7 citations · 30 across the 12 of their papers we have counts for
12 papers
Machine learning evaluation of structural descriptors for supercooled water
Kohei Yoshikawa, Kokoro Shikata, Kang Kim +1
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…
Deep learning of committor and explainable artificial intelligence analysis for identifying reaction coordinates
Toshifumi Mori, Kei-ichi Okazaki, Kang Kim +1
In complex molecular systems, the reaction coordinate (RC) that characterizes transition pathways is essential to understand underlying molecular mechanisms. This review surveys a…
Classification of interfacial water governed by water-polymer interactions in hydrated polymers: A molecular dynamics simulation study of ethylene-based and acrylate polymers
Atsuki Hashimoto, Kokoro Shikata, Kang Kim +1
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 anal…
Deep learning of committor for ion dissociation and interpretable analysis of solvent effects using atom-centered symmetry functions
Kenji Okada, Kazushi Okada, Kei-ichi Okazaki +3
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…
Elucidation of the Correlation between Molecular Conformation and Shear Viscosity of Polymer Melts under Steady-State Shear Flow
Yuhi Sakamaki, Shota Goto, Kang Kim +1
The rheological behavior of polymer melts is strongly influenced by parameters such as chain length, chain stiffness, and architecture. In particular, shear thinning, characterized…
Dual effect of cholesterol on interfacial water dynamics in lipid membranes: Interplay between membrane packing and hydration
Kokoro Shikata, Kento Kasahara, Nozomi Morishita Watanabe +3
Water contained within biological membranes plays a critical role in maintaining the separation between intracellular and extracellular environments and facilitating biochemical pr…
Graph neural network-based structural classification of glass-forming liquids and its interpretation via self-attention mechanism
Kohei Yoshikawa, Kentaro Yano, Shota Goto +2
Glass-forming liquids exhibit slow dynamics below their melting temperatures, maintaining an amorphous structure reminiscent of normal liquids. Distinguishing microscopic structure…
Persistent Homology Reveals the Role of Stiffness in Forming Topological Glasses in Dense Solutions of Ring Polymers
Shota Goto, Takenobu Nakamura, Davide Michieletto +2
Ring polymers are characterized by topology-specific entanglements called threadings. In the limit of large rings, it is conjectured that a "topological glass" should emerge due to…
Atomistic analysis of nematic phase transition in 4-cyano-4--alkyl biphenyl liquid crystals: Sampling for the first-order phase transition and the free-energy decomposition
Shunsuke Ogita, Yoshiki Ishii, Go Watanabe +3
Molecular dynamics (MD) simulations were conducted using the generalized replica exchange method (gREM) on the 4-cyano-4--alkylbiphenyl (CB) system with , 6,…
Investigating the hyperparameter space of deep neural network models for reaction coordinates
Kyohei Kawashima, Takumi Sato, Kei-ichi Okazaki +3
Identifying reaction coordinates (RCs) is a key to understanding the mechanism of reactions in complex systems. Deep neural network (DNN) and machine learning approaches have becom…
Influence of cholesterol on hydrogen-bond dynamics of water molecules in lipid-bilayer systems at varying temperatures
Kokoro Shikata, Kento Kasahara, Nozomi Morishita Watanabe +3
Cholesterol (Chol) plays a crucial role in shaping the intricate physicochemical attributes of biomembranes, exerting considerable influence on water molecules proximal to the memb…
Unveiling interatomic distances influencing the reaction coordinates in alanine dipeptide isomerization: An explainable deep learning approach
Kazushi Okada, Takuma Kikutsuji, Kei-ichi Okazaki +3
The present work shows that the free energy landscape associated with alanine dipeptide isomerization can be effectively represented by specific interatomic distances without expli…