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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 1,513 records · Page 84
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Characterization of immiscible fluid displacement processes with various capillary numbers and viscosity ratios in 3D natural sandstone

We characterize the influence of reservoir conditions upon multiphase flow, we calculated fluid displacements (drainage processes) in 3D pore spaces of Berea sandstone using two-phase lattice Boltzmann (LB) simulations. The results of simulations under various conditions were used to classify the resulting two-phase flow behavior into three typical fluid displacement patterns on the diagram of capillary number (Ca) and viscosity ratio of the two fluids (M). In addition, the saturation of the nonwetting phase was calculated and mapped on the Ca–M diagram. We then characterized dynamic pore-filling events (i.e., Haines jumps) from the pressure variation of the nonwetting phase, and linked this behavior to the occurrence of capillary fingering. The results revealed the onset of capillary fingering in 3D natural rock at a higher Ca than in 2D homogeneous granular models, with the crossover region between typical displacement patterns broader than in the homogeneous granular model. Furthermore, saturation of the nonwetting phase mapped on the Ca–M diagram significantly depends on the rock models. These important differences between two-phase flow in 3D natural rock and in 2D homogeneous models could be due to the heterogeneity of pore geometry in the natural rock and differences in pore connectivity. By quantifying two-phase fluid behavior in the target reservoir rock under various conditions (e.g., saturation mapping on the Ca–M diagram), our approach could provide useful information for investigating suitable reservoir conditions for geo-fluid management (e.g., high CO 2 saturation in CO 2 storage).

58 GEOSCIENCES↗
DOE OSTI2018

Genomic characterization reveals significant divergence within Chlorella sorokiniana (Chlorellales, Trebouxiophyceae)

Selection of highly productive algal strains is crucial for establishing economically viable biomass and bioproduct cultivation systems. Characterization of algal genomes, including understanding strain-specific differences in genome content and architecture is a critical step in this process. Using genomic analyses, we demonstrate significant differences between three strains of Chlorella sorokiniana (strain 1228, UTEX 1230, and DOE1412). We found that unique, strain-specific genes comprise a substantial proportion of each genome, and genomic regions with >80% local nucleotide identity constitute <15% of each genome among the strains, indicating substantial strain specific evolution. Furthermore, cataloging of meiosis and other sex-related genes in C. sorokiniana strains suggests strategic breeding could be utilized to improve biomass and bioproduct yields if a sexual cycle can be characterized. Finally, preliminary investigation of epigenetic machinery suggests the presence of potentially unique transcriptional regulation in each strain. Our data demonstrate that these three C. sorokiniana strains represent significantly different genomic content. Based on these findings, we propose individualized assessment of each strain for potential performance in cultivation systems.

09 BIOMASS FUELS↗
DOE OSTI2019

Functional and phenotypic flow cytometry characterization of Picochlorum soloecismus

Multiple physiological traits essential for efficient cellular function are important when considering the selection and engineering of algal species for biofuel and bioproduct generation. Bioengineering methods have become more ubiquitous producing several novel algal lines with potentially enhanced traits. Complex metabolic interactions, however, require greater depth in characterizing cellular responses to delineate mechanistic understanding. Here, we have developed fluorescence-based high-throughput flow cytometry protocols to facilitate characterization of cell morphology, membrane permeability, metabolic activity, cell viability, intracellular pH, and reactive oxygen species in isolates derived from the species Picochlorum soloecismus. Flow cytometry parameters were optimized for each assay. This suite of molecular flow cytometry probes and procedures can be utilized for rapid screening of optimal phenotypes in microalgae under various environmental conditions as new technical strategies for improving algae strain productivity are established.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Characterization of the quantumness of unsteerable tripartite correlations

Quantumness for a bipartite unsteerable quantum correlation is operationally characterized by the notion of super-unsteerability. Super-unsteerability refers to the requirement of a larger dimension of the random variable that the steering party has to preshare with the party to be steered in the classical simulation protocol to generate an unsteerable correlation than the local Hilbert space dimension of the quantum states (reproducing the given unsteerable correlation) at the steering party’s side. In the present study, this concept of super-unsteerability is generalized by defining the notion of super-bi-unsteerability for tripartite correlations, which is unsteerable across a bipartite cut. Genuine super-bi-unsteerability is defined as the occurrence of super-bi-unsteerability across all possible bipartite cuts. Specific example of genuine super-bi-unsteerability for tripartite correlations has been presented. This study provides a tool to characterize the genuine quantumness of tripartite quantum correlations which are unsteerable across every bipartite cut.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Wave energy resource characterization employing joint distributions in frequency-direction-time domain

Joint and marginal distributions in the frequency, direction, and time domain are employed to demonstrate their value for wave energy resource characterization when full spectra are available. Insights gained through analysis of these distributions support wave energy converter concept design, operation and maintenance. Spatial trends in the wave energy resource and contributing wave energy systems along the continental shelf of the West Coast of the United States are investigated using the most recent two-dimensional wave spectra measurements at four buoys over an eleven year period (2008 to 2018). Resource hot spots and dominant resolved energy resource bands in the frequency-direction-time domain are delineated. Resource attributes, including frequency and directional spreading, and seasonal variability, are characterized using joint distributions and marginal distributions of wave power spectra. North Pacific westerly swells in the winter season, augmented by Aleutian low-pressure southwesterly swells, are the principal suppliers of the dominant resource and main drivers influencing resource attributes. In conclusion, the modification of these systems southward, especially the North Pacific westerly swells, explains the observed spatial resource trends. The dominant resource wave period shifts two seconds to higher wave periods, thirty degrees in the dominant direction band to a more northward orientation, and forward by one month.

16 TIDAL AND WAVE POWER↗
DOE OSTI2021

Characterization of Two Extraordinary AmLi Neutron Sources

Two legacy AmLi sources, MRC-101 and MRC-103, are routinely used for neutron detector characterization and testing campaigns that Pacific Northwest National Laboratory manages for the Defense Threat Reduction Agency within the U.S. Department of Defense. However, applicability of source measurement data has been substantially limited due to the lack of original manufacturer documentation and cross comparison to other sources. This paper summarizes results of the measurement campaign conducted to better quantify source radionuclide content, neutron energy spectrum and emission rate of the AmLi sources. The source characterization study consisted of three major consecutive measurement exercises. First, gamma spectrometry measurements using a high purity germanium detector were used to estimate the radionuclide content and potential impurities of the AmLi sources. Then neutron spectral measurements were taken to determine the unique neutron energy distribution. Finally, assessments of the total neutron yields of the sources were made with measurements in a neutron well counter. The neutron detection efficiency for these measurements was determined via detailed Monte Carlo modeling based on the neutron energy distribution measured with the rotating neutron spectrometer. The most exciting and unexpected finding of the study was a significant contamination of the source material with beryllium, contributing up to 17% to the total neutron emission rate and correspondingly changing the neutron energy spectrum. Also, the obtained lithium-only portion of the measured energy distribution of the sources was compared against several AmLi spectra previously reported by different researchers.

AWCC, AmLi, beryllium contamination, neutron spect↗
DOE OSTI2016

In vivo and in vitro characterization of site-specific recombination of a novel serine integrase from the temperate phage EFC-1

EFC-1 integrase is a site-specific recombinase that belongs to the large family of serine recombinase. In previously study, we isolated the temperate phage EFC-1, and characterized its genomic sequence. Within its genome, Orf28 was predicted encode a 464 amino acid of a putative integrase gene. In this study, EFC-1 integrase was characterized in vitro and in vivo. In vitro assay was performed using purified His-tag fusion integrase. Also, to identify which serine is involved in the catalytic domain, we used site-directed mutagenesis and analyzed by a recombination assay in vitro. In vivo assay involved PCR and confocal microscopy in HEK293 cells, and determined the minimal lengths of attP and attB sites. According to our results, the EFC-1 integrase-mediated recombination was site-specific and unidirectional system in vitro and in vivo. Serine 21 of EFC-1 integrase plays a major role in the catalytic domain, and minimal sizes of attB and attP was defined 48 and 54 bp. Our finding may help develop a useful tool for gene therapy and gene delivery system. - Highlights: • EFC-1 integrase-mediated recombination was site-specific and unidirectional system. • Serine 21 of EFC-1 integrase plays a major role in the catalytic domain. • The functional minimal sizes of attB and attP was defined 48 and 54 bp.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Cloning and functional characterization of a phenolic acid decarboxylase from the liverwort Conocephalum japonicum

Some commercially important vinyl derivatives are produced by the decarboxylation of phenolic acids. Enzymatically, this process can be achieved by phenolic acid decarboxylases (PADs), which are able to act on phenolic acid substrates such as ferulic and p-coumaric acid. Although many microbial PADs have been characterized, little is known regarding their plant homologs. Transcriptome sequencing in the liverworts has identified seven putative PADs, which share a measure of sequence identity with microbial PADs, but are typically much longer proteins. Here, a PAD-encoding gene was isolated from the liverwort species Conocephalum japonicum. The 1197 nt CjPAD cDNA sequence was predicted to be translated into a 398 residue protein. When the gene was heterologously expressed in Escherichia coli, its product exhibited a high level of PAD activity when provided with either p-coumaric or ferulic acid as substrate, along with the conversion of caffeic acid and sinapic acid to their corresponding decarboxylated products. Both N- and C-terminal truncation derivatives were non-functional. The transient expression in tobacco of a GFP/CjPAD fusion gene demonstrated that the CjPAD protein is expressed in the cytoplasm. It is first time a PAD was characterized from plants and the present investigation provided a candidate gene for catalyzing the formation of volatile phenols.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Expression and characterization of the Plasmodium translocon of the exported proteins component EXP2

The malaria parasite Plasmodium falciparum requires the Plasmodium translocon of exported proteins (PTEX) to proliferate in human red blood cells. During the blood stages of malaria, several hundred parasite-encoded proteins are exported from the parasite into the cytosol of red blood cells. PTEX is the translocon for protein export and comprises 5 proteins: EXP2, PTEX150, PTEX88, Hsp101 and TRX2. Among them, EXP2 is thought to constitute the transmembrane pore, whereas the other components seem to play a role in unfolding the luggage proteins or providing a driving force. However, detailed functional and structural characterizations of PTEX proteins have not been performed. In this study, we expressed and characterized the membrane-associated component EXP2. Because expression of EXP2 is lethal to E. coli, EXP2 was expressed as a fusion protein with GST, and the recombinant EXP2 was obtained by protease digestion. The recombinant EXP2 formed pores in bilayer lipid membranes. The inner diameter of the pore was estimated to be approximately 3.5 nm based on electron microscopy images and channel currents. From this size and the molecular mass as determined by size exclusion chromatography and blue native polyacrylamide gel electrophoresis, we determined that the pore comprises approximately 10–12 EXP2 subunits. However, there is a possibility that the pore structure is different in the PTEX complex. These results provide important insights in the protein transport mechanism of PTEX, which will aid in developing new drugs targeting PTEX.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Pharmacological characterization of synthetic serine palmitoyltransferase inhibitors by biochemical and cellular analyses

Highlights: • Tetrahydropyrazolopyridine derivatives were characterized as SPT inhibitors. • The SPT inhibitors exhibited dual inhibitory activities against SPT2 and SPT3. • A SPT inhibitor bound to the SPT2 or SPT3 subunit in SPT enzyme complexes. • One of the SPT inhibitors exhibited a significantly slow dissociation from SPT. • The SPT inhibitors suppressed ceramide content in a non-small-cell lung cancer cell line. Human serine palmitoyltransferase (SPT) is a PLP-dependent enzyme residing in the endoplasmic reticulum. It catalyzes the synthesis of 3-ketodihydrosphingosine (3-KDS) from the substrates palmitoyl-CoA and l-serine. It is a rate-limiting enzyme for sphingolipid synthesis in cells. In the present study, we characterized and pharmacologically profiled a series of tetrahydropyrazolopyridine derivatives that potently inhibit human SPT enzymatic activity, including two cell-active derivatives and one fluorescent-labelled derivative. These SPT inhibitors exhibited dual inhibitory activities against SPT2 and SPT3. We used a fluorescent-labelled probe to molecularly assess the inhibitory mechanism and revealed its binding to the SPT2 or SPT3 subunit in the small subunit (ss) SPTa/SPT1/SPT2/or ssSPTa/SPT1/SPT3 functional complexes. One of the SPT inhibitors exhibited a significantly slow dissociation from the SPT complex. We confirmed that our SPT inhibitors suppressed ceramide content in non-small-cell lung cancer cell line, HCC4006, by performing a target engagement analysis. The potency of ceramide reduction correlated to that observed in a recombinant SPT2 enzyme assay. We thus elucidated and provided a fundamental understanding of the molecular mode of action of SPT inhibitors and developed potent, cell-active SPT inhibitors that can be used to clarify the biological function of SPT.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Identification and functional characterization of three type III polyketide synthases from Aquilaria sinensis calli

Type III polyketide synthases (PKSs) play an important role in biosynthesis of various plant secondary metabolites and plant adaptation to environmental stresses. Aquilaria sinensis (A. sinensis) is the main plant species for production of agarwood, little is known about its PKS family. In this study, AsCHS1 and two new type III PKSs, AsPKS1 and AsPKS2, were isolated and characterized in A. sinensis calli. The comparative sequence and phylogenetic analysis indicated that AsPKS1 and AsPKS2 belonged to non-CHS group different from AsCHS1. The recombinant AsPKS1 and AsPKS2 produced the lactone-type products, suggesting their different enzyme activities from AsCHS1. Three PKS genes had a tissues-specific pattern in A. sinensis. Moreover, we examined the expression profiles of three PKS genes in calli under different abiotic stresses and hormone treatments. AsCHS1 transcript was most significantly induced by salt stress, AsPKS1 abundance was most remarkably enhanced by CdCl{sub 2} treatment, while AsPKS2 expression was most significantly induced by mannitol treatment. Furthermore, AsCHS1, AsPKS1 and AsPKS2 expression was enhanced upon gibberellins (GA3), methyl jasmonate (MeJA), or salicylic acid (SA) treatment, while three PKS genes displayed low transcript levels at the early stage under abscisic acid (ABA) treatment. In addition, three GFP:PKSs fusion proteins were localized in the cytoplasm and cell wall in Nicotiana benthamiana cells. These results indicated the multifunctional role of three type III PKSs in polyketide biosynthesis, plant resistance to abiotic stresses and signal transduction. - Highlights: • Two new PKS genes (AsPKS1 and AsPKS2) were isolated and characterized from A. sinensis. • The recombinant AsPKS1 and AsPKS2 catalyzed lactone-type products in vitro. • AsCHS1, AsPKS1 and AsPKS2 were involved in plant responses to abiotic stresses and hormone stimuli. • Our results also indicated that AsCHS1, AsPKS1 and AsPKS2 were predominantly localized in the cytoplasm and cell wall.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Biophysical characterization of actin bundles generated by the Chlamydia trachomatis Tarp effector

Highlights: • The F-actin binding domain of Tarp is sufficient to bundle filamentous actin. • Actin bundles formed by Tarp are more flexible than that of α-actinin and fascin. • Tarp mediated actin bundling is independent of actin nucleation. Chlamydia trachomatis entry into host cells is mediated by pathogen-directed remodeling of the actin cytoskeleton. The chlamydial type III secreted effector, translocated actin recruiting phosphoprotein (Tarp), has been implicated in the recruitment of actin to the site of internalization. Tarp harbors G-actin binding and proline rich domains required for Tarp-mediated actin nucleation as well as unique F-actin binding domains implicated in the formation of actin bundles. Little is known about the mechanical properties of actin bundles generated by Tarp or the mechanism by which Tarp mediates actin bundle formation. In order to characterize the actin bundles and elucidate the role of different Tarp domains in the bundling process, purified Tarp effectors and Tarp truncation mutants were analyzed using Total Internal Reflection Fluorescence (TIRF) microscopy. Our data indicate that Tarp mediated actin bundling is independent of actin nucleation and the F-actin binding domains are sufficient to bundle actin filaments. Additionally, Tarp-mediated actin bundles demonstrate distinct bending stiffness compared to those crosslinked by the well characterized actin bundling proteins fascin and alpha-actinin, suggesting Tarp may employ a novel actin bundling strategy. The capacity of the Tarp effector to generate novel actin bundles likely contributes to chlamydia's efficient mechanism of entry into human cells.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Molecular characterization of single-chain antibody variable fragments (scFv) specific to Pep27 from Streptococcus pneumoniae

Highlights: • Two antibody fragments specific to pneumococcal autolysis factor Pep27 are selected. • The antibody fragments show sub-micromolar affinity with good selectivity. • Molecular docking supports epitope on Pep27 identified by alanine scanning. Pep27 from Streptococcus pneumoniae is reported to initiate pneumococcal autolysis, thereby constituting a major virulence factor. Although a few antisera recognizing Pep27 have been reported, no monoclonal, well-characterized antibody for Pep27 has been developed. Here we screened two single-chain antibody variable fragments (scFv) using a phage display from a large human synthetic scFv library to select clones E2 and F9. Dissociation constants (K{sub d}) of E2 and F9 were 1.1 μM and 0.50 μM, respectively. E2 and F9 did not cross-react with other pneumococcal and unrelated proteins. The epitopes of Pep27 were localized to residues 24, 26 and 27 by alanine scanning. Molecular docking analysis supported the experimentally investigated epitope. The E2 and F9 clones specifically detected Pep27 in an environment mimicking in vivo conditions, demonstrated in human serum. The scFv clones characterized here represent molecular tools for the detection of pneumococcal diseases with potential for further improvement in affinity.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Identification and characterization of the zinc finger protein SjZF in Schistosoma japonicum

Highlights: • The zinc finger protein SjZF in S. japonicum was identified and characterized. • SjZF was mainly located in the intestinal tract of adult worms and the vitelline glands of females. • The rSjZF induced significant protection against S. japonicum infection in mouse. Schistosomiasis represents one of the most prevalent parasitic infections affecting over 249 million people worldwide. The pathological damage is mainly caused by the eggs laid by female schistosomes. Zinc finger proteins (ZFPs) usually play critical roles in many biological functions. In this study, we cloned, identified and characterized the zinc finger protein SjZF of Schistosoma japonicum. SjZF ortholog proteins were also identified in S. mansoni, S. haematobium, Opisthorchis viverrini and O. sinensis. Fluorescence localization showed that SjZF was particularly expressed in the worm gut of both genders and the vitelline glands of females. In vitro RNAi assay indicated that decreased expression of SjZF could affect the survival rate of adult worms. The immune protection assay indicated that rSjZF did partially protect mice with 54.8% reduction in the worm burden and 34.1% reduction in the liver eggs. Taken in concert, our preliminary results suggest that SjZF may be a potential vaccine candidate for schistosomiasis and may further provide evidence for a possible role of SjZF in the development of schistosomes.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Enzymatic characterization and crystal structure of biosynthetic alanine racemase from Pseudomonas aeruginosa PAO1

Highlights: • The crystal structure of PaAlr was solved. • Sequences and structures were compared among species with two alanine racemases. • d-Lysine was observed in active site, but not covanlently linked, which is somehow similar but different from PaDadX. • Optimal reaction conditions were characterized. Alanine racemase is a pyridoxal-5′-phosphate (PLP)-dependent enzyme that reversibly catalyzes the conversion of l-alanine to d-alanine. d-alanine is an essential constituent in many prokaryotic cell structures. Inhibition of alanine racemase is lethal to prokaryotes, creating an attractive target for designing antibacterial drugs. Here we report the crystal structure of biosynthetic alanine racemase (Alr) from a pathogenic bacteria Pseudomonas aeruginosa PAO1. Structural studies showed that P. aeruginosa Alr (PaAlr) adopts a conserved homodimer structure. A guest substrate d-lysine was observed in the active site and refined to dual-conformation. Two buffer ions, malonate and acetate, were bound in the proximity to d-lysine. Biochemical characterization revealed the optimal reaction conditions for PaAlr.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Characterization of a novel ω-transaminase from a Triassic salt mine metagenome

Highlights: • Metagenome derived from hypersaline environment, formed during Triassic Period. • Novel and active ω-transaminase enzyme synthesized from environmental DNA. • Molecular modeling and docking simulations reveal equivalents to mesophilic enzymes. • Characterization shows different profile to previous halophilic transaminases. Chiral amines are valuable building blocks for the pharmaceutical industry, and are increasingly synthesized by transaminase-mediated (TAm) synthesis. Currently available TAms, primarily isolated from the genomes of cultured mesophilic bacteria, often suffer from a number of drawbacks, including poor substrate range and an inability to tolerate the harsh conditions often demanded by industrial processes. These characteristics have, in part, driven the search for novel biocatalysts from both metagenomic sources and extreme environments. Herein, we report the isolation and characterization of an ω-TAm from a metagenome of a Triassic salt mine in Kilroot, N. Ireland, an extremely hypersaline environment formed circa 220–250 mya. The gene sequence was identified based on homology with existing bacterial TAms, synthesized within a pET28a(+) plasmid and expressed in E. coli BL21 DE3 cells. The resultant 49 kDa protein accepted (S)-methylbenzylamine (MBA) as amino donor and had a specific activity of 0.54 U/mg using α-ketoglutarate (ΑKG) as substrate. Molecular modeling and substrate docking indicated the presence of key residues, conserved in a number of other TAms. Despite the hypersaline environment from which it was isolated, the enzyme displayed low halotolerance, highlighting that not all biocatalysts will demonstrate the extreme characteristics associated with their source environment. This study does however reinforce the viability of mining metagenomic datasets as a means of discovering novel and functional biocatalysts, and adds to a currently scant list of such examples in the field of TAms.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Near-infrared spectroscopy as a green analytical tool for sustainable biomass characterization for biofuels and bioproducts: An overview

Biomass, a widely used renewable energy source, requires characterization to optimize biofuel and bioproduct processes, customize feedstocks, and ensure economic and environmental sustainability. Conventional wet-chemistry methods for biomass analysis are slow, expensive, and require significant reagents and skilled personnel. In contrast, near-infrared (NIR) spectroscopy, a faster, cost-effective, and reagent-free green technology, enables non-destructive biomass analysis with minimal sample preparation. This study provides an overview of the fundamentals of NIR spectroscopy and explores its recent applications for analyzing various biomass properties important to the biofuel and bioproduct industry. The study also critically evaluates the challenges and opportunities of using NIR spectroscopy for biomass analysis. This review aims to guide future research for rapid and high throughput characterization of biomass in the biomass industry, supporting the United Nations’ sustainable development goal (SDG) 7: producing affordable and sustainable energy.

Biofuels↗
DOE OSTI2019

Generation and characterization of carbon fiber microstructure in atomistic simulations

A clear understanding of carbon fiber (CF) microstructure is necessary for the development of high strength CFs. Here, we present an atomistic approach for generating and characterizing realistic mi- crostructures of CFs. Large-scale reactive molecular dynamics simulations are used to generate a set of distinct CF microstructures. Comprehensive characterization of the simulated microstructures is enabled by the development of a suite of computational structural analysis tools capable of evaluation of hy- bridization states of carbon atoms, populations and orientations of individual carbon rings, degree of graphitization, and pore size distribution. The calculation of X-ray diffraction profiles provides a direct link between the structural features of simulated samples and experimental data available for CFs. The CF generation algorithm is shown to produce microstructures with experimental densities and with structural characteristics matching those of PAN-based CFs. The key structural features affecting the properties of CFs, such as the relative fractions of graphitic, turbostratic and amorphous micro- constituents, degree of alignment, pore size distributions, and chemical cross-linking can be effectively controlled in simulations, thus enabling efficient exploration of structureeproperties relationships in CFs. The capabilities of the developed approach are illustrated by performing computational analysis of the mechanical deformation and fracture of CFs under axial tensile loading.

36 MATERIALS SCIENCE↗