Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “SiP”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Abstract Background Linking the identity of wild microbes with their ecophysiological traits and environmental functions is a key ambition for microbial ecologists. Of many techniques that strive for this goal, Stable-isotope probing—SIP—remains among the most comprehensive for studying whole microbial communities in situ. In DNA-SIP, actively growing microorganisms that take up an isotopically heavy substrate build heavier DNA, which can be partitioned by density into multiple fractions and sequenced. However, SIP is relatively low throughput and requires significant hands-on labor. We designed and tested a semi-automated, high-throughput SIP (HT-SIP) pipeline to support well-replicated, temporally resolved amplicon and metagenomics experiments. We applied this pipeline to a soil microhabitat with significant ecological importance—the hyphosphere zone surrounding arbuscular mycorrhizal fungal (AMF) hyphae. AMF form symbiotic relationships with most plant species and play key roles in terrestrial nutrient and carbon cycling. Results Our HT-SIP pipeline for fractionation, cleanup, and nucleic acid quantification of density gradients requires one-sixth of the hands-on labor compared to manual SIP and allows 16 samples to be processed simultaneously. Automated density fractionation increased the reproducibility of SIP gradients compared to manual fractionation, and we show adding a non-ionic detergent to the gradient buffer improved SIP DNA recovery. We applied HT-SIP to 13 C-AMF hyphosphere DNA from a 13 CO 2 plant labeling study and created metagenome-assembled genomes (MAGs) using high-resolution SIP metagenomics (14 metagenomes per gradient). SIP confirmed the AMF Rhizophagus intraradices and associated MAGs were highly enriched (10–33 atom% 13 C), even though the soils’ overall enrichment was low (1.8 atom% 13 C). We assembled 212 13 C-hyphosphere MAGs; the hyphosphere taxa that assimilated the most AMF-derived 13 C were from the phyla Myxococcota, Fibrobacterota, Verrucomicrobiota, and the ammonia-oxidizing archaeon genus Nitrososphaera . Conclusions Our semi-automated HT-SIP approach decreases operator time and improves reproducibility by targeting the most labor-intensive steps of SIP—fraction collection and cleanup. We illustrate this approach in a unique and understudied soil microhabitat—generating MAGs of actively growing microbes living in the AMF hyphosphere (without plant roots). The MAGs’ phylogenetic composition and gene content suggest predation, decomposition, and ammonia oxidation may be key processes in hyphosphere nutrient cycling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Spectral induced polarization (SIP) measurements across a PFAS-contaminated source zone

There is a pressing need for the development of field-scale, in situ screening technologies for assessing variations in aqueous film forming foam (AFFF) concentrations in soils at former fire training and storage sites. Field-scale Spectral Induced Polarization (SIP) geophysical measurements were acquired on a transect crossing an AFFF source zone. Soil samples were acquired from ten locations and used to determine variations in poly- and per-fluoroalkyl substances (PFAS) concentrations in soils and soil texture. These samples were also used to create triplicate soil columns for laboratory-grade SIP measurements. Field and laboratory observations provide evidence that SIP measurements are sensitive to the concentration of AFFF constituents associated with the pore surface in soils. The phase of the SIP measurements on the laboratory samples was linearly correlated with total soil-sorbed PFAS concentration. The phase from the field SIP measurements was highest over the location of maximum PFAS concentration measured on the laboratory samples, although a significant correlation between field-measured phase and laboratory-measured total PFAS concentration was not established. The sensitivity of the SIP response to the removal of soil PFAS using a methanol wash procedure (total PFAS concentration drop of 366 ppb) adds evidence for the case for SIP characterization of AFFF source zones. The results of these studies suggest that SIP might be developed into a field-scale technology for rapid, indirect assessment of AFFF source zones. Such a technology could improve the effectiveness of AFFF source zone characterization at reduced costs.

58 GEOSCIENCES↗
DOE OSTI2020

PFLOTRAN-SIP: A PFLOTRAN Module for Simulating Spectral-Induced Polarization of Electrical Impedance Data

Spectral induced polarization (SIP) is a non-intrusive geophysical method that collects chargeability information (the ability of a material to retain charge) in the time domain or its phase shift in the frequency domain. Although SIP is a temporal method, it cannot measure the dynamics of flow and solute/species transport in the subsurface over long times (i.e., 10–100 s of years). Data collected with the SIP technique need to be coupled with fluid flow and reactive-transport models in order to capture long-term dynamics. To address this challenge, PFLOTRAN-SIP was built to couple SIP data to fluid flow and solute transport processes. Specifically, this framework couples the subsurface flow and transport simulator PFLOTRAN and geoelectrical simulator E4D without sacrificing computational performance. PFLOTRAN solves the coupled flow and solute-transport process models in order to estimate solute concentrations, which were used in Archie’s model to compute bulk electrical conductivities at near-zero frequency. These bulk electrical conductivities were modified while using the Cole–Cole model to account for frequency dependence. Using the estimated frequency-dependent bulk conductivities, E4D simulated the real and complex electrical potential signals for selected frequencies for SIP. These frequency-dependent bulk conductivities contain information that is relevant to geochemical changes in the system. This study demonstrated that the PFLOTRAN-SIP framework is able to detect the presence of a tracer in the subsurface. SIP offers a significant benefit over ERT in the form of greater information content. It provided multiple datasets at different frequencies that better constrained the tracer distribution in the subsurface. Consequently, this framework allows for practitioners of environmental hydrogeophysics and biogeophysics to monitor the subsurface with improved resolution.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Monitoring of In Situ Remediation Technologies with SIP

Deconvoluting the spectral induced polarization (SIP) signal is critical to developing SIP as a robust technology to monitor delivery and subsurface geochemical reactions. Therefore, the primary goal of this project is to elucidate the sensitivity of SIP to geochemical reactions occurring during subsurface remediation. This document presents progress for fiscal year (FY) 2024 toward field-scale SIP monitoring of amendment delivery and reactivity for subsurface remediation. An interdisciplinary critical review team was assembled to review historical SIP data collected under the Deep Vadose Zone program. Based on feedback from the team additional experiments were designed and initiated for the calcium citrate phosphate technology for in situ formation of apatite and additional analysis was conducted with data from sulfur modified iron experiments to consider the potential for scaling monitoring with SIP to the field. In addition, the team outlined a proposed framework for future evaluation of SIP for environmental remediation monitoring to be implemented over the next 2-3 years.

47 OTHER INSTRUMENTATION↗
DOE OSTI2020

Synthesis, Crystal and Electronic Structure of La 2 SiP 4

La 2 SiP 4 (mP-28, Z=4, Wyckoff sequence e 7 , space group P2 1 /c (No. 14), a=10.8230(6) Å, b=7.5208(4) Å, c=7.9189(4) Å, and β=105.389(2)°) which crystallizes in the La 2 CuS 4 structure type is reported here. Instead of isolated CuS 3 triangles bridged by disulfide anions, in the crystal structure of La 2 SiP 4 , one-dimensional zig-zag chains composed of SiP 4 tetrahedra connected by P–P bonds are present. Lanthanum cations fill the voids between the chains and are coordinated by either 9P or 8P+Si atoms. La2SiP4 is a narrow bandgap semiconductor with calculated and measured optical bandgaps of 0.35 eV and 0.85(1) eV, respectively.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

GLBRC Soil Yearlong Incubation 13C-SIP-Lipidomics

Data package for Lipids represent a dynamic, yet stable pool of microbially-derived soil carbon This data is published under a CC0 license. The authors encourage data reuse and request attribution by referencing the below citations for the data packages and associated manuscript. Please cite as: Rempfert KR, Bell SL, Kasanke CP, Kyle JE, Hofmockel KS. 2025. GLBRC Soil Yearlong Incubation 13C-SIP-Lipidomics. [Data Set] PNNL DataHub. doi: Rempfert KR, Bell SL, Kasanke CP, Kyle JE, Hofmockel KS. 2025. MSV000097435: GLBRC soil yearlong incubation 13C-SIP-Lipidomics [Data Set] MassIVE. doi:10.25345/C57659T3K Rempfert KR, Bell SL, Kasanke CP, Kyle JE, Hofmockel KS. 2025. Lipids represent a dynamic, yet stable pool of microbially-derived soil carbon. In Prep This data package consists of compound-specific 13C SIP-lipidomics data from a yearlong tracer incubation experiment designed to investigate microbial lipid persistence in switchgrass bioenergy crop soils. In order to explore how lipid structure may modulate the persistence of C in soil lipids, we leveraged soils from two sites (Michigan - sandy texture, Wisconsin - silty texture) operated by the U.S. Department of Energy-funded Great Lakes Bioenergy Research Center (GLBRC). These sites had comparable climates, identical management practices, but contrasting soil textures, allowing us to assess the variability of lipid accrual or degradation in soils as well as provide insight regarding the degree to which edaphic properties may regulate the retention of soil lipids. Untargeted lipidomics analyses were performed to identify 13C-labeled lipids in the soil microbiome after long-term incubation. Soils were supplemented with 100 micrograms glucose per gram dry soil (99 atom % 13C or natural abundance for paired control) and incubated; samples were collected two months and one year after glucose addition. Lipid extracts (MPLEx) were analyzed by LC-MS/MS and identified using LIQUID. Calculation of isotopic enrichment of lipids was performed by targeted approach using TarMet to quantify lipid isotopologues and IsoCorrectoR to correct for natural abundance isotopes. Contents: Data package contents reported here are the first version and contain downstream analysis files for the raw LC-MS mass spectrometry files (.mzXML) deposited at the MassIVE database repository under accession MSV000097435 (80 experimental runs; 5.85 GB) | MassIVE DOI: 10.25345/C57659T3K. Support files include the additional data download 'Read Me' file containing data descriptor information. Reported data download contents are structured for compliance with project data sharing guidelines, community standards initiatives, and sponsor stakeholder policies supporting FAIR data principles. Data processing software, analysis tools, and data workflows are listed below corresponding to the host repository long-term location. Available Data Downloads (0.3 GB): "GLBRC soil yearlong incubation 13C-SIP-Lipidomics_readme.txt" - 'Read Me' data package content file (txt) "GLBRC_DataPackage_analysis files" - Data processing files (Rmd) and saved intermediate data processing outputs (rds, csv, xlsx) "GLBRC_13C_lipidomics_dataset.xlsx" - processed data in tabular format (xlsx) Linked Software: LIQUID LC-MS Analysis Software | 10.5281/zenodo.6459462 Lipid Mini-On Software Tools | 10.5281/zenodo.1492803 pmartR Omics Statistical Software | 10.5281/zenodo.6108667 xcms (v4.3.3) TarMet (v1.1.1) IsoCorrectoR (1.24.0) Funding Acknowledgments: This research was supported by an Early Career Research Program award funded by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research (OBER) Genomic Science program under FWP 68292, FWP 07880 and EMSL Exploratory Research Project 51095. A portion of this work was performed in the William R. Wiley Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by OBER and located at Pacific Northwest National Laboratory (PNNL). PNNL is a multi-program national laboratory operated by Battelle for the DOE under Contract DE-AC05-76RLO1830.

Rempfert, Kaitlin R [Pacific Northwest National La↗
DOE OSTI2022

Correlative SIP-FISH-Raman-SEM-NanoSIMS links identity, morphology, biochemistry, and physiology of environmental microbes

Microscopic and spectroscopic techniques are commonly applied to study microbial cells but are typically used on separate samples, resulting in population-level datasets that are integrated across different cells with little spatial resolution. To address this shortcoming, we developed a workflow that correlates several microscopic and spectroscopic techniques to generate an in depth analysis of individual cells. By combining stable isotope probing (SIP), fluorescence in situ hybridization (FISH), scanning electron microscopy (SEM), confocal Raman microspectroscopy (Raman), and nano-scale secondary ion mass spectrometry (NanoSIMS), we illustrate how individual cells can be thoroughly interrogated to obtain information about their taxonomic identity, structure, physiology, and metabolic activity. Analysis of an artificial community demonstrated that our correlative approach was able to resolve the activity of single cells using heavy water SIP in conjunction with Raman and/or NanoSIMS and establish their taxonomy and morphology using FISH and SEM. We then applied this workflow to a sample of yet uncultured multicellular magnetotactic bacteria. In addition to establishing their identity and activity, backscatter electron microscopy (BSE), NanoSIMS, and energy-dispersive X-ray spectroscopy (EDS) were employed to characterize the magnetosomes within the cells. By integrating these techniques, we demonstrate a cohesive approach to thoroughly study environmental microbes at single cell resolution.

Schaible, George↗
DOE OSTI2020

Materials Data on SiP by Materials Project

PSi crystallizes in the orthorhombic Cmc2_1 space group. The structure is two-dimensional and consists of two PSi sheets oriented in the (0, 0, 1) direction. there are six inequivalent Si4- sites. In the first Si4- site, Si4- is bonded to one Si4- and three P4+ atoms to form corner-sharing SiSiP3 tetrahedra. The Si–Si bond length is 2.36 Å. There are two shorter (2.29 Å) and one longer (2.31 Å) Si–P bond lengths. In the second Si4- site, Si4- is bonded to one Si4- and three P4+ atoms to form corner-sharing SiSiP3 tetrahedra. There are two shorter (2.29 Å) and one longer (2.31 Å) Si–P bond lengths. In the third Si4- site, Si4- is bonded to one Si4- and three P4+ atoms to form distorted corner-sharing SiSiP3 tetrahedra. The Si–Si bond length is 2.35 Å. There are one shorter (2.27 Å) and two longer (2.28 Å) Si–P bond lengths. In the fourth Si4- site, Si4- is bonded to one Si4- and three P4+ atoms to form distorted corner-sharing SiSiP3 tetrahedra. There are one shorter (2.27 Å) and two longer (2.28 Å) Si–P bond lengths. In the fifth Si4- site, Si4- is bonded to one Si4- and three P4+ atoms to form distorted corner-sharing SiSiP3 tetrahedra. The Si–Si bond length is 2.35 Å. There are one shorter (2.27 Å) and two longer (2.28 Å) Si–P bond lengths. In the sixth Si4- site, Si4- is bonded to one Si4- and three P4+ atoms to form distorted corner-sharing SiSiP3 tetrahedra. There are one shorter (2.27 Å) and two longer (2.28 Å) Si–P bond lengths. There are six inequivalent P4+ sites. In the first P4+ site, P4+ is bonded in a distorted T-shaped geometry to three Si4- atoms. In the second P4+ site, P4+ is bonded in a distorted T-shaped geometry to three Si4- atoms. In the third P4+ site, P4+ is bonded in a distorted T-shaped geometry to three Si4- atoms. In the fourth P4+ site, P4+ is bonded in a distorted T-shaped geometry to three Si4- atoms. In the fifth P4+ site, P4+ is bonded in a distorted T-shaped geometry to three Si4- atoms. In the sixth P4+ site, P4+ is bonded in a distorted T-shaped geometry to three Si4- atoms.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on Co(SiP)3 by Materials Project

CoSi3P3 crystallizes in the monoclinic P2_1 space group. The structure is three-dimensional. there are two inequivalent Co3+ sites. In the first Co3+ site, Co3+ is bonded in a 3-coordinate geometry to three Si4- atoms. There are a spread of Co–Si bond distances ranging from 2.21–2.36 Å. In the second Co3+ site, Co3+ is bonded in a 3-coordinate geometry to three Si4- atoms. All Co–Si bond lengths are 2.25 Å. There are six inequivalent Si4- sites. In the first Si4- site, Si4- is bonded to one Co3+ and three P3+ atoms to form distorted corner-sharing SiCoP3 tetrahedra. There are a spread of Si–P bond distances ranging from 2.31–2.36 Å. In the second Si4- site, Si4- is bonded to one Co3+ and three P3+ atoms to form distorted corner-sharing SiCoP3 tetrahedra. There are one shorter (2.28 Å) and two longer (2.33 Å) Si–P bond lengths. In the third Si4- site, Si4- is bonded in a 4-coordinate geometry to two equivalent Co3+ and two P3+ atoms. There are one shorter (2.29 Å) and one longer (2.40 Å) Si–P bond lengths. In the fourth Si4- site, Si4- is bonded to one Co3+ and three P3+ atoms to form distorted corner-sharing SiCoP3 tetrahedra. There are a spread of Si–P bond distances ranging from 2.27–2.34 Å. In the fifth Si4- site, Si4- is bonded to four P3+ atoms to form corner-sharing SiP4 tetrahedra. There are a spread of Si–P bond distances ranging from 2.25–2.29 Å. In the sixth Si4- site, Si4- is bonded in a distorted rectangular see-saw-like geometry to one Co3+ and three P3+ atoms. There are one shorter (2.28 Å) and two longer (2.33 Å) Si–P bond lengths. There are six inequivalent P3+ sites. In the first P3+ site, P3+ is bonded in a trigonal non-coplanar geometry to three Si4- atoms. In the second P3+ site, P3+ is bonded to four Si4- atoms to form corner-sharing PSi4 tetrahedra. In the third P3+ site, P3+ is bonded in a distorted trigonal non-coplanar geometry to three Si4- atoms. In the fourth P3+ site, P3+ is bonded in a distorted trigonal non-coplanar geometry to three Si4- atoms. In the fifth P3+ site, P3+ is bonded in a distorted trigonal non-coplanar geometry to three Si4- atoms. In the sixth P3+ site, P3+ is bonded in an L-shaped geometry to two Si4- atoms.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on SiP by Materials Project

PSi is Zincblende, Sphalerite structured and crystallizes in the cubic F-43m space group. The structure is three-dimensional. Si4- is bonded to four equivalent P4+ atoms to form corner-sharing SiP4 tetrahedra. All Si–P bond lengths are 2.31 Å. P4+ is bonded to four equivalent Si4- atoms to form corner-sharing PSi4 tetrahedra.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on Fe(SiP)4 by Materials Project

FeSi4P4 crystallizes in the triclinic P1 space group. The structure is three-dimensional. Fe3+ is bonded in a 3-coordinate geometry to three Si4- atoms. There are a spread of Fe–Si bond distances ranging from 2.26–2.28 Å. There are four inequivalent Si4- sites. In the first Si4- site, Si4- is bonded to one Fe3+ and three P+3.25+ atoms to form distorted SiFeP3 tetrahedra that share corners with three equivalent SiP4 tetrahedra and corners with three equivalent SiFeP3 trigonal pyramids. There are two shorter (2.32 Å) and one longer (2.33 Å) Si–P bond lengths. In the second Si4- site, Si4- is bonded to four P+3.25+ atoms to form corner-sharing SiP4 tetrahedra. There are one shorter (2.23 Å) and three longer (2.26 Å) Si–P bond lengths. In the third Si4- site, Si4- is bonded in a distorted rectangular see-saw-like geometry to one Fe3+ and three P+3.25+ atoms. There are one shorter (2.31 Å) and two longer (2.32 Å) Si–P bond lengths. In the fourth Si4- site, Si4- is bonded to one Fe3+ and three P+3.25+ atoms to form distorted corner-sharing SiFeP3 trigonal pyramids. There are one shorter (2.28 Å) and two longer (2.33 Å) Si–P bond lengths. There are four inequivalent P+3.25+ sites. In the first P+3.25+ site, P+3.25+ is bonded in a distorted T-shaped geometry to three Si4- atoms. In the second P+3.25+ site, P+3.25+ is bonded in a distorted trigonal non-coplanar geometry to three Si4- atoms. In the third P+3.25+ site, P+3.25+ is bonded in a tetrahedral geometry to four Si4- atoms. In the fourth P+3.25+ site, P+3.25+ is bonded in a trigonal non-coplanar geometry to three Si4- atoms.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Development and Validation of Low-Cost, High-Reflectance Composite CSP Facets: SIPS Final Report

This work investigates the various challenges associated with developing heliostat structural composite facets using 1 mm glass mirrors. Such facets are desirable for Concentrating Solar Power because 1 mm glass mirrors provide an absolute increase in reflectivity of 2-3 % over the industry standard of 4 mm glass mirrors. Prototypes of paraboloid composite facets with 1 mm glass mirrors were constructed that have a root mean square slope error on the order of 2 mrad while achieving greater than 96% reflectivity. These facets were constructed using a low-quality aluminum mold and a bill of materials that show potential to achieve cost parity with existing 4 mm glass mirrors supported by structural steel. The facets produced were able to survive up to 50 mm hail ball impacts and were robust against accelerated environmental cycling designed to expose durability concerns. Further work is needed to develop a scalable and cost-effective manufacturing process with a similar bill of materials.

14 SOLAR ENERGY↗
DOE OSTI2026

Testing and Validation of Wireless Communication Architecture for Heliostat Fields: SIPS Final Report

This work focuses on the development and testing of a low-cost wireless communication system for heliostat fields, enabling significant capital costs reductions for concentrating solar thermal systems. Outputs of this work include a working demonstration of a multi-node communication system, clear reporting of system performance, and technical documentation of system development and architecture for reproducibility. Through this process, an open-source repository was created for manufacturing hardware at ~$30/heliostat. The system includes software for cybersecurity, achieving sub-second communication latencies and derisking of hardware for eventual scale-up to tens of thousands of heliostats. While the system is not currently off-the-shelf ready, there is now a clearly defined pathway for scaling up and completing the commercial development process.

14 SOLAR ENERGY↗
DOE OSTI2024

MISIP: a data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence and experiment

DNA/RNA-stable isotope probing (SIP) is a powerful tool to link in situ microbial activity to sequencing data. Every SIP dataset captures distinct information about microbial community metabolism, process rates, and population dynamics, offering valuable insights for a wide range of research questions. Data reuse maximizes the information derived from the labor and resource-intensive SIP approaches. Yet, a review of publicly available SIP sequencing metadata showed that critical information necessary for reproducibility and reuse was often missing. Here, we outline the Minimum Information for any Stable Isotope Probing Sequence (MISIP) according to the Minimum Information for any (x) Sequence (MIxS) framework and include examples of MISIP reporting for common SIP experiments. Our objectives are to expand the capacity of MIxS to accommodate SIP-specific metadata and guide SIP users in metadata collection when planning and reporting an experiment. The MISIP standard requires 5 metadata fields—isotope, isotopolog, isotopolog label, labeling approach, and gradient position—and recommends several fields that represent best practices in acquiring and reporting SIP sequencing data (e.g., gradient density and nucleic acid amount). The standard is intended to be used in concert with other MIxS checklists to comprehensively describe the origin of sequence data, such as for marker genes (MISIP-MIMARKS) or metagenomes (MISIP-MIMS), in combination with metadata required by an environmental extension (e.g., soil). The adoption of the proposed data standard will improve the reuse of any sequence derived from a SIP experiment and, by extension, deepen understanding of in situ biogeochemical processes and microbial ecology.

Simpson, Abigayle↗