Multi-level Meta-workflows: New Concept for Regularly Occurring Tasks in Quantum Chemistry

Background: In Quantum Chemistry, many tasks are reoccurring frequently, e.g. geometry optimizations, benchmarking series etc. Here, workflows can help to reduce the time of manual job definition and output extraction. These workflows are executed on computing infrastructures and may require large computing and data resources. Scientific workflows hide these infrastructures and the resources needed to run them. It requires significant efforts and specific expertise to design, implement and test these workflows. Significance: Many of these workflows are complex and monolithic entities that can be used for particular scientific experiments. Hence, their modification is not straightforward and it makes almost impossible to share them. To address these issues we propose developing atomic workflows and embedding them in meta-workflows. Atomic workflows deliver a well-defined research domain specific function. Publishing workflows in repositories enables workflow sharing inside and/or among scientific communities. We formally specify atomic and meta-workflows in order to define data structures to be used in repositories for uploading and sharing them. Additionally, we present a formal description focused at orchestration of atomic workflows into meta-workflows. Conclusions: We investigated the operations that represent basic functionalities in Quantum Chemistry and developed that relevant atomic workflows and combined them into meta-workflows. Having these workflows we defined the structure of the Quantum Chemistry workflow library and uploaded these workflows in the SHIWA Workflow Repository

Low-temperature anharmonicity and symmetry breaking in the sodalite

©2018 Walter de Gruyter GmbH, Berlin/Boston 2018. The aluminosilicate iodide sodalite |Na8I2|[AlSiO4]6 was examined by temperature-dependent neutron time-of-flight powder diffraction from 5 K to 290 K and X-ray diffraction from 298 K to 1200 K. The temperature-dependent properties of the mean structure in space group P4 3n were obtained by Rietveld analysis. A negative slope for the thermal expansion coefficient below 50 K could be observed, and the displacement parameters of the iodide ions indicate anharmonic effects. Local structure models (8×8×8 super cells) were refined against pair-distribution functions calculated from total scattering data collected at 5 K, 165 K and 240 K. The results indicate isotropic displacements for all atoms except for I-atoms, showing the effects of an anharmonic potential around this anion at very low temperatures

Thyroxine modifies the effects of growth hormone in Ames dwarf mice

Ames dwarf (df/df) mice lack growth hormone (GH), thyroid stimulating hormone and prolactin. Treatment of juvenile df/df mice with GH alone stimulates somatic growth, reduces insulin sensitivity and shortens lifespan. Early-life treatment with thyroxine (T4) alone produces modest growth stimulation but does not affect longevity. In this study, we examined the effects of treatment of juvenile Ames dwarf mice with a combination of GH + T4 and compared them to the effects of GH alone. Treatment of female and male dwarfs with GH + T4 between the ages of 2 and 8 weeks rescued somatic growth yet did not reduce lifespan to match normal controls, thus contrasting with the previously reported effects of GH alone. While the male dwarf GH + T4 treatment group had no significant effect on lifespan, the female dwarfs undergoing treatment showed a decrease in maximal longevity. Expression of genes related to GH and insulin signaling in the skeletal muscle and white adipose tissue (WAT) of female dwarfs was differentially affected by treatment with GH + T4 vs. GH alone. Differences in the effects of GH + T4 vs. GH alone on insulin target tissues may contribute to the differential effects of these treatments on longevity

Addressing Research Software Sustainability via Institutes

Research software is essential to modern research, but it requires ongoing human effort to sustain: to continually adapt to changes in dependencies, to fix bugs, and to add new features. Software sustainability institutes, amongst others, develop, maintain, and disseminate best practices for research software sustainability, and build community around them. These practices can both reduce the amount of effort that is needed and create an environment where the effort is appreciated and rewarded. The UK SSI is such an institute, and the US URSSI and the Australian AuSSI are planning to become institutes, and this extended abstract discusses them and the strengths and weaknesses of this approach.Comment: accepted by ICSE 2021 BokSS Workshop (https://bokss.github.io/bokss2021/

The effect of calorie restriction on insulin signaling in skeletal muscle and adipose tissue of Ames dwarf mice

Long-living Ames dwarf (df/df) mice are homozygous for a mutation of the Prop1(df) gene. As a result, mice are deficient in growth hormone (GH), prolactin (PRL) and thyrotropin (TSH). In spite of the hormonal deficiencies, df/df mice live significantly longer and healthier lives compared to their wild type siblings. We studied the effects of calorie restriction (CR) on the expression of insulin signaling genes in skeletal muscle and adipose tissue of normal and df/df mice. The analysis of genes expression showed that CR differentially affects the insulin signaling pathway in these insulin target organs. Moreover, results obtained in both normal and Ames dwarf mice indicate more direct effects of CR on insulin signaling genes in adipose tissue than in skeletal muscle. Interestingly, CR reduced the protein levels of adiponectin in the epididymal adipose tissue of normal and Ames dwarf mice, while elevating adiponectin levels in skeletal muscle and plasma of normal mice only. In conclusion, our findings suggest that both skeletal muscle and adipose tissue are important mediators of insulin effects on longevity. Additionally, the results revealed divergent effects of CR on expression of genes in the insulin signaling pathway of normal and Ames dwarf mice