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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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Initial Experiences with HPE Apollo80 NSP-1 (A64FX) [Slides]
The presentation was targeted to Riken/SNL collaborators.
Cloverleaf on HPE Apollo80 NSP-1 (A64FX) - an update
This presentation gives an update on Cloverleaf performance on A64FX. The backend stalls we reported previously have since been found to be very sensitive to compiler optimization level, at least for CCE. The unrolling and jamming that CCE does with –O3 makes a big difference. Unfortunately we get wrong answers for some of the test cases and need to use –hflex_mp=rigorous to get the 960x960 test to pass. This compiler option disables a lot of the optimizations needed for good performance on A64FX.
Department of Energy NEST Nuclear Search Program (NSP) Maritime Mission
A few high level slides summarizing a mission space for external use (outside USG)
Combinatorial Glycomic Analyses to Direct CAZyme Discovery for the Tailored Degradation of Canola Meal Non-Starch Dietary Polysaccharides
Canola meal (CM), the protein-rich by-product of canola oil extraction, has shown promise as an alternative feedstuff and protein supplement in poultry diets, yet its use has been limited due to the abundance of plant cell wall fibre, specifically non-starch polysaccharides (NSP) and lignin. The addition of exogenous enzymes to promote the digestion of CM NSP in chickens has potential to increase the metabolizable energy of CM. We isolated chicken cecal bacteria from a continuous-flow mini-bioreactor system and selected for those with the ability to metabolize CM NSP. Of 100 isolates identified, Bacteroides spp. and Enterococcus spp. were the most common species with these capabilities. To identify enzymes specifically for the digestion of CM NSP, we used a combination of glycomics techniques, including enzyme-linked immunosorbent assay characterization of the plant cell wall fractions, glycosidic linkage analysis (methylation-GC-MS analysis) of CM NSP and their fractions, bacterial growth profiles using minimal media supplemented with CM NSP, and the sequencing and de novo annotation of bacterial genomes of high-efficiency CM NSP utilizing bacteria. The SACCHARIS pipeline was used to select plant cell wall active enzymes for recombinant production and characterization. This approach represents a multidisciplinary innovation platform to bioprospect endogenous CAZymes from the intestinal microbiota of herbivorous and omnivorous animals which is adaptable to a variety of applications and dietary polysaccharides.
Deploying and Tracking Software with NCCS Software Provisioning
The National Center for Computational Sciences (NCCS) at Oak Ridge National Laboratory has a long history of deploying ground-breaking leadership-class supercomputers for the U.S. Department of Energy. The latest in this line of supercomputers is Frontier, the first supercomputer to break the exascale barrier (1018 floating-point operations per second) on the TOP500 list. Frontier serves a wide array of scientific domains, from traditional simulation-based workloads to newer AI and Machine Learning workloads. To best serve the NCCS user community, NCCS uses Spack to deploy a comprehensive software stack of scientific software packages, providing straightforward access to these packages through Lmod Environment Modules. Maintaining a large software stack while also including multiple new compiler releases each year is a very time-consuming task. Additionally, it is not straightforward to provide a software stack alongside existing vendor-provided software such as the HPE/Cray Programming Environment (CPE), and existing CPE, Spack, and Lmod integration does not allow for multiple versions of GPU libraries such as AMD’s ROCm to be used. To address these challenges and shortcomings, NCCS has developed the NCCS Software Provisioning tool (NSP)1, a tool for deploying and monitoring software stacks on HPC systems. NSP allows NCCS to quickly and effectively provision software stacks from the ground up using template-driven recipes and configuration files. NSP is successfully deployed on Frontier and several other NCCS clusters, enabling the NCCS software team to quickly deploy software stacks for newly-released compilers, expand current software offerings, better support GPU-based software, and monitor Lmod module usage to identify unused software packages that can be removed from the software stack. In this work, we discuss the shortcomings of the previous CPE, Spack, and Lmod usage at NCCS, provide further details on the implementation and structure of NSP, then discuss the benefits that NSP provides.
Mechanistic investigation of SARS-CoV-2 main protease to accelerate design of covalent inhibitors
Targeted covalent inhibition represents one possible strategy to block the function of SARS-CoV-2 Main Protease (M PRO ), an enzyme that plays a critical role in the replication of the novel SARS-CoV-2. Toward the design of covalent inhibitors, we built a covalent inhibitor dataset using deep learning models followed by high throughput virtual screening of these candidates against M PRO . Two top-ranking inhibitors were selected for mechanistic investigations—one with an activated ester warhead that has a piperazine core and the other with an acrylamide warhead. Specifically, we performed a detailed analysis of the free energetics of covalent inhibition by hybrid quantum mechanics/molecular mechanics simulations. Cleavage of a fragment of the non-structured protein (NSP) from the SARS-CoV-2 genome was also simulated for reference. Simulations show that both candidates form more stable enzyme-inhibitor (E-I) complexes than the chosen NSP. It was found that both the NSP fragment and the activated ester inhibitor react with CYS145 of M PRO in a concerted manner, whereas the acrylamide inhibitor follows a stepwise mechanism. Most importantly, the reversible reaction and the subsequent hydrolysis reaction from E-I complexes are less probable when compared to the reactions with an NSP fragment, showing promise for these candidates to be the base for efficient M PRO inhibitors.
MAD: Self-Supervised Masked Anomaly Detection Task for Multivariate Time Series
In this paper, we introduce Masked Anomaly Detection (MAD), a general self-supervised learning task for multivariate time series anomaly detection. With the increasing availability of sensor data from industrial systems, being able to detecting anomalies from streams of multivariate time series data is of significant importance. Given the scarcity of anomalies in real-world applications, the majority of literature has been focusing on modeling normality. The learned normal representations can empower anomaly detection as the model has learned to capture certain key underlying data regularities. A typical formulation is to learn a predictive model, i.e., use a window of time series data to predict future data values. In this paper, we propose an alternative self-supervised learning task. By randomly masking a portion of the inputs and training a model to estimate them using the remaining ones, MAD is an improvement over the traditional left-to-right next step prediction (NSP) task. Our experimental results demonstrate that MAD can achieve better anomaly detection rates over traditional NSP approaches when using exactly the same neural network (NN) base models, and can be modified to run as fast as NSP models during test time on the same hardware, thus making it an ideal upgrade for many existing NSP-based NN anomaly detection models.
Measurement Uncertainty of Highly Asymmetrically Curved Elliptical Mirrors Using Multi-Pitch Slope Stitching Technique
Soft X-ray off-axis elliptical mirrors bring new challenges for X-ray mirror metrology. These highly asymmetrically curved elliptical cylindrical mirrors with a total slope range >10 mrad are extremely challenging to measure. Their total slope range exceeds the measuring range of most angular sensors used for X-ray mirror inspection. To overcome this problem, it is possible to stitch partial slope data by measuring the mirror at different pitch angles (multi-pitch angles). By revisiting the theory of the multi-pitch Nano-accuracy Surface Profiler (NSP), we derive the sampling position error on the mirror surface as a function of the mirror height profile and the measurement error of the pitch rotation center. When measuring “extreme”, highly asymmetrically curved, elliptical mirrors, the calculation of the mirror height profile with iterative reconstruction outperforms the classical “flat assumption” (i.e., assuming that the mirror sag is negligible). As demonstrated by our simulations, a proper tolerance evaluation on the measurement of pitch rotation center is needed to assess the measurement accuracy (systematic error) for these strongly aspherical mirrors using the multi-pitch NSP technique. Taking a real design of an “extreme” elliptical mirror as a case study, we conduct a Monte Carlo simulation to mimic the measurement and characterization process to analyze the impact of several error sources. With the measurement uncertainty of the pitch rotation center, the multi-pitch NSP measurement can estimate the grazing angle θ and the chief ray location x o with their uncertainties, as well as the slope residuals.
Viscosity of the Mercurian Magma Ocean: Implications of Sulfur-Free and Sulfur-Bearing Magma Oceans for Differentiation and Crustal Petrogenesis
Mercury is believed to have had a magma ocean in its early evolution whose solidification dynamics contributed to the planet’s present day surface composition. The surface is characterized by two main geological provinces; the Northern Smooth Plains (NSP),and the Heavily Cratered Terrain (HCT) and Intercratered Terrian (IcT). These provinces are defined by the differences in morphology, composition, and age. The NSP are located in the northern hemisphere and have low Mg/Si, Ca/Si, and S/Si ratios and high Al/Si ratios, and are compositionally analogous to a magnesian alkali basalt. The HCT/IcT cover the majority of the planet and are older than the NSP, and are characterized by high Mg/Si, Ca/Si, and S/Si ratios and low Al/Si ratios. The dichotomy in surface composition motivates the study into the structure of the mantle as a product of magma ocean solidification. Two important and interrelated parameters that determine the efficiency of crystal fractionation during magma ocean solidification are convection vigor and viscosity of the magma ocean. Crystal suspension in a cooling magma ocean could be efficient or inefficient which suggests two end member possibilities for magma ocean solidification. The first is the formation of a compositionally stratified mantle reflecting a cumulate sequence produced along a fractional liquid line of descent. The second is the formation of a well-mixed, batch crystallized mantle by high viscosity and/or vigorously convecting magma ocean. Determining which of these end members, or where on the spectrum between them is most relevant to Mercury’s magma ocean can be experimentally constrained through high P-T falling-sphere viscometry experiments.
Superior removal of As(III) and As(V) from water with Mn-doped β-FeOOH nanospindles on carbon foam
Arsenic pollution of water is one of the severest environmental challenges threatening human health. Iron-based nanomaterials have been demonstrated effective in arsenic removal. However, they generally suffer from low removal efficiency towards highly toxic As(III), loss of active sites owing to agglomeration, and poor reusability. Herein, we report a carbonized melamine foam supported Mn(IV)-doped β-FeOOH nanospindles(CF@Mn-FeOOH NSp) for tackling the technical hurdles. The designed CF@Mn-FeOOH NSp appears as a free-standing monolith through a low-cost and straightforward hydrothermal method. The atomic-scale integration of Mn(IV) into β-FeOOH enables an oxidation-adsorption bifunctionality, where Mn(IV) serves as oxidizer for As(III) and Fe(III) acts as adsorber for As(V). The maximal adsorption capacity for As(V) and As(III) can reach 152 and 107 mg g -1 , respectively. Meanwhile, As in simulated high arsenic groundwater can be decreased to below 10 μg L -1 within 24 h. By simple "filtrating-washing", 85% and 82% of its initial adsorption capacity for As(V) and As(III) can be easily recovered even after 5-cycles reuse. Kinetics and isotherm adsorption study indicate that the arsenic adsorption behavior is mainly through chemical bonding during single-layer adsorbing process. The as-prepared CF@Mn-FeOOH offers a scalable, efficient, and recyclable solution for arsenic removal in groundwater and wastewater from mines and industry.
Synthetic Accessibility and Sodium Ion Conductivity of the Na8–x A x P2O9 (NAP) High-Temperature Sodium Superionic Conductor Framework
Advancement of solid-state electrolytes (SSEs) for all solid-state batteries typically focuses on modification of a known structural framework to improve conductivity, e.g., cation substitution for an immobile ion or varying the concentration of the mobile ions. Novel frameworks can be disruptive by enabling fast ion conduction aided by different structure and diffusion mechanisms, thereby unlocking optimal conductors with different properties. Herein, we perform a high-throughput survey of a structural framework for sodium ion conduction, Na8–x A x P2O9 (NAP), to understand the family’s thermodynamic stability, synthesizability, and ionic conduction. We show that the parent phase Na4TiP2O9 (NTP) undergoes a structural distortion (with accompanying conductivity transition) due to unstable phonons arising from pseudo-Jahn–Teller mode in the 1D titanium chains. Screening compounds in which Ti is substituted by other metals computationally reveal a number of candidates that are predicted to be low in formation energy and have high predicted ionic conductivities. High-throughput experimental and subsequent methodology optimization trials deliver one new compound, Na4SnP2O9 (NSP). X-ray diffraction (XRD), microscopy, and spectroscopy characterization indicate that the room-temperature structure of NSP is similar to the high-temperature, orthorhombic NTP phase but with some small unresolved structural differences. These uncharacterized structural details are speculated to limit the ion conductivity. Temperature-dependent XRD and electrochemical impedance spectroscopy indicate multiple coupled conductivity–structure transitions at a high temperature. We demonstrate the challenges with synthesis development and a priori identification of promising SSE phases as a major bottleneck in new (energy) materials development.
Characterization of two distinct neutrophil serine protease–binding modes within a Staphylococcus aureus innate immune evasion protein family
Extracellular adherence protein domain (EAPs) proteins are a class of innate immune evasion proteins secreted by the human pathogen Staphylococcus aureus. EAPs are potent and selective inhibitors of cathepsin-G (CG) and neutrophil elastase (NE), which are the two most abundant neutrophil serine proteases (NSPs). Previous work from our group has shown that the prototypical EAP, EapH1, relies on plasticity within a single inhibitory site to block the activities of CG and NE. However, whether other EAPs follow similar structure–function relationships is unclear. To address this question, we studied the inhibitory properties of the first (Eap1) and second (Eap2) domains of the modular extracellular adherence protein of S. aureus and determined their structures when bound to CG and NE, respectively. We observed that both Eap1 and Eap2 displayed time-dependent inhibition of CG (on the order of 10 -9 M) and of NE (on the order of 10 -10 M). We also found that whereas the structures of Eap1 and Eap2 bound to CG showed an overall inhibitory mode like that seen previously for EapH1, the structures of Eap1 and Eap2 bound to NE revealed a new inhibitory mode involving a distal region of the EAP domain. Using site-directed mutagenesis of Eap1 and Eap2, along with enzyme assays, we confirmed the roles of interfacial residues in NSP inhibition. Taken together, our work demonstrates that EAPs can form structurally divergent complexes with two closely related serine proteases and further suggests that certain EAPs may be capable of inhibiting two NSPs simultaneously.
Cleavage at the nsp5–nsp6 site of SARS-CoV-2 main protease intermediate precursor is faster from a monomer than a dimer form
Our previous studies of severe acute respiratory syndrome coronavirus 2 main protease (MPro) precursor monomer indicate that the initial N-terminal nonstructural protein (nsp)4/nsp5 cleavage occurs intramolecularly, with a small fraction of the active site loop equilibrium being in the active state. To understand the influence of dimer formation of MPro upon N-terminal cleavage on the subsequent C-terminal nsp5/nsp6 intermolecular cleavage kinetics, the stepwise processing of a monomeric, inactive precursor containing the native terminal cleavage sites of MPro (MBP- (−6) MPro C145A(+3) -GB1-6H, 86.2 kDa) by mature WT MPro (MPro WT ) was investigated. Differential scanning fluorimetry and analytical ultracentrifugation measurements of various MPro constructs suggest that the C145A mutation decreases the dimer dissociation constant (K dimer ) by ∼26-fold, relative to WT C145 and H41A. The monomeric precursor’s nsp4–nsp5 site appears to saturate MProWT’s active sites and cleave faster, followed by a slower first-order cleavage at the C-terminal site. No detectable product resulting from the C-terminal cleavage is observed until most of the N-terminal cleavage is complete. The initial intermediate product (termed MPro C145A-IP ) is a homodimer with an estimated K dimer of <0.05 μM. In contrast, the first-order kinetics observed for the cleavage of the monomeric form of the intermediate product is at least 300 times faster than that of the dimer form. Room-temperature X-ray structure of the MPro C145A-IP –ensitrelvir complex is like that of the MPro WT –ensitrelvir complex and reveals a dynamic C-terminal region including MPro residues 302 to 306. These results are interpreted from the point of view of a mechanism in which nsp5–nsp6 cleavage may occur from a monomeric intermediate, and dimer formation restricts this cleavage.
Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site
Abstract Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the pathogen that causes the disease COVID-19, produces replicase polyproteins 1a and 1ab that contain, respectively, 11 or 16 nonstructural proteins (nsp). Nsp5 is the main protease (M pro ) responsible for cleavage at eleven positions along these polyproteins, including at its own N- and C-terminal boundaries, representing essential processing events for subsequent viral assembly and maturation. We have determined X-ray crystallographic structures of this cysteine protease in its wild-type free active site state at 1.8 Å resolution, in its acyl-enzyme intermediate state with the native C-terminal autocleavage sequence at 1.95 Å resolution and in its product bound state at 2.0 Å resolution by employing an active site mutation (C145A). We characterize the stereochemical features of the acyl-enzyme intermediate including critical hydrogen bonding distances underlying catalysis in the Cys/His dyad and oxyanion hole. We also identify a highly ordered water molecule in a position compatible for a role as the deacylating nucleophile in the catalytic mechanism and characterize the binding groove conformational changes and dimerization interface that occur upon formation of the acyl-enzyme. Collectively, these crystallographic snapshots provide valuable mechanistic and structural insights for future antiviral therapeutic development including revised molecular docking strategies based on M pro inhibition.
Probing remdesivir nucleotide analogue insertion to SARS-CoV-2 RNA dependent RNA polymerase in viral replication
Remdesivir (RDV) prodrug can be metabolized into a triphosphate form nucleotide analogue (RDV-TP) to bind and insert into the active site of viral RNA dependent RNA polymerase (RdRp) to further interfere with viral genome replication. Here in this work, we computationally studied how RDV-TP binds and inserts to the SARS-CoV-2 RdRp active site, in comparison with natural nucleotide substrate adenosine triphosphate (ATP). To do that, we first constructed atomic structural models of an initial binding complex (active site open) and a substrate insertion complex (active site closed), based on high-resolution cryo-EM structures determined recently for SARS-CoV-2 RdRp or non-structural protein (nsp) 12, in complex with accessory protein factors nsp7 and nsp8. By conducting all-atom molecular dynamics simulation with umbrella sampling strategies on the nucleotide insertion between the open and closed state RdRp complexes, our studies show that RDV-TP can initially bind in a comparatively stabilized state to the viral RdRp active site, as it primarily forms base stacking with the template uracil nucleotide (nt +1), which under freely fluctuations supports a low free energy barrier of the RDV-TP insertion (~1.5 kcal mol -1 ). In comparison, the corresponding natural substrate ATP binds initially to the RdRp active site in Watson–Crick base pairing with the template nt, and inserts into the active site with a medium low free energy barrier (~2.6 kcal mol -1 ), when the fluctuations of the template nt are well quenched. The simulations also show that the initial base stacking of RDV-TP with the template can be specifically stabilized by motif C-S759, S682 (near motif B) with the base, and motif G-K500 with the template backbone. Although the RDV-TP insertion can be hindered by motif F-R555/R553 interaction with the triphosphate, the ATP insertion seems to be facilitated by such interactions. The inserted RDV-TP and ATP can be further distinguished by specific sugar interaction with motif B-T687 and motif A-D623, respectively.