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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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DOE OSTI2025

Enzyme Engineering Database (EnzEngDB): a platform for sharing and interpreting sequence–function relationships across protein engineering campaigns

The discovery and engineering of new enzymes is important across the bioeconomy, with diverse applications from foods to pharmaceuticals, sensors to agriculture. However, enzyme engineering, in particular machine learning-guided engineering, is hampered by a lack of data. Currently there exists no database designed to capture and interpret datasets created in this domain, nor are there easy analysis and visualisation tools. We developed the Enzyme Engineering Database to provide a centralized resource and an online analysis tool to consolidate sequence-function data from enzyme engineering campaigns, thereby making three contributions: (i) a database into which researchers can deposit public data, (ii) visualisation and analysis tools for protein engineers to analyse their own data or compare enzyme variants to other engineering campaigns, and (iii) a gold-standard dataset for benchmarking automated extraction along with the first large language model extraction pipeline specific for enzyme engineering campaigns. The Enzyme Engineering Database is accessible at http://enzengdb.org/.

Long, Yueming [California Institute of Technology ↗
DOE OSTI2026

Data for A Generalized Platform for Artificial Intelligence-powered Autonomous Protein Engineering

Proteins are the molecular machines of life with numerous applications in energy, health, and sustainability. However, engineering proteins with desired functions for practical applications remains slow, expensive, and specialist-dependent. Here we report a generally applicable platform for autonomous enzyme engineering that integrates machine learning and large language models with biofoundry automation to eliminate the need for human intervention, judgement, and domain expertise. Requiring only an input protein sequence and a quantifiable way to measure fitness, this automated platform can be applied to engineer a wide array of proteins. As a proof of concept, we engineer Arabidopsis thaliana halide methyltransferase (AtHMT) for a 90-foldimprovement in substrate preference and 16-fold improvement in ethyl-transferase activity, along with developing a Yersinia mollaretii phytase (YmPhytase) variant with 26-fold improvement in activity at neutral pH. This is accomplished in four rounds over 4 weeks, while requiring construction and characterization of fewer than 500 variants for each enzyme. This platform for autonomous experimentation paves the way for rapid advancements across diverse industries, from medicine and biotechnology to renewable energy and sustainable chemistry.

AI/ML↗
DOE OSTI2025

Cyber-Informed Engineering (CIE) – Engineered Controls Database and Use

Cyber-Informed Engineering (CIE) addresses the reality that cyber-attacks on engineered systems can have consequences far beyond data loss or disruption of digital networks. When control systems are compromised, safety, reliability, and performance of the physical process itself may be threatened. This database is meant to establish clear examples and guidance for defining and applying engineered controls in CIE. It explains what engineered controls are, how they differ from information security measures, and how they are integrated into system design. The goal is to ensure that resilience is engineered into systems from the outset. Unlike cybersecurity protections that defend the digital layer, engineered controls act directly at the physical and algorithmic levels to guarantee that unacceptable consequences are prevented or limited. CIE keeps the consequences of a cyber attack from impacting the safety, reliability, and performance of engineered systems.

42 - ENGINEERING↗
DOE OSTI2020

What Questions Would a Systems Engineer Ask to Assess Systems Engineering Models as Credible

Digital Systems Engineering strategies typically call for digital Systems Engineering models to be retained in repositories and certified as an authoritative source of truth (enabling model reuse, qualification, and collaboration). In order for digital Systems Engineering models to be certified as authoritative (credible), they need to be assessed - verified and validated - and with the amount of uncertainty in the model quantified (consider reusing someone else's model without knowing the author). Due to this increasing model complexity, the authors assert that traditional human-based methods for validating, verifying, and uncertainty quantification - such as human-based peer-review sessions - cannot sufficiently establish that a digital Systems Engineering model of a complex system is credible. Digital Systems Engineering models of complex systems can contain millions of nodes and edges. The authors assert that this level of detail is beyond the ability of any group of humans - even working for weeks at a time - to discern and catch every minor model infraction. In contrast, computers are highly effective at discerning infractions with massive amounts of information. The authors suggest that a better approach might be to focus the humans at what model patterns should be assessed and enable the computer to assess the massive details in accordance with those patterns - by running through perhaps 100,000 test loops. In anticipation of future projects to implement and automate the assessment of models at Sandia National Laboratories, a study was initiated to elicit input from a group of 25 Systems Engineering experts. The authors positioning query began with - 'What questions would a Systems Engineer ask to assess Systems Engineering models for credibility?" This report documents the results of that survey.

42 ENGINEERING↗
DOE OSTI2025

Multidimensional Modeling of Mixture Formation in a Hydrogen-Fueled Heavy-Duty Optical Engine With Direct Injection

Hydrogen (H 2 ), as a carbon-free fuel, is considered as one of the most promising solutions to reduce the carbon footprint of hard-to-decarbonize energy and transportation sectors. As such, hydrogen-fueled internal combustion engines (H 2 ICEs) have recently been receiving increasing attention, particularly in applications such as on-road/off-road heavy-duty transport and combined heat and power. The direct injection (DI) of gaseous hydrogen into the combustion chamber offers great potential for achieving high power density and high engine efficiency, while mitigating the risk of backfire and reducing pre-ignition. However, the numerical simulation of H 2 DI system remains a formidable challenge associated with the high computational cost of reproducing compressible supersonic flow and shocks in narrow injector passages and in near-nozzle regions. In general, there is a lack of well-established and validated practices for the modeling of high-pressure H 2 DI in large-bore engines. Here, to this end, this study focuses on computational fluid dynamics (CFD) modeling of the mixture formation process in a heavy-duty optical engine employing a medium-pressure H 2 DI system. Both large eddy simulations (LES) and Reynolds Averaged Navier–Stokes (RANS) simulations are performed and evaluated against optical data. Gaseous hydrogen is injected into the combustion chamber via a centrally located outward opening hollow-cone injector at a pressure of 40 bar. Simulations are carried out for two injection timings, namely, −120 and −60 °CA. The numerical predictions for H 2 distribution in different horizontal and vertical planes during the compression stroke are systematically compared against optical data obtained through planar laser-induced fluorescence (PLIF) measurements. Overall, the LES approach using the Dynamic Structure model is found to have good predictive capabilities for the early jet penetration in terms of length and shape, as well as the later H 2 distributions. However, the unsteady RANS approach with the renormalization group $k - ϵ$ model, which is widely used by industry to model heavy-duty ICEs, significantly underpredicts the H 2 mixing, even at similar mesh resolution to that used in LES. These results indicate that there is a need for the improvement of mixing submodels within the RANS approach when applied to H 2 DI simulations.

LES↗
DOE OSTI2021

The F-box protein gene exo-1 is a target for reverse engineering enzyme hypersecretion in filamentous fungi

Carbohydrate active enzymes (CAZymes) are vital for the lignocellulose-based biorefinery. The development of hypersecreting fungal protein production hosts is therefore a major aim for both academia and industry. However, despite advances in our understanding of their regulation, the number of promising candidate genes for targeted strain engineering remains limited. Here, we resequenced the genome of the classical hypersecreting Neurospora crassa mutant exo-1 and identified the causative point of mutation to reside in the F-box protein–encoding gene, NCU09899. The corresponding deletion strain displayed amylase and invertase activities exceeding those of the carbon catabolite derepressed strain ?cre-1, while glucose repression was still mostly functional in ?exo-1. Surprisingly, RNA sequencing revealed that while plant cell wall degradation genes are broadly misexpressed in ?exo-1, only a small fraction of CAZyme genes and sugar transporters are up-regulated, indicating that EXO-1 affects specific regulatory factors. Aiming to elucidate the underlying mechanism of enzyme hypersecretion, we found the high secretion of amylases and invertase in ?exo-1 to be completely dependent on the transcriptional regulator COL-26. Furthermore, misregulation of COL-26, CRE-1, and cellular carbon and nitrogen metabolism was confirmed by proteomics. Finally, we successfully transferred the hypersecretion trait of the exo-1 disruption by reverse engineering into the industrially deployed fungus Myceliophthora thermophila using CRISPR-Cas9. Our identification of an important F-box protein demonstrates the strength of classical mutants combined with next-generation sequencing to uncover unanticipated candidates for engineering. These data contribute to a more complete understanding of CAZyme regulation and will facilitate targeted engineering of hypersecretion in further organisms of interest.

Gabriel, Raphael↗
DOE OSTI2022

Evaluation of Horizon of Viability Optimization Engine for Sustained Power to Critical Infrastructure: Preprint

In the aftermath of increasingly frequent catastrophic events, a typical scenario is Critical Infrastructure (CI) units being supported by available backup sources with a weak power grid that can be intermittent or absent. Such a scenario is significantly challenging in the sense of reliable supply of power to CI units. In this article, an intelligent optimization scheme termed as Horizon of Viability (HoV) engine is developed to guarantee the viability of a sustained reliable supply of power to the CI units over a time-horizon. The proposed HoV engine generates a cost-optimal portfolio of the locally available generation sources and the loads over a time horizon using a mixed-integer convex programming problem. A Controller hardware-in-the-loop (CHIL) platform is developed to evaluate the control performance of the HoV engine. The experimental results corroborates the efficacy in maintaining the viability of the CI units after a grid interruption event. Further, the proposed HoV optimization scheme performs better compared to existing net-load management schemes in the literature.

disaster resiliency↗
DOE OSTI2026

Engineering Against Digital Risk in CIP Applications: Cyber-Informed Engineering Use Cases

Cyber-Informed Engineering (CIE) addresses the reality that cyber attacks on engineered systems can have consequences far beyond data loss or disruption of digital networks. When control systems are compromised, safety, reliability, and performance of the physical process itself may be threatened. This presentation discusses engineered controls of 7 categories and the CIE database of controls that provides clear examples and guidance for defining and applying engineered controls in CIE. It explains what engineered controls are, how they differ from information security measures, and how they are integrated into system design.

99 - GENERAL AND MISCELLANEOUS↗
DOE OSTI2026

Cyber-Informed Engineering: Incorporating CIE into Engineering Curricula

Cyber-Informed Engineering (CIE) is an engineering approach that mitigates the consequences of cyber risk to critical infrastructure by integrating engineered controls into system design and operation. CIE-focused education is necessary to prepare future engineers and technicians to understand and mitigate digital risk in modern engineered systems. This session explores how universities can incorporate CIE into their curricula, provides examples of how existing universities are already leveraging CIE in their programs, and highlights resources to support adoption.

99 - GENERAL AND MISCELLANEOUS↗
DOE OSTI2024

Cyber-Informed Engineering Adoption in University Engineering Programs: An Overview of CIE Integration Successes at Nine U.S. Educational Institutions

This report examines the adoption of Cyber-Informed Engineering (CIE) in university engineering programs, driven by the need to protect critical energy infrastructure from adversarial threats. CIE equips current and future engineers and technicians with the necessary mindset, skills, and competencies to enhance the resilience of engineered systems against cyber attacks. This report highlights nine academic partners who are incorporating CIE into their curricula through various approaches, including lectures, courses, and certificates.

42 ENGINEERING↗
DOE OSTI2020

Identification of engine oil-derived ash nanoparticles and ash formation process for a gasoline direct-injection engine

Engine oil-derived ash particles emitted from internal combustion (IC) engines are unwanted by-products, after oil is involved in in-cylinder combustion process. Since they typically come out together with particulate emissions, no detail has been reported about their early-stage particles other than agglomerated particles loaded on aftertreatment catalysts and filters. To better understand ash formation process during the combustion process, here differently formulated engine oils were dosed into a fuel system of a gasoline direct injection (GDI) engine that produces low soot mass emissions at normal operating conditions to increase the chances to find stand-alone ash particles separated from soot aggregates in the sub-20-nm size range. In addition to them, ash/soot aggregates in the larger size range were examined using scanning transmission electron microscopy (STEM)-X-ray electron dispersive spectroscopy (XEDS) to present elemental information at different sizes of particles from various oil formulations. The STEM-XEDS results showed that regardless of formulated oil type and particle size, Ca, P and C were always contained, while Zn was occasionally found on relatively large particles, suggesting that these elements get together from an early stage of particle formation. The S, Ca and P K-edge X-ray absorption near edge structure (XANES) analyses were performed for bulk soot containing raw ash. The linear combination approach & cross-checking among XANES results proposed that Ca 5 (OH)(PO 4 ) 2 , Ca 3 (PO 4 ) 2 and Zn 3 (PO 4 ) 2 are potentially major chemical compounds in raw ash particles, when combined with the STEM-XEDS results. Despite many reports that CaSO 4 is a major ash chemical when ash found in DPF/GFP systems was examined, it was observed to be rarely present in raw ashes using the S K-edge XANES analysis, suggesting ash transformation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Engineered Pseudomonas putida simultaneously catabolizes five major components of corn stover lignocellulose: Glucose, xylose, arabinose, p-coumaric acid, and acetic acid

Valorization of all major lignocellulose components, including lignin, cellulose, and hemicellulose is critical for an economically viable bioeconomy. In most biochemical conversion approaches, the standard process separately upgrades sugar hydrolysates and lignin. Here, we present a new process concept based on an engineered microbe that could enable simultaneous upgrading of all lignocellulose streams, which has the ultimate potential to reduce capital cost and enable new metabolic engineering strategies. Specifically, we engineered Pseudomonas putida, a robust microorganism capable of catabolizing aromatic compounds, organic acids, and D-glucose, to utilize D-xylose and L-arabinose by tuning D-xylose transport and pentose phosphate pathway flux. Distinct L-arabinose pathways enabled D-glucose, D-xylose, and L-arabinose co-utilization in minimal medium using model compounds as well as corn stover hydrolysate. After modifying catabolite repression, our engineered P. putida simultaneously co-utilized five representative compounds from cellulose, hemicellulose, and lignin, demonstrating the feasibility of simultaneously upgrading total lignocellulosic biomass to value-added chemicals.

Elmore, Joshua R.↗
DOE OSTI2023

Conduct of Engineering Project Engineer Qualification Standard

This document describes the training and qualification requirements for the Project Engineer (PE) position at the Los Alamos National Laboratory (LANL). Analysis indicates that the Project Engineer position is not required to meet the requirements of DOE Order 426.2, Personnel Selection, Training, Qualification, and Certification Requirements for DOE Nuclear Facilities for “Technical Staff” positions. However, Engineering Services Division (ESD) has decided to hold their Project Engineers to a higher professional standard by developing a qualification program for the PEs.

42 ENGINEERING↗
DOE OSTI2023

Cyber-Informed Engineering Guidance—Implementing CIE in Early Systems Engineering Lifecycle Stages

Traditionally, cybersecurity is not considered in the design process. Design engineers typically focus on building safety and reliability into their products and applications. Security against malicious cyber incidents is often an afterthought, resulting in deployment of security solutions during installation or operation. Unfortunately, waiting to consider cybersecurity until later in the systems engineering lifecycle often results in less effective and more expense security. Idaho National Laboratory (INL) developed the concept of Cyber-Informed Engineering (CIE) in 2015 to provide a framework that enables cybersecurity to be built into systems beginning at the conceptual design stage. In addition to ongoing research by INL, the U.S. Department of Energy (DOE) Office of Cybersecurity, Energy Security, and Emergency Response has recently developed a National CIE Strategy document for incorporating CIE into the design and operation of infrastructure systems reliant on digital monitoring or controls. This paper provides a brief review of this National CIE Strategy as well as a roadmap to historical, current, and future CIE research by INL through the U.S. DOE Office of Nuclear Energy (NE) Cybersecurity Crosscutting Technology Development Program. A near-term focus of the DOE-NE’s research and development is to extend the foundational CIE work into detailed guidance for implementation during initial systems engineering stages in nuclear digital instrumentation and control projects and to demonstrate use of the guidance in an integrated energy systems project.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2026

Data for Metabolic Engineering of Nonmodel Yeast Issatchenkia orientalis SD108 for 5-Aminolevulinic Acid Production

Biological production of 5‐aminolevulinic acid (5‐ALA) has received growing attentionover theyears.However, thereis the tradeoff between 5‐ALA biosynthesis and cell growth because the fermentation broth will become acidic due to the production of 5‐ALA. To address this limitation, we engineered an acid‐tolerant yeast, Issatchenkia orientalis SD108, for 5‐ALA production. We first discovered that the cell growth rate of I. orientalis SD108 was boosted by 5‐ALA and its endogenous ALA synthetase (ALAS) showed higher activity than those homologs from other yeasts. The titer of 5‐ALA was improved from 28mg/L to 120‐, 150‐, and 300mg/L, by optimizing plasmid design, overexpressing a transporter, and increasing gene copy number, respectively. After redirecting the metabolic flux using the pyruvate decarboxylase (PDC) knockout strain (SD108ΔPDC) and culturing with urea, we increased the titer of 5‐ALA to 510mg/L, a 13‐fold enhancement, proving the importance of the newly identified IoALAS with higher activity and the strategic selection of nitrogen sources for knockout strains. This study demonstrates the acid‐tolerant I. orientalis SD108ΔPDC has a high potential for 5‐ALA production at a large scale in the future.

Bioproducts↗
DOE OSTI2020

Engineering the cellulolytic extreme thermophile Caldicellulosiruptor bescii to reduce carboxylic acids to alcohols using plant biomass as the energy source

Abstract Caldicellulosiruptor bescii is the most thermophilic cellulolytic organism yet identified (Topt 78 °C). It grows on untreated plant biomass and has an established genetic system thereby making it a promising microbial platform for lignocellulose conversion to bio-products. Here, we investigated the ability of engineered C. bescii to generate alcohols from carboxylic acids. Expression of aldehyde ferredoxin oxidoreductase (aor from Pyrococcus furiosus) and alcohol dehydrogenase (adhA from Thermoanaerobacter sp. X514) enabled C. bescii to generate ethanol from crystalline cellulose and from biomass by reducing the acetate produced by fermentation. Deletion of lactate dehydrogenase in a strain expressing the AOR–Adh pathway increased ethanol production. Engineered strains also converted exogenously supplied organic acids (isobutyrate and n-caproate) to the corresponding alcohol (isobutanol and hexanol) using both crystalline cellulose and switchgrass as sources of reductant for alcohol production. This is the first instance of an acid to alcohol conversion pathway in a cellulolytic microbe.

Biotechnology & Applied Microbiology↗
DOE OSTI2025

Artificial intelligence–powered biofoundries for protein engineering and metabolic engineering

Synthetic biology is rapidly evolving through the integration of artificial intelligence (AI) and automated biofoundries. This convergence accelerates the design–build–test–learn cycle, shifting protein engineering and metabolic engineering from labor-intensive manual experimentation to autonomous experimentation. This review summarizes recent advances in workflow development, AI models, and their integration with biofoundries for automated or autonomous protein engineering and metabolic engineering. Particularly, we highlight the potential of AI-powered biofoundries for accelerated scientific discovery and innovation in synthetic biology.

Chen, Junyu [Univ. of Illinois at Urbana-Champaign↗
DOE OSTI2025

Research Software Engineering: Introducing a New Computing in Science & Engineering Department

Here, this article introduces the new Research Software Engineering (RSEng) department at Computing in Science & Engineering. Through a conversation with the department coeditors, we highlight why RSEng matters, how it differs from industrial software engineering, what it means to be an RSE, and the scholarly and practical questions that lie ahead. Along the way, we draw on emerging literature, case studies, and community perspectives to frame the profession and practice of RSEng within computational science and engineering.

Lamprecht, Anna-Lena [Univ. of Potsdam (Germany)] ↗