arXiv subjects

Nobuyuki Matubayasi

Publications and source records attributed to Nobuyuki Matubayasi.

28 records · Page 2Linked to original sources

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↗

arXiv2022

Explaining reaction coordinates of alanine dipeptide isomerization obtained from deep neural networks using Explainable Artificial Intelligence (XAI)

A method for obtaining appropriate reaction coordinates is required to identify transition states distinguishing product and reactant in complex molecular systems. Recently, abundant research has been devoted to obtaining reaction coordinates using artificial neural networks from deep learning literature, where many collective variables are typically utilized in the input layer. However, it is difficult to explain the details of which collective variables contribute to the predicted reaction coordinates owing to the complexity of the nonlinear functions in deep neural networks. To overcome this limitation, we used Explainable Artificial Intelligence (XAI) methods of the Local Interpretable Model-agnostic Explanation (LIME) and the game theory-based framework known as Shapley Additive exPlanations (SHAP). We demonstrated that XAI enables us to obtain the degree of contribution of each collective variable to reaction coordinates that is determined by nonlinear regressions with deep learning for the committor of the alanine dipeptide isomerization in vacuum. In particular, both LIME and SHAP provide important features to the predicted reaction coordinates, which are characterized by appropriate dihedral angles consistent with those previously reported from the committor test analysis. The present study offers an AI-aided framework to explain the appropriate reaction coordinates, which acquires considerable significance when the number of degrees of freedom increases.

physics.chem-ph↗

arXiv2021

Simulating the nematic-isotropic phase transition of liquid crystal model via generalized replica-exchange method

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 simulations. The effective temperature is introduced in gREM, allowing the enhanced sampling of configurations in the unstable region, which is intrinsic to the first-order phase transition. The sampling performance was analyzed with different system sizes and compared with that of the temperature replica-exchange method (tREM). It was observed that gREM is capable of sampling configurations at sufficient replica-exchange acceptance ratios even around the NI transition temperature. A bimodal distribution of the order parameter at the transition region was found, which is in agreement with the mean-field theory. In contrast, tREM is ineffective around the transition temperature owing to the potential energy gap between the nematic and isotropic phases.

cond-mat.soft↗

arXiv2021

Effects of chain length on Rouse modes and non-Gaussianity in linear and ring polymer melts

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 polymers by changing the chain length. Rouse-like behavior is observed in ring polymers by quantifying the chain length dependence of the Rouse relaxation time, whereas a crossover from Rouse to reptation behavior is observed in linear polymers. Furthermore, the non-Gaussian parameters of the monomer bead displacement and chain center-of-mass displacement are analyzed. It is found that the non-Gaussianity of ring polymers is remarkably suppressed with slight growth for the center-of-mass dynamics at long chain length, which is in contrast to the growth in linear polymers both for the monomer bead and center-of-mass dynamics.

cond-mat.soft↗

arXiv2021

Understanding the scaling of boson peak through insensitivity of elastic heterogeneity to bending rigidity in polymer glasses

Amorphous materials exhibit peculiar mechanical and vibrational properties, including non-affine elastic responses and excess vibrational states, i.e., the so-called boson peak. For polymer glasses, these properties are considered to be affected by the bending rigidity of the constituent polymer chains. In our recent work [Tomoshige, et al., Sci. Rep. 9 19514 (2019)], we have revealed simple relationships between the variations of vibrational properties and the global elastic properties: the response of the boson peak scales only with that of the global shear modulus. This observation suggests that the spatial heterogeneity of the local shear modulus distribution is insensitive to changes in the bending rigidity. Here, we demonstrate the insensitivity of elastic heterogeneity by directly measuring the local shear modulus distribution. We also study transverse sound wave propagation, which is also shown to scale only with the global shear modulus. Through these analyses, we conclude that the bending rigidity does not alter the spatial heterogeneity of the local shear modulus distribution, which yields vibrational and acoustic properties that are controlled solely by the global shear modulus of a polymer glass.

cond-mat.soft↗

arXiv2020

Learning reaction coordinates via cross-entropy minimization: Application to alanine dipeptide

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 extension of the likelihood maximization approach describing the committor function with a sigmoid. By design, the reaction coordinate as a function of various collective variables is optimized such that the distribution of the committor $p_\mathrm{B}^*$ values generated from molecular dynamics simulations can be described in a sigmoidal manner. We also introduce the $L_2$-norm regularization used in the machine learning field to prevent overfitting when the number of considered collective variables is large. The current method is applied to study the isomerization of alanine dipeptide in vacuum, where 45 dihedral angles are used as candidate variables. The regularization parameter is determined by cross-validation using training and test datasets. It is demonstrated that the optimal reaction coordinate involves important dihedral angles, which are consistent with the previously reported results. Furthermore, the points with $p_\mathrm{B}^*\sim 0.5$ clearly indicate a separatrix distinguishing reactant and product states on the potential of mean force using the extracted dihedral angles.

physics.chem-ph↗

arXiv2019

Boson peak, elasticity, and glass transition temperature in polymer glasses: Effects of the rigidity of chain bending

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 mechanical properties of polymeric glasses are examined by using coarse-grained molecular dynamics simulations, with particular attention to the effects of the bending rigidity of the polymer chains. As the rigidity increases, the system undergoes a glass transition at a higher temperature (under a constant pressure), which decreases the density of the glass phase. The elastic moduli, which are controlled by the decrease of the density and the increase of the rigidity, show a non-monotonic dependence on the rigidity of the polymer chain that arises from the non-affine component. Moreover, a clear boson peak is observed in the vibrational density of states, which depends on the macroscopic shear modulus $G$. In particular, the boson peak frequency is scaled as $ω_\mathrm{BP} \propto \sqrt{G}$. These results provide a positive correlation between the boson peak, shear elasticity, and the glass transition temperature.

cond-mat.soft↗

arXiv2019

Diffusion dynamics of supercooled water modeled with the cage-jump motion and hydrogen-bond rearrangement

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, and after a sufficiently long time, it jumps to escape from the original position by cage-breaking. The clarification of the cage-jump motion is therefore linked to unraveling the fundamental element of the slow dynamics. Here, we develop a cage-jump model for the dynamics of supercooled water. The caged and jumping states of a water molecule are introduced with respect to the hydrogen-bond (H-bond) rearrangement process, and describe the motion in supercooled states. It is then demonstrated from the molecular dynamics simulation of the TIP4P/2005 model that the characteristic length and time scales of cage-jump motions provide a good description of the self-diffusion constant that is determined in turn from the long-time behavior of the mean square displacement. Our cage-jump model thus enables to connect between H-bond dynamics and molecular diffusivity.

cond-mat.soft↗

arXiv2019

Bridging the gap between molecular dynamics and hydrodynamics in nanoscale Brownian motions

Through molecular dynamics simulations, we examined hydrodynamic behavior of the Brownian motion of fullerene particles based on molecular interactions. The solvation free energy and the velocity autocorrelation function (VACF) were calculated by using the Lennard-Jones (LJ) and Weeks-Chandler-Andersen (WCA) potentials for the solute-solvent and solvent-solvent interactions and by changing the size of the fullerene particles. We also measured the diffusion constant of the fullerene particles and the shear viscosity of the host fluid, and then the hydrodynamic radius $a_\mathrm{HD}$ was quantified from the Stokes-Einstein relation. The $a_\mathrm{HD}$ value exceeds that of the gyration radius of the fullerene when the solvation free energy exhibits largely negative values using the LJ potential. In contrast, $a_\mathrm{HD}$ becomes comparable to the size of bare fullerene, when the solvation free energy is positive using the WCA potential. Furthermore, the VACF of the fullerene particles is directly comparable with the analytical expressions utilizing the Navier-Stokes equations both in incompressible and compressible forms. Hydrodynamic long-time tail $t^{-3/2}$ is demonstrated for timescales longer than the kinematic time of the momentum diffusion over the particles' size. However, the VACF in shorter timescales deviates from the hydrodynamic description, particularly for smaller fullerene particles and for the LJ potential. This occurs even though the compressible effect is considered when characterizing the decay of VACF around the sound propagation time scale over the particles' size. These results indicate that the nanoscale Brownian motion is influenced by the solvation structure around the solute particles originating from the molecular interaction.

cond-mat.soft↗

arXiv2018

How do hydrogen bonds break in supercooled water?: Detecting pathways not going through the saddle point of two-dimensional potential of mean force

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-bonds (H-bonds) increases with decreasing temperature. Thus, it is important to clarify the temperature dependence of the H-bond breakage process. This was investigated here using molecular dynamics simulations of TIP4P supercooled water. The two-dimensional (2D) potential of mean force (PMF) is presented using combinations of intermolecular distance and angle between two water molecules. The saddle point of the 2D PMF suggests the presence of the transition state that distinguishes between H-bond and non H-bond states. However, we observed pathways not going through this saddle point particularly at supercooled states, which are due to translational, rather than rotational motions of the molecules. We quantified the characteristic time scales of rotational and translational H-bond breakages. The time scale of translational H-bond breakage shows a non-Arrhenius temperature dependence comparable to that of the H-bond lifetime. This time scale is relevant for the temperature dependence of the transmission coefficient based on the transition state theory. The translational H-bond breakage is also related to cage-jumps observed in glass-forming liquids, which mostly involve spatially correlated molecules. Our findings warrant further exploration of an appropriate free-energy surface or reaction coordinates beyond the geometrical variables of the water dimer to describe a possible saddle point related to collective jump motions.

cond-mat.dis-nn↗