Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “scaffold”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 667 records · Page 37
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

High-quality draft genome sequence of Thermobifida halotolerans DSM 44931

Here, we report the genome sequence of Thermobifida halotolerans DSM 44931, a bacterium that was originally isolated from a salt mine in the Yunnan Province of China. This genome was sequenced using Pacific Biosciences sequencing technology and was assembled into 2 contigs in 2 scaffolds. It has a total length of 5,506,851 bp and a GC content of 71.16%. Functional annotation of this genome provides further metabolic insight into this species.

actinomycete↗
DOE OSTI2020

Draft Genome Sequence of the Biofuel-Relevant Microalga Desmodesmus armatus

A draft genome of 906 scaffolds of 115.8 Mb was created for Desmodesmus armatus , a diploid, lipid- and storage carbohydrate-accumulating microalga proven relevant for large-scale, outdoor cultivation, and serves as a model alga platform for improving photosynthetic efficiency and carbon assimilation for next-generation bioenergy production.

09 BIOMASS FUELS↗
DOE OSTI2021

Metabolic Differentiation of Co-occurring Accumulibacter Clades Revealed through Genome-Resolved Metatranscriptomics

Natural microbial communities consist of closely related taxa that may exhibit phenotypic differences and inhabit distinct niches. However, connecting genetic diversity to ecological properties remains a challenge in microbial ecology due to the lack of pure cultures across the microbial tree of life. “Candidatus Accumulibacter phosphatis” (Accumulibacter) is a polyphosphate-accumulating organism that contributes to the enhanced biological phosphorus removal (EBPR) biotechnological process for removing excess phosphorus from wastewater and preventing eutrophication from downstream receiving waters. Distinct Accumulibacter clades often coexist in full-scale wastewater treatment plants and laboratory-scale enrichment bioreactors and have been hypothesized to inhabit distinct ecological niches. However, since individual strains of the Accumulibacter lineage have not been isolated in pure culture to date, these predictions have been made solely on genome-based comparisons and enrichments with varying strain compositions. Here, we used genome-resolved metagenomics and metatranscriptomics to explore the activity of coexisting Accumulibacter strains in an engineered bioreactor environment. We obtained four high-quality genomes of Accumulibacter strains that were present in the bioreactor ecosystem, one of which is a completely contiguous draft genome scaffolded with long Nanopore reads. We identified core and accessory genes to investigate how gene expression patterns differed among the dominating strains. Using this approach, we were able to identify putative pathways and functions that may confer distinct functions to Accumulibacter strains and provide key functional insights into this biotechnologically significant microbial lineage.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Nutrient limitation shapes functional traits of mycorrhizal fungi and phosphorus-cycling bacteria across an elevation gradient

In nutrient-limited high-elevation ecosystems, plants rely on arbuscular mycorrhizal (AM) fungi to provide mineral phosphorus (P) in the form of phosphate (PO43-). AM fungi gather these nutrients from phosphorus-cycling bacteria (PCBs) that can mineralize PO43- from organic matter and solubilize mineral-bound P. How climate, soil factors, and nutrient limitation influence AM fungi and PCB assembly remains unclear. We collected soil from montane meadows across a 1,000-m elevation gradient on three replicate mountainsides and analyzed AM fungal marker genes, P-cycling genes from shotgun metagenomes, and edaphic measurements. High-elevation soils had nearly 50-fold less soil PO₄³⁻ and 60% more AM fungal hyphae than low-elevation soils. AM fungal turnover was linked to changes in pH, organic carbon, and PO₄³-. The composition of 198 P-cycling genes was influenced by the AM fungal community structure. Drivers of individual PCB functional genes, including pH and organic carbon, varied with gene phylogeny. We found a trade-off in P-cycling strategies across elevation: P-rich, low-elevation soils supported root-colonizing AM fungi and organic P-mineralizing bacteria. P-poor, high-elevation soils were dominated by stress-tolerant AM fungi and mineral P-solubilizing bacteria. Our results suggest that AM fungi and PCB community turnover across elevation are both shaped by pH, organic carbon, and P availability. With continued climate warming, the structure and function of mountaintop ecosystems might shift to resemble lower elevations, disrupting long-established and specialized microbial assemblages, with consequences for P-cycling dynamics and the total P available to plant communities.IMPORTANCEPhosphorus (P) limits plant productivity in high-elevation ecosystems, yet the microbial networks that mobilize P, including arbuscular mycorrhizal (AM) fungi and phosphorus-cycling bacteria (PCBs), remain under-characterized in these nutrient-poor soils. We show that across a 10,00-m elevation gradient, AM fungi and P-cycling gene assemblages shift predictably with pH, organic carbon, and phosphate availability. Higher elevations, with less available P, select for stress-tolerant AM fungal taxa and PCB strategies geared toward mineral solubilization, while low-elevation sites favor root colonization by AM fungi and organic P mineralization. These results suggest that nutrient limitation can constrain microbial community assembly in consistent ways across landscapes. High mountain soils are low in P and rely on a network of underground AM fungi and PCB to deliver nutrients to plants. This study shows how those underground relationships reorganize with elevation and how climate change could collapse long-standing microbial strategies by pushing high-elevation ecosystems toward lowland conditions. As soils warm and dry, the microbial scaffolding that supports alpine plant life may become increasingly unstable.

arbuscular mycorrhizal fungi↗
DOE OSTI2022

SourceFinder: a Machine-Learning-Based Tool for Identification of Chromosomal, Plasmid, and Bacteriophage Sequences from Assemblies

High-throughput genome sequencing technologies enable the investigation of complex genetic interactions, including the horizontal gene transfer of plasmids and bacteriophages. However, identifying these elements from assembled reads remains challenging due to genome sequence plasticity and the difficulty in assembling complete sequences. In this study, we developed a classifier, using random forest, to identify whether sequences originated from bacterial chromosomes, plasmids, or bacteriophages. The classifier was trained on a diverse collection of 23,211 chromosomal, plasmid, and bacteriophage sequences from hundreds of bacterial species. In order to adapt the classifier to incomplete sequences, each complete sequence was subsampled into 5,000 nucleotide fragments and further subdivided into k-mers. This three-class classifier succeeded in identifying chromosomes, plasmids, and bacteriophages using k-mer distributions of complete and partial genome sequences, including simulated metagenomic scaffolds with minimum performance of 0.939 area under the receiver operating characteristic curve (AUC). This classifier, implemented as SourceFinder, has been made available as an online web service to help the community with predicting the chromosomal, plasmid, and bacteriophage sources of assembled bacterial sequence data (https://cge.food.dtu.dk/services/SourceFinder/).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Physical insights into biological memory using phospholipid membranes

Electrical signals may propagate along neuronal membranes in the brain, thus enabling communication between nerve cells. In doing so, lipid bilayers, fundamental scaffolds of all cell membranes, deform and restructure in response to such electrical activity. These changes impact the electromechanical properties of the membrane, which then physically store biological memory. This memory can exist either over a short or long period of time. Traditionally, biological memory is defined by the strengthening or weakening of transmissions between individual neurons. In this report we show that electrical stimulation may also alter the properties of the lipid membrane, thus pointing toward a novel mechanism for memory storage. Furthermore, based on the analysis of existing electrophysiological data, we study molecular mechanisms underlying the long-term potentiation in phospholipid membranes. Finally, we examine possible relationships between the memory capacitive properties of lipid membranes, neuronal learning, and memory.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Solid-Binding Proteins: Bridging Synthesis, Assembly, and Function in Hybrid and Hierarchical Materials Fabrication

There is considerable interest in the development of hybrid organic–inorganic materials because of the potential for harvesting the unique capabilities that each system has to offer. Proteins are an especially attractive organic component owing to the high amount of chemical information encoded in their amino acid sequence, their amenability to molecular and computational (re)design, and the many structures and functions they specify. Genetic installation of solid-binding peptides (SBPs) within protein frameworks affords control over the position and orientation of adhesive and morphogenetic segments, and a path toward predictive synthesis and assembly of functional materials and devices, all while harnessing the built-in properties of the host scaffold. Furthermore, we review the current understanding of the mechanisms through which SBPs bind to technologically relevant interfaces, with an emphasis on the variables that influence the process, and highlight the last decade of progress in the use of solid-binding proteins for hybrid and hierarchical materials synthesis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Characterizing Performance of Electrocatalyst Nanoparticles Infiltrated into Ni-YSZ Cermet Anodes for Solid Oxide Fuel Cells

The infiltration of nanoparticle electrocatalysts into solid oxide fuel cell (SOFC) electrodes has been proven to produce a high density of electrochemically active sites, and reduce charge transfer polarization losses for SOFC electrodes. This is crucial for intermediate temperature operation, as these losses increase greatly at lower temperatures. Nickel-yttria stabilized zirconia (NiYSZ) cermets are low-cost, and exhibit excellent stability, but their main disadvantage stems from nickel coarsening and performance loss over their operational lifetimes. Infiltration of electrocatalyst nanoparticles has been shown to mitigate nickel coarsening and the consequent anode degradation. In this study, the effects of these infiltrants are observed in a standard Ni-YSZ electrode. In addition to nickel, mixed ionic and electronic conducting (MIEC) phases were infiltrated into Ni-YSZ scaffolds and their performances were characterized using electrochemical impedance spectroscopy (EIS). Cross-sectional microscopy of fractured cells was used to compare electrode microstructure and particle statistics. A model is proposed for how the nanoparticle electrocatalysts improve the anode performance.

25 ENERGY STORAGE↗
DOE OSTI2021

Evidence that Surface-Segregated Sr Phases Can Be Removed in LSCF via Ceria Pre-Infiltration, Are Less Apt to Form in SSC

Here Ce 0.9 Gd 0.1 O 1.95−x (GDC) pre-infiltration was performed on 12 vol.% La 0.6 Sr 0.4 Co 0.8 Fe 0.2 O 3−x (LSCF) or Sm 0.5 Sr 0.5 CoO 3−x (SSC) infiltrated GDC Solid Oxide Fuel Cell cathodes. The addition of 7.5 vol.% of ∼40 nm diameter GDC nanoparticles into a ∼30 μ m thick porous scaffold of partially-sintered, sub-micron GDC particles before LSCF infiltration 1) lowered the temperature needed to produce a LSCF-GDC polarization resistance ( R P ) of 0.1 Ohm*cm 2 by ∼50 °C, and 2) reduced the amount of 500 h, 650 °C open-circuit LSCF-GDC R P degradation from ∼37% to ∼6%. In contrast, GDC pre-infiltration had no effect on the initial SSC-GDC R P or the 19% in R P degradation observed during 500 h of 650 °C open-circuit aging. X-Ray Photoelectron Spectroscopy showed that GDC pre-infiltration lowered the concentration of strontium species on the surface of the initial and 650 °C-aged LSCF-GDC, but had no effect on the initial or aged SSC-GDC Sr concentrations. Similarly, Electrochemical Impedance Spectroscopy showed that for both the initial and aged LSCF-GDC, GDC pre-infiltration improved oxygen exchange at the infiltrate-backbone and infiltrate-gas interfaces, but had no effect on the SSC-GDC. Hence, GDC pre-infiltration was concluded to improve LSCF-GDC performance and durability by scavenging exsolved Sr-rich secondary phases that form on the interfaces of LSCF, but not SSC.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Investigating the Catalytic Requirements of Perovskite Fuel Electrodes Using Ultra-Low Metal Loadings

Solid Oxide Fuel Cells (SOFC) with La 0.3 Sr 0.7 TiO 3 (LST)–yttria-stabilized ZrO 2 (YSZ) anodes were prepared by impregnation of LST into porous YSZ scaffolds and then modified by Atomic Layer Deposition (ALD) of Ni, Pt, Pd, Fe, Co. and CeO 2 . Weight loadings as low as 0.01% of Pt, Ni, and Pd were sufficient to decrease anode impedances by orders of magnitude for operation in humidified H 2 at 973 K. The effects of CeO 2 , Co, and Fe were less but still significant. Sintering at higher temperatures was important. Furthermore, possible ways of stabilizing the metal particles and implications for developing ceramic anodes are discussed.

25 ENERGY STORAGE↗
DOE OSTI2025

Electrochemical-Mechanical Coupling Strongly Affects the Performance of Nanopore, Thin-Film, and Solid-State Batteries

Here, the present study focuses on the electrochemical-mechanical (ECM) coupling effects of a thin-film, solid-state battery with only stiff, ceramic materials, in contrast to prior investigations that focus on individual active material particles or aggregations of particles. We model the impacts of ECM couplings including stress-transport and stress-equilibrium potential on the full-cell performance and potential mechanical failure modes of a thin-film battery conformally deposited in a nanopore scaffold, which is an experimentally achievable device. Model results indicate electrode volume changes due to lithium insertion or removal, along with mechanical boundary conditions, result in stress gradients that alter the lithium-ion flux, reduce lithium concentration gradients, and improve cell rate capability. However, the high stress levels in the cell can also lead to mechanics-related failure such as the separation of cell layers. For the parameter set in this work, stress-transport coupling has a much greater influence on rate capability than stress-potential coupling. Optimization of thin-film batteries to harness the benefits of ECM coupling effects requires leveraging geometric design and material selection. The current work underscores the need for further theoretical and experimental investigation into ECM coupling effects in thin-film batteries to enhance their understanding and design optimization.

25 ENERGY STORAGE↗
DOE OSTI2025

Modeling Electrodeposition in 3D Porous Architectures for Solid-State Li-Metal Batteries

Li-metal storage in three-dimensional (3D) electrodes is considered a potential dendrite-mitigation strategy. The large surface area and high porosity of these electrodes result in reduced local Li-plating current densities. The porous topology provides a scaffold for Li-deposition and stripping, maintaining both mechanical integrity and Li accessibility. The goal of this study is to understand how characteristics, such as geometry and material properties, affect the current distribution and deposition pattern. To this end, we developed a computational method to track material growth driven by electrodeposition within a complex geometry. This method ensures that the finite-element discretization remains conforming to the moving boundary while preserving an adequate mesh quality, and thus maintains solution accuracy. Using this new computational tool, we analyze the conditions under which porous anode architectures effectively expand the surface area of the charge-transfer interface, and self-regulate current density and dendrite growth.

3D electrode architectures↗
DOE OSTI2025

Multiscale Modeling Framework for Lithium Nucleation in 3D Porous Carbon Anodes

Porous carbon scaffolds offer a promising route for mitigating non-uniform lithium (Li) plating to enhance the safety and longevity of Li metal batteries. However, the influence of microstructural morphology on Li nucleation is not well understood. Here, we present a multiscale modeling framework to investigate how the porous microstructure of carbon materials affects Li nucleation behavior. Ab initio molecular dynamics simulations quantify the nucleation energy barriers of Li on graphene as a function of Li content, surface curvature, and applied potential, providing key parameters for a classical nucleation theory (CNT) model. From macroscale half-cell simulations, we obtained Li concentration and electrical potential profiles to define boundary conditions for mesoscopic simulations. At the mesoscale, three distinct synthetic 3D microstructures with different porosities and characteristic feature sizes are generated to resolve local distributions of Li flux, current density, and mechanical stress. These outputs are integrated into the CNT model to map spatial variation in nucleation rates. Our findings reveal trade-offs between suppressing nucleation rates and achieving spatial uniformity, offering design guidelines for optimizing porous carbon anodes to balance nucleation control and mechanical integrity.

Materials science↗
DOE OSTI2026

From Powder to Power: Tailored Pre-Milling Strategy that Optimizes Microstructure for Efficient Hydrogen Evolution

The hydrogen evolution reaction (HER) plays a critical role in enabling large-scale electrolytic hydrogen production and advancing future technologies and fuel production. Among non-precious metals, NiMo-based catalysts are particularly attractive due to their capability to promote both water dissociation and hydrogen adsorption in alkaline media. However, conventional NiMo catalysts often suffer from incomplete alloying, particle aggregation, weak metal–support interactions, and surface oxidation, which significantly limit active site utilization, electronic conductivity, and long-term stability. Herein, we report a scalable, solid-state, two-step ball milling strategy for constructing an efficient NiMo/C catalyst for the HER. Pre-milling the metal precursors prior to carbon incorporation promotes efficient solid-state activation, leading to the formation of uniformly alloyed, ultrafine, and defect-rich Ni–Mo nanoparticles with robust metal–carbon interfacial anchoring. Benefiting from this integrated structural design, the optimized NiMo/C catalyst exhibits low overpotentials and Tafel slopes, reduced charge-transfer resistance, and excellent durability under alkaline conditions. Comprehensive structural and surface analysis reveal that the enhanced HER performance can be attributed to the synergistic interplay of homogeneous Ni–Mo alloying, uniform nanoparticle dispersion on a defect-rich carbon scaffold, enhanced accessibility of catalytically active sites, and optimized electronic coupling that stabilizes the catalyst surface. This work highlights the two-step solid-state ball milling strategy as a simple, robust, and scalable route for the preparation of effective and durable non-precious metal HER electrocatalysts, offering practical insights toward large-scale and inexpensive hydrogen production.

Yang, Xiaoxuan [Oak Ridge National Laboratory (ORN↗
DOE OSTI2020

(Invited) All-Solid-State Batteries Using Li 7 La 3 Zr 2 O 12 Garnet Electrolyte Framework

All-solid-state batteries (ASSB) using LLZO (variants of Li 7 La 3 Zr 2 O 12 ) garnet solid electrolyte with lithium metal anode potentially offer higher energy density and improved safety. Rational design of cell architecture as well as manufacturing scalability are key aspects to consider as the technology readiness level advances. A thick composite cathode layer attached to a thin solid electrolyte layer is desirable to obtain superior energy densities. Furthermore, the architecture within the composite cathode may be engineered to contain directional conduction paths of lithium ions or electrons for enhanced rate capabilities. Here, we demonstrate a functioning bulk-type LLZO based all-solid-state battery with a practical form factor incorporating the above described design concepts. Freeze-tape-casting (FTC), a scalable and environmentally friendly ceramic processing method, is used to construct 3D porous LLZO scaffolds composed of vertical arrays of LLZO walls. The thin solid-electrolyte layer is fabricated by tape-casting (TC). By sintering the stacks of FTC and TC green tapes, porous/dense bilayers and porous/dense/porous trilayers of LLZO frameworks are obtained. An ASSB was constructed using a porous/dense bilayer by infiltrating LiNi 0.6 Mn 0.2 Co 0.2 O 2 cathode powder and carbon black into the porous layer and adhering lithium metal foil to the dense side. We find it crucial to introduce a plastic crystal based soft solid electrolyte to the porous layer to electrochemically connect all cathode components, obviating the need for co-sintering to establish contact. The soft nature of the plastic crystal based solid-electrolyte may be able to accommodate the volume change of the cathode material as it cycles. In this device, which contained no liquid component, the initial discharge capacities were similar to those observed in a lithium ion battery configuration using the same cathode powder at C/10 rates.

25 ENERGY STORAGE↗
DOE OSTI2026

TETA Autoresearch [SWR-26-089]

TETA Autoresearch is a template repository based on github.com/karpathy/autoresearch for AI-assisted research science in the TETA group in the Center for Integrated Mobility Sciences (CIMS) center at the National Laboratory of the Rockies. This software is a template for running autonomous research experiments that iteratively improve an ML model for a single optimization objective. Two execution modes share one harness: LLM mode - an agent (e.g. Claude Code) edits a scaffold train.py one change at a time, tagging each experiment, logging reasoning, and pushing results. Defined by program.md. Optimizer mode - an Optuna-backed driver (TPE / CMA-ES / Random) iterates over a domain-defined search space. Defined by optimizers/. RouteE (vehicle energy prediction) is the reference domain under domains/routee/. Adding a new domain is mechanical - see EXTENDING.md.

Reinicke, Nicholas [National Laboratory of the Roc↗
DOE OSTI2020

Methanosarcina acetivorans contains a functional ISC system for iron-sulfur cluster biogenesis

Abstract Background The production of methane by methanogens is dependent on numerous iron-sulfur (Fe-S) cluster proteins; yet, the machinery involved in Fe-S cluster biogenesis in methanogens remains largely unknown. Methanogen genomes encode uncharacterized homologs of the core components of the ISC (IscS and IscU) and SUF (SufBC) Fe-S cluster biogenesis systems found in bacteria and eukaryotes. Methanosarcina acetivorans contains three iscSU and two sufCB gene clusters. Here, we report genetic and biochemical characterization of M. acetivorans iscSU2 . Results Purified IscS2 exhibited pyridoxal 5′- phosphate-dependent release of sulfur from L-cysteine. Incubation of purified IscU2 with IscS2, cysteine, and iron (Fe 2+ ) resulted in the formation of [4Fe-4S] clusters in IscU2. IscU2 transferred a [4Fe-4S] cluster to purified M. acetivorans apo-aconitase. IscU2 also restored the aconitase activity in air-exposed M. acetivorans cell lysate. These biochemical results demonstrate that IscS2 is a cysteine desulfurase and that IscU2 is a Fe-S cluster scaffold. M. acetivorans strain DJL60 deleted of iscSU2 was generated to ascertain the in vivo importance of IscSU2. Strain DJL60 had Fe-S cluster content and growth similar to the parent strain but lower cysteine desulfurase activity. Strain DJL60 also had lower intracellular persulfide content compared to the parent strain when cysteine was an exogenous sulfur source, linking IscSU2 to sulfur metabolism. Conclusions This study establishes that M. acetivorans contains functional IscS and IscU, the core components of the ISC Fe-S cluster biogenesis system and provides the first evidence that ISC operates in methanogens.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Chromosome-level assembly and analysis of Camelina neglecta : a novel diploid model for Camelina biotechnology research

Camelina neglecta is a new diploid Brassicaceae species, which has great research value because of its close relationship with the hexaploid oilseed crop Camelina sativa. Here, we report a chromosome-level assembly of C. neglecta with a total length of 210 Mb. By adopting PacBio sequencing and Hi-C technology, the C. neglecta genome was assembled into 6 chromosomes with scaffold N50 of 29.62 Mb. C. neglecta has undergone the whole-genome triplication (γ) shared among eudicots and two whole-genome duplications (α and β) shared by crucifers, but it has not undergone a specific whole-genome duplication event. By synteny analysis between C. neglecta and C. sativa, we successfully used the method of calculating Ks to distinguish the three subgenomes of C. sativa and determined that C. neglecta was closest to the first subgenome (SG1) of C. sativa. Further, transcriptomic analysis revealed the key genes associated with seed oil biosynthesis and its transcriptional regulation, including SAD, FAD2, FAD3, FAE1, ABI3, WRI1 and FUS3 displaying high expression levels in C. neglecta seeds. The high representability of C. neglecta as a model species for Camelina-based biotechnology research has been demonstrated for the first time. In particular, floral Agrobacterium tumefaciens infiltration-based transformation of C. neglecta, leading to overexpression of CvLPAT2, CpDGAT1 and CvFatB1 transgenes, was demonstrated for medium-chain fatty acid accumulation in C. neglecta seed oil. This study provides an important genomic resource and establishes C. neglecta as a new model for oilseed biotechnology research.

60 APPLIED LIFE SCIENCES↗