Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “intact samples”

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 127 records · Page 7

Optimized purification methods for metallic contaminant removal from directly recycled Li-ion battery cathodes

Metallic contaminants pose a significant challenge to the viability of directly recycling Li-ion batteries. To date, few strategies exist to selectively remove metallic impurities from mixtures of shredded end-of-life material (black mass; BM) without concurrently damaging the structure and electrochemical performance of the target active material. We herein present tailored methods to selectively ionize two major contaminants—Al and Cu—while retaining a representative cathode (LiNi 0.33 Mn 0.33 Co 0.33 O 2 ; NMC-111) intact. This BM purification process is conducted at moderate temperatures in a KOH-based solution matrix. We rationally evaluate approaches to increase both the kinetic corrosion rate and the thermodynamic solubility of Al 0 and Cu 0 , and evaluate the impact of these treatment conditions on the structure, chemistry, and electrochemical performance of NMC. Specifically, we explore the impacts of chloride-based salts, a strong chelating agent, elevated temperature, and sonication on the rate and extent of contaminant corrosion, while concurrently evaluating the effects on NMC. The reported BM purification process is then demonstrated on samples of “simulated BM” containing a practically relevant 1 wt% concentration of Al or Cu. Increasing the kinetic energy of the purifying solution matrix through elevated temperature and sonication accelerates the corrosion of metallic Al and Cu, such that ∼100% corrosion of 75 μm Al and Cu particles is achieved within 2.5 hr. Further, we determine that effective mass transport of ionized species critically impacts the efficacy of Cu corrosion, and that saturated Cl – hinders rather than accelerates Cu corrosion by increasing solution viscosity and introducing competitive pathways for Cu surface passivation. The purification conditions do not induce bulk structural damage to NMC, and electrochemical capacity is maintained in half-cell format. Testing in full cells suggests that a limited quantity of residual surface species are present after treatment, which initially disrupt electrochemical behavior at the graphite anode but are subsequently consumed. Process demonstration on simulated BM suggests that contaminated samples—which prior to treatment show catastrophic electrochemical performance—can be recovered to pristine electrochemical capacity. The reported BM purification method offers a compelling and commercially viable solution to address contamination, particularly in the “fine” fraction of BM where contaminant sizes are on the same order of magnitude as NMC and where traditional separation approaches are unfeasible. Thus, this optimized BM purification technique offers a pathway towards viable direct recycling of BM feedstocks that would otherwise be unusable.

25 ENERGY STORAGE↗

Three-dimensional mapping of mineral in intact shark centra with energy dispersive x-ray diffraction

The centra of shark vertebrae consist of cartilage mineralized by a bioapatite similar to bone's carbonated hy-droxyapatite, and, without a repair mechanism analogous to remodeling in bone, these structures still survive millions of cycles of high-strain loading. The main structures of the centrum are an hourglass-shaped double cone and the intermedialia which supports the cones. Little is known about the nanostructure of shark centra, spe-cifically the relationship between bioapatite and cartilage fibers, and this study uses energy dispersive diffraction (EDD) with polychromatic synchrotron x-radiation to study the spatial organization of the mineral phase and its crystallographic texture. The unique energy-sensitive detector array at beamline 6-BM-B, the Advanced Photon Source, enables EDD to quantify the texture within each sampling volume with one exposure while constructing 3D maps via specimen translation across the sampling volume. Herein this study maps a centrum from two shark orders, a carcharhiniform and a lamniform, with different intermedialia structures. In the blue shark (Prionace glauca, Carcharhiniformes), the bioapatite's c-axes are oriented laterally within the centrum's cone walls but axially within the wide wedges of the intermedialia; the former is interpreted to resist lateral deformation, the latter to support axial loads. In the shortfin mako (Isurus oxyrinchus, Lamniformes), there is some tendency for c-axis variation with position, but the situation is unclear because one dimension of the sampling volume is consid-erably larger than the thickness and spacing of the intermedialia's radially-oriented lamellae. Because elastic modulus in collagen plus bioapatite mineralized tissues varies significantly with both volume fraction of bio-apatite and crystallographic texture, the present 3D EDD-derived maps should inform future 3D numerical models of shark centra under applied load.

59 BASIC BIOLOGICAL SCIENCES↗

Local structure of Sr 2 CuO 3.3 , a 95 K cuprate superconductor without CuO 2 planes

The local structure of the highly “overdoped” 95 K superconductor Sr 2 CuO 3.3 determined by Cu K X-ray absorption fine structure (XAFS) at 62 K in magnetically oriented samples shows that 1) the magnetization is perpendicular to the c axis; 2) at these levels of precision the Cu sublattice is tetragonal in agreement with the crystal structure; the O sublattice has 3) continuous -Cu-O- chains that orient perpendicular to an applied magnetic field; 4) approximately half-filled -Cu-O- chains that orient parallel to this field; 5) a substantial number of apical O vacancies; 6) O ions at some apical positions with expanded Cu-O distances; and 7) interstitial positions that imply highly displaced Sr ions. These results contradict the universally accepted features of cuprates that require intact CuO 2 planes, magnetization along the c axis, and a termination of the superconductivity when the excess charge on the CuO 2 Cu ions exceeds 0.27. These radical differences in charge and structure demonstrate that this compound constitutes a separate class of Cu-O–based superconductors in which the superconductivity originates in a different, more complicated structural unit than CuO 2 planes while retaining exceptionally high transition temperatures.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Unimodal Imaging of Monovalent Metal-Chelator Complexes and Lipids by MALDI Imaging Mass Spectrometry

Careful regulation of monovalent metal ions (M + ) is necessary to maintain a functional cellular system. Of these ions, appropriate sodium (Na + ) and potassium (K + ) concentrations are particularly integral for electrochemical signaling, as well as the secondary transport of nutrients and waste. Dysregulation of M + homeostasis can disrupt these mechanisms, potentially influencing the metabolism of downstream biomolecules such as lipids. Thus, the relationship between M + abundances and related biomolecular distributions must be elucidated to better understand the physiology of healthy and disordered tissues. Traditional techniques for imaging biological metal distributions include SIMS, LA-ICP-MS, and XRF; however, these capabilities are limited to elemental analysis or the analysis of molecular fragments and must be paired with other modalities to visualize distributions of more complex biomolecules within the same or similar samples. Conversely, matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) is a powerful tool often used for mapping such biomolecular distributions, but current methods are unable to detect metals within tissue. This study illustrates a novel methodology that adds metal detection to the MALDI IMS repertoire through which the simultaneous detection of M + metals and lipids is achievable. Using a robotic sprayer for homogeneous application, on-tissue deposition of the chelator deferiprone (DEF) enables subsequent detection of the ionizable metal-chelator complex by MALDI without hindering lipid detection. Our work provides proof-of-concept data for the simultaneous detection of K + , Na + , and intact lipids using MALDI IMS.

59 BASIC BIOLOGICAL SCIENCES↗

Initiator-dependent kinetics of lyotropic liquid crystal-templated thermal polymerization

In this study, we examine the polymerization kinetics with different thermal initiators in lamellar and hexagonal lyotropic liquid crystal (LLC) structures directed by Pluronic L64. Ammonium persulfate is used to initiate the polymerization from the water phase, whereas azobisisobutyronitrile and benzoyl peroxide are employed to commence the reaction through the monomer phase. While the mesophase structure remains intact for all the initiation systems, the kinetics of polymerization and conversion vary significantly. The obtained differential scanning calorimetry (DSC) results reveal that, under same conditions, initiation from water (IFW) system results in enhanced reaction rates as well as higher monomer conversions compared to initiation from oil (IFO) one. Higher termination rate in LLC nanoconfinements induces lower reaction rates in IFO system. Moreover, our work on different LLC structures show that the effect of nanoconfinement on polymerization rate can be minimized through IFW. Chemorheology not only confirms the results obtained from DSC, but also shows that, in similar monomer conversions, the polymers obtained from IFW system exhibit an improved mechanical properties over the samples produced though IFO process.

36 MATERIALS SCIENCE↗

Mapping O 2 concentration in ex-vivo tissue samples on a fast PLIM macro-imager

O 2 PLIM microscopy was employed in various studies, however current platforms have limitations in sensitivity, image acquisition speed, accuracy and general usability. We describe a new PLIM imager based on the Timepix3 camera (Tpx3cam) and its application for imaging of O 2 concentration in various tissue samples stained with a nanoparticle based probe, NanO 2 -IR. Upon passive staining of mouse brain, lung or intestinal tissue surface with minute quantities of NanO 2 -IR or by microinjecting the probe into the lumen of small or large intestine fragments, robust phosphorescence intensity and lifetime signals were produced, which allow mapping of O 2 in the tissue within 20 s. Inhibition of tissue respiration or limitation of O 2 diffusion to tissue produced the anticipated increases or decreases in O 2 levels, respectively. The difference in O 2 concentration between the colonic lumen and air-exposed serosal surface was around 140 µM. Furthermore, subcutaneous injection of 5 µg of the probe in intact organs (a paw or tail of sacrificed mice) enabled efficient O 2 imaging at tissue depths of up to 0.5 mm. Overall, the PLIM imager holds promise for metabolic imaging studies with various ex vivo models of animal tissue, and also for use in live animals.

59 BASIC BIOLOGICAL SCIENCES↗

Carbon dioxide, water vapor and methane soil efflux (soil respiration) in a Pinus palustris root exclusion in Georgetown, SC

This dataset contains processed data from a combination of survey flux chambers and long-term automated flux chambers. Soil flux measurements were conducted from June 2023 through December 2025 in a mature longleaf pine forest in Georgetown, SC. Soil respiration measurements were conducted approximately biweekly for two and a half years, before and after a root exclusion that took place on May 5, 2024. Processed, QAQC’d data for the treatment (root exclusion) and control (roots intact) before and after the root exclusion can be found in the file: 1_DATA_ESS_DOE_HR_RS_HB2_QAQC_Survey_Data_20260223.csv. Two multiday deployments were also conducted prior to the root exclusion using long-term automated chambers to continuously monitor greenhouse gas soil efflux. Processed, QAQC’d data for both long-term deployments can be found in the file: 2_DATA_ESS_DOE_HR_RS_HB2_QAQC_Longterm_Data_20260209.csv. Raw and working data files (.json, .81x, & .82z format) from LI-COR equipment are included for reference and can be accessed using SoilFluxPro software. CSV metadata files describe the raw data and modifications made using SoilFluxPro v5 and Matlab R2024b, as well as formatting and units for processed CSVs. Matlab code is included for reading in the processed CSVs, with sample figures comparing treatment and control. This research was performed as part of the project: “Improving models of stand and watershed carbon and water fluxes with more accurate representations of soil-plant-water dynamics in southern pine ecosystems”, which examines in part the effects hydraulic redistribution on soil efflux of carbon dioxide, water vapor and methane, as well as soil moisture and temperature in a southern pine ecosystem with sandy soils and high water table.

CARBON DIOXIDE FLUX↗

Data for: Spatial access and resource limitations control carbon mineralization in soils

This dataset contains data and code used for the paper "Spatial access and resource limitations control carbon mineralization in soils", https://doi.org/10.1016/j.soilbio.2021.108427. Core-scale soil carbon fluxes are ultimately regulated by pore-scale dynamics of substrate availability and microbial access. These are constrained by physicochemical and biochemical phenomena (e.g. spatial access and hydrologic connectivity, physical occlusion, adsorption-desorption with mineral surfaces, nutrient and resource limitations). We conducted an experiment to determine how spatial access and resource limitations influence core-scale water-soluble soil organic matter (SOM) mineralization, and how these are regulated by antecedent moisture conditions. Intact soil cores were incubated at field-moist vs. drought conditions, after which they were saturated from above (to simulate precipitation) or below (to simulate groundwater recharge). Soluble carbon (acetate) and nitrogen (nitrate) forms were added to some cores during the rewetting process to alleviate potential nutrient limitations. Soil respiration was measured during the incubation, after which pore water was extracted from the saturated soils and analyzed for water soluble organic carbon concentrations and characterization. Our results showed that carbon (C) amendments increased the cumulative carbon dioxide (CO2) evolved from the soil cores, suggesting that the soils were C-limited. Drought and rewetting increased soil respiration, and there was a greater abundance of complex aromatic molecules in pore waters sampled from these soils. This newly available substrate appeared to alleviate nutrient limitations on respiration, because there were no further respiration increases with subsequent C and N amendments. We had hypothesized that respiration would be influenced by wetting direction, as simulated precipitation would mobilize C from the surface. However, as a main effect, this response was seen only in the C-amended soils, indicating that surface-C may not have been bioavailable. At the pore scale (pore water samples), drought and the C, N amendments caused a net loss of identified molecules when the soils were rewet from below, whereas wetting from above caused a net increase in identified molecules, suggesting that fresh inputs stimulated the C-and N-limited microbial populations present deeper in the soil profile. Our experiment highlights the complex and interactive role of antecedent moisture conditions, wetting direction, and resource limitations in driving core-scale C fluxes.This dataset contains a compressed (.zip) archive of the data and R scripts used for this manuscript. The dataset includes files in .csv format, which can be accessed and processed using MS Excel or R. This archive can also be accessed on GitHub at https://github.com/kaizadp/TES_spatial_access_2021 (DOI: 10.5281/zenodo.5522938).

54 ENVIRONMENTAL SCIENCES↗

Double diffraction imaging of x-ray induced structural dynamics in single free nanoparticles

Abstract Because of their high photon flux, x-ray free-electron lasers (FEL) allow to resolve the structure of individual nanoparticles via coherent diffractive imaging (CDI) within a single x-ray pulse. Since the inevitable rapid destruction of the sample limits the achievable resolution, a thorough understanding of the spatiotemporal evolution of matter on the nanoscale following the irradiation is crucial. We present a technique to track x-ray induced structural changes in time and space by recording two consecutive diffraction patterns of the same single, free-flying nanoparticle, acquired separately on two large-area detectors opposite to each other, thus examining both the initial and evolved particle structure. We demonstrate the method at the extreme ultraviolet (XUV) and soft x-ray Free-electron LASer in Hamburg (FLASH), investigating xenon clusters as model systems. By splitting a single XUV pulse, two diffraction patterns from the same particle can be obtained. For focus intensities of about 2 × 10 12 W cm −2 we observe still largely intact clusters even at the longest delays of up to 650 picoseconds of the second pulse, indicating that in the highly absorbing systems the damage remains confined to one side of the cluster. Instead, in case of five times higher flux, the diffraction patterns show clear signatures of disintegration, namely increased diameters and density fluctuations in the fragmenting clusters. Future improvements to the accessible range of dynamics and time resolution of the approach are discussed.

Sauppe, M. (ORCID:0000000163123102)↗

Hexagonal Lattices of HIV Capsid Proteins Explored by Simulations Based on a Thermodynamically Consistent Model

HIV capsid proteins (CAs) may self-assemble into a variety of shapes under in vivo and in vitro conditions. Here, we employed simulations based on a residue-level coarse-grained (CG) model with full conformational flexibility to investigate hexagonal lattices, which are the underlying structural pattern for CA aggregations. Facilitated by enhanced sampling simulations to rigorously calculate CA dimerization and polymerization affinities, we calibrated our model to reproduce the experimentally measured affinities. Here using the calibrated model, we performed unbiased simulations on several large systems consisting of 1512 CA subunits, allowing reversible binding and unbinding of the CAs in a thermodynamically consistent manner. In one simulation, a preassembled hexagonal CA sheet developed spontaneous curvatures reminiscent of those observed in experiments, and the edges of the sheet exhibited local curvatures larger than those of the interior. In other simulations starting with randomly distributed CAs at different concentrations, existing CA assemblies grew by binding free capsomeres to the edges and by merging with other assemblies. At high CA concentrations, rapid establishment of predominant aggregates was followed by much slower adjustments toward more regular hexagonal lattices, with increasing numbers of intact CA hexamers and pentamers being formed. Our approach of adapting a general CG model to specific systems by using experimental binding data represents a practical and effective strategy for simulating and elucidating intricate protein aggregations.

59 BASIC BIOLOGICAL SCIENCES↗

Development of Direct Injection/Ionization Mass Spectrometry Methods for Whole Molecule Characterization

The objective of this work is to adapt ambient ionization mass spectrometry (AMS) techniques for the rapid analysis of intact uranium complexes, stable strontium, cerium, and explosive compounds. The methods used were “soft ionization” techniques, which facilitate the detection of whole molecule complexes. The soft ionization mass spectrometry (MS) techniques that were investigated include paper spray ionization (PSI), matrix-assisted ionization (MAI), electrospray ionization (ESI) and direct analysis in real time (DART). For the first time, PSI-MS methods were successfully developed for whole molecule uranium-containing analytes (uranyl acetate, uranyl nitrate, and uranyl-tributylphosphate complexes). This was also the first demonstration of uranium complex detection and characterization and one of the few examples of inorganic analysis using MAI techniques. Proof of concept experiments also putatively identified matrix-derived ions and ion complexes that have not previously been described in the literature. Additionally, PSI-MS on cotton swipe samples doped with a multi-element standard containing μg levels of U, Bi, Pb, Cd, Fe, and Zn were directly analyzed without purification, representing a major improvement over existing methods. Both PSI and MAI methods demonstrated limits of detection (LODs) in the 10 - 100’s ng for various uranyl species within a range of 10’s ppm - 100’s ppb, dependent on analytical method and analyte species. AMS methods were also developed for other inorganics, including Ce and Sr, and organic explosive residues to address specific challenges in environmental monitoring and forensics. Further refinement and qualification of the AMS techniques developed within this effort would lead to significant cost reduction and timeliness by facilitating the triage and queueing of samples for subsequent more sensitive and time-consuming analyses.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Ultra-high Information-content Chemical Imaging with Broadband Coherent Anti-Stokes Raman and Two-photon Fluorescence Lifetime Microscopy

Raman fingerprint spectroscopy and fluorescence lifetime imaging are emerging tools for studying metabolic profiles of biological specimens. While Raman fingerprint spectroscopy detects intrinsic molecular vibrations that reflect the molecular composition and chemical environment of a sample, fluorescence lifetime imaging measures changes in the excited-state lifetime of fluorophores that are sensitive to their microenvironments. Here, we present a multimodal imaging platform combining broadband coherent anti-Stokes Raman scattering (BCARS) and two-photon fluorescence lifetime imaging (2p-FLIM) microscopy that can acquire biologically relevant Raman fingerprint spectra and fluorescence lifetime signals in vivo and simultaneously. The tremendous chemical information obtained from spatially co-registered BCARS and 2p-FLIM images allows us to characterize the subtle differences between sub-cellular compartments and verify the potential false-positive results generated by fluorescence imaging alone. This is demonstrated by directly comparing the BCARS, 2p-FLIM, and two-photon excitation fluorescence(TPEF) signals simultaneously obtained from the same dye-stained organelle in the live, intact C. elegans expressing a green fluorescent protein (GFP) marker. In this work, we introduce the BCARS/2p-FLIM/TPEF setup scheme, the image acquisition steps, data processing, and representative results showing that the cross-modality imaging method enables rigorous characterization and in vivo detection at sub-cellular resolution. Furthermore, this protocol provides a framework for simultaneous chemical and fluorescence lifetime imaging to improve the accuracy of biological interpretation in complex living systems.

Xu, Haoyu [Georgia Institute of Technology, Atlant↗

Micro- and Nanoscale Surface Analysis of Late Iron Age Glass from Broborg, a Vitrified Swedish Hillfort

Abstract Archaeological glasses with prolonged exposure to biogeochemical processes in the environment can be used to understand glass alteration, which is important for the safe disposal of vitrified nuclear waste. Samples of mafic and felsic glasses with different chemistries, formed from melting amphibolitic and granitoid rocks, were obtained from Broborg, a Swedish Iron Age hillfort. Glasses were excavated from the top of the hillfort wall and from the wall interior. A detailed microscopic, spectroscopic, and diffraction study of surficial textures and chemistries were conducted on these glasses. Felsic glass chemistry was uniform, with a smooth surface showing limited chemical alteration (<150 nm), irrespective of the position in the wall. Mafic glass was heterogeneous, with pyroxene, spinel, feldspar, and quartz crystals in the glassy matrix. Mafic glass surfaces in contact with topsoil were rougher than those within the wall and had carbon-rich material consistent with microbial colonization. Limited evidence for chemical or physical alteration of mafic glass was found; the thin melt film that coated all exposed surfaces remained intact, despite exposure to hydraulically unsaturated conditions, topsoil, and associated microbiome for over 1,500 years. This supports the assumption that aluminosilicate nuclear waste glasses will have a high chemical durability in near-surface disposal facilities.

Matthews, Bethany E. (ORCID:0000000171932583)↗

Investigating Material Properties of Subsurface Rock Formations Modified by Engineering Mineral Precipitation (Final Scientific and Technical Report)

Montana State University’s (MSU) Energy Research Institute (ERI), in collaboration with the Center for Biofilm Engineering (CBE) and the Department of Civil Engineering (CE), has conducted a long‐term research program aimed at developing a novel cementing agent to address wellbore integrity and reduce the unwanted upward migration of fluids and greenhouse gases from the subsurface. The primary technology developed through this research program is known as ureolysis‐induced calcite precipitation (UICP), which harnesses bio‐chemical processes to precipitate calcium carbonate (CaCO 3 ). The same general process can also be called microbially-induced calcium carbonate precipitation (MICP) when microbes provide the process-catalyzing urease enzyme. Both terms are used in this report. Results have conclusively demonstrated that, if properly controlled, UICP can successfully seal fractures, high permeability zones, and compromised cement in the vicinity of wellbores and in nearby caprock. This technology has been successfully deployed to mitigate annular leakage in two test wells and over sixty commercial wells with a 100% success rate. This success in downhole deployment generates consideration of other subsurface applications where UICP could provide benefit to the energy sector, such as shale property modification for unconventional oil and gas recovery. The focus of this research project was to investigate fundamental material and mechanical properties of select shale cores and analyze how these properties change due to engineered mineral precipitation with the intent to control these properties to achieve a range of engineering objectives. Ultimately, the project aim was to identify valuable new areas where application of UICP might contribute to national energy security and environmental protection. The research workplan coupled UICP treatment of core samples, nuclear magnetic resonance (NMR) characterization, and mechanical strength testing at MSU with advanced X‐Ray micro-computed tomography (μCT) imaging and numerical modeling performed by collaborators at two national laboratories, the National Energy Technology Laboratory (NETL) and Lawrence Berkeley National Laboratory (LBNL). Experimental results are useful to inform geo-mechanical models which could be applied to predict mineralized rock formation behavior at field scale. Our findings suggest that NMR and μCT methods to detect and quantify biomineral formation in shale fractures are complementary and consistent with each other. Either could be used to estimate the volume of new mineral formed by UICP in shale fractures. The use of surfactants and guar gum to enhance biomineral precipitation in shale fractures merits further research. UICP can, under some conditions, increase the tensile strength of sealed shale fractures beyond that of the intact shale. These findings demonstrate that continued research in this area may be valuable to understanding and improving shale resource recovery techniques.

58 GEOSCIENCES↗

Spatial access and resource limitations control carbon mineralization in soils

Core-scale soil carbon fluxes are ultimately regulated by pore-scale dynamics of substrate availability and microbial access. These are constrained by physicochemical and biochemical phenomena (e.g. spatial access and hydrologic connectivity, physical occlusion, adsorption-desorption with mineral surfaces, nutrient and resource limitations). We conducted an experiment to determine how spatial access and resource limitations influence core-scale SOM mineralization, and how these are regulated by antecedent moisture conditions. Intact soil cores were incubated at field-moist vs. drought conditions, after which they were saturated from above (to simulate precipitation) or below (to simulate groundwater recharge). Soluble C (acetate) and N (nitrate) forms were added to some cores during the rewetting process to alleviate potential nutrient limitations. Respiration showed evidence of C-limitation, as C amendments increased the cumulative CO 2 evolved. Drought and rewetting increased soil respiration, and these soils also exhibited increased complex aromatic molecules in porewater. This newly available substrate appeared to alleviate nutrient limitations on respiration, because there were no further respiration increases with subsequent C and N amendments. We expected that respiration would be influenced by wetting direction, as simulated precipitation would mobilize C from the surface. However, as a main effect, this response was seen only in the C-amended soils, indicating that surface-C may not have been bioavailable. At the pore scale (porewater samples), compared to the baseline soils, drought and the C, N amendments caused a net loss of identified molecules when the soils were rewet from below, whereas wetting from above caused a net increase in identified molecules. This indicates that as soils were wet from below, the fresh inputs simulated the C-and N-limited microbial populations present deeper in the soil profile. Furthermore, our experiment highlights the complex and interactive role of antecedent moisture conditions, wetting direction, and resource limitations in driving core-scale C fluxes.

59 BASIC BIOLOGICAL SCIENCES↗

StreamGen: Connecting Populations of Streams and Shells to Their Host Galaxies

In this work, we study how the abundance and dynamics of populations of disrupting satellite galaxies change systematically as a function of host galaxy properties. We apply a theoretical model of the phase-mixing process to classify intact satellite galaxies and stellar streamlike and shell-like debris in ∼1500 Milky Way–mass systems generated by a semi-analytic galaxy formation code, SatGen. In particular, we test the effect of host galaxy halo mass, disk mass, ratio of disk scale height to length, and stellar feedback model on disrupting satellite populations. We find that the counts of tidal debris are consistent across all host galaxy models, within a given host mass range, and that all models can have streamlike debris on low-energy orbits, consistent with that observed around the Milky Way. However, we find a preference for streamlike debris on lower-energy orbits in models with a thicker (lower-density) host disk or on higher-energy orbits in models with a more massive host disk. Importantly, we observe significant halo-to-halo variance across all models. These results highlight the importance of simulating and observing large samples of Milky Way–mass galaxies and accounting for variations in host properties when using disrupting satellites in studies of near-field cosmology.

dark matter↗

TopPICR: A Companion R Package for Top-Down Proteomics Data Analysis

Top-down proteomics is the analysis of proteins in their intact form without proteolysis, thus preserving valuable information about post-translational modifications, isoforms, and proteolytic processing. However, it is still a developing field due to limitations in the instrumentation, difficulties with interpretation of complex mass spectra, and a lack of well-established quantification approaches. TopPIC is one of the popular tools for proteoform identification. Here we extended its capabilities into label-free proteoform quantification by developing a companion R package (TopPICR). Key steps in the TopPICR pipeline include filtering identifications, inferring a minimal set of protein accessions explaining the observed sequences, aligning retention times, recalibrating measured masses, clustering features across datasets, and finally compiling feature intensities using the match-between-runs approach. The output of the pipeline is an MSnSet object which makes downstream data analysis seamlessly compatible with packages from the Bioconductor project. It also provides the capability for visualizing proteoforms within the context of the parent protein sequence. The functionality of TopPICR is demonstrated on top-down LC-MS/MS datasets of 10 human-in-mouse xenografts of luminal and basal breast tumor samples.

59 BASIC BIOLOGICAL SCIENCES↗

National User Resource for Biological Accelerator Mass Spectrometry

The National User Resource for Biological Accelerator Mass Spectrometry (User Resource) will provide isotopic analysis (primarily radiocarbon or 14C) by accelerator mass spectrometry (AMS) for NIH- funded researchers across the United States and will be the only User Resource of its type in the United States. The User Resource will provide measurement capability and expertise to a research community that requires highly sensitive, quantitative isotope analyses. Since commissioning a new accelerator mass spectrometer in June 2014, we have measured over 4000 samples a year for collaborators and service users. The User Resource will enable us to continue to meet these research needs, as well as provide for new users whose research programs would benefit from AMS as a measurement tool. The User Resource’s forte will be ultra-high sensitivity quantitation of radiocarbon and selected other radioisotopes for research studies where isotopes are required. Radioisotope labeling studies have been and will continue to be an important tool for addressing many complex biomedical science problems. AMS is a specialized and unique type of mass spectrometry that provides absolute quantitation of radiocarbon and other relevant radioisotopes with extreme sensitivity, having limits of detection in real samples on the order of a few attomol/mg of sample at measurement precisions of ~3%. It is the only instrumental method capable of quantifying radioisotope-labeled agents routinely in real-world samples with such precision and sensitivity. The sensitivity of AMS allows for the quantification of radiolabeled metabolites in extremely complex matrices of cells and organisms at very low concentrations and in small samples. AMS allows studies to be conducted without perturbing metabolism leading to more relevant quantification of metabolic rates and pathways. In addition, it enables quantification of pharmacokinetic and metabolic properties of toxicants at environmentally relevant concentrations in model systems as well as the ability to quantify pharmacokinetics and other molecular endpoints directly in humans. Such quantitative assessments can 1) improve risk assessment for toxicants, 2) address safety and efficacy considerations for therapeutic entities, 3) deepen understanding of xenobiotic and intermediary metabolism, 4) help understand the interactions between critical molecular pathways, and 5) improve efforts to model and predict various metabolic and biological states. These capabilities have been applied in a number of areas including research in carcinogenesis, toxicology, nutrition, pharmacology/drug development and basic biological science. As a NIGMS National Resource the National User Resource for Biological Accelerator Mass Spectrometry will help NIH funded scientists achieve a deeper understanding of the etiology of human health concerns by (1) enabling the quantification of pharmacokinetics and other molecular endpoints directly in humans; (2) offering the ability to conduct quantitative studies using biologics such as proteins or lipids, and thereby reducing the amount of radioisotope usage in biomedical labs; and (3) enabling more relevant studies of metabolic pathways in health and disease through the use of much lower, more biologically-relevant, concentrations of metabolic substrates in cells and intact organisms. Such studies support NIGMS’s basic biomedical research areas that contribute to the understanding of fundamental cellular and physiological principles and enable research supported by the Biophysics, Biomedical Technology, and Computational Biosciences (BBCB); Genetics and Molecular, Cellular, and Developmental Biology (GMCDB); Pharmacology, Physiology, Biological Chemistry (PPBC) and Training, Workforce Development, and Diversity (TWD) Divisions.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗