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

Isolated atoms featuring unique reactivity are at the heart of enzymatic and homogeneous catalysts. In contrast, although the concept has long existed, single-atom heterogeneous catalysts (SACs) have only recently gained prominence. Host materials have similar functions to ligands in homogeneous catalysts, determining the stability, local environment, and electronic properties of isolated atoms and thus providing a platform for tailoring heterogeneous catalysts for targeted applications. Within just a decade, we have witnessed many examples of SACs both disrupting diverse fields of heterogeneous catalysis with their distinctive reactivity and substantially enriching our understanding of molecular processes on surfaces. To date, the term SAC mostly refers to late transition metal-based systems, but numerous examples exist in which isolated atoms of other elements play key catalytic roles. This review provides a compositional encyclopedia of SACs, celebrating the 10th anniversary of the introduction of this term. By defining single-atom catalysis in the broadest sense, we explore the full elemental diversity, joining different areas across the whole periodic table, and discussing historical milestones and recent developments. In particular, we examine the coordination structures and associated properties accessed through distinct single-atom-host combinations and relate them to their main applications in thermo-, electro-, and photocatalysis, revealing trends in element-specific evolution, host design, and uses. Finally, we highlight frontiers in the field, including multimetallic SACs, atom proximity control, and possible applications for multistep and cascade reactions, identifying challenges, and propose directions for future development in this flourishing field.

Single-Atom Catalysts across the Periodic Table.

Furfural and 5-hydroxymethylfurfural stand out as bridges connecting biomass raw materials to the biorefinery industry. Their reductive transformations by hydroconversion are key routes toward a wide variety of chemicals and biofuels, and heterogeneous catalysis plays a central role in these reactions. The catalyst efficiency highly depends on the nature of metals, supports, and additives, on the catalyst preparation procedure, and obviously on reaction conditions to which catalyst and reactants are exposed: solvent, pressure, and temperature. The present review focuses on the roles played by the catalyst at the molecular level in the hydroconversion of furfural and 5-hydroxymethylfurfural in the gas or liquid phases, including catalytic hydrogen transfer routes and electro/photoreduction, into oxygenates or hydrocarbons (e.g., furfuryl alcohol, 2,5-bis(hydroxymethyl)furan, cyclopentanone, 1,5-pentanediol, 2-methylfuran, 2,5-dimethylfuran, furan, furfuryl ethers, etc.). The mechanism of adsorption of the ...

How Catalysts and Experimental Conditions Determine the Selective Hydroconversion of Furfural and 5-Hydroxymethylfurfural.

The Pearl River Estuary is a subtropical estuary and the second largest in China based on discharge volume from the Pearl River. Processes in the estuary vary spatially and temporally (wet vs dry season). In the dry season at the head of the estuary, hypoxic and nearly anoxic conditions occur and NH4 reaches > 600 mu M, NO3 is similar to 300 mu M and nitrite is similar to 60 mu M indicating that nitrification and denitrification may be important dry season processes in the region extending 40 km upstream of the Humen outlet. There are very few biological studies conducted in this upper section of the estuary in either the dry or wet seasons and hence there is a need for further research in this region of the river. In the wet season, the salinity wedge extends to the Hongqimen outlet and oxygen is low (35-80% saturation). Nitrate is similar to 100 mu M, silicate similar to 140 mu M: and phosphate is relatively low at similar to 0.5 mu M, yielding an N:P ratio up to similar to 200:1 in summer. Nutrients decrease in the lower estuary and primary productivity may become potentially P-limited. Eutrophication is not as severe as one would expect from the nutrient inputs from the Pearl River and from Hong Kong's sewage discharge. This estuary shows a remarkable capacity to cope with excessive nutrients. Physical processes such as river discharge, tidal flushing, turbulent dispersion, wind-induced mixing, and estuarine circulation play an important role in controlling the production and accumulation of algal blooms and the potential occurrence of hypoxia. Superimposed on the physical processes of the estuary are the chemical and biological processes involved in the production of the bloom. For example, the 100N:1P ratio indicates that P potentially limits the amount of algal biomass (and potential biological oxygen demand) in summer. While extended periods of hypoxia are rare in Hong Kong waters, episodic events have been reported to occur during late summer due to factors such as low wind, high rainfall and river discharge which result in strong density stratification that significantly dampens vertical mixing processes. Nutrient loads are likely to change over the next several decades and monitoring programs are essential to detect the response of the ecosystem due to the future changes in nutrient loading and the ratio of nutrients. (c) 2008 Elsevier Ltd. All rights reserved.

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Physical–biological coupling in the Pearl River Estuary

Propylene is an important building block for enormous petrochemicals including polypropylene, propylene oxide, acrylonitrile and so forth. Propane dehydrogenation (PDH) is an industrial technology for direct propylene production which has received extensive attention in recent years. With the development of dehydrogenation technologies, the efficient adsorption/activation of propane and subsequential desorption of propylene on the surfaces of heterogeneous catalysts remain scientifically challenging. This review describes recent advances in the fundamental understandings of the PDH process in terms of emerging technologies, catalyst development and new chemistry in regulating the catalyst structures and inhibiting the catalyst deactivation. The active sites, reaction pathways and deactivation mechanisms of PDH over metals and metal oxides as well as their dependent factors are also analysed and discussed, which is expected to enable efficient catalyst design for minimizing the reaction barriers and controlling the selectivity towards propylene. The challenges and perspectives of PDH over heterogeneous catalysts are also proposed for further development.

Propane dehydrogenation: catalyst development, new chemistry, and emerging technologies

This paper examines spatial and temporal variations of mesozooplankton abundance, biomass and community structure during three cruises of July 2002 (summer), January 2003 (winter), and April 2003 (spring) in the Pearl River estuary, China. Zooplankton abundance and biomass fluctuated widely and showed distinct heterogeneity in the Pearl River estuary. A total of 154 species were identified during three surveys. The number of zooplankton species richness was strongly linked to salinity. Hierarchical cluster analysis identified three zooplankton groups during this study. Estuarine, neritic and pelagic groups corresponded to the upper, middle and lower reaches in the Pearl River estuary. The difference among groups could be mainly ascribed to changes in the relative contributions of the dominant species. The fluctuations in the zooplankton abundance, biomass and community structure were determined by the interactive effects of freshwater inflow, tidal and coastal currents, chlorophyll a, salinity and temperature. Significant spatial variability in the distribution of zooplankton species, abundance and biomass can be ascribed to the virtual presence of a horizontal gradient in salinity. (c) 2005 Elsevier Ltd. All rights reserved.

Spatial and temporal variations of mesozooplankton in the Pearl River estuary, China

Covalent-bonding to irreducible SiO2 leads to high-loading and atomically dispersed metal catalysts

Tailoring Pt locations in KL zeolite by improved atomic layer deposition for excellent performance in n-heptane aromatization

Deactivation of Pt/KL catalyst during n-heptane aromatization reaction

Elucidation of intrinsic working principle of single-phase iron carbide and its facet-dependent catalytic behavior remains a substantial challenge in iron-catalyzed Fischer-Tropsch synthesis. Here, we provided in-depth understanding of the iron carbide phase-dependent and facet-dependent properties on theoretically established Fe5C2 particle model through an approach combining Wulff construction, density functional theory, and microkinetics. We studied two key probe reactions, C2 formation via C1+C1 coupling and CH4 formation, by monitoring surface-dependent thermodynamics and microkinetics. Integration of results thereby allows us to assess the macroscopic catalytic properties at single particle level and evaluate contribution from individual exposed surface. The surface (111) and (10 1 - ) are kinetically more viable for C2 formation, whereas CH4 formation is kinetically more facile on surface (010), (110) and (11 1 - ). This study enriches the knowledge of the intrinsic working mechanism for single-phase iron carbide and provides fundamental insights into rational design of improved iron-based Fischer-Tropsch synthesis catalysts.

Junqing Yin

Papers

Spatial and temporal variations of mesozooplankton in the Pearl River estuary, China

Covalent-bonding to irreducible SiO2 leads to high-loading and atomically dispersed metal catalysts

Tailoring Pt locations in KL zeolite by improved atomic layer deposition for excellent performance in n-heptane aromatization

Deactivation of Pt/KL catalyst during n-heptane aromatization reaction

Theoretical exploration of intrinsic facet-dependent CH4 and C2 formation on Fe5C2 particle