Diffusion with a broad class of stochastic diffusion coefficients.

In many physical or biological systems, diffusion can be described by Brownian motions with stochastic diffusion coefficients (DCs). In the present study, we investigate properties of the diffusion with a broad class of stochastic DCs with an approach that is different from subordination. We show that for a finite time, the propagator is non-Gaussian and heavy tailed. This means that when the mean square displacements are the same, for a finite time, some of the diffusing particles with stochastic DCs diffuse farther than the particles with deterministic DCs or exhibiting a fractional Brownian motion. We also show that when a stochastic DC is ergodic, the propagator converges to a Gaussian distribution in the long time limit. The speed of convergence is determined by the autocovariance function of the DC.

Tribo-Chemical Reactions in DLC-Zirconia Sliding under Ethanol Gas Environment.

A reactive force field (ReaxFF) molecular dynamics simulation is performed for the sliding of diamond-like carbon (DLC) and yttria-stabilized zirconia (YSZ) under an ethanol gas environment, motivated by the previous experiment of ultralow friction phenomenon (friction fade-out). We observe (i) dissociation of ethanol into ethoxy and hydrogen, both of which simultaneously adsorb on the YSZ surface, and (ii) dissociation of ethanol into ethyl and hydroxy, the former of which forms a bond with another ethanol molecule and the latter of which adsorbs on the DLC surface. Reaction (i) is enhanced by the sliding motion, but occurs even without it, while reaction (ii) only occurs during sliding with a sufficiently high load pressure. The potentials of mean force for the two reactions are also calculated combining the steered MD and Jarzynski equality. It is shown that the activation energies of reactions (i) and (ii) are significantly lowered by the YSZ and DLC surfaces, respectively, as compared to those in a vacuum. The resultant activation energy is higher for reaction (ii) than for reaction (i).

Leaf-Inspired Host-Guest Complexation-Dictating Supramolecular Gas Sensors.

We report unique conductive leaf-inspired (in particular, stomata-inspired) supramolecular gas sensors in which acetylated cyclodextrin derivatives rule the electric output. The gas sensors consist of polymers bearing acetylated cyclodextrin, adamantane, and carbon black. Host-guest complexes between acetylated cyclodextrin and adamantane corresponding to the closed stomata realize a flexible polymeric matrix. Effective recombination of the cross-links contributes to the robustness. As gas sensors, the supramolecular materials detect ammonia as well as various other gases at 1 ppm in 10 min. The free acetylated cyclodextrin corresponding to open stomata recognized the guest gases to alter the electric resistivity. Interestingly, the conductive device failed to detect ammonia gases at all without acetylated cyclodextrin. The molecular recognition was studied by molecular dynamics simulations. The gas molecules existed stably in the cavity of free acetylated cyclodextrin. These findings show the potential for developing wearable gas sensors.

Reentrant 2D Nanostructured Liquid Crystals by Competition between Molecular Packing and Conformation: Potential Design for Multistep Switching of Ionic Conductivity.

The front cover artwork is provided by Takashi Kato at the University of Tokyo. The image shows three assembled structures of smectic liquid crystals that show reentrant behavior. Read the full text of the Research Article at 10.1002/cphc.202200927.

Reentrant 2D Nanostructured Liquid Crystals by Competition between Molecular Packing and Conformation: Potential Design for Multistep Switching of Ionic Conductivity.

Reentrant phenomena in soft matter and biosystems have attracted considerable attention because their properties are closely related to high functionality. Here, we report a combined experimental and computational study on the self-assembly and reentrant behavior of a single-component thermotropic smectic liquid crystal toward the realization of dynamically functional materials. We have designed and synthesized a mesogenic molecule consisting of an alicyclic trans,trans-bicyclohexyl mesogen and a polar cyclic carbonate group connected by a flexible tetra(oxyethylene) spacer. The molecule exhibits an unprecedented sequence of layered smectic phases, in the order: smectic A-smectic B-reentrant smectic A. Electron density profiles and large-scale molecular dynamics simulations indicate that competition between the stacking of bicyclohexyl mesogens and the conformational flexibility of tetra(oxyethylene) chains induces this unusual reentrant behavior. Ion-conductive reentrant liquid-crystalline materials have been developed, which undergo the multistep conductivity changes in response to temperature. The reentrant liquid crystals have potential as new mesogenic materials exhibiting switching functions.

The effect of electric field on the structural order of water molecules around chitosan between nano gold plates determined by molecular dynamics simulations.

In this paper, we classified the types of water in the vicinity of the chitosan polymer and gold plate by applying an electric field of magnitude 1 V Å-1 in various directions at varying temperatures by using molecular dynamics simulation. The three types of water were categorized by analyzing the data through the tetrahedral order method with four water regions separated in the distance from 1 to 6 Å around polymers. The interaction between water molecules and functional groups, such as hydroxyl, ether, and ester, leads to the formation of intermediate and nonfreezing water. Under an electric field, this formation appeared more clearly due to the transformation of liquid water to crystal cubic ice with two structural formations depending on gold plates at a temperature of 300 K. The enhancement of the tetrahedral order of water in cubic ice is related to the existence of a four-fold H-bonded structure and lower ones in the XES experiment.

Nonpolarizable Force Fields through the Self-Consistent Modeling Scheme with MD and DFT Methods: From Ionic Liquids to Self-Assembled Ionic Liquid Crystals.

A key to achieve the accuracy of molecular dynamics (MD) simulation is the set of force fields used to express the atomistic interactions. In particular, the electrostatic interaction remains the main issue for the precise simulation of various ionic soft materials from ionic liquids to their supramolecular compounds. In this study, we test the nonpolarizable force fields of ionic liquids (ILs) and self-assembled ionic liquid crystals (ILCs) for which the intermolecular charge transfer and intramolecular polarization are significant. The self-consistent modeling scheme is adopted to refine the atomic charges of ionic species in a condensed state through the use of density functional theory (DFT) under the periodic boundary condition. The atomic charges of the generalized amber force field (GAFF) are effectively updated to express the electrostatic properties of ionic molecules obtained by the DFT calculation in condensed phase, which improves the prediction accuracy of ionic conductivity with the obtained force field (GAFF-DFT). The derived DFT charges then suggest that the substitution of a hydrophobic liquid-crystalline moiety into IL-based cations enhances the charge localization of ionic groups in the amphiphilic molecules, leading to the amplification of the electrostatic interactions among the hydrophilic/ionic groups in the presence of hydrophobic moieties. In addition, we focus on an ion-conductive pathway hidden in the self-assembled nanostructure. The MD results indicate that the ionic groups of cation and anion interact strongly for keeping the bicontinuous nanosegregation of ionic nanochannel. The partial fractions of hydrophilic/ionic and hydrophobic nanodomains are then quantified with the volume difference from referenced IL systems, while the calculated ionic conductivity decreases in the self-assembled ILCs more than the occupied volume of ionic nanodomains. These analyses suggest that the mobility of ions in the self-assembled ILCs remains quite restricted even with small tetrafluoroborate anions because of strong attractive interaction among ionic moieties.

Infrared Spectra and Hydrogen-Bond Configurations of Water Molecules at the Interface of Water-Insoluble Polymers under Humidified Conditions.

Elucidating the state of interfacial water, especially the hydrogen-bond configurations, is considered to be key for a better understanding of the functions of polymers that are exhibited in the presence of water. Here, an analysis in this direction is conducted for two water-insoluble biocompatible polymers, poly(2-methoxyethyl acrylate) and cyclic(poly(2-methoxyethyl acrylate)), and a non-biocompatible polymer, poly(n-butyl acrylate), by measuring their IR spectra under humidified conditions and by carrying out theoretical calculations on model complex systems. It is found that the OH stretching bands of water are decomposed into four components, and while the higher-frequency components (with peaks at ∼3610 and ∼3540 cm-1) behave in parallel with the C═O and C-O-C stretching and CH deformation bands of the polymers, the lower-frequency components (with peaks at ∼3430 and ∼3260 cm-1) become pronounced to a greater extent with increasing humidity. From the theoretical calculations, it is shown that the OH stretching frequency that is distributed from ∼3650 to ∼3200 cm-1 is correlated to the hydrogen-bond configurations and is mainly controlled by the electric field that is sensed by the vibrating H atom. By combining these observed and calculated results, the configurations of water at the interface of the polymers are discussed.

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 was simulated using the generalized replica-exchange method (gREM) based on molecular dynamics simulations. The effective temperature is introduced in the gREM, allowing for 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.

Structural order of water molecules around polyrotaxane including PEG, α-cyclodextrin, and α-lipoic acid linker on gold surface by molecular dynamics simulations.

In materials science, water plays an important part, especially at the molecular level. It shows various properties when sorbed onto surfaces of polymers. The structure of the molecular water ensemble in the vicinity of the polymers is under discussion. In this study, we used molecular dynamics methods to analyze the structure of water in the vicinity of the polymer polyrotaxane (PR), composed of α-cyclodextrins (α-CDs), a poly(ethylene glycol) (PEG) axial chain, and α-lipoic acid linkers, at various temperatures. The distribution of water around the functional groups, hydrogen bond network, and tetrahedral order were analyzed to classify the various types of water around the polymer. We found that the tetrahedral order of water had a strained relationship from the XES experiment. Four water regions were separated from each other in the vicinity of 1 to 5 Å around PR. The intermediate and non-freezing water were formed due to the interaction between water molecules and the functional groups, such as hydroxyl, ether, and ester.

Solid Lubricants of Combined Graphene and Iron Nanoparticles for Study of Friction and Stability.

This study focuses on designing solid lubricant particles by combining graphene and iron nanoparticles (namely, graphene-iron (GI) particles) and carrying out studies for behaviors of their lubrication for the iron contact by molecular dynamics simulations. By the annealing process of melting and cooling iron, we can create the lubricant particle, where the iron nanoparticle tightly holds the graphene sheet. In the sliding friction investigations, it is found that the influences of orientation of the graphene sheets inside the contact, size and configuration of the GI particles, and lubrication with the bare iron nanoparticles on friction are strong at low pressure and very slight at high pressure. The GI particles provide stability of the friction coefficient over a wide range of pressure; however, it strongly increases with pressure in the lubrication behaviors by the bare iron particles due to the deformation of the particles. The iron contact in the presence of the GI particles can achieve the ultralow values of the friction coefficient from 0.009 to 0.042. The contact surfaces are not nearly damaged (slightly elastic deformation) with the pressure up to 2.0 GPa. From the comparisons between the results in this study and previous reports, the GI particles have better lubrication than graphene coated on a surface and well stabilize under pressure compared to the different lubricant nanoparticles. The main reason for this is due to the contributions of graphene, besides reduction of the contact area resulted from the configuration of the nanoparticle, which promotes sliding and sharing of the pressure, preventing collision between the lubricant particles.

Molecular insights on confined water in the nanochannels of self-assembled ionic liquid crystal.

Self-assembled ionic liquid crystals can transport water and ions via the periodic nanochannels, and these materials are promising candidates as water treatment membranes. Molecular insights on the water transport process are, however, less investigated because of computational difficulties of ionic soft matters and the self-assembly. Here we report specific behavior of water molecules in the nanochannels by using the self-consistent modeling combining density functional theory and molecular dynamics and the large-scale molecular dynamics calculation. The simulations clearly provide the one-dimensional (1D) and 3D-interconnected nanochannels of self-assembled columnar and bicontinuous structures, respectively, with the precise mesoscale order observed by x-ray diffraction measurement. Water molecules are then confined inside the nanochannels with the formation of hydrogen bonding network. The quantitative analyses of free energetics and anisotropic diffusivity reveal that, the mesoscale geometry of 1D nanodomain profits the nature of water transport via advantages of dissolution and diffusion mechanisms inside the ionic nanochannels.

Higher-order structure of polymer melt described by persistent homology.

The optimal method of the polymer Materials Informatics (MI) has not been developed because the amorphous nature of the higher-order structure affects these properties. We have now tried to develop the polymer MI's descriptor of the higher-order structure using persistent homology as the topological method. We have experimentally studied the influence of the MD simulation cell size as the higher-order structure of the polymer on its electrical properties important for a soft material sensor or actuator device. The all-atom MD simulation of the polymer has been calculated and the obtained atomic coordinate has been analyzed by the persistent homology. The change in the higher-order structure by different cell size simulations affects the dielectric constant, although these changes are not described by a radial distribution function (RDF). On the other hand, using the 2nd order persistent diagram (PD), it was found that when the cell size is small, the island-shaped distribution become smoother as the cell size increased. There is the same tendency for the condition of change in the monomer ratio, the polymer chain length or temperature. As a result, the persistent homology may express the higher-order structure generated by the MD simulation as a descriptor of the polymer MI.

Generic transport coefficients of a confined electrolyte solution.

Physical parameters characterizing electrokinetic transport in a confined electrolyte solution are reconstructed from the generic transport coefficients obtained within the classical nonequilibrium statistical thermodynamic framework. The electro-osmotic flow, the diffusio-osmotic flow, the osmotic current, as well as the pressure-driven Poiseuille-type flow, the electric conduction, and the ion diffusion are described by this set of transport coefficients. The reconstruction is demonstrated for an aqueous NaCl solution between two parallel charged surfaces with a nanoscale gap, by using the molecular dynamic (MD) simulations. A Green-Kubo approach is employed to evaluate the transport coefficients in the linear-response regime, and the fluxes induced by the pressure, electric, and chemical potential fields are compared with the results of nonequilibrium MD simulations. Using this numerical scheme, the influence of the salt concentration on the transport coefficients is investigated. Anomalous reversal of diffusio-osmotic current, as well as that of electro-osmotic flow, is observed at high surface charge densities and high added-salt concentrations.

Boundary condition at a two-phase interface in the lattice Boltzmann method for the convection-diffusion equation.

A boundary scheme in the lattice Boltzmann method (LBM) for the convection-diffusion equation, which correctly realizes the internal boundary condition at the interface between two phases with different transport properties, is presented. The difficulty in satisfying the continuity of flux at the interface in a transient analysis, which is inherent in the conventional LBM, is overcome by modifying the collision operator and the streaming process of the LBM. An asymptotic analysis of the scheme is carried out in order to clarify the role played by the adjustable parameters involved in the scheme. As a result, the internal boundary condition is shown to be satisfied with second-order accuracy with respect to the lattice interval, if we assign appropriate values to the adjustable parameters. In addition, two specific problems are numerically analyzed, and comparison with the analytical solutions of the problems numerically validates the proposed scheme.

Molecular dynamics simulation of electrokinetic flow of an aqueous electrolyte solution in nanochannels.

Electrokinetic flows of an aqueous NaCl solution in nanochannels with negatively charged surfaces are studied using molecular dynamics simulations. The four transport coefficients that characterize the response to weak electric and pressure fields, namely, the coefficients for the electrical current in response to the electric field (M(jj)) and the pressure field (M(jm)), and those for the mass flow in response to the same fields (M(mj) and M(mm)), are obtained in the linear regime using a Green-Kubo approach. Nonequilibrium simulations with explicit external fields are also carried out, and the current and mass flows are directly obtained. The two methods exhibit good agreement even for large external field strengths, and Onsager's reciprocal relation (M(jm) = M(mj)) is numerically confirmed in both approaches. The influence of the surface charge density on the flow is also considered. The values of the transport coefficients are found to be smaller for larger surface charge density, because the counter-ions strongly bound near the channel surface interfere with the charge and mass flows. A reversal of the streaming current and of the reciprocal electro-osmotic flow, with a change of sign of M(mj) due to the excess co-ions, takes places for very high surface charge density.

Mechanism of ultra low friction of multilayer graphene studied by coarse-grained molecular simulation.

Coarse-grained Metropolis Monte Carlo Brownian Dynamics simulations are used to clarify the ultralow friction mechanism of a transfer film of multilayered graphene sheets. Each circular graphene sheet consists of 400 to 1,000,000 atoms confined between the upper and lower sliders and are allowed to move in 3 translational and 1 rotational directions due to thermal motion at 300 K. The sheet-sheet interaction energy is calculated by the sum of the pair potential of the sp2 carbons. The sliding simulations are done by moving the upper slider at a constant velocity. In the monolayer case, the friction force shows a stick-slip like curve and the average of the force is high. In the multilayer case, the friction force does not show any oscillation and the average of the force is very low. This is because the entire transfer film has an internal degree of freedom in the multilayer case and the lowest sheet of the layer is able to follow the equipotential surface of the lower slider.

Electric polarizability of DNA in aqueous salt solution.

Monte Carlo simulations are performed to determine the anisotropy of the electric polarizability of a model DNA fragment in aqueous salt solution. By taking into consideration the participation of coions in the electroneutrality condition, at every simulation step, we obtain a list of counterions constituting the net charge arranged in increasing order of their distance from the DNA and calculate the contribution to the dipole moment from the first n counterions in the list. We define a partial polarizability tensor due to these n counterions to understand the origin of the polarizability in close relation to the solution structure. The ionic distributions are described by the counterion condensation theory. Characteristic features of the electric properties of polyelectrolytes are reproduced. The anisotropy of the electric polarizability Deltaalpha of DNA decreases with the addition of salt, yielding values comparable to experiment. The effect of electrophoretic motion of the polyion is examined by estimating its upper limit.