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Structures of liquid water are controversial not only in supercooled polyamorphism but also in stable bulk liquids in the high temperature and pressure range. Several experimental studies in bulk liquid have assumed the existence of three different liquid water structures. If indeed the three liquid water structures are different, they should be clearly distinguished by some measure other than density that characterizes the difference in structural order. In this study, whether the three different bulk liquid water structures are real or not is numerically verified based on molecular simulations using a reliable water molecular model. Since these liquid water structures have been suggested to be related to three different crystal structures (i.e., ice Ih, III, and V), liquid structures are sampled from the vicinity of the ice Ih-liquid coexistence point, the ice III-V-liquid triple point, and the ice V-VI-liquid triple point, respectively. An attempt is made to introduce local order parameters (LOPs) as an indicator to distinguish these structures. A fast and exhaustive LOP search is performed by the molecular assembly structure learning package for Identifying order parameters. The selected LOP distinguishes the molecular structures of three different stable liquid waters with high accuracy, providing numerical evidence that these structural orders differ from each other. Furthermore, regions of the liquid water structures are drawn on a phase diagram using the LOP, demonstrating their consistency with experimental studies. [ABSTRACT FROM AUTHOR]

Positron annihilation lifetime spectroscopy (PALS) enables the nondestructive measurement of nanoscale cavities in materials. In this study, a strategy was proposed for mapping PALS measurement data of isotactic polypropylene to classical molecular dynamics (CMD) simulations. The discrepancy between simulated and experimental glass transition temperatures was resolved by shortening the polymer chains, rather than adjusting for the temperature, using the Williams–Landel–Ferry (WLF) equation. The effective probe radii of ortho-positronium (o-Ps), determined by comparing PALS data with CMD simulations, were ∼0.8 nm, which was consistent with the o-Ps size given by the solution of the Schrödinger equation. The free-volume fraction corresponding to the effective probe radius was 12.3% at the glass transition temperature, close to the value estimated using Simha–Boyer theory. The cavity number density was proportional to the effective probe radius and decreased with temperature. The o-Ps effective probe radius was proportional to both the critical probe radius and the −1/3 power of the monomer number density, and increased with increasing temperature. These findings suggest that combining PALS measurements with CMD simulations may provide insight into cavities in polymeric materials without relying on the WLF equation. [ABSTRACT FROM AUTHOR]

Identifying molecular structures of water and ice helps reveal the chemical nature of liquid and solid water. Real-space geometrical information on molecular systems can be precisely obtained from molecular simulations, but classifying the resulting structure is a non-trivial task. Order parameters are ordinarily introduced to effectively distinguish different structures. Many order parameters have been developed for various kinds of structures, such as body-centered cubic, face-centered cubic, hexagonal close-packed, and liquid. Order parameters for water have also been suggested but need further study. There has been no thorough investigation of the classification capability of many existing order parameters. In this work, we investigate the capability of 493 order parameters to classify the three structures of ice: Ih, Ic, and liquid. A total of 159 767 496 combinations of the order parameters are also considered. The investigation is automatically and systematically performed by machine learning. We find the best set of two bond-orientational order parameters, Q4 and Q8, to distinguish the three structures with high accuracy and robustness. A set of three order parameters is also suggested for better accuracy. [ABSTRACT FROM AUTHOR]

Determining local structures of molecular systems helps the scientific and technological understanding of the function of materials. Molecular simulations provide microscopic information on molecular systems, but analyzing the resulting local structures is a non-trivial task. Many kinds of order parameters have been developed for detecting such local structures. Bond-orientational order parameters are promising for classifying local structures and have been used to analyze systems with such structures as body-centered cubic, face-centered cubic, hexagonal close-packed, and liquid. A specific set of order parameters derived from Lechner's definitional equation are widely used to classify complex local structures. However, there has been no thorough investigation of the classification capability of other Lechner parameters, despite their potential to precisely distinguish local structures. In this work, we evaluate the classification capability of 112 species of bond-orientational order parameters including Lechner's definitions. A total of 234 248 combinations of these parameters are also evaluated. The evaluation is systematically and automatically performed using machine learning techniques. To distinguish the four types of local structures, we determine the better set of two order parameters by comparing with a conventional set. A set of three order parameters is also suggested for better accuracy. Therefore, the machine learning scheme in the present study enables the systematic, accurate, and automatic mining of effective order parameters for classifying crystal structures. [ABSTRACT FROM AUTHOR]

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 105 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. [ABSTRACT FROM AUTHOR]

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, rc. However, the estimation of the electrostatic potential profile and dipole orientational function is poor. The Wolf method cannot estimate electrostatic configuration at rc <= Lz/2 (Lz 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 rc = Lz/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 rc = Lz/3. In spite of this shortcoming, the IPSn method gives the most accurate result in estimating the surface tension at rc = Lz/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 rc 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. [ABSTRACT FROM AUTHOR]

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, rc, 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 rc. Thus the deviation becomes insignificant (less than 1%) at rc greater than 2.2 nm. The distance dependent Kirkwood factor Gk(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 Gk(r) of cutofflike method greatly deviate from that of the Ewald sum. However, the discrepancy of Gk(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. [ABSTRACT FROM AUTHOR]

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 3σ. The IPS method is an effective technique for estimating the transport coefficients of the Lennard-Jones liquid in a homogeneous system. [ABSTRACT FROM AUTHOR]