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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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At least 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

TEMPI: An Interposed MPI Library with Canonical Representation of MPI Datatypes [Slides]

These points are covered in this presentation: Distributed GPU stencil, non-contiguous data; Equivalence of strided datatypes and minimal representation; GPU communication methods; Deploying on managed systems; Large messages and MPI datatypes; Translation and canonicalization; Automatic model-driven transfer method selection; and Interposed library implementation.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

TEMPI: An Interposed MPI Library with Canonical Representation of MPI Datatypes [Poster]

TEMPI provides a transparent non-contiguous data-handling layer compatible with various MPIs. MPI Datatypes are a powerful abstraction for allowing an MPI implementation to operate on non-contiguous data. CUDA-aware MPI implementations must also manage transfer of such data between the host system and GPU. The non-unique and recursive nature of MPI datatypes mean that providing fast GPU handling is a challenge. The same noncontiguous pattern may be described in a variety of ways, all of which should be treated equivalently by an implementation. This work introduces a novel technique to do this for strided datatypes. Methods for transferring non-contiguous data between the CPU and GPU depends on the properties of the data layout. This work shows that a simple performance model can accurately select the fastest method. Unfortunately, the combination of MPI software and system hardware available may not provide sufficient performance. The contributions of this work are deployed on OLCF Summit through an interposer library which does not require privileged access to the system to use

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Canonical Vegetation Simulations

LANL employed the FIRETEC model to produce a suite of simulations of flow around trees and forests. The purpose of this suite of simulations is to provide detailed simulations of the effects of various types of trees and groups of trees including the mean velocity and turbulence fields. This suite includes various tree densities ranging from individual trees, wind breaks (i.e., lateral rows of trees), orchards, and forests of various densities. In addition to the simulations that we have already run, we have developed tools to facilitate more simulations in the future.

58 GEOSCIENCES↗
DOE OSTI2021

A priori examination of reduced chemistry models derived from canonical stirred reactors using three-dimensional direct numerical simulation datasets

Data-driven approaches to construct reduced chemical kinetic models, that rely heavily on thermo-chemical datasets with full chemical kinetics, have been gaining popularity. Datasets from direct numerical simulations (DNS) under three-dimensional (3-D) realistic turbulent flow conditions are desirable but limited to carefully designed parametric conditions due to the computational cost. Constructing datasets from a large ensemble of zero-dimensional stirred reactors like perfectly stirred reactor (PSR) and partially stirred reactor (PaSR) is a computationally efficient solution to consider the turbulence-chemistry interactions and cover a broad range of parametric conditions. In this paper, we derive reduced chemistry models from solutions of a large number of PSR and PaSR reactors using autoencoder (AE) neural networks and principal component analysis (PCA), and conduct a priori examination of the reduced models in three temporally evolving 3-D DNS jet flames featuring local extinction and re-ignition. The results show that the reduced models derived from PaSR datasets, i.e., AE-PaSR and PCA-PaSR, generally show significant improvement over the ones derived from PSR datasets. Among all the reduced models, AE-PaSR shows the best agreement with DNS results on the reconstruction accuracy and the representation of temporally evolving local extinction and re-ignition events.

Zhang, Pei↗
DOE OSTI2020

MassIVE MSV000085948 - Utilization of syringyl lignin-derived compounds and production of 2-pyrone-4,6-dicarboxylic acid by Pseudomonas putida KT2440: Lignin is an abundant aromatic polymer formed in plants by coupling reactions of p-coumaryl, coniferyl, and sinapyl alcohols. Pseudomonas putida KT2440 (P. putida KT2440), a robust soil bacterium, naturally catabolizes many aromatic compounds derived from lignin as carbon and energy sources and has been extensively engineered to valorize guaiacyl (G) and p-hydroxyphenyl (H) lignin-derived aromatic species to valuable chemicals. However, only a few studies report the capacity of Pseudomonads to grow on syringyl (S) lignin-derived compounds. In this work, we demonstrate that P. putida KT2440 catabolizes syringate in the presence of an auxiliary energy source. Overexpression of vanAB, encoding a native Rieske non-heme iron monooxygenase, enabled catabolism of syringate and syringaldehyde without an additional carbon and energy source. In vitro biochemical characterization of VanAB confirmed that this enzyme O-demethylates syringate to 3-O-methylgallate and, subsequently, 3-O-methylgallate to gallate, albeit 4- and 55-fold less efficiently than vanillate, respectively. Transcriptomics and proteomics experiments demonstrate that the galADBC transcripts and enzymes required for gallate catabolism are induced when vanAB is overexpressed during cultivation in syringate. Further, we show that that the endogenous protocatechuate-3,4-dioxygenase PcaHG ring-opens gallate to produce 2-pyrone-4,6-dicarboxylic acid (PDC), a promising bio-based chemical. Constitutive overexpression of vanAB and pcaHG along with galA deletion enabled PDC production from SA at a 70% (mol/mol) yield. Furthermore, leveraging the LigAB dioxygenase from Sphingobium sp. SYK-6 and VanAB O-demethylase from Pseudomonas sp. HR199 enabled simultaneous conversion of monomers with S-, G-, and H-type functionality to PDC at 82% (mol/mol) yield. Overall, this study elucidates a native pathway for catabolism of syringyl lignin-derived compounds in P. putida KT2440 and demonstrates the potential of this robust host for biological funneling of substrates derived from all three canonical monolignols.

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Beckham, Gregg↗
DOE OSTI2023

Dual incorporation of non-canonical amino acids enables production of post-translationally modified selenoproteins

Post-translational modifications (PTMs) can occur on almost all amino acids in eukaryotes as a key mechanism for regulating protein function. The ability to study the role of these modifications in various biological processes requires techniques to modify proteins site-specifically. One strategy for this is genetic code expansion (GCE) in bacteria. The low frequency of post-translational modifications in bacteria makes it a preferred host to study whether the presence of a post-translational modification influences a protein’s function. Genetic code expansion employs orthogonal translation systems engineered to incorporate a modified amino acid at a designated protein position. Selenoproteins, proteins containing selenocysteine, are also known to be post-translationally modified. Selenoproteins have essential roles in oxidative stress, immune response, cell maintenance, and skeletal muscle regeneration. Their complicated biosynthesis mechanism has been a hurdle in our understanding of selenoprotein functions. As technologies for selenocysteine insertion have recently improved, we wanted to create a genetic system that would allow the study of post-translational modifications in selenoproteins. By combining genetic code expansion techniques and selenocysteine insertion technologies, we were able to recode stop codons for insertion of N ε -acetyl- l -lysine and selenocysteine, respectively, into multiple proteins. The specificity of these amino acids for their assigned position and the simplicity of reverting the modified amino acid via mutagenesis of the codon sequence demonstrates the capacity of this method to study selenoproteins and the role of their post-translational modifications. Moreover, the evidence that Sec insertion technology can be combined with genetic code expansion tools further expands the chemical biology applications.

59 BASIC BIOLOGICAL SCIENCES↗