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DOE OSTI2021

Viral Fate and Transport for COVID-19 - NVBL

The NVBL Viral Fate and Transport Team includes researchers from eleven DOE national laboratories and is utilizing unique experimental facilities combined with physics-based and data-driven modeling and simulation to study the transmission, transport, and fate of SARSCoV-2. The team was focused on understanding and ultimately predicting SARS-CoV-2 viability in varied environments with the goal of rapidly informing strategies that guide the nation’s resumption of normal activities. The primary goals of this project include prioritizing administrative and engineering controls that reduce the risk of SARS-CoV-2 transmission within an enclosed environment; identifying the chemical and physical properties that influence binding of SARS-CoV-2 to common surfaces; and understanding the contribution of environmental reservoirs and conditions on transmission and resurgence of SARS-CoV-2.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Viral Fate and Transport for COVID-19

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

CrossLink: General Overview [Slides]

Problem: Traditional mesh generation approaches are labor intensive and have limited robustness when applied to parametric design exploration and optimization of complex geometries. While automatic mesh generation approaches exist, they tend to generate tetrahedral or mixed-hybrid meshes which are generally unsuitable for physics applications with strong shock waves, thin boundary layers, and strong gradients. In addition, simulations sizes in the billions of cells are becoming more common with traditional mesh generation methods quickly reaching scalability limits. Solution: CrossLink offers a topology-based mesh generation approach with unstructured block-filling methods and a scalable mesh generation engine. In addition, CrossLink incorporates a python-based API for seamless workflow integration and robust repeatability of the geometry handling and mesh generation process. This makes it ideal for parametric design study and optimization of complex geometries. Finally, future versions of CrossLink will offer a parametric mesh capability that optimizes a high-order mesh and enables reconstruction of the final mesh in memory by the physics solver.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

An Assessment of Machine Learning Applied to Ultrasonic Nondestructive Evaluation

In the United States, the nuclear industry performs inservice inspection (ISI) through nondestructive examination (NDE) methods in accordance with guidelines specified in the American Society of Mechanical Engineers (ASME) Boiler and Pressure Vessel Code (BPVC), Section XI, Rules for Inservice Inspection of Nuclear Power Plant Components. Ultrasonic nondestructive testing and evaluation (NDT&E) is one of the more commonly used techniques for inspecting Class 1 structural components in nuclear power systems. As the number of qualified NDE inspectors declines, the nuclear industry is looking to take advantage of advances in automation to enhance inspection capabilities. Advances in computational power, cloud-based computing, and machine learning algorithms make automated data analysis possible. Machine learning (ML) has shown huge potential in automated data analyses for ultrasonic NDE in the context of weld inspections.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2024

Oscilloscope Data Push Program

Data acquisition (DAQ) is a complex and costly process. Creating DAQ systems for analyzing a system requires expensive electronics and a dedicated team of engineers for support, posing a challenge for users who readily need data. This project is a proof of concept to create a temporary or one-off DAQ system using equipment commonly available to every team. We aim to automate the data acquisition process from the Rohde \& Schwarz RTO 1044 oscilloscope, convert the acquired binary data into floating point values, and store the results in a CSV file format. By developing a Python program to handle these tasks, we seek to reduce the manual effort involved in data collection, significantly increasing efficiency.

Osei-Tutu, Jason↗

DOE OSTI2022

Site-Differentiated Iron–Sulfur Cluster Ligation Affects Flavin-Based Electron Bifurcation Activity

Electron bifurcation is an elegant mechanism of biological energy conversion that effectively couples three different physiologically relevant substrates. As such, enzymes that perform this function often play critical roles in modulating cellular redox metabolism. One such enzyme is NADH-dependent reduced-ferredoxin: NADP+ oxidoreductase (NfnSL), which couples the thermodynamically favorable reduction of NAD+ to drive the unfavorable reduction of ferredoxin from NADPH. The interaction of NfnSL with its substrates is constrained to strict stoichiometric conditions, which ensures minimal energy losses from non-productive intramolecular electron transfer reactions. However, the determinants for this are not well understood. One curious feature of NfnSL is that both initial acceptors of bifurcated electrons are unique iron–sulfur (FeS) clusters containing one non-cysteinyl ligand each. The biochemical impact and mechanistic roles of site-differentiated FeS ligands are enigmatic, despite their incidence in many redox active enzymes. Herein, we describe the biochemical study of wild-type NfnSL and a variant in which one of the site-differentiated ligands has been replaced with a cysteine. Results of dye-based steady-state kinetics experiments, substrate-binding measurements, biochemical activity assays, and assessments of electron distribution across the enzyme indicate that this site-differentiated ligand in NfnSL plays a role in maintaining fidelity of the coordinated reactions performed by the two electron transfer pathways. Given the commonality of these cofactors, our findings have broad implications beyond electron bifurcation and mechanistic biochemistry and may inform on means of modulating the redox balance of the cell for targeted metabolic engineering approaches.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Structure-function analysis of the FCRL5–IgG1 Fc complex reveals an unappreciated pathway for B cell modulation by Fc-attenuated IgG

The Fc region of therapeutic IgG antibodies is often engineered to remove or “silence” Fc effector functions, but it remains unclear whether these mutations eliminate all Fc-mediated effector activity. Human Fc receptor-like 5 (FCRL5/FcRH5) is a low-affinity IgG Fc receptor expressed on B cells and is an actively pursued antibody target in multiple myeloma. Here, we show that common Fc function-silencing mutations do not impair FCRL5-mediated activity and therefore attenuate, rather than eliminate, Fc effector function. The crystal structure of the FCRL5-IgG1 Fc complex, solved at 3.4 Å resolution, revealed that FCRL5 binds IgG1 Fc in a 1:1 complex through a binding mode distinct from that of classical Fcγ receptors, explaining why mutations that attenuate Fc effector function spare FCRL5 binding. Fc-engineered antibodies that selectively engage FCRL5 inhibited B cell receptor-induced Ca 2+ flux in FCRL5-expressing B cells. These findings demonstrate that Fc-attenuated therapeutic IgG retains the ability to engage FCRL5, identifying an unappreciated pathway for B cell modulation.

Herpers, Bart M. [Department of Biomedical Enginee↗

DOE OSTI2022

Automated fault detection and diagnosis deployment Internet of Things solution for building energy system

The building sector is the highest energy consumer and ranks first in terms of carbon emissions among all sectors. To address these issues, decarbonization and electrification in the building energy sector are two critical missions of the new US administration. For decarbonization, the new administration has set a target to reduce greenhouse gas emissions by 50–52% by 2030 and targeting a carbon-neutral economy by 2050. For electrification, the goal is to achieve 100% clean electricity by 2035. Such decarbonization and electrification in the building sector require that energy consumption in buildings be reduced significantly. Therefore, the building sector must continuously adopt new technologies to achieve its energy and carbon emission goals. One of the most fundamental technologies is the Internet of Things (IoT). IoT has proven to be an effective solution for the building domain, including building information/energy modeling, smart buildings, etc. Although much progress has been made in the development of IoT-based building energy systems, there is still a lack of reliable, scalable, and affordable IoT-based automated fault and degradation diagnostic (AFDD) solutions. Such solutions would enable deployment of advanced algorithms into real systems to archive the projected energy benefits. Here, this study reviews existing IoT solutions developed for building energy–related application and developed a simple but effective AFDD IoT deployment solution, including developing a suitable IoT architecture and conducting easy and scalable deployment by leveraging a common cloud-based IoT service.

42 ENGINEERING↗

DOE OSTI2024

Intermittent cluster dynamics and temporal fractional diffusion in a bulk metallic glass

Glassy solids evolve towards lower-energy structural states by physical aging. This can be characterized by structural relaxation times, the assessment of which is essential for understanding the glass’ time-dependent property changes. Conducted over short times, a continuous increase of relaxation times with time is seen, suggesting a time-dependent dissipative transport mechanism. By focusing on micro-structural rearrangements at the atomic-scale, we demonstrate the emergence of sub-diffusive anomalous transport and therefore temporal fractional diffusion in a metallic glass, which we track via coherent x-ray scattering conducted over more than 300,000 s. At the longest probed decorrelation times, a transition from classical stretched exponential to a power-law behavior occurs, which in concert with atomistic simulations reveals collective and intermittent atomic motion. Our observations give a physical basis for classical stretched exponential relaxation behavior, uncover a new power-law governed collective transport regime for metallic glasses at long and practically relevant time-scales, and demonstrate a rich and highly non-monotonous aging response in a glassy solid, thereby challenging the common framework of homogeneous aging and atomic scale diffusion.

42 ENGINEERING↗

DOE OSTI2023

Rapid, Approximate Multi-Axis Vibration Testing [Thesis]

The aerospace industry uses vibration shaker tables to perform component durability testing. In these tests a component, piece of equipment, or entire system is attached to a shaker table where it is subjected to dynamic excitation. The goal is to understand how the article under test will perform in its service environment without having to run it through its entire service life via field testing. In a vibration test, an aerospace system or component is qualified if it is shown to survive a test meant to replicate its lifetime service conditions. The test is designed based on recorded field data. To develop a test, a system is taken through all of its intended environments, e.g., transportation, launch, and reentry. Acceleration data measured from these environments is then brought back to the lab and imported into a shaker table controller. The controller then drives a vibration test intended to mimic the acceleration conditions experienced by the system or specific components of the system in the field. However, it is often difficult to match the measured field response in a lab test. This is largely due to the test’s boundary conditions and excitation methods. In a lab test, a shaker table is the excitation source. The two most common shaker table types, differentiated by their number of independent degrees of freedom, are single-axis and multi-axis shaker tables. Multi-axis shakers have the ability to reproduce service environments more realistically, as real accelerations inevitably produce multiple degrees of freedom of excitation simultaneously. Figure 1 depicts a generic multi-axis testing setup on a three-axis shaker table. Often multi-axis tests use six-degree-of-freedom (6DOF) shaker tables. Yet multi-axis shakers are not yet common in the aerospace industry due in part to their high cost and the difficulty for shaker controllers to handle the added complexity. Single-axis shaker tables are much more common. They are not as expensive to purchase and have a wide range of control software options.

42 ENGINEERING↗

DOE OSTI2022

Realizing "Net-Zero-Carbon" Sustainable Aviation Fuel

The aviation industry needs renewable and fungible jet fuel - commonly referred to as sustainable aviation fuel (SAF) - to minimize emissions and increase efficiencies. SAF can displace the same, if not more, CO2 equivalent emissions (CO2eq), reduce contrail formation, and increase engine-aircraft efficiencies. Flight represents ~10% of transportation greenhouse gas emissions, with the global consumption of ~400 billion liters of fossil jet fuel in 2019 releasing over 900 million tons of CO2eq. Even with impacts from the COVID-19 global pandemic, the aviation sector is projected to grow with passenger miles expected to double by 2050, relative to 2010. As such, there is an urgent need to produce drop-in aviation fuel from renewables with a dramatically lower carbon footprint.

biojet↗

DOE OSTI2020

Generation of a highly attenuated strain of Pseudomonas aeruginosa for commercial production of alginate

Alginate is an important polysaccharide that is commonly used as a gelling agent in foods, cosmetics and healthcare products. Currently, all alginate used commercially is extracted from brown seaweed. However, with environmental changes such as increasing ocean temperature and the increasing number of biotechnological uses of alginates with specific properties, there is an emerging need for more reliable and customizable sources of alginate. An alternative to seaweed for alginate production is Pseudomonas aeruginosa, a common Gram-negative bacterium that can form alginate containing biofilms. However, P. aeruginosa is an opportunistic pathogen that can cause life-threatening infections in immunocompromised patients. Therefore, we sought to engineer a non-pathogenic P. aeruginosa strain that is safe for commercial production of alginate. Using a homologous recombination strategy, we sequentially deleted five key pathogenicity genes from the P. aeruginosa chromosome, resulting in the marker-free strain PGN5. Intraperitoneal injection of mice with PGN5 resulted in 0% mortality, while injection with wild-type P. aeruginosa resulted in 95% mortality, providing evidence that the systemic virulence of PGN5 is highly attenuated. Importantly, PGN5 produces large amounts of alginate in response to overexpression of MucE, an activator of alginate biosynthesis. The alginate produced by PGN5 is structurally identical to alginate produced by wildtype P. aeruginosa, indicating that the alginate biosynthetic pathway remains functional in this modified strain. The genetic versatility of P. aeruginosa will allow us to further engineer PGN5 to produce alginates with specific chemical compositions and physical properties to meet different industrial and biomedical needs.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Coupled diffusion-deformation-damage model for polymers used in hydrogen infrastructure

The soft materials used in the infrastructure of hydrogen storage and distribution systems are vulnerable because exposure to high-pressure hydrogen can lead to mechanical damage and property degradation. Some materials, such as polymers, can undergo mechanical failure due to a phenomenon wherein hydrogen gas diffuses through the polymer chains and occupies preexisting cavities or voids inside the polymer material. If the hydrogen gas pressure is reduced more quickly than hydrogen can diffuse back out of the polymer which is necessary for some applications, the trapped hydrogen gas instead escapes by rupturing the material, causing surface blistering or permanent damage. In this study, a continuum mechanics-based fully coupled diffusion-deformation model with damage is developed to predict the stress distribution and damage propagation while the polymer undergoes rapid decompression failure. The hyperelastic material model, along with the maximum principal strain failure theory, was chosen for this study as it represents the nonlinear material response with brittle failure observed in uniaxial tensile tests perfectly. EPDM polymer was chosen for this study because of its commercial availability and common use in hydrogen storage and distribution system. It has superior mechanical properties, high and low temperature resistance, and certain compounds work well in hydrogen gas. This work is useful for design engineers to alter the parameters while manufacturing polymer composites to increase their performance in a high-pressure hydrogen environment.

Kulkarni, Shank S.↗

DOE OSTI2024

Recognizing Institutions that Prepare Students for 21st Century Building Careers

Buildings play a significant role in reaching the White House's goal of a net-zero emissions economy by 2050, so it is critical that building professionals are prepared to design and construct high-efficiency, low-carbon buildings powered by renewables. The U.S. Department of Energy's Zero Energy Design Designation recognizes post-secondary academic programs that prepare students for 21st century building careers. ZEDD is a three-year designation, and as of 2023 almost 40 programs of study from more than 25 institutions have been recognized and supported by DOE for their great work. The University of Cincinnati received the ZEDD designation for the Net Zero Energy Design Track in Architectural Engineering Program. Tracks, majors, minors, and certificates are all eligible for ZEDD. In recent interviews with faculty from the University of Cincinnati and Appalachian State University about their experiences with ZEDD, many common topics came up. Both faculty members mentioned their students who graduate with ZEDD on their resume are often the only people in their future design firms who understand and can create net zero energy designs.

buildings↗

DOE OSTI2020

Programmable gene regulation for metabolic engineering using decoy transcription factor binding sites

Abstract Transcription factor decoy binding sites are short DNA sequences that can titrate a transcription factor away from its natural binding site, therefore regulating gene expression. In this study, we harness synthetic transcription factor decoy systems to regulate gene expression for metabolic pathways in Escherichia coli. We show that transcription factor decoys can effectively regulate expression of native and heterologous genes. Tunability of the decoy can be engineered via changes in copy number or modifications to the DNA decoy site sequence. Using arginine biosynthesis as a showcase, we observed a 16-fold increase in arginine production when we introduced the decoy system to steer metabolic flux towards increased arginine biosynthesis, with negligible growth differences compared to the wild type strain. The decoy-based production strain retains high genetic integrity; in contrast to a gene knock-out approach where mutations were common, we detected no mutations in the production system using the decoy-based strain. We further show that transcription factor decoys are amenable to multiplexed library screening by demonstrating enhanced tolerance to pinene with a combinatorial decoy library. Our study shows that transcription factor decoy binding sites are a powerful and compact tool for metabolic engineering.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

An Innovative High Throughput Genome Releaser for Rapid and Efficient PCR Screening

High-throughput PCR screening is vital in synthetic biology and metabolic engineering as it allows researchers to rapidly analyze and detect numerous targeted genetic mutation in the genome. Current challenges for high-throughput PCR screening in synthetic biology include efficiently preparing genomic DNA, optimizing protocols for diverse sample types, managing contamination risks, and effectively analyzing the large volumes of data generated while ensuring consistent and accurate results. In this study, we present the development of a High Throughput Genome Releaser (HTGR), an innovative device addressing common challenges in screening PCR. This genome DNA releaser is designed based on a squash method for rapid, cost-effective, and efficient DNA release, optimized for subsequent PCR reactions. After experimenting with various synthetic materials, we selected a plastic that closely replicates the smooth surface and compression properties of microscope slides, ensuring reliable performance. We engineered a device featuring a 96-Well Plate and a shear applicator, operable both manually and automatically, and compatible with standard liquid-handling robot platform. This compatibility enhances ease of use in high-throughput PCR workflows. Additionally, we developed software to support its automatic functions. Our results demonstrated that the specially engineered 96-Well Plate and HTGR can effectively squash fungal spores , which release enough genome DNA for PCR screening. The genome releaser facilitates the preparation of PCR-amplifiable genomic DNA substrate from 96 samples within minutes, eliminates the need for extraction buffers, and is adaptable to a wide range of microorganisms and cells, which could significantly advance biomanufacturing processes.

Yuan, Guoliang [BATTELLE (PACIFIC NW LAB)]↗

DOE OSTI2020

A control-oriented combustion model framework for compression ignition engines operating on low-reactivity fuel

This work focuses on zero-dimensional modeling of the heat release rate in a compression ignition engine operating on gasoline-like fuels. Due to the properties of gasoline, such as high volatility and longer ignition delay than diesel, the injection strategies can vary significantly from the operation with conventional diesel fuel. Different injection strategies are commonly used to achieve varying degrees of in-cylinder stratification in order to shape the combustion event and maximize efficiency. The proposed zero-dimensional combustion model was developed to account for the different stages in combustion caused by the fuel stratification. As the ignition delay model is an integral part of the entire combustion process and significantly affects the prediction accuracy, special attention has been paid to local phenomena influencing ignition delay. A one-dimensional spray model by Musculus and Kattke was employed in conjunction with a Lagrangian tracking approach in order to estimate the local air–fuel ratio within the spray tip, as a proxy for reactivity. The local air–fuel ratio, in-cylinder temperature and pressure were used in an integral fashion to estimate the ignition delay. Heat release rates were modeled using first-order non-linear differential equations. The proposed combustion model was validated against experimental data of a heavy-duty compression ignition engine with up to three injection events at mostly 1038 r/min and 14 bar brake mean effective pressure. Further validation of the model was carried out at other engine loads and speeds. Model prediction errors in CA50 of less than 1 °CA across all conditions were found. Modeling results of other combustion metrics such as combustion duration and indicated mean effective pressure are also highly satisfactory. In addition, the model has been shown to be capable of estimating the ringing intensity for most conditions.

Pamminger, Michael↗

DOE OSTI2022

A colorimetric method to measure in vitro nitrogenase functionality for engineering nitrogen fixation

Biological nitrogen fixation (BNF) is the reduction of N 2 into NH 3 in a group of prokaryotes by an extremely O 2 -sensitive protein complex called nitrogenase. Transfer of the BNF pathway directly into plants, rather than by association with microorganisms, could generate crops that are less dependent on synthetic nitrogen fertilizers and increase agricultural productivity and sustainability. In the laboratory, nitrogenase activity is commonly determined by measuring ethylene produced from the nitrogenase-dependent reduction of acetylene (ARA) using a gas chromatograph. The ARA is not well suited for analysis of large sample sets nor easily adapted to automated robotic determination of nitrogenase activities. Here, we show that a reduced sulfonated viologen derivative (S 2 V red ) assay can replace the ARA for simultaneous analysis of isolated nitrogenase proteins using a microplate reader. We used the S 2 V red to screen a library of NifH nitrogenase components targeted to mitochondria in yeast. Two NifH proteins presented properties of great interest for engineering of nitrogen fixation in plants, namely NifM independency, to reduce the number of genes to be transferred to the eukaryotic host; and O 2 resistance, to expand the half-life of NifH iron-sulfur cluster in a eukaryotic cell. This study established that NifH from Dehalococcoides ethenogenes did not require NifM for solubility, [Fe-S] cluster occupancy or functionality, and that NifH from Geobacter sulfurreducens was more resistant to O 2 exposure than the other NifH proteins tested. It demonstrates that nitrogenase components with specific biochemical properties such as a wider range of O 2 tolerance exist in Nature, and that their identification should be an area of focus for the engineering of nitrogen-fixing crops.

59 BASIC BIOLOGICAL SCIENCES↗