Yoshiyuki Hirano¹, Kanta Nambu¹, Tsukasa Aso², Masanori Hara³ and Susumu Fujiwara⁴
1 Department of integrated health sciences, Graduate school of medicine, Nagoya University, Japan
2 Electronics and Computer Engineering, National Institute of Technology, Toyama College, Japan
3 Faculty of Science, Academic Assembly, University of Toyama, Japan
4 Faculty of Materials Science and Engineering, Kyoto Institute of Technology, Japan

Abstract
Ionizing radiation induces DNA damage both directly and indirectly through hydroxyl radicals (·OH) generated by water radiolysis. The indirect action involves hydrogen abstraction from deoxyribose, leading to DNA damage such as base release and strand breaks. The probability of such events depends on the accessibility of specific hydrogen atoms to ·OHradicals. Previous computational studies have examined naked DNA fragments; however, the effect of nucleosomal organization has not been addressed. Here, we performed molecular dynamics (MD) simulations usingLAMMPS(Large-scale Atomic Molecular Massively Parallel Simulator) to evaluate the accessibility of ·OHradicals to deoxyribose hydrogens in both 12-bp naked B-typeDNAand nucleosomal DNA containing histone proteins. The accessibility to the hydrogens increased, following the order H1′≈H2′≈H3′＜H4′＜H5′, consistent with previous studies. Accessibility was approximately proportional to the solvent accessible surface area (SASA), supporting SASA as a practical predictor of accessibility even in base-dependent differences were observed. In nucleosomal DNA, accessibility of hydrogens facing the histone core was significantly reduced compared to solvent-facing hydrogens, despite comparable SASA values. This reduction suggests that histones physically hinder ·OHradical penetration. These findings highlight the importance of considering protein–DNA complexes when modeling indirect radiation effects.

https://doi.org/10.1088/1402-4896/ae3446
ACCEPTED FOR PUBLICATION :6 January 2026

Shun Fukagawa ^a, Tsukasa Aso ^b, Yuya Tanbo ^b, Yoshiyuki Hirano ^c, Susumu Fujiwara ^d, Masanori Hara ^e

a Advanced Course, National Institute of Technology, Toyama College, Imizu 9330293, Japan
b Electronics and Computer Engineering, National Institute of Technology, Toyama College, Imizu 9330293, Japan
c Department of integrated health sciences, Graduate school of medicine, Nagoya University, Nagoya 4618673, Japan
d Faculty of Materials Science and Engineering, Kyoto Institute of Technology, Kyoto 6068585, Japan
e Faculty of Science, Academic Assembly, University of Toyama, Toyama 9308555, Japan

Abstract
Accurate simulation of radiation-induced DNA damage requires geometry models that preserve atomic structure while satisfying Geant4-DNA constraints. We present PDBDNAConv, a modular software suite that provides an automated pipeline for converting Protein Data Bank (PDB) structures into simulation-ready geometries. The software reconstructs hierarchical DNA models based on atomic structure using ellipsoidal approximation categorized for sugar, phosphate, and base moieties in nucleotide to reduce geometric complexes. Geometric overlaps are automatically detected and resolved to ensure valid geometry construction. Structured output is serialized in JSON format for interoperability and seamless integration into Geant4-DNA simulations. The exported JSON files are loadable by an example Geant4-DNA application through developed geometry construction classes that enable atomic-scale analysis of direct and indirect DNA damage.

https://doi.org/10.1016/j.softx.2026.102746
Accepted:21 May 2026

Ichiro Nishii ^a, Tomone Suganuma ^a, Takahiko Horiai ^b, Yuui Yokota ^c , Masao Yoshino ^c, Makoto Nakajima ^a, Masanori Hara ^d, Keisuke Shigemori ^a, Kohei Yamanoi ^a

a Institute of Laser Engineering, The University of Osaka, 2-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
b National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8565, Japan
c Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
d Faculty of Science, Academic Assembly, University of Toyama, 3190 Gofuku, Toyama, 930-8555, Japan

Abstract
Tritium in water is difficult to monitor because the low-energy beta particles emitted by tritium are strongly selfabsorbed. Although liquid scintillation counting provides high sensitivity, it requires sample preparation and generates radioactive organic liquid waste, limiting its suitability for on-site continuous monitoring. In this study, we investigated the inorganic single-crystal scintillator (La,Gd)₂Si₂O₇:Ce (Ce:La-GPS) for tritiated water measurements. The as-grown sample showed long-term afterglow that increased the count rate in the region of interest for tritium detection, but air annealing at 1200 ℃ suppressed the afterglow to the background level. The annealed sample exhibited a light output of approximately 35,000 photons/MeV and an energy resolution of 5.5% at 662 keV under ¹³⁷Cs gamma-ray excitation. Immersion measurements in tritiated water showed a linear counting response, with a minimum detectable activity of 3.85 MBq/L for a 600 s measurement. These results indicate that Ce:La-GPS is a promising solid scintillator for high-activity tritiated water monitoring, while application to low-level monitoring will require increasing the effective scintillator surface area.

https://doi.org/10.1016/j.optmat.2026.118252
Accepted:10 June 2026