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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Potential for functional divergence in ectomycorrhizal fungal communities across a precipitation gradient

Abstract Functional traits influence the assembly of microbial communities, but identifying these traits in the environment has remained challenging. We studied ectomycorrhizal fungal (EMF) communities inhabiting Populus trichocarpa roots distributed across a precipitation gradient in the Pacific Northwest, USA. We profiled these communities using taxonomic (meta-barcoding) and functional (metagenomic) approaches. We hypothesized that genes involved in fungal drought-stress tolerance and fungal mediated plant water uptake would be most abundant in drier soils. We were unable to detect support for this hypothesis; instead, the abundance of genes involved in melanin synthesis, hydrophobins, aquaporins, trehalose-synthases, and other gene families exhibited no significant shifts across the gradient. Finally, we studied variation in sequence homology for certain genes, finding that fungal communities in dry soils are composed of distinct aquaporin and hydrophobin gene sequences. Altogether, our results suggest that while EMF communities exhibit significant compositional shifts across this gradient, coupled functional turnover, at least as inferred using community metagenomics is limited. Accordingly, the consequences of these distinct EMF communities on plant water uptake remain critically unknown, and future studies targeting the expression of genes involved in drought stress tolerance are required.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Machine-learning enabled thermodynamic model for the design of new rare-earth compounds

We employ a descriptor based machine-learning approach to assess the effect of chemical alloying on formation-enthalpy of rare-earth intermetallics. Application of machine-learning approaches in rare-earth intermetallic design have been sparse due to limited availability of reliable datasets. In this work, we developed an ‘in-house’ rare-earth database with more than 600 + compounds, each entry was populated with formation enthalpy and related atomic features using high-throughput density-functional theory (DFT). The SISSO (sure independence screening and sparsifying operator) based machine-learning method with meaningful atomic features was used for training and testing the formation enthalpies of rare earth compounds. The complex lattice function coupled with the machine-learning model was used to explore the effect of transition metal alloying on the energy stability of Ce based cubic Laves phases (MgCu 2 type). The SISSO predictions show good agreement with high-fidelity DFT calculations and X-ray powder diffraction measurements. Our study provides quantitative guidance for compositional considerations within a machine-learning model and discovering new metastable materials. The electronic-structure of Ce-Fe-Cu based compound was also analyzed to get an in-depth understanding of the electronic origin of phase stability. The interpretable analytical models in combination with density-functional theory and experiments provide a fast and reliable design guide for discovering technologically useful materials.

36 MATERIALS SCIENCE↗
DOE OSTI2024

The Effective Fragment Molecular Orbital Method: Achieving High Scalability and Accuracy for Large Systems

The effective fragment molecular orbital (EFMO) method has been developed to predict the total energy of a very large molecular system accurately (with respect to the underlying quantum mechanical method) and efficiently by taking advantage of the locality of strong chemical interactions and employing a two-level hierarchical parallelism. The accuracy of the EFMO method is partly attributed to the accurate and robust intermolecular interaction prediction between distant fragments, in particular, the many-body polarization and dispersion effects, which require the generation of static and dynamic polarizability tensors by solving the coupled perturbed Hartree–Fock (CPHF) and time-dependent HF (TDHF) equations, respectively. Solving the CPHF and TDHF equations is the main EFMO computational bottleneck due to the inefficient (serial) and I/O-intensive implementation of the CPHF and TDHF solvers. In this work, the efficiency and scalability of the EFMO method are significantly improved with a new CPU memory-based implementation for solving the CPHF and TDHF equations that are parallelized by either message passing interface (MPI) or hybrid MPI/OpenMP. Here, the accuracy of the EFMO method is demonstrated for both covalently bonded systems and noncovalently bound molecular clusters by systematically examining the effects of basis sets and a key distance-related cutoff parameter, R cut . R cut determines whether a fragment pair (dimer) is treated by the chosen ab initio method or calculated using the effective fragment potential (EFP) method (separated dimers). Decreasing the value of Rcut increases the number of separated (EFP) dimers, thereby decreasing the computational effort. It is demonstrated that excellent accuracy (<1 kcal/mol error per fragment) can be achieved when using a sufficiently large basis set with diffuse functions coupled with a small R cut value. With the new parallel implementation, the total EFMO wall time is substantially reduced, especially with a high number of MPI ranks. Given a sufficient workload, nearly ideal strong scaling is achieved for the CPHF and TDHF parts of the calculation. For the first time, EFMO calculations with the inclusion of long-range polarization and dispersion interactions on a hydrated mesoporous silica nanoparticle with explicit water solvent molecules (more than 15k atoms) are achieved on a massively parallel supercomputer using nearly 1000 physical nodes. In addition, EFMO calculations on the carbinolamine formation step of an amine-catalyzed aldol reaction at the nanoscale with explicit solvent effects are presented.

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

Vacancy Mediated Electrooxidation of 5‐Hydroxymethyl Furfuryl Using Defect Engineered Layered Double Hydroxide Electrocatalysts

Abstract Electrochemical biomass oxidation coupled with hydrogen evolution offers a promising route to generate value‐added chemicals and clean energy. The complex adsorption behavior of 5‐hydroxymethyl furfural (HMF) and hydroxyl ions (OH − ) on the electrocatalyst surface during HMF electrooxidation reaction (HMFOR) necessitates an in‐depth understanding of active sites available for adsorption. Herein, oxygen vacancy (V O ) defects are introduced in NiFe layered double hydroxide (LDH) using Ce dopants to manipulate electronic structure. Synchrotron‐based HE‐XRD and XAS indicate negligible V O in La‐doped NiFe while Ce doping leads to V O defects due to flexible Ce redox (Ce 3+ ↔ Ce 4+ ). The V O ‐rich Ce‐NiFe exhibits higher Faradic efficiency of ≈90% to produce 2,5‐furan dicarboxylic acid (FDCA), far greater than ≈60% for NiFe V O in Ce‐NiFe act as alternative active sites for OH − adsorption, hence reducing adsorption competition for the same metal sites. DFT calculation results corroborate experimental findings by showcasing that the presence of V O in Ce‐NiFe manipulates the adsorption energies and facilitates the chemical adsorption OH − in V O to improve HMFOR. In situ HE‐XRD derived pair distribution function coupled to RMC simulations confirm OH − trapping in V O and HMF adsorption on metal centers as evident by interlayer distance evolution. Taken together, this work showcases routes for dual‐site electrocatalyst design for improved biomass electrooxidation.

Chemistry↗
DOE OSTI2022

Codesigning Alloy Compositions of CdSe y Te 1− y Absorbers and Mg x Zn 1− x O Contacts to Increase Solar Cell Efficiency

Thin‐film solar cells such as CdTe are a major commercial photovoltaic technology, with more than 25 GW installed worldwide and levelized costs of electricity competitive with fossil fuels. Further progress may result from integrating CdSe y Te 1− y absorbers with Mg x Zn 1− x O contacts, but the device efficiency is difficult to maximize due to coupled dependence on chemical composition of both alloys. Herein, a high‐throughput approach is demonstrated to codesign chemical compositions in alloyed Mg x Zn 1− x O/CdSe y Te 1− y thin‐film solar cells, using combinatorial libraries of PV devices with orthogonal composition gradients in CdSe y Te 1− y absorbers and Mg x Zn 1− x O contacts. It is found that the solar cell performance is a strong and coupled function of both elemental compositions, with efficiency up to 17.7% ( V OC = 836 mV, fill factor = 69%, J SC = 30.6 mA cm −2 ) at atomic compositions of Mg/(Mg + Zn) ≈18% and average Se/(Se + Te) ≈4%. These performance trends among >100 devices are explained by >100 ns lifetime of photoexcited charge carriers at the Mg x Zn 1− x O/CdSe y Te 1− y interface where strong Se accumulation is also observed. This study reports the optimal compositions of the commercially relevant Mg x Zn 1− x O/CdSe y Te 1− y solar cells and demonstrates a general approach to codesigning performance of alloyed thin‐film solar cells and other optoelectronic devices.

14 SOLAR ENERGY↗
DOE OSTI2023

Tangent functional connectomes uncover more unique phenotypic traits

Functional connectomes (FCs) containing pairwise estimations of functional couplings between pairs of brain regions are commonly represented by correlation matrices. As symmetric positive definite matrices, FCs can be transformed via tangent space projections, resulting into tangent-FCs. Tangent-FCs have led to more accurate models predicting brain conditions or aging. Motivated by the fact that tangent-FCs seem to be better biomarkers than FCs, we hypothesized that tangent-FCs have also a higher fingerprint. We explored the effects of six factors: fMRI condition, scan length, parcellation granularity, reference matrix, main-diagonal regularization, and distance metric. Our results showed that identification rates are systematically higher when using tangent-FCs across the “fingerprint gradient” (here including test-retest, monozygotic and dizygotic twins). Highest identification rates were achieved when minimally (0.01) regularizing FCs while performing tangent space projection using Riemann reference matrix and using correlation distance to compare the resulting tangent-FCs. Such configuration was validated in a second dataset (resting-state).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Molecular Modeling and Molecular Dynamics Simulation of a Packed and Intact Bacterial Microcompartment

Bacterial microcompartments (BMCs) are protein-bound organelles found in some bacteria which encapsulate enzymes for enhanced catalytic activity. These compartments spatially sequester enzymes within semipermeable shell proteins and are packed full of enzyme cargoes and metabolites as they fulfill their function. Coupling together recent SAXS and proteomics work, it is possible to develop molecular models for these microcompartments and interrogate enzyme and metabolite dynamics within. Our primary goal of this study is to quantify the permeability of metabolite glyceraldehyde-3-phosphate (G3P) and dihydroxyacetone phosphate (DHAP) across the BMC shell through classical molecular dynamics simulation. The Haliangium ochraceum model of BMC shell (PDB: 6MZX) was used to model an intact BMC of approximately 10 million atoms. Working at this scale presented its own challenges in managing large data sets, with multiple challenges and hardware advances discussed that facilitated this work. Over approximately 750 ns of aggregate simulation, we see multiple permeation events for these metabolites that were added at high concentration through the pores present within BMC shell tiles. When compared to independent permeability estimates for the same metabolites determined through replica exchange umbrella sampling simulations, the permeabilities varied by approximately 3 orders of magnitude. Regardless, the permeability coefficients for both G3P and DHAP are highly similar and very high, such that only very small concentration gradients can be maintained across the BMC shell between the cytosol and BMC interior. The large simulation systems also facilitated comparisons for molecular diffusivity in the crowded environment within the BMC shell. By our estimates, the viscosity within a packed BMC shell is at least 10-fold higher than it would be in neat solution and is the real driver for varying permeability estimates we obtained through simulation. These findings will be used as design inputs for future bioengineering efforts to make products from BMCs, highlighting how permeable BMC shells can be.

Diffusion↗
DOE OSTI2021

Manipulation of Exciton Dynamics in Single-Layer WSe 2 Using a Toroidal Dielectric Metasurface

Recent advances in emerging atomically thin transition metal dichalcogenide semiconductors with strong light–matter interactions and tunable optical properties provide novel approaches for realizing new material functionalities. Coupling two-dimensional semiconductors with all-dielectric resonant nanostructures represents an especially attractive opportunity for manipulating optical properties in both the near-field and far-field regimes. In this work, by integrating single-layer WSe 2 and titanium oxide (TiO 2 ) dielectric metasurfaces with toroidal resonances, we realized robust exciton emission enhancement over 1 order of magnitude at both room and low temperatures. Furthermore, we could control exciton dynamics and annihilation by using temperature to tailor the spectral overlap of excitonic and toroidal resonances, allowing us to selectively enhance the Purcell effect. Our results provide rich physical insight into the strong light–matter interactions in single-layer TMDs coupled with toroidal dielectric metasurfaces, with important implications for optoelectronics and photonics applications.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Reduction of spectroscopic overlap across the Z = 8 shell in neutron-rich nuclei

The recent discovery and spectroscopic measurements of 27 O and 28 O suggests the disappearance of the N = 20 shell structure in these neutron-rich oxygen isotopes. We measured one- and two-proton removal cross sections from 27 F and 29 N, respectively, extracting spectroscopic factors and comparing them to shell model overlap functions coupled with eikonal reaction model calculations. The invariant mass technique was used to reconstruct the two-body ( 24 O + n) and three-body ( 24 O + 2n) decay energies from knockout reactions of 27 F (106.2 MeV/u) and 29 Ne (112.8 MeV/u) beams impinging on a 9 Be target. The one-proton removal from 27 F strongly populated the ground state of 26 O and the extracted cross section of $3.4^{+0.3}_{-1.5}$ mb agrees with eikonal model calculations that are normalized by the shell model spectroscopic factors and account for the systematic reduction factor observed for single nucleon removal reactions within the models used. For the two-proton removal reaction from 29 Ne an upper limit of 0.08 mb was extracted for populating states in 27 O decaying though the ground state of 26 O. The measured upper limit for the population of the ground state of 26 O in the two-proton removal reaction from 29 Ne indicates a significant difference in the underlying nuclear structure of 27 F and 29 Ne.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Role of carboxysomes in cyanobacterial CO 2 assimilation: CO 2 concentrating mechanisms and metabolon implications

Many carbon-fixing organisms have evolved CO 2 concentrating mechanisms (CCMs) to enhance the delivery of CO 2 to RuBisCO, while minimizing reactions with the competitive inhibitor, molecular O 2 . These distinct types of CCMs have been extensively studied using genetics, biochemistry, cell imaging, mass spectrometry, and metabolic flux analysis. Highlighted in this paper, the cyanobacterial CCM features a bacterial microcompartment (BMC) called ‘carboxysome’ in which RuBisCO is co-encapsulated with the enzyme carbonic anhydrase (CA) within a semi-permeable protein shell. Further, the cyanobacterial CCM is capable of increasing CO 2 around RuBisCO, leading to one of the most efficient processes known for fixing ambient CO 2 . The carboxysome life cycle is dynamic and creates a unique subcellular environment that promotes activity of the Calvin–Benson (CB) cycle. The carboxysome may function within a larger cellular metabolon, physical association of functionally coupled proteins, to enhance metabolite channelling and carbon flux. In light of CCMs, synthetic biology approaches have been used to improve enzyme complex for CO 2 fixations. Research on CCM-associated metabolons has also inspired biologists to engineer multi-step pathways by providing anchoring points for enzyme cascades to channel intermediate metabolites towards valuable products.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1975

High and low energy secondary cosmic rays in the atmosphere

A rapporteur paper is presented on the subject of secondary cosmic rays in the earth atmosphere. The response of cosmic ray detectors to environmental factors is discussed treating both interplanetary and near-earth effects. The energy response characteristics of cosmic ray detectors are considered, examining the response characteristics of the underground vertical muon telescope at London and presenting the upper cut-off rigidity for some coupling functions. Cosmic-ray produced electrons and photons in the atmosphere are discussed.

Ahluwalia, H. S.↗
NASA NTRS1979

Prediction of the occurrence and intensity of magnetospheric substorms

The solar wind and IMF data obtained by the Venus probe Mariner 5 (at a distance of 460 earth radii) and by the earthbound Explorer 34 satellite, on June 24, 25, and 26, 1967 were examined. It is demonstrated that the occurrence and intensity of magnetospheric substorms can be predicted about 1-3 hours prior to their onsets by monitoring the energy coupling function at a distance of a few hundred earth radii upstream of the solar wind. It appears that the 'epsilon signal' propagates with different speeds, perhaps depending on the propagation time of disturbances which increase epsilon.

Akasofu, S.-I.↗
NASA NTRS1980

Interplanetary shock waves and magnetospheric substorms

It is shown that substorm activity after a storm sudden commencement (SSC) depends on whether or not an interplanetary shock wave is accompanied by a large increase of the solar wind-magnetosphere energy coupling function. It has long been thought that substorm activity associated with an SSC results from sudden conversion of magnetic energy stored in the magnetotail, and that this conversion is triggered by the shock wave. However, the present result implies that the magnetospheric substorm is not a sudden conversion of stored magnetic energy, but is a direct consequence of increased efficiency of the solar wind-magnetosphere dynamo.

Akasofu, S.-I.↗
NASA NTRS1980

Middle atmosphere electric fields

A review is presented describing the classical picture relative to sources of electric fields in the middle atmosphere, the coupling of these sources and factors which cause variations in the coupling functions. Measurement techniques for middle atmosphere electric fields and results of measurement attempts are also given.

Maynard, N. C.↗
NASA NTRS1981

Solar wind control of auroral zone geomagnetic activity

Solar wind magnetosphere energy coupling functions are analyzed using linear prediction filtering with 2.5 minute data. The relationship of auroral zone geomagnetic activity to solar wind power input functions are examined, and a least squares prediction filter, or impulse response function is designed from the data. Computed impulse response functions are observed to have characteristics of a low pass filter with time delay. The AL index is found well related to solar wind energy functions, although the AU index shows a poor relationship. High frequency variations of auroral indices and substorm expansions are not predictable with solar wind information alone, suggesting influence by internal magnetospheric processes. Finally, the epsilon parameter shows a poorer relationship with auroral geomagnetic activity than a power parameter, having a VBs solar wind dependency.

Clauer, C. R.↗
NASA NTRS1981

Magnetospheric substorms - A newly emerging model

A surge of progress in magnetospheric substorm studies is expected by the following three recent developments: (1) the finding of the solar wind-magnetosphere energy coupling function epsilon, (2) the determination of the Pedersen current distribution over the entire polar region, and (3) a new understanding of the auroral potential structure. In this paper, the significance of the three developments and the newly emerging model of magnetospheric substorms is described.

Akasofu, S.-I.↗
NASA NTRS1984

Algal culture studies related to a Closed Ecological Life Support System (CELSS)

In many respects, algae would be the ideal plant component for a biologically based controlled life support system, since they are eminently suited to the closely coupled functions of atmosphere regeneration and food production. Scenedesmus obliquus and Spirulina platensis were grown in three continuous culture apparatuses. Culture vessels their operation and relative merits are described. Both light and nitrogen utilization efficiency are examined. Long term culture issues are detailed and a discussion of a plasmid search in Spirulina is included.

Radmer, R.↗