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At least 217 records · Page 12

All sources NASA NTRS DOE OSTI

DOE OSTI2022

Rationalizing nitrogen-doped secondary carbon particles for practical lithium-sulfur batteries

Nanostructured carbon host materials are widely used to improve both sulfur utilization rate and reaction kinetics in lithium-sulfur (Li-S) batteries. However, high complexity/cost of materials synthesis and difficulty in processing nano-materials into high-mass-loading electrodes are still significant barriers to the development of low-cost and high-energy Li-S batteries. In this study, we reported a generic and scalable synthesis approach to prepare nitrogen-doped secondary carbon particles. By using nitrogen-containing precursor as an integration reagent, the nanosized Ketjen Black particles were integrated into micron-size secondary ones and nitrogen-doped (NKB) simultaneously through a one-step heat treatment. With NKB as an example material, the effects of particle integration degree on the secondary particles’ structures, pore volume and connectivity, sulfur loading capability, and cell performance were studied and discussed. At an optimal integration condition, the NKB particles had significantly improved particle dimensions with well-maintained high specific surface area and pore volume. Here, contributed by the micron size and high pore volume, the NKB/S were successfully used for high-sulfur-loading cathodes (4–7 mg s /cm -2 ) and were able to deliver a specific capacity of ~1100 mAh g -1 at a low-porosity (50%) and lean-electrolyte conditions (E/S =4 µL/mg -1 ). Feasibility of the materials for practical use was validated through scaling up synthesis (40 g/batch), large-area electrode coating, and practical pouch cell (1.6 Ah) assembly and test.

25 ENERGY STORAGE↗

DOE OSTI2025

Overcoming Secondary Nucleation of Misoriented Domains during Wafer-Scale Epitaxy of Single-Crystal Graphene on Ge(110)

The wafer-scale synthesis of single-crystal graphene on technologically important substrates is a major challenge inhibiting the development of next-generation devices that harness the exceptional electronic, thermal, and mechanical properties of single-crystal graphene. Here, in this work, the factors controlling the domain orientation of graphene grown epitaxially on Ge(110) are elucidated, and this insight is utilized to produce graphene with minimal polycrystallinity. In the early stages of growth, most graphene islands have unidirectionally aligned lattices. However, we discover a secondary nucleation phenomenon in which misoriented graphene domains nucleate near/from the island edges, introducing defective grain boundaries and significantly increasing polycrystallinity throughout growth. We find that secondary nucleation occurs when islands grow over Ge steps, which form because of an interplay between the island growth and Ge surface topography evolution. Strategies for suppressing secondary nucleation are developed, enabling the synthesis of graphene in which the predominant crystal orientation has high coverage >99% and low rotational spread <0.6°. This work overcomes the irreproducibility of graphene epitaxy on Ge(110) reported in the literature, providing a route toward the large-area synthesis of single-crystal graphene on technologically useful semiconductors.

chemical vapor deposition↗

DOE OSTI2021

Direct Aerobic Generation of a Ferric Hydroperoxo Intermediate Via a Preorganized Secondary Coordination Sphere

Enzymes exert control over the reactivity of metal centers with precise tuning of the secondary coordination sphere of active sites. One particularly elegant illustration of this principle is in the controlled delivery of proton and electron equivalents in order to activate abundant but kinetically inert oxidants such as O 2 for oxidative chemistry. Chemists have drawn inspiration from biology in designing molecular systems where the secondary coordination sphere can shuttle protons or electrons to substrates. However, a biomimetic activation of O 2 requires the transfer of both protons and electrons, and molecular systems where ancillary ligands are designed to provide both of these equivalents are comparatively rare. Here, we report the use of a dihydrazonopyrrole (DHP) ligand complexed to Fe to perform exactly such a biomimetic activation of O 2 . In the presence of O 2 , this complex directly generates a high spin Fe(III)-hydroperoxo intermediate which features a DHP• ligand radical via ligand-based transfer of an H atom. This system displays oxidative reactivity and ultimately releases hydrogen peroxide, providing insight on how secondary coordination sphere interactions influence the evolution of oxidizing intermediates in Fe-mediated aerobic oxidations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Capturing Secondary Kinetic Instabilities in Three‐Dimensional Dayside Reconnection Using an Improved Gradient‐Based Closure

Magnetic reconnection is a highly dynamic process that excites a wide variety of kinetic waves and instabilities. Transverse current sheet instabilities such as the lower-hybrid drift and secondary drift-kink instabilities in particular have been shown by kinetic simulations to modify the reconnection and introduce significant turbulence and mixing to the reconnection layer. Past studies using the ten-moment fluid model to capture important kinetic physics such as the electron inertia and full representation of the pressure tensor proved advantageous to a two-fluid representation of reconnection, but the model struggled when using a local relaxation closure for the heat flux to replicate the current sheet instabilities and subsequent mixing seen in kinetic simulations. This work uses the Gkeyll software framework to perform simulations of asymmetric reconnection based on the 16 October 2015 MMS crossing of a diffusion region, the Burch event. An improved gradient-based heat flux closure is implemented, showing significant improvement in secondary kinetic instabilities that grow in the current sheet. These instabilities generate turbulence which leads to growth of secondary magnetic islands and flux ropes.

Bradshaw, K. [Princeton University, NJ (United Sta↗

DOE OSTI2025

Microbial secondary metabolites: advancements to accelerate discovery towards application

Microbial secondary metabolites not only have key roles in microbial processes and relationships but are also valued in various sectors of today’s economy, especially in human health and agriculture. The advent of genome sequencing has revealed a previously untapped reservoir of biosynthetic capacity for secondary metabolites indicating that there are new biochemistries, roles and applications of these molecules to be discovered. New predictive tools for biosynthetic gene clusters (BGCs) and their associated pathways have provided insights into this new diversity. Advanced molecular and synthetic biology tools and workflows including cell-based and cell-free expression facilitate the study of previously uncharacterized BGCs, accelerating the discovery of new metabolites and broadening our understanding of biosynthetic enzymology and the regulation of BGCs. These are complemented by new developments in metabolite detection and identification technologies, all of which are important for unlocking new chemistries that are encoded by BGCs. This renaissance of secondary metabolite research and development is catalysing toolbox development to power the bioeconomy.

Dinglasan, Jaime Lorenzo N↗

DOE OSTI2022

New proposed ITER divertor design using carbon insert on tungsten to mitigate ELMs and secondary radiation effects on nearby components

Abstract Building a successful device for the magnetic fusion energy production is a great challenge. ITER is an international project of the tokamak based magnetic fusion design being developed for the demonstration of the feasibility of thermonuclear technologies for future realization of successful commercial fusion energy. A key obstacle to a successful magnetic fusion energy production is however, the performance during abnormal events including plasma disruptions and edge-localized modes (ELMs). A credible reactor design must tolerate at least a few of these transient events without serious consequences such as melting of the structure. This paper investigates and compares the performance of the current ITER tokamak design during two types of transient events, i.e., ELMs occurring at normal operation and disruptions during abnormal operation. We simulated the divertor components response using our integrated 3D HEIGHTS package. The simulations include self-consistent modeling of the interaction of the released core plasma particles with the initial solid divertor material, energy deposition processes, vaporization of divertor material, secondary plasma formation and MHD evolution, incident core particles collisions and scattering from this dense secondary plasma, photon radiation of secondary plasma, and the resulting heat loads on nearby components. Our simulations showed that using a small carbon insert around the strike point can significantly reduce the overall expected damage on the tungsten dome structure, reflector plates, and prevent tungsten vaporization and its potential core plasma contamination.

47 OTHER INSTRUMENTATION↗

DOE OSTI2022

Molecular dynamics simulations of the secondary-binding site in disaccharide-modified glycopeptide antibiotics

Oritavancin is a semisynthetic glycopeptide antibiotic used to treat severe infections by multidrug-resistant Gram-positive pathogens. Oritavancin is known to be a thousand times more potent than vancomycin against Gram-positive bacteria due to the additional interactions with bacterial peptidoglycan (PG) facilitated by a secondary-binding site. The presence of this secondary-binding site is evident in desleucyl-oritavancin, an Edman degradation product of oritavancin, still retaining its potency against Gram-positive bacteria, whereas desleucyl-vancomycin is devoid of any antimicrobial activities. Herein, using explicit solvent molecular dynamics (MD) simulations, steered MD simulations, and umbrella sampling, we show evidence of a secondary-binding site mediated by the disaccharide-modified hydrophobic sidechain of oritavancin interactions with the pentaglycyl-bridge segment of the PG. The interactions were characterized through comparison to the interaction of PG with chloroeremomycin, vancomycin, and the desleucyl analogs of the glycopeptides. Our results show that the enhanced binding of oritavancin to PG over the binding of the other complexes studied is due to an increase in the hydrophobic effect, electrostatic and van der Waals interactions, and not the average number of hydrogen bonds. Our ranking of the binding interactions of the biomolecular complexes directly correlates with the order based on their experimental minimum inhibitory concentrations. The results of our simulations provide insight into the modification of glycopeptides to increase their antimicrobial activities or the design of novel antibiotics against pathogenic Gram-positive bacteria.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Closed-form theoretical model of the secondary drop size in partial coalescence—Capturing pertinent timescales and viscous forces

One of the most important outcomes of partial drop coalescence is the ratio of the secondary drop radius to the primary drop radius, known as the drop ratio, ri. This ratio is thought to be approximately constant and independent of physical parameters of the fluids involved. However, here we reveal that ambient fluid viscosity can alter the size of the secondary drop and the drop ratio consequently. Using scaling analysis, we derive a model that predicts the behavior of the drop ratio as a function of the Ohnesorge number, a dimensionless ratio of viscous to inertial forces. In addition, we present our experimental results of coalescing drops on a planar interface under the influence of surface tension gradients. A high-speed digital camera is used to observe the evolution of drops as they coalesce with a bulk liquid. We show that this process is influenced by the surface tension gradient between the drop and the bulk liquid. The ratio of the secondary drop to the primary drop in partial coalescence is smaller than the reported values for coalescence without a surface tension gradient. The analytical model derived through this study is based on a new modified Ohnesorge number that includes surface tension gradients. Our analytical model is compared against other models and the results illustrate good agreement with our experimental findings and experimental data in the literature.

42 ENGINEERING↗

DOE OSTI2021

Diagnosing plasma magnetization in inertial confinement fusion implosions using secondary deuterium-tritium reactions

Diagnosing plasma magnetization in inertial confinement fusion implosions is important for understanding how magnetic fields affect implosion dynamics and to assess plasma conditions in magnetized implosion experiments. Secondary deuterium–tritium (DT) reactions provide two diagnostic signatures to infer neutron-averaged magnetization. Magnetically confining fusion tritons from deuterium–deuterium (DD) reactions in the hot spot increases their path lengths and energy loss, leading to an increase in the secondary DT reaction yield. In addition, the distribution of magnetically confined DD-triton is anisotropic, and this drives anisotropy in the secondary DT neutron spectra along different lines of sight. Implosion parameter space as well as sensitivity to the applied B-field, fuel ρR, temperature, and hot-spot shape will be examined using Monte Carlo and 2D radiation-magnetohydrodynamic simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2023

Impact of photoexcitation on secondary electron emission: A Monte Carlo study

Understanding the transport of photogenerated charge carriers in semiconductors is crucial for applications in photovoltaics, optoelectronics, and photo-detectors. While recent experimental studies using scanning ultrafast electron microscopy (SUEM) have demonstrated that the local change in the secondary electron emission induced by photoexcitation enables direct visualization of the photocarrier dynamics in space and time, the origin of the corresponding image contrast still remains unclear. Here, we investigate the impact of photoexcitation on secondary electron emissions from semiconductors using a Monte Carlo simulation aided by time-dependent density functional theory. Particularly, we examine two photoinduced effects: the generation of photocarriers in the sample bulk and the surface photovoltage (SPV) effect. Using doped silicon as a model system and focusing on primary electron energies below 1 keV, we found that both the hot photocarrier effect immediately after photoexcitation and the SPV effect play dominant roles in changing the secondary electron yield (SEY), while the distribution of photocarriers in the bulk leads to a negligible change in SEY. Our work provides insights into electron–matter interaction under photo-illumination and paves the way toward a quantitative interpretation of the SUEM contrasts.

Physics↗

DOE OSTI2024

Secondary structure determines electron transport in peptides

Proteins play a key role in biological electron transport, but the structure–function relationships governing the electronic properties of peptides are not fully understood. Despite recent progress, understanding the link between peptide conformational flexibility, hierarchical structures, and electron transport pathways has been challenging. Here, we use single-molecule experiments, molecular dynamics (MD) simulations, nonequilibrium Green’s function-density functional theory (NEGF-DFT), and unsupervised machine learning to understand the role of secondary structure on electron transport in peptides. Our results reveal a two-state molecular conductance behavior for peptides across several different amino acid sequences. MD simulations and Gaussian mixture modeling are used to show that this two-state molecular conductance behavior arises due to the conformational flexibility of peptide backbones, with a high-conductance state arising due to a more defined secondary structure (beta turn or 3 10 helices) and a low-conductance state occurring for extended peptide structures. These results highlight the importance of helical conformations on electron transport in peptides. Conformer selection for the peptide structures is rationalized using principal component analysis of intramolecular hydrogen bonding distances along peptide backbones. Molecular conformations from MD simulations are used to model charge transport in NEGF-DFT calculations, and the results are in reasonable qualitative agreement with experiments. Projected density of states calculations and molecular orbital visualizations are further used to understand the role of amino acid side chains on transport. Overall, our results show that secondary structure plays a key role in electron transport in peptides, which provides broad avenues for understanding the electronic properties of proteins.

Science & Technology - Other Topics↗

DOE OSTI2020

Skeletides: A Modular, Simplified Physical Model of Protein Secondary Structure

Three-dimensional (3D) models are essential for visualization and conceptual understanding of complex architectures such as protein structure. Although there is a plethora of software platforms that allow digital depictions of protein structure at an atomic level in silico, physical models are needed to convey an intuitive understanding of biomolecular architecture. However, it is a challenge to represent all the relevant features of proteins in a single physical model due to their sheer structural complexity. Here, we describe a modular protein model that focuses only on representation of the secondary structure—the underlying structural skeleton. The simplified model consists of amino acid units, which can be linked together to reproduce the two most fundamental structural features of protein secondary structure: the relative positions of the amino acid alpha carbon atoms, and the intra-main chain hydrogen bonding pattern. We use 3D printing and magnets to create a set of three modular amino acid building blocks, which when linked together into a chain, can faithfully represent alpha helices, beta sheets, and turns. These simple to make models can be used to quickly assemble the alpha carbon trace of an entire protein domain, which conveys a tactile experience of the complexity of protein skeletal architecture. These models highlight the modularity of protein structure: where a single structural unit, the amino acid, can be linked together to form a larger, regular secondary structure. These models also have a propensity to spontaneously organize into alpha helices and beta sheets, as demonstrated by their ability to autonomously assemble when placed in a circulating water tank. These models provide a missing educational tool to expand knowledge of protein structure, foster deeper insight into protein folding, and inspire greater interest in biomacromolecular architecture.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Microbial community dynamics in the soil-root continuum are linked with plant species turnover during secondary succession

Grazing exclusion and land abandonment are commonly adopted to restore degraded ecosystems in semiarid and arid regions worldwide. However, the temporal variation in the soil- versus root-associated microbiome over plant species turnover during secondary succession has rarely been quantified. Using the chronosequence restored from fenced grassland and abandoned farmlands on the Loess Plateau of China, we characterized the dynamics of the soil- and root-associated microbiome of host plant with different dominance statuses during secondary succession from 0 to 40 years. Our results revealed that the root microhabitat, the host plant and their interactions were the main contributors to the bacterial community shift (R 2 = 15.5%, 8.1%, and 22.3%, respectively), and plant interspecies replacement had a greater effect on the shift in the root-associated microbial community than intraspecies replacement did during succession. The root-associated bacterial community of pioneer plants was particularly responsive to succession, especially the endosphere community. Endosphere microbial diversity was positively correlated with host plant coverage change, and the diversity and abundance of taxon recruitment into the endosphere of pioneer plants from the surrounding environment decreased as succession progressed. The community assembly processes also indicated that the endosphere microbiota are strongly selected in younger host plants, whereas stochastic processes dominate in aged host plants. Our study provides evidence of the unique response of the root-associated microbiome to the replacement of plant species during secondary succession, and the function of endosphere microbes should be considered when studying plant–microbe feedback.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Siderophores and secondary metabolites produced by Ganoderma adspersum

Ganoderma adspersum is a white-rot wood-degrading basidiomycete of ecological, biotechnological and medicinal interest. In addition to its role in lignin degradation, it produces bioactive metabolites with reported antimicrobial and antioxidant activities. However, the mechanisms of iron acquisition, including siderophore-mediated pathways, remain poorly characterized in Ganoderma species. Improved understanding of these systems is essential to elucidate their contributions to fungal physiology, secondary metabolism and ecological adaptation. In this study, the genome of G. adspersum was sequenced for the first time and screened for genes that may be involved in the production of secondary metabolites. A gene cluster was identified as potentially involved in iron uptake. In particular, genes related to non-ribosomal peptide synthetases were detected next to a gene encoding a monooxygenase and indicated a potential hydroxamate-family siderophore. Liquid chromatography (LC)-ES-MS analysis of secondary metabolites secreted by G. adspersum into the growth medium under iron-limiting conditions revealed a group of previously undescribed siderophores. Genome and MS/MS analysis suggested that these structures might be related to the coprinoferrin family of siderophores. Aside from siderophores, the genome and LC-MS analysis revealed G. adspersum to be a prolific producer of a variety of triterpenoids and sesquiterpenoids, in agreement with previous findings. This is the first description of the genome sequence of G. adspersum and its siderophores.

Reyes, Carolina [Laboratory for Cellulose and Wood↗

DOE OSTI2020

Methods to Synchronize and Control the Secondary Side Active Rectifier in Wireless Power Transfer Systems

This paper presents practical analog circuit-based methods to synchronize the secondary side active bridge of different wireless power transfer (WPT) systems with their primary side. The synchronization is necessary for proper operation of any WPT system with an active bridge on the secondary. The proposed schemes use only secondary side signals without the need of any information from the primary side. Simulation results presented validate the proposed schemes.

Mukherjee, Subho↗

DOE OSTI2021

Ecological generalism drives hyperdiversity of secondary metabolite gene clusters in xylarialean endophytes

Although secondary metabolites are typically associated with competitive or pathogenic interactions, the high bioactivity of endophytic fungi in the Xylariales, coupled with their abundance and broad host ranges spanning all lineages of land plants and lichens, suggests that enhanced secondary metabolism might facilitate symbioses with phylogenetically diverse hosts. Here, we examined secondary metabolite gene clusters (SMGCs) across 96 Xylariales genomes in two clades (Xylariaceae s.l. and Hypoxylaceae), including 88 newly sequenced genomes of endophytes and closely related saprotrophs and pathogens. We paired genomic data with extensive metadata on endophyte hosts and substrates, enabling us to examine genomic factors related to the breadth of symbiotic interactions and ecological roles. All genomes contain hyperabundant SMGCs; however, Xylariaceae have increased numbers of gene duplications, horizontal gene transfers (HGTs) and SMGCs. Enhanced metabolic diversity of endophytes is associated with a greater diversity of hosts and increased capacity for lignocellulose decomposition. Our results suggest that, as host and substrate generalists, Xylariaceae endophytes experience greater selection to diversify SMGCs compared with more ecologically specialised Hypoxylaceae species. Altogether, our results provide new evidence that SMGCs may facilitate symbiosis with phylogenetically diverse hosts, highlighting the importance of microbial symbioses to drive fungal metabolic diversity.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Analysis of useful ion yield for Si in GaN by secondary ion mass spectrometry

The optimum detection levels that can be achieved by a secondary ion mass spectrometer are dependent on how efficiently a particular species of interest can be ionized and detected. One can determine in advance whether the analysis of a particular ion in the sample is possible, if the useful ion yield is known. The useful ion yield depends on the element, instrument transmission, the analytical conditions, the sample matrix, etc. The value of the useful ion yield for a species can diverge from one instrument type to another due to its different transmission and ionization probabilities. However, the same tendencies in the results may be expected for all types of instruments. In this paper, the authors present a quantitative secondary ion mass spectrometry analysis of the useful ion yield for the silicon dopant species in a gallium nitride matrix grown by metal organic chemical vapor deposition. Positively ionized cesium was used as the primary ion beam, and its energy was varied in the range from 0.5 to 5 kV. A quadrupole mass analyzer was utilized to collect secondary ion species of interest. The analysis results can be used to determine the primary beam energies for optimal Si sensitivity.

Senevirathna, M. K. Indika (ORCID:0000000243575029↗

DOE OSTI2025

Quorum sensing modulates microbial community structure through regulation of secondary metabolites

Bacteria are recognized for their diverse metabolic capabilities, yet the impact of microbe-microbe interactions on multispecies community structure and dynamics is poorly understood. Cell-to-cell signaling in the form of quorum sensing (QS) often regulates secondary metabolite production and microbial interactions. Here, we examine how acylhomoserine lactone (AHL)-mediated QS impacts microbial community structure in a 10-member synthetic community of isolates from Populus deltoides . To explore the role of QS in microbial community structure and dynamics, we disrupted AHL signaling by exogenous addition of AiiA-lactonase, an enzyme that cleaves the lactone ring. Microbial community structure resulting from signal inactivation, as measured by 16S rRNA amplicon sequencing and secondary metabolite production, was assessed after successive passaging of the community. Further, we investigated the impact of quorum quenching on specific microbe-microbe interactions using pairwise inhibition assays. Our results indicate that AHL inactivation alters the relative abundance of dominant community members at later passages but does not impact the overall membership in the community. Quorum quenching significantly alters the metabolic profile in lactonase-treated communities. This metabolic alteration impacts microbe-microbe interactions through decreased inhibition of other community members. Together, these results indicate that QS impacts microbial community structure through the regulation of secondary metabolites in dominant members and that the membership of microbial communities can be relatively stable despite changes in metabolic profiles.

59 BASIC BIOLOGICAL SCIENCES↗