Published papers

© 2018 National Academy of Sciences. All rights reserved. Akin to bulk water, water confined to an isolated nanoslit can show a wealth of new 2D phases of ice and amorphous ice, as well as unusual phase behavior. Indeed, 2D water phases, such as bilayer hexagonal ice and monolayer square ice, have been detected in the laboratory, confirming earlier computational predictions. Herein, we report theoretical evidence of a hitherto unreported state, namely, bilayer very low density amorphous ice (BL-VLDA), as well as evidence of a strong first-order transition between BL-VLDA and the BL amorphous ice (BL-A), and a weak first-order transition between BL-VLDA and the BL very low density liquid (BL-VLDL) water. The diffusivity of BL-VLDA is typically in the range of 10 −9 cm 2 /s to 10 −10 cm 2 /s. Similar to bulk (3D) water, 2D water can exhibit two forms of liquid in the deeply supercooled state. However, unlike supercooled bulk water, for which the two forms of liquid can coexist and merge into one at a critical point, the 2D BL-VLDL and BL high-density liquid (BL-HDL) phases are separated by the highly stable solid phase of BL-A whose melting line exhibits the isochore end point (IEP) near 220 K in the temperature−pressure diagram. Above the IEP temperature, BL-VLDL and BL-HDL are indistinguishable. At negative pressures, the metastable BL-VLDL exhibits a spatially and temporally heterogeneous structure induced by dynamic changes in the nanodomains, a feature much less pronounced in the BL-HDL.

© 2018 Author(s). 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.

© 2019 Author(s). 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.

© 2018 The Royal Society of Chemistry. The oxygen evolution reaction (OER) is an important reaction in the field of renewable energy and is utilized in electrochemical water splitting for hydrogen fuel production and rechargeable metal-air batteries. Herein, we report a new oxygen evolution reaction mechanism originating from oxygen vacancies, which remarkably enhances the OER activity of oxygen deficient electrocatalysts. The OER activity of Sr 2 VFeAsO 3-δ is drastically enhanced above the lattice oxygen vacancy of δ = 0.5, exhibiting ∼300 mV lower overpotential and 80 times higher specific activity at 1.7 V vs. RHE. Surprisingly, the initially low OER activity of Sr 2 VFeAsO 3-δ (δ < 0.5) is enhanced to the level of state-of-the-art OER catalysts simply by introducing higher concentrations of oxygen vacancies. Density functional theory (DFT) calculations clarify that the oxygen vacancies are initially dominated by one of the crystallographic sites, while two types of crystallographic sites become fully accessible for δ > 0.5. As a result, the distance between OH - coupled oxygen-vacant sites becomes sufficiently short to enable direct O-O bond formation as in photosystem II. Thus, we found that the OER activity of oxygen deficient electrocatalysts is controllable by the variety of lattice oxygen vacancies, which suggests that oxygen deficient layered superconductors are promising OER catalysts for energy conversion technologies.

© 2020 The Royal Society of Chemistry. 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.

© 2019 The Royal Society of Chemistry. Anisotropic dodecahedral (D) water cages found in semiclathrate hydrates have unique gas selectivity due to their varied shapes. Herein, the D cages incorporating ideally isotropic rare gases, i.e., Xe, Kr and Ar, were characterized by crystal structure analyses. Stabilization mechanisms of the semiclathrate hydrates by the D cages are discussed.

© 2019 American Chemical Society. The Aurivillius phases of complex bismuth oxides have attracted considerable attention because of their lattice polarization (ferroelectricity) and photocatalytic activity. We report a first-principles exploration of Bi2WO6 and the crystal engineering through replacing W6+ by pentavalent (Nb5+ and Ta5+) and tetravalent (Ti4+ and Sn4+) ions, with charge neutrality maintained by the formation of a mixed anion oxyhalide sublattice. We find that Bi2SnO4F2 is thermodynamically unstable, in contrast to Bi2TaO5F, Bi2NbO5F, and Bi2TiO4F2. The electric dipoles introduced by chemical substitutions in the parent compound are found to suppress the spontaneous polarization from 61.55 μC/cm2 to below 15.50 μC/cm2. Analysis of the trends in electronic structure, surface structure, and ionization potentials is reported. This family of materials can be further extended with control of layer thicknesses and choice of compensating halide species.

© 2020 Pua et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The study of molecular dynamics simulations is largely facilitated by analysis and visualization toolsets. However, these toolsets are often designed for specific use cases and those only, while scripting extensions to such toolsets is often exceedingly complicated. To overcome this problem, we designed a software application called AViS which focuses on the extensibility of analysis. By utilizing the dataflow programming (DFP) paradigm, algorithms can be defined by execution graphs, and arbitrary data can be transferred between nodes using visual connectors. Extension nodes can be implemented in either Python, C++, and Fortran, and combined in the same algorithm. AViS offers a comprehensive collection of nodes for sophisticated visualization state modifications, thus greatly simplifying the rules for writing extensions. Input files can also be read from the server automatically, and data is fetched automatically to improve memory usage. In addition, the visualization system of AViS uses physically-based rendering techniques, improving the 3D perception of molecular structures for interactive visualization. By performing two case studies on complex molecular systems, we show that the DFP workflow offers a much higher level of flexibility and extensibility when compared to legacy workflows.

© 2019 The Royal Society of Chemistry. Molecular dynamics (MD) simulation is a powerful computational method to observe molecular behavior. Although the detection of molecular behavior that characterizes systems is an important task in the study of MD, it is typically difficult and depends on human expert knowledge. Therefore, we propose a novel analysis scheme for MD data using deep neural networks. A key aspect of our scheme is the estimation of statistical distances between different ensembles that are probability distributions over the possible states of systems. This allows us to build low-dimensional embeddings of ensembles to visualize differences between systems in a compact metric space. Furthermore, the molecular behavior that contributes to the differences between systems can also be detected using the trained function of deep neural networks. The applicability of our scheme is demonstrated using three types of MD data. Our scheme could be a powerful tool to clarify the underlying physics in the molecular systems.

© 2020 Author(s). Among the many different types of molecules that form clathrate hydrates, H2 is unique as it can easily diffuse into and out of clathrate cages, a process that involves the physical-chemical interactions between guest (H2) and host (water) molecules, and is unlike any other molecular system. The dynamic and nano-scale process of H2 diffusion into binary structure II hydrates, where the large cages are occupied by larger molecules, was studied using molecular dynamics simulation. As the H2 molecules diffused from one cage to another, two types of diffusion processes were observed: (i) when moving between a pair of large cages, the H2 molecules pass through the central part of the hexagonal rings; (ii) however, when the H2 molecules move from a large cage to a small one, it requires one of the pentagonal rings to partially break, as this allows the H2 molecule to pass through the widened space. While the diffusion of H2 molecules between large cages was found to occur more frequently, the presence of SF6 molecules in the large cages was found to inhibit diffusion. Therefore, in order to attain higher H2 storage capacities in binary hydrates, it is suggested that there is an optimal number of large cages that should be occupied by SF6 molecules.

© 2019 American Chemical Society. We developed a computational method to establish an interaction surface using virtual companion particles. Upon the implementation of this new method, wetting behaviors of liquid droplets on highly textured solid surfaces can be investigated by molecular dynamics (MD) simulations. The interactions between atoms in the liquid droplets and the "interaction surface" depend only on the distance from the atom to the surface. Textured surfaces with nanopillars can be modeled by setting the range of pillars. The interactions with the droplet atoms can be calculated by using the potential function of the virtual particles which are placed interactively on the range of pillars and the bottom surfaces. The positions of the virtual particles are determined so as to minimize the distance from the droplet atoms and can be set independently of the lattice structures of the solid surfaces. Hence, we can design various pillar shapes (e.g., cylindrical, cone, and pyramidal shapes) for the textured surfaces. Such a method can be useful for the MD simulation of wetting behavior on a complex rough surface with a simple and yet effective procedure.

© 2019, Springer Science+Business Media, LLC, part of Springer Nature. Rhodopsin is a light-driven G protein-coupled receptor mediating signal transduction in eyes. The molecular dynamics (MD) simulations are powerful computational tools to investigate molecular behavior of proteins and internal water molecules which are related to the function of proteins; however, the MD simulations of the rhodopsin require several technical setups for accurate calculations. This chapter discusses practical methods for setting up the MD simulations of the rhodopsin [preparation of initial systems, condition files for MD simulation package GROMACS, and data analysis]. The data analysis includes the root mean square deviation (RMSD) and mapping of accessibility of water molecules.

© Published under licence by IOP Publishing Ltd. Carbon nanotubes (CNTs) have shown a great promise for nanofluidic-based applications such as for separation membranes. Water confined in nanotubes has different properties compared with those in bulk. Therefore, to develop a membrane with CNTs, it is very important to clarify the behavior of water in CNTs. In this study, we show effects of an electric field on water in a CNT by molecular dynamics simulation. An electric field aligns the dipole moment of water molecules and induces formation of an ordered structure in a CNT. As a result, the electrostatic interaction between water molecules within the structure becomes stronger. Strengthening of the electrostatics interaction facilitates water molecules preferring to fill a CNT over alcohol molecules. This indicates a strong separation effect for water-alcohol solutions.

© the Owner Societies. Carbon nanotubes (CNTs) are a promising candidate for separation membranes because of their ability to transport substances at very high flow rates. However, there is a tradeoff between achieving a high selectivity using small pore sizes and the reduction of water flux. Here, using molecular dynamics simulations, we report that CNTs can effectively separate water-methanol mixtures under an electric field. Without an electric field and under piston pressure, both water and methanol flow through a CNT, resulting in no separation effect. In contrast, under an electric field and high piston pressure, CNTs allow selective water permeation while rejecting the permeation of methanol molecules. This separation effect is caused by the ordered structures of water molecules in the CNT. A high filtering effect is observed under the conditions of high methanol concentration in the solution or even with large-diameter CNTs up to 3.39 nm. As long as the ordered structure of water in the CNTs can be maintained, the strong filtering effect can be maintained.

© 2020 The Author(s) High mobility group box 1 (HMGB1) is a damage-associated molecular pattern (DAMP) molecule that triggers the progression of several pro-inflammatory diseases such as diabetes, Alzheimer's disease and cancer, by inducing signals upon interaction with the receptors such as the receptor for advanced glycation end-products (RAGE) and toll-like receptors (TLRs). The acidic C-terminal tail of HMGB1 is an intrinsically disordered region of the protein which is known to determine the interaction of HMGB1 to DNA and histones. This study characterizes its structural properties using a combination of circular dichroism (CD) and molecular dynamics (MD) simulations. The full-length and tail-less forms of HMGB1 were compared to rationalise the role of the acidic tail in maintaining the stability of the entire structure of HMGB1 in atomistic detail. Consistent with experimental data, the acidic tail was predicted to adopt an extended conformation that allows it to make a range of hydrogen-bonding and electrostatic interactions with the box-like domains that stabilize the overall structure of HMGB1. Absence of the acidic tail was predicted to increase structural fluctuations of all amino acids, leading to changes in secondary structure from α-helical to more hydrophilic turns along with increased exposure of multiple amino acids to the surrounding solvent. These structural changes reveal the intrinsic conformational dynamics of HMGB1 that are likely to affect the accessibility of its receptors.

© 2018 Author(s). Anatase TiO2 nanocrystals have received considerable attention owing to their promising applications in photocatalysis, photovoltaics, and fuel cells. Although experimental evidence has shown that the performance of nanocrystals can be significantly improved through reduction, the mechanistic basis of this enhancement remains unclear. To shed a light on the chemistry of reduced anatase TiO2 nanocrystals, density functional theory were used to investigate the properties of defects and excess electrons. We demonstrated that oxygen vacancies are stable both on the surface and at the sub-surface of the nanocrystal, while titanium interstitials prefer sub-surface sites. Different defect locations possessed different excess electron structures, which contributed to deep and shallow states in the band gap of the nanocrystals. Furthermore, valence band tailing was observed, resulting in band gap narrowing. The theoretical results presented here deepen our understanding, and show the potential of defects to considerably change the macroscopic properties of anatase TiO2 nanocrystals.

© 2018 American Chemical Society. Water dynamics is of predominant importance in life, and it plays a critical role in chemical and biological systems. Many studies have reported nonbulk and anomalous dynamics of water molecules; however, a general method to detect the anomalous dynamics is yet to be established. Here, we develop a detection approach for the anomalous dynamics of a water molecule. Using a time series of the dipole vector of a water molecule, our approach achieves single-molecule detection of the anomalous dynamics for all water molecules in the system. Moreover, our approach quantifies the anomalous dynamics of a water molecule, which enables users to compare between different systems. In addition to the applicability, our approach has computational efficiency because it never calculates interactions with any other molecules. Experiments on five different systems of molecular dynamics simulations illustrate that our approach successfully detects the change points of water-molecule dynamics. These results demonstrate that our approach is a useful tool and provides a better understanding of dynamics of water molecules.

© 2018 The Author(s). Truncation is still chosen for many long-range intermolecular interaction calculations to efficiently compute free-boundary systems, macromolecular systems and net-charge molecular systems, for example. Advanced truncation methods have been developed for long-range intermolecular interactions. Every truncation method can be implemented as one of two basic cut-off schemes, namely either an atom-based or a group-based cut-off scheme. The former computes interactions of "atoms" inside the cut-off radius, whereas the latter computes interactions of "molecules" inside the cut-off radius. In this work, the effect of group-based cut-off is investigated for isotropic periodic sum (IPS) techniques, which are promising cut-off treatments to attain advanced accuracy for many types of molecular system. The effect of group-based cut-off is clearly different from that of atom-based cut-off, and severe artefacts are observed in some cases. However, no severe discrepancy from the Ewald sum is observed with the extended IPS techniques.

© 2017 Informa UK Limited, trading as Taylor & Francis Group. A homogeneous metastable liquid system and a heterogeneous system with an immersed impurity were used to investigate the cavitation and crystallisation characteristics by molecular dynamics. An isochoric quench was conducted to the systems, which initially produced a cavity, where the entire system subsequently crystallised. The systems with the impurities showed an overall increase in the crystal nucleation rate and a modest but clear shape effect was observed. Similar to previous droplet condensation studies, a clear curvature effect was observed to influence the rate of the phenomenon. At the onset of quenching, crystallisation occurred on the faces of the seed, so a flat surface promoted local crystallisation, which propagated the formation of the cavity, and thereafter increased the density of the metastable liquid, so to advance overall crystallisation within the system.

© 2018 the Owner Societies. Photovoltaics is one of the key areas in renewable energy research with remarkable progress made every year. Here we consider the case of a photoactive material and study its structural composition and the resulting consequences for the fundamental processes driving solar energy conversion. A multiscale approach is used to characterize essential molecular properties of the light-absorbing layer. A selection of bulk-representative pairs of donor/acceptor molecules is extracted from the molecular dynamics simulation of the bulk heterojunction and analyzed at increasing levels of detail. Significantly increased ground state energies together with an array of additional structural characteristics are identified that all point towards an auxiliary role of the material's structural organization in mediating charge-transfer and -separation. Mechanistic studies of the type presented here can provide important insights into fundamental principles governing solar energy conversion in next-generation photovoltaic devices.