arXiv subjects

Susumu Fujiwara

Publications and source records attributed to Susumu Fujiwara.

5 recordsLinked to original sources

arXiv2026

Findings of sub-$T_\mathrm{g}$ endotherm in vapor-deposited ultrastable phenolphthalein glass

We have performed heat capacity measurements for physically vapor-deposited phenolphthalein glass using conventional and in-house high-sensitivity differential scanning calorimetry. As a result, we found that phenolphthalein forms an ultrastable glass when deposited at 313 K, about 0.86 times the ordinary glass transition temperature of 361 K. In addition, we observed a large endotherm (sub-$T_\mathrm{g}$ endotherm) between deposition and the ordinary glass transition temperature. From an enthalpy perspective, the integrated enthalpy of the sub-$T_\mathrm{g}$ endotherm increased with decreasing film thickness following an inverse-power dependence, whose exponent increased as the deposition rate decreased. In particular, the integrated enthalpy of the sub-$T_\mathrm{g}$ endotherm was comparable in magnitude to the enthalpy of fusion of crystalline phenolphthalein. To investigate the structural origin of the sub-$T_\mathrm{g}$ endotherm, we performed wide-angle X-ray diffraction and in situ atomic force microscopy. As a result, we found that while the stable structure is linked to an anisotropic amorphous structure consistent with past research on ultrastable glasses, the appearance of the sub-$T_\mathrm{g}$ endotherm is associated with surface morphological relaxation, as suggested by atomic force microscopy.

cond-mat.soft↗

arXiv2024

Reactive Molecular Dynamics Simulation on DNA Double Strand Breaks Induced by Hydrogen Elimination

We propose a scar model to reproduce how double-strand breaks occur in the telomeric DNA damaged by the effect of the $β$-decay of tritium to helium. In this scar model, the two hydrogens bonded to the 5$^\prime$ carbon connecting the pent saccharides and phosphate are removed. Molecular dynamics simulations using the reactive force field are carried out for 10 cases for the telomeric DNA consisting of 16 base pairs (32 nucleotides). It results in double-strand breaks (DSBs) being observed for structures with more than 24 scars. For 16 scar cases, only single-strand breaks (SSB) are observed. Moreover, in the case of $\left\{16, 0 \right\}$ and $\left\{ 0, 16 \right\},$ where only one of the strands had scars, SSB occurs only in the scarred strand. Secondly, in the $\left\{16, 8 \right\}$ and $\left\{ 8, 16 \right\}$ cases, DSBs occurs. Therefore, we conclude that the following conditions are necessary for DSBs:(i) Scars must occur on both the L and R strands. (ii) A large number of scars (24 or more) must occur in close proximity to each other.

cond-mat.soft↗

arXiv2020

Icosahedral order in liquid and glassy phases of cyclohexane

We performed all-atom molecular dynamics simulations for bulk cyclohexane and analysed the short- and medium-range structures in supercooled and glassy states by using the Voronoi tessellation technique. From the analyses of both the potential energy of the system and the radial distribution function of molecules, cyclohexane was found to be vitrified as the temperature decreased. Furthermore, the icosahedral-like structures are dominant at all temperatures and grow in a supercooled liquid, whereas the face-centred cubic structures do not grow when the temperature decreases. It was also ascertained that the icosahedral-like structure is more dominant than the full-icosahedral one. The network of the distorted icosahedron spreads throughout the system at low temperatures. Our simulation demonstrates the stability of the icosahedral structure even in a non-spherical molecule such as cyclohexane.

cond-mat.dis-nn↗

arXiv2019

Hydrogen bond analysis of confined water in mesoporous silica using the reactive force field

The structural and dynamical properties of water confined in nanoporous silica with a pore diameter of 2.7 nm were investigated by performing large-scale molecular dynamics simulations using the reactive force field. The radial distribution function and diffusion coefficient of water were calculated, and the values at the center of the pore agreed well with experimental values for real water. In addition, the pore was divided into thin coaxial layers, and the average number of hydrogen bonds, hydrogen bond lifetime, and hydrogen bond strength were calculated as a function of the radial distance from the pore central axis. The analysis showed that hydrogen bonds involving silanol (Si-OH) have a longer lifetime, although the average number of hydrogen bonds per atom does not change from that at the pore center. The longer lifetime, as well as smaller diffusion coefficient, of these hydrogen bonds is attributed to their greater strength.

cond-mat.soft↗

arXiv2000

Rigidity of Orientationally Ordered Domains of Short Chain Molecules

By molecular dynamics simulation, discovered is a strange rigid-like nature for a hexagonally packed domain of short chain molecules. In spite of the non-bonded short-range interaction potential (Lennard-Jones potential) among chain molecules, the packed domain gives rise to a resultant global moment of inertia. Accordingly, as two domains encounter obliquely, they rotate so as to be parallel to each other keeping their overall structures as if they were rigid bodies.

cond-mat.soft↗