Optimizing the Gravitational Tree Algorithm for Many-Core Processors

Gravitational $N$-body simulations calculate numerous interactions between particles. The tree algorithm reduces these calculations by constructing a hierarchical oct-tree structure and approximating gravitational forces on particles. Over the last three decades, the tree algorithm has been extensively used in large-scale simulations, and its parallelization in distributed memory environments has been well studied. However, recent supercomputers are equipped with many CPU cores per node, and optimizations of the tree construction in shared memory environments are becoming crucial. We propose a novel tree construction method in contrast to the conventional top-down approach. It first creates all leaf cells without traversing the tree and then constructs the remaining cells by a bottom-up approach. We evaluated the performance of our novel method on the supercomputer Fugaku and an Intel machine. On a single thread, our method accelerates one of the most time-consuming processes of the conventional tree construction method by a factor of above 3.0 on Fugaku and 2.2 on the Intel machine. Furthermore, as the number of threads increases, our parallel tree construction time reduces considerably. Compared to the conventional sequential tree construction method, we achieve a speedup of over 45 on 48 threads of Fugaku and more than 56 on 112 threads of the Intel machine. In stark contrast to the conventional method, the tree construction with our method no longer constitutes a bottleneck in the tree algorithm, even when using many threads.Comment: 12 pages, 6 figures, accepted by MNRA

Tissue and Cellular Localization of NADH-Dependent Glutamate Synthase Protein in Leaves of Spinach

Tissue and cellular localization of NADH-dependent glutamate synthase (NADH-GOGAT, EC1.4. 1.14) in young leaves of dicotyledonous spinach (Spinacia oleacea) was investigated using the immunocytological method with an affinity-purified anti-NADH-GOGAT immunoglobulin G. Immunoblotting analysis showed this antibody specifically cross-reacted with NADH-GOGAT protein in crude soluble proteins from young leaf blades of spinach. When transverse sections (10μm in thickness) prepared from the paraffin-embedded young leaf blades of spinach were stained with the anti-NADH-GOGAT antibody, strong signals for NADH-GOGAT protein were detected in companion cells of large vascular bundles. Weak signals for the NADH-GOGAT protein were also detected in vascular parenchyma cells and mesophyll cells of young leaves. Ferredoxin (Fd)-GOGAT (EC 1.4.7.1) protein was mainly located in mesophyll cells and signals for the protein were also detected in companion cells and xylemparenchyma cells of large vascular bundles. By the way, in young leaf blades of monocotyledonous rice, NADH-GOGAT protein specifically located in vascular cells and Fd-GOGAT protein was abundant in mesophyll cells (Hayakawa et al., 1994). The differences of functions in young leaves for NADH-GOGAT proteins between monocotyledonous rice and dicotyledonous spinach are discussed

Mammalian Lgl Forms a Protein Complex with PAR-6 and aPKC Independently of PAR-3 to Regulate Epithelial Cell Polarity

AbstractBackground: Epithelial cells have apicobasal polarity and an asymmetric junctional complex that provides the bases for development and tissue maintenance. In both vertebrates and invertebrates, the evolutionarily conserved protein complex, PAR-6/aPKC/PAR-3, localizes to the subapical region and plays critical roles in the establishment of a junctional complex and cell polarity. In Drosophila, another set of proteins called tumor suppressors, such as Lgl, which localize separately to the basolateral membrane domain but genetically interact with the subapical proteins, also contribute to the establishment of cell polarity. However, how physically separated proteins interact remains to be clarified.Results: We show that mammalian Lgl competes for PAR-3 in forming an independent complex with PAR-6/aPKC. During cell polarization, mLgl initially colocalizes with PAR-6/aPKC at the cell-cell contact region and is phosphorylated by aPKC, followed by segregation from apical PAR-6/aPKC to the basolateral membrane after cells are polarized. Overexpression studies establish that increased amounts of the mLgl/PAR-6/aPKC complex suppress the formation of epithelial junctions; this contrasts with the previous observation that the complex containing PAR-3 promotes it.Conclusions: These results indicate that PAR-6/aPKC selectively interacts with either mLgl or PAR-3 under the control of aPKC activity to regulate epithelial cell polarity

Preparation and characterization of SiO2-coated submicron-sized L10 Fe-Pt particles

The development of magnets with higher performance is attracting increasing interest. The optimization of their microstructure is essential to enhance their properties, and a microstructure comprising magnetically isolated hard magnetic grains of a single-domain size has been proposed as an ideal structure for enhancing the coercivity of magnets. To obtain magnets with an ideal structure, we consider the fabrication of magnets by an approach based on core/shell nanoparticles with a hard magnetic core and a non-magnetic shell. In this study, to obtain particles for our proposed approach, we attempted to fabricate L10 Fe-Pt/SiO2-core/shell particles with submicron-sized cores less than the critical single-domain size. The fabrication of such core/shell particles was confirmed from morphology observations and XRD analysis of the particles. Although the formation of more desirable core/shell particles with submicron-sized single-crystal cores in the single-domain size range was not achieved, the fabricated core/shell particles showed a high coercivity of 25 kOe