arXiv subjects

Kazushi Okada

Publications and source records attributed to Kazushi Okada.

6 recordsLinked to original sources

arXiv2026

Deep learning of committor for ion dissociation and interpretable analysis of solvent effects using atom-centered symmetry functions

The association and dissociation of ion pairs in water are fundamental to physical chemistry, yet their reaction coordinates are complex, involving not only interionic distance but also solvent-mediated hydration structures. These processes are often represented by free-energy landscapes constructed from collective variables (CVs), such as interionic distance and water bridging structures; however, it remains uncertain whether such representations reliably capture the transition pathways between the two associated and dissociated states. In this study, we employ deep learning to identify reaction coordinates for NaCl ion pair association and dissociation in water, using the committor as a quantitative measure of progress along the transition pathway through the transition state. The solvent environment surrounding the ions is encoded through descriptors based on atom-centered symmetry functions (ACSFs), which serve as input variables for the neural network. In addition, an explainable artificial intelligence technique is applied to identify ACSFs that contribute to the reaction coordinate. A comparative analysis of their correlation with CVs representing water bridging structures, such as interionic water density and the number of water molecules coordinating both ions, further provides a molecular-level interpretation of the ion association-dissociation mechanism in water.

physics.chem-ph↗

arXiv2024

Unveiling interatomic distances influencing the reaction coordinates in alanine dipeptide isomerization: An explainable deep learning approach

The present work shows that the free energy landscape associated with alanine dipeptide isomerization can be effectively represented by specific interatomic distances without explicit reference to dihedral angles. Conventionally, two stable states of alanine dipeptide in vacuum, i.e., C$7_{\mathrm{eq}}$ ($β$-sheet structure) and C$7_{\mathrm{ax}}$ (left handed $α$-helix structure), have been primarily characterized using the main chain dihedral angles, $φ$ (C-N-C$_α$-C) and $ψ$ (N-C$_α$-C-N). However, our recent deep learning combined with "Explainable AI" (XAI) framework has shown that the transition state can be adequately captured by a free energy landscape using $φ$ and $θ$ (O-C-N-C$_α$) [T. Kikutsuji, et al. J. Chem. Phys. 156, 154108 (2022)]. In perspective of extending these insights to other collective variables, a more detailed characterization of transition state is required. In this work, we employ the interatomic distances and bond angles as input variables for deep learning, rather than the conventional and more elaborate dihedral angles. Our approach utilizes deep learning to investigate whether changes in the main chain dihedral angle can be expressed in terms of interatomic distances and bond angles. Furthermore, by incorporating XAI into our predictive analysis, we quantified the importance of each input variable and succeeded in clarifying the specific interatomic distance that affects the transition state. The results indicate that constructing a free energy landscape based on using the identified interatomic distance can clearly distinguish between the two stable states and provide a comprehensive explanation for the energy barrier crossing.

physics.chem-ph↗

arXiv2018

"Slow-Scanning" in Ground-Based Mid-Infrared Observation

Chopping observations with a tip-tilt secondary mirror have conventionally been used in ground-based mid-infrared observations. However, it is not practical for next generation large telescopes to have a large tip-tilt mirror that moves at a frequency larger than a few Hz. We propose an alternative observing method, a "slow-scanning" observation. Images are continuously captured as movie data, while the field-of-view is slowly moved. The signal from an astronomical object is extracted from the movie data by a low-rank and sparse matrix decomposition. The performance of the "slow-scanning" observation was tested in an experimental observation with Subaru/COMICS. The quality of a resultant image in the "slow-scanning" observation was as good as in a conventional chopping observation with COMICS, at least for a bright point-source object. The observational efficiency in the "slow-scanning" observation was better than that in the chopping observation. The results suggest that the "slow-scanning" observation can be a competitive method for the Subaru telescope and be of potential interest to other ground-based facilities to avoid chopping.

astro-ph.IM↗

arXiv2018

Mid-infrared Multi-wavelength Imaging of Ophiuchus\,IRS\,48\,Transitional Disk

Transitional disks around the Herbig Ae/Be stars are fascinating targets in the contexts of disk evolution and also planet formation. Oph IRS 48 is one of such Herbig Ae stars, which shows an inner dust cavity and azimuthally lopsided large dust distribution. We present new images of Oph IRS 48 at eight mid-infrared (MIR) wavelengths from 8.59 to 24.6\,$μ{\rm m}$ taken with the COMICS mounted on the 8.2\,m Subaru Telescope. The N-band (7 to 13\,$μ{\rm m}$) images show that the flux distribution is centrally peaked with a slight spatial extent, while the Q-band (17 to 25\,$μ{\rm m}$) images show asymmetric double peaks (east and west). Using 18.8 and 24.6\,$μ$m images, we derived the dust temperature at both east and west peaks to be 135$\pm$22 K. Thus, the asymmetry may not be attributed to a difference in the temperature. % thus other reason is necessary to explain the asymmetry of east and west peaks in Q-band. Comparing our results with previous modeling works, we conclude that the inner disk is aligned to the outer disk. A shadow casted by the optically thick inner disk has a great influence on the morphology of MIR thermal emission from the outer disk.

astro-ph.EP↗

arXiv2015

ANIR : Atacama Near-Infrared Camera for the 1.0-m miniTAO Telescope

We have developed a near-infrared camera called ANIR (Atacama Near-InfraRed camera) for the University of Tokyo Atacama Observatory 1.0m telescope (miniTAO) installed at the summit of Cerro Chajnantor (5640 m above sea level) in northern Chile. The camera provides a field of view of 5'.1 $\times$ 5'.1 with a spatial resolution of 0".298 /pixel in the wavelength range of 0.95 to 2.4 $μ$m. Taking advantage of the dry site, the camera is capable of hydrogen Paschen-$α$ (Pa$α$, $λ=$1.8751 $μ$m in air) narrow-band imaging observations, at which wavelength ground-based observations have been quite difficult due to deep atmospheric absorption mainly from water vapor. We have been successfully obtaining Pa$α$ images of Galactic objects and nearby galaxies since the first-light observation in 2009 with ANIR. The throughputs at the narrow-band filters ($N1875$, $N191$) including the atmospheric absorption show larger dispersion (~10%) than those at broad-band filters (a few %), indicating that they are affected by temporal fluctuations in Precipitable Water Vapor (PWV) above the site. We evaluate the PWV content via the atmospheric transmittance at the narrow-band filters, and derive that the median and the dispersion of the distribution of the PWV are 0.40+/-0.30 mm for $N1875$ and 0.37+/-0.21 mm for $N191$, which are remarkably smaller (49+/-38% for $N1875$ and 59+/-26% for $N191$) than radiometry measurements at the base of Cerro Chajnantor (5100 m alt.). The decrease in PWV can be explained by the altitude of the site when we assume that the vertical distribution of the water vapor is approximated at an exponential profile with scale heights within 0.3-1.9 km (previously observed values at night). We thus conclude that miniTAO/ANIR at the summit of Cerro Chajnantor indeed provides us an excellent capability for a "ground-based" Pa$α$ observation.

astro-ph.IM↗

arXiv2014

Ground-based Pa$α$ Narrow-band Imaging of Local Luminous Infrared Galaxies I: Star Formation Rates and Surface Densities

Luminous infrared galaxies (LIRGs) are enshrouded by a large amount of dust, produced by their active star formation, and it is difficult to measure their activity in the optical wavelength. We have carried out Pa$α$ narrow-band imaging observations of 38 nearby star-forming galaxies including 33 LIRGs listed in $IRAS$ RBGS catalog with the Atacama Near InfraRed camera (ANIR) on the University of Tokyo Atacama Observatory (TAO) 1.0 m telescope (miniTAO). Star formation rates (SFRs) estimated from the Pa$α$ fluxes, corrected for dust extinction using the Balmer Decrement Method (typically $A_V$ $\sim$ 4.3 mag), show a good correlation with those from the bolometric infrared luminosity of $IRAS$ data within a scatter of 0.27 dex. This suggests that the correction of dust extinction for Pa$α$ flux is sufficient in our sample. We measure the physical sizes and the surface density of infrared luminosities ($Σ_{L(\mathrm{IR})}$) and $SFR$ ($Σ_{SFR}$) of star-forming region for individual galaxies, and find that most of the galaxies follow a sequence of local ultra luminous or luminous infrared galaxies (U/LIRGs) on the $L(\mathrm{IR})$-$Σ_{L(\mathrm{IR})}$ and $SFR$-$Σ_{SFR}$ plane. We confirm that a transition of the sequence from normal galaxies to U/LIRGs is seen at $L(\mathrm{IR})=8\times10^{10}$ $L_{\odot}$. Also, we find that there is a large scatter in physical size, different from those of normal galaxies or ULIRGs. Considering the fact that most of U/LIRGs are merging or interacting galaxies, this scatter may be caused by strong external factors or differences of their merging stage.

astro-ph.GA↗