Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “assembly pathways”

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 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Brockarchaeota, a novel archaeal phylum with unique and versatile carbon cycling pathways

Geothermal environments, such as hot springs and hydrothermal vents, are hotspots for carbon cycling and contain many poorly described microbial taxa. Here, we reconstructed 15 archaeal metagenome-assembled genomes (MAGs) from terrestrial hot spring sediments in China and deep-sea hydrothermal vent sediments in Guaymas Basin, Gulf of California. Phylogenetic analyses of these MAGs indicate that they form a distinct group within the TACK superphylum, and thus we propose their classification as a new phylum, ‘Brockarchaeota’, named after Thomas Brock for his seminal research in hot springs. Based on the MAG sequence information, we infer that some Brockarchaeota are uniquely capable of mediating non-methanogenic anaerobic methylotrophy, via the tetrahydrofolate methyl branch of the Wood-Ljungdahl pathway and reductive glycine pathway. The hydrothermal vent genotypes appear to be obligate fermenters of plant-derived polysaccharides that rely mostly on substrate-level phosphorylation, as they seem to lack most respiratory complexes. In contrast, hot spring lineages have alternate pathways to increase their ATP yield, including anaerobic methylotrophy of methanol and trimethylamine, and potentially use geothermally derived mercury, arsenic, or hydrogen. Their broad distribution and their apparent anaerobic metabolic versatility indicate that Brockarchaeota may occupy previously overlooked roles in anaerobic carbon cycling.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Predictive CRISPR-mediated gene downregulation for enhanced production of sustainable aviation fuel precursor in Pseudomonas putida

CRISPR interference (CRISPRi) has emerged as a valuable tool for redirecting metabolic flux to enhance bioproduction. However, its application is often constrained by two challenges: (i) rationally identifying effective gene targets for downregulation and (ii) efficiently constructing multiplexed CRISPRi systems. In this study, we address both challenges by integrating a computational prioritization tool with a versatile assembly method for building multiplexed CRISPRi systems. FluxRETAP (Flux-Reaction Target Prioritization) accurately identified gene targets whose knockdown led to substantial increase of isoprenol titers in Pseudomonas putida KT2440, outperforming a conventional non-computational, pathway-guided target selection. The highest isoprenol titer of nearly 1.5 g/L was achieved by knocking down PP_4118 (a gene encoding α-ketoglutarate dehydrogenase). The use of VAMMPIRE (Versatile Assembly Method for MultiPlexing CRISPRi-mediated downREgulation) enabled accurate assembly of CRISPRi constructs containing up to five sgRNA arrays, reducing context dependency and achieving uniform, position-independent gene downregulation. The integration of FluxRETAP and VAMMPIRE has the potential to advance metabolic engineering by rapidly identifying CRISPRi-mediated knockdowns and knockdown combinations that enhance bioproduction titers, with potential applicability to other microbial systems.

CRISPR interference↗
DOE OSTI2020

Photoresponsive Structured Liquids Enabled by Molecular Recognition at Liquid–Liquid Interfaces

Using host-guest molecular recognition at the oil-water interface, a new type of photoresponsive nanoparticle surfactant (NPS) was designed and prepared to structure liquids. With the help of a polymeric surfactant, the interfacial host-guest interactions can be significantly enhanced, leading to the rapid formation and assembly of a NP monolayer and offering sufficient binding energy to hold the NPs in a jammed state. The assembly of the NPSs can be reversibly manipulated via a photoswitchable jamming-to-unjamming transition, endowing the interface as well as the macroscopic assemblies with responsiveness to the external trigger (photons). Finally, this study for the first time opens a pathway for the construction of multiresponsive, structured all-liquid systems by introducing host-guest chemistry, showing promising potential applications in encapsulation, delivery systems, and unique microfluidic devices.

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

Ce IV 70 Oxosulfate Rings, Frameworks, Supramolecular Assembly, and Redox Activity**

Abstract M IV molecular oxo‐clusters (M=Zr, Hf, Ce, Th, U, Np, Pu) are prolific in bottoms‐up material design, catalysis, and elucidating reaction pathways in nature and in synthesis. Here we introduce Ce 70 , a wheel‐shaped oxo‐cluster, [Ce IV 70 (OH) 36 (O) 64 (SO 4 ) 60 (H 2 O) 10 ] 4− . Ce 70 crystallizes into intricate high pore volume frameworks with divalent transition metals and Ce‐monomer linkers. Eight crystal‐structures feature four framework types in which the Ce 70 ‐rings are linked as propellers, in offset‐stacks, in a tartan pattern, and as isolated rings. Small‐angle X‐ray scattering of Ce 70 dissolved in butylamine, with and without added cations (Ce IV , alkaline earths, Mn II ), shows the metals‘ differentiating roles in ring linking, leading to supramolecular assemblies. The large acidic pores and abundant terminal sulfates provide ion‐exchange behavior, demonstrated with U IV and Nd III . Frameworks featuring Ce III/IV ‐monomer linkers demonstrate both oxidation and reduction. This study opens the door to mixed‐metal, highly porous framework catalysts, and new clusters for metal‐organic framework design

Colliard, Ian↗
DOE OSTI2022

Functional Insights of Salinity Stress-Related Pathways in Metagenome-Resolved Methanothrix Genomes

Recently, methanogenic archaea belonging to the genus Methanothrix were reported to have a fundamental role in maintaining stable ecosystem functioning in anaerobic bioreactors under different configurations/conditions. In this study, we reconstructed three Methanothrix metagenome-assembled genomes (MAGs) from granular sludge collected from saline upflow anaerobic sludge blanket (UASB) reactors, where Methanothrix harundinacea was previously implicated with the formation of compact and stable granules under elevated salinity levels (up to 20 g/L Na + ). Genome annotation and pathway analysis of the Methanothrix MAGs revealed a genetic repertoire supporting their growth under high salinity. Specifically, the most dominant Methanothrix (MAG_279), classified as a subspecies of Methanothrix_A harundinacea_D, had the potential to augment its salinity resistance through the production of different glycoconjugates via the N-glycosylation process, and via the production of compatible solutes as N ε -acetyl-β-lysine and ectoine. The stabilization and reinforcement of the cell membrane via the production of isoprenoids was identified as an additional stress-related pathway in this microorganism. The improved understanding of the salinity stress-related mechanisms of M. harundinacea highlights its ecological niche in extreme conditions, opening new perspectives for high-efficiency methanisation of organic waste at high salinities, as well as the possible persistence of this methanogen in highly-saline natural anaerobic environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Modular cell-free expression plasmids to accelerate biological design in cells

Industrial biotechnology aims to produce high-value products from renewable resources. This can be challenging because model microorganisms—organisms that are easy to use like Escherichia coli—often lack the machinery required to utilize desired feedstocks like lignocellulosic biomass or syngas. Non-model organisms, such as Clostridium, are industrially proven and have desirable metabolic features but have several hurdles to mainstream use. Namely, these species grow more slowly than conventional laboratory microbes, and genetic tools for engineering them are far less prevalent. To address these hurdles for accelerating cellular design, cell-free synthetic biology has matured as an approach for characterizing non-model organisms and rapidly testing metabolic pathways in vitro. Unfortunately, cell-free systems can require specialized DNA architectures with minimal regulation that are not compatible with cellular expression. In this work, we develop a modular vector system that allows for T7 expression of desired enzymes for cell-free expression and direct Golden Gate assembly into Clostridium expression vectors. Utilizing the Joint Genome Institute’s DNA Synthesis Community Science Program, we designed and synthesized these plasmids and genes required for our projects allowing us to shuttle DNA easily between our in vitro and in vivo experiments. We next validated that these vectors were sufficient for cell-free expression of functional enzymes, performing on par with the previous state-of-the-art. Lastly, we demonstrated automated six-part DNA assemblies for Clostridium autoethanogenum expression with efficiencies ranging from 68% to 90%. We anticipate this system of plasmids will enable a framework for facile testing of biosynthetic pathways in vitro and in vivo by shortening development cycles.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2007

International Space Station Research: Accomplishments and Pathways for Exploration and Fundamental Research

Beginning with the launch of the European Columbus module planned for December 2007, we approach a transition in the assembly of the International Space Station (ISS) that is of great importance for the sciences. During the following 18 months, we will operate the first experiments in Columbus physical science resource facilities and also launch and commission the Japanese Kibo module. In addition, two Multi-purpose Logistics Module (MPLM) flights will deliver the U.S. Combustion Integrated Rack (CIR) and Fluids Integrated Rack (FIR) along with their first science experiments. These facilities provide significant new capabilities for basic and applied physical science research in microgravity. New life support technologies will come online throughout 2008, and we will reach the milestone of a 6-person crew planned for April 2009. A larger crew enables significant more scientific use of all the facilities for the life of ISS. Planning for the use of the International Space Station as a national laboratory is also maturing as we near the completion of assembly, enabling access to ISS as a research platform for other government agencies and the private sector. The latest updates on National Laboratory implementation will also be provided in this presentation. At the same time as these significant increases in scientific capability, there have been significant ongoing accomplishments in NASA's early ISS research both exploration related and fundamental research. These accomplishments will be reviewed in context as harbingers of the capabilities of the International Space Station when assembly is complete. The Vision for Space Exploration serves to focus NASA's applied investigations in the physical sciences. However, the broader capability of the space station as a National Laboratory and as a nexus for international collaboration will also influence the study of gravity-dependent processes by researchers around the world.

Robinson, Julie A.↗
DOE OSTI2024

Driving forces for particle-based crystallization: From experiments to theory and simulations

The multi-step crystallization processes involving the formation of stable building blocks that subsequently assemble into a crystal are ubiquitous in mineral formation and biomineralization and are particularly attractive in materials synthesis. Utilizing these pathways offers the approach to overcoming the restrictions on the expression of various crystal faces imposed by the interfacial energy during monomer-by-monomer growth to unlock the breadth of architectures with unique properties. Further, controlling particle-based crystallization proved challenging despite its promise due to the complex interdependence of interfacial forces and their non-linear dependence on synthesis parameters. Here, the status of the development of state-of-the-art approaches to measuring interparticle forces and predictive theoretical models of particle-based crystallization are reviewed.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Designing a Zn–Ag Catalyst Matrix and Electrolyzer System for CO 2 Conversion to CO and Beyond

CO 2 emissions can be transformed into high-added-value commodities through CO 2 electrocatalysis; however, efficient low-cost electrocatalysts are needed for global scale-up. Inspired by other emerging technologies, the authors report the development of a gas diffusion electrode containing highly dispersed Ag sites in a low-cost Zn matrix. Here, this catalyst shows unprecedented Ag mass activity for CO production: –614 mA cm –2 at 0.17 mg of Ag. Subsequent electrolyte engineering demonstrates that halide anions can further improve stability and activity of the Zn–Ag catalyst, outperforming pure Ag and Au. Membrane electrode assemblies are constructed and coupled to a microbial process that converts the CO to acetate and ethanol. Combined, these concepts present pathways to design catalysts and systems for CO 2 conversion toward sought-after products.

36 MATERIALS SCIENCE↗
DOE OSTI2023

The first two chromosome‐scale genome assemblies of American hazelnut enable comparative genomic analysis of the genus Corylus

Summary The native, perennial shrub American hazelnut ( Corylus americana ) is cultivated in the Midwestern United States for its significant ecological benefits, as well as its high‐value nut crop. Implementation of modern breeding methods and quantitative genetic analyses of C. americana requires high‐quality reference genomes, a resource that is currently lacking. We therefore developed the first chromosome‐scale assemblies for this species using the accessions ‘Rush’ and ‘Winkler’. Genomes were assembled using HiFi PacBio reads and Arima Hi‐C data, and Oxford Nanopore reads and a high‐density genetic map were used to perform error correction. N50 scores are 31.9 Mb and 35.3 Mb, with 90.2% and 97.1% of the total genome assembled into the 11 pseudomolecules, for ‘Rush’ and ‘Winkler’, respectively. Gene prediction was performed using custom RNAseq libraries and protein homology data. ‘Rush’ has a BUSCO score of 99.0 for its assembly and 99.0 for its annotation, while ‘Winkler’ had corresponding scores of 96.9 and 96.5, indicating high‐quality assemblies. These two independent assemblies enable unbiased assessment of structural variation within C. americana , as well as patterns of syntenic relationships across the Corylus genus. Furthermore, we identified high‐density SNP marker sets from genotyping‐by‐sequencing data using 1343 C. americana , C. avellana and C. americana × C. avellana hybrids, in order to assess population structure in natural and breeding populations. Finally, the transcriptomes of these assemblies, as well as several other recently published Corylus genomes, were utilized to perform phylogenetic analysis of sporophytic self‐incompatibility (SSI) in hazelnut, providing evidence of unique molecular pathways governing self‐incompatibility in Corylus .

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Scrambling Signal Modularity in Bottom-up Assembled Synthetic Pseudomonas Consortia Reveals Robust Information Transfer

There is immense potential in crafting synthetic microbial communities for application in human health, agriculture, the environment, and even biomanufacturing where an appropriately constructed consortium can be assembled with tremendous biosynthetic or degradative capabilities. In many of these cases, bacterial signaling serves as a form of intercellular information transfer that guides the collective’s behavior. Such communication is complex, as many signals, signal disruptors, microbial species, physical barriers, and spatiotemporal constraints may be involved. Here, in this work, we demonstrate that a multisignal pathway for molecular information transfer within a consortium of several Pseudomonas spp. can be scrambled (genetically and organizationally) while the original message is still effectively conveyed. Assembled from the bottom up, we have employed two types of signaling molecules (i) a redox active secondary metabolite (rhizospheric signal, phloroglucinol), and (ii) a bacterial quorum sensing signal (3-oxo-C12 acylhomoserine lactone, AI-1). These signals can be intraconverted and acted upon by designated community members. We show how the order in which the signals are received, transduced, and subsequently transmitted can be rearranged with minimal impact on the intended outcome. In the consortial context, we found this messaging structure can be remarkably robust. Inspired by rhizospheric molecular signaling mechanisms, this work provides a conceptual framework for designing signaling and information transfer processes within assembled communities.

Biological and medical sciences↗
DOE OSTI2021

Ce IV 70 oxosulfate rings, frameworks, supramolecular assembly and redox activity

M IV molecular oxo-clusters (M=Zr, Hf, Ce, Th, U, Np, Pu) are prolific in bottoms-up material design, catalysis, and elucidating reaction pathways in nature and in synthesis. Here we introduce Ce 70 , a wheel-shaped oxo-cluster, [Ce IV 70 -(OH) 36 (O) 64 (SO 4 ) 60 (H 2 O) 10 ] 4- . Ce 70 crystallizes into intricate high pore volume frameworks with divalent transition metals and Ce-monomer linkers. Eight crystal-structures feature four framework types in which the Ce 70 -rings are linked as propellers, in offset-stacks, in a tartan pattern, and as isolated rings. In this work, small-angle X-ray scattering of Ce 70 dissolved in butylamine, with and without added cations (Ce IV , alkaline earths, Mn II ), shows the metals‘ differentiating roles in ring linking, leading to supramolecular assemblies. The large acidic pores and abundant terminal sulfates provide ion-exchange behavior, demonstrated with U IV and Nd III . Frameworks featuring Ce III/IV -monomer linkers demonstrate both oxidation and reduction. Furthermore, this study opens the door to mixed-metal, highly porous framework catalysts, and new clusters for metal-organic framework design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Large-Area Periodic Arrays of Atomically Flat Single-Crystal Gold Nanotriangles Formed Directly on Substrate Surfaces

The advancement of nanoenabled wafer-based devices requires the establishment of core competencies related to the deterministic positioning of nanometric building blocks over large areas. Within this realm, plasmonic single-crystal gold nanotriangles represent one of the most attractive nanoscale components but where the formation of addressable arrays at scale has heretofore proven impracticable. In this work, a benchtop process is presented for the formation of large-area periodic arrays of gold nanotriangles. The devised growth pathway sees the formation of an array of defect-laden seeds using lithographic and vapor-phase assembly processes followed by their placement in a growth solution promoting planar growth and threefold symmetric side-faceting. The nanotriangles formed in this high-yield synthesis distinguish themselves in that they are epitaxially aligned with the underlying substrate, grown to thicknesses that are not readily obtainable in colloidal syntheses, and present atomically flat pristine surfaces exhibiting gold atoms with a close-packed structure. As such, they express crisp and unambiguous plasmonic modes and form photoactive surfaces with highly tunable and readily modeled plasmon resonances. The devised methods, hence, advance the integration of single-crystal gold nanotriangles into device platforms and provide an overall fabrication strategy that is adaptable to other nanomaterials.

42 ENGINEERING↗
DOE OSTI2020

Mechanism and Reaction Energy Landscape for Apiose Cross-Linking by Boric Acid in Rhamnogalacturonan II

Rhamnogalacturonan II (RG-II)—the most complex polysaccharide known in nature—exists as a borate cross-linked dimer in the plant primary cell wall. Boric acid facilitates the formation of this cross-link on the apiosyl residues of RG-II’s side chain A. Here, we detail the reaction mechanism for the cross-linking process with ab initio calculations coupled with transition state theory. We determine the formation of the first ester linkage to be the rate-limiting step of the mechanism. Our findings demonstrate that the regio- and stereospecific nature of subsequent steps in the reaction itinerary presents four distinct energetically plausible reaction pathways. This has significant implications for the overall structure of the cross-linked RG-II dimer assembly. Finally, our transition state and reaction path analyses reveal key geometric insights that corroborate previous experimental hypotheses on borate ester formation reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Ion-Assisted Nanoscale Material Engineering in Atomic Layers

Achieving deterministic control over the properties of low-dimensional materials with nanoscale precision is a long-sought goal. Mastering this capability has a transformative effect on the design of multifunctional electrical and optical devices. Here, we present an ion-assisted synthetic technique that enables precise control over the material composition and energy landscape of two-dimensional (2D) atomic crystals. Our method transforms binary transition-metal dichalcogenides, like MoSe2, into ternary MoS2αSe2(1-α) alloys with systematically adjustable compositions, α. By piecewise assembly of the lateral, compositionally modulated MoS2αSe2(1-α) segments within 2D atomic layers, we present a synthetic pathway toward the realization of multicompositional designer materials. Our technique enables the fabrication of advanced 2D structures with arbitrary boundaries, dimensions as small as 30 nm, and fully customizable energy landscapes. Our optical characterizations further showcase the potential for implementing tailored optoelectronics in these engineered 2D crystals.

2D materials↗
DOE OSTI2022

Multiple sources of aerobic methane production in aquatic ecosystems include bacterial photosynthesis

Aquatic ecosystems are globally significant sources of the greenhouse gas methane to the atmosphere. Until recently, methane production was thought to be a strictly anaerobic process confined primarily to anoxic sediments. However, supersaturation of methane in oxygenated waters has been consistently observed in lakes and the ocean (termed the ‘methane paradox’), indicating that methane can be produced under oxic conditions through unclear mechanisms. Here we show aerobic methane production from multiple sources in freshwater incubation experiments under different treatments and based on biogeochemical, metagenomic, and metatranscriptomic data. We find that aerobic methane production appears to be associated with (bacterio)chlorophyll metabolism and photosynthesis, as well as with Proteobacterial degradation of methylphosphonate. Genes encoding pathways for putative photosynthetic- and methylphosphonate-based methane production also co-occur in Proteobacterial metagenome-assembled genomes. Our findings provide insight into known mechanisms of aerobic methane production, and suggest a potential co-occurring mechanism associated with bacterial photosynthesis in aquatic ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structural basis for ATG9A recruitment to the ULK1 complex in mitophagy initiation

The assembly of the autophagy initiation machinery nucleates autophagosome biogenesis, including in the PINK1- and Parkin-dependent mitophagy pathway implicated in Parkinson’s disease. The structural interaction between the sole transmembrane autophagy protein, autophagy-related protein 9A (ATG9A), and components of the Unc-51–like autophagy activating kinase (ULK1) complex is one of the major missing links needed to complete a structural map of autophagy initiation. We determined the 2.4-Å x-ray crystallographic structure of the ternary structure of ATG9A carboxyl-terminal tail bound to the ATG13:ATG101 Hop1/Rev7/Mad2 (HORMA) dimer, which is part of the ULK1 complex. We term the interacting portion of the extreme carboxyl-terminal part of the ATG9A tail the “HORMA dimer–interacting region” (HDIR). This structure shows that the HDIR binds to the HORMA domain of ATG101 by β sheet complementation such that the ATG9A tail resides in a deep cleft at the ATG13:ATG101 interface. Disruption of this complex in cells impairs damage-induced PINK1/Parkin mitophagy mediated by the cargo receptor NDP52.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Molecular insights into the in situ early-stage assembly of metal–organic frameworks on cellulose nanofibrils

The integration of metal–organic frameworks (MOFs) into renewable matrices, including those derived from cellulose, to create cellulose/MOF hybrids has attracted significant interest due to the synergistic combination of cellulosic biopolymer properties and MOFs' multifunctional features. The interfacial interactions between cellulose and MOF not only ensure stable bonding, but ultimately also determine the bulk physical properties of the macroscopic composites. However, the mechanistic understanding of the in situ assembly between the two materials remains unclear. In this study, we employ a combination study of synthesis, experimental characterization, and molecular dynamics simulations to explore the early-stage assembly of a cellulose/MOF hybrid. Our results revealed that the growth of MOF clusters on the 2,2,6,6-tetramethyl-1-piperidinyloxy oxidized cellulose nanofibrils (TOCNF) follows an inhomogeneous sequential transformation pathway. The carboxylates of TOCNF form coordination-like bonds with the metal ions, while the hydroxyl groups of TOCNF form hydrogen bonds with MOF ligands. These interactions provide the initial nucleation sites that mediate the growth of MOF clusters and also guide the assembly of larger MOF clusters onto the TOCNF substrate. In conclusion, the fundamental insights into the in situ assembly of MOF nanoparticles on cellulosic substrates are essential for the rational design of high-performance materials with tailored morphology and optimized properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗