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At least 757 records · Page 42

All sources NASA NTRS DOE OSTI

DOE OSTI2021

Modular polyketide synthase contains two reaction chambers that operate asynchronously

Type I modular polyketide synthases are homodimeric multidomain assembly line enzymes that synthesize a variety of polyketide natural products by performing polyketide chain extension and β-keto group modification reactions. We determined the 2.4-angstrom-resolution x-ray crystal structure and the 3.1-angstrom-resolution cryo–electron microscopy structure of the Lsd14 polyketide synthase, stalled at the transacylation and condensation steps, respectively. These structures revealed how the constituent domains are positioned relative to each other, how they rearrange depending on the step in the reaction cycle, and the specific interactions formed between the domains. Like the evolutionarily related mammalian fatty acid synthase, Lsd14 contains two reaction chambers, but only one chamber in Lsd14 has the full complement of catalytic domains, indicating that only one chamber produces the polyketide product at any given time.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes

While numerous computational frameworks and workflows are available for recovering prokaryote and eukaryote genomes from metagenome data, only a limited number of pipelines are designed specifically for viromics analysis. With many viromics tools developed in the last few years alone, it can be challenging for scientists with limited bioinformatics experience to easily recover, evaluate quality, annotate genes, dereplicate, assign taxonomy, and calculate relative abundance and coverage of viral genomes using state-of-the-art methods and standards. Here, we describe Modular Viromics Pipeline (MVP) v.1.0, a user-friendly pipeline written in Python and providing a simple framework to perform standard viromics analyses. MVP combines multiple tools to enable viral genome identification, characterization of genome quality, filtering, clustering, taxonomic and functional annotation, genome binning, and comprehensive summaries of results that can be used for downstream ecological analyses. Overall, MVP provides a standardized and reproducible pipeline for both extensive and robust characterization of viruses from large-scale sequencing data including metagenomes, metatranscriptomes, viromes, and isolate genomes. As a typical use case, we show how the entire MVP pipeline can be applied to a set of 20 metagenomes from wetland sediments using only 10 modules executed via command lines, leading to the identification of 11,656 viral contigs and 8,145 viral operational taxonomic units (vOTUs) displaying a clear beta-diversity pattern. Further, acting as a dynamic wrapper, MVP is designed to continuously incorporate updates and integrate new tools, ensuring its ongoing relevance in the rapidly evolving field of viromics. MVP is available at https://gitlab.com/ccoclet/mvp and as versioned packages in PyPi and Conda.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2014

Modular approach for modeling cell motility

Modeling cell movement is a challenging task since the motility machinery is highly complex. Moreover, there is a rather broad diversity of different cell types. In order to obtain insights into generic features of the motility mechanisms of several distinct cell types, we propose a modular approach that starts with a minimal model, consisting of a phase field description of the moving cell boundary and a simplified internal dynamics. We discuss how this starting point can be extended to increase the level of detail, and how the internal dynamics "module" can be changed/adjusted to properly model various cell types. The former route allows studying specific processes involved in cell motility in the framework of a self-organized moving domain, and the latter might permit to put different cellular motility mechanisms into a unified framework.

Ziebert, F.↗

DOE OSTI2022

SODA Synthesizer: an Open-source, Multi-level, Modular, Extensible Compiler from High-level Frameworks to Silicon

The SODA Synthesizer is an open-source modular, end-to-end hardware compiler framework. The SODA frontend, developed in MLIR, performs system-level design, code partitioning, and high-level optimizations to prepare the specifications for the hardware synthesis. The backend is based on a state-of-the-art high-level synthesis tool, and generates the final hardware design. The backend can interface with logic synthesis tools for field programmable gate arrays or with commercial and open-source logic synthesis tools for application-specific integrated circuits. We discuss the opportunities and challenges in integrating with commercial and open-source tools both at the frontend and backend, and the unique opportunities that an open-source hardware design ecosystem provides.

Bohm Agostini, Nicolas↗

DOE OSTI2025

OmniFed: A Modular Framework for Configurable Federated Learning from Edge to HPC

Federated Learning (FL) is critical for edge and High Performance Computing (HPC) where data is not centralized and privacy is crucial. We present OmniFed, a modular framework designed around decoupling and clear separation of concerns for configuration, orchestration, communication, and training logic. Its architecture supports configuration-driven prototyping and code-level override-what-you-need customization. We also support different topologies, mixed communication protocols within a single deployment, and popular training algorithms. It also offers optional privacy mechanisms including Differential Privacy (DP), Homomorphic Encryption (HE), and Secure Aggregation (SA), as well as compression strategies. These capabilities are exposed through well-defined extension points, allowing users to customize topology and orchestration, learning logic, and privacy/compression plugins, all while preserving the integrity of the core system. We evaluate multiple models and algorithms to measure various performance metrics. By unifying topology configuration, mixed-protocol communication, and pluggable modules in one stack, OmniFed streamlines FL deployment across heterogeneous environments. Github repository is available at https://github.com/at-aaims/OmniFed.

Tyagi, Sahil [ORNL] (ORCID:0009000783144745)↗

DOE OSTI2017

Efficient and Extensible Quasi-Explicit Modular Nonlinear Multiscale Battery Model: GH-MSMD

Complex physics and long computation time hinder the adoption of computer aided engineering models in the design of large-format battery cells and systems. A modular, efficient battery simulation model -- the multiscale multidomain (MSMD) model -- was previously introduced to aid the scale-up of Li-ion material and electrode designs to complete cell and pack designs, capturing electrochemical interplay with 3-D electronic current pathways and thermal response. Here, this paper enhances the computational efficiency of the MSMD model using a separation of time-scales principle to decompose model field variables. The decomposition provides a quasi-explicit linkage between the multiple length-scale domains and thus reduces time-consuming nested iteration when solving model equations across multiple domains. In addition to particle-, electrode- and cell-length scales treated in the previous work, the present formulation extends to bus bar- and multi-cell module-length scales. We provide example simulations for several variants of GH electrode-domain models.

30 DIRECT ENERGY CONVERSION↗

DOE OSTI2024

MODAQ (Modular Offshore Data Acquisition System) [SWR-24-58]

The National Renewable Energy Laboratory (NREL) has developed a data acquisition system to support laboratory (component) and in-water validation and testing of Marine Renewable Energy (MRE) technologies. The Modular Ocean Data AcQuisition System (MODAQ) is a robust system built on industrial grade hardware that can acquire high-quality and summary data from many sensor and instrument types. MODAQ includes modules to perform real-time QC screening, system health monitoring, and send alerts. MODAQ is also part of a larger data management, processing, visualization, and archiving system.

Raye, Robert↗

DOE OSTI2024

MODAQ 2.0 (Modular Ocean Data AcQuisition System v2.0) [SWR-24-138]

MODAQ 2.0 is the continuation of the Modular Ocean/Offshore Data AcQuisition system which offers new benefits of being based on generally available hardware and open-source development tools. The MODAQ 2.0 project is the amalgamation of ROS packages, tools, and guidance for developing data acquisition and control applications for marine energy devices using a ROS2 based architecture. The MODAQ 2.0 Reference Design includes several packages that are targeted for the marine energy sector and allow most developers with a basic background in programming to spin up a high-quality DAQ and control system. It is comprised of multiple software repositories which can be found at the MODAQ2 GitHub Organization: https://github.com/NREL-MODAQ2

Nichols, Casey↗

DOE OSTI2024

Control And Optimization Modular Modeling Application For Nuclear Deployment

The purpose of the COMMAND code is to provide a flexible, scalable tool for use in developing, integrating, and testing the technologies necessary for achieving autonomous operations of advanced nuclear reactors. The code enables users to efficiently implement custom simulations and experiments by combining key methods from different software modules. These modules are focused on: modeling and simulation tools, such as nuclear simulation tools used for high-fidelity modeling (e.g., Reactor Excursion and Leak Analysis Program [RELAP5-3D] and Monte Carlo N-Particle [MCNP]); machine learning and optimization tools (e.g., anomaly detection and data-driven modeling techniques); advanced control in its digital, high-performance, and supervisory control forms (e.g., proportional integral derivative (PID) control and model predictive control (MPC); and integration with hardware through industrial communication protocols. To ensure flexibility and scalability, COMMAND was designed to be both modular—the software “pieces” all inherit from generic building blocks and can be combined and connected to create complicated simulations—and high performing—designed for parallel processing, enabling simulations and experiments to take advantage of multi-core computers, servers, and nodes. The code is written in the Python programming language due to the language's popularity, active community, and open-source and cross-platform nature. Maintaining consistency with other simulation tools used within the nuclear energy community, users implement simulations and experiments through text input files, which define components, parameters, connections, etc., through lines of text. Given that COMMAND is written in Python, these input files are native Python scripts, and so use the standard Python structure and formatting. This also enables users to take advantage of Python's extensive package library to develop custom capabilities for their specific use cases.

Faber, Jacob [Idaho National Laboratory (INL), Ida↗

DOE OSTI2018

Modular assembly of transposable element arrays by microsatellite targeting in the guayule and rice genomes

Background: Guayule ( Parthenium argentatum A. Gray) is a rubber-producing desert shrub native to Mexico and the United States. Guayule represents an alternative to Hevea brasiliensis as a source for commercial natural rubber. The efficient application of modern molecular/genetic tools to guayule improvement requires characterization of its genome. Results: The 1.6 Gb guayule genome was sequenced, assembled and annotated. The final 1.5 Gb assembly, while fragmented (N50 = 22 kb), maps > 95% of the shotgun reads and is essentially complete. Approximately 40,000 transcribed, protein encoding genes were annotated on the assembly. Further characterization of this genome revealed 15 families of small, microsatellite-associated, transposable elements (TEs) with unexpected chromosomal distribution profiles. These SaTar (Satellite Targeted) elements, which are non-autonomous Mu-like elements (MULEs), were frequently observed in multimeric linear arrays of unrelated individual elements within which no individual element is interrupted by another. This uniformly non-nested TE multimer architecture has not been previously described in either eukaryotic or prokaryotic genomes. Five families of similarly distributed non-autonomous MULEs (microsatellite associated, modularly assembled) were characterized in the rice genome. Families of TEs with similar structures and distribution profiles were identified in sorghum and citrus. Conclusion: The sequencing and assembly of the guayule genome provides a foundation for application of current crop improvement technologies to this plant. In addition, characterization of this genome revealed SaTar elements with distribution profiles unique among TEs. Satar targeting appears based on an alternative MULE recombination mechanism with the potential to impact gene evolution.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

Development and testing of a prototype modular tritium and carbon-14 gas environmental monitoring system

Increasing quantities of radioactive waste are being placed into storage facilities. Many of the waste products contain organic materials which may undergo degradation leading to the release of tritium and carbon-14 species into waste containers and potentially into the environment. Monitoring for radioactive gas releases are required for environmental regulatory compliance and for radiation protection of facility workers. Research is currently being undertaken at the National Physical Laboratory (NPL) as part of a European Metrology Research Programme (EMRP) project MetroRWM to adapt and automate existing environmental sampling techniques for tritium and carbon-14 species. An innovative modular system is being developed which will lead to the introduction of an on-site small scale system capable of gas collection, liquid scintillation sample preparation and measurement. This paper outlines the evaluation of a liquid scintillation system that has been performed to date using active solutions of spiked trapping medium of similar activity concentrations to those anticipated in a waste repository. This system will operate using pre-set conditions for quench and luminescence derived from these and subsequent trials, unlike most other counters for which corrections for these phenomena are applied post measurement. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2013

Representative Source Terms and the Influence of Reactor Attributes on Functional Containment in Modular High-Temperature Gas-Cooled Reactors

Modular high-temperature gas-cooled reactors (MHTGRs) offer a high degree of passive safety. The low power density of the reactor and the high heat capacity of the graphite core result in slow transients that do not challenge the integrity of the robust TRISO fuel. Another benefit of this fuel form and the surrounding graphite is their superior ability to retain fission products under all anticipated normal and off-normal conditions, which limits reactor accident source terms to very low values. In this paper, we develop estimates of the source term for a generic MHTGR to illustrate the performance of the radionuclide barriers that comprise the MHTGR functional containment. We also examine the influence of initial fuel quality, fuel performance/failure, reactor outlet temperature, and retention outside of the reactor core on the resultant source term to the environment.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2016

Modular synthetic inverters from zinc finger proteins and small RNAs

Synthetic zinc finger proteins (ZFPs) can be created to target promoter DNA sequences, repressing transcription. The binding of small RNA (sRNA) to ZFP mRNA creates an ultrasensitive response to generate higher effective Hill coefficients. Here we combined three “off the shelf” ZFPs and three sRNAs to create new modular inverters in E. coli and quantify their behavior using induction fold. We found a general ordering of the effects of the ZFPs and sRNAs on induction fold that mostly held true when combining these parts. We then attempted to construct a ring oscillator using our new inverters. In conclusion, our chosen parts performed insufficiently to create oscillations, but we include future directions for improvement upon our work presented here.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Bypassing the Pentose Phosphate Pathway: Towards Modular Utilization of Xylose

The efficient use of hemicellulose in the plant cell wall is critical for the economic conversion of plant biomass to renewable fuels and chemicals. Previously, the yeast Saccharomyces cerevisiae has been engineered to convert the hemicellulose-derived pentose sugars xylose and arabinose to D-xylulose-5-phosphate for conversion via the pentose phosphate pathway (PPP). However, efficient pentose utilization requires PPP optimization and may interfere with its roles in NADPH and pentose production. Here, we developed an alternative xylose utilization pathway that largely bypasses the PPP. In the new pathway, D-xylulose is converted to D-xylulose-1-phosphate, a novel metabolite to S. cerevisiae, which is then cleaved to glycolaldehyde and dihydroxyacetone phosphate. This synthetic pathway served as a platform for the biosynthesis of ethanol and ethylene glycol. The use of D-xylulose-1-phosphate as an entry point for xylose metabolism opens the way for optimizing chemical conversion of pentose sugars in S. cerevisiae in a modular fashion.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Modular Adaptive Packing for Integrally Cooled Absorbers

Process intensification is one cornerstone in ION Clean Energy’s (ION) efforts to lowering CO2 capture cost. ION has modeled, designed, and fabricated an innovative gas-liquid contactor known as Modular Adaptive Packing (MAP). During two successful SBIR Phase I and II projects entitled: “Rapid Design and Testing of Novel Gas-Liquid Contacting Devices for Post-Combustion CO2 Capture via 3D-printing”, ION developed and proved this new technology at bench scale. MAP, a 3D-printed lattice-structured packing, combines the absorber gas/liquid contactor with an innovative in-situ heat-exchanger. Thanks to the capabilities of 3D-printing, the lattice structure of MAP contains hollow channels through which coolant water can be pumped to remove the heat of reaction from CO2 absorption. ION refers to this novel method of heat exchange as intracooling. After 25.4 cm (10 in) diameter MAP modules were fabricated, ION built and tested a packing characterization rig at its pilot facility in Boulder, Colorado, U.S.A. To provide baseline results for the characterization rig, ION tested Sulzer’s Mellapak™ 250Y (MP250Y) as a standard structured packing. ION’s MAP was then compared directly to the baseline MP250Y packing to evaluate key indicators including pressure drop, liquid hold-up, and effective area. MAP has a higher pressure drop than MP250Y at the same gas velocities in addition to greater liquid holdup. However, ION found that MAP displays a higher wetting coverage of 93% compared to 65% for MP250Y and reduces shearing forces that result in undesirable droplet formation. Using Optimized Gas Treating’s (OGT) rate-based simulation software ProTreat®, a conceptual evaluation of MAP was modeled for a CO2 absorber using 30 wt% MEA solvent over a range of lean loadings at 90% CO2 capture from a coal-fired power plant. ION modeled a 25-meter column absorber for both the standard MP250Y packing and a hybrid column. The hybrid absorber contained 10 m of MP250Y packing at the top and bottom with the middle 5 meters comprised of MAP. Compared to a traditional intercooled absorber, MAP can remove 22% more heat and increase overall MEA carrying capacity by 4% without increasing overall pressure drop.

20 FOSSIL-FUELED POWER PLANTS↗

DOE OSTI2020

Beurling-Selberg extremization and modular bootstrap at high energies

We consider previously derived upper and lower bounds on the number of operators in a window of scaling dimensions [\Delta - \delta,\Delta + \delta] [ Δ − δ , Δ + δ ] at asymptotically large \Delta Δ in 2d unitary modular invariant CFTs. These bounds depend on a choice of functions that majorize and minorize the characteristic function of the interval [\Delta - \delta,\Delta + \delta] [ Δ − δ , Δ + δ ] and have Fourier transforms of finite support. The optimization of the bounds over this choice turns out to be exactly the Beurling-Selberg extremization problem, widely known in analytic number theory. We review solutions of this problem and present the corresponding bounds on the number of operators for any \delta \geq 0 δ ≥ 0 . When 2\delta \in \mathbb Z_{\geq 0} 2 δ ∈ ℤ ≥ 0 the bounds are saturated by known partition functions with integer-spaced spectra. Similar results apply to operators of fixed spin and Virasoro primaries in c>1 c > 1 theories.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2012

Next Generation Solvent – Materials Compatibility with Polymer Components within Modular CausticSide Solvent Extraction Unit (Final Report)

The Office of Waste Processing, within the Office of Technology Innovation and Development, is funding the development of an enhanced solvent for deployment at the Savannah River Site for removal of cesium from High Level Waste. The technical effort is collaboration between Oak Ridge National Laboratory (ORNL), Savannah River National Laboratory (SRNL), and Argonne National Laboratory. The first deployment target for the technology is within the Modular Caustic-Side Solvent Extraction Unit (MCU). Deployment of a new chemical within an existing facility requires verification that the chemical components are compatible with the installed equipment. In the instance of a new organic solvent, the primary focus is on compatibility of the solvent with organic polymers used in the facility. This report provides the data from exposing these polymers to the Next Generation Solvent (NGS). The test was conducted over six months. An assessment of the dimensional stability of polymers present in MCU (i.e., PEEK, Grafoil, Tefzel and Isolast) in the modified NGS (where the concentration of LIX®79 and MaxCalix was varied systematically) showed that LIX®79 selectively affected Tefzel and its different grades (by an increase in size and lowering its density). The copolymer structure of Tefzel and possibly its porosity allows for the easier diffusion of LIX®79. Tefzel is used as the seat material in some of the valves at MCU. Long term exposure to LIX®79, may make the valves hard to operate over time due to the seat material (Tefzel) increasing in size. However, since the physical changes of Tefzel in the improved solvent are comparable to the changes in the CSSX baseline solvent, no design changes are needed with respect to the Tefzel seating material. PEEK, Grafoil and Isolast were not affected by LIX®79 and MaxCalix within six months of exposure. The initial rapid weight gain observed in every polymer is assigned to the finite and limited uptake of Isopar® L/Modifier by the polymers probably due to the polymers porosity and rough surfaces. Spectroscopic data on the organic liquid and the polymer surfaces showed no preferential adsorption of any component in the NGS to the polymers and with the exception of CPVC, no leachate was observed in the NGS from any of the polymers studied. The testing shows no major concerns for compatibility over the short duration of these tests but does indicate that longer duration exposure studies are warranted, especially for Tefzel. However, the physical changes experienced by Tefzel in the improved solvent were comparable to the physical changes obtained when Tefzel is placed in CSSX baseline solvent. Therefore, there is no effect of the improved solvent beyond those observed in CSSX baseline solvent.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2012

NREL Wind Turbine Blade Structural Testing of the Modular Wind Energy MW45 Blade: Cooperative Research and Development Final Report, CRADA Number CRD-09-354

This CRADA was a purely funds-in CRADA with Modular Wind Energy (MWE). MWE had a need to perform full-scale testing of a 45-m wind turbine blade. NREL/NWTC provided the capabilities, facilities, and equipment to test this large-scale MWE wind turbine blade. Full-scale testing is required to demonstrate the ability of the wind turbine blade to withstand static design load cases and demonstrate thefatigue durability. Structural testing is also necessary to meet international blade testing certification requirements. Through this CRADA, MWE would obtain test results necessary for product development and certification, and NREL would benefit by working with an industrial partner to better understand the unique test requirements for wind turbine blades with advanced structural designs.

17 WIND ENERGY↗