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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Atom Probe characterization of neutron irradiated commercial ZIRLO® and AXIOM X2® alloys

As part of the Mechanistic Understanding of ZIrconium Corrosion (MUZIC) program, this team has been instrumental to obtain EPRI and Westinghouse sponsorships to prepare the neutron irradiated ZIRLO® and X2® from Vogtle nuclear power plant and ship them from Studsvik’s (Sweden) hot cells to Idaho National Laboratory (INL) to be part of the NSUF library. The uniqueness of these sets of neutron irradiated alloys is that they are at the same two extremes of the fuel cycles, allowing us to study the microchemistry evolution as a function of irradiation doses, exposure time and solute content. Advanced commercial Zirconium-Niobium (Zr-Nb) alloys, such as ZIRLO® and AXIOM®, have been developed by Westinghouse to enhance the corrosion resistance of fuel cladding material for longer service time. This study specifically aims at investigating the neutron irradiation induced Nb redistribution in AXIOM® X2® to understand the effect of neutron irradiation induced microchemistry changes and the irradiation enhanced corrosion resistance observed in ZrNb alloys. The detailed sample information on chemical composition and irradiation is given in shown in Table 1a and 1b respectively. To study the neutron IIP/nanoclusters and Nb concentration in the solid solution, atom probe tomography (APT) is the primary tool to obtain reliable chemical information. APT specimens were prepared in shielded focused ion beam (FIB) at the Irradiated Materials Characterization Laboratory (IMCL) at INL followed by APT analysis at CAES facility using LEAP 4000XR

36 MATERIALS SCIENCE↗
DOE OSTI2024

LevSeq: Rapid Generation of Sequence-Function Data for Directed Evolution and Machine Learning

Sequence-function data provides valuable information about the protein functional landscape but is rarely obtained during directed evolution campaigns. Here, we present Long-read every variant Sequencing (LevSeq), a pipeline that combines a dual barcoding strategy with nanopore sequencing to rapidly generate sequence-function data for entire protein-coding genes. LevSeq integrates into existing protein engineering workflows and comes with open-source software for data analysis and visualization. The pipeline facilitates data-driven protein engineering by consolidating sequence-function data to inform directed evolution and provide the requisite data for machine learning-guided protein engineering (MLPE). LevSeq enables quality control of mutagenesis libraries prior to screening, which reduces time and resource costs. Simulation studies demonstrate LevSeq’s ability to accurately detect variants under various experimental conditions. Lastly, we show LevSeq’s utility in engineering protoglobins for new-to-nature chemistry. Widespread adoption of LevSeq and sharing of the data will enhance our understanding of protein sequence-function landscapes and empower data-driven directed evolution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Proceedings for the Workshop on Applied Nuclear Data Activities 2024

The Workshop for Applied Nuclear Data Activities (WANDA) is designed to increase communication among nuclear data (ND) users in multidisciplinary federal programs, ND producers, ND funders, and other ND experts. It also presents an opportunity to cross-pollinate ideas as well as introduce ND gaps identified by federal programs to ND experts and ND capabilities to the various federal ND users. WANDA 2024 included five technical sessions, three of which focused on Fusion Energy Sciences (FES)—FES Fusion Neutronics, FES Tritium Production, and FES Material Damage—and two stand-alone sessions—Isotopes and Targetry for Nuclear Data and Uncertainty Quantification. The FES sessions successfully brought new voices to the WANDA discussions, expanding the application space in which nuclear data are critical. FES programs need accurate nuclear data with realistic uncertainty quantification to properly estimate, for example, shielding, activation, tritium production, helium production, structural material integrity, and superconducting magnet operation. This includes a variety of projectile (neutrons, photons, charged particles) and target atoms. One of the action items common to all the FES sessions was a need to perform sensitivity studies to identify the prioritization of nuclear data needs. The Isotopes and Targetry session highlighted the many capabilities available to produce high-quality targets for nuclear data measurements, including 3D printing with spherical powders, combustion synthesis coupled with spin coating & electrospraying, inkjet printing, and isotopic doping. These new methods open doors for more accurate measurement, but it was also stressed that sample characterization following any method of fabrication is of the highest importance to accurately interpret nuclear data measurement results that used that sample. The Uncertainty Quantification (UQ) session was broken into two categories: nuclear data uncertainty quantification and the use of that uncertainty quantification. Thematic to the UQ session was the loss of information when going from nuclear data measurement, to evaluation, to evaluated file, and finally to neutron transport calculations. Current evaluated ND libraries typically only contain covariances, which assume that the probability distributions are Gaussian. Beyond being a simplified assumption for many evaluations, this can lead to negative values on many observables when attempting to sample the covariance. The covariance format, however, is very efficient in that a simple set of linear equations can transform uncertainty from parameters or cross sections to the application of interest. Focused collaboration is needed between nuclear data evaluators and nuclear data users to ensure that needs are being met.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Augmented DNA Nanoarchitectures: A Structural Library of 3D Self-Assembling Tensegrity Triangle Variants

The DNA tensegrity triangle is known to reliably self-assemble into a 3D rhombohedral crystalline lattice via sticky-end cohesion. Here, in this study, the library of accessible motifs is expanded through covalent extensions of intertriangle regions and sticky-end-coordinated linkages of adjacent triangles with double helical segments using both geometrically symmetric and asymmetric configurations. The molecular structures of 18 self-assembled architectures at resolutions of 3.32–9.32 Å are reported; the observed cell dimensions, cavity sizes, and cross-sectional areas agree with theoretical expectations. These data demonstrate that fine control over triclinic and rhombohedral crystal parameters and the customizability of more complex 3D DNA lattices are attainable via rational design. It is anticipated that augmented DNA architectures may be fine-tuned for the self-assembly of designer nanocages, guest–host complexes, and proscriptive 3D nanomaterials, as originally envisioned. Finally, designer asymmetric crystalline building blocks can be seen as a first step toward controlling and encoding information in three dimensions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

PETSc/TAO Users Manual (Rev. 3.19)

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) and the Toolkit for Advanced Optimization (TAO) for the numerical solution of partial differential equations and related problems on high-performance computers. PETSc/TAO is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication. PETSc/TAO includes a large suite of parallel linear solvers, nonlinear solvers, time integrators, and opti mization that may be used in application codes written in Fortran, C, C++, and Python (via petsc4py; see Getting Started). PETSc provides many of the mechanisms needed within parallel application codes, such as parallel matrix and vector assembly routines. The library is organized hierarchically, enabling users to employ the level of abstraction that is most appropriate for a particular problem. By using techniques of object-oriented programming, PETSc provides enormous flexibility for users. PETSc is a sophisticated set of software tools; as such, for some users it initially has a much steeper learning curve than packages such as MATLAB or a simple subroutine library. In particular, for individuals without some computer science background, experience programming in C, C++, python, or Fortran and experience using a debugger such as gdb or lldb, it may require a significant amount of time to take full advantage of the features that enable efficient software use. However, the power of the PETSc design and the algorithms it incorporates may make the efficient implementation of many application codes simpler than “rolling them” yourself. For many tasks a package such as MATLAB is often the best tool; PETSc is not intended for the classes of problems for which effective MATLAB code can be written. There are several packages, built on PETSc, that may satisfy your needs without requiring directly using PETSc. We recommend reviewing these packages functionality before starting to code directly with PETSc. PETSc can be used to provide a “MPI parallel linear solver” in an otherwise sequential, or OpenMP parallel code. This approach cannot provide extremely large improvements in the application time by utilizing large numbers of MPI processes but can still improve the performance. Certainly all parts of a previously sequential code need not be parallelized but the matrix generation portion must be parallelized to expect true scalability to large numbers of MPI processes. See PCMPI for details on how to utilize the PETSc MPI linear solver server. Since PETSc is under continued development, small changes in usage and calling sequences of routines will occur. PETSc has been supported for twenty-five years; see mailing list information on our website for information on contacting support.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Non-target RNA depletion strategy to improve sensitivity of next-generation sequencing for the detection of RNA viruses in poultry

PCR-based assays have become the benchmark for detecting pathogens of poultry and other livestock; however, these techniques are limited in their ability to detect multiple infecting agents, provide limited genetic information on the pathogen, and, for RNA viruses, must be reviewed frequently to assure high sensitivity and specificity. In contrast, untargeted, high-throughput sequencing can rapidly detect all infecting agents in a sample while providing genomic sequence information to allow more in-depth characterization of viruses. Although next-generation sequencing (NGS) offers many advantages, one of its primary limitations is low sensitivity to pathogens given the abundance of host and other non-target sequences in sequencing libraries. We explored methods for improving the sensitivity of NGS to detect respiratory and enteric viruses in poultry from RNA extracts of swab samples. We employed commercial and custom-designed negative enrichment strategies to selectively deplete the most abundant rRNA reads from the host and non-target bacteria; host RNA was diminished from up to 40% of total reads to as low as 3%, and the total number of reads assigned to abundant bacterial classes were reduced greatly. Our treatment resulted in up to a 700-fold increase in the number of viral reads, detection of a greater number of viral agents, and higher average genome coverage for pathogens. Depletion assays added only 2 h to the NGS library preparation workflow. Custom depletion probe design offered significant cost savings (US$7–12 per sample) compared to commercial kits (US$30–50 per sample).

Parris, D. Joshua↗
DOE OSTI2020

Statistically Steady State Large-Eddy Simulations Forced by an Idealized GCM: 1. Forcing Framework and Simulation Characteristics

Using large-eddy simulations (LES) systematically has the potential to inform parameterizations of subgrid-scale (SGS) processes in general circulation models (GCMs), such as turbulence, convection, and clouds. Here we show how LES can be run to emulate grid columns of GCMs to generate a library of LES across a cross-section of dynamical regimes. The LES setup replicates the thermodynamic and water budgets in GCM grid columns. Resolved horizontal and vertical transports of heat and water and large-scale pressure gradients from the GCM are prescribed as forcing in the LES. The LES satisfies the same (slab-ocean) surface boundary conditions as the GCM, leaving the LES temperatures free to adjust. Radiative transfer is treated in a unied but highly idealized manner (a semi-gray atmosphere without cloud radiative effects) in both the GCM and LES. We show that the LES with these forcing and boundary conditions reaches statistically steady states without nudging to reference profiles. These steady states provide a training dataset for developing GCM parameterizations. The same LES setup also provides a good basis for studying the cloud response to global warming.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

An automatically curated first-principles database of ferroelectrics

Ferroelectric materials have technological applications in information storage and electronic devices. The ferroelectric polar phase can be controlled with external fields, chemical substitution and size-effects in bulk and ultrathin film form, providing a platform for future technologies and for exploratory research. In this work, we integrate spin-polarized density functional theory (DFT) calculations, crystal structure databases, symmetry tools, workflow software, and a custom analysis toolkit to build a library of known, previously-proposed, and newly-proposed ferroelectric materials. With our automated workflow, we screen over 67,000 candidate materials from the Materials Project database to generate a dataset of 255 ferroelectric candidates, and propose 126 new ferroelectric materials. We benchmark our results against experimental data and previous first-principles results. The data provided includes atomic structures, output files, and DFT values of band gaps, energies, and the spontaneous polarization for each ferroelectric candidate. Finally, we contribute our workflow and analysis code to the open-source python packages atomate and pymatgen so others can conduct analogous symmetry driven searches for ferroelectrics and related phenomena.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Mammalian Chromosome Analysis and Sorting by Flow Cytometry

The analysis of chromosomes by flow cytometry is termed flow cytogenetics, and it involves the analysis and sorting of single mitotic chromosomes in suspension. The study of flow karyograms provides insight into chromosome number and structure to provide information on chromosomal DNA content and can enable the detection of deletions, translocations, or any forms of aneuploidy. Beyond its clinical applications, flow cytogenetics greatly contributed to the Human Genome Project through the ability to sort pure populations of chromosomes for gene mapping, cloning, and the construction of DNA libraries. Maximizing the potential of these important applications of flow cytogenetics relies on precise instrument setup and optimal sample processing, both of which impact the accuracy and quality of the data that are generated. This article is a compilation of the existing protocols that describe the stepwise methodology of accumulating, isolating, and staining metaphase chromosomes to prepare single-chromosome suspensions for flow cytometric analysis and sorting. Although the chromosome preparation protocols have remained largely unchanged, cytometer technology has advanced dramatically since these protocols were originally developed. Advances in cytometry technologies offer new and exciting approaches for understanding and monitoring chromosomal aberrations, but the hallmark of these protocols remains their simplicity in methodologies and reagent requirements and the accuracy of data resolvable to every chromosome of the cell.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Monitoring leaf phenology in moist tropical forests by applying a superpixel-based deep learning method to time-series images of tree canopies

Tropical leaf phenology-particularly its variability at the tree-crown scale-dominates the seasonality of carbon and water fluxes. However, given enormous species diversity, accurate means of monitoring leaf phenology in tropical forests is still lacking. Time series of the Green Chromatic Coordinate (GCC) metric derived from tower-based red-green-blue (RGB) phenocams have been widely used to monitor leaf phenology in temperate forests, but its application in the tropics remains problematic. To improve monitoring of tropical phenology, we explored the use of a deep learning model (i.e. superpixel-based Residual Networks 50, SP-ResNet50) to automatically differentiate leaves from non-leaves in phenocam images and to derive leaf fraction at the tree-crown scale. To evaluate our model, we used a year of data from six phenocams in two contrasting forests in Panama. Here, we first built a comprehensive library of leaf and non-leaf pixels across various acquisition times, exposure conditions and specific phenocams. We then divided this library into training and testing components. We evaluated the model at three levels: 1) superpixel level with a testing set, 2) crown level by comparing the model-derived leaf fractions with those derived using image-specific supervised classification, and 3) temporally using all daily images to assess the diurnal stability of the model-derived leaf fraction. Finally, we compared the model-derived leaf fraction phenology with leaf phenology derived from GCC. Our results show that: 1) the SP-ResNet50 model accurately differentiates leaves from non-leaves (overall accuracy of 93%) and is robust across all three levels of evaluations; 2) the model accurately quantifies leaf fraction phenology across tree-crowns and forest ecosystems; and 3) the combined use of leaf fraction and GCC helps infer the timing of leaf emergence, maturation and senescence, critical information for modeling photosynthetic seasonality of tropical forests. Collectively, this study offers an improved means for automated tropical phenology monitoring using phenocams.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Systematic characterization of gene function in the photosynthetic alga Chlamydomonas reinhardtii

Most genes in photosynthetic organisms remain functionally uncharacterized. Here, using a barcoded mutant library of the model eukaryotic alga Chlamydomonas reinhardtii, we determined the phenotypes of more than 58,000 mutants under more than 121 different environmental growth conditions and chemical treatments. A total of 59% of genes are represented by at least one mutant that showed a phenotype, providing clues to the functions of thousands of genes. Mutant phenotypic profiles place uncharacterized genes into functional pathways such as DNA repair, photosynthesis, the CO 2 -concentrating mechanism and ciliogenesis. We illustrate the value of this resource by validating phenotypes and gene functions, including three new components of an actin cytoskeleton defense pathway. The data also inform phenotype discovery in land plants; mutants in Arabidopsis thaliana genes exhibit phenotypes similar to those we observed in their Chlamydomonas homologs. We anticipate that this resource will guide the functional characterization of genes across the tree of life.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Arginine off-kilter: guanidinium is not as planar as restraints denote

Crystallographic refinement of macromolecular structures relies on stereochemical restraints to mitigate the typically poor data-to-parameter ratio. For proteins, each amino acid has a unique set of geometry restraints which represent stereochemical information such as bond lengths, valence angles, torsion angles, dihedrals and planes. It has been shown that the geometry in refined structures can differ significantly from that present in libraries; for example, it was recently reported that the guanidinium moiety in arginine is not symmetric. In this work, the asymmetry of the N ∊ —C ζ —N η1 and N ∊ —C ζ —N η2 valence angles in the guanidinium moiety is confirmed. In addition, it was found that the C δ atom can deviate significantly (more than 20°) from the guanidinium plane. This requires the relaxation of the planar restraint for the C δ atom, as it otherwise causes the other atoms in the group to compensate by distorting the guanidinium core plane. A new set of restraints for the arginine side chain have therefore been formulated, and are available in the software package Phenix , that take into account the asymmetry of the group and the planar deviation of the C δ atom. This is an example of the need to regularly revisit the geometric restraint libraries used in macromolecular refinement so that they reflect the best knowledge of the structural chemistry of their components available at the time.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Nanobodies as potential tools for microbiological testing of live biotherapeutic products

Nanobodies are highly specific binding domains derived from naturally occurring single chain camelid antibodies. Live biotherapeutic products (LBPs) are biological products containing preparations of live organisms, such as Lactobacillus, that are intended for use as drugs, i.e. to address a specific disease or condition. Demonstrating potency of multi-strain LBPs can be challenging. The approach investigated here is to use strain-specific nanobody reagents in LBP potency assays. Llamas were immunized with radiation-killed Lactobacillus jensenii or L. crispatus whole cell preparations. A nanobody phage-display library was constructed and panned against bacterial preparations to identify nanobodies specific for each species. Nanobody-encoding DNA sequences were subcloned and the nanobodies were expressed, purified, and characterized. Colony immunoblots and flow cytometry showed that binding by Lj75 and Lj94 nanobodies were limited to a subset of L. jensenii strains while binding by Lc38 and Lc58 nanobodies were limited to L. crispatus strains. Mass spectrometry was used to demonstrate that Lj75 specifically bound a peptidase of L. jensenii, and that Lc58 bound an S-layer protein of L. crispatus. The utility of fluorescent nanobodies in evaluating multi-strain LBP potency assays was assessed by evaluating a L. crispatus and L. jensenii mixture by fluorescence microscopy, flow cytometry, and colony immunoblots. Our results showed that the fluorescent nanobody labelling enabled differentiation and quantitation of the strains in mixture by these methods. Development of these nanobody reagents represents a potential advance in LBP testing, informing the advancement of future LBP potency assays and, thereby, facilitation of clinical investigation of LBPs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

MnEdgeNet for accurate decomposition of mixed oxidation states for Mn XAS and EELS L2,3 edges without reference and calibration

Accurate decomposition of the mixed Mn oxidation states is highly important for characterizing the electronic structures, charge transfer and redox centers for electronic, and electrocatalytic and energy storage materials that contain Mn. Electron energy loss spectroscopy (EELS) and soft X-ray absorption spectroscopy (XAS) measurements of the Mn L2,3 edges are widely used for this purpose. To date, although the measurements of the Mn L2,3 edges are straightforward given the sample is prepared properly, an accurate decomposition of the mix valence states of Mn remains non-trivial. For both EELS and XAS, 2+, 3+, and 4+ reference spectra need to be taken on the same instrument/beamline and preferably in the same experimental session because the instrumental resolution and the energy axis offset could vary from one session to another. To circumvent this hurdle, in this study, we adopted a deep learning approach and developed a calibration-free and reference-free method to decompose the oxidation state of Mn L2,3 edges for both EELS and XAS. A deep learning regression model is trained to accurately predict the composition of the mix valence state of Mn. To synthesize physics-informed and ground-truth labeled training datasets, we created a forward model that takes into account plural scattering, instrumentation broadening, noise, and energy axis offset. With that, we created a 1.2 million-spectrum database with 1-by-3 oxidation state composition ground truth vectors. The library includes a sufficient variety of data including both EELS and XAS spectra. By training on this large database, our convolutional neural network achieves 85% accuracy on the validation dataset. We tested the model and found it is robust against noise (down to PSNR of 10) and plural scattering (up to t/λ = 1). We further validated the model against spectral data that were not used in training. In particular, the model shows high accuracy and high sensitivity for the decomposition of Mn 3 O 4 , MnO, Mn 2 O 3 , and MnO 2 . The accurate decomposition of Mn 3 O 4 experimental data shows the model is quantitatively correct and can be deployed for real experimental data. Our model will not only be a valuable tool to researchers and material scientists but also can assist experienced electron microscopists and synchrotron scientists in the automated analysis of Mn L edge data.

25 ENERGY STORAGE↗
DOE OSTI2022

Development of a Gibbs Energy Minimiser for the MOOSE-based Corrosion Modelling App Yellowjacket and Validation of MSTDB

Nuclear materials are highly complex multiscale, multiphysics systems,and an effective prediction of nuclear reactor performance and safety requires simulation capabilities that tightly couple different physical phenomena. The Idaho National Laboratory’s Multiphysics Object Oriented Simulation Environment (MOOSE) provides the computational foundation for performing such simulations. With the move towards advanced reactors, such as the Molten Salt Reactor (MSR), that employ high temperature fluids compared to conventional reactors, corrosion has become a problem of great interest. A new application called Yellowjacket is currently under development to directly couple thermodynamic equilibrium and kinetics with phase field models in order to model corrosion in MSRs. As part of Yellowjacket, a Gibbs energy minimiser is being developed to perform thermochemical equilibrium calculations for a range of different materials, which is currently in its infancy. This report describes the further progress towards the development of Yellowjacket Gibbs energy minimiser. Ontario Tech University is developing a new Gibbs energy minimiser for Yellowjacket which is the primary contribution of this work. The aim to develop a thermochemistry solver for the MOOSE framework following the same development philosophy and using the same tools and libraries. A special focus is on performance, documentation and SQA. Furthermore through a scope extension partway through the fiscal year a thorough assessment of the MSTDB-TC v1.3 was performed at Ontario Tech University in the context of continuous improvement and quality assurance. The objective of the work was to have an arm’s length review of the database to give confidence that the database is performing as it was intended while assessing its current state to give recommendations to future developments. This assessment involved two parts: A) a quantitative assessment, and B) a qualitative assessment. Part A involved developing an automated test-suite that would compute values from the database using Thermochimica with comparisons to experimental measurements for validation purposes, which gives confidence to the database’s stakeholders that its functioning properly. Part B involved reviewing all binary systems in the database and making a qualitative assessment with two performance indicators: comprehensiveness and overall confidence. It is important to note that the models in the database are empirical, which is to say that the quality of any model is highly dependent on the experimental data used to inform its development.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2024

Coupling Metabolic Source Isotopic Pair Labeling and Genome Wide Association for Metabolite and Gene Annotation in Plants (Final Technical Report)

In this project, we applied our labeling pipeline to Arabidopsis and sorghum by feeding tissues with isotopically labeled versions of commercially available amino acids to identify all metabolite features that incorporate the label. In sorghum, we fed five accessions, sampled across the diversity of sorghum, to identify the precursor-of-origin for metabolites that vary between accessions as well as those that may be missing from a single reference genotype. This provided us with precursor-of-origin annotation for thousands of unknown metabolites. We then used GWA to map genes responsible for the synthesis of precursor-of-origin classified metabolites. For sorghum leaf and root ducible metabolites, we performed untargeted metabolomics on leaf and root tissues from 300 diverse genotyped sorghum inbred lines. The amino acid precursor-of-origin metabolite library were then used to identify the corresponding metabolites in the GWA data sets and to identify novel gene-metabolite associations. Finally, we utilized existing and newly generated sequenced EMS mutants of sorghum to validate the predicted gene-metabolite relationships that our labelling analysis identified. In parallel, we conducted similar feeding experiments in Arabidopsis to categorize metabolites based on precursor-of-origin, identify those that vary across our existing Arabidopsis metabolite GWA dataset, and identify genes required for the synthesis of each metabolite. To provide an independent test of gene annotation and pathway involvement, we tested the GWA gene-metabolite associations in Arabidopsis by analyzing the metabolic phenotypes of gene knockouts. Genes of particular interest from both sorghum and Arabidopsis were studied in detail by directly measuring the activity of the corresponding enzymes following heterologous expression. In summary, this work classified as-yet-unknown amino acid-derived metabolites and identified genes involved in their production generated through “omics” technologies. This information was used to validate gene function and identify new metabolism in Arabidopsis and sorghum.

09 BIOMASS FUELS↗
DOE OSTI2023

Optimizing Irregular Communication with Neighborhood Collectives and Locality-Aware Parallelism

Irregular communication often limits both the performance and scalability of parallel applications. Typically, applications individually implement irregular communication as point-to-point, and any optimizations are integrated directly into the application. As a result, these optimizations lack portability. It is difficult to optimize point-to-point messages within MPI, as the interface for single messages provides no information on the collection of all communication to be performed. However, the persistent neighbor collective API, released in the MPI 4 standard, provides an interface for portable optimizations of irregular communication within MPI libraries. This paper presents methods for implementing existing optimizations for irregular communication within neighborhood collectives, analyzes the impact of replacing point-to-point communication in existing codebases such as Hypre BoomerAMG with neighborhood collectives, and finally shows up to a 1.38x speedup on sparse matrix-vector multiplication communication within a BoomerAMG solve through the use of our optimized neighbor collectives. Here, the authors analyze three implementations of persistent neighborhood collectives for Alltoallv: an unoptimized wrapper of standard point-to-point communication, and two locality-aware aggregating methods. The second locality-aware implementation exposes an non-standard interface to perform additional optimization, and the authors present the additional 0.07x speedup from the extended interface. All optimizations are available in an open-source codebase, MPI Advance, which sits on top of MPI, allowing for optimizations to be added into existing codebases regardless of the system MPI install.

AMG↗
DOE OSTI2020

Active- and transfer-learning applied to microscale-macroscale coupling to simulate viscoelastic flows

Active- and transfer-learning are applied to microscale dynamics of polymer flows for the multiscale discovery of effective constitutive approximations required in viscoelastic flow simulation. The result is macroscopic rheology directly connected to a microstructural model. Micro and macroscale simulations are adaptively coupled by means of Gaussian process regression (GPR) to run the expensive microscale computations only as necessary. This multiscale method is demonstrated with flows of a polymer solution as a model system. At the microscale level dissipative particle dynamics (DPD) is employed to model the fluid as a suspension of bead-spring micro-structures subjected to steady shear flow. The results yield the non-Newtonian viscosity and the first normal stress difference at strain rates as training data used in a GPR model. DPD parameters are calibrated with respect to experimental data for a real polymer solution. Compliance with these data requires adjustment of the DPD model's cutoff radius, which then becomes a function of the second invariant of the strain rate tensor. The FENE-P model is chosen for the macroscale description using the spectral element method (SEM) to simulate channel flow and flow past a circular cylinder. The DPD results at the lowest possible shear strain rate yield an estimate of the zero-shear rate viscosity, which allows the initiation of the macroscale flow by SEM as a Newtonian fluid. The resulting strain-rate field is surveyed to determine additional shear strain rate sampling points for the DPD system. This new information allows an initial fitting of parameters of the constitutive equation followed by new SEM simulations at the macroscale. Additionally, guided by active-learning GPR to select new sampling points, this process continues until convergence is achieved. The effectiveness of this new simulation paradigm for viscoelastic flows is tested with different macroscale operating conditions. The effective closure learned in the channel simulation is then transferred directly to the flow past a circular cylinder at low Reynolds number, where the results show that only two additional DPD simulations are required to achieve a satisfactory constitutive model. With an increase of the Reynolds number, the active-learning scheme automatically detects the inaccuracy of the learned constitutive model, and initiates additional DPD simulations for the extra data needed to once again close the microscale-macroscale coupled system. This new paradigm of active- and transfer-learning for multiscale modeling is readily applicable to other microscale-macroscale coupled simulations of complex fluids and other materials. Furthermore, the coupling between microscale and macroscale solvers can be seamlessly implemented with our open source multiscale universal interface (MUI) library.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗