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Molecular dynamics simulations of nucleation of a supersaturated Lennard-Jones vapor in slit nanopores are carried out. In this study we extend a previous work [K. Yasuoka, G. T. Gao, and X. C. Zeng, J. Chem. Phys. 112, 4279 (2000)] in that the walls of the slit are treated as actual atomic walls serving as both the confining solid surfaces and a thermostat. The walls are fixed in place in a fcc lattice structure and wall atoms are subjected to a stiff biharmonic potential thereby bounded to lattice sites. The two walls of the slit have an identical surface [fcc (100)], but different strength of attractive interaction with the vapor particles--one is strongly adsorbing and another is weakly adsorbing. Heterogeneous nucleation of the supersaturated vapor in the slit is investigated and events of nucleus formation are monitored in real time. A comparison with the previous simulation (using rigid structureless walls) leads to useful insight into the influence of the wall model to the nucleus formation. In particular, it is found that although the adsorbed particles on the structureless wall diffuse faster than those on the atomic wall, the rate of nucleus formation on the structureless wall is actually about one order of magnitude lower. A detailed analysis of particle and cluster-formation flux indicates that the rate of nucleus formation on the wall is more sensitive to the kinetics of adsorption of gas particles onto the wall than the diffusion rate of adsorbed particles. The higher flux of cluster formation on the atomic wall is apparently due to the higher rate of deposition of monomers onto the wall. © 2001 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations of nucleation of Lennard-Jones vapor confined in a slit pore have been performed. The walls of the slit pore are structureless walls; each wall interacts with vapor molecules via Lennard-Jones 9-3 potential. The rate of nucleation in the steady state is determined by analyzing time evolution of the cluster size distribution. At the same vapor density and temperature, the nucleation rate in the slit pore is higher than in the homogeneous vapor [K. Yasuoka and M. Matsumoto, J. Chem. Phys. 109, 8451 (1998)], irrespective of the strength of attraction between the wall and vapor molecules. However, this attraction strongly affects the process of nucleus formation: if the attraction is weak (a drying wall), nuclei tend to form in the middle of the pore, whereas if the attraction is strong (a wetting wall), the nucleus formation originates from two sources, the surface diffusion of adsorbed molecules and deposition of clusters formed in the middle of the pore. © 2000 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Carbon nanotubes (CNTs) have potential applications in separation membranes and nanofluidic devices. It is well known that the behavior of water molecules confined in CNTs is affected by surface functional groups and external electric fields, leading to structural changes. The understanding of these structural changes of water within various CNTs is crucial, particularly in the context of material separation. While there have been many investigations into the effects of individual specific functional groups, a comprehensive understanding of the effect of these functional groups and the electric fields they generate on water molecules remains elusive. In this study, we investigate the properties of water molecules in tip-charged CNTs of (8,8), (10,10), and (12,12) chiral vectors with positive charges at one tip and negative charges at the other tip. Abstraction of ionized functional groups as tip charges enables a comprehensive understanding that is independent of individual functional groups. The symmetrically arranged tip-charges spontaneously generate a strong and symmetric electric field in the CNTs. However, the strength and directionality of the electric field are non-uniform and complex. In the interiors of (8,8) and (10,10) tip-charged CNTs, helical and square structures, which have disturbances caused by the non-uniformity of the electric field, are observed. The properties of the water molecules differed significantly in the center of the CNTs and near positive and negative charges, despite the electric field symmetry. In (12,12) tip-charged CNTs with 12 charges, a local ring structure is observed in the vicinity of negative charges but not in the vicinity of positive charges. It is concluded that the water structures in tip-charged CNTs have different characteristics from those in plain CNTs under a uniform electric field., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Clathrate hydrates continue to be the focus of active research efforts due to their use in energy resources, transportation, and storage-related applications. Therefore, it is crucial to define their essential characteristics from a molecular standpoint. Understanding molecular structure in particular is crucial because it aids in understanding the mechanisms that lead to the formation or dissociation of clathrate hydrates. In the past, a wide variety of order parameters have been employed to classify and evaluate hydrate structures. An alternative approach to inventing bespoke order parameters is to apply machine learning techniques to automatically generate effective order parameters. In earlier work, we suggested a method for automatically designing novel parameters for ice and liquid water structures with Graph Neural Networks (GNNs). In this work, we use a GNN to implement our method, which can independently produce feature representations of the molecular structures. By using the TeaNet-type model in our method, it is possible to directly learn the molecular geometry and topology. This enables us to build novel parameters without prior knowledge of suitable order parameters for the structure type, discover structural differences, and classify molecular structures with high accuracy. We use this approach to classify the structures of clathrate hydrate structures: sI, sII, and sH. This innovative approach provides an appealing and highly accurate replacement for the traditional order parameters. Furthermore, our method makes clear the process of automatically designing a universal parameter for liquid water, ice, and clathrate hydrate to analyze their structures and phases., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

We propose a method to build full-atomistic (FA) amorphous polymer structures using reverse-mapping from coarse-grained (CG) models. In this method, three models with different resolutions are utilized, namely the CG1, CG2, and FA models. It is assumed that the CG1 model is more abstract than the CG2 model. The CG1 is utilized to equilibrate the system, and then sequential reverse-mapping procedures from the CG1 to the CG2 models and from the CG2 to the FA models are conducted. A mapping relation between the CG1 and the FA models is necessary to generate a polymer structure with a given density and radius of chains. Actually, we have used the Kremer-Grest (KG) model as the CG1 and the monomer-level CG model as the CG2 model. Utilizing the mapping relation, we have developed a scheme that constructs an FA polymer model from the KG model. In the scheme, the KG model, the monomer level CG model, and the FA model are successively constructed. The scheme is applied to polyethylene (PE), cis 1,4-polybutadiene (PB), and poly(methyl methacrylate) (PMMA). As a validation, the structures of PE and PB constructed by the scheme were carefully checked through comparison with those obtained using long-time FA molecular dynamics (MD) simulations. We found that both short- and long-range chain structures constructed by the scheme reproduced those obtained by the FA MD simulations. Then, as an interesting application, the scheme is applied to generate an entangled PMMA structure. The results showed that the scheme provides an efficient and easy way to construct amorphous structures of FA polymers., (© 2023 Author(s). Published under an exclusive license by AIP Publishing.)

Molecular dynamics simulation produces three-dimensional data on molecular structures. The classification of molecular structure is an important task. Conventionally, various order parameters are used to classify different structures of liquid and crystal. Recently, machine learning (ML) methods have been proposed based on order parameters to find optimal choices or use them as input features of neural networks. Conventional ML methods still require manual operation, such as calculating the conventional order parameters and manipulating data to impose rotational/translational invariance. Conversely, deep learning models that satisfy invariance are useful because they can automatically learn and classify three-dimensional structural features. However, in addition to the difficulty of making the learned features explainable, deep learning models require information on large structures for highly accurate classification, making it difficult to use the obtained parameters for structural analysis. In this work, we apply two types of graph neural network models, the graph convolutional network (GCN) and the tensor embedded atom network (TeaNet), to classify the structures of Lennard-Jones (LJ) systems and water systems. Both models satisfy invariance, while GCN uses only length information between nodes. TeaNet uses length and orientation information between nodes and edges, allowing it to recognize molecular geometry efficiently. TeaNet achieved a highly accurate classification with an extremely small molecular structure, i.e., when the number of input molecules is 17 for the LJ system and 9 for the water system, the accuracy is 98.9% and 99.8%, respectively. This is an advantage of our method over conventional order parameters and ML methods such as GCN, which require a large molecular structure or the information of wider area neighbors. Furthermore, we verified that TeaNet could build novel order parameters without manual operation. Because TeaNet can recognize extremely small local structures with high accuracy, all structures can be mapped to a low-dimensional parameter space that can explain structural features. TeaNet offers an alternative to conventional order parameters because of its novelty., (© 2023 Author(s). Published under an exclusive license by AIP Publishing.)

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≲10 8 s -1 . However, the shear viscosities at γ̇≲10 8 s -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.

Water confined in carbon nanotubes (CNTs) has been intensively studied because of its unique properties and potential for various applications and is often embedded in silicon nitride (Si 3 N 4 ) membranes. However, the understanding of the influence of Si 3 N 4 on the properties of water in CNTs lacks clarity. In this study, we performed molecular dynamics simulations to investigate the effect of the Si 3 N 4 membrane on water molecules inside CNTs. The internal electric field generated in the CNTs by the point charges of the Si 3 N 4 membrane changes the structure and dynamical properties of water in the nanotubes, causing it to attain a disordered structure. The Si 3 N 4 membrane decreases the diffusivity of water in the CNTs; this is because the Coulomb potential energy (i.e., electrostatic interaction) of water decreases owing to the presence of Si 3 N 4 , whereas the Lennard-Jones potential energy (i.e., van der Waals interaction) does not change significantly. Furthermore, electrostatic interactions make the water structure more stable in the CNTs. As a result, the Si 3 N 4 membrane enhances the separation effect of the water-methanol mixture with CNTs in the presence of an external electric field. Furthermore, the threshold of the external electric field strength to induce water-methanol separation with CNTs is reduced owing to the presence of a silicon nitride membrane.

Among the many different types of molecules that form clathrate hydrates, H 2 is unique as it can easily diffuse into and out of clathrate cages, a process that involves the physical-chemical interactions between guest (H 2 ) and host (water) molecules, and is unlike any other molecular system. The dynamic and nano-scale process of H 2 diffusion into binary structure II hydrates, where the large cages are occupied by larger molecules, was studied using molecular dynamics simulation. As the H 2 molecules diffused from one cage to another, two types of diffusion processes were observed: (i) when moving between a pair of large cages, the H 2 molecules pass through the central part of the hexagonal rings; (ii) however, when the H 2 molecules move from a large cage to a small one, it requires one of the pentagonal rings to partially break, as this allows the H 2 molecule to pass through the widened space. While the diffusion of H 2 molecules between large cages was found to occur more frequently, the presence of SF 6 molecules in the large cages was found to inhibit diffusion. Therefore, in order to attain higher H 2 storage capacities in binary hydrates, it is suggested that there is an optimal number of large cages that should be occupied by SF 6 molecules.

In this paper, equilibrium properties of structure II hydrates of hydrogen were determined from Monte Carlo simulations in the isothermal-isobaric Gibbs ensemble. Water and hydrogen molecules are described by the TIP4P/Ice and Silvera-Goldman models, respectively. The use of the Gibbs ensemble has many key advantages for the simulation of hydrates. By the separation of hydrogen vapor and hydrate phases into their own domains, coupled with transfer moves of hydrogen molecules between domains, cage occupancies were determined. Furthermore, the choice of this ensemble also allows equilibrium lattice constants and guest molecule chemical potentials to be straightforwardly estimated. Results for hydrogen mass fractions indicate reasonable agreement with prior simulation data and theoretical models, while detailed analysis of cage occupancy distributions and neighboring cage pair occupancy combinations gives valuable insight into the behavior of this hydrate at the inter-cage scale. These results will aid in the construction of theoretical models, for which knowledge of the occupancy of neighboring cages is of great importance. In support of previous experimental and theoretical works, we also find evidence of double occupancy of a few small cages inside of the hydrate stability zone, albeit at very high pressures; approximately 0.1% of small cages are doubly occupied at 300 MPa, for temperatures of 225 K and 250 K.

The nucleation process of anisotropic particles often differs from that of their spherically symmetric counterparts. Despite a large body of work on the structure of droplets of anisotropic particles, their formation process remains poorly understood. In this study, homogeneous nucleation of uniaxial anisotropic particles was studied. Through structural analysis of cluster development and the formation free energy during the nucleation stage, it was revealed that the nucleation of uniaxial particles begins from highly ordered states. There is, however, a marked decrease in orientational order within the cluster before critical nucleus size is attained. Further investigation on variations in the molecular interactions demonstrates how droplet elongation and the direction of the nematic ordering director relative to the axis of elongation can both be controlled according to the nature of the molecular anisotropy.

Studies on homogeneous nucleation have been conducted for decades, but a large gap between experiment and theory persists when evaluating the nucleation rate because the classical nucleation theory (CNT) with all its modifications still cannot fully incorporate the kinetics of homogeneous nucleation. Recent large-scale molecular dynamics (MD) simulations on homogeneous nucleation estimated a nucleation rate around the same order of magnitude as that obtained in experiments. This immensely improved agreement between experiment and theory is exciting because MD can provide detailed information on molecular trajectories. Therefore, a better understanding of the kinetics of homogeneous nucleation can now be obtained. In this study, large-scale MD simulations on homogeneous nucleation were performed. Through kinetic analysis of the simulation results, the nucleation rate, free energy barrier, and critical cluster size were found. Although the nucleation rates directly obtained from the simulations differed from those calculated from the CNT by 8-13 orders of magnitude, when the parameters calculated from the molecular trajectories were substituted into the classical theory, the discrepancy between the nucleation rates decreased to within an order of magnitude. This proves that the fundamental formulation of the theoretical equation is physically sound. We also calculated the cluster formation free energy and confirmed that the free energy barrier decreases with increasing supersaturation ratio. The estimated barrier height was twice that determined by theory, whereas the critical cluster size showed very good agreement between simulation and theory.

To develop prediction methods of three-phase equilibrium (coexistence) conditions of methane hydrate by molecular simulations, we examined the use of NVT (isometric-isothermal) molecular dynamics (MD) simulations. NVT MD simulations of coexisting solid hydrate, liquid water, and vapor methane phases were performed at four different temperatures, namely, 285, 290, 295, and 300 K. NVT simulations do not require complex pressure control schemes in multi-phase systems, and the growth or dissociation of the hydrate phase can lead to significant pressure changes in the approach toward equilibrium conditions. We found that the calculated equilibrium pressures tended to be higher than those reported by previous NPT (isobaric-isothermal) simulation studies using the same water model. The deviations of equilibrium conditions from previous simulation studies are mainly attributable to the employed calculation methods of pressure and Lennard-Jones interactions. We monitored the pressure in the methane phase, far from the interfaces with other phases, and confirmed that it was higher than the total pressure of the system calculated by previous studies. This fact clearly highlights the difficulties associated with the pressure calculation and control for multi-phase systems. The treatment of Lennard-Jones interactions without tail corrections in MD simulations also contributes to the overestimation of equilibrium pressure. Although improvements are still required to obtain accurate equilibrium conditions, NVT MD simulations exhibit potential for the prediction of equilibrium conditions of multi-phase systems.

Many recent experimental studies have been conducted on constructing nanorods and nanowires to use in a wide range of applications. In this study, molecular dynamics is used to directly examine the condensation rate of nanorods and the results are compared with other basic configurations such as cubes or spheres. According to previous studies conducted by Suh and Yasuoka [J. Phys. Chem. B 115, 10631 (2011); 116, 14637 (2012)], a simple change in the configuration of the seed produces a shape effect, where the curvature of the solid seed surface directly affects the growth generating an orderly difference depending on the curvature. Nanoscale cuboids or nanorods were studied to find an aspect ratio effect when condensation occurs on the surface. Various aspect ratios were examined for different nanorod sizes over a wide range of supersaturation ratios. The results show that the growth rate of the nanorod is independent of the supersaturation ratio, which was also observed for the sphere and cube. The growth rate for the rod fell between those of the cube and the sphere, and this is due to an increase in the surface area of the nanorod compared to the cube and curvature effect in comparison with the sphere. A clear size dependence of the seed was observed, which is also similar to the cube and sphere. Furthermore, no aspect ratio influence was seen for the growth rate. This does not mean that the actual amount of condensation is the same for longer seeds, but rather from the definition of the growth rate, the amount of accumulation per unit area is the same for all seed lengths.

Carbon nanotubes (CNTs) are promising for water transport through membranes and for use as nano-pumps. The development of CNT-based nanofluidic devices, however, requires a better understanding of the properties of water molecules in CNTs because they can be very different from those in the bulk. Using all-atom molecular dynamics simulations, we investigate the effect of axial electric fields on the structure of water molecules in CNTs having diameters ranging from (7,7) to (10,10). The water dipole moments were aligned parallel to the electric field, which increases the density of water inside the CNTs and forms ordered ice-like structures. The electric field induces the transition from liquid to ice nanotubes in a wide range of CNT diameters. Moreover, we found an increase in the lifetime of hydrogen bonds for water structures in the CNTs. Fast librational motion breaks some hydrogen bonds, but the molecular pairs do not separate and the hydrogen bonds reform. Thus, hydrogen bonds maintain the water structure in the CNTs, and the water molecules move collectively, decreasing the axial diffusion coefficient and permeation rate.

Liquid-solid and solid-solid phase transitions of a monolayer water confined between two parallel hydrophobic surfaces are studied by molecular dynamics simulations. The solid phase considered is the high-density rhombic monolayer ice. Based on the computed free energy surface, it is found that at a certain width of the slit nanopore, the monolayer water exhibits not only a high freezing point but also a low energy barrier to crystallization. Moreover, through analyzing the oxygen-hydrogen-oxygen angle distribution and oxygen-hydrogen radial distribution, the high-density monolayer ice is classified as either a flat ice or a puckered ice. The transition between a flat ice and a puckered ice reflects a trade-off between the water-wall interactions and the electrostatic interactions among water molecules.

How do lipid molecules in membranes perform a flip-flop? The flip-flops of lipid molecules play a crucial role in the formation and flexibility of membranes. However, little has been determined about the behavior of flip-flops, either experimentally, or in molecular dynamics simulations. Here, we provide numerical results of the flip-flops of model lipid molecules in a model membrane and investigate the statistical properties, using millisecond-order coarse-grained molecular simulations (dissipative particle dynamics). We find that there are three different ways of flip-flops, which can be clearly characterized by their paths on the free energy surface. Furthermore, we found that the probability of the number of the flip-flops is well fitted by the Poisson distribution, and the probability density function for the inter-occurrence times of flip-flops coincides with that of the forward recurrence times. These results indicate that the occurrence of flip-flops is a Poisson process, which will play an important role in the flexibilities of membranes.

A novel route to the exponential trapping-time distribution within a solidlike state in water clusters is described. We propose a simple homogeneous network (SHN) model to investigate dynamics on the potential energy networks of water clusters. In this model, it is shown that the trapping-time distribution in a solidlike state follows the exponential distribution, whereas the trapping-time distribution in local potential minima within the solidlike state is not exponential. To confirm the exponential trapping-time distribution in a solidlike state, we investigate water clusters, (H2O)6 and (H2O)12, by molecular dynamics simulations. These clusters change dynamically from solidlike to liquidlike state and vice versa. We find that the probability density functions of trapping times in a solidlike state are described by the exponential distribution whereas those of interevent times of large fluctuations in potential energy within the solidlike state follow the Weibull distributions. The results provide a clear evidence that transition dynamics between solidlike and liquidlike states in water clusters are well described by the SHN model, suggesting that the exponential trapping-time distribution within a solidlike state originates from the homogeneous connectivity in the potential energy network.

Position and orientation of water protons need to be specified when the molecular simulation studies are performed for clathrate hydrates. Positions of oxygen atoms in water are experimentally determined by X-ray diffraction analysis of clathrate hydrate structures, but positions of water hydrogen atoms in the lattice are disordered. This study reports a determination of the water proton coordinates in unit cell of structure I (sI), II (sII), and H (sH) clathrate hydrates that satisfy the ice rules, have the lowest potential energy configuration for the protons, and give a net zero dipole moment. Possible proton coordinates in the unit cell were chosen by analyzing the symmetry of protons on the hexagonal or pentagonal faces in the hydrate cages and generating all possible proton distributions which satisfy the ice rules. We found that in the sI and sII unit cells, proton distributions with small net dipole moments have fairly narrow potential energy spreads of about 1 kJ∕mol. The total Coulomb potential on a test unit charge placed in the cage center for the minimum energy∕minimum dipole unit cell configurations was calculated. In the sI small cages, the Coulomb potential energy spread in each class of cage is less than 0.1 kJ∕mol, while the potential energy spread increases to values up to 6 kJ∕mol in sH and 15 kJ∕mol in the sII cages. The guest environments inside the cages can therefore be substantially different in the sII case. Cartesian coordinates for oxygen and hydrogen atoms in the sI, sII, and sH unit cells are reported for reference.

Vibrational spectra of guest molecules in clathrate hydrates are frequently measured to determine the characteristic signatures of the molecular environment and dynamical properties of guest-host interactions. Here, we present results of our study on the vibrational frequencies of methane molecules in structure H clathrate hydrates, namely, in the 5(12) and 4(3)5(6)6(3) cages, as the frequencies of stretching vibrational modes in these environments are still unclear. The vibrational spectra of methane molecules in structure H clathrate hydrate were obtained from ab initio molecular dynamics simulation and computed from Fourier transform of autocorrelation functions for each distinct vibrational mode. The calculated symmetric and asymmetric stretching vibrational frequencies of methane molecules were found to be lower in the 4(3)5(6)6(3) cages than in the 5(12) cages (3.8 cm(-1) for symmetric stretching and 6.0 cm(-1) for asymmetric stretching). The C-H bond length and average distance between methane molecules and host-water molecules in 4(3)5(6)6(3) cages were slightly longer than those in the 5(12) cages.

We performed molecular dynamics simulations of systems that consisted of the ice nucleation protein and the quasi-two-dimensional water cluster on it. The angle distributions, percolation probabilities, mean cluster sizes, cluster size distributions, and hydrogen bond relaxation times were analyzed. We concluded that the behavior of the water clusters on the ice nucleation protein was elaborately intertwined by the interaction between the ice nucleation protein and water, the interaction between the water molecules and the effect of temperature. The percolation probability and mean cluster size depended on the interactions and temperatures.

Vibrational frequencies of guest molecules in clathrate hydrates reflect the molecular environment and dynamical behavior of molecules. A detailed understanding of the mechanism for the vibrational frequency changes of the guest molecules in the clathrate hydrate cages is still incomplete. In this study, molecular vibrations of methane molecules in a structure I clathrate hydrate are calculated from ab initio molecular dynamics simulation. The vibrational spectra of methane are computed by Fourier transform of autocorrelation functions, which reveal distinct separation of each vibrational mode. Calculated symmetric and asymmetric stretching vibrational frequencies of methane molecules are lower in the large cages than in the small cages (8 and 16 cm(-1) for symmetric and asymmetric stretching, respectively). These changes are closely linked with the C-H bond length. The vibrational frequencies for the bending and rocking vibrational modes nearly overlap in each of the cages., (© 2012 American Institute of Physics)

An IPS/Tree method which is a combination of the isotropic periodic sum (IPS) method and tree-based method was developed for large-scale molecular dynamics simulations, such as biological and polymer systems, that need hundreds of thousands of molecules. The tree-based method uses a hierarchical tree structure to reduce the calculation cost of long-range interactions. IPS/Tree is an efficient method like IPS/DFFT, which is a combination of the IPS method and FFT in calculating large-scale systems that require massively parallel computers. The IPS method has two different versions: IPSn and IPSp. The basic idea is the same expect for the fact that the IPSn method is applied to calculations for point charges, while the IPSp method is used to calculate polar molecules. The concept of the IPS/Tree method is available for both IPSn and IPSp as IPSn/Tree and IPSp/Tree. Even though the accuracy of the Coulomb forces with tree-based method is well known, the accuracy for the combination of the IPS and tree-based methods is unclear. Therefore, in order to evaluate the accuracy of the IPS/Tree method, we performed molecular dynamics simulations for 32,000 bulk water molecules, which contains around 10(5) point charges. IPSn/Tree and IPSp/Tree were both applied to study the interaction calculations of Coulombic forces. The accuracy of the Coulombic forces and other physical properties of bulk water systems were evaluated. The IPSp/Tree method not only has reasonably small error in estimating Coulombic forces but the error was almost the same as the theoretical error of the ordinary tree-based method. These facts show that the algorithm of the tree-based method can be successfully applied to the IPSp method. On the other hand, the IPSn/Tree has a relatively large error, which seems to have been derived from the interaction treatment of the original IPSn method. The self-diffusion and radial distribution functions of water were calculated each by both the IPSn/Tree and IPSp/Tree methods, where both methods showed reasonable agreement with the Ewald method. In conclusion, the IPSp/Tree method is a potentially fast and sufficiently accurate technique for predicting transport coefficients and liquid structures of water in a homogeneous system.

As a more economical but similarly accurate computation method than the Ewald sum, the isotropic periodic sum (IPS) method for nonpolar molecules (IPSn) and polar molecules (IPSp), along with the Wolf method are of interest, but the cutoff radius dependence is an important issue. To evaluate the cutoff radius effect of the three methods, a water-vapor interfacial system has been studied by molecular dynamics. The Wolf method can produce adequate results for surface tension compared to that of the Ewald sum (within 2.9%) at a long enough cutoff radius, r(c). However, the estimation of the electrostatic potential profile and dipole orientational function is poor. The Wolf method cannot estimate electrostatic configuration at r(c) ≤ L(z)∕2 (L(z) is the longest lattice of the system). We have found that the convergence of the surface tension and the electrostatic configuration of the IPSn method is faster than that of the IPSp method. Moreover, the IPSn method is most accurate among the three methods for the same cutoff radius. Furthermore, the behavior of the surface tension against the cutoff radius shows a greater difference for the IPSn and IPSp method. The surface tension of the IPSp method fluctuates and presents a similar result to that of the Ewald sum, but the surface tension for the IPSn method greatly deviates near r(c) = L(z)∕3. The cause of this deviation is the difference between the interfacial configuration of the water surface and the cutoff treatment of the IPS method. The deviation becomes insignificant far from r(c) = L(z)∕3. In spite of this shortcoming, the IPSn method gives the most accurate result in estimating the surface tension at r(c) = L(z)∕2. From all the results in this work, the IPSn and IPSp method have been found to be more accurate than the Wolf method. In conclusion, the surface tension and structure of water-vapor interface can be calculated by the IPSn method when r(c) is greater than or equal to the longest lattice of the system. The IPSp method and the Wolf method require a longer cutoff radius than the longest lattice of the system to estimate interfacial properties.

Molecular dynamics simulations have been performed to examine the thermodynamic properties of methane/water interface using two different water models, the TIP4P/2005 and SPC/E, and two sets of combining rules. The density profiles, interfacial tensions, surface excesses, surface pressures, and coexisting densities are calculated over a wide range of pressure conditions. The TIP4P/2005 water model was used, with an optimized combining rule between water and methane fit to the solubility, to provide good predictions of interfacial properties. The use of the infinite dilution approximation to calculate the surface excesses from the interfacial tensions is examined comparing the surface pressures obtained by different approaches. It is shown that both the change of methane solubilities in pressure and position of maximum methane density profile at the interface are independent of pressure up to about 2 MPa. We have also calculated the adsorption enthalpies and entropies to describe the temperature dependency of the adsorption.

The surface tension, vapor-liquid equilibrium densities, and equilibrium pressure for common water models were calculated using molecular dynamics simulations over temperatures ranging from the melting to the critical points. The TIP4P/2005 and TIP4P-i models produced better values for the surface tension than the other water models. We also examined the correlation of the data to scaling temperatures based on the critical and melting temperatures. The reduced temperature (T/T(c)) gives consistent equilibrium densities and pressure, and the shifted temperature T + (T(c, exp) - T(c, sim)) gives consistent surface tension among all models considered in this study. The modified fixed charge model which has the same Lennard-Jones parameters as the TIP4P-FQ model but uses an adjustable molecular dipole moment is also simulated to find the differences in the vapor-liquid coexistence properties between fixed and fluctuating charge models. The TIP4P-FQ model (2.72 Debye) gives the best estimate of the experimental surface tension. The equilibrium vapor density and pressure are unaffected by changes in the dipole moment as well as the surface tension and liquid density.

Molecular dynamics simulation has been applied for water to compare the isotropic periodic sum (IPS) method [X. Wu and B. R. Brooks, J. Chem. Phys. 122, 044107 (2005)] with the Ewald sum based on the diffusion coefficient and liquid structure. The IPS method gives a good estimation for the self-diffusion coefficient at a cutoff radius, r(c), greater than 2.2 nm; however, the radial distribution function g(r) has a notable deviation. The peak of this deviation appears at specific intermolecular distances which are near each cutoff radius and decrease in proportion to the inverse of the cube of r(c). Thus the deviation becomes insignificant (less than 1%) at r(c) greater than 2.2 nm. The distance dependent Kirkwood factor G(k)(r) was also calculated, and since the truncation of a long-range interaction of the cutofflike method (such as cutoff with or without the switch function and the reaction field) shows serious shortcomings for dipole-dipole correlations in bulk water systems, this was observed by comparing the shape to that of the Ewald sum [Y. Yonetani, J. Chem. Phys. 124, 204501 (2006); D. van der Spoel and P. J. van Maaren, J. Chem. Theory Comput. 2, 1 (2006)]. The G(k)(r) of cutofflike method greatly deviate from that of the Ewald sum. However, the discrepancy of G(k)(r) for the IPS method was found to be much less than that of other typical cutofflike methods. In conclusion, the IPS method is an adequately accurate technique for estimating transport coefficients and the liquid structure of water in a homogeneous system at long cutoff distances.

We conducted a molecular dynamics simulation of the binary nucleation in the vapor mixture consisting of water and a small amount of sulfuric acid and investigated the microscopic process in relation to the structure of the hydrate (binary cluster composed of sulfuric acid and water). It was observed that the nucleation rate increased with the concentration of sulfuric acid. It was found that the formation of the hydrate is stable as long as its size is small enough, and the hydrate growth by coagulation played a major part in the enhanced nucleation. The rate of coagulation became larger by the uptake of more sulfuric acid in the hydrate, while it was suppressed with increasing the hydration number. We found that such features came from the structure of the small hydrate which was a multishell structure composed of an inner shell of sulfuric acid and diffused outer shell of water.

Using the simple point charge/extended water model, we performed molecular dynamics simulations of homogeneous vapor-liquid nucleation at various values of temperature T and supersaturation S, from which the nucleation rate J, critical nucleus size n(*), and the cluster formation free energy DeltaG were derived. As well as providing lots of simulation data, the results were compared with theories on homogeneous nucleation, including the classical, semi-phenomenological, and scaled models, but none of these gave a satisfactory explanation for our results. It was found that two main factors made the theories fail: (1) The average cluster structure including the nonspherical shape and the core structure that is not like the bulk liquid and (2) the forward rate which is larger than assumed by the theories by about one order of magnitude. The quantitative evaluation of these factors is left for future investigations.

Molecular dynamics simulations of a Lennard-Jones (LJ) liquid were applied to compare the isotropic periodic sum (IPS) method [X. Wu and B. R. Brooks, J. Chem. Phys. 122, 044107 (2005)], which can reduce the calculation cost of long-range interactions, such as the Lennard-Jones and Coulombic ones, with the cutoff method for the transport coefficients which includes the self-diffusion coefficient, bulk viscosity, and thermal conductivity. The self-diffusion coefficient, bulk viscosity, and thermal conductivity were estimated with reasonable accuracy if the cutoff distance of the LJ potential for the IPS method was greater than 3sigma. The IPS method is an effective technique for estimating the transport coefficients of the Lennard-Jones liquid in a homogeneous system.

More than 100 micros dissipative particle dynamics simulations were carried out to investigate the spontaneous formation process of threadlike micelles from the random configuration for surfactant molecules. Stable spherical micelles were formed during the earlier stage. These spherical micelles fused to each other and grew into rodlike and threadlike micelles during the later stage. The length and radius of a micelle were estimated by tracing the backbone positions and the distance between the head group particles and the backbone of the micelles, respectively. The ratio of the largest to the smallest principal moments of inertia for each micelle was calculated as the micelle shape.

The free energy differences are calculated for various type-I and type-II clathrate hydrates based on molecular-dynamics simulations, thereby evaluating the thermodynamic stability of the hydrates depending on the chemical species of the guest substances. The simulation systems consist of 27 unit cells, that is, 1242 water molecules and 216 guest molecules for type-I hydrates, and 3672 water molecules and 648 guest molecules for type-II hydrates. The water molecules are described by TIP4P potential, while the guest molecules are described by one-site Lennard-Jones potential, U=4epsilon{(sigma/r)12-(sigma/r)6}, where U is the potential energy, r is the particle distance, sigma is the particle diameter, and epsilon is the energy well depth. The optimal values of sigma that yield the minimum free energy (the best thermodynamic stability) were determined to be 0.39 nm for the type-I hydrates and 0.37 nm for the type-II hydrates.

A molecular dynamics simulation of vapor phase nucleation has been performed with 40,000 Lennard-Jones particles for the target gas and 0-160,000 particles for the carrier gas. Three carrier gas models are adopted, including a soft-core model, a Lennard-Jones model, and a modified Lennard-Jones model in which the attractive interaction can be adjusted. The effect of the carrier-gas pressure is assessed through computing and comparing the rate of nucleation and cluster size distribution. It is found that the effect of the carrier-gas pressure can be strongly dependent on the carrier-gas model. A positive effect (enhancement of the nucleation rate) is found with the soft-core potential model, whereas negligible effect is found with the Lennard-Jones potential model. For the modified Lennard-Jones potential with a weak attractive interaction, the carrier-gas effect is positive. However, the effect is negligible with a stronger attractive interaction between the target and carrier-gas particles. A reason for the negligible effect is that the carrier-gas particles are adsorbed on the cluster surface when the density of target and carrier-gas particles are comparable. When the density of carrier-gas particles are four times that of the target particles, the carrier-gas particles tend to mix with the target particles in the clusters.

A molecular-dynamics (MD) simulation of structure-H hydrates was performed under constant pressure and temperature with 6120 TIP4P water molecules, 900 OPLS-UA methane molecules, and 180 large molecular guest substance (LMGS) molecules. The LMGS molecules were represented in the form of a one-site Lennard-Jones (LJ) model using the LJ parameters sigma and epsilon. In order to clarify the thermodynamic stability of structure-H hydrates, we calculated the free-energy difference, changing on the sigma and epsilon only of the LMGS molecules. In this simulation, stable crystals of structure-H hydrates and a minimum value of DeltaG were obtained at sigma approximately 6.2 A and large values of epsilon. All simulations were performed using the special-purpose computer hardware MDGRAPE-2.

We performed large-scale molecular-dynamics simulation of nanoscale hydrophobic interaction manifested by the formation of nanobubble between nanometer-sized hydrophobic clusters at constrained equilibrium. Particular attention is placed on the tendency of formation and stability of nanobubbles in between model nanoassemblies which are composed of hydrophobic clusters (or patches) embedded in a hydrophilic substrate. On the basis of physical behavior of nanobubble formation, we observed a change from short-range molecular hydrophobic interaction to midrange nanoscopic interaction when the length scale of hydrophobe approaches to about 1 nm. We investigated the behavior of nanobubble formation with several different patterns of nonpolar-site distribution on the nanoassemblies but always keeping a constant ratio of nonpolar to polar monomer sites. Dynamical properties of confined water molecules in between nanoassemblies are also calculated.