An efficient MPI/OpenMP parallelization of the Hartree-Fock method for the second generation of Intel Xeon Phi processor

Modern OpenMP threading techniques are used to convert the MPI-only Hartree-Fock code in the GAMESS program to a hybrid MPI/OpenMP algorithm. Two separate implementations that differ by the sharing or replication of key data structures among threads are considered, density and Fock matrices. All implementations are benchmarked on a super-computer of 3,000 Intel Xeon Phi processors. With 64 cores per processor, scaling numbers are reported on up to 192,000 cores. The hybrid MPI/OpenMP implementation reduces the memory footprint by approximately 200 times compared to the legacy code. The MPI/OpenMP code was shown to run up to six times faster than the original for a range of molecular system sizes.Comment: SC17 conference paper, 12 pages, 7 figure

Intracellular Membrane Transport in Vascular Endothelial Cells

The main component of blood and lymphatic vessels is the endothelium covering their luminal surface. It plays a significant role in many cardiovascular diseases. Tremendous progress has been made in deciphering of molecular mechanisms involved into intracellular transport. However, molecular machines are mostly characterized in vitro. It is important to adapt this knowledge to the situation existing in tissues and organs. Moreover, contradictions have accumulated within the field related to the function of endothelial cells (ECs) and their trans-endothelial pathways. This has induced necessity for the re-evaluation of several mechanisms related to the function of vascular ECs and intracellular transport and transcytosis there. Here, we analyze available data related to intracellular transport within ECs and re-examine several hypotheses about the role of different mechanisms in transcytosis across ECs. We propose a new classification of vascular endothelium and hypotheses related to the functional role of caveolae and mechanisms of lipid transport through ECs.</p

Improving the Theoretical and Methodological Framework for Implementing Digital Twin Technology in Various Sectors of Agriculture

The aim of this study is to systematize and improve the theoretical and methodological framework for implementing digital twin technology. The study focuses on digital twins in agriculture. This paper is designed to solve the scientific problem associated with the development of a methodological framework for the implementation of digital twins in the work of agricultural organizations. Using methods of analysis of socio-economic phenomena and processes on the basis of a set of scientific approaches, economic-statistical analysis, and others, the study considers the importance of digital twins of agricultural machinery and equipment, identifies trends in agriculture determined by digitalization, and suggests promising areas for digital twins of agricultural machinery and equipment. This paper also examines the theoretical basis for the implementation of digital twin technology in the agricultural sector of production. New research results complement the theoretical provisions on the essence of digital twin technology; develop the methodological provisions of digital twin technology, represented by the study of their significance, principles, and features of operation. The study may be seen as academically novel as it reveals the prerequisites for implementing digital technology in agriculture as well as clarifies and improves the theoretical and methodological provisions of the application of digital twin technology in various sectors of agriculture. Doi: 10.28991/ESJ-2023-07-04-05 Full Text: PD

Superpolynomials for toric knots from evolution induced by cut-and-join operators

The colored HOMFLY polynomials, which describe Wilson loop averages in Chern-Simons theory, possess an especially simple representation for torus knots, which begins from quantum R-matrix and ends up with a trivially-looking split W representation familiar from character calculus applications to matrix models and Hurwitz theory. Substitution of MacDonald polynomials for characters in these formulas provides a very simple description of "superpolynomials", much simpler than the recently studied alternative which deforms relation to the WZNW theory and explicitly involves the Littlewood-Richardson coefficients. A lot of explicit expressions are presented for different representations (Young diagrams), many of them new. In particular, we provide the superpolynomial P_[1]^[m,km\pm 1] for arbitrary m and k. The procedure is not restricted to the fundamental (all antisymmetric) representations and the torus knots, still in these cases some subtleties persist.Comment: 23 pages + Tables (51 pages

Morphogenesis of post-Golgi transport carriers

The trans-Golgi network (TGN) is one of the main, if not the main, sorting stations in the process of intracellular protein trafficking. It is therefore of central importance to understand how the key players in the TGN-based sorting and delivery process, the post-Golgi carriers (PGCs), form and function. Over the last few years, modern morphological approaches have generated new insights into the questions of PGC biogenesis, structure and dynamics. Here, we present a view by which the “lifecycle” of a PGC consists of several distinct stages: the formation of TGN tubular export domains (where different cargoes are segregated from each other and from the Golgi enzymes); the docking of these tubular domains onto molecular motors and their extrusion towards the cell periphery along microtubules; the fission of the forming PGC from the donor membrane; and the delivery of the newly formed PGC to its specific acceptor organelle. It is now important to add the many molecular machineries that have been described as operating at the TGN to this “morphofunctional map” of the TGN export process

A comparative study of hydrophilic phosphine hexanuclear rhenium cluster complexes’ toxicity

Octahedral rhenium cluster compound Na2H8[{Re6Se8}(P(C2H4CONH2)(C2H4COO)2)6] has recently emerged as a very promising X-ray contrast agent for biomedical applications. However, the synthesis of this compound is rather challenging due to difficulty to control the hydrolysis of initial P(C2H4CN)3 ligand during the reaction process. Therefore, in this report we compare the in vitro and in vivo toxicity of Na2H8[{Re6Se8}(P(C2H4CONH2)(C2H4COO)2)6] with those of related compounds featuring fully hydrolysed form of the phosphine ligand, namely Na2H14[{Re6Q8}(P(C2H4COO)3)6] (Q = S or Se). Our results demonstrate that cytotoxicity and acute in vivo toxicity of the complex Na2H8[{Re6Se8}(P(C2H4CONH2)(C2H4COO)2)6] solutions were considerably lower than those of compounds with fully hydrolysed ligand P(C2H4COOH)3. Such behavior can be explained by the higher osmolality of Na2H14[{Re6Q8}(P(C2H4COO)3)6] versus Na2H8[{Re6Se8}(P(C2H4CONH2)(C2H4COO)2)6]

A two-step approach for producing an ultrafine-grain structure in Cu-30Zn brass

A two-step approach involving cryogenic rolling and subsequent recrystallization annealing was developed to produce an ultrafine-grain structure in Cu-30Zn brass. The material so processed was characterized by a mean grain size of 0.5 μm, fraction of high-angle boundaries of 90 pct., a weak crystallographic texture, and strength twice that of initial material