Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

Intermolecular And Surface Forces

Structure and nanostructure in ionic liquids.

Roles of water for chemical reactions in high-temperature water

The past few decades have shown a rapid and continuous exhaustion of the available energy resources which may lead to serious energy global crises. Researchers have been focusing on developing new and renewable energy resources to meet the increasing fuel demand and reduce greenhouse gas emissions. A surge of research effort is also being directed towards replacing fossil fuel based vehicles with hybrid and electric alternatives. Energy storage is now seen as a critical element in future "smart grid and electric vehicle" applications. Electrochemical energy storage systems offer the best combination of efficiency, cost and flexibility, with redox flow battery systems currently leading the way in this aspect. In this work, a panoramic overview is presented for the various redox flow battery systems and their hybrid alternatives. Relevant published work is reported and critically discussed. A comprehensive study of the available technologies is conducted in terms of technical aspects as well as economic and environmental consequences. Some of the flow battery limitations and technical challenges are also discussed and a range of further research opportunities are presented. Of the flow battery technologies that have been investigated, the all-vanadium redox flow battery has received the most attention and has shown most promise in various pre-commercial to commercial stationary applications to date, while new developments in hybrid redox fuel cells are promising to lead the way for future applications in mechanically and electrically "refuelable" electric vehicles.

https://iopscience.iop.org/article/10.1149/1.3599565/pdf

Progress in Flow Battery Research and Development

We investigate the dissociation of methane hydrate in liquid water using molecular dynamics simulations. As dissociation of the hydrate proceeds, methane molecules are released into the aqueous phase and eventually they form bubbles. It is shown that this bubble formation, which causes change in the methane concentration in the aqueous phase, significantly affects the dissociation kinetics of methane hydrate. A large system size employed in this study makes it possible to analyze the effects of the change in the methane concentration and the formation of bubbles on the dissociation kinetics in detail. It is found that the dissociation rate decreases with time until the bubble formation and then it turns to increase. It is also demonstrated that methane hydrate can exist as a metastable superheated solid if there exists no bubble.

Effect of bubble formation on the dissociation of methane hydrate in water: a molecular dynamics study.

Thermodynamic properties of aqueous mixtures of hydrophilic compounds 2. Aminoethanol and its methyl derivatives

Membrane area fluctuation of the lipid bilayer has been investigated based upon two-dimensional Voronoi tessellation analysis for the centers of mass of the lipid molecules projected on the bilayer plane. Long-time trajectories of the molecules used in the analysis have been generated by molecular dynamics calculations. The single-molecular area defined by Voronoi polygon showed a broad Gaussian distribution, from which area distribution of the membrane composed of N lipid molecules may satisfactorily be predicted. The fluctuation was found to be caused mainly by thermal motions of the alkyl chains. The number of gauche conformation and alkyl chain length was strongly correlated to the molecular area. Head group motions, however, showed little contribution to the fluctuation. Geometry of Voronoi polygons and the number of nearest neighbor molecules showed rather broad distribution due to the thermal fluctuation. This is in contrast to the structure found in the ripple, gel, and crystal phases. Formation of large pores in the membrane was also investigated.

A Voronoi analysis of lipid area fluctuation in a bilayer

A series of molecular dynamics calculations for water has been carried out along an isochore at 1 g/cm3 and an isotherm at 600 K in order to examine microscopic properties of water in the sub- and supercritical states. A polarizable potential model proposed by Dang (RPOL model) was employed to take into account the state dependence of intermolecular interaction. Along the isochore, fluid structure changes from tetrahedral icelike structure at room temperature to simple-liquidlike one at high temperatures. Orientational correlation between a tagged molecule and its neighbors is reduced substantially with increasing temperature, though hydrogen bonds between two molecules persist even at 600 K. As temperature increases, the number of the hydrogen bonds per molecule decreases monotonically from 3.2 at 280 K to 1.9 at 600 K. The activation barrier for diffusion at 600 K is about half as large as that at room temperature. A collective polarization relaxation loses collective character above the temperature whe...

A molecular dynamics study of sub- and supercritical water using a polarizable potential model

By the use of umbrella‐sampling technique in the Monte Carlo method proposed by Torrie and Valleau, reliable data have been established for the Helmoholtz free energy of mixing in some selected models of Lennard‐Jones liquid mixtures. The variational method in perturbation theory is found to account for these Monte Carlo data. Validity of some representative semiempirical theories is discussed and it is found that none of them can reproduce the present Monte Carlo results reasonably well. Finally the phase stability of the present models is discussed in terms of both the free energy of mixing and local composition values recently obtained from our molecular dynamics calculations.

Susumu Okazaki

Papers

Effect of bubble formation on the dissociation of methane hydrate in water: a molecular dynamics study.

Thermodynamic properties of aqueous mixtures of hydrophilic compounds 2. Aminoethanol and its methyl derivatives

A Voronoi analysis of lipid area fluctuation in a bilayer

A molecular dynamics study of sub- and supercritical water using a polarizable potential model

Free energy of mixing, phase stability, and local composition in Lennard‐Jones liquid mixtures