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

Approaches, Derivatives and Applications Vasilios Georgakilas,† Michal Otyepka,‡ Athanasios B. Bourlinos,‡ Vimlesh Chandra, Namdong Kim, K. Christian Kemp, Pavel Hobza,‡,§,⊥ Radek Zboril,*,‡ and Kwang S. Kim* †Institute of Materials Science, NCSR “Demokritos”, Ag. Paraskevi Attikis, 15310 Athens, Greece ‡Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, Korea Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo naḿ. 2, 166 10 Prague 6, Czech Republic

Functionalization of Graphene: Covalent and Non-Covalent Approaches, Derivatives and Applications

Heteroatom doping can endow graphene with various new or improved electromagnetic, physicochemical, optical, and structural properties. This greatly extends the arsenal of graphene materials and their potential for a spectrum of applications. Considering the latest developments, we comprehensively and critically discuss the syntheses, properties and emerging applications of the growing family of heteroatom-doped graphene materials. The advantages, disadvantages, and preferential doping features of current synthesis approaches are compared, aiming to provide clues for developing new and controllable synthetic routes. We emphasize the distinct properties resulting from various dopants, different doping levels and configurations, and synergistic effects from co-dopants, hoping to assist a better understanding of doped graphene materials. The mechanisms underlying their advantageous uses for energy storage, energy conversion, sensing, and gas storage are highlighted, aiming to stimulate more competent applications.

/pdf/heteroatom-doped-graphene-materials-syntheses-properties-and-2gkc1nc0vf.pdf

Heteroatom-doped graphene materials: syntheses, properties and applications

There is enormous interest in the use of graphene-based materials for energy storage. This article discusses the progress that has been accomplished in the development of chemical, electrochemical, and electrical energy storage systems using graphene. We summarize the theoretical and experimental work on graphene-based hydrogen storage systems, lithium batteries, and supercapacitors. Even though the research on the use of graphene for energy storage began very recently, the explosive growth of the research conducted in this area makes this minireview timely.

Graphene-based nanomaterials for energy storage

In this review, we discuss the most recent progress on graphene-related nanomaterials, including doped graphene and derived graphene nanoribbons, graphene oxide, graphane, fluorographene, graphyne, graphdiyne, and porous graphene, from both experimental and theoretical perspectives, and emphasize tuning their stability, electronic and magnetic properties by chemical functionalization.

Graphene-related nanomaterials: tuning properties by functionalization

The spillover phenomenon, which essentially involves transfer of H from a metal catalyst to a graphitic receptor, has been considered promising for efficient hydrogen storage. An open question about the spillover mechanism is how a H atom binds to graphene instead of forming the thermodynamically preferred H2. Usingabinitiocalculations,weshowthatthecatalystsaturationprovidesawaytotheadsorptionofhydrogenon the receptor by increasing the H chemical potential to a spillover favorable range. Although it is energetically unfavorable for the spillover to occur on a pristine graphene surface, presence of a phase of hydrogenated graphene facilitates the spillover by significantly improving the CH binding. We show that thermodynamic spillover can occur, both from the free-standing and from the receptor-supported clusters. Further, the computed energy barrier of the motion of a H from the catalyst to the hydrogenated graphene is small (0.7 eV) and can be overcome at operational temperatures.

/pdf/h-spillover-through-the-catalyst-saturation-an-ab-initio-4che8i35w8.pdf

H-Spillover through the Catalyst Saturation: An Ab Initio Thermodynamics Study.

Using ab initio methods we have investigated the fluorination of graphene and find that different stoichiometric phases can be formed without a nucleation barrier, with the complete “2D-Teflon” CF phase being thermodynamically most stable. The fluorinated graphene is an insulator and turns out to be a perfect matrix-host for patterning nanoroads and quantum dots of pristine graphene. The electronic and magnetic properties of the nanoroads can be tuned by varying the edge orientation and width. The energy gaps between the highest occupied and lowest unoccupied molecular orbitals (HOMO-LUMO) of quantum dots are size-dependent and show a confinement typical of Dirac fermions. Furthermore, we study the effect of different basic coverage of F on graphene (with stoichiometries CF and C4F) on the band gaps, and show the suitability of these materials to host quantum dots of graphene with unique electronic properties.

/pdf/patterning-nanoroads-and-quantum-dots-on-fluorinated-4vzbq3cdbb.pdf

Patterning nanoroads and quantum dots on fluorinated graphene

Using ab initio methods we have investigated the fluorination of graphene and find that different stoichiometric phases can be formed without a nucleation barrier, with the complete "2D-Teflon" CF phase being thermodynamically most stable. The fluorinated graphene is an insulator and turns out to be a perfect matrix-host for patterning nanoroads and quantum dots of pristine graphene. The electronic and magnetic properties of the nanoroads can be tuned by varying the edge orientation and width. The energy gaps between the highest occupied and lowest unoccupied molecular orbitals (HOMO-LUMO) of quantum dots are size-dependent and show a confinement typical of Dirac fermions. Furthermore, we study the effect of different basic coverage of F on graphene (with stoichiometries CF and C$_{4}$F) on the band gaps, and show the suitability of these materials to host quantum dots of graphene with unique electronic properties.

http://absimage.aps.org/image/MAR11/MWS_MAR11-2010-006689.pdf

http://www.owlnet.rice.edu/~biy/Selected%20papers/10DRM_grAphenes.pdf

The ultimate diamond slab: GraphAne versus graphEne

Catalytic nucleation of carbon nanotubes (CNTs) remains a challenge for the theory: Which factors and forces decide if the gathering sp2-network of atoms will adhere to the catalyst particle and fully cover it or the graphitic cap will liberate itself to extend into a hollow filament? This intimate mechanism cannot be seen in experiment, yet it can be investigated through comprehensive molecular dynamics. We systematically vary the adhesion strength (Wad) of the graphitic cap to the catalyst and temperature T (and C diffusion rate). Observations allow us to build a statistically representative map of CNT nucleation and define the conditions for growth or metal encapsulation in a fullerene-shell (catalyst poisoning). It shows clearly that weak Wad, sufficient thermal kinetic energy (high T) or fast C diffusion favor the CNT nucleation. In particular, below 600 K carbon-diffusion on the catalyst surface limits the growth, but at higher T it fully depends on cap lift-off. Informed choice of parameters allowe...

/pdf/nanotube-nucleation-versus-carbon-catalyst-adhesion-probed-32171rsxvu.pdf

Morgana de Avila Ribas

Papers

H-Spillover through the Catalyst Saturation: An Ab Initio Thermodynamics Study.

Patterning nanoroads and quantum dots on fluorinated graphene

Patterning nanoroads and quantum dots on fluorinated graphene

The ultimate diamond slab: GraphAne versus graphEne

Nanotube nucleation versus carbon-catalyst adhesion--probed by molecular dynamics simulations.