OpenMP in VASP: Threading and SIMD

The Vienna Ab initio Simulation Package (VASP) is a widely used electronic structure code that originally exploits process-level parallelism through the Message Passing Interface (MPI) for work distribution within and across nodes. Architectural changes of modern parallel processors urge programmers to address thread- and data-level parallelism as well to benefit most from the available compute resources within a node. We describe for VASP how to approach for an MPI + OpenMP parallelization including data-level parallelism through OpenMP SIMD constructs together with a generic high-level vector coding scheme. We can demonstrate an improved scalability of VASP and more than 20% gain over the MPI-only version as well as a 2× increased performance of collective operations using the multiple-endpoint MPI feature. The high-level vector coding scheme applied to VASP's general gradient approximation routine gives up 9× performance gain on AVX512 platforms with the Intel compiler.     

Dichroismus und Doppelbrechung des Kalomelkristalls im gesamten Bereich seiner Transparenz

Ohne Zusammenfassung     

CATALOGIC 301C model – validation and improvement

In Europe, REACH legislation encourages the use of alternative in silico methods such as (Q)SAR models. According to the recent progress of Chemical Substances Control Law (CSCL) in Japan, (Q)SAR predictions are also utilized as supporting evidence for the assessment of bioaccumulation potential of chemicals along with read across. Currently, the effective use of read across and QSARs is examined for other hazards, including biodegradability. This paper describes the results of external validation and improvement of CATALOGIC 301C model based on more than 1000 tested new chemical substances of the publication schedule under CSCL. CATALOGIC 301C model meets all REACH requirements to be used for biodegradability assessment. The model formalism built on scientific understanding for the microbial degradation of chemicals has a well-defined and transparent applicability domain. The model predictions are adequate for the evaluation of the ready degradability of chemicals.     

A green synthesis of isatoic anhydrides from isatins with urea-hydrogen peroxide complex and ultrasound

The oxidation of isatins at room temperature, using the cheap and environmentally friendly urea-hydrogen peroxide complex and ultrasonic irradiation, has been investigated. The ultrasonic irradiation dramatically reduces the reaction time. With easy and reproducible reaction procedures, different isatoic anhydrides were obtained in excellent yield and with high purity.     

A Novel Squarylium Dye for Monitoring Oxidative Processes in Lipid Membranes

A novel squaraine probe SQ-1 has been found to be appropriate for monitoring the peroxidation processes in membrane systems. Formation of free radicals was triggered by methemoglobin (metHb) or cytochrome c (cyt c) binding to the model lipid membranes composed of zwitterionic lipid phosphatidylcholine (PC) and anionic lipid cardiolipin (CL). Protein association with the lipid vesicles was followed by drastic quenching of SQ-1 fluorescence. The observed spectral changes were suppressed in the presence of free radical scavengers, butylated hydroxytoluene (BHT) and thiourea (TM) suggesting that SQ-1 decolorization can be attributed to its reactions with lipid radicals.     

Ultrafast excited-state dynamics of DNA fluorescent intercalators: new insight into the fluorescence enhancement mechanism

The excited-state dynamics of the DNA bisintercalator YOYO-1 and of two derivatives has been investigated using ultrafast fluorescence up-conversion and time-correlated single photon counting. The free dyes in water exist in two forms: nonaggregated dyes and intramolecular H-type aggregates, the latter form being only very weakly fluorescent because of excitonic interaction. The excited-state dynamics of the nonaggregated dyes is dominated by a nonradiative decay with a time constant of the order of 5 ps associated with large amplitude motion around the monomethine bridge of the cyanine chromophores. The strong fluorescence enhancement observed upon binding of the dyes to DNA is due to both the inhibition of this nonradiative deactivation of the nonaggregated dyes and the dissociation of the aggregates and thus to the disruption of the excitonic interaction. However, the interaction between the two chromophoric moieties in DNA is sufficient to enable ultrafast hopping of the excitation energy as revealed by the decay of the fluorescence anisotropy. Finally, these dyes act as solvation probes since a dynamic fluorescence Stokes shift was observed both in bulk water and in DNA. Very similar time scales were found in bulk water and in DNA.     

The thermodynamic properties and solvation of lithium halides in N-methylpyrrolidone at 298.15 K

The heat capacity and density of solutions of lithium chloride, bromide, and iodide in N-methylpyrrolidone (I) were determined by calorimetry and densimetry techniques. The standard partial molar heat capacities and volumes ( $\overline {C^\circ _{p2} } $ and $\overline {V^\circ _2 } $ ) of lithium halides in I were calculated. The $\overline {C^\circ _{pi} } $ and $\overline {V^\circ _i } $ values for halogen and lithium ions in I were determined. The coordination numbers of the Li⁺, Cl^?, Br^?, and I^? ions in solutions in I at 298.15 K were calculated.     

Lignans from Linum species of sections Syllinum and Linum

The aryltetralin lignans 6-methoxypodophyllotoxin, 5'-demethoxy-6-methoxypodophyllotoxin as well as the corresponding 8'-epimers 6-methoxypicropodophyllin, and 5'-demethoxy-6-methoxypicropodophyllin were isolated from suspension cultures of Linum cariense, and 4'-demethyl-6-methoxypodophyllotoxin together with 6-methoxypodophyllotoxin from plants of L. tauricum, which both belong to section Syllinum of the genus Linum. Cell cultures of L. altaicum, L. austriacum ssp. euxinum and L. lewisii belonging to section Linum accumulate the naphthalene lignans justicidin B and isojusticidin B. The different lignans were identified by HPLC and spectroscopic methods.     

Active Oxygen in Oxide Catalytic Systems for Environmental Catalysis

Summary. The effect of the synthesis conditions of individual and modified with Mn Ni- and Co-oxide systems on the content and the mobility of their active oxygen has been studied by means of chemical and IR spectral analyses. The results obtained show that the main part of the active oxygen in Ni-oxide system is located on the catalyst’s surface (O_s ^* is approximately 73% of the total active oxygen), while Co-oxide system is characterized by much lower surface active oxygen content. Ni- and Co-oxide systems modified with Mn have comparatively higher active oxygen content as compared to the individual ones. Data of the IR spectral analysis reveal that Mn, as a modifying component, affects the mobility of the active oxygen, the latter contributing to the activity of oxide systems in oxidation processes. The high content of loosely bonded active oxygen formed during the synthesis determines a high catalytic activity of the studied samples in reactions of complete oxidation in the low temperature region.