Article
Biochemistry & Molecular Biology
Giuseppe Porpora, Francesco Rusciano, Raffaele Pastore, Francesco Greco
Summary: Glass transition is an intriguing open issue in molecular liquids, and recent research has found that the relationship between macroscopic timescales and cage-jump quantities changes on approaching the glass transition.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Materials Science, Multidisciplinary
J. Q. Wu, H. P. Zhang, M. Z. Li
Summary: The relationship between structure and relaxation dynamics in metallic glass-forming liquids was studied through classical molecular dynamics simulations. It was found that the Debye-Waller factor decreases with increasing five-fold local symmetry and a new equation describing this relationship was derived. These findings suggest a common structural basis for both short-time beta-relaxation and long-time alpha-relaxation dynamics.
COMPUTATIONAL MATERIALS SCIENCE
(2022)
Review
Chemistry, Multidisciplinary
Indrajit Tah, Anoop Mutneja, Smarajit Karmakar
Summary: Glasses are prevalent in nature and play a significant role in our daily lives. The dynamics of glass-forming systems, ranging from microscopic to macroscopic scales, exhibit slow and heterogeneous behaviors. Recent research has shown that there are growing dynamic and static correlation lengths associated with the observed dynamical heterogeneity and rapid rise in viscosity, highlighting the complexity of glassy dynamics.
Article
Physics, Multidisciplinary
Gerhard Jung, Giulio Biroli, Ludovic Berthier
Summary: We propose GlassMLP, a machine learning framework that utilizes physics-inspired structural input to predict long-time dynamics in deeply supercooled liquids. Our deep neural network shows superior performance compared to existing methods, requiring less training data and fitting parameters. GlassMLP accurately predicts four-point dynamic correlations and the geometry of dynamic heterogeneity. The transferability across system sizes enables efficient study of temperature-dependent spatial dynamic correlations, revealing significant changes in the geometry of rearranging regions.
PHYSICAL REVIEW LETTERS
(2023)
Article
Materials Science, Ceramics
Fumiya Noritake
Summary: Accurate knowledge of the diffusion mechanism of network-forming elements in silicate liquids is crucial for understanding transport properties. While previous studies have focused on alkali diffusion, this research uses molecular dynamics simulations to reveal that oxygen atoms diffuse via a site exchange mechanism, while silicon diffusion involves bond-exchange events leading to network deformation.
JOURNAL OF NON-CRYSTALLINE SOLIDS
(2021)
Article
Multidisciplinary Sciences
Baicheng Mei, Yuxing Zhou, Kenneth S. Schweizer
Summary: Understanding the activated dynamics in diverse glass-forming liquids over a wide time range is a challenge in physics, physical chemistry, and materials science. Currently, there is still a lack of a predictive theory that covers both noncooperative and cooperative relaxation. Experimental data has validated a recent microscopic dynamical theory prediction, providing a different conceptual view of the global relaxation map.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Materials Science, Multidisciplinary
Heng Kang, Yanhui Zhang, Ji Wang, Shidong Feng, Limin Wang
Summary: The research reveals the significance of local symmetry in the dynamics of metallic glass-forming liquids, with local symmetry entropy playing a role in rearrangements and diffusion. The diffusion coefficient can be described by a scaling with local symmetry entropy, which also shows a linear correlation with two-pair entropy, indicating a contribution to the decrease of thermodynamic entropy in undercooled liquids during the cooling process.
MODELLING AND SIMULATION IN MATERIALS SCIENCE AND ENGINEERING
(2021)
Article
Chemistry, Multidisciplinary
Mengtan Liu, Ryan D. McGillicuddy, Hung Vuong, Songsheng Tao, Adam H. Slavney, Miguel Gonzalez, Simon J. L. Billinge, Jarad A. Mason
Summary: Molten phases of metal-organic networks offer exciting opportunities for using coordination chemistry principles to access liquids and glasses with unique and tunable structures and properties. General thermodynamic strategies provide increased enthalpic and entropic driving force for reversible, low-temperature melting transitions in extended coordination solids, illustrated through a systematic study of bis(acetamide)-based networks with record-low melting temperatures. Weak coordination bonds, conformationally flexible bridging ligands, and weak electrostatic interactions contribute to the low melting temperatures of these compounds, reducing enthalpy and increasing entropy of fusion.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Materials Science, Multidisciplinary
Yuan-wei Pu, Li-li Zhou, Yong-chao Liang, Ze-an Tian, Qian Chen, Li Zhang, Jia-jun Ma, Yun-fei Mo, Rang-su Liu, Ting-hong Gao, Quan Xie
Summary: In this study, the effects of adding trace elements on the glass-forming ability (GFA) of metallic glasses were investigated through molecular dynamics simulations. The results showed that the GFA becomes stronger with the increase of Y element, which can promote the formation of topologically close-packed (TCP) clusters and hinder the crystallization process.
JOURNAL OF MATERIALS RESEARCH AND TECHNOLOGY-JMR&T
(2022)
Article
Materials Science, Multidisciplinary
B. Q. Wu, L. T. Kong, J. F. Li
Summary: This study thoroughly investigated the glass-forming ability of Cu-Ag alloys at different compositions using molecular dynamics simulations. The results showed that the eutectic alloy exhibited the best glass-forming ability, with a critical cooling rate significantly lower than that of pure metals. The number of densely packed icosahedral-like clusters increased with increasing solute content in the alloy. While the dynamical properties of Cu-Ag melts were composition-independent at high temperatures, they clearly changed with composition at low temperatures.
Article
Materials Science, Multidisciplinary
Y. J. Lu, C. C. Guo, H. S. Huang, J. A. Gao, H. R. Qin, W. H. Wang
Summary: The study investigates the aging process of supercooled Cu50Zr50 glass-forming liquid, revealing a multi-mode dynamics accompanied by a quantized hierarchy of mobile clusters. An aging model is proposed to describe the aging dynamics as a weighted average over quantized dynamic modes. This model predicts the heterogeneous dynamics in aging and equilibration of supercooled metallic liquids, shedding light on the intrinsic aspects influencing the aging process.
Article
Chemistry, Physical
B. Yao, Z. Wojnarowska, M. Paluch
Summary: The ultimate aim of researchers is to predict the properties of matter based on molecular structure, but achieving this goal is still challenging. By comparing two compounds, benzene and cyclohexane, which differ only in the type of six-carbon ring, the study demonstrates how aromaticity affects the relaxation dynamics behavior of supercooled liquid and glass. Through experiments under ambient and elevated pressure, the researchers identified which dynamic and thermodynamic quantities are sensitive to such structural differences and which are not.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Chemistry, Physical
Xiao-Juan Ma, Rui Zhang
Summary: This study systematically investigates the cooperative activated hopping dynamics of matrix and penetrant particles in binary sphere mixture systems. It is found that in high activation barrier cases, the long-range elastic distortion generated by a matrix particle hopping over its cage confinement always generates a nonnegligible elastic barrier. The study also reveals that increasing the penetrant-to-matrix size ratio or the penetrant-matrix cross-attraction strength universally enlarges the composition window of matrix/penetrant cooperative activated hopping dynamics.
Article
Physics, Multidisciplinary
W. J. Jiang, M. Z. Li
Summary: A study on the structure-dynamics correlations in CuZr metallic glass-forming liquids using classical molecular dynamics simulations revealed an increase in correlation between structure order parameters and dynamics with increasing coarse-graining length, showing a characteristic length scale. The characteristic correlation length displays a non-monotonic temperature evolution near the glass transition temperature, with no sensitivity to the specific structure order parameters considered. These findings provide new insights into the structure-dynamics correlation in glass transition.
Article
Materials Science, Ceramics
Y. X. Chen, S. P. Pan, X. Q. Lu, H. Kang, Y. H. Zhang, M. Zhang, S. D. Feng, K. L. Ngai, L. M. Wang
Summary: The study reveals the existence of unusual caged dynamics in metallic glass-forming liquids with strong atomic interactions. The mechanism of caged dynamics is found to be related to chemical order, Voronoi polyhedra, and covalent-like bonds.
JOURNAL OF NON-CRYSTALLINE SOLIDS
(2022)
Article
Chemistry, Physical
Manish Maurya, Atanu K. Metya, Jayant K. Singh, Shinji Saito
Summary: The study reveals that the local structure in the core region of a water droplet is similar to that in liquid water, while the local structure of water molecules at the solid/water and air/water interfaces mainly consists of three-coordinated molecules that are greatly distorted from a tetrahedral structure.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Biophysics
Mahroof Kalathingal, Takashi Sumikama, Shigetoshi Oiki, Shinji Saito
Summary: This study investigates the dynamic mechanism of the vectorial insertion of polytheonamide B (pTB), a prefolded cytotoxic peptide. The all-atom molecular dynamics simulations reveal that the insertion of pTB involves three phases - landing, penetration, and equilibration, with an energy cost of 4.3 kcal/mol at the membrane surface. The membrane insertion of pTB can occur through either trapped or untrapped pathways, with membrane anchoring by the hydrophobic N-terminal blocking group playing a crucial role in the landing phase.
BIOPHYSICAL JOURNAL
(2021)
Article
Chemistry, Physical
Yoshihiro Matsumura, Shinji Saito
Summary: This study investigates the microscopic aspects of dynamic disorder in a protein's isomerization dynamics, shedding light on the transition from slow modulation to fast modulation. Through theoretical modeling and analysis, the research uncovers the microscopic origins of dynamic disorder in complex molecular processes.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Shota Goto, Kang Kim, Nobuyuki Matubayasi
Summary: The dynamics of ring polymer melts were studied using molecular dynamics simulations. Rouse-like behavior was observed in ring polymers, while a crossover from Rouse to reptation behavior was observed in linear polymers. Non-Gaussianity of ring polymers was found to be significantly suppressed at long chain lengths, in contrast to the growth in linear polymers.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Taichi Inagaki, Shinji Saito
Summary: In this paper, a new hybrid method called potential scaling HMC (PS-HMC) is introduced to study complex chemical processes. By modulating the trajectory and gradually flattening the potential energy surface, the PS-HMC method is capable of constructing the canonical ensemble with a multimodal distribution. Applications to different molecular processes demonstrate the feasibility and features of this new method.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Kengo Takemoto, Yoshiki Ishii, Hitoshi Washizu, Kang Kim, Nobuyuki Matubayasi
Summary: The nematic-isotropic phase transition of 4-cyano-4'-pentylbiphenyl was simulated using the generalized replica-exchange method, and compared with the temperature replica-exchange method. The results showed that the generalized replica-exchange method was effective in sampling configurations around the transition temperature and exhibited a bimodal distribution of the order parameter, while the temperature replica-exchange method was ineffective due to the energy gap between the nematic and isotropic phases.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Zhe Zhu, Masahiro Higashi, Shinji Saito
Summary: This study investigates the electronic properties of chlorophyll in different solvents using quantum mechanical and molecular mechanical calculations. By optimizing the parameters of the functional, the experimental results were successfully reproduced, showing changes in the electronic distribution within the molecule. Furthermore, it was observed that the polarity of the solvent and hydrogen bonding affect the excitation energy and its distribution.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Takuma Kikutsuji, Yusuke Mori, Kei-ichi Okazaki, Toshifumi Mori, Kang Kim, Nobuyuki Matubayasi
Summary: This study uses Explainable Artificial Intelligence (XAI) methods to explain the appropriate reaction coordinates in complex molecular systems. The contribution of each collective variable to reaction coordinates is determined using nonlinear regressions with deep learning. The results show that XAI methods provide important features consistent with previous experimental results.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Multidisciplinary Sciences
Yoshihiko Furuike, Atsushi Mukaiyama, Shin-Ichi Koda, Damien Simon, Dongyan Ouyang, Kumiko Ito-Miwa, Shinji Saito, Eiki Yamashita, Taeko Nishiwaki-Ohkawa, Kazuki Terauchi, Takao Kondo, Shuji Akiyama
Summary: KaiC is a dual ATPase that drives the circadian clock system of cyanobacteria through the coordination of its N-terminal and C-terminal active sites. The activities of these two sites are regulated differently and their delicate interactions drive the assembly and disassembly cycle of KaiA and KaiB.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemical Research Methods
Shin-Ichi Koda, Shinji Saito
Summary: The formation of the clock protein complex in cyanobacteria relies on the slow KaiB-KaiC interaction, which is promoted by inhibiting ADP/ATP exchange through accumulating ADP molecules. This inhibition not only accelerates complex formation, but also contributes to period robustness under environmental perturbations. Moreover, the stabilization of the binding-competent C1 by KaiB binding and relatively fast ADP/ATP exchange in the binding-incompetent C1 are essential for this simultaneous promotion and acceleration.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Chemistry, Physical
Toshifumi Mori, Shinji Saito
Summary: The slow intrinsic dynamics of Pin1 play a role in isomerization reactions by affecting the residues near the ligand binding site, with conformational transitions at the 3(10) helix being particularly significant.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Multidisciplinary
Tsuyoshi Kato, Shinji Saito
Summary: In this study, the authors proposed a numerical solution to the inverse Kohn-Sham problem using an integral equation. The accuracy of the calculated exchange-correlation potentials was quantified by evaluating the exchange and correlation energies based on the virial theorem and comparing with the exact ground-state electronic energy. The results showed that the numerical solutions of the integral equation were accurate in reproducing the Kohn-Sham potential and satisfying the virial theorem.
JOURNAL OF THE CHINESE CHEMICAL SOCIETY
(2023)
Article
Chemistry, Physical
Kokoro Shikata, Takuma Kikutsuji, Nobuhiro Yasoshima, Kang Kim, Nobuyuki Matubayasi
Summary: Polymers with functional groups can form hydrogen bonds with water molecules, which creates a strong H-bond network that affects their bulk properties. This study used molecular dynamics simulations to investigate the H-bonding dynamics of water molecules in three poly(meth)acrylates. The results showed that as the water content decreased, the H-bonding dynamics slowed down significantly. The diffusion of water molecules and its relationship with H-bond breakage were also analyzed. The findings suggest that the impact of polymer functional groups on H-bonding dynamics is dependent on the specific interactions between the water molecules and the polymer.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Taichi Inagaki, Miho Hatanaka, Shinji Saito
Summary: In this study, the intermolecular vibration and relaxation dynamics of a water film and a water droplet on a graphene surface were investigated using low-frequency Raman spectra calculated from molecular dynamics simulations. The results showed that the interfacial water systems exhibited weakened libration and enhanced intermolecular hydrogen bond stretching compared to bulk water, indicating softened orientation motion. The study also revealed slower collective polarizability relaxation in the water droplet, which was attributed to positive correlation between induced polarizabilities caused by structural fluctuations. The research demonstrated the revealing capability of low-frequency Raman spectroscopy on the anisotropic and finite effects of intermolecular dynamics in water films and droplets.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Polymer Science
Shota Goto, Kang Kim, Nobuyuki Matubayasi
Summary: This study investigates the static and dynamic behavior of ring polymer melts by molecular dynamics simulations, focusing on the effect of chain stiffness and monomer density. It is found that the dynamics of ring polymers are influenced by excluded volume interactions between centers of mass, as indicated by the increasing non-Gaussianity in the displacement distribution with higher monomer density and stiffness. The relationship between the radius of gyration and monomer density varies with chain stiffness, which can be attributed to the competition between repulsive forces inside and between rings. The dynamic heterogeneity of bond-breakage is coupled with the non-Gaussianity in ring polymer melts, emphasizing the importance of the bond-breaking method in determining the intermolecular dynamics. Overall, this study provides insights into the factors governing the dynamic behaviors of ring polymers.
