Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “directed assembly”

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 361 records · Page 20
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Hydrodynamics of thermally driven chiral suspensions

Considerable effort has been directed towards the characterization of chiral mesoscale structures, as shown in chiral protein assemblies and carbon nanotubes. Here, we establish a thermally driven hydrodynamic description for the actuation and separation of mesoscale chiral structures in a fluid medium. Cross-flow of a Newtonian liquid with a thermal gradient gives rise to an effective torque that propels each particle of a chiral suspension according to its handedness. In turn, the chiral suspension alters the liquid flow, which thus acquires a transverse (chiral) velocity component. Since observation of the predicted effects requires a low degree of sophistication, our work provides an efficient and inexpensive approach to test and calibrate chiral particle propulsion and separation strategies.

Mechanics↗
DOE OSTI2021

Gradient-Informed Design Optimization of Select Nuclear Systems

In this work, we present a gradient-informed design optimization of nuclear reactor core components based on neutronics objectives with both continuous and discrete materials. The main argument in favor of using gradient-informed design optimization is that it scales well with increasing dimensionality of the design space. First, a challenge problem with 121 free parameters is solved with a gradient-informed method and then with a genetic algorithm. Then, a challenge problem to optimize the flux profile of a simplified assembly with eight axial zones is solved. Both challenge problems are solved using directly calculated derivatives from Tools for Sensitivity and Uncertainty Analysis Methodology Implementation (TSUNAMI) in the SCALE package. Furthermore, we demonstrate how a discrete optimization problem—selection of materials for 121 voxels—can be lifted into a continuous problem with mixed materials. In the continuous space, adjoint-based gradients are well-defined, and gradient descent is applicable. Then, a forcing function is introduced that with the selection of an appropriately sized hyperparameter can be used to guide the optimized continuous solution back into a discrete solution. This paper presents an account of the challenges that were faced when applying a gradient-informed optimization algorithm using a Monte Carlo calculation to estimate the gradient information and compares a gradient descent optimization method to a genetic algorithm optimization of the same geometry. Overall, this work demonstrates the potential use of adjoint-based gradient calculations in design optimization of nuclear systems.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2020

Mathematical modeling of hepatitis C RNA replication, exosome secretion and virus release

Hepatitis C virus (HCV) causes acute hepatitis C and can lead to life-threatening complications if it becomes chronic. The HCV genome is a single plus strand of RNA. Its intracellular replication is a spatiotemporally coordinated process of RNA translation upon cell infection, RNA synthesis within a replication compartment, and virus particle production. While HCV is mainly transmitted via mature infectious virus particles, it has also been suggested that HCV-infected cells can secrete HCV RNA carrying exosomes that can infect cells in a receptor independent manner. In order to gain insight into these two routes of transmission, we developed a series of intracellular HCV replication models that include HCV RNA secretion and/or virus assembly and release. Fitting our models to in vitro data, in which cells were infected with HCV, suggests that initially most secreted HCV RNA derives from intracellular cytosolic plus-strand RNA, but subsequently secreted HCV RNA derives equally from the cytoplasm and the replication compartments. Furthermore, our model fits to the data suggest that the rate of virus assembly and release is limited by host cell resources. Including the effects of direct acting antivirals in our models, we found that in spite of decreasing intracellular HCV RNA and extracellular virus concentration, low level HCV RNA secretion may continue as long as intracellular RNA is available. This may possibly explain the presence of detectable levels of plasma HCV RNA at the end of treatment even in patients that ultimately attain a sustained virologic response.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Diagnostic and predictive capabilities of the TCR digital platform

The Transformational Challenge Reactor program is leveraging additive manufacturing technologies to fabricate the nuclear components required to assemble a microreactor core. Compared with traditional manufacturing processes, additive manufacturing allows for direct observation of the interior of the component during manufacturing. This unique capability promises significant possibilities for creating a new paradigm for nuclear component qualification by leveraging in-situ process data. This report describes FY21 efforts to predict material tensile properties based on data collected during the laser powder bed fusion printing process. The primary focus of this report is the test campaign designed to generate the large quantities of training data required to implement artificial intelligence algorithms that can predict these material properties. Preliminary prediction results and a demonstration of the overall data collection, analysis, and visualization pipeline are also provided.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2024

Electron Density Measurements Using USPR (Final Scientific/Technical Report)

UC Davis has fabricated an ultrashort pulse reflectometer (USPR) diagnostic instrument for electron density profile measurements on compact, short duration, magnetically-confined fusion-energy concept devices such as spheromaks and FRCs. The USPR system transmits extremely short duration (~few nsec) chirped waveforms that together span 29 to 75 GHz. These chirped waveforms illuminate and reflect from the target plasma, with each frequency component reflecting from a different density layer (higher frequencies probe deeper into the plasma before reflecting). The reflected waveforms are split into roughly 42 different frequencies; time-of-flight (TOF) measurements made at each frequency with high resolution (~25 psec measurement resolution which corresponds to ~5 mm). These TOF data may then be inverted via software to generate electron density profiles with high time resolution (~10 μsec). At the heart of the system is a field programmable gate array (FPGA) based controller which collects and processes all of the USPR data in addition to generating all of the control signals required for maximum flexibility. The FPGA controller has the software flexibility to be easily reconfigured for different plasma devices, and the entire system sufficiently compact to be easily and quickly transported between devices. A high speed impulse generator was transformed into a set of three ultrashort pulse transmitter chirps using a combination of dispersive waveguide, frequency doublers and high-pass filters. A mm-wave controller was fabricated to sequentially switch between the three chirps, directing the chirps one-by-one to three different mm-wave assemblies spanning 29-75 GHz. Each mm-wave assembly consists of a high power active multiplier chain which converts the transmitter chirp to higher frequencies, and a broadband mixer which downconverts the reflected waveform to the 2-18 GHz range of the UPSR receiver. The 16-channel receiver (shared by all 3 mm-wave assemblies) was fabricated employing custom TOF modules capable of operating at a high 1 MHz sampling rate. Laboratory testing of the full system revealed the presence of unwanted harmonics from the multiplication process, with interference observed in the downconverted reflections at selected frequency channels that could not be completely filtered out. Additional interference effects arising from internal reflections within the mm-wave assemblies were minimized using a high-speed switch which served to “gate out” much of these reflections. The USPR diagnostic was transported and installed onto the HIT-SIU plasma device, becoming operational on 11/08/2022. Although designed to span 3 distinct mm-wave bands, the HIT-SIU plasmas at this time were sufficiently low density such that only the lowest of the three bands was likely to have strong plasma reflections. The system was then set to operate on only the lowest band (assembly #1), with data collected every 1 μsec rather than 3 μsec which would have been the case when cycling through all three bands. Connected to HIT-SIU, time-varying plasma reflections were observed on 9 of 16 possible frequency channels. Close examination of the data collected revealed issues previously unobserved in laboratory testing, associated with (a) reflections from the small aperture horns required for operation within the HIT-SIU device, and (b) a dependence of the recorded TOF with the threshold voltage of a given channel. Plans were made to address each of these issues before undertaking any future campaigns.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Degradation Effects at the Porous Transport Layer/Catalyst Layer Interface in Polymer Electrolyte Membrane Water Electrolyzer

The porous transport layer (PTL)/catalyst layer (CL) interface plays a crucial role in the achievement of high performance and efficiency in polymer electrolyte membrane water electrolyzers (PEMWEs). This study investigated the effects of the PTL/CL interface on the degradation of membrane electrode assemblies (MEAs) during a 4000 h test, comparing the MEAs assembled with uncoated and Ir-coated Ti PTLs. Our results show that compared to an uncoated PTL/CL interface, an optimized interface formed when using a platinum group metal (PGM) coating, i.e., an iridium layer at the PTL/CL interface, and reduced the degradation of the MEA. The agglomeration and formation of voids and cracks could be found for both MEAs after the long-term test, but the incorporation of an Ir coating on the PTL did not affect the morphology change or oxidation of IrO x in the catalyst layer. In addition, our studies suggest that the ionomer loss and restructuring of the anodic MEA can also be reduced by Ir coating of the PTL/CL interface. Optimization of the PTL/CL interface improves the performance and durability of a PEMWE.

30 DIRECT ENERGY CONVERSION↗
DOE OSTI2022

helixCAM: A platform for programmable cellular assembly in bacteria and human cells

Interactions between cells are indispensable for signaling and creating structure. The ability to direct precise cell-cell interactions would be powerful for engineering tissues, understanding signaling pathways, and directing immune cell targeting. In humans, intercellular interactions are mediated by cell adhesion molecules (CAMs). However, endogenous CAMs are natively expressed by many cells and tend to have cross-reactivity, making them unsuitable for programming specific interactions. Here, we showcase “helixCAM,” a platform for engineering synthetic CAMs by presenting coiled-coil peptides on the cell surface. helixCAMs were able to create specific cell-cell interactions and direct patterned aggregate formation in bacteria and human cells. Based on coiled-coil interaction principles, we built a set of rationally designed helixCAM libraries, which led to the discovery of additional high-performance helixCAM pairs. Finally, we applied this helixCAM toolkit for various multicellular engineering applications, such as spherical layering, adherent cell targeting, and surface patterning.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Folding at the Microscale: Enabling Multifunctional 3D Origami‐Architected Metamaterials

Abstract Mechanical metamaterials inspired by the Japanese art of paper folding have gained considerable attention because of their potential to yield deployable and highly tunable assemblies. The inherent foldability of origami structures enlarges the material design space with remarkable properties such as auxeticity and high deformation recoverability and deployability, the latter being key in applications where spatial constraints are pivotal. This work integrates the results of the design, 3D direct laser writing fabrication, and in situ scanning electron microscopic mechanical characterization of microscale origami metamaterials, based on the multimodal assembly of Miura‐Ori tubes. The origami‐architected metamaterials, achieved by means of microfabrication, display remarkable mechanical properties: stiffness and Poisson’s ratio tunable anisotropy, large degree of shape recoverability, multistability, and even reversible auxeticity whereby the metamaterial switches Poisson’s ratio sign during deformation. The findings here reported underscore the scalable and multifunctional nature of origami designs, and pave the way toward harnessing the power of origami engineering at small scales.

Lin, Zhaowen↗
DOE OSTI2025

Current-Activated Reactive Ultrafast Joining (CARUJ)

We have demonstrated Current Activated Reactive Ultrafast Joining (CARUJ) as a novel approach for rapid fabrication of similar and dissimilar materials, such as ceramic-ceramic and ceramic-metal joint assemblies. The CARUJ technology utilizes resistive heating of carbon-based materials to apply localized heat at, (through or around) joint zones at rates of 10 1 -10 2 ˚C/min, enabling joining at time scales considerably shorter (several minutes as opposed to hours) than conventional approaches for similar systems. Herein, we present our findings while evaluating the CARUJ concept. Three methods of heat application were evaluated: (i) using carbon joule heating elements to apply heat directly through the joint interface; (ii) using flexible joule heating elements to locally apply heat around the assembly interface; and (iii) non-contact heating of the joint assembly using inductive power. Schemes (ii) and (iii) proved to be the most effective in producing mechanically sound reliable joints. We demonstrated single-step fabrication of dense SiC-SiC joints with a Si- SiC interface using minimal pressure (1–2 MPa) in under 30 minutes. Measured average joint strengths of about 15 MPa are initially achieved for joined bodies when tested in single lap offset (SLO) compressive shear, while tuning of the interfacial composition along with a reduction in interlayer thickness, results in improved joint strengths of approximately 43 MPa. We further demonstrated SiC-SiC joining using Active Brazing Alloys (ABAs) proof of concept joining of tubular geometries. The versatility of CARUJ is demonstrated by utilizing non-contact heating via induction, to join dissimilar materials systems of SiC, SS316 and MAX phase ceramics with ABA interlayers. The localized and rapid heat application realizes a versatile material joining technique that can be extended for joining components at the plant site.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Shape-Shifting Peptide Nanomaterials: Surface Asymmetry Enables pH-Dependent Formation and Interconversion of Collagen Tubes and Sheets

The fabrication of dynamic, transformable biomaterials that respond to environmental cues represents a significant step forward in the development of synthetic materials that rival their highly functional, natural counterparts. In this work, we describe the design and synthesis of crystalline supramolecular architectures from charge-complementary heteromeric pairs of collagen-mimetic peptides (CMPs). Under appropriate conditions, CMP pairs spontaneously assemble into either 1D ultraporous (pore diameter >100 nm) tubes or 2D bilayer nanosheets due to the structural asymmetry that arises from heteromeric self-association. Crystalline collagen tubes represent a heretofore unobserved morphology of this common biomaterial. In-depth structural characterization from a suite of biophysical methods, including TEM, AFM, high-resolution cryo-EM, and SAXS/WAXS measurements, reveals that the sheet and tube assemblies possess a similar underlying lattice structure. The experimental evidence suggests that the tubular structures are a consequence of the self-scrolling of incipient 2D layers of collagen triple helices and that the scrolling direction determines the formation of two distinct structural isoforms. Furthermore, we show that nanosheets and tubes can spontaneously interconvert through manipulation of the assembly pH and systematic adjustment of the CMP sequence. Altogether, we establish initial guidelines for the construction of dynamically responsive 1D and 2D assemblies that undergo a structurally programmed morphological transition.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Non-equilibrium molecular dynamics studies of thermal diffusion of hydrogen isotopes in low concentration zirconium hydrides

Tritium permeability in zirconium-based tritium getter critically impacts tritium storage and environmental safety during operation of tritium-producing burnable absorber rods (TPBARs). Previous experiments indicated that during irradiation operation, the hydrogen equilibrium pressured is increased. Further experimental and modeling studies suggested that the enhanced tritium release observed for reactor scale assemblies might be related to a thermal diffusion known as the Soret effect. A direct measurement of the Soret factor, however, has not been performed. To improve TPBAR and other nuclear applications, here we have applied two non-equilibrium molecular dynamics methods to study thermal diffusion of hydrogen isotopes in low-concentration zirconium hydrides. One of the methods produces sufficiently converged results to distinguish crystal orientation, isotope type, and concentration effects. In conclusion, with this method, crystal orientation, isotope type, and concentration effects are discussed.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Mechanistic Insights into Dinitrogen Reduction to Ammonia in Light-Controlled Nanocrystal:Nitrogenase Complexes

Developing systems that can efficiently capture photon energy and convert this energy into fuels and chemicals requires understanding how to assemble molecular components with diverse functions into complete systems possessing selectivity and efficiency in directing charge carriers to catalytic reactions. There are many challenges to achieving this goal. One promising approach is the development of hybrid systems that combine semiconductor nanocrystals (NCs) for light capture and enzymes as efficient catalysts. Such biohybrid systems capitalize on the tunable electronic and optical properties of NCs while leveraging the unmatched specificity and efficiency of enzymes in catalyzing chemical reactions, thereby offering opportunities to surpass the limitations of each component alone. Here, we focus on recent progress in developing a biohybrid system that combines CdS NCs for photon capture with the enzyme nitrogenase to accomplish light-driven dinitrogen (N 2 ) reduction to ammonia (NH 3 ). Integrating light-harvesting materials with biological catalysts requires a deep understanding of NC properties, protein stability, and electron transfer (ET), making it an inherently multidisciplinary problem. The reduction of N 2 to NH 3 is a challenging reaction, with a high demand in both agriculture and industrial chemical production. This reaction is intrinsically energy intensive, due to the need to activate the N≡N triple bond. The current standard industrial approach to N 2 reduction, the Haber−Bosch reaction, obtains the necessary energy input from fossil fuels, whereas biological systems capable of N 2 reduction utilize the hydrolysis of ATP as their energy source. Replacing these costly, energy-intensive inputs with renewable light energy represents a critical step toward sustainable NH 3 production. Recent progress has demonstrated that semiconductor CdS NCs can be coupled to the catalytic component of nitrogenase, the MoFe protein, to form a biohybrid CdS NC:MoFe protein complex, enabling light-driven N 2 reduction rather than energy input from fossil fuels or ATP. This illustrates how inorganic NCs can functionally replace the natural Fe protein partner, yielding a biohybrid catalyst that enables controlled electron delivery and provides not only light-driven NH 3 production but also new approaches for probing enzyme catalytic function. The CdS NC:MoFe protein biohybrid system enables light-initiated electron delivery at ambient temperature, as well as temperatures below freezing, allowing for stabilization and spectroscopic characterization of key reaction intermediates. These findings highlight how photochemical biohybrids can serve as both functional catalysts and mechanistic probes. Beyond studies of the nitrogenase mechanism, studies of the CdS NC:MoFe system reveal how variables such as NC size, electrostatic binding interactions, and sacrificial electron donors (SEDs) govern complex stability, charge transfer efficiency, and catalytic performance. In addition, studies of nitrogenase and the high activation barrier for N 2 reduction are enabling investigations of new and interesting questions regarding the properties and limitations of NC biocatalysis. In this Account, we describe the key features of CdS NC:MoFe protein biohybrids and the parameters for optimal light-driven N 2 reduction, and how controlling ET with light illuminates the path to new insights into the nitrogenase mechanism.

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

Bounds on galaxy stochasticity from halo occupation distribution modeling

The joint probability distribution of matter overdensity and galaxy counts in cells is a powerful probe of cosmology, and the extent to which variance in galaxy counts at fixed matter density deviates from Poisson shot noise is not fully understood. The lack of informed bounds on this stochasticity is currently the limiting factor in constraining cosmology with the galaxy–matter probability distribution function (PDF). We investigate stochasticity in the conditional distribution of galaxy counts along lines of sight with fixed matter density, and we present a halo occupation distribution (HOD)-based approach for obtaining plausible ranges for stochasticity parameters. To probe the high-dimensional space of possible galaxy–matter connections, we derive a set of HODs that conserve the galaxies’ linear bias and number density to produce RED M A G I C-like galaxy catalogs within the A BACUS S UMMIT suite of N -body simulations. We study the impact of individual HOD parameters and cosmology on stochasticity and perform a Monte Carlo search in HOD parameter space subject to the constraints on bias and density. In mock catalogs generated by the selected HODs, shot noise in galaxy counts spans both sub-Poisson and super-Poisson values, ranging from 80% to 133% of Poisson variance for cells with mean matter density. Nearly all of the derived HODs show a positive relationship between local matter density and stochasticity. For galaxy catalogs with higher stochasticity, modeling galaxy bias to second order is required for an accurate description of the conditional PDF of galaxy counts at fixed matter density. The presence of galaxy assembly bias also substantially extends the range of stochasticity in the super-Poisson direction. This HOD-based approach leverages degrees of freedom in the galaxy–halo connection to obtain informed bounds on nuisance model parameters and can be adapted to study other parametrizations of shot noise in galaxy counts, in particular to motivate prior ranges on stochasticity for cosmological analyses.

Britt, Dylan (ORCID:000000019905601X)↗
DOE OSTI2022

Measurement of laser absorption in underdense plasmas using near-field imaging of the incident and transmitted beams

Measurements of laser absorption in high-temperature, underdense plasmas produced at the Omega Laser Facility are made using two near-field imaging detectors that diagnose the spatial profile and energy of the port P9 beam before and after it transmits through the plasma. The incident beam is sampled using a partial reflection from a full-aperture, (30 cm-diam) uncoated wedge pickoff located before the target chamber vacuum window and final focus lens assembly. A concave mirror reduces the reflected beam size, allowing it to be recorded directly using a charged-coupled device (CCD) camera. The P9 transmitted beam diagnostic (P9TBD) characterizes the transmitted light by terminating the expanded beam on a semi-transparent diffuser and imaging the illuminated surface using a lens and CCD camera. The P9TBD samples a numerical aperture twice as large as the input beam, allowing the energy of transmitted beams with moderate levels of beam spray to be measured accurately. Calibration shots with no plasma provide a path to infer absorption without absolute photometric calibration of either detector. Lastly, the cross-calibration between the two detectors was measured to remain stable at ±200 ppm, enabling measurements of total beam absorption below 1% with ±0.07% error.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

High spatial resolution direct conversion amorphous selenium X-ray detectors with monolithically integrated CMOS readout

Recent progress in the field of micron-scale spatial resolution direct conversion X-ray detectors for high-energy synchrotron light sources serve applications ranging from nondestructive and noninvasive microscopy techniques which provide insight into the structure and morphology of crystals, to medical diagnostic measurement devices. Amorphous selenium ( a -Se) as a wide-bandgap thermally evaporated photoconductor exhibits ultra-low thermal generation rates for dark carriers and has been extensively used in X-ray medical imaging. Being an amorphous material, it can further be deposited over large areas at room temperatures and at substantially lower costs as compared to crystalline semiconductors. Here, to address the demands for a high-energy and high spatial resolution X-ray detector for synchrotron light source applications, we have thermally evaporated a -Se on a Mixed-Mode Pixel Array Detector (MM-PAD) Application Specific Integrated Circuit (ASIC). The ASIC format consists of 128 × 128 square pixels each 150 μm on a side. A 200 μm a -Se layer was directly deposited on the ASIC followed by a metal top electrode. The completed detector assembly was tested with 45 kV Ag and 23 kV Cu X-ray tube sources. The detector fabrication, performances, Modulation Transfer Function (MTF) measurements, and simulations are reported.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Mesocrystal growth through oriented sliding and attachment of nanoplates

Oriented attachment is a critical, yet poorly understood, crystal growth pathway based on the self-assembly of nanocrystals. During oriented attachment, solvent-separated particles align and coalesce through forces that enable precise rotation and translation. While prior studies emphasized intragap forces driving crystallographic alignment, the forces enabling uniform stacking and superlattice formation remain unclear. Here, we demonstrate how macroscopic gibbsite mesocrystals emerge from nanoplates guided into staggered positions by directional sliding. Electron microscopy and X-ray scattering reveal the monoclinic superlattice structure, based on nanoplate stacking with a uniform ≈50° stagger along the gibbsite [010] direction. In situ liquid-cell TEM captures preferential sliding along the gibbsite [010] direction, decelerating with increasing particle overlap. Molecular dynamics simulations reveal that this staggered arrangement corresponds to a global free-energy minimum, rather than full alignment. The simulations also confirm that sliding along the [010] direction is energetically favored and provide insight into the role of interfacial water in achieving long-range ordered assemblies. These insights highlight the energy landscape’s role in oriented attachment, with implications for material synthesis and hierarchical structures in nature.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Visualizing Assembly Dynamics of All‐Liquid 3D Architectures

Abstract To better exploit all‐liquid 3D architectures, it is essential to understand dynamic processes that occur during printing one liquid in a second immiscible liquid. Here, the interfacial assembly and transition of 5,10,15,20‐tetrakis(4‐sulfonatophenyl) porphyrin (H 6 TPPS) over time provides an opportunity to monitor the interfacial behavior of nanoparticle surfactants (NPSs) during all‐liquid printing. The formation of J‐aggregates of H 4 TPPS 2− at the interface and the interfacial conversion of the J‐aggregates of H 4 TPPS 2− to H‐aggregates of H 2 TPPS 4− is demonstrated by interfacial rheology and in situ atomic force microscopy. Equally important are the chromogenic changes that are characteristic of the state of aggregation, where J‐aggregates are green in color and H‐aggregates are red in color. In all‐liquid 3D printed structures, the conversion in the aggregate state with time is reflected in a spatially varying change in the color, providing a simple, direct means of assessing the aggregation state of the molecules and the mechanical properties of the assemblies, linking a macroscopic observable (color) to mechanical properties.

Gu, Pei‐Yang↗
DOE OSTI2022

Metagenome-assembled genome extraction and analysis from microbiomes using KBase

Uncultivated Bacteria and Archaea account for the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only become possible recently. In order to realize the hope of capturing Earth’s microbial genetic complement and to facilitate the investigation of the functional roles of specific lineages in a given ecosystem, technologies that accelerate the recovery of high-quality genomes are necessary. We present a series of analysis steps and data products for the extraction of high-quality metagenome-assembled genomes (MAGs) from microbiomes using the U.S. Department of Energy Systems Biology Knowledgebase (KBase) platform (http://www.kbase.us/). Overall, these steps take about a day to obtain extracted genomes when starting from smaller environmental shotgun read libraries, or up to about a week from larger libraries. In KBase, the process is end-to-end, allowing a user to go from the initial sequencing reads all the way through to MAGs, which can then be analyzed with other KBase capabilities such as phylogenetic placement, functional assignment, metabolic modeling, pangenome functional profiling, RNA-Seq and others. While portions of such capabilities are available individually from other resources, the combination of the intuitive usability, data interoperability and integration of tools in a freely available computational resource makes KBase a powerful platform for obtaining MAGs from microbiomes. While this workflow offers tools for each of the key steps in the genome extraction process, it also provides a scaffold that can be easily extended with additional MAG recovery and analysis tools, via the KBase software development kit (SDK).

59 BASIC BIOLOGICAL SCIENCES↗