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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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DOE OSTI2024

Extreme-scale workflows: A perspective from the JLESC international community

The Joint Laboratory for Extreme-Scale Computing (JLESC) focuses on software challenges in high-performance computing systems to meet the needs of today’s science campaigns, which often require large resources, consist of multiple tasks, and generate vast amounts of data. In this context, extreme-scale workflows have been the key factor in enabling scientific discoveries by helping scientists automate the dependencies and data exchanges between workflow tasks, instead of managing those manually. Here, in this paper, we present representative extreme-scale workflows and feature workflow systems developed by JLESC participating institutions. We present lessons learned while developing these tools, alongside with the open challenges and future research directions in the field of extreme-scale workflows.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

A terminology for scientific workflow systems

The term “scientific workflow” has evolved over the last two decades to encompass a broad range of compositions of interdependent compute tasks and data movements. It has also become an umbrella term for processing in modern scientific applications. Today, many scientific applications can be considered as workflows made of multiple dependent steps, and hundreds of workflow systems have been developed to manage and run these scientific workflows. However, no turnkey solution has emerged from the field to address the diversity of scientific processes and the infrastructure on which they are supposed to be implemented. Instead, new research problems requiring the execution of scientific workflows with some novel feature often lead to the development of an entirely new workflow system. A direct consequence of this situation is that many existing workflow management systems (WMSs) share some salient features, offer similar functionalities, and can manage the same categories of workflows but at the same time also have some distinct capabilities that can be important for specific applications. This situation makes researchers who develop workflows face the complex question of selecting a WMS. This selection can be driven by technical considerations, to find the system that is the most appropriate for their application and for the computing and storage resources available to them, or other factors such as reputation, adoption, strong community support, or long-term sustainability. To address this problem, a group of WMS developers and practitioners joined their efforts to produce a community-based terminology of WMSs. This paper summarizes their findings and introduces this new terminology to characterize WMSs. Furthermore, this terminology is composed of fives axes: workflow structure and characteristics, composition, orchestration, data management, and metadata capture. Each axis comprises several concepts that capture the prominent features of WMSs. Based on this terminology, this paper also presents a classification of 23 existing WMSs according to the proposed axes and terms.

Community-based terminology↗
DOE OSTI2023

An empirical calibration of the serpentine-water oxygen isotope fractionation at T = 25–100°C

The ability to precisely constrain the physical–chemical conditions of serpentinization, such as temperature and fluid source, is limited by the accuracy of calibrations for oxygen isotope fractionation between serpentine and water – i.e., 1000 lnα( serpentine-water ) – which disagree by up to 20‰ when extrapolated to T<200°C. In this study, we present a new empirical calibration of 1000 lnα( serpentine-water ) aiming to improve applications of oxygen isotope geochemistry to very low-T serpentinization (T<100°C). We used the high-spatial resolution capabilities of Secondary Ion Mass Spectrometry (SIMS) to analyze oxygen isotope ratios in mineral pairs of calcite + serpentine, quartz + serpentine and talc + serpentine co-crystallized at scales≤50μm in six serpentinite samples from the Samail ophiolite (Oman). SIMS analysis shows that the mineral pairs are relatively homogenous in oxygen isotope ratios with variability in δ 18 O values ≤2‰ (2s). Clumped isotope thermometry and petrological constraints indicate crystallization temperatures from 25 to 100°C for the investigated samples. These independent constraints on temperature allowed us to derive 1000 lnα( serpentine-water ) by combining Δ 18 O( quartz-serpentine ), Δ 18 O( talc-serpentine ) and Δ 18 O( calcite-serpentine ) measured by SIMS in the investigated samples with Δ 18 O( quartz-water ), Δ 18 O( talc-water ) and Δ 18 O( calcite-water ) calibrations available in the literature. Our empirical calibration of 1000 lnα( serpentine-water ) = 1.04±0.20 (2SE) × 10 6 /T 2 (T in K), from T = 25 to 100°C, is within uncertainty of former high-temperature empirical calibrations extrapolated to T<100°C and matches experimental calibrations when extrapolated to T=250°C. In conclusion, the new serpentine-water calibration enables more accurate reconstructions of fluid-rock interactions occurring during low-temperature serpentinization processes in various tectonic settings.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Tracking alternative versions of the galactose gene network in the genus Saccharomyces and their expansion after domestication

When Saccharomyces cerevisiae grows on mixtures of glucose and galactose, galactose utilization is repressed by glucose, and induction of the GAL gene network only occurs when glucose is exhausted. Contrary to reference GAL alleles, alternative alleles support faster growth on galactose, thus enabling distinct galactose utilization strategies maintained by balancing selection. Here, we report on new wild populations of Saccharomyces cerevisiae harboring alternative GAL versions and, for the first time, of Saccharomyces paradoxus alternative alleles. We also show that the non-functional GAL version found earlier in Saccharomyces kudriavzevii is phylogenetically related to the alternative versions, which constitutes a case of trans-specific maintenance of highly divergent alleles. Strains harboring the different GAL network variants show different levels of alleviation of glucose repression and growth proficiency on galactose. We propose that domestication involved specialization toward thriving in milk from a generalist ancestor partially adapted to galactose consumption in the plant niche.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Discovery of amivantamab (JNJ-61186372), a bispecific antibody targeting EGFR and MET

A bispecific antibody (BsAb) targeting the epidermal growth factor receptor (EGFR) and mesenchymal–epithelial transition factor (MET) pathways represents a novel approach to overcome resistance to targeted therapies in patients with non–small cell lung cancer. In this study, we sequentially screened a panel of BsAbs in a combinatorial approach to select the optimal bispecific molecule. The BsAbs were derived from different EGFR and MET parental monoclonal antibodies. Initially, molecules were screened for EGFR and MET binding on tumor cell lines and lack of agonistic activity toward MET. Hits were identified and further screened based on their potential to induce untoward cell proliferation and cross-phosphorylation of EGFR by MET via receptor colocalization in the absence of ligand. After the final step, we selected the EGFR and MET arms for the lead BsAb and added low fucose Fc engineering to generate amivantamab (JNJ-61186372). The crystal structure of the anti-MET Fab of amivantamab bound to MET was solved, and the interaction between the two molecules in atomic details was elucidated. Amivantamab antagonized the hepatocyte growth factor (HGF)-induced signaling by binding to MET Sema domain and thereby blocking HGF β-chain—Sema engagement. The amivantamab EGFR epitope was mapped to EGFR domain III and residues K443, K465, I467, and S468. Furthermore, amivantamab showed superior antitumor activity over small molecule EGFR and MET inhibitors in the HCC827-HGF in vivo model. Based on its unique mode of action, amivantamab may provide benefit to patients with malignancies associated with aberrant EGFR and MET signaling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Functional analysis of a conserved site mutation in the DNA end processing enzyme PNKP leading to ataxia with oculomotor apraxia type 4 in humans

Polynucleotide kinase 3'-phosphatase (PNKP), an essential DNA end-processing enzyme in mammals with 3'-phosphatase and 5'-kinase activities, plays a pivotal role in multiple DNA repair pathways. Its functional deficiency has been etiologically linked to various neurological disorders. Recent reports have shown that mutation at a conserved glutamine (Gln) in PNKP leads to late-onset ataxia with oculomotor apraxia type 4 (AOA4) in humans and embryonic lethality in pigs. However, the molecular mechanism underlying such phenotypes remains elusive. Here, we report that the enzymatic activities of the mutant versus WT PNKP are comparable; however, cells expressing mutant PNKP and peripheral blood mononuclear cells (PBMCs) of AOA4 patients showed a significant amount of DNA double-strand break accumulation and consequent activation of the DNA damage response. Further investigation revealed that the nuclear localization of mutant PNKP is severely abrogated, and the mutant proteins remain primarily in the cytoplasm. Western blot analysis of AOA4 patient-derived PBMCs also revealed the presence of mutated PNKP predominantly in the cytoplasm. To understand the molecular determinants, we identified that mutation at a conserved Gln residue impedes the interaction of PNKP with importin alpha but not with importin beta, two highly conserved proteins that mediate the import of proteins from the cytoplasm into the nucleus. Collectively, our data suggest that the absence of PNKP in the nucleus leads to constant activation of the DNA damage response due to persistent accumulation of double-strand breaks in the mutant cells, triggering death of vulnerable brain cells—a potential cause of neurodegeneration in AOA4 patients.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

The dependence of aluminum lattice orientation on semiconductor lattice parameter in planar InAs/Al hybrid heterostructures

We present a detailed study of 7-nm thick Al layers epitaxially grown on In x Al 1-x As or Al 1-x Ga x Sb y As 1-y (0 0 1) semiconductors using high-resolution transmission electron microscopy (HRTEM) and synchrotron X-ray diffraction (XRD). These techniques provide high spatial and high reciprocal space resolution information about Al lattice orientations and interfacial structure, highlighting the existence of a strong correlation between the surface lattice parameter of the semiconductor and the normal orientation of the aluminum film. The normal orientation of Al layers is found to be [1 1 1] when the in-plane semiconductor surface lattice parameter, a S , is smaller than 5.98 Å, and is [1 1 0] when aS is larger than this value. In the transition between these lattice parameters where one orientation is preferred, both orientations may be observed. Concomitant with the change in normal orientation is an inversion in the strain state of the aluminum film. When the normal orientation is [1 1 1], the Al film is compressively strained; while for [1 1 0] normal orientations, the Al in-plane strain is tensile. An energy balance model, accounting for surface, interfacial, side-face, and strain energy, and the registry of lattice planes across the semiconductor/aluminum interface provide explanations for the observed normal orientation and strain inversion.

36 MATERIALS SCIENCE↗