near-atomic level of resolution for proteins and macromolecular complexes. Samples are immobilized by vitrification and this sample can be maintained at liquid nitrogen temperatures in the vacuum of the electron microscope with negligible sublimation. Due to the low electron doses needed to avoid radiation damage, averaging over tens of thousands to hundreds of thousands of particle images is used to achieve a high signal-to-noise ratio. An alternative approach has been proposed where samples are at room temperature in the liquid state, maintained in the vacuum of the electron microscope by thin film enclosures that are relatively transparent to electrons while preventing evaporation of the liquid. A paper has argued that using this liquid-phase approach, higher resolution (3.2 Å) can be achieved than using cryo-EM (3.4 Å) when imaging and reconstructing adeno-associated virus particles. I show here that these assertions are untrue, and that basic principles in mathematics and physics would need to be violated to achieve the stated resolution in the liquid state. Thus, high resolution liquid phase EM of macromolecules remains science fiction.

High-confidence placement of low-occupancy fragments into electron density using the anomalous signal of sulfur and halogen atoms.

Fragment-based drug design using X-ray crystallography is a powerful technique to enable the development of new lead compounds, or probe molecules, against biological targets. This study addresses the need to determine fragment binding orientations for low-occupancy fragments with incomplete electron density, an essential step before further development of the molecule. Halogen atoms play multiple roles in drug discovery due to their unique combination of electronegativity, steric effects and hydrophobic properties. Fragments incorporating halogen atoms serve as promising starting points in hit-to-lead development as they often establish halogen bonds with target proteins, potentially enhancing binding affinity and selectivity, as well as counteracting drug resistance. Here, the aim was to unambiguously identify the binding orientations of fragment hits for SARS-CoV-2 nonstructural protein 1 (nsp1) which contain a combination of sulfur and/or chlorine, bromine and iodine substituents. The binding orientations of carefully selected nsp1 analogue hits were focused on by employing their anomalous scattering combined with Pan-Dataset Density Analysis (PanDDA). Anomalous difference Fourier maps derived from the diffraction data collected at both standard and long-wavelength X-rays were compared. The discrepancies observed in the maps of iodine-containing fragments collected at different energies were attributed to site-specific radiation-damage stemming from the strong X-ray absorption of I atoms, which is likely to cause cleavage of the C-I bond. A reliable and effective data-collection strategy to unambiguously determine the binding orientations of low-occupancy fragments containing sulfur and/or halogen atoms while mitigating radiation damage is presented.

Temperature Effects of Nuclear and Electronic Stopping Power on Si and C Radiation Damage in 3C-SiC.

Silicon carbide has been considered a material for use in the construction of advanced high-temperature nuclear reactors. However, one of the most important design issues for future reactors is the development of structural defects in SiC under a strong irradiation field at high temperatures. To understand how high temperatures affect radiation damage, SiC single crystals were irradiated at room temperature and after being heated to 800 °C with carbon and silicon ions of energies ranging between 0.5 and 21 MeV. The number of displaced atoms and the disorder parameters have been estimated by using the channeling Rutherford backscattering spectrometry. The experimentally determined depth profiles of induced defects at room temperature agree very well with theoretical calculations assuming its proportionality to the electronic and nuclear-stopping power values. On the other hand, a significant reduction in the number of crystal defects was observed for irradiations performed at high temperatures or for samples annealed after irradiation. Additionally, indications of saturation of the crystal defect concentration were observed for higher fluences and the irradiation of previously defected samples.

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.

Phase-separated super-enhancers confer an innate radioresistance on genomic DNA.

Recently, biomolecular condensates formed through liquid-liquid phase separation have been widely reported to regulate key intracellular processes involved in cell biology and pathogenesis. BRD4 is a nuclear protein instrumental to the establishment of phase-separated super-enhancers (SEs) to direct the transcription of important genes. We previously observed that protein droplets of BRD4 became hydrophobic as their size increase, implying an ability of SEs to limit the ionization of water molecules by irradiation. Here, we aim to establish if SEs confer radiation resistance in cancer cells. We established an in vitro DNA damage assay that measures the effect of radicals provoked by the Fenton reaction on DNA integrity. This revealed that DNA damage was markedly reduced when BRD4 underwent phase separation with DNA. Accordingly, co-focal imaging analyses revealed that SE foci and DNA damage foci are mutually exclusive in irradiated cells. Lastly, we observed that the radioresistance of cancer cells was significantly reduced when irradiation was combined with ARV-771, a BRD4 de-stabilizer. Our data revealed the existence of innately radioresistant genomic regions driven by phase separation in cancer cells. The disruption of these phase-separated components enfolding genomic DNA may represent a novel strategy to augment the effects of radiotherapy.

Doses for X-ray and electron diffraction: New features in RADDOSE-3D including intensity decay models.

New features in the dose estimation program RADDOSE-3D are summarised. They include the facility to enter a diffraction intensity decay model which modifies the "Diffraction Weighted Dose" output from a "Fluence Weighted Dose" to a "Diffraction-Decay Weighted Dose", a description of RADDOSE-ED for use in electron diffraction experiments, where dose is historically quoted in electrons/Å2 rather than in gray (Gy), and finally the development of a RADDOSE-3D GUI, enabling easy access to all the options available in the program.

Identifying and avoiding radiation damage in macromolecular crystallography.

Radiation damage remains one of the major impediments to accurate structure solution in macromolecular crystallography. The artefacts of radiation damage can manifest as structural changes that result in incorrect biological interpretations being drawn from a model, they can reduce the resolution to which data can be collected and they can even prevent structure solution entirely. In this article, we discuss how to identify and mitigate against the effects of radiation damage at each stage in the macromolecular crystal structure-solution pipeline.

Effects on Lung Tissue After Breast Cancer Radiation: Comparing Photon and Proton Therapies.

Purpose: In breast cancer, improved treatment approaches that reduce injury to lung tissue and early diagnosis and intervention for lung toxicity are increasingly important in survivorship. The aims of this study are to (1) compare lung tissue radiographic changes in women treated with conventional photon radiation therapy and those treated with proton therapy (PT), (2) assess the volume of lung irradiated to 5 Gy (V5) and 20 Gy (V20) by treatment modality, and (3) quantify the effects of V5, V20, time, and smoking history on the severity of tissue radiographic changes. Patients and Methods: A prospective observational study of female breast cancer patients was conducted to monitor postradiation subclinical lung tissue radiographic changes. Repeated follow-up x-ray computed tomography scans were acquired through 2 years after treatment. In-house software was used to quantify an internally normalized measure of pulmonary tissue density change over time from the computed tomography scans, emphasizing the 6- and 12-month time points. Results: Compared with photon therapy, PT was associated with significantly lower lung V5 and V20. Lung V20 (but not V5) correlated significantly with increased subclinical lung tissue radiographic changes 6 months after treatment, and neither correlated with lung effects at 12 months. Significant lung tissue density changes were present in photon therapy patients at 6 and 12 months but not in PT patients. Significant lung tissue density change persisted at 12 months in ever-smokers but not in never-smokers. Conclusion: Patients treated with PT had significantly lower radiation exposure to the lungs and less statistically significant tissue density change, suggesting decreased injury and/or improved recovery compared to photon therapy. These findings motivate additional studies in larger, randomized, and more diverse cohorts to further investigate the contributions of treatment modality and smoking regarding the short- and long-term radiographic effects of radiation on lung tissue.