研究者詳細 - 荒井　規允

論文 - 荒井　規允

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Molecular modelling of active oil droplet propulsion: Insights from dissipative particle dynamics simulation

Sasaki, K; Ishiwatari, Y; Ueno, K; Kojima, T; Banno, T; Arai, N

CHEMICAL PHYSICS LETTERS 857 2024年12月

研究論文（学術雑誌）, 最終著者, 査読有り, ISSN 0009-2614

This study employed dissipative particle dynamics (DPD) simulations to investigate the self-propelled motion of oil droplets in water–oil–surfactant systems. It is the first attempt to replicate self-propulsion models of oil droplets at the molecular level, contrasting previous simulations focused on Brownian motion and hydrodynamic behaviour of colloidal particles. The DPD model reproduced droplet propulsion and visualised internal Marangoni flow, showing that larger droplet radii and greater interfacial tension differences increase propulsion speeds. Additionally, surfactants with stronger oil–oil repulsion enhanced propulsion speed, suggesting that surfactant-induced local structures are crucial for the self-propulsion mechanism.

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Corrigendum to “Poly(vinyl alcohol)-modified poly(methyl methacrylate) particles for solid-stabilized oil-in-water emulsions” [Colloids Surf. A: Physicochem. Eng. Asp. 697 (2024) 134433]

Takashi Yamazaki, Kojiro Suzuki, Yusei Kobayashi, Noriyoshi Arai, Toshikazu Tsuji

Colloids and Surfaces A: Physicochemical and Engineering Aspects （Elsevier BV） 135683 - 135683 2024年11月

研究論文（学術雑誌）, 査読有り, ISSN 0927-7757

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Poly(vinyl alcohol)-modified poly(methyl methacrylate) particles for solid-stabilized oil-in-water emulsions

Yamazaki, T; Suzuki, K; Kobayashi, Y; Arai, N; Tsuji, T

COLLOIDS AND SURFACES A-PHYSICOCHEMICAL AND ENGINEERING ASPECTS （Elsevier BV） 697 134433 - 134433 2024年09月

研究論文（学術雑誌）, 査読有り, ISSN 0927-7757

In this study, submicron poly(methyl methacrylate) (PMMA) particles with surfaces modified using poly(vinyl alcohol) (PVA) (PMMA-PVA) were produced to formulate solid-stabilized oil-in-water (O/W) emulsions including high internal phase emulsions with a dispersed phase of over 74 %. The high-internal phase emulsions stabilized by PMMA–PVA exhibited gel-like behavior, and the oil droplets exhibited faceted shapes. PVA with a degree of saponification of 80 and 88 mol% was used as the surface modifier rather than PVA with > 96 mol%, assisting in the formation of a robust adsorbed layer on the PMMA particles. Coarse-grained molecular simulations revealed that the partially-hydrolyzed PVA exhibited a better adsorption behavior compared to the fully-hydrolyzed PVA, being thermodynamically adsorbed onto the PMMA surface in water owing to stable adsorption via its hydrophobic acetyl groups. Furthermore, PMMA–PVA reduced the interfacial tension as the degree of saponification of PVA decreased. Simulation and experimental results suggested that the acetyl groups of PVA not only adsorbed onto the PMMA surface but also promoted adsorption between PMMA and the oil–water interface. Overall, the findings of this study underscore the potency of PMMA–PVA as a particulate stabilizer for formulating O/W high internal phase emulsions.

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Coarse-grained molecular simulation of the effect of liquid crystal molecular pitch on structure in cylindrical confinement

Sato, T; Tsujinoue, H; Arai, N; Takahashi, KZ

PHYSICAL REVIEW E 110 （ 1 ） 014701 2024年07月

研究論文（学術雑誌）, 査読有り, ISSN 2470-0045

Blue phases (BPs) consist of three-dimensional self-assembled structures formed by a double-twisted columnar arrangement of liquid crystal molecules. Although their unique optical and structural properties render BPs particularly useful for applications such as liquid crystal displays, BPs typically appear in a narrow temperature range between the isotropic and nematic phases. This thermodynamic instability impedes their practical applicability. However, the simulations we present here showed that, in a quasi-one-dimensional system confined to nanospace, a phase equivalent to the BP appears and persists between the nematic and smectic phases. Confinement to a nanotube (NT) with a relatively small radius enables the BP to be maintained over a wide temperature range, whereas for an NT with a relatively larger radius, the BP appears only in a very narrow temperature range between the aforementioned phases. We additionally showed that the pitch of the BP is dependent on and can be controlled by adjusting the radius of the NTs. This finding has significant implications for the potential application of these materials in fields such as photonics and chiral separation technologies.

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Design strategy for blends of biodegradable polyester and thermoplastic starch based on a molecular dynamics study of the phase-separated interface

Yamaguchi, A; Arai, S; Arai, N

CARBOHYDRATE POLYMERS （Carbohydrate Polymers） 333 122005 2024年06月

研究論文（学術雑誌）, 最終著者, 査読有り, ISSN 0144-8617

Molecular insight into the phase-separated interface formed when biodegradable polyesters and thermoplastic starch (TPS) are melt-blended is valuable for the design of composites. In this study, eight different interfaces combining four major biodegradable polyesters (PLA, PBS, PHB and PBAT) and two TPSs [unmodified TPS (nTPS) and citrate-modified TPS (cTPS)] were investigated by using molecular dynamics (MD) simulations. According to the MD simulation results, PBS, PHB and PBAT diffuse readily into the TPS and form compatible interfaces, whereas PLA is less compatible with the TPS. The results of tensile simulations show that PBS and PBAT adhere well to TPS; in particular, PBS/cTPS and PBAT/cTPS exhibit high interfacial-fracture energy (G). Both PLA and PHB blended with TPS exhibit low G because PLA is less compatible with TPS and PHB and TPS have low electrostatic interaction. The reason for the high G of PBS/cTPS and PBAT/cTPS is thought to be a combination of three factors: (i) formation of a deep compatible interface, (ii) suppression of void growth by electrostatic interactions and (iii) absorption of strain energy by a change in the conformation of the molecular chains. These three interfacial adhesion mechanisms should be considered when designing biodegradable polyester/TPS blends with good mechanical properties.

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In-layer inhomogeneity of molecular dynamics in quasi-liquid layers of ice.

Yasuda I, Endo K, Arai N, Yasuoka K

Communications chemistry 7 （ 1 ） 117 2024年05月

研究論文（学術雑誌）, 査読有り, ISSN 2399-3669

Quasi-liquid layers (QLLs) are present on the surface of ice and play a significant role in its distinctive chemical and physical properties. These layers exhibit considerable heterogeneity across different scales ranging from nanometers to millimeters. Although the formation of partially ice-like structures has been proposed, the molecular-level understanding of this heterogeneity remains unclear. Here, we examined the heterogeneity of molecular dynamics on QLLs based on molecular dynamics simulations and machine learning analysis of the simulation data. We demonstrated that the molecular dynamics of QLLs do not comprise a mixture of solid- and liquid water molecules. Rather, molecules having similar behaviors form dynamical domains that are associated with the dynamical heterogeneity of supercooled water. Nonetheless, molecules in the domains frequently switch their dynamical state. Furthermore, while there is no observable characteristic domain size, the long-range ordering strongly depends on the temperature and crystal face. Instead of a mixture of static solid- and liquid-like regions, our results indicate the presence of heterogeneous molecular dynamics in QLLs, which offers molecular-level insights into the surface properties of ice.

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Cholesteric liquid crystal phase variations within nanotubes: an in-depth analysis of the influences of twist radius and molecular pitch

Yamada, K; Arai, N

LIQUID CRYSTALS （Liquid Crystals） 51 （ 7 ） 1204 - 1214 2024年05月

研究論文（学術雑誌）, 最終著者, 責任著者, 査読有り, ISSN 0267-8292

This study investigates the self-assembly and phase transitions of cholesteric liquid crystals (CLCs) when confined in nanotubes, specifically focusing on the variations in their molecular structures. A dissipative particle dynamics method was used to investigate how the changes in helix radius ((Formula presented.)) and pitch ((Formula presented.)) affect the behaviour of the LCs. For pitches of 24, 12, and 6, the orientation order parameter ((Formula presented.)) showed distinct trends during cooling. Smaller helix radii resulted in isotropic to nematic to smectic phase transitions, whereas larger radii resulted in a novel smectic phase with spiral structures (Sm (Formula presented.)). Circumferential local-order parameters ((Formula presented.) and (Formula presented.)) were introduced to better characterise the phases, and a disordered spiral-structure phase (Sm (Formula presented.)) with local perturbations was observed. The transitions between isotropic, nematic, and smectic phases, highlighting the influence of the pitch and helix radius, were observed from the phase diagrams. Smaller pitches and radii prevented the formation of stable structures; however, specific combinations induced characteristic spiral structures in the smectic phase. These results provide new insights into the self-assembly of confined CLCs, which have potential applications in the design of photonic devices and LC-based sensors. This study advances our understanding of phase control in quasi-one-dimensional systems and highlights the importance of molecular variations in liquid crystal behaviour.

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Supramolecular copolymerization of hydrophobic and hydrophilic monomers in liquid crystalline media

Morishita, D; Itoh, Y; Furukawa, K; Arai, N; Zhang, XJ; Aida, T

CHEMICAL SCIENCE （Chemical Science） 15 （ 11 ） 4068 - 4074 2024年

研究論文（学術雑誌）, 査読有り, ISSN 2041-6520

In the case of covalent polymers, immiscible polymers can be integrated by covalently linking them together, but such a strategy is not possible in supramolecular polymers. Here we report the supramolecular copolymerization of two porphyrin-based monomers, C10P2H and TEGPCu with side chains bearing cyanobiphenyl (CB) groups at the ends of hydrophobic alkyl or hydrophilic tetraethylene glycol chains, respectively. These monomers undergo self-sorting supramolecular polymerization in highly diluted solutions ([monomer] = 3.4 × 10−9 mol% (2.0 × 10−8 mol L−1)) in nonpolar media due to the incompatibility of the side chains. Surprisingly, these monomers undergo supramolecular copolymerization under high concentration conditions ([monomer] = 7.7 mol%) in the medium of 4-cyano-4′-pentyloxybiphenyl (5OCB) to form a columnar liquid crystalline phase under thermodynamic conditions, where the individual columns are composed of supramolecular block copolymers. The combination of CB ends of both monomers and the 5OCB medium is essential for the two monomers to form an integrated structure in a condensed system without phase separation.

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Machine learning prediction of self-assembly and analysis of molecular structure dependence on the critical packing parameter

Ishiwatari, Y; Yokoyama, T; Kojima, T; Banno, T; Arai, N

MOLECULAR SYSTEMS DESIGN & ENGINEERING （Molecular Systems Design and Engineering） 9 （ 1 ） 20 - 28 2024年

研究論文（学術雑誌）, 査読有り, ISSN 2058-9689

Amphiphilic molecules spontaneously form self-assembly structures depending on physical conditions such as the molecular structure, concentration, and temperature. These structures exhibit various functionalities according to their morphology. The critical packing parameter (CPP) is used to correlate self-organized structures with the chemical composition. However, accurately calculating it requires information about both the molecular shape and molecular aggregates, making it challenging to apply directly in molecular design. We aimed to predict the self-assembled structure of a molecule directly from its chemical structure and to analyze the factors influencing it using machine learning. Dissipative particle dynamics simulations were used to reproduce many self-assembly structures comprising various chemical structures, and their CPPs were calculated. Machine learning models were built using the chemical structures as input data and the CPPs as output data. As a result, both random forest and the gated recurrent unit showed high prediction accuracy. Feature importance analysis and sample size dependence revealed that the amphiphilic nature of molecules significantly influences the self-assembly structures. Additionally, selecting an appropriate molecular structure representation for each algorithm is crucial. The study results should contribute to product development in the fields of materials science, materials chemistry, and medical materials.

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Mechanisms underlying the stability and instability of concentrated oil-in-water emulsions: Effect of the chemical structure of amphiphilic polymers

Suzuki, K; Kobayashi, Y; Yamazaki, T; Tsuji, T; Arai, N

JOURNAL OF MOLECULAR LIQUIDS （Journal of Molecular Liquids） 394 123749 - 123749 2023年12月

研究論文（学術雑誌）, 査読有り, ISSN 0167-7322

Despite extensive experimentation to efficiently prepare concentrated oil-in-water (O/W) emulsions with sufficient stability, the effect of the chemical structure of the polymeric surfactants on the emulsion stability is not yet understood in detail at the molecular level. We investigated the effect of the degree of saponification and arrangement of the hydrophobic (acetyl) groups of poly(vinyl alcohol) (PVA) on the stability of the concentrated emulsion via a combination of experiments and coarse-grained molecular simulations. This was accomplished by varying the degree of saponification and the arrangement of the hydrophobic groups on PVA, and by systematically changing the volume fraction of PVA molecules. The stability of the emulsion was adversely affected by the presence of an excess or the complete absence of hydrophobic groups on PVA. The former situation promotes the aggregation of PVA molecules with each other; conversely, fully saponified PVA molecules penetrate the water phase, thereby decreasing the number of PVA molecules at the O/W interface. Thus, the depletion of the interface of PVA molecules increases the interfacial tension, and, consequently, destabilizes the interface. Adjustment of the degree of saponification to a suitable value (80%) led to the formation of stable, concentrated emulsions with a smaller amount of PVA. For PVA with an appropriate degree of saponification, the interfacial behavior of concentrated O/W emulsions was to a lesser extent affected by the arrangement of the hydrophobic groups of PVA compared to the degree of saponification. Furthermore, the individual PVA chains at the interface had planar conformations, regardless of the arrangement of the hydrophobic groups. Our results indicate that careful tuning of the degree of saponification, rather than the arrangement of the hydrophobic groups of PVA, is necessary to control the interfacial stability of concentrated O/W emulsions using PVA. The findings of this study provide support for departing from empirical trial-and-error approaches and may facilitate the development of emulsifiers with enhanced performance.

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Predicting the Performance of Functional Materials Composed of Polymeric Multicomponent Systems Using Artificial Intelligence—Formulations of Cleansing Foams as an Example

Masugu Hamaguchi, Hideki Miwake, Ryoichi Nakatake, Noriyoshi Arai

Polymers 2023年10月

研究論文（学術雑誌）, 査読有り

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The Relationship between Nanostructured Bio-Inspired Material Surfaces and the Free Energy Barrier Using Coarse-Grained Molecular Dynamics

Meng, F; Arai, N

BIOMIMETICS （Biomimetics） 8 （ 6 ） 2023年09月

研究論文（学術雑誌）, 査読有り

Bio-inspired (biomimetic) materials, which are inspired by living organisms, offer exciting opportunities for the development of advanced functionalities. Among them, bio-inspired superhydrophobic surfaces have attracted considerable interest due to their potential applications in self-cleaning surfaces and reducing fluid resistance. Although the mechanism of superhydrophobicity is understood to be the free energy barrier between the Cassie and Wenzel states, the solid-surface technology to control the free energy barrier is still unclear. Therefore, previous studies have fabricated solid surfaces with desired properties through trial and error by measuring contact angles. In contrast, our study directly evaluates the free energy barrier using molecular simulations and attempts to relate it to solid-surface parameters. Through a series of simulations, we explore the behavior of water droplets on surfaces with varying values of surface pillar spacing and surface pillar height. The results show that the free energy barrier increases significantly as the pillar spacing decreases and/or as the pillar height increases. Our study goes beyond traditional approaches by exploring the relationship between free energy barriers, surface parameters, and hydrophobicity, providing a more direct and quantified method to evaluate surface hydrophobicity. This knowledge contributes significantly to material design by providing valuable insights into the relationship between surface parameters, free energy barriers, and hydrophilicity/hydrophobicity.

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Molecular insight into toughening induced by core-shell structure formation in starch-blended bioplastic composites

Yamaguchi Akihiro, Arai Satoshi, Arai Noriyoshi

CARBOHYDRATE POLYMERS （Carbohydrate Polymers） 315 120974 2023年09月

研究論文（学術雑誌）, 査読有り, ISSN 0144-8617

Binary and ternary blends with poly(lactic acid) (PLA), poly(butylene succinate) (PBS), and thermoplastic starch (TPS) were prepared by a melt process to produce biodegradable biomass plastics with both economical and good mechanical properties. The mechanical and structural properties of each blend were evaluated. Molecular dynamics (MD) simulations were also conducted to examine the mechanisms underlying the mechanical and structural properties. PLA/PBS/TPS blends showed improved mechanical properties compared with PLA/TPS blends. The PLA/PBS/TPS blends with a TPS ratio of 25–40 wt% showed higher impact strength than PLA/PBS blends. Morphology observations showed that in the PLA/PBS/TPS blends, a structure similar to that of core-shell particles with TPS as the embedding phase and PBS as the coating phase was formed, and that the trends in morphology and impact strength changes were consistent. The MD simulations suggested that PBS and TPS tightly adhered to each other in a stable structure at a specific intermolecular distance. From these results, it is clear that PLA/PBS/TPS blends are toughened by the formation of a core-shell structure in which the TPS core and the PBS shell adhered well together and stress concentration and energy absorption occurred in the vicinity of the core-shell structure.

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Aggregation of amphiphilic nanocubes in equilibrium and under shear

Yokoyama Takahiro, Kobayashi Yusei, Arai Noriyoshi, Nikoubashman Arash

SOFT MATTER （Soft Matter） 19 （ 34 ） 6480 - 6489 2023年08月

研究論文（学術雑誌）, 査読有り, ISSN 1744-683X

We investigate the self-assembly of amphiphilic nanocubes into finite-sized aggregates in equilibrium and under shear, using molecular dynamics (MD) simulations and kinetic Monte Carlo (KMC) calculations. These patchy nanoparticles combine both interaction and shape anisotropy, making them valuable models for studying folded proteins and DNA-functionalized nanoparticles. The nanocubes can self-assemble into various finite-sized aggregates ranging from rods to self-avoiding random walks, depending on the number and placement of the hydrophobic faces. Our study focuses on suspensions containing multi- and one-patch cubes, with their ratio systematically varied. When the binding energy is comparable to the thermal energy, the aggregates consist of only few cubes that spontaneously associate/dissociate. However, highly stable aggregates emerge when the binding energy exceeds the thermal energy. Generally, the mean aggregation number of the self-assembled clusters increases with the number of hydrophobic faces and decreases with increasing fraction of one-patch cubes. In sheared suspensions, the more frequent collisions between nanocube clusters lead to faster aggregation dynamics but also to smaller terminal steady-state mean cluster sizes. The results from the MD and KMC simulations are in excellent agreement for all investigated two-patch cases, whereas the three-patch cubes form systematically smaller clusters in the MD simulations compared to the KMC calculations due to finite-size effects and slow aggregation kinetics. By analyzing the rate kernels, we are able to identify the primary mechanisms responsible for (shear-induced) cluster growth and breakup. This understanding allows us to tune nanoparticle and process parameters to achieve desired cluster sizes and shapes.

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Reproduction of super-multicomponent self-assembled structures and their functionality using coarse-grained molecular simulation - the example of cleansing agents

Yokoyama Takahiro, Miwake Hideki, Hamaguchi Masugu, Nakatake Ryoichi, Arai Noriyoshi

MOLECULAR SYSTEMS DESIGN & ENGINEERING （Molecular Systems Design and Engineering） 8 （ 4 ） 538 - 550 2023年04月

研究論文（学術雑誌）, 査読有り, ISSN 2058-9689

Self-assembly of multi-component systems can provide a large variety of functions, which is impossible for a single-component system, and those multi-component derived functional materials attract attention in various fields such as biomedical, engineering, and materials science. This gives multi-component systems importance, but molecular elucidation of such systems is a major challenge, since this type of complex system has large degrees of freedom. In this study, we focused on cleansing agents as multi-component systems, which are cosmetics products mainly used to remove oily compounds such as makeup, and are multi-component aqueous solutions consisting of many surfactants, moisturizers, and pH regulators. Our aim is to link the macroscopic properties of multi-component systems with the mesoscale structures to elucidate the molecular evidence of functions. We have studied the self-assembled morphologies of cleansing agents using coarse-grained molecular simulations as mesoscale structures and compared them to cleansing performance as a macroscopic property. From the simulation results of morphologies and the experimental results of performance, the key features which explain their functionalities were examined. As a result, it was quantitatively shown that the distribution of specific particles or molecules such as hydrophobic particles both in the bulk state and when they are applied on dirty surfaces is one of the clues to explain the performance. Through molecular designing based on this result, it will be much easier to reach the desired property or performance in the field of multi-component functional materials. Thus, this molecular simulation method will push the field of materials science and materials informatics forward.

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Wetting hysteresis induces effective unidirectional water transport through a fluctuating nanochannel

Arai Noriyoshi, Yamamoto Eiji, Koishi Takahiro, Hirano Yoshinori, Yasuoka Kenji, Ebisuzaki Toshikazu

NANOSCALE HORIZONS （Nanoscale Horizons） 8 （ 5 ） 652 - 661 2023年02月

研究論文（学術雑誌）, 査読有り, ISSN 2055-6756

We propose a water pump that actively transports water molecules through nanochannels. Spatially asymmetric noise fluctuations imposed on the channel radius cause unidirectional water flow without osmotic pressure, which can be attributed to hysteresis in the cyclic transition between the wetting/drying states. We show that the water transport depends on fluctuations, such as white, Brownian, and pink noises. Because of the high-frequency components in white noise, fast switching of open and closed states inhibits channel wetting. Conversely, pink and Brownian noises generate high-pass filtered net flow. Brownian fluctuation leads to a faster water transport rate, whereas pink noise has a higher capability to overcome pressure differences in the opposite direction. A trade-off relationship exists between the resonant frequency of the fluctuation and the flow amplification. The proposed pump can be considered as an analogy for the reversed Carnot cycle, which is the upper limit of the energy conversion efficiency.

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Combining Molecular Dynamics and Machine Learning to Analyze Shear Thinning for Alkane and Globular Lubricants in the Low Shear Regime

Yasuda I., Kobayashi Y., Endo K., Hayakawa Y., Fujiwara K., Yajima K., Arai N., Yasuoka K.

ACS Applied Materials and Interfaces （ACS Applied Materials and Interfaces） 15 （ 6 ） 8567 - 8578 2023年02月

研究論文（学術雑誌）, 査読有り, ISSN 19448244

Lubricants with desirable frictional properties are important in achieving an energy-saving society. Lubricants at the interfaces of mechanical components are confined under high shear rates and pressures and behave quite differently from the bulk material. Computational approaches such as nonequilibrium molecular dynamics (NEMD) simulations have been performed to probe the molecular behavior of lubricants. However, the low-shear-velocity regions of the materials have rarely been simulated owing to the expensive calculations necessary to do so, and the molecular dynamics under shear velocities comparable with that in the experiments are not clearly understood. In this study, we performed NEMD simulations of extremely confined lubricants, i.e., two molecular layers for four types of lubricants confined in mica walls, under shear velocities from 0.001 to 1 m/s. While we confirmed shear thinning, the velocity profiles could not show the flow behavior when the shear velocity was much slower than thermal fluctuations. Therefore, we used an unsupervised machine learning approach to detect molecular movements that contribute to shear thinning. First, we extracted the simple features of molecular movements from large amounts of MD data, which were found to correlate with the effective viscosity. Subsequently, the extracted features were interpreted by examining the trajectories contributing to these features. The magnitude of diffusion corresponded to the viscosity, and the location of slips that varied depending on the spherical and chain lubricants was irrelevant. Finally, we attempted to apply a modified Stokes-Einstein relation at equilibrium to the nonequilibrium and confined systems. While systems with low shear rates obeyed the relation sufficiently, large deviations were observed under large shear rates.

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Effect of temperature on the structure and drug-release behaviour of inclusion complex of beta-cyclodextrin with cyclophosphamide: a molecular dynamics study

Sakai Seiga, Hirano Yoshinori, Kobayashi Yusei, Arai Noriyoshi

SOFT MATTER （Soft Matter） 19 （ 16 ） 2902 - 2907 2023年

研究論文（学術雑誌）, 査読有り, ISSN 1744-683X

Cyclodextrins (CDs) are suitable drug carriers because of their doughnut-shaped cavities with hydrophilic outer and hydrophobic inner surfaces. Temperature-responsive CD-based drug carriers are expected to be one of the most promising candidates for drug delivery systems. In this study, we performed molecular dynamics simulations of the inclusion complex of β-CD with cyclophosphamide (CP) at temperatures from 300 K to 400 K to investigate the temperature dependency of the release behaviour of CP and structural changes of β-CD in an aqueous solution. We analysed the distance between the centres of mass of β-CD and CP and the radius of gyration of β-CD. The CP molecule was released from the β-CD cavity at 400 K, whereas two different inclusion complexes, partially and completely, were observed at T < 400 K. β-CD encapsulating a CP molecule had a more spherical shape and rigidity than β-CD without a CP, and the rigidity of their inclusion complex decreased with increasing temperature. Our findings provide fundamental insights into the behaviours of the β-CD/CP complex and drug release at the molecular level and can facilitate the development of new temperature-responsive drug delivery systems with CD nanocarriers triggered by localised temperature increases using focused ultrasound.

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Unsupervised deep learning for molecular dynamics simulations: a novel analysis of protein-ligand interactions in SARS-CoV-2 M<SUP>pro</SUP>

Mustali, J; Yasuda, I; Hirano, Y; Yasuoka, K; Gautieri, A; Arai, N

RSC ADVANCES （RSC Advances） 13 （ 48 ） 34249 - 34261 2023年

研究論文（学術雑誌）, 査読有り

Molecular dynamics (MD) simulations, which are central to drug discovery, offer detailed insights into protein-ligand interactions. However, analyzing large MD datasets remains a challenge. Current machine-learning solutions are predominantly supervised and have data labelling and standardisation issues. In this study, we adopted an unsupervised deep-learning framework, previously benchmarked for rigid proteins, to study the more flexible SARS-CoV-2 main protease (Mpro). We ran MD simulations of Mpro with various ligands and refined the data by focusing on binding-site residues and time frames in stable protein conformations. The optimal descriptor chosen was the distance between the residues and the center of the binding pocket. Using this approach, a local dynamic ensemble was generated and fed into our neural network to compute Wasserstein distances across system pairs, revealing ligand-induced conformational differences in Mpro. Dimensionality reduction yielded an embedding map that correlated ligand-induced dynamics and binding affinity. Notably, the high-affinity compounds showed pronounced effects on the protein's conformations. We also identified the key residues that contributed to these differences. Our findings emphasize the potential of combining unsupervised deep learning with MD simulations to extract valuable information and accelerate drug discovery.

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Correlation between ordering and shear thinning in confined OMCTS liquids

Kobayashi Yusei, Arai Noriyoshi, Yasuoka Kenji

JOURNAL OF CHEMICAL PHYSICS （Journal of Chemical Physics） 157 （ 11 ） 114506 2022年09月

研究論文（学術雑誌）, 査読有り, ISSN 0021-9606

Despite decades of extensive research, the behavior of confined liquids, particularly in the mixed/boundary lubrication regime, remains unelucidated. This can be attributed to several factors, including the difficulty to make direct experimental observations of the behavior of lubricant molecules under nonequilibrium conditions, the high computational cost of molecular simulations to reach steady state, and the low signal-to-noise ratio at extremely low shear rates corresponding to actual operating conditions. In this regard, we studied the correlation between the structure formation and shear viscosity of octamethylcyclotetrasiloxane confined between two mica surfaces in a mixed/boundary lubrication regime. Three different surface separations - corresponding to two-, three-, and five-layered structures - were considered to analyze the effect of confinement. The orientational distributions with one specific peak for n = 2 and two distributions, including a parallel orientation with the surface normal for n > 2, were observed at rest. The confined liquids exhibited a distinct shear-thinning behavior independent of surface separations for a relatively low shear rate, γ˙≲108s-1. However, the shear viscosities at γ˙≲108s-1 depended on the number of layered structures. Newtonian behavior was observed with further increase in the shear rate. Furthermore, we found a strong correlation between the degree of molecular orientation and the shear viscosity of the confined liquids. The magnitude of the shear viscosity of the confined liquids can primarily be determined by the degree of molecular orientation, and shear thinning originates from the vanishing of specific orientational distributions with increasing shear rate.

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