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

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At least 1,747 records · Page 97
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

World Record Demonstration of > 30% Thermophotovoltaic Conversion Efficiency

Thermophotovoltaic (TPV) devices are solid-state heat engines that convert thermal radiation into electricity using semiconductor diodes, and have applications in energy storage, primary power conversion, and waste heat recovery. Higher temperature emitters and wider band gap photovoltaics (PVs) generally afford higher TPV efficiencies. High temperature emitters are accessible in thermal energy storage applications. We have demonstrated a world record 31% +/- 2% TPV conversion efficiency with a 0.9 cm2 GaAs-based PV device under a 2430 °C thermal emitter, producing an electrical output power of 2.23 W. Critical to the result was the cell’s high reflectance of photon energies below the device band gap. Unlike solar PV, for which sub-band gap (SBG) light is lost, a TPV cell can reflect and recycle SBG light to the thermal emitter. The demonstration was made on a custom-built measurement platform in which a ~100 cm2 graphite thermal emitter was heated under vacuum up to 2430 °C. The TPV efficiency was evaluated by comparing the measured electrical output power of the TPV with the calorimetrically measured total net power incident on the cell. The measured TPV efficiency as a function of thermal emitter temperature was corroborated by our full system modeling predictions. As far as the authors are aware, this is the highest TPV conversion efficiency ever measured, and device improvements should yield > 40% efficiency in the near future.

27 ARPA - Advanced Research Projects Agency-Energy↗
DOE OSTI2019

The spatial scale dependence of diazotrophic and bacterial community assembly in paddy soil

Aim: The factors driving microbial community β-diversity (variation in composition) at different spatial scales yield fundamental insights into the mechanisms that maintain ecosystem biodiversity, which as yet are uncertain. In this work, we explore whether spatial scale-dependent patterns of β-diversity vary between microbial functional groups and bacterial taxa (i.e., diazotrophic and bacterial communities) across local to regional scales (from metres to hundreds of kilometres). Location: Eastern China. Time period: October and November 2015. Major taxa studied: Diazotrophic and bacterial communities. Methods: We use two complementary statistical tools to unveil biotic mechanisms (i.e., species association) underlying variation in β-diversity of diazotrophic and bacterial communities. We examined distance–decay slopes of both communities at the local (1–113 m), meso- (3.4–39 km) and regional (103–668 km) scales. We used an environmentally constrained checkerboard score and topological features of association networks as indices of species association. We then calculated contributions of species association, abiotic factors and geographical distance to explain community β-diversity. The scale-dependent distance–decay relationships were also examined in ubiquitous (high occupancy across samples) and endemic communities of diazotrophs and bacteria. Results: Diazotrophs displayed steeper distance–decay slopes than bacteria, suggesting that the β-diversity of diazotrophic communities was more variable. The distance–decay slopes were dependent on spatial scales in both communities, owing to different contributions of geographical distance, abiotic factors and species association at three spatial scales. Intriguingly, species association was greater and contributed more to community β-diversity than other forces at the local scale, implying that species association could greatly alter community structures. Main conclusions: Drivers of diazotrophic and bacterial community β-diversity depended on spatial scales, resulting in different distance–decay patterns. Moreover, this was the first study to use two methods to demonstrate that species association played important, but as yet unrecognized, roles in driving spatial scale-dependent β-diversity.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Investigating the RTA Treatment of Ohmic Contacts to n-Layers of Heterobipolar Nanoheterostructures

The preparation of ohmic contacts to heterobipolar nanostructures has a number of characteristic features. In addition to the basic requirement of minimizing contact resistance, contacts to this type of structures have a transition layer whose depth of penetration must not exceed the emitter layer’s thickness, due to the possibility of short-circuiting the emitter base p–n junction. In this work, the effect the main technological parameters of rapid thermal annealing have on a contact’s characteristics are examined, and the process of obtaining a low-resistance ohmic contact to heterobipolar transistor layers is optimized. Ohmic contacts to the n-layers of heterobipolar nanoheterostructures based on gallium arsenide and produced via layer-by-layer electron-beam deposition of Ge/Au/Ni/Au are considered. The diffusion distribution profiles of doping with Ge impurities are calculated as a function of the time and temperature of rapid thermal annealing, and are examined via scanning electron microscopy. It is found that rapid thermal annealing for 60 s at a temperature of 398°C yields ohmic contacts with low resistance, smooth surface morphology, and the minimum size of the transition layer.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Modulation of phytochrome signaling networks for improved biomass accumulation using a bioenergy crop model

Plant growth and development, including stem elongation, flowering time, and shade-avoidance habits, are affected by wavelength composition (i.e., light quality) of the light environment. the molecular mechanisms underlying light perception and signaling pathways in plants have been best characterized in Arabidopsis thaliana where dozens of genes have been implicated in converging, complementary, and antagonistic pathways communicating light quality cues perceived by the phytochrome (red/far-red) cryptochrome (blue) and phototropin (blue) photorecptors. Light perception and signaling have been studied in grasses, including rice and sorghum but in much less detail than in Arabidopsis. During the course of the Mocker lab's DOE-funded wrok generating a gene expression atlas in Brachypodium distachyon we observed that Brachypodium plants grown in continuous monochromatic red light or continuous white light enriched in far-red light accumulated significantly more biomass and exhibited significantly greater seed yield than plants grown in monochromatic blue light or white light. This phenomenon was also observed in two other grasses, switchgrass and rice. We will systematically manipulate the expression of genes predicted to function in Brachypodium phytochrome signaling and assess the phenotypic consequences in transgenic Brachypodium plants in terms of morphology, stature, biomass accumulation, and cell wall composition. We will also interrogate direct interactions between candidate phytochrome signaling transcription factors and target promoters using a high-throughput yeast one-hybrid system. Brachypodium distachyon has emerged as a model grass species and is closely related to candidate feedstock crops for bioethanol production. Identification of genes capable of modifying growth characteristics of Brachypodium, when misexpressed, in particular increasing biomass accumulation, by modulating photoreceptor signaling will provide valuable candidates for manipulation in biomass and biofuel feedstock grass crops through targeted breeding or engineering efforts.

09 BIOMASS FUELS↗
DOE OSTI2024

Bilocal Field Theory for Composite Scalar Bosons

We give a bilocal field theory description of a composite scalar with an extended binding potential that reduces to the Nambu–Jona-Lasinio (NJL) model in the pointlike limit. This provides a description of the internal dynamics of the bound state and features a static internal wave function, $\phi(\vec{r})$, in the center-of-mass frame that satisfies a Schrödinger–Klein–Gordon equation with eigenvalues m 2 . We analyze the “coloron” model (single perturbative massive gluon exchange) which yields a UV completion of the NJL model. This has a BCS-like enhancement of its interaction, ∝N c the number of colors, and is classically critical with g critical remarkably close to the NJL quantum critical coupling. Negative eigenvalues for m 2 lead to spontaneous symmetry breaking, and the Yukawa coupling of the bound state to constituent fermions is emergent.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2016

THE MASS AND SIZE DISTRIBUTION OF PLANETESIMALS FORMED BY THE STREAMING INSTABILITY. I. THE ROLE OF SELF-GRAVITY

We study the formation of planetesimals in protoplanetary disks from the gravitational collapse of solid over-densities generated via the streaming instability. To carry out these studies, we implement and test a particle-mesh self-gravity module for the Athena code that enables the simulation of aerodynamically coupled systems of gas and collisionless self-gravitating solid particles. Upon employment of our algorithm to planetesimal formation simulations, we find that (when a direct comparison is possible) the Athena simulations yield predicted planetesimal properties that agree well with those found in prior work using different numerical techniques. In particular, the gravitational collapse of streaming-initiated clumps leads to an initial planetesimal mass function that is well-represented by a power law, dN/dM{sub p}∝M{sub p}{sup −p}, with p≃1.6±0.1, which equates to a differential size distribution of dN/dR{sub p}∝R{sub p}{sup −q}, with q≃2.8±0.1. We find no significant trends with resolution from a convergence study of up to 512{sup 3} grid zones and N{sub par}≈1.5×10{sup 8} particles. Likewise, the power-law slope appears indifferent to changes in the relative strength of self-gravity and tidal shear, and to the time when (for reasons of numerical economy) self-gravity is turned on, though the strength of these claims is limited by small number statistics. For a typically assumed radial distribution of minimum mass solar nebula solids (assumed here to have dimensionless stopping time τ=0.3), our results support the hypothesis that bodies on the scale of large asteroids or Kuiper Belt Objects could have formed as the high-mass tail of a primordial planetesimal population.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Gauge constrained algorithm of variational discrete action theory at N = 3 for the multiorbital Hubbard model

The recently developed variational discrete action theory (VDAT) provides a systematic variational approach to the ground state of the quantum many-body problem, where the quality of the solution is controlled by an integer N, and increasing N monotonically approaches the exact solution. VDAT can be exactly evaluated in the d = ∞ multiorbital Hubbard model using the self-consistent canonical discrete action theory (SCDA), which requires a self-consistency condition for the integer time Green's functions. Previous work demonstrates that N = 3 accurately captures multiorbital Mott/Hund physics at a cost similar to the Gutzwiller approximation. Here we employ a gauge constraint to automatically satisfy the self-consistency condition of the SCDA at N = 3, yielding an even more efficient algorithm with enhanced numerical stability. We derive closed form expressions of the gauge constrained algorithm for the multiorbital Hubbard model with general density-density interactions, allowing VDAT at N = 3 to be straightforwardly applied to the seven-orbital Hubbard model. We present results and a performance analysis using N = 2 and N = 3 for the SU⁡(2⁢N orb ) Hubbard model in d = ∞ with N orb = 2–8, and compare to numerically exact dynamical mean-field theory solutions where available. Finally, the developments in this work will greatly facilitate the application of VDAT at N = 3 to strongly correlated electron materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2026

Group-Additivity–Embedded Multiscale Modeling for Electric Field-Enhanced Nanocatalysis

Elucidating structure-performance relationships remains a central challenge in field-enhanced catalysis, where nanoparticles exhibit nonuniform surface sites with site-dependent responses to electric fields. Low-coordination sites (edges, corners, and tips) are particularly electric field-sensitive (EF), leading to nonuniform charge distribution, adsorption energies, and catalytic activity. Here, using ammonia decomposition on a ruthenium cluster as a model system, we develop a transferable multiscale framework integrating density functional theory, group additivity (GA), Brønsted-Evans-Polanyi scaling, and microkinetic modeling to predict EF-dependent activity across nonuniform cluster sites. Across sites and fields, the nitrogen adsorption energy (E N ) emerges as the governing descriptor, yielding robust volcano relationships whose optimum shifts systematically with field: negative fields strengthen N binding via electron accumulation, while positive fields weaken N binding via charge depletion, moving the optimal E N toward weaker binding. Microkinetic analysis shows that N≡N bond formation remains the key kinetic bottleneck over most conditions; positive fields lower the effective barrier and, critically, increase the fraction of near-optimal active sites, leading to a net enhancement in overall activity relative to zero-field and negative-field cases. By capturing EF- and site-dependent energetics with high accuracy and low computational cost, this GA-embedded multi-scale simulation workflow provides a physically interpretable route to predict and design field-enhanced nanocatalysis.

ammonia decomposition↗
DOE OSTI2026

Development of male-sterile lines of Setaria viridis to accelerate C 4 model plant genetics

Setaria viridis is a diploid C 4 grass in the Poaceae family, notable for its rapid life cycle of 6–8 weeks from sowing to seed—much shorter than the 4–5 months required by crops such as Zea mays and Sorghum bicolor . This fast growth makes S. viridis a valuable model for C 4 crop research. Genetic crosses are essential for studying gene function, but manual crossing is labor-intensive and time-consuming. Here, to address this, we developed a male-sterile line by targeting the S. viridis ortholog of Setaria italica NO POLLEN 1 ( SiNP1 ), which encodes a glucose–methanol–choline oxidoreductase required for pollen exine formation. Using Cas9 and TREX2 -mediated genome editing, we generated SiNP1 knockouts in both the S. viridis ME034V and A10.1 backgrounds that were fully male-sterile. Backcrossing T 0 male-sterile plants to ME034V wild-type followed by selfing yielded a stable BC 1 F 2 line homozygous for a 59 bp deletion in the S. viridis NO POLLEN 1 gene, easily genotyped by PCR and maintained by heterozygous siblings. Using this line, we developed a simple and efficient crossing protocol that eliminates the need for emasculation. This method enables a single person to perform up to 100 crosses per day—compared to 15 using traditional methods—and yields 20–32 F 1 hybrid seeds per panicle with 100% genetic purity. We also quantified pollen flow and outcrossing frequencies under greenhouse conditions to develop optimal bagging strategies and prevent unintended pollination. This resource accelerates genetic research in S. viridis , enhancing its utility as a premier C 4 model for mapping and functional genomics.

C4 research↗
DOE OSTI2018

One 3-oxoacyl-(acyl-Carrier-protein) reductase functions as 17β-hydroxysteroid dehydrogenase in the estrogen-degrading Pseudomonas putida SJTE-1

Highlights: • A novel NAD-dependent 3-oxoacyl-(ACP) reductase induced by 17β-estradiol functions as the 17β-hydroxysteroid dehydrogenase. Pseudomonas putida SJTE-1 can utilize 17β-estradiol (E2) as its carbon source, while the enzymes for E2 transformation in this strain is still unclear. 17β-hydroxysteroid dehydrogenases (17β-HSD) can catalyze the reduction/oxidation at C{sub 17} site of steroid hormone specifically, critical for steroid transformation. Here a novel 3-oxoacyl-(acyl-carrier protein) (ACP) reductase (ANI02794.1) was identified as it could bβ-estradiol, and was proved to be capable of functioning as 17β-HSD. Sequences alignment showed it contained the two consensus regions and the conserved residues of short-chain dehydrogenase/reductase (SDR). Its encoding gene was cloned and over-expressed in Escherichia coli BL21(DE3) strain, and the recombinant protein was purified by the metal-ion affinity chromatography with the yield of 18 mg/L culture. HPLC (High Performance Liquid Chromatography) detection showed this enzyme could convert 17β-estradiol into estrone using NAD{sup +} as cofactor. Its K{sub m} value was 0.082 mM and its V{sub max} value was 0.81 mM/s; its transformation efficiency of 17β-estradiol into estrone was over 96.6% in five minutes. Its optimal temperature was 37 °C and optimal was pH 9.0; the divalent ions had different effects on the enzymatic activity. In conclusion, this 3-oxoacyl-ACP reductase functioned as 17β-HSD in P. putida SJTE-1 and played important role in its estrogen metabolism.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Rb 4 CuSb 2 Cl 11 and Rb 2 In 0.91(0.2) Sb 0.09 Cl 5 ·H 2 O: Wide Band Gap 0D Metal Halide Semiconductors

Herein, we report the discovery, structural and photophysical characterization of a new zero-dimensional (0D) lead-free all-inorganic halide, Rb 4 CuSb 2 Cl 11 , which adopts a new structure type. Single-crystal X-ray diffraction (SCXRD) shows that the structure consists of isolated, distorted seesaw [SbCl 4 ] − and trigonal planar [CuCl 3 ] 2− units, separated by Rb + cations that provide charge balance. Optoelectronic measurements and density functional theory (DFT) calculations indicate an indirect band gap of 2.89 eV, making it a candidate for wide-bandgap optoelectronic applications. Electrical resistivity was measured at 1.29 × 10 10 Ω·cm, and the trap-state density (n trap ) was found to be 7.44 × 10 10 cm −3 . Attempts to synthesize substitution analogs of Rb 4 CuSb 2 Cl 11 led to the synthesis of Rb 2 In 0.91(0.2) Sb 0.09 Cl 5 ·H 2 O, which was erroneously reported as Rb 2 SbCl 5 O in a previous study. Rb 2 In 0.91(0.2) Sb 0.09 Cl 5 ·H 2 O adopts a vacancyordered perovskite structure and exhibits broad-band yellow emission under UV excitation. The measured photoluminescence quantum yield (PLQY) for Rb 2 In 0.91 (0.2)Sb 0.09 Cl 5 ·H 2 O is 18.2%. These findings add to the growing class of quaternary metal halides with multiple cation and anion compositions, expanding the chemical phase space for the discovery of new materials with functional properties.

Crystal structure↗
DOE OSTI2025

Modification and analysis of context-specific genome-scale metabolic models: methane-utilizing microbial chassis as a case study

ABSTRACT Context-specific genome-scale model (CS-GSM) reconstruction is becoming an efficient strategy for integrating and cross-comparing experimental multi-scale data to explore the relationship between cellular genotypes, facilitating fundamental or applied research discoveries. However, the application of CS modeling for non-conventional microbes is still challenging. Here, we present a graphical user interface that integrates COBRApy, EscherPy, and RIPTiDe, Python-based tools within the BioUML platform, and streamlines the reconstruction and interrogation of the CS genome-scale metabolic frameworks via Jupyter Notebook. The approach was tested using -omics data collected for Methylotuvimicrobium alcaliphilum 20Z R , a prominent microbial chassis for methane capturing and valorization. We optimized the previously reconstructed whole genome-scale metabolic network by adjusting the flux distribution using gene expression data. The outputs of the automatically reconstructed CS metabolic network were comparable to manually optimized i IA409 models for Ca-growth conditions. However, the CS model questions the reversibility of the phosphoketolase pathway and suggests higher flux via primary oxidation pathways. The model also highlighted unresolved carbon partitioning between assimilatory and catabolic pathways at the formaldehyde-formate node. Only a very few genes and only one enzyme with a predicted function in C1 metabolism, a homolog of the formaldehyde oxidation enzyme ( fae1-2 ), showed a significant change in expression in La-growth conditions. The CS-GSM predictions agreed with the experimental measurements under the assumption that the Fae1-2 is a part of the tetrahydrofolate-linked pathway. The cellular roles of the tungsten (W)-dependent formate dehydrogenase ( fdhAB ) and fae homologs ( fae1-2 and fae3 ) were investigated via mutagenesis. The phenotype of the f dhAB mutant followed the model prediction. Furthermore, a more significant reduction of the biomass yield was observed during growth in La-supplemented media, confirming a higher flux through formate. M. alcaliphilum 20Z R mutants lacking fae1-2 did not display any significant defects in methane or methanol-dependent growth. However, contrary to fae1, the fae1-2 homolog failed to restore the formaldehyde-activating enzyme function in complementation tests. Overall, the presented data suggest that the developed computational workflow supports the reconstruction and validation of CS-GSM networks of non-model microbes. IMPORTANCE The interrogation of various types of data is a routine strategy to explore the relationship between genotype and phenotype. An efficient approach for integrating and cross-comparing experimental multi-scale data in the context of whole-genome-based metabolic network reconstruction becomes a powerful tool that facilitates fundamental and applied research discoveries. The present study describes the reconstruction of a context-specific (CS) model for the methane-utilizing bacterium, Methylotuvimicrobium alcaliphilum 20Z R . M. alcaliphilum 20Z R is becoming an attractive microbial platform for the production of biofuels, chemicals, pharmaceuticals, and bio-sorbents for capturing atmospheric methane. We demonstrate that this pipeline can help reconstruct metabolic models that are similar to manually curated networks. Furthermore, the model is able to highlight previously overlooked pathways, thus advancing fundamental knowledge of non-model microbial systems or promoting their development toward biotechnological or environmental implementations.

Kulyashov, M. A.↗
DOE OSTI2021

Parton distributions and lattice-QCD calculations: Toward 3D structure

The strong force which binds hadrons is described by the theory of quantum chromodynamics (QCD). Determining the character and manifestations of QCD is one of the most important and challenging outstanding issues necessary for a comprehensive understanding of the structure of hadrons. Within the context of the QCD parton picture, the parton distribution functions (PDFs) have been remarkably successful in describing a wide variety of processes. However, these PDFs have generally been confined to the description of collinear partons within the hadron. New experiments and facilities provide the opportunity to additionally explore the transverse structure of hadrons which is described by generalized parton distributions (GPDs) and transverse-momentum-dependent parton distribution functions (TMD PDFs). In our previous report Lin et al. (2018), we compared and contrasted the two main approaches used to determine the collinear PDFs: the first based on perturbative QCD factorization theorems, and the second based on lattice-QCD calculations. In the present report, we provide an update of recent progress on the collinear PDFs, and also expand the scope to encompass the generalized PDFs (GPDs and TMD PDFs). We review the current state of the various calculations, and consider what new data might be available in the near future. We also examine how a shared effort can foster dialog between the PDF and lattice-QCD communities, and yield improvements for these generalized PDFs.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2017

Shapes and features of the primordial bispectrum

If time-dependent disruptions from slow-roll occur during inflation, the correlation functions of the primordial curvature perturbation should have scale-dependent features, a case which is marginally supported from the cosmic microwave background (CMB) data. We offer a new approach to analyze the appearance of such features in the primordial bispectrum that yields new consistency relations and justifies the search of oscillating patterns modulated by orthogonal and local templates. Under the assumption of sharp features, we find that the cubic couplings of the curvature perturbation can be expressed in terms of the bispectrum in two specific momentum configurations, for example local and equilateral. This allows us to derive consistency relations among different bispectrum shapes, which in principle could be tested in future CMB surveys. Furthermore, based on the form of the consistency relations, we construct new two-parameter templates for features that include all the known shapes.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

Role of baryon number conservation in measurements of fluctuations

Here, I discuss the role and impact of net-baryon number conservation in measurements of net-proton fluctuations in heavy-ion collisions. I show that the magnitude of the fluctuations is entirely determined by the strength of two particle correlations. At LHC and top RHIC energy, this implies the fluctuations are proportional to the integral of the balance function (BF), B pp¯ of protons and antiprotons, while in the context of the RHIC beam energy scan (BES), one must also account for correlations of stopped protons. The integral of B pp¯ measured in a 4π detector depends on the relative cross sections of processes yielding pp¯ and those balancing the proton baryon number via the production of other antibaryons. The accepted integral of B pp¯ further depends on the shape and width of the BF relative to the width of the acceptance. The magnitude of the measured second-order cumulant of net-proton fluctuations thus has much less to do with QCD susceptibilities than with the creation/transport of baryons and antibaryons in heavy-ion collisions, and most particularly the impact of radial flow on the width of the BF. I thus advocate that net-proton fluctuations should be studied by means of differential BF measurements rather than with integral correlators. I also derive an expression of net-baryon fluctuations in terms of integrals of balance functions of identified baryon pairs and argue that measurements of such balance functions would enable a better understanding of the collision system expansion dynamics, the hadronization chemistry, and an experimental assessment of the strength of net-baryon fluctuations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Electronegative metal dopants improve switching variability in Al 2 ⁢O 3 resistive switching devices

Resistive random-access memories are promising for nonvolatile memory and brain-inspired computing applications. High variability and low yield of these devices are key drawbacks hindering reliable training of physical neural networks. In this paper, we show that doping an oxide electrolyte, Al 2 ⁢O 3 , with electronegative metals makes resistive switching significantly more reproducible, surpassing the reproducibility requirements for obtaining reliable hardware neuromorphic circuits. Based on density functional theory calculations, the underlying mechanism is hypothesized to be the ease of creating oxygen vacancies in the vicinity of electronegative dopants due to the capture of the associated electrons by dopant midgap states and the weakening of Al-O bonds. These oxygen vacancies and vacancy clusters also bind significantly to the dopant, thereby serving as preferential sites and building blocks in the formation of conducting paths. Throughout this work, we validate this theory experimentally by implanting different dopants over a range of electronegativities in devices made of multiple alternating layers of Al 2 ⁢O 3 and WN and find superior repeatability and yield with highly electronegative metals, Au, Pt, and Pd. These devices also exhibit a gradual SET transition, enabling multibit switching that is desirable for analog computing.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Modeling central metabolism and energy biosynthesis across microbial life

Here, automatically generated bacterial metabolic models, and even some curated models, lack accuracy in predicting energy yields due to poor representation of key pathways in energy biosynthesis and the electron transport chain (ETC). Further compounding the problem, complex interlinking pathways in genome-scale metabolic models, and the need for extensive gapfilling to support complex biomass reactions, often results in predicting unrealistic yields or unrealistic physiological flux profiles. As a result, to overcome this challenge, we developed methods and tools to build high quality core metabolic models (CMM) representing accurate energy biosynthesis based on a well studied, phylogenetically diverse set of model organisms. We compare these models to explore the variability of core pathways across all microbial life, and by analyzing the ability of our core models to synthesize ATP and essential biomass precursors, we evaluate the extent to which the core metabolic pathways and functional ETCs are known for all microbes. 6,600 (80 %) of our models were found to have some type of aerobic ETC, whereas 5,100 (62 %) have an anaerobic ETC, and 1,279 (15 %) do not have any ETC. Using our manually curated ETC and energy biosynthesis pathways with no gapfilling at all, we predict accurate ATP yields for nearly 5586 (70 %) of the models under aerobic and anaerobic growth conditions. This study revealed gaps in our knowledge of the central pathways that result in 2,495 (30 %) CMMs being unable to produce ATP under any of the tested conditions. We then established a methodology for the systematic identification and correction of inconsistent annotations using core metabolic models coupled with phylogenetic analysis. In conclusion, we predict accurate energy yields based on our improved annotations in energy biosynthesis pathways and the implementation of diverse ETC reactions across the microbial tree of life. We highlighted missing annotations that were essential to energy biosynthesis in our models. We examine the diversity of these pathways across all microbial life and enable the scientific community to explore the analyses generated from this large-scale analysis of over 8000 microbial genomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Configurations, band structures and photocurrent responses of 4-(4-oxopyridin-1(4H)-yl)phthalic acid and its metal-organic frameworks

4-(4-oxopyridin-1(4 H)-yl)phthalic acid (H{sub 2}L) and three H{sub 2}L-based metal-organic frameworks (MOFs) formulated as ZnL(DPE)(H{sub 2}O)·H{sub 2}O (DPE=(E)-1, 2-di(pyridine −4-yl)ethene) (1), CdL(H{sub 2}O){sub 2} (2) and CdL (3) were synthesized and structurally characterized by single-crystal X-ray diffraction. The free H{sub 2}L ligand shows an enol-form and the L{sup 2−} ligand in the three MOFs exists as the keto-form. Density functional theory (DFT) calculations indicate H{sub 2}L and the three MOFs possess different band structures. Due to the existence of the N-donor, DPE in MOF 1, the conduction band (CB) minimum and band gap of MOF 1 are much lower than those of H{sub 2}L. And MOF 1 yielded much larger photocurrent density than H{sub 2}L upon visible light illumination. Electrochemical impedance spectroscopy (EIS) shows the interfacial charge transfer impedance in the presence of MOF 1 is lower than that in the presence of H{sub 2}L. The hydrous MOF 2 and the anhydrous MOF 3 are both constructed by Cd(II) and L{sup 2−}, and they can be reversibly transformed to each other. However, MOFs 2 and 3 possess different CB minimums and VB maximums, and their band gaps are much larger than that of MOF 1. - Graphical abstract: The free ligand, 4-(4-oxopyridin-1(4H)-yl)phthalic acid (H{sub 2}L) shows different configuration from its three MOFs, and they possess different band structures. MOF 1 yielded much larger visible-light-driven photocurrent density than H{sub 2}L. The hydrous MOF 2 and the anhydrous MOF 3 can be transformed to each other, and they have larger band gaps than MOF 1.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗