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At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Environmental stress mediates groundwater microbial community assembly

Community assembly describes how different ecological processes shape microbial community composition and structure. How environmental factors impact community assembly remains elusive. Here we sampled microbial communities and >200 biogeochemical variables in groundwater at the Oak Ridge Field Research Center, a former nuclear waste disposal site, and developed a theoretical framework to conceptualize the relationships between community assembly processes and environmental stresses. We found that stochastic assembly processes were critical (>60% on average) in shaping community structure, but their relative importance decreased as stress increased. Dispersal limitation and ‘drift’ related to random birth and death had negative correlations with stresses, whereas the selection processes leading to dissimilar communities increased with stresses, primarily related to pH, cobalt and molybdenum. Assembly mechanisms also varied greatly among different phylogenetic groups. As a result, our findings highlight the importance of microbial dispersal limitation and environmental heterogeneity in ecosystem restoration and management.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Construction and characterization of a genome-scale ordered mutant collection of Bacteroides thetaiotaomicron

Ordered transposon-insertion collections, in which specific transposon-insertion mutants are stored as monocultures in a genome-scale collection, represent a promising tool for genetic dissection of human gut microbiota members. However, publicly available collections are scarce and the construction methodology remains in early stages of development. Here, we describe the assembly of a genome-scale ordered collection of transposon-insertion mutants in the model gut anaerobe Bacteroides thetaiotaomicron VPI-5482 that we created as a resource for the research community. We used flow cytometry to sort single cells from a pooled library, located mutants within this initial progenitor collection by applying a pooling strategy with barcode sequencing, and re-arrayed specific mutants to create a condensed collection with single-insertion strains covering >2500 genes. To demonstrate the potential of the condensed collection for phenotypic screening, we analyzed growth dynamics and cell morphology. We identified both growth defects and altered cell shape in mutants disrupting sphingolipid synthesis and thiamine scavenging. Finally, we analyzed the process of assembling the B. theta condensed collection to identify inefficiencies that limited coverage. We demonstrate as part of this analysis that the process of assembling an ordered collection can be accurately modeled using barcode sequencing data. We expect that utilization of this ordered collection will accelerate research into B. theta physiology and that lessons learned while assembling the collection will inform future efforts to assemble ordered mutant collections for an increasing number of gut microbiota members.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Embedded anchoring of multi-material assemblies by friction riveting process

In this paper, we report on work that focused on extending the capability and broaden the applicability of the friction-riveting process for joining stacks composed of a wide range of multi-layer polymer-to-metals and similar and dissimilar metals. We first present direct experimental evidence of our use of this process to join aluminum-to-steel dissimilar metals with steel rivets. We have demonstrated for the first time the use of magnesium as a rivet material for joining carbon fiber reinforced polymer (CFRP) stacks, aluminum as a rivet material to laminate magnesium to CFRP, and aluminum-to-aluminum similar metal joining and aluminum-to-steel dissimilar metal joining with steel rivets. Our work sheds light on detailed process parameter optimization and the corresponding process response behavior, thus advancing our understanding of this complex joining method for a wide range of material combinations.

Friction-riveting, magnesium rivet, carbon fiber r↗
DOE OSTI2024

Impacts of Fast Critical Assembly Fuel Discards on Liquid Waste Processes

The Savannah River Nuclear Solutions (SRNS) Fast Critical Assembly (FCA) mission is reestablishing the electrolytic dissolver for processing of Pu and Pu-U materials clad in stainless steel (SS). H-Canyon is planning to dissolve and neutralize FCA fuel without recovering the special nuclear material (i.e., Pu) prior to discarding to the Concentration, Storage, and Transfer Facilities (CSTF) operated by the Savannah River Mission Completion (SRMC) Liquid Waste (LW) Organization. The FCA discards will be combined with sludge in the CSTF after Low Temperature Aluminum Dissolution (LTAD) if needed. The combined waste will be washed, concentrated, and vitrified at the Defense Waste Processing Facility (DWPF). The high level waste canisters produced will be temporarily stored in the Glass Waste Storage Buildings prior to transfer to a future federal repository. Decants from LTAD and sludge washing will be combined with DWPF recycle and dissolved salt cake to prepare salt batches for processing in the Salt Waste Processing Facility. The resulting decontaminated salt solution will be processed in the Saltstone Production Facility.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2025

Sequence Programmable Order–Disorder Transitions in Supramolecular Assembly of Peptide Nanofibers

Protein–protein interactions determine the assembly of complexes that are responsible for numerous key biological processes. The assembly of many natural protein complexes is mediated by post-translational structural changes and environmental stimuli. In this study, we show that incorporation of adjacent lysine residues results in the pH-tunable stability of peptide secondary structure and assembly, allowing for the incorporation of complementary order-inducing motifs. The strategic placement of cysteine pairs in the same peptide sequence results in redox-dependent disulfide staple formation, inducing a transition from random coil to β-sheet conformation and subsequent supramolecular nanofiber assembly from otherwise disordered peptide monomers. Spectroscopic, imaging, molecular dynamics, and kinetic studies highlight the critical role of sequence motif location, oligomerization, and the competitive interplay between intra- and interpeptide disulfide bonding in determining assembly outcomes. We extend this approach to demonstrate phosphorylation-dependent assembly from the design of the same parent peptide sequence, suggesting a general approach to the design of diverse stimulus-responsive peptide sequences for supramolecular assembly. Furthermore, these findings also provide a framework for investigating sequence-dependent pathways in amyloid fiber formation with potential implications for neurodegenerative disease research.

Disulfides↗
DOE OSTI2025

Shaping Symmetry and Molding Morphology of Triply-Periodic Network Assemblies via Molecular Design and Processing of Block Copolymers

This project aimed to uncover molecular design rules for block copolymer (BCP) assemblies of triply-periodic network (TPN) phases, which are highly sought after, yet elusive, nanostructures for many functional material applications that rely on their combination of symmetry and polycontinuous domain connectivity [R1, R2], such as topological-photonics, supercapacitors and ultrafiltration media. While they have been a target of “bottom up” approaches to nanostructured, hybrid materials, the ability to manipulate the tubular network morphology of TPN assemblies beyond the cubic double-gyroid (DG) phase has advanced relatively little.

36 MATERIALS SCIENCE↗
DOE OSTI2020

DUCTED ASSEMBLY STEADY STATE HEAT TRANSFER SOFTWARE

The Ducted Assembly Steady State Heat transfer software (DASSH) performs full core, steady state, subchannel temperature calculations for hexagonal, ducted assemblies. DASSH is targeted for use in the early stages of the reactor design process when assembly characteristics may not be defined or are undergoing considerable changes. DASSH provides a relatively rapid assessment of the temperature and flow distribution to inform reactor design updates and analysis.

ATZ, MILOSIVO↗
DOE OSTI2021

Ducted Assembly Steady-State Heat Transfer Software (DASSH)

The Ducted Assembly Steady-State Heat transfer software (DASSH) is being developed at Argonne National Laboratory to perform a steady-state thermal fluids calculation to determine the coolant flow and temperature distribution for a hexagonal reactor core configuration with ducted assemblies. DASSH is intended to be used in the early stages of the reactor design process when assembly components can be undefined or are undergoing considerable design changes. DASSH provides a rapid assessment of the temperature and flow distribution to allow quick characterization of the system and identification of problem areas. This document is a guide for DASSH users. It summarizes the core capabilities of DASSH and highlights differences between DASSH and SE2-ANL. Instructions for obtaining and installing DASSH are provided along with some guidelines and recommendations for newer Python users. It covers the structure of the input file, provides directions for running DASSH, describes the various output files produced by the code, and provides instructions for visualizing data. Examples demonstrating various DASSH options are included. DASSH is under active development, so it is anticipated that this guide will grow and evolve as the code is updated.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2023

Automated Progress Monitoring in Modular Construction Factories Using Computer Vision and Building Information Modeling

Modular construction methods have recently gained interest due to the advantages offered in terms of safety, quality, and productivity for projects. In this method, a significant portion of the construction is performed off-site in factories where modular components are built in different workstations, assembled on the production line, and shipped to the site for installation. Due to the labor-intensive nature of tasks, cycle times in modular construction factories are highly variable, which commonly leads to major bottlenecks and delays in construction projects. To remedy this effect, recent methods rely on sensors such as RFID to monitor the production process, which is reportedly expensive, and intrusive to the work process. Recently, computer vision-based methods have been proposed to track the production process in modular construction factories. However, these methods overlook monitoring the assembly process on the production line. Therefore, this paper presents a method to monitor the assembly process by integrating computer vision-based methods with Building Information Modeling (BIM). The proposed method detects the modular units using object segmentation; superimposes the installation area with the corresponding 2D region using BIM, and identifies the installation of the components using image processing techniques. The proposed method has been validated using surveillance videos captured from a modular construction factory in the US. Successful implementation of the proposed method can lead to timely identification of delays during the assembly process and reduce delays in modular integrated construction projects.

building information modeling↗
DOE OSTI2024

Positioning Accuracy in a Concurrent Robot-CNC Hybrid Manufacturing System

Abstract Additive manufacturing (AM) has gained notoriety for offering advantages over traditional manufacturing methods, such as increased design complexity and flexibility. However, it has not found widespread use beyond rapid prototyping. One hindrance to the acceptance of AM processes in industry is the time and cost of fabrication per component. While metal AM by itself can be inexpensive, extra manufacturing steps in the form of subtractive manufacturing (SM) may need to be performed to reach final part tolerances, leading to hybrid additive-subtractive manufacturing (HASM) of a part, which increases time and cost. A potential area to reduce cost is through increasing the efficiency of the HASM process by conducting additive and subtractive manufacturing simultaneously. Usually, HASM is performed in a process where AM is completed in one machine or cell and transferred to another machine or cell for SM in a sequential assembly line process. This efficiency decreases part cost, but high aspect ratio parts or parts with internal geometry that require interleaved additive deposition and machining cannot be produced. One unexplored solution to simultaneous HASM that allows for interleaved operations is to operate the deposition head and machining spindle concurrently within the same machine envelope, known as concurrent HASM (CHASM). In this type of process, both AM and SM occur simultaneously on a batch of small parts or a single large part, maintaining a high efficiency without sacrificing the full range of complex geometries that AM allows for. A potential approach to the single-machine method could be to combine a robot and mill within the same envelope. A challenge to this approach, however, is control of both systems. Most machine controllers have limited external communication or, if a robot has been integrated, only offer movement of either the robot or mill at any given time. As a result, systems must pause either the AM or SM process to switch between them rather than working simultaneously. The present work investigates the positional accuracy of such a CHASM system comprised of a robotic arm and a 3-axis mill. Open-loop tests with limited communication between machines are performed on the system to verify positional error during concurrent robot-mill movements. Under certain conditions, it is demonstrated that position error can stay within 2 mm for the duration of a single layer; however, these tests show that, generally, the open-loop positioning performance of the system is inadequate for CHASM without part-specific hand-tuning of parameters. Based on these results, a set of requirements for successful robot-CNC CHASM is proposed for future integrations.

Goodwin, Jesse↗
DOE OSTI2022

Robotic four-dimensional pixel assembly of van der Waals solids

Van der Waals (vdW) solids can be engineered with atomically precise vertical composition through the assembly of layered two-dimensional materials. However, the artisanal assembly of structures from micromechanically exfoliated flakes is not compatible with scalable and rapid manufacturing. Further engineering of vdW solids requires precisely designed and controlled composition over all three spatial dimensions and interlayer rotation. Here, we report a robotic four-dimensional pixel assembly method for manufacturing vdW solids with unprecedented speed, deliberate design, large area and angle control. We used the robotic assembly of prepatterned 'pixels' made from atomically thin two-dimensional components. Wafer-scale two-dimensional material films were grown, patterned through a clean, contact-free process and assembled using engineered adhesive stamps actuated by a high-vacuum robot. We fabricated vdW solids with up to 80 individual layers, consisting of 100 x 100 μm 2 areas with predesigned patterned shapes, laterally/vertically programmed composition and controlled interlayer angle. This enabled efficient optical spectroscopic assays of the vdW solids, revealing new excitonic and absorbance layer dependencies in MoS 2 . Furthermore, we fabricated twisted $N$-layer assemblies, where we observed atomic reconstruction of twisted four-layer WS 2 at high interlayer twist angles of >= 4°. In conclusion, our method enables the rapid manufacturing of atomically resolved quantum materials, which could help realize the full potential of vdW heterostructures as a platform for novel physics and advanced electronic technologies.

42 ENGINEERING↗
DOE OSTI2021

DOE JGI Metagenome Workflow

The DOE Joint Genome Institute (JGI) Metagenome Workflow performs metagenome data processing, including assembly; structural, functional, and taxonomic annotation; and binning of metagenomic data sets that are subsequently included into the Integrated Microbial Genomes and Microbiomes (IMG/M) (I.-M. A. Chen, K. Chu, K. Palaniappan, A. Ratner, et al., Nucleic Acids Res, 49:D751–D763, 2021, https://doi.org/10.1093/nar/gkaa939) comparative analysis system and provided for download via the JGI data portal (https://genome.jgi.doe.gov/portal/). This workflow scales to run on thousands of metagenome samples per year, which can vary by the complexity of microbial communities and sequencing depth. Here, we describe the different tools, databases, and parameters used at different steps of the workflow to help with the interpretation of metagenome data available in IMG and to enable researchers to apply this workflow to their own data. We use 20 publicly available sediment metagenomes to illustrate the computing requirements for the different steps and highlight the typical results of data processing. The workflow modules for read filtering and metagenome assembly are available as a workflow description language (WDL) file (https://code.jgi.doe.gov/BFoster/jgi_meta_wdl). The workflow modules for annotation and binning are provided as a service to the user community at https://img.jgi.doe.gov/submit and require filling out the project and associated metadata descriptions in the Genomes OnLine Database (GOLD) (S. Mukherjee, D. Stamatis, J. Bertsch, G. Ovchinnikova, et al., Nucleic Acids Res, 49:D723–D733, 2021, https://doi.org/10.1093/nar/gkaa983).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Depth-dependent Metagenome-Assembled Genomes of Agricultural Soils under Managed Aquifer Recharge

Abstract Managed Aquifer Recharge (MAR) systems, which intentionally replenish groundwater aquifers with excess water, are critical for addressing water scarcity exacerbated by demographic shifts and climate variability. To date, little is known about the functional diversity of the soil microbiome at different soil depth inhabiting agricultural soils used for MAR. Knowing the functional diversity is pivotal in regulating nutrient cycling and maintaining soil health. Metagenomics, particularly Metagenome-Assembled Genomes (MAGs), provide a powerful tool to explore the diversity of uncultivated soil microbes, facilitating in-depth investigations into microbial functions. In a field experiment conducted in a California vineyard, we sequenced soil DNA before and after water application of MAR. Through this process, we assembled 146 medium and 14 high-quality MAGs, uncovering a wide array of archaeal and bacterial taxa across different soil depths. These findings advance our understanding of the microbial ecology and functional diversity of soils used for MAR, contributing to the development of more informed and sustainable land management strategies.

Science & Technology - Other Topics↗
DOE OSTI2021

Differential structure and functional gene response to geochemistry associated with the suspended and attached shallow aquifer microbiomes from the Illinois Basin, IL

Despite the clear ecological significance of the microbiomes inhabiting groundwater and connected ecosystems, our current understanding of their habitats, functionality, and the ecological processes controlling their assembly have been limited. In this study, an efficient pipeline combining geochemistry, high-throughput Fluidigm TM functional gene amplification and sequencing was developed to analyze the suspended and attached microbial communities inhabiting five groundwater monitoring wells in the Illinois Basin, USA. The dominant taxa in the suspended and the attached microbial communities exhibited significantly different spatial and temporal changes in both alpha- and beta-diversity. Further analyses of representative functional genes affiliated with N 2 fixation (nifH), methane oxidation (pmoA), and sulfate reduction (dsrB, and aprA), suggested functional redundancy within the shallow aquifer microbiomes. While more diversified functional gene taxa were observed for the suspended microbial communities than the attached ones except for pmoA, different levels of changes over time and space were observed between these functional genes. Notably, deterministic and stochastic ecological processes shaped the assembly of microbial communities and functional gene reservoirs differently. While homogenous selection was the prevailing process controlling assembly of microbial communities, the neutral processes (e.g., dispersal limitation, drift and others) were more important for the functional genes. The results suggest complex and changing shallow aquifer microbiomes, whose functionality and assembly vary even between the spatially proximate habitats and fractions. As a result, this research underscored the importance to include all the interface components for a more holistic understanding of the biogeochemical processes in aquifer ecosystems, which is also instructive for practical applications.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Self-assembly for electronics

Self-assembly, a process in which molecules, polymers, and particles are driven by local interactions to organize into patterns and functional structures, is being exploited in advancing silicon electronics and in emerging, unconventional electronics. Additionally, silicon electronics has relied on lithographic patterning of polymer resists at progressively smaller lengths to scale down device dimensions. Yet, this has become increasingly difficult and costly. Assembly of block copolymers and colloidal nanoparticles allows resolution enhancement and the definition of essential shapes to pattern circuits and memory devices. As we look to a future in which electronics are integrated at large numbers and in new forms for the Internet of Things and wearable and implantable technologies, we also explore a broader material set. Semiconductor nanoparticles and biomolecules are prized for their size-, shape-, and composition-dependent properties and for their solution-based assembly and integration into devices that are enabling unconventional manufacturing and new device functions.

36 MATERIALS SCIENCE↗
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

DIVA/DeviceEditor (DIVA) v5.1

The DIVA software interfaces a process in which researchers design their DNA with a web-based graphical user interface (DeviceEditor), submit their designs to a central queue, and a few weeks later receive their sequence-verified clonal constructs. Each researcher independently designs the DNA to be constructed with a web-based BioCAD tool, and presses a button to submit their designs to a central queue. Researchers have web-based access to their DNA design queues, and can track the progress of their submitted designs as they progress from "evaluation", to "waiting for reagents", to "in progress", to "complete". Researchers access their completed constructs through the central DNA repository. Along the way, all DNA construction success/failure rates are captured in a central database. his success/failure rate data can be leveraged to refine the DNA assembly design process.

Lane, Stephen↗
DOE OSTI2025

AlloSHP: deconvoluting single homeologous polymorphism for phylogenetic analysis of allopolyploids

Background The genomic and evolutionary study of allopolyploid organisms involves multiple copies of homeologous chromosomes, making their assembly, annotation, and phylogenetic analysis challenging. Bioinformatics tools and protocols have been developed to study polyploid genomes, but sometimes require the assembly of their genomes, or at least the genes, limiting their use. Results We have developed AlloSHP, a command-line tool for detecting and extracting single homeologous polymorphisms (SHPs) from the subgenomes of allopolyploid species. This tool integrates three main algorithms, WGA, VCF2ALIGNMENT and VCF2SYNTENY, and allows the detection of SHPs for the study of diploid-polyploid complexes with available diploid progenitor genomes, without assembling and annotating the genomes of the allopolyploids under study. AlloSHP has been validated on three diploid-polyploid plant complexes, Brachypodium, Brassica, and Triticum-Aegilops, and a set of synthetic hybrid yeasts and their progenitors of the genus Saccharomyces. The results and congruent phylogenies obtained from the four datasets demonstrate the potential of AlloSHP for the evolutionary analysis of allopolyploids with a wide range of ploidy and genome sizes. Conclusions AlloSHP combines the strategies of simultaneous mapping against multiple reference genomes and syntenic alignment of these genomes to call SHPs, using as input data a single VCF file and the reference genomes of the known or closest extant diploid progenitor species. This novel approach provides a valuable tool for the evolutionary study of allopolyploid species, both at the interspecific and intraspecific levels, allowing the simultaneous analysis of a large number of accessions and avoiding the complex process of assembling polyploid genomes.

Allopolyploids↗