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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

TUTORIAL: A new custom metabolic model for iron-oxidizing bacteria

In this tutorial narrative, we introduce a novel template developed to enable the creation of stoichiometric genome-scale metabolic models for iron-oxidizing bacteria. We demonstrate the development of this template by applying it to Sideroxydans lithotrophicus ES-1, and validate our model using transcriptomic data (Published in Zhou et al., 2022 AEM). Below, we further show that our template facilitates the modeling of mixotrophic iron-oxidizing bacteria and metagenome-assembled genomes (MAGs), by applying our template to the MAG of the mixotrophic iron oxidizer Leptothrix ochracea (Published in Tothero et al, 2024). This work represents the first instance of a generalized and adaptable template for modeling diverse iron-oxidizing microbial systems, expanding the accessibility and applicability of metabolic modeling in this field.

genome-scale model↗
DOE OSTI2024

Comparative proteomics of a versatile, marine, iron-oxidizing chemolithoautotroph

This study conducted a comparative proteomic analysis to identify potential genetic markers for the biological function of chemolithoautotrophic iron oxidation in the marine bacterium Ghiorsea bivora. To date, this is the only characterized species in the class Zetaproteobacteria that is not an obligate iron-oxidizer, providing a unique opportunity to investigate differential protein expression to identify key genes involved in iron-oxidation at circumneutral pH. Over 1000 proteins were identified under both iron- and hydrogen-oxidizing conditions, with differentially expressed proteins found in both treatments. Notably, a gene cluster upregulated during iron oxidation was identified. This cluster contains genes encoding for cytochromes that share sequence similarity with the known iron-oxidase, Cyc2. Interestingly, these cytochromes, conserved in both Bacteria and Archaea, do not exhibit the typical β-barrel structure of Cyc2. This cluster potentially encodes a biological nanowire-like transmembrane complex containing multiple redox proteins spanning the inner membrane, periplasm, outer membrane, and extracellular space. The upregulation of key genes associated with this complex during iron-oxidizing conditions was confirmed by quantitative reverse transcription-PCR. These findings were further supported by electromicrobiological methods, which demonstrated negative current production by G. bivora in a three-electrode system poised at a cathodic potential. This research provides significant insights into the biological function of chemolithoautotrophic iron oxidation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Microstructural dependence of defect formation in iron-oxide thin films

In this report passivating iron-oxide films are grown atop iron films simulating the corrosion process in a nuclear reactor environment. Two oxide films grown via physical vapor deposition at 600 °C and room temperature exhibited dense-epitactic and columnar-polycrystalline, microstructures respectively. A third oxide film grown in open air at 600 °C exhibited an eqiuaxed, porous morphology. Cubic maghemite and magnetite phases in each oxide film were identified via grazing incidence X-ray diffraction. Positron annihilation spectroscopy was used to characterize point defects and measure their depth and size distributions in each oxide layer and showed a range of average positron lifetimes from 0.23 ns in the high temperature, vapor deposited film, 0.35 ns in the room temperature-grown film, and 0.31 ns in the thermally grown oxide. These data indicate that the film morphology, which varies greatly in these films, leads to very different defect content. Finally, four-dimensional scanning transmission electron microscopy was used to measure the internal stress of each film and was correlated to the strain state presented in the X-ray diffraction spectra. The defect formation in each film is reasoned through using a thin film growth model.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Temperature trends and correlation between SQUID superparamagnetic relaxometry and dc-magnetization on model iron-oxide nanoparticles

Structural properties of iron-oxide nanoparticles deeply affect their magnetic performance in many applications such as with superparamagnetic relaxometry, when employed as cell-targeted magnetic nanoparticles for in vivo diagnostics. In this work, we present a detailed characterization of model nanoparticles for this application, with an average size of ~25 nm and a narrow size dispersion (σ < 7%). Considering the intrinsic structural properties of these model nanoparticles, the study of temperature dependence and correlation between dc-magnetization and superconducting quantum interference detector-relaxometry are discussed based on known theoretical predictions and computer simulations of the magnetic dipole moment and characteristic decay constants. Furthermore, computer simulations provide support in clarifying how important the overall collective magnetization is affected by particle size dispersion, which has a direct role on sustaining the magnetic relaxation signal in the temperature range required in preclinical and clinical settings.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Effect of Dipole Interactions on Blocking Temperature and Relaxation Dynamics of Superparamagnetic Iron-Oxide (Fe 3 O 4 ) Nanoparticle Systems

The effects of dipole interactions on magnetic nanoparticle magnetization and relaxation dynamics were investigated using five nanoparticle (NP) systems with different surfactants, carrier liquids, size distributions, inter-particle spacing, and NP confinement. Dipole interactions were found to play a crucial role in modifying the blocking temperature behavior of the superparamagnetic nanoparticles, where stronger interactions were found to increase the blocking temperatures. Consequently, the blocking temperature of a densely packed nanoparticle system with stronger dipolar interactions was found to be substantially higher than those of the discrete nanoparticle systems. The frequencies of the dominant relaxation mechanisms were determined by magnetic susceptibility measurements in the frequency range of 100 Hz–7 GHz. The loss mechanisms were identified in terms of Brownian relaxation (1 kHz–10 kHz) and gyromagnetic resonance of Fe 3 O 4 (~1.12 GHz). It was observed that the microwave absorption of the Fe 3 O 4 nanoparticles depend on the local environment surrounding the NPs, as well as the long-range dipole–dipole interactions. These significant findings will be profoundly important in magnetic hyperthermia medical therapeutics and energy applications.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Antibacterial activity of iron oxide, iron nitride, and tobramycin conjugated nanoparticles against Pseudomonas aeruginosa biofilms

Novel methods are necessary to reduce morbidity and mortality of patients suffering from infections with Pseudomonas aeruginosa. Being the most common infectious species of the Pseudomonas genus, P. aeruginosa is the primary Gram-negative etiology responsible for nosocomial infections. Due to the ubiquity and high adaptability of this species, an effective universal treatment method for P. aeruginosa infection still eludes investigators, despite the extensive research in this area. Results We report bacterial inhibition by iron-oxide (nominally magnetite) nanoparticles (NPs) alone, having a mean hydrodynamic diameter of ~ 16 nm, as well as alginate-capped iron-oxide NPs. Alginate capping increased the average hydrodynamic diameter to ~ 230 nm. We also investigated alginate-capped iron-oxide NP-drug conjugates, with a practically unchanged hydrodynamic diameter of ~ 232 nm. Susceptibility and minimum inhibitory concentration (MIC) of the NPs, NP-tobramycin conjugates, and tobramycin alone were determined in the PAO1 bacterial colonies. Investigations into susceptibility using the disk diffusion method were done after 3 days of biofilm growth and after 60 days of growth. MIC of all compounds of interest was determined after 60-days of growth, to ensure thorough establishment of biofilm colonies. Conclusions Positive inhibition is reported for uncapped and alginate-capped iron-oxide NPs, and the corresponding MICs are presented. We report zero susceptibility to iron-oxide NPs capped with polyethylene glycol, suggesting that the capping agent plays a major role in enabling bactericidal ability in of the nanocomposite. Our findings suggest that the alginate-coated nanocomposites investigated in this study have the potential to overcome the bacterial biofilm barrier. Magnetic field application increases the action, likely via enhanced diffusion of the iron-oxide NPs and NP-drug conjugates through mucin and alginate barriers, which are characteristic of cystic-fibrosis respiratory infections. We demonstrate that iron-oxide NPs coated with alginate, as well as alginate-coated magnetite–tobramycin conjugates inhibit P. aeruginosa growth and biofilm formation in established colonies. We have also determined that susceptibility to tobramycin decreases for longer culture times. However, susceptibility to the iron-oxide NP compounds did not demonstrate any comparable decrease with increasing culture time. These findings imply that iron-oxide NPs are promising lower-cost alternatives to silver NPs in antibacterial coatings, solutions, and drugs, as well as other applications in which microbial abolition or infestation prevention is sought.

Biotechnology & Applied Microbiology↗
DOE OSTI2024

Quantifying microbial roles in environmental iron oxidation via an integrated kinetics, `omics and metabolic modeling study (Final Report)

Iron oxyhydroxides are extremely reactive components of environmental systems, and therefore exert a strong influence on biogeochemical cycles. These oxyhydroxides strongly adsorb many biologically-relevant elements, including organic carbon and phosphate, as well as a wide range of metals including uranium and actinide species. Thus, the formation mechanism of iron oxyhydroxides are key to understanding both nutrient and contaminant cycling. Microorganisms can catalyze iron oxidation and promote the formation of Fe biominerals and thus are increasingly recognized as important players in biogeochemical cycling. However, it is completely unknown how much of environmental iron oxidation is biologically mediated versus abiotic, and various challenges in studying microbial iron oxidation have hindered accurate incorporation into hydrobiogeochemical models. The overarching goal of our work was to quantify and constrain microbial iron oxidation rates and use ‘omics to gain insight into the controls on this process, while developing tools to enable integration of biotic iron oxidation into hydrobiogeochemical models. Our work focused on the Savannah River Site (SRS) in South Carolina, where extensive microbial iron oxidation has been observed. At Tims Branch, part of the Argonne National Laboratory Wetland Hydrobiogeochemistry Science Focus Area (Argonne SFA), where groundwater discharges into a stream, iron-oxidizing microbial mats form and appear to be a major sink of uranium. In the wetlands that surround Tims Branch, there are wide swaths of iron microbial mats and flocs (mobilized mat). We measured biotic and abiotic iron oxidation rates using mats and water sampled from these sites and found that iron oxidation is primarily carried out by chemolithotrophic microorganisms. The resulting rate constants can be incorporated into models. These mats were characterized by metagenomics and metatranscriptomics, which showed that aerobic chemolithotrophs were the dominant iron-oxidizing bacteria (FeOB), and these included Gallionellaceae and Leptothrix, and possibly Rhodoferax, which is known as an Fe-reducer but may also oxidize Fe(II). This demonstrated that diverse FeOB can coexist and suggests that there are a range of niches and therefore drivers of chemolithotrophic iron oxidation. Analysis of reconstructed genomes strongly suggests that a major factor in diversity is carbon source, as genomes contained varied pathways for autotrophy and heterotrophy. We performed an in-depth analysis of Leptothrix ochracea genomes, since this sheath-former is one of the primary mat builders, yet its physiology remained unresolved. A combination of genomics, transcriptomics, and metabolic modeling suggest that L. ochracea grows mixotrophically using a combination of Fe(II) and organics for energy and both inorganic and organic carbon to create biomass. This contrasts with the largely autotrophic Gallionellaceae (Gallionella, Sideroxydans, and Ferriphaselus) also present in the mats and flocs. Remarkably, multiple FeOB, both Leptothrix and Gallionellaceae, showed activity in response to Fe(II) in live mat incubations. We tracked the gene expression of individual MAGs to Fe(II) and found that various autotrophic and heterotrophic FeOB responded to Fe(II), increasing expression of both carbon fixation and organic utilization genes. The results of the integrated field, kinetics, and omics studies give detailed insight into 1) the taxa that oxidize Fe, and 2) how they connect Fe, C, and N cycles. Towards the goal of connecting omics data to hydrobiogeochemical models, we worked with the KBase team to create a template metabolic model for chemolithotrophic iron oxidation. We initially modeled the well-characterized isolate Gallionellaceae Sideroxydans lithotrophicus, and also applied the model to the mixotroph L. ochracea. In all, we have characterized diverse FeOB in a representative wetland system and solved key problems that enable better incorporation of iron-oxidizing microbes into hydrobiogeochemical models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Genetically Controlled Iron Oxide Biomineralization in Encapsulin Nanocompartments for Magnetic Manipulation of a Mammalian Cell Line

Magnetic nanoparticles have proven invaluable for biomechanical investigations due to their ability to exert localized forces. However, cellular delivery of exogenous magnetic agents often results in endosomal entrapment, thereby limiting their utility for manipulating subcellular structures. This study characterizes and exploits fully genetically controlled biomineralization of iron-oxide cores inside encapsulin nanocompartments to enable magnetic-activated cell sorting (MACS) and magnetic cell manipulation. The fraction of MACS-retained cells showed substantial overexpression of encapsulins and exhibited both para- and ferrimagnetic responses with magnetic moments of 10 -15 A m 2 per cell, comparable to standard exogenous labels for MACS. Electron microscopy revealed that MACS-retained cells contained densely packed agglomerates of ≈30 nm iron oxide cores consisting of ultrafine quasicrystalline ordered nuclei within an amorphous matrix of iron, oxygen, and phosphorus. Scanning transmission X-ray microscopy, X-ray absorption spectroscopy, and Raman microspectroscopy confirmed that the iron-oxide species are consistent with ferric oxide (Fe 2 O 3 ). In addition, the encapsulin-overexpressing MACS-retained cells can be manipulated by a magnetic needle and regrown in patterns determined by magnetic gradients. This study demonstrates that the formation of quasicrystalline iron oxide with mixed para/ferrimagnetic behavior in the cytosol of mammalian cells enables magnetic manipulation without the delivery of exogenous agents.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Gallionellaceae in rice root plaque: metabolic roles in iron oxidation, nutrient cycling, and plant interactions

On the roots of wetland plants such as rice, Fe(II) oxidation forms Fe(III) oxyhydroxide-rich plaques that modulate plant nutrient and metal uptake. The microbial roles in catalyzing this oxidation have been debated and it is unclear if these iron-oxidizers mediate other important biogeochemical and plant interactions. To investigate this, we studied the microbial communities, metagenomes, and geochemistry of iron plaque on field-grown rice, plus the surrounding rhizosphere and bulk soil. Plaque iron content (per mass root) increased over the growing season, showing continuous deposition. Analysis of 16S rRNA genes showed abundant Fe(II)-oxidizing and Fe(III)-reducing bacteria (FeOB and FeRB) in plaque, rhizosphere, and bulk soil. FeOB were enriched in relative abundance in plaque, suggesting FeOB affinity for the root surface. Gallionellaceae FeOB Sideroxydans were enriched during vegetative and early reproductive rice growth stages, while a Gallionella was enriched during reproduction through grain maturity, suggesting distinct FeOB niches over the rice life cycle. FeRB Anaeromyxobacter and Geobacter increased in plaque later, during reproduction and grain ripening, corresponding to increased plaque iron. Metagenome-assembled genomes revealed that Gallionellaceae may grow mixotrophically using both Fe(II) and organics. The Sideroxydans are facultative, able to use non-Fe substrates, which may allow colonization of rice roots early in the season. FeOB genomes suggest adaptations for interacting with plants, including colonization, plant immunity defense, utilization of plant organics, and nitrogen fixation. Taken together, our results strongly suggest that rhizoplane and rhizosphere FeOB can specifically associate with rice roots, catalyzing iron plaque formation, with the potential to contribute to plant growth.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Oxidation rates and redox stabilization of ferrous iron in trioctahedral smectites

Iron(II)-bearing trioctahedral smectites (saponites) form during anoxic alteration of basaltic rock. They are predicted to have been widespread on the early Earth and are observed in the oceanic subsurface today. Smectite structures, including the occupancy of sites in the octahedral sheet, affect iron redox behavior but the rates and products of trioctahedral smectite oxidation have been largely unexplored to date. In this study we synthesized two Fe(II)-bearing trioctahedral smectites, one moderate (22 wt% Fe) and one high (27 wt% Fe) in iron content. We then examined the rate, extent, and products of their oxidation by dissolved oxygen, nitrite, and hydrogen peroxide. Dissolved oxygen caused partial oxidation of Fe(II) in the smectites with 14 to 43% of Fe(II) unoxidized after 20 to 30 days of exposure. The rate and extent of oxidation correlated with the dissolved oxygen concentration and the Fe(II) content of the clay. The incomplete oxidation in these experiments is consistent with the mixed-valent trioctahedral smectites observed in oxidized natural samples but contrasts with the complete reoxidation by oxygen shown by chemically- or microbially-reduced dioctahedral smectites. Oxidation of structural Fe(II) by 5 mmol L -1 nitrite was negligible for the moderate-iron smectite and yielded only ~17% oxidation after 54 days of reaction for the high-iron smectite. Hydrogen peroxide caused rapid and near-complete oxidation of both clays. Powder X-ray diffraction, variable-temperature Mössbauer spectroscopy, and extended X-ray absorption fine structure spectroscopy together detected no crystalline or short-range-ordered secondary phases and show that oxidized iron remained in the trioctahedral smectite structure. The recalcitrant Fe(II) pool in oxidized trioctahedral smectites exists in less distorted sites than Fe(II) in the initial clays. Its unreactive nature at prolonged reaction times indicates an elevated redox potential generated by the local coordination environment. Slower oxidation rates create a larger recalcitrant Fe(II) pool, suggesting kinetic competition between oxidation and a process involved in redox stabilization, such as electron exchange between octahedral iron sites or deprotonation of hydroxyl groups in the structure. The resistance to complete oxidation of trioctahedral ferrous smectites and their full retention of iron demonstrates that transitions from anoxic to oxic conditions generate mixed-valence smectites rather than a mixture of new phases. Identifying the diagenetic products of mixed-valent trioctahedral smectites may provide an indicator in the rock record of past redox cycling. In conclusion, substantial portions of structural Fe(II) in trioctahedral smectites display slow abiotic oxidation kinetics and represent potential electron donors for both microaerophilic iron oxidizing and nitrate-reducing, iron-oxidizing microorganisms in altered mafic rocks and related settings.

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

Pseudo-viscous modeling of transport in dense granular flows for thermal energy storage applications

Dense, granular flows were examined to effectively capture and model bulk viscous properties in thin packed beds. A modified Couette cell with particle image velocimetry was used to experimentally determine pseudo-viscosity properties of four particulate media with varying morphologies: (1) iron oxide-coated SiO 2 particles, (2) CARBOBEAD CP30-60 particles, (3) CARBOBEAD CP40-100 particles, and (4) Al 2 O 3 beads. The pseudo-viscosity functions were fitted using a power law to correlate the measured shear stress as a function of measured shear rate. The pseudo-viscous functions were used as inputs to computation fluid dynamics models for a single-phase viscous fluid to predict granular flow profiles. Steady-state free surface velocity profiles at angular velocities <7 rad/s predicted by the model were in good agreement with the experimental particle image velocimetry measurements, resulting in Pearson correlation coefficients of 0.97 for iron-oxide coated SiO 2 particles and 0.95 for CP30-60 particles. As a result, this alternative approach to measuring pseudo-viscous properties under shearing and modeling bulk transport behavior of granular flow using computation fluid dynamics model offered significant reduction in computational load compared to discrete element methods.

14 SOLAR ENERGY↗
DOE OSTI2025

Pathways to Electrochemical Ironmaking at Scale Via the Direct Reduction of Fe 2 O 3

Electrochemical ironmaking can provide an energy efficient, zero-emissions alternative to traditional methods of ironmaking, but the scalability of low-temperature electrochemical cells may be constrained by reactor throughput and the availability of acceptable feedstocks. Electrodes directly converting solid iron-oxide particles to metal circumvent traditional mass-transport limitations but are sensitive to both the particle size and nanoscale morphology of reactants. Furthermore, the effect of these properties on reactor throughput has not been systematically studied at model electrowinning surfaces. Here, we have used size-controlled, homologous α-Fe 2 O 3 particles to study how the nanoscale morphology of oxides influences the obtainable current density toward Fe metal and integrated these results in a technoeconomic model for alkaline iron electrowinning systems. Micron-scale α-Fe 2 O 3 with nanoscale porosity can be used to form Fe at current densities commensurate with industrial water electrolysis (>0.6 A cm –2 ) in the absence of external convection, providing a path to cost-competitive and scalable ironmaking using electrochemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Improved constraints on hematite refractive index for estimating climatic effects of dust aerosols

Abstract Uncertainty in desert dust composition poses a big challenge to understanding Earth’s climate across different epochs. Of particular concern is hematite, an iron-oxide mineral dominating the solar absorption by dust particles, for which current estimates of absorption capacity vary by over two orders of magnitude. Here, we show that laboratory measurements of dust composition, absorption, and scattering provide valuable constraints on the absorption potential of hematite, substantially narrowing its range of plausible values. The success of this constraint is supported by results from an atmospheric transport model compared with station-based measurements. Additionally, we identify substantial bias in simulating hematite abundance in dust aerosols with current soil mineralogy descriptions, underscoring the necessity for improved data sources. Encouragingly, the next-generation imaging spectroscopy remote sensing data hold promise for capturing the spatial variability of hematite. These insights have implications for enhancing dust modeling, thus contributing to efforts in climate change mitigation and adaptation.

Environmental Sciences & Ecology↗
DOE OSTI2026

Activating magnetite ores for aqueous ironmaking at high current densities

Low-temperature electrochemical cells reducing iron oxides to metal in alkaline electrolytes can support fully electrified steelmaking processes. Previous studies on these cells have primarily focused on high-surface-area hematite, Fe 2 O 3 , reactants whereas attempts to reduce suspensions of magnetite, Fe 3 O 4 —one of the two feedstocks for existing ironmaking reactors—have generally been limited to low rates of reaction (<30 mA cm −2 ). Here, in this study, we control the crystalline domain size of Fe 2 O 3 and Fe 3 O 4 particles in 10 M NaOH electrolytes to study how the nanoscale morphology of oxides controls the rate of electrochemical ironmaking. Rotating-ring disk electrode measurements of Fe 2+ , in situ Raman spectroscopy of the electrode surface, and ex situ electron microscopy were consistent with a hypothesized passivation process at Fe 3 O 4 surfaces that may prevent the continuous formation of soluble intermediates. Sufficiently small (<100 nm diameter) oxide particles yielded Fe partial current densities >160 mA cm −2 , a fivefold increase relative to previously reported rates for Fe 3 O 4 suspensions and comparable to active Fe 2 O 3 . Electron microscopy revealed that electrodeposited films were composed of micron-scale crystalline Fe domains with a porous film of Fe 3 O 4 nanoparticles and supports a model where Fe is grown primarily from soluble Fe 2+ intermediates. Based on these insights, inactive blast-furnace-grade iron-oxides were transformed into high surface area nanoparticles (1.6 to 229.2 m 2 g −1 ) via reprecipitation, leading to a ninefold enhancement in faradaic efficiency and an Fe partial current density of 120 mA cm −2 . When integrated with chlor-iron cells producing reagents for reprecipitation, this approach could lead to a cost-competitive process for electrochemical ironmaking from industrially relevant feedstocks.

TEM↗
DOE OSTI2020

FeGenie: a comprehensive tool for the identification of iron genes and iron gene neighborhoods in genomes and metagenome assemblies

Iron is a micronutrient for nearly all life on Earth. It can be used as an electron donor and electron acceptor by iron-oxidizing and iron-reducing microorganisms and is used in a variety of biological processes, including photosynthesis and respiration. While it is the fourth most abundant metal in the Earth’s crust, iron is often limiting for growth in oxic environments because it is readily oxidized and precipitated. Much of our understanding of how microorganisms compete for and utilize iron is based on laboratory experiments. However, the advent of next-generation sequencing and surge in publicly available sequence data has made it possible to probe the structure and function of microbial communities in the environment. To bridge the gap between our understanding of iron acquisition, iron redox cycling, iron storage, and magnetosome formation in model microorganisms and the plethora of sequence data available from environmental studies, we have created a comprehensive database of hidden Markov models (HMMs) based on genes related to iron acquisition, storage, and reduction/oxidation in Bacteria and Archaea. Along with this database, we present FeGenie, a bioinformatics tool that accepts genome and metagenome assemblies as input and uses our comprehensive HMM database to annotate provided datasets with respect to iron-related genes and gene neighborhood. An important contribution of this tool is the efficient identification of genes involved in iron oxidation and dissimilatory iron reduction, which have been largely overlooked by standard annotation pipelines. We validated FeGenie against a selected set of 28 isolate genomes and showcase its utility in exploring iron genes present in 27 metagenomes, 4 isolate genomes from human oral biofilms, and 17 genomes from candidate organisms, including members of the candidate phyla radiation. We show that FeGenie accurately identifies iron genes in isolates. Furthermore, analysis of metagenomes using FeGenie demonstrates that the iron gene repertoire and abundance of each environment is correlated with iron richness. While this tool will not replace the reliability of culture-dependent analyses of microbial physiology, it provides reliable predictions derived from the most up-to-date genetic markers. FeGenie’s database will be maintained and continually updated as new genes are discovered.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Electron transfer calculations between edge sharing octahedra in hematite, goethite, and annite

A key reaction underlying the charge transport in iron containing oxides, clays, micas is the Fe$^{2+}$-Fe$^{3+}$ exchange reaction between edge-sharing iron octahedra. These reactions facilitate conduction in these minerals by the thermally-activated hopping of small polarons across the lattice. Depending on the mineral and local charge state the small polaron can either encase an electron or hole. The probability for conduction of small polarons depends strongly on the height and adiabicity of the reaction barrier, with larger and more diabatic barriers yielding slow conduction associated with either weak coupling or a large prerequisite rearrangement of the lattice during charge transport. To model these reactions, a first principle electron transfer (ET) method was developed to model the small polaron hopping between the edge-sharing octahedra sites in hematite ($e^{-}$ polaron), goethite ($e^{-}$ polaron), and annite ($h^{+}$ polaron) bulk structures. The ET method is based on electronic structure methods (i.e., plane-wave Density Functional Theory) capable of performing calculations with periodic cells and large size systems efficiently while at the same time being accurate enough to be used in the estimation of the electron-transfer coupling matrix element, $V_{AB}$, and the electron transfer transmission factor, $\kappa_{el}$. Additionally, the calculations confirmed the existence of small polarons in all three minerals, and the reactions were predicted to be strongly adiabatic. It was found that transfer of a hole in the octahedral layer of annite had an adiabatic barrier of $0.311$ eV, and the transfer of an extra electron in hematite and goethite had adiabatic barriers of $0.242$ eV and $0.232$ eV respectively. The electronic coupling parameters,$V_{AB}$, were found to be $0.188$ eV, $0.196$ eV, and $0.102$ eV respectively for hematite, goethite, and annite. While similar bonding topologies pertain, the underlying basis for the differences is the subtle differences in local structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗