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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 397 records · Page 22
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

The relationship between gene traits and transcription in soil microbial communities varies by environmental stimulus

Codon and nucleotide frequencies are known to relate to the rate of gene transcription, yet how these traits shape transcriptional profiles of soil microbial communities remains unclear. Here we test the prediction that functional genes with high codon optimization and energetically lower cost nucleotides (i.e., nucleotides requiring less adenosine triphosphate (ATP) for synthesis) have higher transcriptional expression in a soil microbial community. In laboratory incubations, we subjected an agricultural soil to two separate short-term environmental changes: labile carbon (glucose) addition or a sudden 30-min increase in temperature from 20 °C to 60 °C. Using the total genomic codon frequencies to predict preferred codon usage for each taxon, we then estimated codon optimization for each transcript. On the community level, we found a higher average level of codon optimization after the addition of glucose. Synonymous nucleotide composition in the transcript pool also shifted towards energetically cheaper nucleotides, favoring uracil (U) over adenine (A) and cytosine (C) over guanine (G). Similarly, we found that encoded amino acid usage shifted towards energetically cheaper amino acids in response to labile carbon. In contrast, in communities responding to heat shock, there were no significant differences in the averaged gene traits of expressed transcripts. We used metagenome-assembled-genomes to further examine the ability of gene traits to predict transcriptional responses within and between taxa. We found that traits of individual genes could not reliably predict the level of transcription of a gene within or between taxa—highlighting the limits of this approach. However, we did find that when traits were averaged across several related genes, codon optimization was able to predict levels of transcription in metabolic pathways associated with growth and nutrient uptake in response to glucose. Similar relationships were not observed in response to heat, or for functions associated with stress—such as genes associated with sporulation or heat shock. These results demonstrate that gene traits, such as codon usage, nucleotide selection, and amino acid selection, relate to the transcriptional expression of genes in soil microbial communities and suggests that these relationships may be dependent on both gene function and the specific type of environmental stimuli.

Biological and medical sciences↗
DOE OSTI2021

On the Stochastic Stability of Deep Markov Models

Deep Markov models (DMM) are generative models which are scalable and expressive generalization of Markov models for representation, learning, and inference problems. However, the fundamental stochastic stability guarantees of such models have not been thoroughly investigated. In this paper, we present a novel stability analysis method and provide sufficient conditions of DMM's stochastic stability. The proposed stability analysis is based on the contraction of probabilistic maps modeled by deep neural networks. We make connections between the spectral properties of neural network's weights and different types of used activation function on the stability and overall dynamic behavior of DMMs with Gaussian distributions. Based on the theory, we propose a few practical methods for designing constrained DMMs with guaranteed stability. We empirically substantiate our theoretical results via intuitive numerical experiments using the proposed stability constraints.

Drgona, Jan↗
DOE OSTI2024

Relative State Counting for Semiclassical Black Holes

It has been shown that entropy differences between certain states of perturbative quantum gravity can be computed without specifying an ultraviolet completion. This is analogous to the situation in classical statistical mechanics, where entropy differences are defined but absolute entropy is not. Unlike in classical statistical mechanics, however, the entropy differences computed in perturbative quantum gravity do not have a clear physical interpretation. Here we construct a family of perturbative black hole states for which the entropy difference can be interpreted as a relative counting of states. Conceptually, this Letter begins with the algebra of mass fluctuations around a fixed black hole background, and points out that while this is a type I algebra, it is not a factor and therefore has no canonical definition of entropy. As in previous work, coupling the mass fluctuations to quantum matter embeds the mass algebra within a type II factor, in which entropy differences (but not absolute entropies) are well defined. It is then shown that for microcanonical wave functions of mass fluctuation, the type II entropy difference equals the logarithm of the dimension of the extra Hilbert space that is needed to map one microcanonical window to another using gauge-invariant unitaries. The Letter closes with comments on type II entropy difference in a more general class of states, where the von Neumann entropy difference does not have a physical interpretation, but “one-shot” entropy differences do. Published by the American Physical Society 2024

Akers, Chris (ORCID:0000000227929827)↗
DOE OSTI2020

Regulation and Maturation of the Shewanella oneidensis Sulfite Reductase SirA

Shewanella oneidensis, a metal reducer and facultative anaerobe, expresses a large number of c-type cytochromes, many of which function as anaerobic reductases. All of these proteins contain the typical heme-binding motif CXXCH and require the Ccm proteins for maturation. Two c-type cytochrome reductases also possess atypical heme-binding sites, the NrfA nitrite reductase (CXXCK) and the SirA sulfte reductase (CX12NKGCH). S. oneidensis MR-1 encodes two cytochrome c synthetases (CcmF and SirE) and two apocytochrome c chaperones (CcmI and SirG). SirE located in the sir gene cluster is required for the maturation of SirA, but not NrfA. Here we show that maturation of SirA requires the combined function of the two apocytochrome c chaperones CcmI and SirG. Loss of either protein resulted in decreased sulfte reductase. Furthermore, SirA was not detected in a mutant that lacked both chaperones, perhaps due to misfolding or instability. These results suggest that CcmI interacts with SirEFG during SirA maturation, and with CcmF during maturation of NrfA. Additionally, we show that CRP regulates expression of sirA via the newly identifed transcriptional regulatory protein, SirR.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Dispersive Dark Excitons in van der Waals Ferromagnet CrI 3

Spin-flip dark excitons are optical-dipole-forbidden quasiparticles with remarkable potential in optoelectronics, especially when they are realized within cleavable van der Waals materials. Despite this potential, dark excitons have not yet been definitively identified in ferromagnetic van der Waals materials. Here, we report two dark excitons in a model ferromagnetic material CrI 3 using high-resolution resonant inelastic x-ray scattering and show that they feature narrower linewidths compared to the bright excitons previously reported in this material. These excitons are shown to have spin-flip character, to disperse as a function of momentum, and to change through the ferromagnetic transition temperature. Given the versatility of van der Waals materials, these excitons hold promise for new types of magneto-optical functionality.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Approximating and incorporating model uncertainty in an inversion for seismic source functions: Preliminary results

We present preliminary work on propagating model uncertainty into the estimation of the time domain source time functions of the seismic source. Our method is based on an estimated model covariance function, which we estimate from the data. The model covariance function is then used to construct a suite of surrogate Greens functions which we use in a Monte Carlo type inversion scheme. The result is a probability density function of the six independent source time functions, each of which corresponds to an individual component of the seismic moment tensor. We compare the results of our method with those obtained using a computationally expensive finite difference Monte Carlo method and find that our new method produces results that are deficient in low frequencies. The advantage of our new method, which we term the Karhunen-Loeve Monte Carlo (KLMC) method, is that is several orders of magnitude faster than our current method, which uses a finite difference scheme to produce the suite of forward models.

42 ENGINEERING↗
DOE OSTI2020

Multi-organ media compositions and methods of their use

Disclosed herein are media for culture of cells, tissues, and/or organs. The media formulations disclosed herein can be used to support growth, viability, and/or function of one or more than one cell type, tissue, or organ. In some embodiments, one or more cell types, tissues, organ devices, and/or organs are contacted with a disclosed culture medium under conditions sufficient to support growth, viability, and/or function of the cell types, tissues, and/or organs. The disclosed media can be used in methods of culturing multiple cell types, and in some examples, is used in a platform device including one or more organ devices, for example, by circulating the medium through the one or more organ devices in the platform.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Distinguishing Leptothrix and Sphaerotilus genera by an integrated genomic-phenotypic analysis supported by new Leptothrix genomes

The Sphaerotilus-Leptothrix group of bacteria includes one of the first described microorganisms, Leptothrix ochracea, an uncultured type strain, plus isolates of Leptothrix and Sphaerotilus. This group is unified by the ability to form sheaths and oxidize metals, although L. ochracea exhibits obvious ecological, morphological, and functional differences from the rest of Sphaerotilus-Leptothrix. Recently, there have been calls to combine the group into one genus, Sphaerotilus; however, these studies lacked adequate genomic representation of L. ochracea. Here, we present a comprehensive comparative genomic analysis of the Sphaerotilus-Leptothrix group, including expanded representation of L. ochracea, a closely related novel species, Leptothrix toolikensis, and two new isolates (Leptothrix mechoopdaensis). Analysis of 38 genomes resolves three phylogenetic and functional groups: the ochracea-type Leptothrix (Group 1), the mobilis-type Leptothrix (Group 2), and Sphaerotilus (Group 3). Group 1 genomes form a separate genus based on average nucleotide identity and alignment fraction. The genomes clearly diverge from the rest of Sphaerotilus-Leptothrix in phylogeny, size, and metabolic potential. Group 1 genomes are much smaller (2.59–3.04 Mb) than those of Groups 2 (4.55–6.06 Mb) and 3 (3.94–5.07 Mb), while encoding more metal oxidases and fewer carbohydrate-active enzymes. Group 2 clusters with Group 3 phylogenetically and is similar in organic carbon metabolisms but maintains more metal oxidation genes. Group 2 members lack homogeneity in phenotype and genotype, suggesting that additional isolates and genomes are needed for confident classification. However, Group 1 genomes (L. ochracea and L. toolikensis) show clear divergence, precluding their inclusion in Sphaerotilus and supporting the retention of the genus Leptothrix.

Leptothrix↗
DOE OSTI2025

Stage-resolved gene regulatory network analysis reveals developmental reprogramming and genes with robust stem-preferred expression in sorghum

Sorghum bicolor is a deep-rooted, heat- and drought-tolerant crop that thrives on marginal lands and is increasingly valued for its applications in biofuel, bioenergy, and biopolymer production. The sorghum stem, which can reach 4–5 m in length, serves as the primary reservoir of both lignocellulosic biomass and soluble sugars, making it a promising bioenergy feedstock. Although recent advances in genetic, genomic, and transcriptomic resources have improved our understanding of sorghum biology, comprehensive genome-wide analyses of functional dynamics across diverse organ types and developmental stages remain limited. In particular, candidate genes with stem preferred expression pattern or their associated cis-regulatory elements, which may program key stem-related functions and enable organ- or tissue-specific engineering, have not yet been identified.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Photoinduced electric effects in various plasmonic materials

Photoinduced voltages associated with surface plasmon polariton excitations are studied both theoretically and experimentally in various plasmonic systems as the function of material, wavelength, and type of structure. Experimental photovoltage normalized to the absorbed power shows a general decrease upon an increase in the wavelength, enhancement in the nanostructured samples, and a strong variation in the magnitude as a function of the material, which are not in line with the theoretical predictions of the simple plasmonic pressure approach. Furthermore, the results can be used for clarification of the mechanisms and further development of an adequate theoretcial approach to the plasmon drag effect.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2021

Systematic Evaluation of Carbon Hosts for High-Energy Rechargeable Lithium-Metal Batteries

Rechargeable lithium batteries (RLBs) have attracted wide attention for achieving high energy and low cost, but the poor stability of the Li anode has remained as a large challenge. In the last several years, great efforts have been made to develop carbon anode structures for RLB applications. A wide range of carbon structures as well as many chemical modification strategies have been investigated to improve the Coulombic efficiency and extend the cycle life of the anodes or the cells. However, currently there is no clear conclusion on key factors that determine the performance of such the types of carbon structures due to the wide range of experimental conditions used in such studies. In this study, we systematically evaluated and compared the electrochemical properties of representative carbon anode materials as well as chemically functionalized carbon materials in different electrolytes. We have found that chemical functionalization, metallic loading, and the types of micro or nano-structures all have an effect on Li deposition/stripping process, but by far the most critical factor is the nature of the electrolytes. All carbon materials produced poor Coulombic efficiency and cycle life in conventional carbonate or ether-based electrolytes. However, when a Li metal compatible is used, the average Coulombic efficiency of Li metal deposition on all carbon structures is increased to 99% or higher. This study provides critical lessons on the directions for carbon anodes for RLBs. Based on these findings, we constructed Li metal coin cells using prelithiated hard carbon, LiNi0.6Mn0.2Co0.2O2 (NMC622) cathode, and compatible electrolyte and tested the cells under conditions of lean electrolyte, lean Li metal and high cathode loading required for more than 300 Wh kg-1 specific energy. More than 200 stable cycles were demonstrated with over 80% capacity retention. Furthermore, the existing challenges and potential approaches have been discussed to further extend the cyclability of lithium-metal batteries under practical conditions.

Liu, Yao↗
DOE OSTI2020

Functional equations and separation of variables for exact g -function

The g-function is a measure of degrees of freedom associated to a boundary of two-dimensional quantum field theories. In integrable theories, it can be computed exactly in a form of the Fredholm determinant, but it is often hard to evaluate numerically. In this paper, we derive functional equations — or equivalently integral equations of the thermodynamic Bethe ansatz (TBA) type — which directly compute the g-function in the simplest integrable theory; the sinh-Gordon theory at the self-dual point. The derivation is based on the classic result by Tracy and Widom on the relation between Fredholm determinants and TBA, which was used also in the context of topological string. We demonstrate the efficiency of our formulation through the numerical computation and compare the results in the UV limit with the Liouville CFT. As a side result, we present multiple integrals of Q-functions which we conjecture to describe a universal part of the g-function, and discuss its implication to integrable spin chains.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Monte Carlo Explicitly Correlated Second-Order Many-Body Green’s Function Calculations of Semiconductor Band Gaps

A systematically converging series of ab initio, post-density-functional, size-consistent, electron-correlated approximations is desired for predictive computing of felectronic band structures of insulating, semiconducting, and metallic solids. A series that meets all of these desiderata (except the applicability to metals) is ab initio many-body Green's function theory based on Gaussian-type-orbital (GTO) basis sets. Here, its leading-order approximation, the second-order Green's function (GF2) method in the diagonal and frequency-independent approximations with the aug-cc-pVDZ basis set, is applied to the fundamental band gaps of three semiconductors (diamond, silicon, and silicon carbide in the zincblende structure) using cluster models. Corrections are made to the basis-set-incompleteness errors by the explicit-correlation (F12) ansatz (GF2-F12) for the valence band edges. The crystals are modeled as surface-passivated clusters of increasing sizes, whose wave functions are expanded by up to 2709 GTO basis functions. Immense computational costs of these calculations are overcome by the highly scalable stochastic algorithm of the Monte Carlo GF2-F12 method, whose operation cost per state increases only as a cubic power of system size, which has a tiny memory footprint and easily achieves near-perfect parallel efficiency on thousands of CPUs or on hundreds of GPUs. The correlated, F12-corrected highest-occupied and lowest-unoccupied molecular-orbital energy (HOMO-LUMO) gap is 5.78 ± 0.07 eV for C 87 H 76 as compared with the experimental value of the fundamental (indirect) band gap of bulk diamond at 5.48 eV. The correlated, F12-corrected HOMO-LUMO gaps for Si 75 H 76 and Si 32 C 43 H 76 are 2.56 ± 0.15 eV and 3.50 ± 0.12 eV, respectively, which are expected to decrease further with increasing cluster sizes. As a result, the experimental fundamental (indirect) band gaps of bulk silicon and silicon carbide are 1.17 eV and 2.42 eV, respectively.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Crystal structures of OrfX1, OrfX2 and the OrfX1–OrfX3 complex from the orfX gene cluster of botulinum neurotoxin E1

Botulinum neurotoxins (BoNTs) are among the most lethal toxins known to humans, comprising seven established serotypes termed BoNT/A–G encoded in two types of gene clusters (ha and orfX) in BoNT-producing clostridia. The ha cluster encodes four non-toxic neurotoxin-associated proteins (NAPs) that assemble with BoNTs to protect and enhance their oral toxicity. However, the structure and function of the orfX-type NAPs remain largely unknown. Here, we report the crystal structures for OrfX1, OrfX2, and an OrfX1–OrfX3 complex, which are encoded in the orfX cluster of a BoNT/E1-producing Clostridium botulinum strain associated with human foodborne botulism. These structures lay the foundation for future studies on the potential roles of OrfX proteins in oral intoxication and pathogenesis of BoNTs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Strong-coupling anisotropic s-wave superconductivity in the type-II Weyl semimetal TaIrTe 4

TaIrTe 4 is a recently discovered type-II Weyl semimetal, hosting only four Weyl points. In this work, we study the cleaved TaIrTe 4 crystal using scanning tunneling microscopy/spectroscopy and find that it also hosts a superconducting state with a transition temperature of 3.9 K. From Dynes function fitting, the superconducting phase is consistent with anisotropic s-wave pairing, with a superconducting gap of 1.31 meV. This value leads to a value of 2Δ max /k B T C = 7.81 , much larger than the 3.53 predicted by Bardeen-Cooper-Schrieffer theory for weak-coupling superconductors. The critical field is found to be 0.7 T based on the analysis of tunneling conductance as a function of magnetic field. Two types of nonmagnetic defects on the TaIrTe 4 surface are observed, neither of which induce bound states inside the superconducting gap, further supporting conventional s-wave superconductivity in the TaIrTe 4 system.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Decoding crops one cell at a time: from cell atlases to single-cell genetics

Understanding the mechanisms underlying key agricultural traits remains a central challenge in crop research, but recent advances in technologies are providing powerful tools to address this issue. Among these, single-cell and spatial transcriptomics have revealed tissue heterogeneity and spatial organization, offering unique insights into cellular gene expression dynamics and the coordinated activity of multiple cell types. These approaches help uncover how specific cell types contribute to agricultural traits and refine candidate loci lists through integration with trait-associated loci. Additionally, single-cell and spatial transcriptomics have the potential to serve as cell-level readout platforms integrating cellular perturbations, enabling high-throughput discovery of causal relationships between genotype and gene expression at the cellular level in plants. Successful implementation will accelerate the identification of key genetic variants for crop improvement. Furthermore we review lessons learned from application of single-cell screening in mammalian cells, highlight major technical and biological barriers to its use in plants, and outline potential strategies to overcome these challenges. Together, the widespread application and integration of single-cell and spatial transcriptomics with other technologies enable not only the descriptive cataloging of cell states but also the causal interrogation of sequence functions and regulatory networks at cell type resolution, ultimately advancing gene function studies and accelerating crop improvement.

Cellular heterogeneity↗
DOE OSTI2025

The Stochastic Gause Predator-Prey model: Noise-induced extinctions and invariance

We consider the Gause predator-prey with general bounded or sub‑linear functional responses, – which includes those of Holling types Ⅰ–Ⅳ. – and multiplicative Gaussian noise. In contrast to previous studies, the prey in our model follows logistic dynamics while the predator's population is solely regulated by consumption of the prey. To ensure well-posedeness, we derive explicit Lyapunov‐type criteria ensuring global positivity and moment boundedness of solutions. We find conditions for noise‑induced extinctions, proving that stochasticity can drive either population to collapse even when the deterministic analogue predicts stable coexistence. In the case when the predator becomes extinct, we establish a limiting distribution for the predator's population. Last, for functional responses of Holling type Ⅰ, we provide sufficient conditions on the intensity of the noise for the existence and uniqueness of a stationary distribution.

Gause model↗
DOE OSTI2023

A data driven approach for cross-slip modelling in continuum dislocation dynamics

Cross-slip is a thermally activated process by which screw dislocation changes its glide plane to another slip plane sharing the same Burgers vector. The rate at which this process happens is determined by a Boltzmann type expression that is a function of the screw segment length and the stress acting on the dislocation. In continuum dislocation dynamics (CDD), the information regarding the length of the screw dislocation segment and local stress state on dislocations are lost due to the coarse-grained representation of the density. Here, in this work, a data driven approach to characterize the lost information by analyzing the discrete dislocation configurations is proposed to enable cross-slip modeling in the CDD framework in terms of the coarse-grained dislocation density and stress fields. The analysis showed that the screw segment length follows an exponential distribution, and the stress fluctuations, defined as the difference between the stress on the dislocations and the mean field stress in CDD, follows a Lorentzian distribution. A novel approach for cross slip implementation in CDD employing the screw segment length and stress fluctuation statistics was proposed and rigorously tested by comparing the CDD cross-slip rates with discrete dislocation dynamics (DDD) rates. This approach has been applied in conjunction with three cross-slip models used in DDD simulations differing mainly in the functional form of cross slip activation energy. It was found that different cross-slip activation energy formulations yielded different cross-slip rates, yet the effect on mechanical stress-strain response and dislocation density evolution was minimal for the [001] type loading.

42 ENGINEERING↗