Structure and dynamics of amphiphilic patchy cubes in a nanoslit under shear.

Patchy nanocubes are intriguing materials with simple shapes and space-filling and multidirectional bonding properties. Previous studies have revealed various mesoscopic structures such as colloidal crystals in the solid regime and rod-like or fractal-like aggregates in the liquid regime of the phase diagram. Recent studies have also shown that mesoscopic structural properties, such as an average cluster size M and orientational order, in amphiphilic nanocube suspensions are associated with macroscopic viscosity changes, mainly owing to differences in cluster shape among patch arrangements. Although many studies have been conducted on the self-assembled structures of nanocubes in bulk, little is known about their self-assembly in nanoscale spaces or structural changes under shear. In this study, we investigated mixtures of one- and two-patch amphiphilic nanocubes confined in two flat parallel plates at rest and under shear using molecular dynamics simulations coupled with multiparticle collision dynamics. We considered two different patch arrangements for the two-patch particles and two different slit widths H to determine the degree of confinement in constant volume fractions in the liquid regime of the phase diagram. We revealed two unique cluster morphologies that have not been previously observed under bulk conditions. At rest, the size of the rod-like aggregates increased with decreasing H, whereas that of the fractal-like aggregates remained constant. Under weak shear with strong confinement, the rod-like aggregates maintained a larger M than the fractal-like aggregates, which were more rigid and maintained a larger M than the rod-like aggregates under bulk conditions.

Monascus pigment prevent the oxidative cytotoxicity in myotube derived hydrogen peroxide.

The amounts of Reactive oxygen species (ROS) become higher by strenuous exercises which consume larger amounts of oxygen in active muscles. Since these ROS directly injured muscles, the high ROS concentration involves muscle fatigue. Thus, an immediate ROS scavenging system in the muscle is desired. Since Monascus pigment (MP) involves physiologically active substances which scavenge ROS, it may be a clue to save the muscle injury. However, there are no reports examining MP effects on oxidative stress in skeletal muscle. In this study, we investigated the effect and mechanism of MP on skeletal muscle cells damaged by oxidative stress. The ability to directly eliminate ROS was evaluated by mixing MP solutions with •OH and O2 •-, a type of ROS. The effect of peroxidation in C2C12 cells was evaluated by cell viability assay and Western blotting. MP scavenges •OH and O2 •-. MP treatment increases the survival rate under oxidative stress. At that time, the expression of catalase was increased: the enzyme change H2O2 into H2O to rescue the cells under oxidative stress. We conclude that monascus pigment suppressed myotube damage under oxidative stress by both non-enzymatic ROS scavenging and up-regulation of catalase expression.

Thermal transport of confined water molecules in quasi-one-dimensional nanotubes.

Dimensions and molecular structures play pivotal roles in the principle of heat conduction. The dimensional characteristics of a solution within nanoscale systems depend on the degrees of confinement. However, the influence of such variations on heat transfer remains inadequately understood. Here, we perform quasi-one-dimensional non-equilibrium molecular dynamics simulations to calculate the thermal conductivity of water molecules confined in carbon nanotubes. The structure of water molecules is determined depending on the nanotube radius, forming a single-file, a single-layer, and a double-layer structure, corresponding to an increasing radius order. We reveal that the thermal conductivity of liquid water has a sublinear dependency on nanotube length exclusively when water molecules form a single file. A stronger confinement leads to behavioral and structural characteristics closely resembling a one-dimensional nature. Moreover, single-layer-structured water molecules exhibit enhanced thermal conductivity. We elucidate that this is due to the increase in the local water density and the absence of transitions to another layer, which typically occurs in systems with double-layer water structures within relatively large radius nanotubes.

Aggregation of amphiphilic nanocubes in equilibrium and under shear.

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.

Identification of Cyclocybe erebia metabolites that affect the circadian rhythm of Eluc expression under control of Bmal1 promoter in mouse fibroblast cells.

Pharmacological intervention of circadian rhythms is a potentially useful approach for ameliorating various health problems caused by disturbed circadian rhythms including sleep disorder and metabolic diseases. To find compounds that affect circadian rhythms, we screened mushroom extracts using mouse cells expressing the luciferase gene under the control of the mouse Bmal1 promoter. The culture filtrate extract from the basidiomycete Cyclocybe erebia enhanced the oscillation of bioluminescence caused by the expression of the luciferase gene and prolonged the period of bioluminescence. Bioassay-guided fractionation of the extract resulted in purification of compounds 1 and 2. Spectroscopic analyses along with single-crystal X-ray diffraction analysis, revealed that these compounds were diterpenoids with a unique skeleton and a fused ring system comprising 3-, 7-, and 5-membered rings. Compounds 1 and 2 were named cyclocircadins A and B, respectively. These findings suggested that natural diterpenoids could be a source of compounds with the activity affecting circadian rhythms.

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

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 ß-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 ß-CD in an aqueous solution. We analysed the distance between the centres of mass of ß-CD and CP and the radius of gyration of ß-CD. The CP molecule was released from the ß-CD cavity at 400 K, whereas two different inclusion complexes, partially and completely, were observed at T < 400 K. ß-CD encapsulating a CP molecule had a more spherical shape and rigidity than ß-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 ß-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.

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

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.

Correlation between ordering and shear thinning in confined OMCTS liquids.

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, γ̇≲108s-1. However, the shear viscosities at γ̇≲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.

Self-Assembly of Amphiphilic Cubes in Suspension.

We study the self-assembly of amphiphilic cubic colloids using molecular dynamics as well as rejection-free kinetic Monte Carlo simulations. We vary both the number and location of the solvophobic faces (patches) on the cubes at several colloid volume fractions and determine the resulting size and shape distributions of the self-assembled aggregates. When the binding energy is comparable to the thermal energy of the system, aggregates typically consist of only few spontaneously associating/dissociating colloids. Increasing the binding energy (or lowering the temperature) leads to the emergence of highly stable aggregates, e.g., small dimers in pure suspensions of one-patch cubes or large (system-spanning) aggregates in suspensions of multipatch colloids. In mixtures of one- and multipatch cubes, the average aggregation number increases with increasing number of solvophobic faces on the multipatch cubes as well with increasing fraction of multipatch cubes. The resulting aggregate shapes range from elongated rods over fractal objects to compact spheres, depending on the number and arrangement of solvophobic patches on the cubic colloids. Our findings establish the complex self-assembly pathways for a class of building blocks that combine both interaction and shape anisotropy, with the potential of forming hierarchically ordered superstructures.

Molecular Insight into the Possible Mechanism of Drag Reduction of Surfactant Aqueous Solution in Pipe Flow.

The phenomenon of drag reduction (known as the "Toms effect") has many industrial and engineering applications, but a definitive molecular-level theory has not yet been constructed. This is due both to the multiscale nature of complex fluids and to the difficulty of directly observing self-assembled structures in nonequilibrium states. On the basis of a large-scale coarse-grained molecular simulation that we conducted, we propose a possible mechanism of turbulence suppression in surfactant aqueous solution. We demonstrate that maintaining sufficiently large micellar structures and a homogeneous radial distribution of surfactant molecules is necessary to obtain the drag-reduction effect. This is the first molecular-simulation evidence that a micellar structure is responsible for drag reduction in pipe flow, and should help in understanding the mechanisms underlying drag reduction by surfactant molecules under nonequilibrium conditions.

Effect of chemical design of grafted polymers on the self-assembled morphology of polymer-tethered nanoparticles in nanotubes.

There is a clear relationship between the self-assembling architecture of nanoparticles (NPs) and their physical properties, and they are currently used in a variety of applications, including optical sensors. Polymer-tethered NPs, which are created by grafting polymers onto NPs to control the self-assembly of NPs, have attracted considerable attention. Recent synthetic techniques have made it possible to synthesize a wide variety of polymers and thereby create NPs with many types of surfaces. However, self-assembled structures have not been systematically classified because of the large number of tuning parameters such as the polymer length and graft density. In this study, by using coarse-grained molecular simulation, we investigated the changes in the self-assembled structure of polymer-tethered NP solutions confined in nanotubes due to the chemical properties of polymers. Three types of tethered polymer NP models were examined: homo hydrophilic, diblock hydrophilic-hydrophobic (HI-HO), and diblock hydrophobic-hydrophilic. Under strong confinement, the NPs were dispersed in single file at low axial pressure. As the pressure increased, multilayered lamellar was observed in the HI-HO model. In contrast, under weak confinement, the difference in the pressure at which the phases emerge, depending on the model, was significant. By changing the chemical properties of the grafted polymer, the thermodynamic conditions (the axial pressure in this study) under which the phases appear is altered, although the coordination of NPs remains almost unchanged. Our simulation offers a theoretical guide for controlling the morphologies of self-assembled polymer-tethered NPs, a novel system that may find applications in nanooptical devices or for nanopatterning.

Self-assembly of polymer-tethered nanoparticles with uniform and Janus surfaces in nanotubes.

In this study, a coarse-grained molecular simulation was performed to investigate the morphologies and phase diagrams of self-assembled polymer-tethered nanoparticles (NPs) confined in nanotubes (NTs). Unlike ordinary NPs, polymer-tethered NPs have two distinct characteristic lengths, which are key factors that determine their self-assembly. Herein, two distinct types of NT walls and three types of polymer-tethered NPs were considered: hydrophilic and hydrophobic walls, and hydrophilic, hydrophobic, and Janus surfaces. First, the qualitative phase diagrams of the axial pressure, Pz, versus the ratio of the NT radius to the NP radius, L, were derived. The results revealed that diverse self-assembled morphologies, which are not formed in non-tethered NPs, were observed in the polymer-tethered NPs. For example, three types of ordered structures with different structural characteristic lengths, depending on Pz, were obtained. In addition, the effect of the chemical nature of the polymer-tethered NP surface on the self-assembled morphology confined in NTs was investigated. Clusters of water molecules were formed, particularly in the hydrophobic polymer-tethered NPs, and these clusters caused the structural distortion of the NP. Moreover, in the polymer-tethered NPs with the Janus amphiphilic surface, the hydrophobic and hydrophilic polymer tethered NPs assembled in the axial direction to form an ordered structure, and a double-helix structure was formed at L = 3.0 in the hydrophobic NT. The results of these simulations indicate that the self-assembly behaviours of polymer-tethered NPs can be qualitatively predicted based on the chemical nature of the NT walls and the surface design of the polymer-tethered NP.

Structure and Shear Response of Janus Colloid-Polymer Mixtures in Solution.

We investigate the structure and rheological properties of dilute colloid-polymer mixtures at rest and under shear via molecular simulations that take into account hydrodynamic interactions. Mixtures of amphiphilic Janus colloids (JCs) and hydrophobic/amphiphilic polymers are considered for various solvent qualities and polymer concentrations. Free polymers, small polymer droplets, and hybrid aggregates coexist in mixtures with slightly hydrophobic homopolymers. As the solvent quality worsens, all polymers aggregate into small droplets, covered and stabilized by the JCs. In mixtures with amphiphilic polymers, we observe the coexistence of free polymers, purely polymeric micelles, and hybrid aggregates. At low shear rates, all mixtures exhibit a Newtonian-like response with intrinsic shear viscosities that are up to 2 times as large as of pure suspensions of nonadsorbing colloids at the same concentration. Furthermore, the mean aggregation number increases slightly due to the flow-enhanced collision of aggregates. At larger shear rates, however, the aggregates break up, the polymers align in the flow direction, and the mixtures exhibit shear-thinning. This shear-induced breakup occurs at stronger shear compared to pure JC suspensions, indicating that the adsorbed polymers reinforce the hybrid aggregates.

Effect of the Janus Amphiphilic Wall on the Viscosity Behavior of Aqueous Surfactant Solutions.

The effects of the chemical nature of an interface are one of the key parameters which can affect self-assembly and rheological behavior. To date, several studies have reported self-assembled structures and rheological behaviors in the development of various functional materials. In this study, we investigated the self-assembly and viscosity behavior of aqueous surfactant solutions confined in three types of Janus amphiphilic nanotubes (JANTs), which have two, four, and eight sequential domains, respectively, using molecular simulation. We found that the viscosity behavior depends on the surfactant concentration and the chemical nature of the wall surface. For instance, although the concentration levels of the surfactants are the same (c = 10%), completely different viscosity behaviors were observed in the two sequential domains (Newtonian-like) and the four and eight sequential domains (strong shear-thinning) of the JANTs. Our simulations demonstrated how the rheological properties of aqueous surfactant solutions, including viscosity and velocity profiles, can be controlled by the chemical nature of the JANT wall surface, effect of confinement, and their self-assembly structures. Considering the foregoing, we hope that our study offers new knowledge on nanofluid systems.

A biointerface effect on the self-assembly of ribonucleic acids: a possible mechanism of RNA polymerisation in the self-replication cycle.

Despite decades of intensive research, many questions remain on the formation and growth of the first cells on Earth. Here, we used computer simulation to compare the self-assembly process of ribonucleic acids in two environments: enclosed in a vesicle-cell membrane and in the bulk. The self-assembly was found to be more favoured in the former environment, and the origin of such a biointerface effect was identified. These results will contribute to a better understanding of the origin of life on the primitive Earth.

Structure and dynamics of amphiphilic Janus spheres and spherocylinders under shear.

We study the structure formation and flow properties of colloidal dispersions comprised of Janus spheres, Janus spherocylinders, and their mixtures, using hybrid molecular dynamics simulations that take into account hydrodynamic interactions. We systematically vary the Janus balance and the shape anisotropy of the particles, and explore a range of colloid volume fractions in the liquid regime of the phase diagram. At rest, Janus spheres with small hydrophobic patches form spherical micelles for all investigated colloid concentrations. In contrast, Janus spheres with an entirely hydrophobic hemisphere aggregate to larger worm-like micelles and network-like structures. Janus spherocylinders exhibit a similar self-assembly behavior. At small and intermediate shear, we observe deformation and rearrangement of the micelles, accompanied by a Newtonian-like rheology with slightly higher shear viscosity compared to homoparticle dispersions at the same concentration. As the shear rate is increased further, the micelles eventually break up into small dimers and free particles, causing a distinct shear-thinning of the dispersions. The network-like structures exhibit a similar flow behavior at high shear rates, but for weak shear we find an almost threefold increase of the shear viscosity and a distinct shear-thinning behavior due to the fracturing of the intertwined networks. In general, we identify a strong correlation between the size of the aggregates and the rheology of the dispersions, allowing for the determination of dynamic properties solely based on structural information.

Replica exchange dissipative particle dynamics method on threadlike micellar aqueous solutions.

The self-assembly of surfactant molecules can spontaneously result in a variety of micelle morphologies, such as spherical micelles, threadlike micelles, and vesicles, and it is therefore crucial to predict and control the self-assembly to achieve a helpful process in the fields of materials chemistry and engineering. A dissipative particle dynamics (DPD) method used in a coarse-grained molecular simulation is applied to simulate various self-assembling soft matter systems because it can handle greater length and time scales than a typical molecular dynamics simulation (MD). It should be noted that the thorough sampling of a system is not assured at low temperatures because of large complex systems with coarse-grained representations. In this article, we demonstrate that the replica exchange method (REM) is very effective for even a DPD in which the energy barrier is comparatively lower than that of a MD. A replica exchange on DPD (REDPD) simulation for threadlike micellar aqueous solutions was conducted, and the values of the potential energy and the mean aggregation number were compared. As a result, the correct values and a self-assembled structure within a low-temperature range can only be obtained through the REDPD.

The Production of a Rat Model That Inhibits Phosphoenolpyruvate Carboxykinase (PEPCK), a Rate-Limiting Enzyme of Hepatic Gluconeogenesis.

We previously showed that taurine administration contributed to the extension of time to exhaustion through exercise-induced hypoglycemia restraint, and we suggested that the activation of hepatic gluconeogenesis was initiated before the exercise with the taurine administration. We hypothesize that the extension effect of exercise duration with the taurine administration is restrained in the rats which inhibited hepatic gluconeogenesis. In this study, we aimed to produce a rat model that inhibited hepatic gluconeogenesis as a first step in testing our hypothesis.F344 male rats of 8 weeks after birth were purchased. The blood samples were collected via jugular vein catheter to perform the pyruvate tolerance test (PTT) with the intraperitoneal administration, and to determine the optimal time point of blood glucose measurement. 3-mercaptopicolinic acids (3MPA) was used as an inhibitor of PEPCK. The rats were divided into three groups, Non-dosage control (CON) group, 30 mg/kg・BW 3MPA (3MPA 30) group, and 300 mg/kg・BW 3MPA (3MPA 300) group.The blood glucose level showed a significant peak 15 min after pyruvate administration. The change of the blood glucose level after the PTT in 3MPA 300 group was significantly smaller than that of the CON group at this time point. These results show we could prepare the rat model that inhibited hepatic gluconeogenesis.

Janus or homogeneous nanoparticle mediated self-assembly of polymer electrolyte fuel cell membranes.

The functionality of polymer electrolyte fuel cell membranes depends on the self-assembled structure of the graft polymer. To control self-assembly, nanoparticles (NPs) are often used as catalysts. Hence, we investigate the effect of hydrophilic (HI), hydrophobic (HO), and Janus nanoparticles (JNPs) for the self-assembly of graft polymers using dissipative particle dynamics (DPD) simulations. We found that the differences that appeared among the self-assembled structures of water depended on the concentration of PEFC. We also calculated the diffusion constant of water (D(H2O)) from the slopes of the time-averaged mean square displacement (MSD) curves. HI NPs had the largest effect in suppressing the diffusion of water because the HI NPs incorporated into the water particles. It was also seen that D(H2O) with various NPs gradually decreased as the number of NPs increased for three PEFC concentrations (70%, 80%, and 90%). Thus, a close correlation between the position and chemical composition of NPs in polymer electrolyte fuel cell (PEFC) membrane systems has been found. Moreover, the mean square radius of gyration 〈R g〉 and the mean square end-to-end distance 〈R〉 was calculated to analyse the self-assembled structures of PEFC. The 〈R g〉 and 〈R〉 increased as the concentration of PEFC was increased, with and without various NPs.

Programmed Self-Assembly of Branched Nanocrystals with an Amphiphilic Surface Pattern.

Site-selective surface modification on the shape-controlled nanocrystals is a key approach in the programmed self-assembly of inorganic colloidal materials. This study demonstrates a simple methodology to gain self-assemblies of semiconductor nanocrystals with branched shapes through tip-to-tip attachment. Short-chained water-soluble cationic thiols are employed as a surface ligand for CdSe tetrapods and CdSe/CdS core/shell octapods. Because of the less affinity of arm-tip to the surface ligands compared to the arm-side wall, the tip-surface becomes uncapped to give a hydrophobic nature, affording an amphiphilic surface pattern. The amphiphilic tetrapods aggregated into porous agglomerates through tip-to-tip connection in water, while they afforded a hexagonally arranged Kagome-like two-dimensional (2D) assembly by the simple casting of aqueous dispersion with the aid of a convective self-assembly mechanism. A 2D net-like assembly was similarly obtained from amphiphilic octapods. A dissipative particle dynamics simulation using a planar tripod model with an amphiphilic surface pattern reproduced the formation of the Kagome-like assembly in a 2D confined space, demonstrating that the lateral diffusion of nanoparticles and the firm contacts between the hydrophobic tips play crucial roles in the self-assembly.