64 citations · 253 across the 11 of their papers we have counts for
11 papers
Unraveling the glass-like dynamic heterogeneity in ring polymer melts: From semi-flexible to stiff chain
Shota Goto, Kang Kim, Nobuyuki Matubayasi
Ring polymers are an intriguing class of polymers with unique physical properties, and understanding their behavior is important for developing accurate theoretical models. In this…
Revealing the hidden dynamics of confined water in acrylate polymers: Insights from hydrogen-bond lifetime analysis
Kokoro Shikata, Takuma Kikutsuji, Nobuhiro Yasoshima +2
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…
Explaining reaction coordinates of alanine dipeptide isomerization obtained from deep neural networks using Explainable Artificial Intelligence (XAI)
Takuma Kikutsuji, Yusuke Mori, Kei-ichi Okazaki +3
A method for obtaining appropriate reaction coordinates is required to identify transition states distinguishing product and reactant in complex molecular systems. Recently, abunda…
Simulating the nematic-isotropic phase transition of liquid crystal model via generalized replica-exchange method
Kengo Takemoto, Yoshiki Ishii, Hitoshi Washizu +2
The nematic-isotropic (NI) phase transition of 4-cyano-4'-pentylbiphenyl (5CB) was simulated using the generalized replica-exchange method (gREM) based on molecular dynamics simula…
Effects of chain length on Rouse modes and non-Gaussianity in linear and ring polymer melts
Shota Goto, Kang Kim, Nobuyuki Matubayasi
The dynamics of ring polymer melts are studied via molecular dynamics simulations of the Kremer-Grest bead-spring model. Rouse mode analysis is performed in comparison with linear…
Understanding the scaling of boson peak through insensitivity of elastic heterogeneity to bending rigidity in polymer glasses
Naoya Tomoshige, Shota Goto, Hideyuki Mizuno +3
Amorphous materials exhibit peculiar mechanical and vibrational properties, including non-affine elastic responses and excess vibrational states, i.e., the so-called boson peak. Fo…
Learning reaction coordinates via cross-entropy minimization: Application to alanine dipeptide
Yusuke Mori, Kei-ichi Okazaki, Toshifumi Mori +2
We propose a cross-entropy minimization method for finding the reaction coordinate from a large number of collective variables in complex molecular systems. This method is an exten…
Boson peak, elasticity, and glass transition temperature in polymer glasses: Effects of the rigidity of chain bending
Naoya Tomoshige, Hideyuki Mizuno, Tatsuya Mori +2
The excess low-frequency vibrational spectrum, called boson peak, and non-affine elastic response are the most important particularities of glasses. Herein, the vibrational and mec…
Diffusion dynamics of supercooled water modeled with the cage-jump motion and hydrogen-bond rearrangement
Takuma Kikutsuji, Kang Kim, Nobuyuki Matubayasi
The slow dynamics of glass-forming liquids is generally ascribed to the cage-jump motion. In the cage-jump picture, a molecule remains in a cage formed by neighboring molecules, an…
Bridging the gap between molecular dynamics and hydrodynamics in nanoscale Brownian motions
Keisuke Mizuta, Yoshiki Ishii, Kang Kim +1
Through molecular dynamics simulations, we examined hydrodynamic behavior of the Brownian motion of fullerene particles based on molecular interactions. The solvation free energy a…
How do hydrogen bonds break in supercooled water?: Detecting pathways not going through the saddle point of two-dimensional potential of mean force
Takuma Kikutsuji, Kang Kim, Nobuyuki Matubayasi
Supercooled water exhibits remarkably slow dynamics similar to the behavior observed for various glass-forming liquids. The local order of tetrahedral structures due to hydrogen-bo…