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DOE OSTI2020

Reactivity, Mechanism, and Assembly of the Alternative Nitrogenases

Biological nitrogen fixation is catalyzed by the enzyme nitrogenase, which facilitates the cleavage of the relatively inert triple bond of N 2 . Nitrogenase is most commonly associated with the molybdenum–iron cofactor called FeMoco or the M-cluster, and it has been the subject of extensive structural and spectroscopic characterization over the past 60 years. In the late 1980s and early 1990s, two “alternative nitrogenase” systems were discovered, isolated, and found to incorporate V or Fe in place of Mo. These systems are regulated by separate gene clusters; however, there is a high degree of structural and functional similarity between each nitrogenase. Limited studies with the V- and Fe-nitrogenases initially demonstrated that these enzymes were analogously active as the Mo-nitrogenase, but more recent investigations have found capabilities that are unique to the alternative systems. In this review, we will discuss the reactivity, biosynthetic, and mechanistic proposals for the alternative nitrogenases as well as their electronic and structural properties in comparison to the well-characterized Mo-dependent system. Studies over the past 10 years have been particularly fruitful, though key aspects about V- and Fe-nitrogenases remain unexplored.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Application of the metabolic modeling pipeline in KBase to categorize reactions, predict essential genes, and predict pathways in an isolate genome

The DOE Systems Biology Knowledgebase (KBase) platform offers a range of powerful tools for the reconstruction, refinement, and analysis of genome-scale metabolic models built from microbial isolate genomes. In this chapter, we describe and demonstrate these tools in action with an analysis of isoprene production in the Bacillus subtilis DSM genome. Two different methods are applied to build initial metabolic models for the DSM genome, then the models are gapfilled in three different growth conditions. Next, flux balance analysis (FBA) and flux variability analysis (FVA) techniques are applied to both study the growth of these models in minimal media and classify reactions within each model based on essentiality and functionality. The models are applied with the FBA method to predict essential genes, which are then compared to an updated list of essential genes obtained for B. subtilis 168, a very similar strain to the DSM isolate. The models are also applied to simulate Biolog growth conditions, and these results are compared with Biolog data collected for B. subtilis 168. Finally, the DSM metabolic models are applied to explore the pathways and genes responsible for producing isoprene in this strain. These studies demonstrate the accuracy and utility of models generated from the KBase pipelines, as well as exploring the tools available for analyzing these models.

DOE knowledgebase↗

DOE OSTI2021

Application of the Metabolic Modeling Pipeline in KBase to Categorize Reactions, Predict Essential Genes, and Predict Pathways in an Isolate Genome

Allen, Benjamin↗

DOE OSTI2025

Coupling to rotational manifolds to improve gas-phase pump–probe spectroscopic models

The physical picture of gas-phase optical transitions is normally presented as an isolated two-level system balanced by upward and downward processes. Isolated models assume a phenomenological treatment of collisional dephasing but do not strictly account for collisional population exchange with the rotational baths. While this assumption is valid under low-intensity conditions, where excitation is rate-limiting, isolated models can deviate from Beer’s Law at sufficient pressures and monochromatic intensities when both collisional broadening and power broadening are comparable to (or greater than) lifetime broadening, which are not uncommon conditions for cavity enhanced spectroscopies in the mid-IR spectral range. Although this problem has been addressed by rate-equation models for linear absorption measurements, a general treatment for multi-level quantum mechanical models suitable for non-linear absorption measurements (two-photon/two-color/pump–probe) is lacking. Isolated models require physical parameter inputs that disagree with expected values by at least an order of magnitude. These non-physical models undermine the ability to predict non-linear signal strengths under untested conditions and thereby limit the potential to optimize the sensitivity of non-linear spectroscopies and to expand their analytical applications (e.g., new analytes and/or buffer gases, changes in cavity free-spectral-range, changes in intracavity powers or wavelengths, and accurate investigation of physical phenomena). In this study, we derive bath-coupled models for gaseous pump–probe spectroscopy by application of the quantum Lindblad equation and detailed balance. Bath-coupled models are shown to fit data consistently across variations in intensity and agree with all physically expected values.

Cavity ring-down spectroscopy↗

DOE OSTI2023

Insights into the physiological and genomic characterization of three bacterial isolates from a highly alkaline, terrestrial serpentinizing system

The terrestrial serpentinite-hosted ecosystem known as “The Cedars” is home to a diverse microbial community persisting under highly alkaline (pH ~ 12) and reducing (Eh < -550 mV) conditions. This extreme environment presents particular difficulties for microbial life, and efforts to isolate microorganisms from The Cedars over the past decade have remained challenging. Herein, we report the initial physiological assessment and/or full genomic characterization of three isolates: Paenibacillus sp. Cedars (‘Paeni-Cedars’), Alishewanella sp. BS5-314 (‘Ali-BS5-314’), and Anaerobacillus sp. CMMVII (‘Anaero-CMMVII’). Paeni-Cedars is a Gram-positive, rod-shaped, mesophilic facultative anaerobe that grows between pH 7–10 (minimum pH tested was 7), temperatures 20–40°C, and 0–3% NaCl concentration. The addition of 10–20 mM CaCl 2 enhanced growth, and iron reduction was observed in the following order, 2-line ferrihydrite > magnetite > serpentinite ~ chromite ~ hematite. Genome analysis identified genes for flavin-mediated iron reduction and synthesis of a bacillibactin-like, catechol-type siderophore. Ali-BS5-314 is a Gram-negative, rod-shaped, mesophilic, facultative anaerobic alkaliphile that grows between pH 10–12 and temperatures 10–40°C, with limited growth observed 1–5% NaCl. Nitrate is used as a terminal electron acceptor under anaerobic conditions, which was corroborated by genome analysis. The Ali-BS5-314 genome also includes genes for benzoate-like compound metabolism. Anaero-CMMVII remained difficult to cultivate for physiological studies; however, growth was observed between pH 9–12, with the addition of 0.01–1% yeast extract. Anaero-CMMVII is a probable oxygen-tolerant anaerobic alkaliphile with hydrogenotrophic respiration coupled with nitrate reduction, as determined by genome analysis. Based on single-copy genes, ANI, AAI and dDDH analyses, Paeni-Cedars and Ali-BS5-314 are related to other species (P. glucanolyticus and A. aestuarii, respectively), and Anaero-CMMVII represents a new species. The characterization of these three isolates demonstrate the range of ecophysiological adaptations and metabolisms present in serpentinite-hosted ecosystems, including mineral reduction, alkaliphily, and siderophore production.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Isolation and characterization of 24 phages infecting the plant growth-promoting rhizobacterium Klebsiella sp. M5al

Bacteriophages largely impact bacterial communities via lysis, gene transfer, and metabolic reprogramming and thus are increasingly thought to alter nutrient and energy cycling across many of Earth’s ecosystems. However, there are few model systems to mechanistically and quantitatively study phage-bacteria interactions, especially in soil systems. Here, we isolated, sequenced, and genomically characterized 24 novel phages infectingKlebsiellasp. M5al, a plant growth-promoting, nonencapsulated rhizosphere-associated bacterium, and compared many of their features against all 565 sequenced, dsDNAKlebsiellaphage genomes. Taxonomic analyses revealed that theseKlebsiellaphages belong to three known phage families (Autographiviridae,Drexlerviridae, andStraboviridae) and two newly proposed phage families (CandidatusMavericviridaeand Ca.Rivulusviridae). At the phage family level, we found that core genes were often phage-centric proteins, such as structural proteins for the phage head and tail and DNA packaging proteins. In contrast, genes involved in transcription, translation, or hypothetical proteins were commonly not shared or flexible genes. Ecologically, we assessed the phages’ ubiquity in recent large-scale metagenomic datasets, which revealed they were not widespread, as well as a possible direct role in reprogramming specific metabolisms during infection by screening their genomes for phage-encoded auxiliary metabolic genes (AMGs). Even though AMGs are common in the environmental literature, only one of our phage families,Straboviridae, contained AMGs, and the types of AMGs were correlated at the genus level. Host range phenotyping revealed the phages had a wide range of infectivity, infecting between 1–14 of our 22 bacterial strain panel that included pathogenicKlebsiellaandRaoultellastrains. This indicates that not all capsule-independent Klebsiella phages have broad host ranges. Together, these isolates, with corresponding genome, AMG, and host range analyses, help build theKlebsiellamodel system for studying phage-host interactions of rhizosphere-associated bacteria.

Science & Technology - Other Topics↗

DOE OSTI2021

Evaluation of Centralized Model-Based FLISR in a Lab Setup: Preprint

Utilities are installing advanced distribution management systems (ADMS) around the globe to improve the sensing and control of distribution systems. ADMS is becoming a critical component to improve the resiliency and reliability of distribution systems. These management systems host a multitude of applications that can be used to sense, control, and operate distribution systems. Fault location, isolation, and service restoration (FLISR) is one of the ADMS applications that is critical to improving resilience during fault conditions. FLISR applications use smart, controllable devices that are installed in the distribution system for FLISR operation. These controllable devices include distributed energy resources (DER) and reclosers. Evaluating such ADMS applications before installation in the field can help de-risk the field implementation and avoid costly failures in the field. This paper presents a background on experimental setup that are typically used to evaluate ADMS applications. This is followed by briefly presenting the setup used to evaluate the FLISR application in an off-the-shelf ADMS tool. Finally, results from the evaluation experiments are presented.

94 GMLC - Grid Modernization Laboratory Consortium↗

DOE OSTI2023

Utah FORGE 1-2409: Zonal Isolation Solution for Geothermal Wells - Workshop Presentation

This is a presentation on the Zonal Isolation Solution for Geothermal Wells project by PetroQuip Energy Services, presented by VP of operations Robert Coon. The project's objective was to design and develop a multi-stage system for zonally isolating fluids inside and outside of geothermal well casings. This presentation was featured in the Utah FORGE R&D Annual Workshop on September 7, 2023. The workshop provided a valuable opportunity to explore the progress made in each of the 17 Research and Development projects funded under Solicitation 2020-1 which aim to enhance our understanding of the crucial factors influencing the development of Enhanced Geothermal Systems (EGS) reservoirs and resources.

15 GEOTHERMAL ENERGY↗

DOE OSTI2024

Residual resistance ratio measurement system for Nb 3 Sn wires extracted from Rutherford cables

Residual resistance ratio (RRR) of superconducting strands is an important parameter for magnet electrical stability. RRR serves as a measure of the low-temperature electrical conductivity of the copper within a conductor that has a copper stabilization matrix. For Nb 3 Sn, due to the need of a reaction heat treatment, the technical requirements for high quality measurements of strands extracted from Rutherford cables are particularly demanding. Quality of wire, cabling deformation, heat treatment temperature, heat treatment atmosphere, sample handling, and measurement methods can all affect the RRR. Therefore, as an integral part of the electrical quality control (QC) of Nb 3 Sn Rutherford cables manufactured at the Lawrence Berkeley National Laboratory, it was prudent that we established a RRR measurement system that can isolate the assessment of cable-fabrication-related impacts from sample preparation and measurement factors. Here we describe a bespoke cryocooler-based measurement system, capable of measuring RRR of over 80 samples in a single cooldown. The samples are mounted on custom-designed printed circuit boards that accommodate the shape of strands extracted from a Rutherford cable without added deformation, which we will show is critical in ensuring that the measurements accurately represent the RRR values of the conductor within the cable. Using this sample mounting solution, we routinely measure the overall RRR of the strand as well as individual intra-strand sections corresponding to both cable edges and cable broad faces with high reproducibility. Such measurements provide valuable information on the variation of RRR along the length of the strands as well as across strand productions and cable runs over time.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2021

Evaluation of Centralized Model Based FLISR in a Lab Setup

94 GMLC - Grid Modernization Laboratory Consortium↗

DOE OSTI2023

A Review of Distributed Secondary Control Architectures in Islanded-Inverter-Based Microgrids

The increasing energy demand, the shortage of energy resources, and the environmental challenges faced by conventional power-generation systems are some of the ongoing challenges faced by modern power systems. Therefore, many efforts have been made by the scientific community to develop comprehensive solutions to overcome these issues. For instance, current technological advances have allowed the integration of distributed generators into the power systems, promoting the use of microgrids to overcome these issues. However, the use of renewable distributed generators have introduced new challenges to the traditional control system schemes. To overcome these challenges, a hierarchical control approach has been proposed for distributed renewable sources. In other words, the control scheme have been divided into three hierarchical levels, primary, secondary, and tertiary, to overcome the new challenges present in modern power systems. Due to extensiveness of this topic, this overview is focused on secondary control systems, mainly for AC isolated microgrids. To improve the power quality of modern systems, several secondary control schemes have been proposed to overcome the well-known problem of frequency and voltage deviation. Some of these schemes have also introduced adequate active/reactive power sharing techniques to optimize the utilization of resources. Additionally, other secondary control schemes have also focused on reducing the communication load, to lower the network cost and adding robustness against communication problems. This article presents an insight of the different control techniques used to overcome power quality and communication problems. A comprehensive overview of distributed secondary control techniques for islanded microgrids is presented. In addition, the implementation of these techniques is explained in an orderly and sequential manner.

14 SOLAR ENERGY↗

DOE OSTI2022

Using discrete Bayesian networks for diagnosing and isolating cross-level faults in HVAC systems

Fault detection and diagnosis (FDD) technologies are critical to ensure satisfactory building performance, such as reducing energy wastes and negative impacts on occupant comfort and productivity. Existing FDD technologies mainly focus on component-level FDD solutions, which could lead to mis-diagnosis of cross-level faults in heating, ventilating, and air-conditioning (HVAC) systems. Cross-level faults are those faults that occur in one component or subsystem, but cause operational abnormalities in other components or subsystems, and result in a building level performance degradation. How to effectively diagnose the root cause of a cross-level fault is the focus of this study. Here, this paper presents a novel discrete Bayesian Network (DisBN)-based method for diagnosing cross-level faults in an HVAC system commonly used in commercial buildings. A two-level DisBN structure model is developed in this study. The parameters used in the DisBN model are obtained either from expert knowledge or through machine-learning strategies from normal system operation data. Meanwhile, the probability parameters are discretized to incorporate the uncertainties associated with typical expert knowledge. Thus, the developed DisBN method addresses the challenges many other BN based FDD methods face, i.e., the lack of fault data for BN parameter training. The developed DisBN represents causal relationships between a fault and its cross-level system impacts (i.e., fault symptoms or fault indicators) by considering how fault impacts propagate across different levels in an HVAC system. A weather and schedule information-based Pattern Matching (WPM) method is employed to automatically create WPM baseline data sets for each incoming real time snapshot data from the building systems. Consequently, BN inference and real-time diagnostics are achieved by comparing incoming snapshot data and the WPM baseline data set. The proposed method is evaluated using experimental fault data collected in a campus building. Fault diagnosis results demonstrate that the WPM-DisBN method is effective at locating the root causes of cross-level faults in an HVAC system.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2021

A tool for assessing demand side management and operating strategies for isolated microgrids

Globally, power system operators are exploring ways to leverage the capabilities of smart meters to implement fine-grained demand side management (DSM). Here this paper presents a new simulation tool to evaluate operating strategies for smart-meter-enabled (SME) islanded microgrids being advanced for sustainable rural electrification in emerging economies. Based on MATLAB/Simulink, the tool's component-level models of small microgrids can be easily configured. Alternative rule-based operating strategies are implemented with controllable supply and storage components as well as other components driven by external factors (e.g., weather and time of day). To account for the wide range of possible operating conditions in real-world applications, statistical metrics can be evaluated using Monte Carlo (MC) methods based on user-defined, time-dependent probability distributions for demands, supplies, and environmental variables. Features of the tool are demonstrated with case studies for a representative microgrid in rural Rwanda.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2023

A long path-length optical property measurement device for highly transparent detector media

Measurements of the optical properties of highly transparent liquids are necessary for large-scale detectors that seek to detect optical signatures in kiloton-scale or larger volumes. Detailed understanding of the attenuation and scattering properties of fill media is critical to the ability to accurately simulate detector performance, and yet is often unavailable until in-situ measurements can be performed. Moreover, in-situ measurements may rely on effective attenuation lengths or other approximations to characterize performance, rather than absolute measurements of attenuation and scattering. To better understand the optical properties of potential fill media and purification schemes, a system has been developed which provides simultaneous attenuation and differential scattering cross-section measurements for highly transparent liquids. This horizontal, adjustable path-length “long-arm” system provides excellent isolation from the atmosphere, a high degree of vibration insensitivity, and a simple and reliable method of calibration. Further, scattering measurements can be carried out simultaneously at ports along the beamline equipped with optics allowing the selection of scatter angle and polarization. This enables both reliable quantitative scatter measurements and phase-function separation. This system has been extensively tested using deionized (DI) water as a benchmark, and has demonstrated repeatable measurements of attenuation lengths exceeding 100 m and scattering lengths approaching 1 km.

47 OTHER INSTRUMENTATION↗

DOE OSTI2022

Acoustic focusing of microplastics in microfabricated and steel tube devices: An experimental study on the effects from particle size and medium density

The contamination of aquatic systems with microplastics is becoming a severe threat to living organisms. Microplastics found in the environment consist of a wide range of particle sizes thus give rise to several challenges to current purification methods. Acoustic focusing has been utilized as a particle concentrating method in biological and non-biological applications. In this study, we investigate the feasibility of using acoustic focusing technology to isolate microplastics in aqueous samples and find that a two-stage mechanism is essential to concentrate microplastics of wide size ranges of the same material. We demonstrate for the first time experimentally that when the particle size is comparable to the resonance wavelength, they deviate from typical pressure nodal focusing and show pressure antinodal focusing. Further, we have expanded microplastics isolation beyond microfluidic systems and demonstrate their extraction capabilities relatively at higher flow rates using microplastics of polystyrene, polyethylene, and polymethyl methacrylate ranging from 6 µm to 300 µm diameter and in devices fabricated with cylindrical steel tubes. We could extract 70% of microplastics smaller than 180 µm and 82% of microplastics greater than 180 µm in diameter from an aqueous sample at a flow rate of 12 mL/min. In conclusion, we demonstrate that small microplastics focus on acoustic pressure nodes regardless of the medium density. However, focusing of large microplastics of the same material depends on the medium density.

42 ENGINEERING↗

DOE OSTI2023

Design of a Multi-Chemistry Battery Pack System for Behind-the-Meter Storage Applications

Battery management systems (BMS) are essential for a battery pack's safe operation and longevity. This paper presents an active balancing method-based BMS for different cell chemistry structures to be used in behind-the-meter storage (BTMS) applications. The proposed system utilizes modular isolated dual active bridge (DAB) DC/DC converters to actively balance the battery pack through a low voltage (LV) bus. A supervisory controller monitors all the cell voltage, current, and state of charge (SOC) values. Based on the estimation of the SOCs, reference currents for the DAB converters are generated by the supervisory controller. Detailed modeling and the control approach of the modular DAB converters are presented in the paper. Moreover, the control strategy of the supervisory control is also analyzed. The proposed method and structure can be extended to any combination of the number of cells to design the battery pack. Simulation results are provided for a system consisting of three cells in parallel to form a cell block and three cell blocks in series to form the battery module. Experimental results are provided for three modular DAB converters operating with a LiFeMnPO4 prismatic cell with 3.2V, 20Ah rated values.

battery management systems↗

DOE OSTI2020

Success Using A Granular-Activated Carbon Filtration Swab to Rehabilitate Westbay{sup R} Multi-level Groundwater Monitoring Wells at the INL - 20544

In November 2015, tetrachloroethylene (PCE) was discovered in groundwater samples collected from a Westbay{sup R} multi-level groundwater monitoring well at the Idaho National Laboratory (INL).a Subsequent investigation determined that PCE was not present in the groundwater. The detected PCE was instead due to inadvertent contamination of the internal tubing fluid in the Westbay well-monitoring system, which is isolated from the surrounding groundwater. Further investigation showed that three of the 11 Westbay wells at the INL contained PCE-contaminated tubing fluid at concentrations above the U.S. Environmental Protection Agency's maximum contaminant level for drinking water (5 μg/L). Loose sediment at the bottom of some Westbay wells was also found to contain PCE; the three wells were then identified for rehabilitation as part of the INL well maintenance program. The unique construction of the Westbay wells - i.e., the small diameter (5.72 cm [2.25 in.]) and the depths of the tubing fluid ranging from 144.8 to 419 m (475 to 1,376 ft) below ground surface - posed unique challenges to the rehabilitation. Because the tubing fluid provides structural integrity, the fluid cannot be removed and then replaced without damaging the integrity of the Westbay well. Additionally, the small diameter of the systems and the associated depths limit the availability of equipment that can be used for the rehabilitation. After an evaluation of potential methods, it was determined that the use of an in-well, custom-fabricated, granular-activated-carbon filtration swab deployed via a wire line would provide the safest and most cost-effective method for rehabilitation. Westbay well rehabilitation started at well MIDDLE-2051 in late June 2018 and paused in December 2018 for the season. The PCE concentration in the tubing fluid at MIDDLE-2051 was initially reduced to a maximum concentration of 3.81 μg/L from a maximum of 642 μg/L, while the concentration of PCE in the sediment had been reduced from 5,360 to 2,270 μg/kg. Sampling was performed at MIDDLE-2051 again in August 2019, and the tubing fluid increased to a maximum concentration of 45.4 μg/L, while the concentration in the sediment decreased further to 1,890 μg/kg due to desorption of PCE from the sediment to the tubing fluid. Rehabilitation resumed at well MIDDLE-2050A in late August 2019, and the PCE concentration in the tubing fluid had been reduced to a maximum concentration of 19.0 μg/L. Although the method has been shown to be time-consuming, it has proven to be effective and safe for personnel performing the work and to the integrity of the well. Future sample data results at all wells will help determine an estimated completion of the rehabilitation. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2024

Differential cross-sections for events with missing transverse momentum and jets measured with the ATLAS detector in 13 TeV proton-proton collisions

Measurements of inclusive, differential cross-sections for the production of events with missing transverse momentum in association with jets in proton-proton collisions at √s = 13 TeV are presented. The measurements are made with the ATLAS detector using an integrated luminosity of 140 fb –1 and include measurements of dijet distributions in a region in which vector-boson fusion processes are enhanced. They are unfolded to correct for detector resolution and efficiency within the fiducial acceptance, and are designed to allow robust comparisons with a wide range of theoretical predictions. A measurement of differential cross sections for the Z → νν process is made. The measurements are generally well-described by Standard Model predictions except for the dijet invariant mass distribution. Auxiliary measurements of the hadronic system recoiling against isolated leptons, and photons, are also made in the same phase space. Ratios between the measured distributions are then derived, to take advantage of cancellations in modelling effects and some of the major systematic uncertainties. These measurements are sensitive to new phenomena, and provide a mechanism to easily set constraints on phenomenological models. To illustrate the robustness of the approach, these ratios are compared with two common Dark Matter models, where the constraints derived from the measurement are comparable to those set by dedicated detector-level searches.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗