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

Metal–Organic Frameworks for Separations

Kenji Sumida, David L. Rogow, Jarad A. Mason, Thomas M. McDonald, Eric D. Bloch, Zoey R. Herm, Tae-Hyun Bae, Jeffrey R. Long

Carbon Dioxide Capture in Metal–Organic Frameworks

Molecular conductance junctions are structures in which single molecules or small groups of molecules conduct electrical current between two electrodes. In such junctions, the connection between the molecule and the electrodes greatly affects the current-voltage characteristics. Despite several experimental and theoretical advances, including the understanding of simple systems, there is still limited correspondence between experimental and theoretical studies of these systems.

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Electron transport in molecular wire junctions.

A series of porous crystalline materials known as metal–organic materials are prepared, and a full sorption study shows that controlled pore size (rather than large surface area) coupled with appropriate chemistry lead to materials exhibiting fast and highly selective CO2 sorption. Metal organic frameworks are porous crystalline materials widely studied as potential gas separation and storage materials for clean energy applications. A general trend in this field has been the development of materials with the largest possible surface area with the aim of maximizing uptake of gases. In this paper the authors generate a series of metal organic frameworks and carry out sorption experiments that suggest that surface area may not be as important as was thought. Rather, pore size, coupled with appropriate chemistry, are the keys to fast CO2 uptake and strong CO2 sorption. Materials designed on these principles attain high selectivity for CO2 over nitrogen, oxygen, methane and hydrogen even in the presence of moisture. The energy costs associated with the separation and purification of industrial commodities, such as gases, fine chemicals and fresh water, currently represent around 15 per cent of global energy production, and the demand for such commodities is projected to triple by 2050 (ref. 1). The challenge of developing effective separation and purification technologies that have much smaller energy footprints is greater for carbon dioxide (CO2) than for other gases; in addition to its involvement in climate change, CO2 is an impurity in natural gas, biogas (natural gas produced from biomass), syngas (CO/H2, the main source of hydrogen in refineries) and many other gas streams. In the context of porous crystalline materials that can exploit both equilibrium and kinetic selectivity, size selectivity and targeted molecular recognition are attractive characteristics for CO2 separation and capture, as exemplified by zeolites 5A and 13X (ref. 2), as well as metal–organic materials (MOMs)3,4,5,6,7,8,9. Here we report that a crystal engineering7 or reticular chemistry5,9 strategy that controls pore functionality and size in a series of MOMs with coordinately saturated metal centres and periodically arrayed hexafluorosilicate (SiF62−) anions enables a ‘sweet spot’ of kinetics and thermodynamics that offers high volumetric uptake at low CO2 partial pressure (less than 0.15 bar). Most importantly, such MOMs offer an unprecedented CO2 sorption selectivity over N2, H2 and CH4, even in the presence of moisture. These MOMs are therefore relevant to CO2 separation in the context of post-combustion (flue gas, CO2/N2), pre-combustion (shifted synthesis gas stream, CO2/H2) and natural gas upgrading (natural gas clean-up, CO2/CH4).

https://sqma.myweb.usf.edu/pages/pictures/publications/P_65.pdf

Porous materials with optimal adsorption thermodynamics and kinetics for CO2 separation

Understanding the molecular details of CO(2)-sorbent interactions is critical for the design of better carbon-capture systems. Here we report crystallographic resolution of CO(2) molecules and their binding domains in a metal-organic framework functionalized with amine groups. Accompanying computational studies that modeled the gas sorption isotherms, high heat of adsorption, and CO(2) lattice positions showed high agreement on all three fronts. The modeling apportioned specific binding interactions for each CO(2) molecule, including substantial cooperative binding effects among the guest molecules. The validation of the capacity of such simulations to accurately model molecular-scale binding bodes well for the theory-aided development of amine-based CO(2) sorbents. The analysis shows that the combination of appropriate pore size, strongly interacting amine functional groups, and the cooperative binding of CO(2) guest molecules is responsible for the low-pressure binding and large uptake of CO(2) in this sorbent material.

http://science.sciencemag.org/content/sci/330/6004/650.full.pdf

Direct Observation and Quantification of CO2 Binding Within an Amine-Functionalized Nanoporous Solid

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.

/pdf/water-proton-configurations-in-structures-i-ii-and-h-mok6z5ej82.pdf

Water proton configurations in structures I, II, and H clathrate hydrate unit cells.

Molecular dynamics simulations are used to study the dynamics and transport properties of 12 room-temperature ionic liquids of the 1-alkyl-3-methylimidazolium [amim]+ (alkyl=methyl, ethyl, propyl, and butyl) family with PF6−, NO3−, and Cl− counterions. The explicit atom transferable force field of Canongia Lopes et al. [J. Phys. Chem. B 108, 2038 (2004)] is used in the simulations. In this first part, the dynamics of the ionic liquids are characterized by studying the mean-square displacement (MSD) and the velocity autocorrelation function (VACF) for the centers of mass of the ions at 400 K. Trajectory averaging was employed to evaluate the diffusion coefficients at two temperatures from the linear slope of MSD(t) functions in the range of 150–300 ps and from the integration of the VACF(t) functions at 400 K. Detailed comparisons are made between the diffusion results from the MSD and VACF methods. The diffusion coefficients from the integration of the VACFs are closer to experimental values than the diff...

Molecular dynamics simulation of imidazolium-based ionic liquids. I. Dynamics and diffusion coefficient

Molecular dynamics simulations are performed to determine the melting points of aluminum nanoparticles of 55−1000 atoms with the Streitz−Mintmire [Phys. Rev. B 1994, 50, 11996] variable-charge electrostatic plus potential. The melting of the nanoparticles is characterized by studying the temperature dependence of the potential energy and Lindemann index. Nanoparticles with less than 850 atoms show bistability between the solid and liquid phases over temperature ranges below the point of complete melting. The potential energy of a nanoparticle in the bistable region alternates between values corresponding to the solid and liquid phases. This bistability is characteristic of dynamic coexistence melting. At higher temperatures, only the liquid state is stable. Nanoparticles with more than 850 atoms undergo a sharp solid−liquid-phase transition characteristic of the bulk solid phase. The variation of the melting point with the effective nanoparticle radius is also determined.

Molecular dynamics simulations of the melting of aluminum nanoparticles.

Molecular-dynamics simulations are used to study the stability of structure II hydrogen clathrates with different H2 guest occupancies. Simulations are done at pressures of 2.5kbars and 1.013bars and for temperatures ranging from 100to250K. For a structure II unit cell with 136 water molecules, H2 guest molecule occupancies of 0–64 are studied with uniform occupancies among each type of cage. The simulations show that at 100K and 2.5kbars, the most stable configurations have single occupancy in the small cages and quadruple occupancy in the large cages. The optimum occupancy for the large cages decreases as the temperature is raised. Double occupancy in the small cages increases the energy of the structures and causes tetragonal distortion in the unit cell. The spatial distribution of the hydrogen guest molecules in the cages is determined by studying the guest-water and guest-guest radial distribution functions at various temperatures.

Saman Alavi

Papers

Direct Observation and Quantification of CO2 Binding Within an Amine-Functionalized Nanoporous Solid

Water proton configurations in structures I, II, and H clathrate hydrate unit cells.

Molecular dynamics simulation of imidazolium-based ionic liquids. I. Dynamics and diffusion coefficient

Molecular dynamics simulations of the melting of aluminum nanoparticles.

Molecular-dynamics study of structure II hydrogen clathrates.