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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.

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At least 127 records · Page 7

Data for "RT-EZ: A Golden Gate Assembly Toolkit for Streamlined Genetic Engineering of Rhodotorula toruloides"

For economic and sustainable biomanufacturing, the oleaginous yeast Rhodotorula toruloides has emerged as a promising platform for producing biofuels, pharmaceuticals, and other valuable chemicals. However, genetic manipulation of R. toruloides has been limited by its high GC content and the lack of a replicating plasmid, necessitating gene integration into the genome of the yeast. To address these challenges, we developed the RT-EZ ( R. toruloides Efficient Zipper) toolkit, a versatile tool based on Golden Gate assembly, designed to streamline R. toruloides engineering with improved efficiency and flexibility. The RT-EZ toolkit simplifies vector construction by incorporating new features such as bidirectional promoters and 2A peptides, color-based screening using RFP, and sequences optimized for both Agrobacterium tumefaciens-mediated transformation (ATMT) and easy linearization, enabling straightforward selection and transformation. Notably, the RT-EZ kit can be used to construct an expression cassette with four different genes in one assembly reaction, significantly improving vector construction speed and efficiency. The utility of the RT-EZ toolkit was demonstrated through the successful synthesis of arachidonic acid in R. toruloides by coexpressing fatty acid elongases and desaturases. This result underscores the potential of the RT-EZ toolkit to advance synthetic biology in R. toruloides , providing a streamlined method for addressing genetic engineering challenges in the yeast.

gene editing↗

RT-EZ: A Golden Gate Assembly Toolkit for Streamlined Genetic Engineering of Rhodotorula toruloides

For economic and sustainable biomanufacturing, the oleaginous yeast Rhodotorula toruloides has emerged as a promising platform for producing biofuels, pharmaceuticals, and other valuable chemicals. However, genetic manipulation of R. toruloides has been limited by its high GC content and the lack of a replicating plasmid, necessitating gene integration into the genome of the yeast. To address these challenges, we developed the RT-EZ (R. toruloides Efficient Zipper) toolkit, a versatile tool based on Golden Gate assembly, designed to streamline R. toruloides engineering with improved efficiency and flexibility. The RT-EZ toolkit simplifies vector construction by incorporating new features such as bidirectional promoters and 2A peptides, color-based screening using RFP, and sequences optimized for both Agrobacterium tumefaciens-mediated transformation (ATMT) and easy linearization, enabling straightforward selection and transformation. Notably, the RT-EZ kit can be used to construct an expression cassette with four different genes in one assembly reaction, significantly improving vector construction speed and efficiency. The utility of the RT-EZ toolkit was demonstrated through the successful synthesis of arachidonic acid in R. toruloides by coexpressing fatty acid elongases and desaturases. Furthermore, this result underscores the potential of the RT-EZ toolkit to advance synthetic biology in R. toruloides, providing a streamlined method for addressing genetic engineering challenges in the yeast.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Python Library for Monte Carlo Simulations with Ab Initio and Machine-Learned Interatomic Potentials

There is a growing need in the simulation community for software that provides a transparent, reproducible, usable, and extensible (TRUE) Monte Carlo (MC) simulation framework employing energies from ab initio methods and machine-learning interatomic potentials (MLIPs). We introduce a Python library (ASE-MC) that adds Monte Carlo functionality to the Atomic Simulation Environment (ASE) package. Now, we can combine the powerful tools used to build systems and perform ab initio and MLIP in ASE with MC simulation algorithms to sample the configurational space with a concise Python script. After presenting the design philosophy, we demonstrate the flexibility of our approach using selected examples. These example simulations include liquid water described with a message-passing MLIP in the canonical and isothermal–isobaric ensembles, sampling the characteristic dihedral angle of biphenyl and comparing an MLIP to first-principles calculations, and a grand canonical Monte Carlo simulation of ammonia adsorption on Pt(111). These examples showcase the main features of the software, which include flexibility in the choice of ab initio or MLIP engine, ab initio or MLIP grand canonical MC with cavity bias insertions and deletions, the ability to add custom MC moves to the move set, and how users can condense complex MC workflows into a single Python script. Finally, this library serves as a framework for reproducible Monte Carlo simulations, facilitating easy reproduction of the work and application to new systems.

97 MATHEMATICS AND COMPUTING↗

Melt Pool characteristics on surface roughness and printability of 316L stainless steel in laser powder bed fusion

Purpose Surface quality and porosity significantly influence the structural and functional properties of the final product. This study aims to establish and explain the underlying relationships among processing parameters, top surface roughness and porosity level in additively manufactured 316L stainless steel. Design/methodology/approach A systematic variation of printing process parameters was conducted to print cubic samples based on laser power, speed and their combinations of energy density. Melt pool morphologies and dimensions, surface roughness quantified by arithmetic mean height (Sa) and porosity levels were characterized via optical confocal microscopy. Findings The study reveals that the laser power required to achieve optimal top surface quality increases with the volumetric energy density (VED) levels. A smooth top surface (Sa < 15 µm) or a rough surface with humps at high VEDs (VED > 133.3 J/mm 3 ) can serve as indicators for fully dense bulk samples, while rough top surfaces resulting from melt pool discontinuity correlate with high porosity levels. Under insufficient VED, melt pool discontinuity dominates the top surface. At high VEDs, surface quality improves with increased power as mitigation of melt pool discontinuity, followed by the deterioration with hump formation. Originality/value This study reveals and summarizes the formation mechanism of dominant features on top surface features and offers a potential method to predict the porosity by observing the top surface features with consideration of processing conditions.

Engineering↗

Machine Learning for Predictive Performance Analysis in Charged Particle Beam Tools

Imaging methods driven by probes, electrons, and ions have played a dominant role in modern science and engineering. Opportunities for machine vision and AI that focus on consumer problems like driving and feature recognition, are now presenting themselves for automating aspects of the scientific processes. This proposal aims to enable and drive discovery in ultra-low energy implantation by taking advantage of faster processing, flexible control and detection methods, and architecture-agnostic workflows that will result in higher efficiency and shorter scientific development cycles. Custom microscope control, collection and analysis hardware will provide a framework for conducting novel in situ experiments revealing unprecedented insight into surface dynamics at the nanoscale. Ion implantation is a key capability for the semiconductor industry. As devices shrink, novel materials enter the manufacturing line, and quantum technologies transition to being more mainstream. Traditional implantation methods fall short in terms of energy, ion species, and positional precision. Here we demonstrate 1 keV focused ion beam Au implantation into Si and validate the results via atom probe tomography. We show the Au implant depth at 1 keV is 0.8 nm and that identical results for low energy ion implants can be achieved by either lowering the column voltage, or decelerating ions using bias – while maintaining a sub-micron beam focus. We compare our experimental results to static calculations using SRIM and dynamic calculations using binary collision approximation codes TRIDYN and IMSIL. A large discrepancy between the static and dynamic simulation is found that is due to lattice enrichment with high stopping power Au and surface sputtering. Additionally, we demonstrate how model details are particularly important to the simulation of these low-energy heavy-ion implantations. Finally, we discuss how our results pave a way to much lower implantation energies, while maintaining high spatial resolution.

47 OTHER INSTRUMENTATION↗

Defect engineering in nickel via electrodeposition following low temperature annealing

Electrodeposited nickel coatings are characterized by high densities of crystalline defects including dislocations, growth twins, and hydrogen bubbles/voids, arising from the non-equilibrium nature of deposition. While these metastable features influence as-deposited properties, their evolution under low temperature annealing remains unexplored. Here, in this study, we demonstrate that low temperature annealing (200 °C) induces significant microstructural rearrangement without grain growth, enabling defect engineering through thermally assisted dislocation motion and twin boundary migration. Notably, we observe faceted twin boundaries and dislocation organization into extended networks, which have been rarely reported under such annealing conditions. These transformations are attributed to hydrogen-assisted defect mobility, facilitated by the release or redistribution of hydrogen trapped during deposition. These structural transformations correlate with a significant enhancement in mechanical properties, including a twofold increase in yield strength and improved ductility. Our findings highlight the role of trapped hydrogen in mediating low-temperature defect mobility and twin boundary evolution, offering a unique pathway for microstructural tuning of metallic coatings through controlled annealing.

36 - MATERIALS SCIENCE↗

FLEX-FUEL MIXING CONTROLLED COMBUSTION ENABLED BY PRECHAMBER IGNITION

There is an imminent need to displace fossil diesel fuel with cleaner burning, domestically produced, renewable fuels for use in heavy-duty engines. Bioethanol is a prime candidate as it widely adopted in the U.S. as a gasoline additive ranging in volume percentage from 10% (E10) up to 85% (E85). Direct substitution of market available ethanol-gasoline blends for diesel fuel is not plausible as the stark reactivity differences would not constitute the same ignition quality nor achieve auto-ignition at all. This work focuses on the development of prechamber enabled mixing-controlled combustion (PC-MCC) as an advanced combustion strategy to facilitate reliable ignition and diffusion style combustion ethanol-gasoline fuel blends. PC-MCC involves integration of an actively fueled prechamber (PC) into a conventional compression ignition combustion system. When ignited, the PC ejects hot turbulent jets into the main combustion chamber that then interact with the direct injected fuel, prompting immediate ignition. The PC jet flames provide a robust thermal ignition source that allows the engine to operate agnostic of fuel composition, or flex-fuel. Computational fluid dynamics (CFD) modeling was used to assess critical design features of the PC while garnering insights into the ignition strategies that facilitate robust performance. A key finding was the ignition performance benefits of fuel-rich PC operation which yield exothermic jets. Based on the numerical findings, a prototype igniter was tested experimentally on both single and multi-cylinder engine platforms at a variety of operating conditions. The experimental results indicate flex-fuel PC-MCC is well capable of diesel-like combustion processes by demonstrating matched or improved gross thermal efficiencies and load variability within 2%. Fuel grade ethanol (E98) exhibited consistently lower NOx and immeasurable soot across the load space. E98 also demonstrated a significant improvement in thermal efficiency at light loads.

Zeman, Jared↗

Design of Novel Hot Gas Component for Gas Turbine Engines Enabled by Materials and Additive Manufacturing Process Development

This CRADA project was the result of a project award under FOA-DOE-0001980. The overarching FOA project team consisted of researchers from Carpenter Technology Corporation (CTC), Solar Turbines Incorporated (Solar), Pennsylvania State University (PSU), University of California-Santa Barbara (UCSB), and Oak Ridge National Laboratory (ORNL). Evaluations were conducted on two high-γ’ superalloys that were designed by CTC and the UCSB. One alloy named GammaPrint-700 (GP-700) is a cobalt-base superalloy. The other alloy named GammaPrint-1100 (GP-1100) is a nickel-base (Ni-base) superalloy. PSU provided expertise and experimental testing of the thermal performance of AM micro-cooling architectures. ORNL provided expertise with the AM superalloy materials characterization and AM processing science. Solar provided turbine component design expertise. The focus of this CRADA report is to document the efforts between ORNL and CTC towards the development of superalloys designed for AM. The project goal was to use an AM processable high-temperature superalloy and design for Additive Manufacturing (DfAM) techniques to design an efficient turbine component (i.e. a turbine tip shoe) with enhanced cooling features that can only be fabricated through additive manufacturing (AM). The efficiencies of existing combined heat and power (CHP) engines are capped by both component design and materials limitations. However, AM of a tip shoe component from a γ’strengthened superalloy offers the design flexibility to increase the efficiency and power of an industrial gas turbine. This project brought about advancements in the DfAM tip shoe design space and in the area of high temperature superalloys processable through laser powder bed fusion (LPBF) AM. State of art computation design tools were utilized to optimize unique cooling features into a tip shoe component design. A two-prong materials development approach was taken to support development of the AM tip shoe geometry. The first approach centered on investigating the processability and the appropriate process science for the industry standard high-γ’ nickel-base (Ni-base) superalloy Mar-M247. This superalloy is typically cast and considered non-weldable by traditional welding standards. In the course of this work, the alloy was not deemed feasible for process scale-up due to significant cracking issues during printing. The second approach focused on the development and evaluation of a novel cobalt-base superalloy, GammaPrint™-700 (GP-700 and a Ni-base superalloy, GammaPrint™-1100 (GP-1100) designed to mitigate the significant AM processing issues with Mar-M247. The processability of these two alloys were investigated through electron beam melting (EBM) binder-jet AM (BJAM), and LPBF as a risk mitigation for manufacturability. To be considered a candidate material for down-selection to proceed to fullscale AM tip shoe engine testing trials, the high temperature creep rupture strength was required to achieve at a minimum, a Larsen Miller Parameter (LMP) increase of 10.9% over the baseline material LPBF AM Hastelloy X.

36 MATERIALS SCIENCE↗

Design of Novel Hot Gas Component for Gas Turbine Engines Enabled by Materials and Additive Manufacturing Process Development

This CRADA project was the result of a project award under FOA-DOE-0001980. The overarching FOA project team consisted of researchers from Carpenter Technology Corporation (CTC), Solar Turbines Incorporated (Solar), Pennsylvania State University (PSU), University of California-Santa Barbara (UCSB), and Oak Ridge National Laboratory (ORNL). Evaluations were conducted on two high-γ’ superalloys that were designed by CTC and the UCSB. One alloy named GammaPrint-700 (GP-700) is a cobalt-base superalloy. The other alloy named GammaPrint-1100 (GP-1100) is a nickel-base (Ni-base) superalloy. PSU provided expertise and experimental testing of the thermal performance of AM micro-cooling architectures. ORNL provided expertise with the AM superalloy materials characterization and AM processing science. Solar provided turbine component design expertise. The focus of this CRADA report is to document the efforts between ORNL and CTC towards the development of superalloys designed for AM. The project goal was to use an AM processable high-temperature superalloy and design for Additive Manufacturing (DfAM) techniques to design an efficient turbine component (i.e. a turbine tip shoe) with enhanced cooling features that can only be fabricated through additive manufacturing (AM). The efficiencies of existing combined heat and power (CHP) engines are capped by both component design and materials limitations. However, AM of a tip shoe component from a γ’strengthened superalloy offers the design flexibility to increase the efficiency and power of an industrial gas turbine. This project brought about advancements in the DfAM tip shoe design space and in the area of high temperature superalloys processable through laser powder bed fusion (LPBF) AM. State of art computation design tools were utilized to optimize unique cooling features into a tip shoe component design. A two-prong materials development approach was taken to support development of the AM tip shoe geometry. The first approach centered on investigating the processability and the appropriate process science for the industry standard high-γ’ nickel-base (Ni-base) superalloy Mar-M247. This superalloy is typically cast and considered non-weldable by traditional welding standards. In the course of this work, the alloy was not deemed feasible for process scale-up due to significant cracking issues during printing. The second approach focused on the development and evaluation of a novel cobalt-base superalloy, GammaPrint™-700 (GP-700 and a Ni-base superalloy, GammaPrint™-1100 (GP-1100) designed to mitigate the significant AM processing issues with Mar-M247. The processability of these two alloys were investigated through electron beam melting (EBM) binder-jet AM (BJAM), and LPBF as a risk mitigation for manufacturability. To be considered a candidate material for down-selection to proceed to full-scale AM tip shoe engine testing trials, the high temperature creep rupture strength was required to achieve at a minimum, a Larsen Miller Parameter (LMP) increase of 10.9% over the baseline material LPBF AM Hastelloy X.

99 GENERAL AND MISCELLANEOUS↗

Rapid curing dynamics of PEG-thiol-ene resins allow facile 3D bioprinting and in-air cell-laden microgel fabrication

Thiol-norbornene photoclick hydrogels are highly efficient in tissue engineering applications due to their fast gelation, cytocompatibility, and tunability. In this work, we utilized the advantageous features of polyethylene glycol (PEG)-thiol-ene resins to enable fabrication of complex and heterogeneous tissue scaffolds using 3D bioprinting and in-air drop encapsulation techniques. We demonstrated that photoclickable PEG-thiol-ene resins could be tuned by varying the ratio of PEG-dithiol to PEG norbornene to generate a wide range of mechanical stiffness (0.5–12 kPa) and swelling ratios. Importantly, all formulations maintained a constant, rapid gelation time (<0.5 s). We used this resin in biological projection microstereolithography (BioPµSL) to print complex structures with geometric fidelity and demonstrated biocompatibility by printing cell-laden microgrids. Moreover, the rapid gelling kinetics of this resin permitted high-throughput fabrication of tunable, cell-laden microgels in air using a biological in-air drop encapsulation apparatus (BioIDEA). We demonstrated that these microgels could support cell viability and be assembled into a gradient structure. This PEG-thiol-ene resin, along with BioPµSL and BioIDEA technology, will allow rapid fabrication of complex and heterogeneous tissues that mimic native tissues with cellular and mechanical gradients. The engineered tissue scaffolds with a controlled microscale porosity could be utilized in applications including gradient tissue engineering, biosensing, and in vitro tissue models.

36 MATERIALS SCIENCE↗

MCP-eGridGPT (MCP-Enabled Chatbot with Electrical Power System Analysis and Interactive Visualization Tool) [SWR-25-126]

This software is an advanced chatbot system that integrates the Model Context Protocol (MCP) to provide intelligent electrical power system analysis and automated visualization generation. The system enables users to interact with complex electrical engineering tools through natural language, automatically analyzes power system data for voltage violations and grid health assessment, and generates professional interactive HTML dashboards and reports. Key features include dynamic tool discovery from MCP servers, multi-LLM provider support, intelligent data interpretation using large language models, automated chart generation, and a web-based interface for real-time analysis. The software bridges sophisticated electrical engineering analysis with user-friendly interfaces, making power system diagnostics accessible through conversational AI.

Choi, Seong [National Laboratory of the Rockies (N↗

Tunable Electronic Energy Level Alignment and Exciton Diversity in Organic–Inorganic van der Waals Heterostructures

van der Waals stacking of two-dimensional (2D) materials offers a powerful platform for engineering material interfaces with tailored electronic and optical properties. While most van der Waals multilayers have featured inorganic monolayers, incorporating molecular monolayers introduces additional degrees of tunability and functionality. Here, in this study, we investigate hybrid bilayers composed of atomically thin perylene-based molecular crystals interfaced with monolayer transition metal dichalcogenides (TMDs), specifically MoS 2 and WS 2 . Using the ab initio many-body perturbation theory within the GW approximation and the Bethe-Salpeter equation approach, we predict emergent properties beyond those of the isolated constituent systems. Notably, we find substantial renormalization of monolayer molecular crystal band gap due to TMD-induced polarization. Furthermore, by varying the TMD monolayer, we demonstrate tuning of the energy level alignment of the bilayer and subsequent control over a diversity of lowest-energy excitons, which include strongly bound hybrid excitons and long-lived charge-transfer excitons. These findings establish organic-inorganic van der Waals heterostructures as a promising class of materials for tunable optoelectronic devices and quantum excitonic phenomena, expanding the design space for low-dimensional systems.

GW-BSE calculations↗

Feature Pathway Graphs using Random Forest Regressors

SAND2025-04671O Feature Pathway Graphs using Random Forest Regressors is a software tool that uses machine learning to determine pathways of influence between features in data sets. It can be used as a surrogate method for casual discovery. The output creates pathway graphs between features of interest. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Peterson, Matthew↗

Identifying microbial functional guilds performing cryptic organotrophic and lithotrophic redox cycles in anaerobic granular biofilms

Granular biofilms used in anaerobic digester systems contain diverse microbial populations that interact to hydrolyze organic matter and produce methane within controlled environments. Prior research investigated the feasibility of utilizing granular biofilms obtained from an anaerobic digester to remove nitrate without the addition of exogenous electron donors. These granules possessed a unique structure of alternating light and dark iron sulfide and pyrite rich layers that potentially served as both an electron source and sink, linking carbon, nitrogen, sulfur, and iron cycles. To characterize the functional roles of diverse microbial populations enriched within these layered biofilms, we analyzed metagenomes obtained from three different granules. Comparisons between the functional gene content of forty metagenome assembled genomes (MAGs) identified phylogenetically cohesive functional guilds. Each of these functional MAG clusters was assigned to specific steps in anaerobic digestion (hydrolysis, acidogenesis, acetogenesis, and methanogenesis) and anaerobic respiration (denitrification and sulfate reduction). Comparisons with metagenomes derived from a variety of natural and engineered ecosystems confirmed that the enriched denitrifying bacteria were similar to populations typically found in wetlands and biological nitrogen removal systems. Analysis of read alignments to individual genes within the forty MAGs identified conserved genomic features that were representative of the functions that distinguished functional guilds. Overall, this research illustrates the utility of functional based classification of microorganisms for characterizing ecosystem functions and highlights the potential application of engineered ecosystems to serve as experimental models for complex natural ecosystems.

Ecosystem engineering↗

Nanopolysaccharide Builder: A User-Friendly Tool for Atomistic Models of Polysaccharide-Based Nanostructures

Here, we introduce Nanopolysaccharide Builder (NPB), a user-friendly software tool designed to construct polysaccharide nanostructures─mainly those based on cellulose, chitin, and chitosan─using experimental data or user-defined parameters. NPB enables the generation of cellulose and chitin allomorphs with customizable biochemical topologies and also facilitates the construction of large bundles that replicate nanostructures found in biological support systems, including plant cell walls and arthropod cuticles. The software outputs atomic Cartesian coordinates in Protein Data Bank (PDB) format and also provides atom connectivity files in PSF and PARM formats, ensuring seamless integration with major molecular dynamics (MD) engines such as NAMD, CHARMM, GROMACS, AMBER, OpenMM, and LAMMPS. Built on an interactive visualization framework, NPB features a graphical user interface (GUI) and supports both macOS and Linux operating systems. By enabling detailed atomic-scale studies of polysaccharide evolution in extracellular matrices and cell walls of algae, bacteria, fungi, and plants, NPB is poised to advance AI-guided research in sustainable chemical development and biomass utilization.

Wan, Zhangmin [Univ. of British Columbia, Vancouve↗

Detector Interface for Streaming, Control, and Open-source integration (DISCO) v1.0.0

This suite consists of a multi-package ecosystem featuring detector emulators, EPICS areaDetector drivers, and remote server frameworks designed for the Advanced Light Source (ALS). Engineered for high-bandwidth devices—including VFCCD, Timepix3, Timepix4, and related pixel detectors—the software simulates hardware, wraps vendor SDKs into remote-callable servers, and integrates with open-source control systems. Key Capabilities: Distributed SDK Architecture: Server packages wrap hardware-specific SDKs, allowing areaDetector drivers to execute remote framework calls. This isolates proprietary libraries from the EPICS IOC, enhancing stability and enabling distributed computing across beamline networks. Device Support: Custom drivers for VFCCD, the Timepix family, and similar sensors optimize the data path from hardware control to high-speed transport. Full-Stack Emulation: Sophisticated emulator packages allow end-to-end pipeline testing and software development without requiring physical hardware or beam time. Integrated Workflows: Supports high-bandwidth streaming for real-time analysis and robust, metadata-rich file-based workflows (e.g., HDF5/NeXus). By standardizing interfaces across heterogeneous hardware, this suite reduces technical debt. It provides the ALS with a scalable, open-source solution to manage massive data rates within a unified control environment.

Mahl, Johannes [Lawrence Berkeley National Laborat↗

Engineering Layer For System Analysis

ELSA offers various utility classes and methods to streamline the definition of regions, materials, and geometries in nuclear simulations. Key features include generating OpenMC regions, managing material properties, and providing convenient abstractions for complex geometrical and physical configurations. Additionally, ELSA supports the creation of submodels, enabling users to build modular and reusable components for their simulations. The codebase also includes robust extrusion and revolution capabilities, facilitating the efficient creation of 3D parametric geometries from 2D profiles through linear and rotational transformations.

Ferney, Paul [Idaho National Laboratory (INL), Ida↗

HELPR Version 1.1.0 User Guide

Hydrogen Extremely Low Probability of Rupture (HELPR) is a modular probabilistic fracture mechanics modeling platform developed to assess structural integrity of pipelines for transmission and distribution of hydrogen. HELPR couples fatigue and fracture engineering models with probabilistic methods to generate fast predictions and enables quantification of prediction uncertainty and sensitivity. This user manual serves as a guide through the various analysis features HELPR contains.

08 HYDROGEN↗