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

Single-layer metal dichalcogenides are two-dimensional semiconductors that present strong potential for electronic and sensing applications complementary to that of graphene.

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Electronics and optoelectronics of two-dimensional transition metal dichalcogenides.

We present a method for calculating the stability of reaction intermediates of electrochemical processes on the basis of electronic structure calculations. We used that method in combination with detailed density functional calculations to develop a detailed description of the free-energy landscape of the electrochemical oxygen reduction reaction over Pt(111) as a function of applied bias. This allowed us to identify the origin of the overpotential found for this reaction. Adsorbed oxygen and hydroxyl are found to be very stable intermediates at potentials close to equilibrium, and the calculated rate constant for the activated proton/electron transfer to adsorbed oxygen or hydroxyl can account quantitatively for the observed kinetics. On the basis of a database of calculated oxygen and hydroxyl adsorption energies, the trends in the oxygen reduction rate for a large number of different transition and noble metals can be accounted for. Alternative reaction mechanisms involving proton/electron transfer to ...

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Origin of the Overpotential for Oxygen Reduction at a Fuel-Cell Cathode

TiO2 photocatalysis and related surface phenomena

Platinum-based heterogeneous catalysts are critical to many important commercial chemical processes, but their efficiency is extremely low on a per metal atom basis, because only the surface active-site atoms are used. Catalysts with single-atom dispersions are thus highly desirable to maximize atom efficiency, but making them is challenging. Here we report the synthesis of a single-atom catalyst that consists of only isolated single Pt atoms anchored to the surfaces of iron oxide nanocrystallites. This single-atom catalyst has extremely high atom efficiency and shows excellent stability and high activity for both CO oxidation and preferential oxidation of CO in H-2. Density functional theory calculations show that the high catalytic activity correlates with the partially vacant 5d orbitals of the positively charged, high-valent Pt atoms, which help to reduce both the CO adsorption energy and the activation barriers for CO oxidation.

Single-atom catalysis of CO oxidation using Pt1/FeOx

The interaction of nitric oxide, NO, with the stepped Pd(211) surface is studied using density functional theory slab calculations. Calculated chemisorption energies and geometries reveal that surface sites are not populated in a sequential manner as the NO coverage is increased. This comes about through mutual NO interactions that reorganize the adsorbates during the adsorption. The finding of nonsequential site population allows a reinterpretation of existing experimental data.

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Adsorbate Reorganization at Steps: NO on Pd(211)

The interaction of graphene with various metal surfaces is investigated using density functional theory and the meta-generalized gradient approximation (MGGA) M06-L functional. We demonstrate that this method is of comparable accuracy to the random-phase approximation (RPA). With M06-L we study large systems inaccessible to RPA with H adsorbed on graphene on a selected strongly (Ni) and a selected weakly (Pt) interacting substrate. Very stable graphane-like clusters, where every other C atom binds to a H atom above and every other to a metal atom below, are found on both substrates. Such graphane-like clusters have been proposed to be responsible for opening a band gap in graphene. On Ni we find that the binding energies of the H clusters are almost constant with the cluster size, whereas on Pt the binding energies increase with the cluster size. Comparing the Perdew-Burke-Ernzerhof and M06-L functionals we demonstrate the importance of accounting for dispersive interactions.

https://phys.au.dk/fileadmin/site_files/forskning/surfacedynamics/pdf/andersen_2012.pdf

Graphene on metal surfaces and its hydrogen adsorption: A meta-GGA functional study

Promoting and poisoning effects of Na and Cl coadsorption on CO oxidation over MgO-supported Au nanoparticles

Pathways for the dissociative adsorption of NO on the planar Pd(111) and the stepped Pd(211) surfaces are calculated using density functional theory. The pathways with the smallest energy barriers for the dissociation are found to be very similar on the two types of Pd surfaces. The stepped surface exhibits the smallest energy barrier, because this surface binds the molecular NO and the atomic N and O, more strongly than does the flat surface.

Reactivity of a stepped surface NO dissociation on Pd(211)

Surface coordination networks formed by co- adsorption of metal atoms and organic ligands have interesting properties, for example regarding catalysis and data storage. Surface coordination networks studied to date have typically been based on single metal atom centers. The formation of a novel surface coordination network is now demonstrated that is based on network nodes in the form of clusters consisting of three Cu adatoms. The network forms by deposition of tetrahydroxybenzene (THB) on Cu(111) under UHV condi- tions. As shown from a combination of scanning tunneling microscopy, X-ray photoelectron spectroscopy, and density functional theory calculations, all four hydroxy groups of THB dehydrogenate upon thermal activation at 440 K. This highly reactive ligand binds to Cu adatom trimers, which are resolved by high-resolution STM. The network creates an ordered array of mono-dispersed metal clusters constituting a two-dimen- sional analogue of metal-organic frameworks.

Bjørk Hammer

Papers

Adsorbate Reorganization at Steps: NO on Pd(211)

Graphene on metal surfaces and its hydrogen adsorption: A meta-GGA functional study

Promoting and poisoning effects of Na and Cl coadsorption on CO oxidation over MgO-supported Au nanoparticles

Reactivity of a stepped surface NO dissociation on Pd(211)

A surface coordination network based on copper adatom trimers.