arXiv subjects

Kokoro Shikata

Publications and source records attributed to Kokoro Shikata.

5 recordsLinked to original sources

arXiv2026

Machine learning evaluation of structural descriptors for supercooled water

The anomalous behavior of liquid water is widely associated with a liquid-liquid phase transition between high- and low-density states in the supercooled regime. At the microscopic level, tetrahedral hydrogen-bond networks govern these properties, motivating structural descriptors that characterize local molecular environments. These structural descriptors quantify features such as tetrahedral order, local density, and the separation between the first and second coordination shells; however, they have largely been proposed independently, with limited systematic comparison. Here we evaluate 16 previously proposed descriptors using a neural-network-based temperature classification framework, enabling an objective assessment of their ability to distinguish temperature-dependent structural changes in supercooled water. We further apply an explainable artificial intelligence method that identifies the structural features responsible for the model predictions. This approach reveals how different descriptors encode local structural information and establishes a data-driven framework for benchmarking structural descriptors in liquid water.

cond-mat.soft↗

arXiv2026

Classification of interfacial water governed by water-polymer interactions in hydrated polymers: A molecular dynamics simulation study of ethylene-based and acrylate polymers

We perform molecular dynamics simulations to investigate hydration structures and dynamics in seven water-containing polymers: PVA, PHEA, PHEMA, PBA, PMEMA, PEG, and PMEA. The analysis integrates four perspectives: the water-content dependence of the glass transition temperature $T_g$, polymer chain fluctuations characterized by dihedral angle distributions, hydrogen-bond lifetimes $τ_{\mathrm{HB}}$ between water and polymer functional groups, and the localization and exchange dynamics of confined water quantified by the distinct part of van Hove correlation function. Hydroxyl-containing polymers (PVA, PHEA, and PHEMA) exhibit relatively high dry-state $T_g$ values and its pronounced depression upon hydration. Chain fluctuations are limited, and $τ_{\mathrm{HB}}$ follows Arrhenius behavior, forming localized hydration shells. In contrast, PMEMA and PBA show low equilibrium water contents and hydrophobic character; although their dry-state $T_g$ values are moderately lower and less sensitive to water content, chain fluctuations remain small, and $τ_{\mathrm{HB}}$ also obeys Arrhenius behavior, with hydrophobic aggregation promoting water localization. PEG and PMEA display low dry-state $T_g$ values and weak water-content dependence. Greater rotational freedom around ether or methoxy oxygen atoms leads to larger chain fluctuations and loosely bound water. Below $T_g$, $τ_{\mathrm{HB}}$ between water and ether or methoxy oxygen atoms exhibits super-Arrhenius behavior. These results clarify three hydration types: highly hydrated (PVA, PHEA, and PHEMA), hydrophobic (PMEMA and PBA), and flexibly hydrated (PEG and PMEA), and provide a molecular-level framework for interpreting interfacial water governed by water-polymer interactions.

cond-mat.soft↗

arXiv2025

Dual effect of cholesterol on interfacial water dynamics in lipid membranes: Interplay between membrane packing and hydration

Water contained within biological membranes plays a critical role in maintaining the separation between intracellular and extracellular environments and facilitating biochemical processes. Variations in membrane composition and temperature lead to phase state changes in lipid membranes, which in turn influence the structure and dynamics of the associated interfacial water. In this study, molecular dynamics simulations were performed on binary membranes composed of dipalmitoylphosphatidylcholine (DPPC) or palmitoyl sphingomyelin (PSM) mixed with cholesterol (Chol). To elucidate the effects of Chol on interfacial water, we examined the orientation and hydrogen-bonding behavior of water molecules spanning from the membrane interior to the interface. As the Chol concentration increased, a transient slow down in water dynamics was observed in the ripple phase at 303 K. Conversely, at higher Chol concentrations, water dynamics were accelerated relative to pure lipid membranes across all temperatures studied. Specifically, at a Chol concentration of 50%, the hydrogen bond lifetime in DPPC membranes decreased to approximately 0.5-0.7 times that of pure lipid membranes. This nonmonotonic behavior is attributed to the combined effects of membrane packing induced by Chol and a reduced density of lipid molecules in the hydrophilic region, offering key insights for modulating the dynamical properties of interfacial water.

cond-mat.soft↗

arXiv2024

Influence of cholesterol on hydrogen-bond dynamics of water molecules in lipid-bilayer systems at varying temperatures

Cholesterol (Chol) plays a crucial role in shaping the intricate physicochemical attributes of biomembranes, exerting considerable influence on water molecules proximal to the membrane interface. In this study, we conducted molecular dynamics simulations on the bilayers of two lipid species, dipalmitoyl phosphatidylcholine (DPPC) and palmitoyl sphingomyelin (PSM); they are distinct with respect to the structures of the hydrogen-bond (H-bond) acceptors. Our investigation focuses on the dynamic properties and H-bonds of water molecules in the lipid-membrane systems, with particular emphasis on the influence of Chol at varying temperatures. Notably, in the gel phase at 303 K, the presence of Chol extends the lifetimes of H-bonds of the oxygen atoms acting as H-bond acceptors within DPPC with water molecules by a factor of 1.5 to 2.5. In the liquid-crystalline phase at 323 K, on the other hand, H-bonding dynamics with lipid membranes remain largely unaffected by Chol. This observed shift in H-bonding states serves as a crucial key to unraveling the subtle control mechanisms governing water dynamics in lipid-membrane systems.

cond-mat.soft↗

arXiv2023

Revealing the hidden dynamics of confined water in acrylate polymers: Insights from hydrogen-bond lifetime analysis

Polymers contain functional groups that participate in hydrogen bond (H-bond) with water molecules, establishing a robust H-bond network that influences bulk properties. This study utilized molecular dynamics (MD) simulations to examine the H-bonding dynamics of water molecules confined within three poly(meth)acrylates: poly(2-methoxyethyl acrylate) (PMEA), poly(2-hydroxyethyl methacrylate) (PHEMA), and poly(1-methoxymethyl acrylate) (PMC1A). Results showed that H-bonding dynamics significantly slowed as the water content decreased. Additionally, the diffusion of water molecules and its correlation with H-bond breakage were analyzed. Our findings suggest that when the H-bonds between water molecules and the methoxy oxygen of PMEA are disrupted, those water molecules persist in close proximity and do not diffuse on a picosecond timescale. In contrast, the water molecules H-bonded with the hydroxy oxygen of PHEMA and the methoxy oxygen of PMC1A diffuse concomitantly with the breakage of H-bonds. These results provide an in-depth understanding of the impact of polymer functional groups on H-bonding dynamics.

cond-mat.soft↗