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At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Life history strategies of soil bacterial communities across global terrestrial biomes

The life history strategies of soil microbes determine their metabolic potential and their response to environmental changes. Yet these strategies remain poorly understood. Here we use shotgun metagenomes from terrestrial biomes to characterize overarching covariations of the genomic traits that capture dominant life history strategies in bacterial communities. The emerging patterns show a triangle of life history strategies shaped by two trait dimensions, supporting previous theoretical and isolate-based studies. The first dimension ranges from streamlined genomes with simple metabolisms to larger genomes and expanded metabolic capacities. As metabolic capacities expand, bacterial communities increasingly differentiate along a second dimension that reflects a trade-off between increasing capacities for environmental responsiveness or for nutrient recycling. Random forest analyses show that soil pH, C:N ratio and precipitation patterns together drive the dominant life history strategy of soil bacterial communities and their biogeographic distribution. Finally, our findings provide a trait-based framework to compare life history strategies of soil bacteria.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Diel mercury concentration variations in a mercury-impacted stream

Here, filtered and particulate mercury (Hg) and methylmercury (MMHg), and associated water chemistry parameters, were evaluated bi-hourly for several 30 h periods during the summer and winter seasons at several distinct locations (downstream forested, midstream urban/suburban, upstream industrial) along a creek contaminated with high levels of inorganic Hg to determine if biogeochemical Hg and MMHg cycles respond to the daily photocycle. In summer particulate Hg and MMHg concentrations doubled overnight (excluding the upstream industrial site) concurrent with increases in turbidity and total suspended sediment; no such pattern was evident in winter. Seasonal and diel changes in the activity of macrobiota affecting the suspension of contaminated sediments are likely responsible for these patterns as other potential explanatory variables (e.g., instrument drift, pH, discharge) could not account for the range and timing of our observations. Diel patterns in filtered Hg (Hg D ) were significant only at locations and times of the year when channel shading was not present and daytime concentrations increased 22–89% above nighttime minima likely caused by direct and indirect photochemical reactions. Relationships between Hg D and dissolved organic carbon (DOC) concentration or character were inconsistent between sites. Unlike Hg D , there were significant diel patterns in filtered MMHg (MMHg D ) at all sites and times of year, with summer concentrations peaking in mid to late afternoon while the timing differed in winter, with concentrations peaking after sunset. Daily variability in MMHg D concentration ranged between 25 and 75%. The results imply key controls on net methylation occur within the stream or on the stream bed and include factors such as small-scale temperature changes in the water column and photosynthetic activity of stream biofilm. With respect to stream monitoring, results from this study indicate (1) consistent timing in stream Hg and MMHg sampling is required for accurate assessment of long-term trends, (2) in situ measurements of turbidity can be used to quantify diel dynamics of both particulate Hg and MMHg concentrations, and (3) in situ fluorescing dissolved organic matter (FDOM), a potential proxy for DOC, was not capable of resolving diel dynamics of filtered Hg or MMHg.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Exceedance Response Action (ERA) Level 1 Report and ERA Level 2 Action Plan

This report consolidates the requirements for an Exceedance Response Action (ERA) Level 1 and ERA Level 2 Action Plan for pH. A discharger’s baseline status for any given parameter changes to Level 1 status if sampling results indicate a Numeric Action Level (NAL) exceedance for that same parameter. NAL exceedance can be either of the following: (1) Instantaneous maximum NAL exceedance: Occurs when two or more analytical results for any single parameter within a reporting year exceed the instantaneous maximum NAL (for example for pH a value less than 6 or a value greater than 9); and (2) Annual NAL exceedance: Occurs when the average of all the analytical results for a parameter within a reporting year exceeds the annual NAL. A Discharger’s Level 1 status for any given parameter changes to Level 2 status if sampling results indicate a Numeric Action Level (NAL) exceedance for the same parameter while a Discharger is in Level 1.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Charge regulation mechanism in end-tethered weak polyampholytes

Weak polyampholytes, containing oppositely charged dissociable groups, are expected to be responsive to changes in ionic conditions. Here, we determine structural and thermodynamic properties, including the charged groups’ degrees of dissociation, of end-tethered weak polyampholyte layers as a function of salt concentration, pH, and the solvent quality. For diblock weak polyampholytes grafted by their acidic blocks, we find that the acidic monomers increase their charge while the basic monomers decrease their charge with decreasing salt concentration for pH values less than the pK a value of both monomers and vice versa when the pH > pK a . This complex charge regulation occurs because the electrostatic attraction between oppositely charged blocks is stronger than the repulsion between monomers with the same charge in both good and poor solvents when the screening by salt ions is weak. This is shown by the retraction of the top block into the bottom layer. In the case of poor solvent conditions to the basic block (the top block), we find lateral segregation of basic monomers into micelles, forming a two-dimensional hexagonal pattern on the surface at intermediate and high pH values for monovalent salt concentrations from 0.01 to 0.1 M. When the solvent is poor to both blocks, we find lateral segregation of the grafted acidic block into lamellae with longitudinal undulations of low and high acidic monomer density. By exploiting weak block polyampholytes, our work expands the parameter space for creating responsive surfaces stable over a wide range of pH and salt concentration.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Ab Initio Electron-Phonon Interactions in Correlated Electron Systems

Electron-phonon ( e - ph ) interactions are pervasive in condensed matter, governing phenomena such as transport, superconductivity, charge-density waves, polarons, and metal-insulator transitions. First-principles approaches enable accurate calculations of e - ph interactions in a wide range of solids. However, they remain an open challenge in correlated electron systems (CES), where density functional theory often fails to describe the ground state. Therefore reliable e - ph calculations remain out of reach for many transition metal oxides, high-temperature superconductors, Mott insulators, planetary materials, and multiferroics. Here we show first-principles calculations of e - ph interactions in CES, using the framework of Hubbard-corrected density functional theory ( DFT + U ) and its linear response extension ( DFPT + U ), which can describe the electronic structure and lattice dynamics of many CES. We showcase the accuracy of this approach for a prototypical Mott system, CoO, carrying out a detailed investigation of its e - ph interactions and electron spectral functions. While standard DFPT gives unphysically divergent and short-ranged e - ph interactions, DFPT + U is shown to remove the divergences and properly account for the long-range Fröhlich interaction, allowing us to model polaron effects in a Mott insulator. Our work establishes a broadly applicable and affordable approach for quantitative studies of e - ph interactions in CES, a novel theoretical tool to interpret experiments in this broad class of materials.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Neutron spin echo shows pHLIP is capable of retarding membrane thickness fluctuations

In this study, cell membranes are responsible for a range of biological processes that require interactions between lipids and proteins. While the effects of lipids on proteins are becoming better understood, our knowledge of how protein conformational changes influence membrane dynamics remains rudimentary. Here, we performed experiments and computer simulations to study the dynamic response of a lipid membrane to changes in the conformational state of pH-low insertion peptide (pHLIP), which transitions from a surface-associated (SA) state at neutral or basic pH to a transmembrane (TM) α-helix under acidic conditions. Our results show that TM-pHLIP significantly slows down membrane thickness fluctuations due to an increase in effective membrane viscosity. Our findings suggest a possible membrane regulatory mechanism, where the TM helix affects lipid chain conformations, and subsequently alters membrane fluctuations and viscosity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Bio-Oil Impact on Water Diffusion and Durability of Bitumen: Influence of Aging and Salinity

Bio-oils derived from inexpensive biomass offer environmentally friendly options for modifying bitumen for improved durability or rejuvenating aged material, although their impact on bitumen moisture resistance can be mixed. A better understanding of water diffusion into bitumen and its interactions with bio-oil compounds would aid the development of effective bio-oils. In this study, the effect of water exposure on bio-oil-modified bitumen blends was examined by de-wetting contact angle measurements and differential FTIR spectroscopy. The bio-oils improved the anti-stripping behavior of the bitumen but also increased water absorption which could weaken cohesive strength. Short-term thermal aging increased water diffusion for all bitumen blends including the control, probably due to the presence of more oxidized compounds. Negative peaks of alkanes and polar groups in the differential FTIR data suggest the co-diffusion of surfactant molecules towards the bitumen-water interface. Basic pH increased de-wetting of some bitumen blends from silica, possibly by attacking the silica surface itself. The presence of salt in solution altered the bitumen surface composition through the formation of salt complexes with bitumen or bio-oil compounds. In particular, the formation of calcium-carboxylate complexes appeared to greatly improve anti-stripping effects of bio-oils. Water diffusion into most of the bitumen blends was insensitive to pH or salt concentration except for a few notable outliers. Identifying the compounds responsible for increasing or decreasing water diffusion in these outlier cases would be valuable developing future bio-oil formations that avoid or promote those compounds.

Hung, Albert M.↗
DOE OSTI2023

Grid-Tied PV Inverter with Oversized Power Module to Increase its Low-Voltage Ride Through (LVRT) Capabilities and VAR Support

This paper proposes a novel design for grid-tied 3-ph Photovoltaic (PV) inverter to improve its low-voltage ride through (LVRT) response while significantly increasing its voltampere reactive (VAR) support during voltage sags. The literature available on LVRT for PV inverters can be grouped in solutions that dissipate the excess energy and those that temporary stores this energy. This paper proposes a third solution; oversizing inverter hardware components to safely transferring all the energy excess back to while maintaining the semiconductor under the maximum temperature limits. The advantages of the proposed approach are: 1) Improved LVRT capabilities and stable dc-link voltage control at MPP during sags. 2) Increased VAR support during voltage sags. 3) Increased use of renewable energy as all active power is injected back to the grid during voltage sags. Finally, the proposed solution is more cost effective compared with solutions that incorporate energy storage because only a few inverter components are required to be oversized. This paper also presents a detailed power loss analysis, which determined that that oversizing the power semiconductors has minimal impact in the inverter losses while significatively reducing the diode and IGBT conduction losses during both normal operation and grid fault conditions.

Ferrari Maglia, Max↗
DOE OSTI2021

Effects of pH on an IDP conformational ensemble explored by molecular dynamics simulation

The conformational ensemble of intrinsically disordered proteins, such as α-synuclein, are responsible for their function and malfunction. Misfolding of α-synuclein can lead to neurodegenerative diseases, and the ability to study their conformations and those of other intrinsically disordered proteins under varying physiological conditions can be crucial to understanding and preventing pathologies. In contrast to well-folded peptides, a consensus feature of IDPs is their low hydropathy and high charge, which makes their conformations sensitive to pH perturbation. We examine a prominent member of this subset of IDPs, α-synuclein, using a divide-and-conquer scheme that provides enhanced sampling of IDP structural ensembles. We constructed conformational ensembles of α-synuclein under neutral (pH ~ 7) and low (pH ~ 3) pH conditions and compared our results with available information obtained from smFRET, SAXS, and NMR studies. Specifically, α-synuclein has been found to in a more compact state at low pH conditions and the structural changes observed are consistent with those from experiments. We also characterize the conformational and dynamic differences between these ensembles and discussed the implication on promoting pathogenic fibril formation. We find that under low pH conditions, neutralization of negatively charged residues leads to compaction of the C-terminal portion of α-synuclein while internal reorganization allows α-synuclein to maintain its overall end-to-end distance. Here, we also observe different levels of intra-protein interaction between three regions of α-synuclein at varying pH and a shift towards more hydrophilic interactions with decreasing pH.

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

Methanogenesis and Acetogenesis in Hydrogenotrophy with Carbonate Minerals: Dependence on Mineral Surface Area, Biofilm Growth, and Microbial Community

The production, storage, and use of hydrogen are anticipated to grow substantially to achieve energy and climate goals. Consequently, microbial communities in many terrestrial and subsurface Earth environments could be exposed to elevated hydrogen concentrations. Hydrogen stimulates metabolic processes that reduce aqueous chemical species, such as bicarbonate or sulfate, that can exchange with solid mineral phases, but the controls on microbial hydrogenotrophy with mineral sources of electron acceptors are not fully understood. Herein, we applied laboratory experiments and biogeochemical modeling to study the response of a natural microbial community to an elevated partial pressure of hydrogen in the presence of carbonate minerals of varying composition, solubility, and size. Experimental incubations and simulation results showed that hydrogen consumption by microbial communities was initially dominated by sulfate reduction and, subsequently, transitioned to acetogenesis and methanogenesis. The rates of acetogenesis and methanogenesis were not correlated with the solubility of carbonate minerals. Instead, we observed strong linear correlations between the rates and surface area of carbonate minerals. Methane and acetate production slowed down in all incubations after about 2 weeks of incubation, although biogeochemical modeling predicted that the metabolic processes were not thermodynamically limited. Electron microscopy and infrared spectroscopy showed that biofilms with diverse microorganisms grew on the carbonates during this period. The methane δ13C value significantly increased, consistent with slower growth at elevated pH. This work highlights that microbial communities form biofilm on carbonate mineral surfaces as a response to hydrogen and that biofilm formation could pose a strong kinetic limitation to hydrogenotrophic metabolism utilizing carbonate minerals.

Acetobacterium↗
DOE OSTI2024

Uranium and Nickel Partitioning in a Contaminated Riparian Wetland

Uranium (U) and nickel (Ni) released 50 years ago have been immobilized in the Tims Branch wetlands located on the Savannah River Site in the United States. Sediments were collected from seven locations to identify the factors responsible for this attenuation. Ni and U contents in the solids were significantly correlated, suggesting that depositional as opposed to chemical processes contributed to their spatial distribution. Based on sequential extractions, 63 ± 16% of the U was partitioned into the organic fraction, whereas Ni was distributed between several sediment fractions. An inverse pH-organic matter (OM) correlation and positive correlations of OM with total U and organic-bound U/Ni suggest that increased OM preservation and binding to the mineral surfaces were likely responsible for Ni- and especially U-sediment retention (Tims Branch pH = 4.84 ± 0.68). EXAFS analysis indicated the predominance of U(VI) coordinated with clay minerals (~65%), together with ~35% coordinated to either OM (in areas with elevated OM levels) or iron oxides. The desorption-Kd coefficients of U (3972 ± 1370 L/kg) and Ni (30 ± 8 L/kg) indicate that dissolved Ni poses a greater long-term risk than dissolved U for migrating downstream. This study suggests that a delicate balance of geochemical properties controls whether wetlands behave as sinks or sources of contaminants.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗
DOE OSTI2025

Quantifying Stern layer water alignment before and during the oxygen evolution reaction

While water’s oxygen is the electron source in the industrially important oxygen evolution reaction, the strong absorber problem clouds our view of how the Stern layer water molecules orient themselves in response to applied potentials. Here, we report nonlinear optical measurements on nickel electrodes held at pH 13 indicating a disorder-to-order transition in the Stern layer water molecules before the onset of Faradaic current. A full water monolayer (1.1 × 10 15 centimeter −2 ) aligns with oxygen atoms pointing toward the electrode at +0.8 volt and the associated work is 80 kilojoule per mole. Our experiments identify water flipping energetics as a target for understanding overpotentials, advance molecular electrochemistry, provide benchmarks for electrical double layer models, and serve as a diagnostic tool for understanding electrocatalysis.

Science & Technology - Other Topics↗
DOE OSTI2024

Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase

Chitin is an abundant biopolymer and pathogen-associated molecular pattern that stimulates a host innate immune response. Mammals express chitin-binding and chitin-degrading proteins to remove chitin from the body. One of these proteins, Acidic Mammalian Chitinase (AMCase), is an enzyme known for its ability to function under acidic conditions in the stomach but is also active in tissues with more neutral pHs, such as the lung. Here, we used a combination of biochemical, structural, and computational modeling approaches to examine how the mouse homolog (mAMCase) can act in both acidic and neutral environments. We measured kinetic properties of mAMCase activity across a broad pH range, quantifying its unusual dual activity optima at pH 2 and 7. We also solved high-resolution crystal structures of mAMCase in complex with oligomeric GlcNAcn, the building block of chitin, where we identified extensive conformational ligand heterogeneity. Leveraging these data, we conducted molecular dynamics simulations that suggest how a key catalytic residue could be protonated via distinct mechanisms in each of the two environmental pH ranges. These results integrate structural, biochemical, and computational approaches to deliver a more complete understanding of the catalytic mechanism governing mAMCase activity at different pH. Engineering proteins with tunable pH optima may provide new opportunities to develop improved enzyme variants, including AMCase, for therapeutic purposes in chitin degradation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Investigating Soil Organic Matter Complexation using Spectral Induced Polarization

Spectral induced polarization (SIP) laboratory experiments were conducted to determine the sensitivity of this method to the formation of soil organic matter (SOM) complexes, with a long-term goal of field-scale monitoring. There are few SIP experiments that have explored this topic, yet understanding the dynamic behavior and interactions of SOM at the field scale could provide insight into soil fertility and health which influences crop yields, microorganisms that degrade organic pollutants, and carbon stabilization. We present the results of three experiments where the iron oxide, ferrihydrite (Fhy), was used to coat different media, and then the OM compound pentaglycine (PG) was pulse injected to form SOM complexes. SIP data was collected during these injections to capture any surface complexation changes. These experiments were performed in 1) a fluidic cell containing a micromodel, 2) a column containing Fhy coated ceramic beads and 3) a column containing Fhy coated Accusand®. Our results show a higher frequency response (defined here as > 1 Hz) in all three experiments, with the largest amplitude response after the first PG injection (Figure S.1). The repeatability of this response is encouraging and supporting data collected on the Accusand® experiment provides preliminary insight into the mechanisms controlling the SIP signatures. Sampling of fluid conductivity $σ_w$ and pH may indicate deprotonation of SOM occurring or rapid adsorption and release of protons from the Fhy sites. However additional experiments are needed to identify and confirm the primary and secondary reactions impacting the SIP response. We are looking towards other opportunities to continue this work, particularly to repeat experiments while collecting supporting datasets.

58 GEOSCIENCES↗
DOE OSTI2020

Programmable Dynamic Self-Assembly of DNA Nanostructures (Final Technical Report)

This technical report summarizes our research toward the synthesis of active biomolecular materials that take advantage of the biological properties of DNA and RNA, but can operate in non-biological contexts. Our approach takes inspiration from the dynamic assembly and disassembly of cytoskeletal filaments inside cells, and focuses on the generation of artificial filaments with comparable adaptation and responsiveness. We report the construction of DNA nanotube systems that assemble and disassemble reversibly in response to a variety of molecular stimuli including other nucleic acids (DNA and RNA), enzymes, and pH, as well as our progress on developing a reaction network framework to regulate self-assembly. Our DNA polymers are active in that they rely on the programmable energetics of hybridization and on the kinetics of enzymatic reactions to perform assembly and disassembly. Results include experiments and computational models. The research described here was performed between June 15, 2016 and June 15, 2019 at the University of California at Riverside with the support of the collaborative award DE-SC0010595 to PI Elisa Franco at UC Riverside and PI Rebecca Schulman at Johns Hopkins. The report focuses on the research performed by the team of PI Franco. The report also details work performed during a no-cost extension (June 15, 2019 - December 15, 2019) awarded to PI Guillermo Aguilar and PI Franco.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Environmental impact of solution pH on the formation and migration of iron colloids in deep subsurface energy systems

Deep subsurface stimulation processes often promote fluid-rock interactions that can lead to the formation of small colloidal particles that are suspected to migrate through the rock matrix, partially or fully clog pores and microfractures, and promote the mobilization of contaminants. Thus, the goal of this work is to understand the geochemical changes of the host rock in response to reservoir stimulation that promote the formation and migration of colloids. Two different carbonate-rich shales were exposed to different solution pHs (pH = 2 and 7). In this study, iron and other mineral transformations at the shale-fluid interface were first characterized by synchrotron-based XRF mapping. Then, colloids that were able to migrate from the shale into the bulk fluid were characterized by synchrotron-based extended X-ray absorption structure (EXAFS), scanning electron microscopy (SEM), and single-particle inductively coupled plasma time-of-flight mass spectrometry (sp-icpTOF-MS). When exposed to the pH = 2 solution, extensive mineral dissolution and secondary precipitation was observed; iron-(oxyhydr)oxide colloids colocated with silicates were observed by SEM at the fluid-shale interfaces, and the mobilization of chromium and nickel with these iron colloids into the bulk fluid was detected by sp-icpTOF-MS. Iron EXAFS spectra of the solution at the shale-fluid interface suggests the rapid (within minutes) formation of ferrihydrite-like nanoparticles. Thus, we demonstrate that the pH neutralization promotes the mobilization of existing silicate minerals and the rapid formation of new iron colloids. These Fe colloids have the potential to migrate through the shale matrix and mobilize other heavy metals (such as Cr and Ni, in this study) and impacting groundwater quality, as well produced waters from these hydraulic fracturing operations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Bacterial exometabolites influence Chlamydomonas cell cycle and double algal productivity

Algal-bacterial interactions provide clues to algal physiology, but mutualistic interactions are complicated by dynamic exchange. In this study, we characterized the response of Chlamydomonas reinhardtii to the presence of a putative alga-benefitting commensal bacterium ( Arthrobacter strain ‘P2b’). Co-cultivation promoted chlorophyll content, biomass, average cell size, and number of dividing cells, relative to axenic cultures. Addition of bacterial spent medium (whole, size-fractionated and heat-treated) had similar effects, indicating P2b does not require algal interaction to promote growth. Nutrients and pH were excluded as putative effectors, collectively indicating a commensal interaction mediated by Arthrobacter -released small exometabolite(s). Proteogenomic comparison revealed similar response to co-cultivation and spent media, including differential cell cycle regulation, extensive downregulation of flagellar genes and histones, carbonic anhydrase and RubisCO downregulation, upregulation of some chlorophyll, amino acid and carbohydrate biosynthesis genes, and changes to redox and Fe homeostasis. Further, Arthrobacter protein expression indicated some highly expressed putative secondary metabolites. Together, these results revealed that low molecular weight bacterial metabolites can elicit major physiological changes in algal cell cycle regulation, perhaps through a more productive G1 phase, that lead to substantial increases in photosynthetically-produced biomass. This work illustrates that model commensal interactions can be used to shed light on algal response to stimulating bacteria.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Development of carbon nanosensor for vinpocetine at zinc oxide modified carbon matrix with anionic surfactant for clinical application

A nano-level sensing method was formulated for the trace-level detection and determination of vinpocetine (VIN) at a zinc oxide nanomaterial-based carbon matrix with immobilised anionic surfactant sodium dodecyl sulfate (ZnO-SDS/CPE) using cyclic voltammetry (CV) and square wave voltammetry (SWV) approaches. The catalytic properties of ZnO impact the electron rate of VIN activity, resulting in a threefold increase in the VIN peak response with the ZnO-SDS-modified sensor. Here, the effects of several factors, including scan rate, pH, accumulation length, modifier amount, and concentration, were investigated on the VIN peak current. The electro-oxidation of VIN by pH study involves one proton and one electron. The CV method also investigated the effect of scan rate. The charge transfer coefficient (α) is obtained to be 0.58, and the heterogeneous rate constant (k°) is estimated to be 4.46 s⁻¹. The concentration effect of VIN was studied using the SWV method. Specifically, the SWV methodology achieved the lowest detection limit compared to previously published approaches, with estimated values of the Limit of Detection (LOD) and Limit of Quantification (LOQ) being 2.2 × 10⁻⁸ M and 7.7 × 10⁻⁸ M, respectively. The trace level of VIN in tablet and urine samples was determined using the modified sensor. Moreover, the sensor demonstrates particular reproducibility and long-term stability, making it suitable for real-time applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗