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JAEA Reports

Survey of computational methods of cross sections for thermal neutron scattering by liquids

Ichihara, Akira

JAEA-Review 2019-046, 36 Pages, 2020/03

JAEA-Review-2019-046.pdf:1.55MB

Toward the revision of JENDL-4.0, we conducted a literature survey on how to compute the cross section of thermal neutrons scattered by a liquid. This report summarizes the computational methods for evaluating thermal neutron cross sections with molecular dynamics simulations. The cross section can be expressed with a function called as scattering law. For light and heavy water, the scattering law data instead of the cross sections have been provided in nuclear databases. In this report we review the formulations of the scattering laws. The scattering laws can be derived from both the intermediate scattering function and the space-time correlation function. Features of the derived scattering laws are briefly explained. It is shown that the scattering law data can be evaluated using a molecular dynamics simulation of the liquid that is the target of thermal neutrons.

Journal Articles

Molecular dynamics simulations of physical properties of water and cations in montmorillonite interlayer; Application to diffusion model

Yotsuji, Kenji*; Tachi, Yukio; Kawamura, Katsuyuki*; Arima, Tatsumi*; Sakuma, Hiroshi*

Nendo Kagaku, 58(1), p.8 - 25, 2019/00

Molecular dynamics (MD) simulations were conducted to investigate physical properties of water and cations in montmorillonite interlayer nanopores. The swelling behaviors and hydration states were firstly evaluated as functions of interlayer cations and layer charge. The diffusion coefficients of water and cations in interlayer nanopores were decreased in comparison with those in bulk water and came closer to those in bulk water when basal spacing increased. The viscosity coefficients of interlayer water estimated indicated a significant effect of viscoelectricity at 1- and 2-layer hydration states and higher layer charge of montmorillonite. These trends from MD calculations were confirmed to be consistent with existing measured data and previous MD simulation. In addition, model and parameter related to viscoelectric effect used in the diffusion model was refined based on comparative discussion between MD simulations and measurements. The series of MD calculations could provide atomic level understanding for the developments and improvements of the diffusion model for compacted montmorillonite.

Journal Articles

Diffusion and adsorption of uranyl ion in clays; Molecular dynamics study

Arima, Tatsumi*; Idemitsu, Kazuya*; Inagaki, Yaohiro*; Kawamura, Katsuyuki*; Tachi, Yukio; Yotsuji, Kenji

Progress in Nuclear Energy, 92, p.286 - 297, 2016/09

 Times Cited Count:4 Percentile:44.9(Nuclear Science & Technology)

Diffusion and adsorption behavior of uranyl (UO$$_2^{2+}$$) species is important for the performance assessment of radioactive waste disposal. The diffusion behaviors of UO$$_2^{2+}$$, K$$^{+}$$, CO$$_3^{2-}$$ and Cl$$^{-}$$ and H$$_{2}$$O in the aqueous solutions were evaluated by molecular dynamics (MD) calculations. The diffusion coefficient (De) of UO$$_2^{2+}$$ is the smallest and is 26% less than the self-diffusion coefficient of H$$_{2}$$O. For the aqueous solution with high concentration of carbonate ions, uranyl carbonate complexes: UO$$_{2}$$CO$$_{3}$$ and UO$$_{2}$$(CO$$_{3}$$)$$^{2-}$$ can be observed. For the clay (montmorillonite or illite)-aqueous solution systems, the adsorption and diffusion behaviors of UO$$_2^{2+}$$ and K$$^{+}$$ were evaluated by MD calculations. The distribution coefficients (Kd) increase with the layer charge of clay, and Kd of UO$$_2^{2+}$$ might be smaller than that of K$$^{+}$$. Further, their two-dimensional diffusion coefficients were relatively small in the adsorption layer and were extremely small for illite with higher layer charge.

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:6 Percentile:64.99(Chemistry, Physical)

Journal Articles

Mechanisms of oxygen reduction reactions for carbon alloy catalysts via first principles molecular dynamics

Ikeda, Takashi; Hou, Z.*; Chai, G.-L.*; Terakura, Kiyoyuki*

Hyomen Kagaku, 36(7), p.345 - 350, 2015/07

Carbon alloy catalysts (CACs) are one of promising candidates for platinum-substitute cathode catalysts for polymer electrolyte fuel cells. We have investigated possible mechanisms of oxygen reduction reactions (ORRs) for CACs via first-principles-based molecular dynamics simulations. In this contribution, we review possible ORRs at likely catalytic sites of CACs suggested from our simulations.

Journal Articles

Infrared absorption and Raman scattering spectra of water under pressure via first principles molecular dynamics

Ikeda, Takashi

Journal of Chemical Physics, 141(4), p.044501_1 - 044501_8, 2014/07

 Times Cited Count:9 Percentile:55.54(Chemistry, Physical)

From both the polarized and depolarized Raman scattering spectra of supercritical water a peak located at around 1600 cm$$^{-1}$$, attributed normally to bending mode of water molecules, was experimentally observed to vanish, whereas the corresponding peak remains clearly visible in the measured infrared (IR) absorption spectrum. In this computational study a theoretical formulation for analyzing the IR and Raman spectra is developed via first principles molecular dynamics combined with the modern polarization theory. We demonstrate that the experimentally observed peculiar behavior of the IR and Raman spectra for water are well reproduced in our computational scheme. We discuss the origins of a feature observed at 1600 cm$$^{-1}$$ in Raman spectra of ambient water.

Journal Articles

DNA strand break; Structural and electrostatic properties studied by molecular dynamics simulation

Kotulic Bunta, J.*; Laaksonen, A.*; Pinak, M.; Nemoto, Toshiyuki*

Computational Biology and Chemistry, 30(2), p.112 - 119, 2006/04

 Times Cited Count:3 Percentile:76.47(Biology)

Due to their lethal consequences, single and double strand breaks are among the most important and dangerous DNA lesions. This work defines and analyzes a DNA with single strand break as a template study for future complex analyses of biologically serious double strand break damage and its enzymatic repair mechanisms. Besides a non-damaged DNA serving as a reference system, system with open valences of the atoms at the strand break ends as well as a system with filled valences was simulated. As for the results, the system with open valences is partly disrupted, and the system with filled valences is stabilized by forming new hydrogen bonds between two strand endings.

Journal Articles

Enzymatic recognition of radiation-produced oxidative DNA lesion; Molecular dynamics approach

Pinak, M.

Modern Methods for Theoretical Physical Chemistry of Biopolymers, p.191 - 210, 2006/00

Results of molecular dynamics (MD) studies of several lesions on DNA and their respective repair enzymes are presented. Main focus is to describe structural and energy changes in DNA molecule with the respect to proper recognition of the lesion by respective repair enzyme. Pyrimidine and purine lesions were studied using MD simulation code Amber and respective force field modified for each lesion. The significant structural changes as breaking of hydrogen bonds network opening and bending the DNA double helix were observed. This collapsing of the double helical structure around the lesion is considered to facilitate docking of the repair enzyme into the DNA. Specific values of electrostatic interaction energy that enables repair enzyme to discriminate lesion from non-damaged site were also detected at several lesion sites.

Journal Articles

Hydration structure of Y$$^{3+}$$ and La$$^{3+}$$ compared; An Application of metadynamics

Ikeda, Takashi; Hirata, Masaru; Kimura, Takaumi

Journal of Chemical Physics, 122(24), p.244507_1 - 244507_5, 2005/06

 Times Cited Count:41 Percentile:17.98(Chemistry, Physical)

We studied the hydration structures of Y$$^{3+}$$ and La$$^{3+}$$ in aqueous solutions by applying the metadynamics method recently introduced as a tool to explore reaction pathways based on the Car-Parrinello molecular dynamics. By employing the metal-water oxygen coordination number as a collective variable of the metadynamics a couple of aqua and chloro-aqua complexes are successfully generated within the time scales of 10 ps. The reconstructed free energy surface captures the characteristics of the hydration of the light and heavy trivalent rare-earth ions. The present study demonstrates that the metadynamics based on the Car-Parrinello molecular dynamics is a promising tool for exploring the free energy surface of complicated systems such as solutions.

Journal Articles

Molecular dynamics simulation of clustered DNA damage sites containing 8-oxoguanine and abasic site

Fujimoto, Hirofumi*; Pinak, M.; Nemoto, Toshiyuki*; O'Neill, P.*; Kume, Etsuo; Saito, Kimiaki; Maekawa, Hideaki*

Journal of Computational Chemistry, 26(8), p.788 - 798, 2005/06

 Times Cited Count:20 Percentile:43.06(Chemistry, Multidisciplinary)

Clustered DNA damage sites induced by ionizing radiation have been suggested to have serious consequences to organisms. In this study, approaches based on molecular dynamics (MD) simulation have been applied to examine conformational changes and energetic properties of DNA molecules containing clustered damage sites consisting of 2 lesioned sites, 8-oxoG and AP site. After 1 nanosecond of MD simulation, one of the 6 DNA molecules containing a clustered damage site develop specific characteristic features: sharp bending at the lesioned site and weakening or complete loss of electrostatic interaction energy between 8-oxoG and bases locating on the complementary strand. From these results it is suggested that these changes would make it difficult for the repair enzyme to bind to the lesions within the clustered damage site and thereby result in a reduction of its repair capacity.

Journal Articles

A Severe artifact in simulation of liquid water using a long cut-off length; Appearance of a strange layer structure

Yonetani, Yoshiteru

Chemical Physics Letters, 406(1-3), p.49 - 53, 2005/04

 Times Cited Count:46 Percentile:15.24(Chemistry, Physical)

We report that a severe artifact appeared in molecular dynamics simulation of bulk water using the long cut-off length 18 AA ; Our result shows that increasing the cut-off length does not always improve the simulation result. Moreover, the use of the long cut-off length can lead to a spurious result. It is suggested that the simulation of solvated biomolecules using such a long cut-off length, which has been often performed, may contain an unexpected artifact.

Journal Articles

An Observation of a nascent fractal pattern in MD simulation for a fragmentation of an fcc lattice

Chikazumi, Shimpei*; Iwamoto, Akira

Chaos, Solitons and Fractals, 23(1), p.73 - 78, 2005/01

To seek for a possible origin of fractal pattern in nature, we perform a molecular dynamics simulation for a fragmentation of an infinite fcc lattice. The fragmentation is induced by the initial condition of the model that the lattice particles have the Hubble-type radial expansion velocities. As time proceeds, the average density decreases and density fluctuation develops. By using the box counting method, it is found that the frequency-size plot of the density follows instantaneously a universal power-law for each Hubble constant up to the size of a cross-over. This cross-over size corresponds to the maximum size of fluctuation and is found to obey a dynamical scaling law as a function of time. This instantaneous generation of a nascent fractal is purely of dynamical origin and it shows us a new formation mechanism of a fractal patters different from the traditional criticality concept.

Journal Articles

Direct ab initio molecular dynamics study of the two photodissociation channels of formic acid

Kurosaki, Yuzuru; Yokoyama, Keiichi; Teranishi, Yoshiaki

Chemical Physics, 308(3), p.325 - 334, 2005/01

 Times Cited Count:19 Percentile:42.78(Chemistry, Physical)

A total of $$sim$$ 1200 trajectories have been integrated for the two dissociation channels of formic acid, HCOOH $$rightarrow$$ H$$_{2}$$O + CO (1) and HCOOH $$rightarrow$$ CO$$_{2}$$ + H$$_{2}$$ (2), which occur with 248 and 193 nm photons, using the direct ab initio molecular dynamics method at the RMP2(full)/cc-pVDZ level of theory. It was found that the percentage of the energy distributed to a relative translational mode in reaction 2 is much larger than that in reaction 1. This is mainly due to the difference in the geometry of transition state (TS); the H$$_{2}$$O geometry in the TS of reaction 1 was predicted to significantly deviate from the equilibrium one, whereas the CO$$_{2}$$ and H$$_{2}$$ geometries in the TS of reaction 2 were found to be more similar to their equilibrium ones. It was also found that the product diatomic molecules, CO and H$$_{2}$$, are both vibrationally and rotationally excited. The calculated relative population of the vibrationally excited CO for the 248 nm photodissociation was consistent with experiment.

JAEA Reports

Molecular dynamics simulation studies of radiation damaged DNA molecules and repair enzymes

Pinak, M.

JAERI 1346, 25 Pages, 2004/12

JAERI-1346.pdf:3.84MB

Molecular dynamics (MD) studies on several radiation damages to DNA - thymine dimer, thymine glycol8-oxoguanine and their recognition by repair enzymes are introduced in order to describe on the stepwise description of molecular process observed at radiation lesion sites. In all cases the significant structural changes in the DNA double helical structure were observed: (a) the breaking of hydrogen bonds network between complementary bases and resulting opening of the double helix (8-oxoguanine); (b) the sharp bending of the DNA helix centered at the lesion site (thymine dimer, thymine glycol); and (c) the flipping-out base on the strand complementary to the lesion (8-oxoguanine). The specific values of electrostatic interaction energy were found at the lesion sites (thymine dimmer: -10kcal/mol, thymine glycol: -26kcal/mol, 8-oxoguanine: -48kcal/mol).

Journal Articles

Photoemission study of the translational energy induced oxidation processes on Cu(111)

Moritani, Kosuke; Okada, Michio*; Sato, Seiichi*; Goto, Seishiro*; Kasai, Toshio*; Yoshigoe, Akitaka; Teraoka, Yuden

Journal of Vacuum Science and Technology A, 22(4), p.1625 - 1630, 2004/08

 Times Cited Count:18 Percentile:40.74(Materials Science, Coatings & Films)

We studied the oxidation of Cu{111} surface with a hyperthermal O$$_{2}$$ molecular beam (HOMB) using X-ray photoemission spectroscopy (XPS) in conjunction with a synchrotron radiation (SR) source. The efficiency of oxidation with 0.6-eV-HOMB is higher thab that with 2.3-eV-HOMB under $$theta$$ $$leq$$ 0.5ML. Ont the other hand, further oxidation occurs rather inefficiency under $$theta$$ $$geq$$ 0.5ML. In this region, efficiency of oxidation with 2.3-eV-HOMB is higher than 0.6-eV-HOMB. We found that such slow oxidation process of Cu can be interpreted in terms of a collision-induced-adsorption mechanism. These results suggest that we can control the oxidation process of Cu by using HOMB.

Journal Articles

Large scale MD simulation of 8-oxoguanine and AP site multiple lesioned DNA molecule combined with biomolecular visualization software

Fujimoto, Hirofumi; Pinak, M.; Nemoto, Toshiyuki*; Sakamoto, Kiyotaka*; Yamada, Kazuyuki*; Hoshi, Yoshiyuki*; Kume, Etsuo

Journal of Molecular Structure; THEOCHEM, 681(1-3), p.1 - 8, 2004/01

We developed the novel system, Fujitsu Bio Molecular Visualization System (F-BMVS), that enables to produce real pictures and an animation by arranging them along a time series of a large scale simulation of biomolecules associated with a molecular dynamics (MD) simulation program. This animation system is used to study the results of molecular dynamics code, AMBER, in order to find structural differences on the lesioned DNA comparing with non-damaged DNA. These structural differences would be a factor that guides a repair enzyme to discriminate a lesion from non-damaged DNA region.

Journal Articles

Spatiotemporal behavior of void collapse in shocked solids

Hatano, Takahiro

Physical Review Letters, 92(1), p.015503_1 - 015503_4, 2004/01

 Times Cited Count:35 Percentile:19.75(Physics, Multidisciplinary)

Molecular dynamics simulations on a three dimensional defective Lennard-Jones solid containing a void are performed in order to investigate detailed properties of hot spot generation. In addition to the temperature, I monitor the number of energetically colliding particles per unit volume which characterizes the intensity of shock-enhanced chemistry. The quantity is found to saturate for nanoscale voids and to be maximized after voids have completely collapsed. It makes an apparent comparison to the temperature which requires much larger void for the enhancement and becomes maximum during the early stage of the collapse. It is also found that the average velocity and the temperature of ejected molecules inside a cubic void are enhanced during the collapse because of the focusing of momentum and energy towards the center line of a void.

Journal Articles

Structural transformation of methane hydrate from cage clathrate to filled ice

Ikeda, Takashi; Terakura, Kiyoyuki*

Journal of Chemical Physics, 119(13), p.6784 - 6788, 2003/10

 Times Cited Count:24 Percentile:36.01(Chemistry, Physical)

The structural, dynamical, and electronic properties of methane hydrate under pressure and at room temperature are investigated using the $textit{ab initio}$ constant pressure molecular dynamics method. Cage structures in cubic structure I are destroyed at 4.5GPa. After the breakdown of cage structures water molecules form a channel surrounding a chain of methane molecules prominent in MH-III. In our MH-III there exists a single peak of C-D stretching mode showing blueshift in agreement with experiment. Our study supports the existence of $textquotedblleft filled icetextquotedblright proposed by Loveday textit{et al.}$ [Phys. Rev. Lett. $textbf{87}$, 215501 (2001).]

Journal Articles

Pressure-induced structural phase transitions and solid-state reactions in hydrogen bromide and hydrogen sulfide

Ikeda, Takashi

Koatsuryoku No Kagaku To Gijutsu, 13(3), p.224 - 231, 2003/08

Applying pressure to hydrogen-bonded crystals hydrogen bromide and hydrogen sulfide alters significantly the bonding nature and induces various kinds of phenomena: order-disorder transition, hydrogen-bond symmetrization, and molecular dissociation accompanied by the solid-state reactions. This article reviews the relationship between pressure-induced structural phase transitions and solid-state reactions, revealed from the cooperative works between high pressure experiments and the ab initio molecular dynamics simulations.

Journal Articles

SiO mass spectrometry and Si-2p photoemission spectroscopy for the study of oxidation reaction dynamics of Si(001) surface by supersonic O$$_{2}$$ molecular beams under 1000 K

Teraoka, Yuden; Yoshigoe, Akitaka; Moritani, Kosuke

Japanese Journal of Applied Physics, Part 1, 42(7B), p.4671 - 4675, 2003/07

 Times Cited Count:4 Percentile:78.51(Physics, Applied)

The oxidation reaction mechanisms for Si(001) by O$$_{2}$$ molecules have been investigated in a surface temperature region from 860 K to 1300 K and in an incident energy region from 0.6 eV to 3.0 eV. Synchrotron Radiation photoemission spectroscopy was used for surface analysis. Si-2p photoemission spectra were measured during molecular beam irradiation so that their dependences on surface temperature and incident energy were clarified. SiO molecules, desorbed from the surface at high temperature region, were also detected by a quadrupole mass analyzer using $$^{18}$$O$$_{2}$$ molecular beams to measure SiO desorption yield depending on surface temperature and incident energy. Consequently, a reaction scheme, oxide layers formation, etching, and coexistence of both reactions, is determined by the incident energy under 1000 K.

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