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Journal Articles

First-principles simulation of an ejected electron produced by monochromatic deposition energy to water at the femtosecond order

Kai, Takeshi; Toigawa, Tomohiro; Matsuya, Yusuke; Hirata, Yuho; Tezuka, Tomoya*; Tsuchida, Hidetsugu*; Yokoya, Akinari*

RSC Advances (Internet), 13(46), p.32371 - 32380, 2023/11

Although scientific knowledge of photolysis and radiolysis of water is widely used in the life sciences and other fields, the formation mechanism of the spatial distribution of hydrated electrons (spur) resulting from energy deposition to water is still not well understood. The chemical reaction times of hydrated electrons, OH radicals, and H$$_{3}$$O$$^{+}$$ in the spur strongly depend on the spur radius. In our previous study, we elucidated the mechanism at a specific given energy (12.4 eV) by first-principles calculations. In the present study, we performed first-principles calculations of the spur radius at the deposition energies of 11-19 eV. The calculated spur radius is 3-10 nm, which is consistent with the experimental prediction (~4 nm) for the energy range of 8-12.4 eV, and the spur radius gradually increases with increasing energy. The spur radius is a new scientific knowledge and is expected to be widely used for estimating radiation DNA damage.

Journal Articles

Incorporation of a bromine atom into DNA-related molecules changes their electronic properties

Hirato, Misaki*; Yokoya, Akinari*; Baba, Yuji*; Mori, Seiji*; Fujii, Kentaro*; Wada, Shinichi*; Izumi, Yudai*; Haga, Yoshinori

Physical Chemistry Chemical Physics, 25(21), p.14836 - 14847, 2023/05

 Times Cited Count:0 Percentile:0.01(Chemistry, Physical)

Journal Articles

Nature of the physicochemical process in water photolysis uncovered by a computer simulation

Kai, Takeshi; Toigawa, Tomohiro; Ukai, Masatoshi*; Fujii, Kentaro*; Watanabe, Ritsuko*; Yokoya, Akinari*

Journal of Chemical Physics, 158(16), p.164103_1 - 164103_8, 2023/04

New insight into water radiolysis and photolysis is indispensable in the dramatic progress of sciences and technologies in various research areas. In the radiation field, reactive hydrated electrons are considerably produced along radiation tracks. Although the formation results from a transient dynamic correlation between ejected electrons and water, the individual mechanisms of electron thermalization, delocalization, and polarization are unknown. Using a dynamic Monte Carlo code, we show herein that the ejected electrons are immediately delocalized by molecular excitations in parallel with phonon polarization and gradually thermalized by momentum transfer with an orientation polarization in a simultaneous manner. Our results show that these mechanisms heavily depend on the intermolecular vibration and rotation modes peculiar to water. We expect our approach to be a powerful technique for connecting physical and chemical processes in various solvents.

Journal Articles

Initial yield of hydrated electron production from water radiolysis based on first-principles calculation

Kai, Takeshi; Toigawa, Tomohiro; Matsuya, Yusuke*; Hirata, Yuho; Tezuka, Tomoya*; Tsuchida, Hidetsugu*; Yokoya, Akinari*

RSC Advances (Internet), 13(11), p.7076 - 7086, 2023/03

 Times Cited Count:1 Percentile:79.55(Chemistry, Multidisciplinary)

Scientific insights of water radiolysis are widely used in the life sciences and so on, however, the formation mechanism of radicals, a product of water radiolysis, is still not well understood. We are challenging to develop a simulation code to solve this formation mechanism from the viewpoint of radiation physics. Our first-principles calculations have revealed that the behavior of secondary electrons in water is governed not only by collisional effects but also by polarization effects. Furthermore, from the predicted ratio of ionization to electronic excitation, based on the spatial distribution of secondary electrons, we successfully reproduce the initial yield of hydrated electrons predicted in terms of radiation chemistry. The code provides us a reasonable spatiotemporal connection from radiation physics to radiation chemistry. Our findings are expected to provide newly scientific insights for understanding the earliest stages of water radiolysis.

Journal Articles

Dense radical formation in L-alanine-3,3,3-d3 and L-alanine-d4 by 1.5 keV soft X-ray irradiation

Nakagawa, Seiko*; Oka, Toshitaka; Fujii, Kentaro*; Yokoya, Akinari*

Radiation Physics and Chemistry, 192, p.109884_1 - 109884_5, 2022/03

 Times Cited Count:0 Percentile:35.78(Chemistry, Physical)

Radicals produced in crystalline L-alanine-3,3,3-d3 and L-alanine-d4 were observed by the electron spin resonance (ESR) technique during 1.5 keV soft X-ray irradiation. The line width of the ESR spectra obtained by the soft X-ray irradiation was 1.5 times wider than that of hard X-rays from a previous report, meaning a higher density of radicals. The efficiency of the radical yield by the soft X-ray irradiation was 10$$^{-6}$$ relative to that by $$gamma$$-irradiation. For the soft X-ray irradiation, many radicals will be lost by the efficient radical-radical recombination due to the higher density of the radicals, just as the high-LET irradiation by heavy ions. We concluded that the high LET nature of the lower energy photons leads to the dense radical formation in the crystalline alanine powder.

Journal Articles

Electronic properties of DNA-related molecules containing a bromine atom

Hirato, Misaki*; Onizawa, Misato*; Baba, Yuji*; Haga, Yoshinori; Fujii, Kentaro*; Wada, Shinichi*; Yokoya, Akinari*

International Journal of Radiation Biology, 7 Pages, 2020/00

 Times Cited Count:2 Percentile:25.41(Biology)

Journal Articles

Recent progress of radiation physicochemical process (third part)

Kai, Takeshi; Yokoya, Akinari*; Fujii, Kentaro*; Watanabe, Ritsuko*

Hoshasen Kagaku (Internet), (106), p.21 - 29, 2018/11

It is thought to that the biological effects such as cell death or mutation are induced by complex DNA damage which are formed by several damage sites within a few nm. As the prediction of complex DNA damage at an electron track end, we report our outcomes. These results indicate that DNA damage sites comprising multiple nucleobase lesions with a single strand breaks can be formed by multiple collisions of the electrons within 1 nm. This multiple damage site cannot be processed by base excision repair enzymes. Pre-hydrated electrons can also be produced resulting in an additional base lesion over a few nm from the multi-damage site. This clustered damage site may be finally converted into a double strand break. These DSBs include another base lesion(s) at their termini that escape from the base excision process and which may result in biological effect. Our simulation is useful to reveal phenomena involved in radiation physico-chemistry as well as the DNA damage prediction.

Journal Articles

A Significant role of non-thermal equilibrated electrons in the formation of deleterious complex DNA damage

Kai, Takeshi; Yokoya, Akinari*; Ukai, Masatoshi*; Fujii, Kentaro*; Toigawa, Tomohiro; Watanabe, Ritsuko*

Physical Chemistry Chemical Physics, 20(4), p.2838 - 2844, 2018/01

 Times Cited Count:19 Percentile:76.27(Chemistry, Physical)

It is thought that complex DNA damage which induces in radiation biological effects is formed at radiation track end. Thus, the earliest stage of water radiolysis at the electron track end was studied to predict DNA damage. These results indicate that DNA damage sites comprising multiple nucleobase lesions with a single strand breaks can therefore be formed by multiple collisions of the electrons within three base pairs (3bp) of a DNA strand. This multiple damage site cannot be processed by base excision repair enzymes. However, pre-hydrated electrons can also be produced resulting in an additional base lesion more than 3bp away from the multi-damage site. This clustered damage site may be finally converted into a double strand break (DSB) when base excision enzymes process the additional base lesions. These DSBs include another base lesion(s) at their termini that escape from the base excision process and which may result in biological effects such as mutation in surviving cells.

Journal Articles

Reactivity of an antioxidant, edaravone, with reactive oxygen species and its chemical repair properties against oxidative damage on DNA

Hata, Kuniki; Lin, M.*; Yokoya, Akinari*; Fujii, Kentaro*; Yamashita, Shinichi*; Muroya, Yusa*; Katsumura, Yosuke*

Hoshasen Kagaku (Internet), (103), p.29 - 34, 2017/04

Reactivity of edaravone (3-methyl-1-phenyl-2-pyrazolin-5-one), which is known to show high antioxidative properties, with oxidative species, such as hydroxyl radical ($${}^{bullet}$$OH) and azide radical (N$$^{bullet}$$$$_{3}$$), was investigated by a pulse radiolysis experiment, and generation behavior of edaravone radicals produced through these reactions were observed. It was shown that OH-adducts are produced by the reaction with $${}^{bullet}$$OH in contrast to the other oxidative radicals, which react with edaravone by an electron transfer reaction. Chemical repair properties of edaravone against DNA lesions produced by reactions of DNA with oxidative species were also investigated by a pulse radiolysis experiment with deoxyguanosine monophosphate (dGMP) and a $$gamma$$-radiolysis experiment with plasmid DNA solutions. It was observed that edaravone reduced dGMP radicals just after produced in a dilute aqueous solution and inhibited some base lesions on plasmid DNA more effectively than single strand breaks. These results show that edaravone may protect living system from oxidative stress, such as radiation, by not only scavenging oxidative species but also reducing precursors of DNA leisons.

Journal Articles

Dynamic behavior of secondary electrons produced by a high-energy electron in liquid water

Kai, Takeshi; Yokoya, Akinari*; Fujii, Kentaro*; Watanabe, Ritsuko*

Yodenshi Kagaku, (8), p.11 - 17, 2017/03

It is thought to that the biological effects such as cell death or mutation are induced by complex DNA damage which are formed by several damage sites within a few nm. We calculated dynamic behavior of secondary electrons produced by primary electron and positon of high energy in water whose composition ratio is similar to biological context. The secondary electrons induce the ionization or electronic excitation near the parent cations. The decelerated electrons about 10% are distributed to their parent cations by the attractive Coulombic force. From the results, we predicted the following formation mechanism for the complex DNA damage. The electrons ejected from DNA could induce the ionization or the electronic excitation within the DNA. The electrons attracted by the Coulombic force are pre-hydrated in water layer of the DNA. The pre-hydrated electrons could induce to the DNA damage by dissociative electron transfer. As the results, the complex DNA damage with 1 nm could be formed by the interaction of not only the primary electron or positon but also the secondary electrons.

Journal Articles

Deceleration processes of secondary electrons produced by a high-energy Auger electron in a biological context

Kai, Takeshi; Yokoya, Akinari; Ukai, Masatoshi; Fujii, Kentaro; Watanabe, Ritsuko

International Journal of Radiation Biology, 92(11), p.654 - 659, 2016/11

 Times Cited Count:9 Percentile:69.2(Biology)

Journal Articles

Dynamic behavior of secondary electrons in liquid water at the earliest stage upon irradiation; Implications for DNA damage localization mechanism

Kai, Takeshi; Yokoya, Akinari*; Ukai, Masatoshi*; Fujii, Kentaro*; Watanabe, Ritsuko*

Journal of Physical Chemistry A, 120(42), p.8228 - 8233, 2016/10

 Times Cited Count:16 Percentile:61.57(Chemistry, Physical)

Low energy secondary electrons produced by an ionizing radiation in a living cell may involve in formation of complexed DNA damage. We performed theoretical study for numerical calculation of dynamic behavior of the electrons to imply a formation of radiation damage to DNA. The decelerating electrons are gradually attracted to their parent cations by the Coulombic force within hundreds of fs, and about 12.6 % of electrons are finally distributed within 2 nm from the cations. The collision fraction of the ionization and excitation within 1 nm from the cation was estimated to be about 40 %. From those analyses, we suggested a process of DNA damage that the secondary electrons may cause highly localized lesions around a cation in DNA molecule through additional dissociative electron transfer as well as the ionization or the excitation if the electrons are ejected from DNA. The localized damage may involve ultimately in biological effects such as cell death or mutation induction.

Journal Articles

Recent progress of radiation physicochemical process (first part)

Kai, Takeshi; Yokoya, Akinari; Fujii, Kentaro; Watanabe, Ritsuko

Hoshasen Kagaku (Internet), (101), p.3 - 11, 2016/04

Behavior analysis of low energy electrons in liquid water provides the fundamentals for successive radiation chemistry, and it makes analysis of DNA damage implication involved in the electrons possible. We have progressed theoretical studies for radiation physicochemical process of liquid water to clear the role of low-energy secondary electrons damage to DNA. The process has included many unknown factors for the DNA damage so far. Based on the results, we implied a newly formation process of unrepair DNA damage produced by the secondary electrons assumed that it was ejected from DNA by impact of a high energy electron. We report our outcomes separately in three manuscripts entitled "Recent progress of radiation physicochemical process (first, second, third parts)" to journal of radiation chemistry. In this first part, we outline recent status of studies for the DNA damage and the radiation physicochemical process, we also show calculation method of electron impact cross sections involved strongly in electron deceleration in liquid water in the topics of our outcomes. From the calculated results, we also report our prediction, which are different from previous one, for electron thermalization.

Journal Articles

Ultraviolet circular dichroism spectroscopy for protein structural study

Izumi, Yudai; Yamamoto, Satoshi*; Fujii, Kentaro; Yokoya, Akinari

Hoshasen Seibutsu Kenkyu, 51(1), p.91 - 106, 2016/03

no abstracts in English

Journal Articles

Low-dose radiation risk and individual variation in radiation sensitivity in Fukushima

Fukunaga, Hisanori*; Yokoya, Akinari

Journal of Radiation Research, 57(1), p.98 - 100, 2016/01

 Times Cited Count:8 Percentile:85.99(Biology)

Journal Articles

Recent progress of radiation physicochemical process (second part)

Kai, Takeshi; Yokoya, Akinari*; Fujii, Kentaro*; Watanabe, Ritsuko*

Hoshasen Kagaku (Internet), (102), p.49 - 56, 2016/00

Behavior analysis of low energy electrons in liquid water provides the fundamentals for successive radiation chemistry, and it makes analysis of DNA damage implication involved in the electrons possible. We have progressed theoretical studies for radiation physicochemical process of water to clear the role of secondary electrons damage to DNA. The process has included many unknown factors for the DNA damage so far. We implied a newly formation process of unrepair DNA damage produced by the secondary electrons. We report our outcomes separately in three manuscripts entitled "Recent progress of radiation physicochemical process (first, second, third parts)". In this second part, we show calculated results of thermalization lengths and times of electrons in water to verify a dynamic Monte Carlo code developed in this study. From the calculated results, we also report our prediction, which are different from previous one, for thermalization and pre-hydration processes.

Journal Articles

Cellular automaton-based model for radiation-induced bystander effects

Hattori, Yuya; Yokoya, Akinari; Watanabe, Ritsuko

BMC Systems Biology (Internet), 9, p.90_1 - 90_22, 2015/12

 Times Cited Count:17 Percentile:66.94(Mathematical & Computational Biology)

The radiation-induced bystander effect is a biological response observed in non-irradiated cells surrounding an irradiated cell, which is known to be caused by two intercellular signaling pathways. However, the behavior of the signals is largely unknown. To investigate the role of these signaling pathways, we developed a mathematical model to describe the cellular response to direct irradiation and the bystander effect, with a particular focus on cell-cycle modification. The analysis of model dynamics revealed that bystander effect on cell cycle modification was different between low-dose irradiation and high-dose irradiation. We demonstrated that signaling through both pathways induced cell cycle modification via the bystander effect. By simulating various special and temporal conditions of irradiation and cell characteristics, our model will be a powerful tool for the analysis of the bystander effect.

Journal Articles

Investigation of the fragmentation of core-ionised deoxyribose; A Study as a function of the tautomeric form

Herv$'e$ du Penhoat, M.-A.*; Kamol Ghose, K.*; Gaigeot, M.-P.*; Vuilleumier, R.*; Fujii, Kentaro; Yokoya, Akinari; Politis, M.-F.*

Physical Chemistry Chemical Physics, 17(48), p.32375 - 32383, 2015/12

 Times Cited Count:8 Percentile:32.07(Chemistry, Physical)

Journal Articles

Secondary structure alterations of histones H2A and H2B in X-irradiated human cancer cells; Altered histones persist in cells for at least 24 hours

Izumi, Yudai; Yamamoto, Satoshi*; Fujii, Kentaro; Yokoya, Akinari

Radiation Research, 184(5), p.554 - 558, 2015/11

 Times Cited Count:7 Percentile:33.45(Biology)

Journal Articles

Thermal equilibrium and prehydration processes of electrons injected into liquid water calculated by dynamic Monte Carlo method

Kai, Takeshi; Yokoya, Akinari; Ukai, Masatoshi*; Fujii, Kentaro; Watanabe, Ritsuko

Radiation Physics and Chemistry, 115, p.1 - 5, 2015/10

 Times Cited Count:29 Percentile:93.68(Chemistry, Physical)

Role of secondary electrons on DNA damage have not been understood sufficiently because there still exists a lack of study for thermalization process of an electron in liquid phase. We calculated thermalization lengths and spatial distributions of an electron in liquid water using cross sections for rotation and phonon excitations in a liquid phase. Obtained thermalization lengths are in good agreement with experimental results reported by literatures. Thermalization time was also estimated from time evolution of spatial distributions of the incident electron to be hundreds femtoseconds. From these results, we predict that thermalization and pre-hydration of electron might progress simultaneously. These electrons possibly cause damage in biological molecules in a cell. Particularly severe types of DNA damage consisting of proximately located multiple lesions are potentially induced by reaction of DNA with the thermalized electrons by dissociative electron transfer.

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