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DOE OSTI2020

A missense variant remote from the active site impairs stability of human phosphoglucomutase 1

Abstract Missense variants of human phosphoglucomutase 1 (PGM1) cause the inherited metabolic disease known as PGM1 deficiency. This condition is categorised as both a glycogen storage disease and a congenital disorder of glycosylation. Approximately 20 missense variants of PGM1 are linked to PGM1 deficiency, and biochemical studies have suggested that they fall into two general categories: those affecting the active site and catalytic efficiency, and those that appear to impair protein folding and/or stability. In this study, we characterise a novel variant of Arg422, a residue distal from the active site of PGM1 and the site of a previously identified disease‐related variant (Arg422Trp). In prior studies, the R422W variant was found to produce insoluble protein in a recombinant expression system, precluding further in vitro characterisation. Here we investigate an alternative variant of this residue, Arg422Gln, which is amenable to experimental characterisation presumably due to its more conservative physicochemical substitution. Biochemical, crystallographic, and computational studies of R422Q establish that this variant causes only minor changes in catalytic efficiency and 3D structure, but is nonetheless dramatically reduced in stability. Unexpectedly, binding of a substrate analog is found to further destabilise the protein, in contrast to its stabilising effect on wild‐type PGM1 and several other missense variants. This work establishes Arg422 as a lynchpin residue for the stability of PGM1 and supports the impairment of protein stability as a pathomechanism for variants that cause PGM1 deficiency. Synopsis Biochemical and structural studies of a missense variant far from the active site of human PGM1 identify a residue with a key role in enzyme stability.

Stiers, Kyle M.↗

DOE OSTI2024

2023 Southeast Decarbonization Workshop

Decarbonization refers to a large-scale shift away from fossil fuel sources for energy production and toward energy sources, energy end-use practices, and land management approaches that do not result in a net increase of carbon dioxide in the atmosphere. Decarbonization in the Southeastern United States is distinguished from that of other regions in the country by its potential impact on historically underserved populations and the ways this region’s human–environmental systems are predicted to fare in a climate-altered world. In parallel, ensuring a clean energy transition requires the ability to engage entire communities that are motivated to learn, build, and encourage the spread of so-called clean tech. In contrast to other technology trends from the past century, the foundation of clean tech is a shared sense of purpose—a collective strategy to mitigate the threats of climate change and support a better environment for everyone. As seen in the Office of Science and Technology Policy’s (OSTP’s) Net-Zero Technology Action Plan (2023), decarbonization is best accelerated by simultaneous investments in Innovation, Demonstration, and Deployment of technology in tandem with intentional policy and community-based solutions. The 2023 Southeast Decarbonization Workshop, hosted by the Georgia Institute of Technology (Georgia Tech) and Oak Ridge National Laboratory (ORNL), aimed to bring together members of our communities and a group of regional experts to strategize about opportunities in this important area, as well as to incorporate the important pillar of System Interactions to bridge the gap between clean tech’s intent and its impact.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

ReVise: A Human-AI Interface for Incremental Algorithmic Recourse

The recent adoption of artificial intelligence in socio-technical systems raises concerns about the black-box nature of the resulting decisions in fields such as hiring, finance, admissions, etc. If data subjects—such as job applicants, loan applicants, and students—receive an unfavorable outcome, they may be interested in algorithmic recourse, which involves updating certain features to yield a more favorable result when re-evaluated by algorithmic decision-making. Unfortunately, when individuals do not fully understand the incremental steps needed to change their circumstances, they risk following misguided paths that can lead to significant, long-term adverse consequences. Existing recourse approaches focus exclusively on the final recourse goal but neglect the possible incremental steps to reach the goal with real-life constraints, user preferences, and model artifacts. To address this gap, we formulate a visual analytic workflow for incremental recourse planning in collaboration with AI/ML experts and contribute an interactive visualization interface that helps data subjects efficiently navigate the recourse alternatives and make an informed decision. We also present one of the many usage scenarios, developed during exploratory feedback sessions with twelve graduate students using a real-world dataset, which demonstrates that our approach can be instrumental for data subjects in choosing a suitable recourse path.

algorithmic recourse↗

DOE OSTI2020

Potential for Transport of Cesium as Bio-colloids in a High Ionic Strength System

The Waste Isolation Pilot Plant (WIPP) is a deep geologic repository for long-term disposal of transuranic, radioactive waste that is a byproduct from the nation's nuclear defense program. Most likely release scenario → human intrusion (potentially through drilling) (US DOE 1995; 1996). Brine may proceed through the Rustler formation (the most transmissive layer) (Perkins et al., 1999). There is a need to investigate halophilic microbes including their mobility in the Rustler formation and the potential for enhancing transport of cesium as a bio-colloid. Objectives: To quantify the change in mobility of Cs by interaction with microbes (Chromohalobacter) that may be present near Waste Isolation Pilot Plant. What is Chromohalobacter?: a halophilic microbe, isolated from near the WIPP site, able to thrive in the high salt concentrations relevant to the repository. Does the microbe growth phase effect uptake of Cs? Experiments conducted with actively growing and stationary phase Chromohalobacter. Uptake may differ if Cs{sup +} is mistaken for K{sup +} in an actively growing (Log) phase versus stationary phase microbes (not actively reproducing). Materials: 1'' Teflon column packed with 1 gram of dolomite [355-500 μm, CaMg(CO{sub 3}){sub 2}] connected to a syringe pump and fraction collector via Teflon tubing. Chromohalobacter (100 million cells/mL) and dolomite collected near the WIPP. Synthetic brine - 15% NaCl (w/v ∼2.78 M) + 3 mM NaHCO{sub 3}. Methodology: Negative Control 5,000 ppb Cs initially injected into mini-columns with brine. Injection solution was then switched to only brine. Cs Experiments with Stationary Phase Chromo: Set 1: Viable stationary Chromo injected into minicolumns after reaction with 200 ppb Cs. Injection solution was then switched to only brine (without Cs or microbes). Set 2: Stressed stationary Chromo initially injected into mini-columns after reaction with 200 ppb Cs. Then, switched to brine only. Cs Experiments with Log phase Chromo: Set 1: Chromo injected into mini-columns after reaction with 5,000 ppb Cs. Injection then switched to only brine (without Cs or microbes). Set 2: Chromo grown with 5,000 ppb Cs and spiked with additional Cs before injection into columns. Preliminary Conclusions: Cs was not taken up or mobilized by Chromohalobacter in the actively growing or stationary phases or under stressed conditions. Competition may have occurred between Cs and K{sup +} at lower ionic strength, significantly greater concentrations of K{sup +} were present. Results suggest that Chromohalobacter can selectively uptake K{sup +} in the presence of Cs{sup +}. Future Research: K{sup +} and Cs{sup +} uptake will be monitored at high ionic strength in K{sup +} depleted media to consider uptake of Cs in the absence of K.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2020

Twist again: Dynamically and reversibly controllable chirality in liquid crystalline elastomer microposts

Photoresponsive liquid crystalline elastomers (LCEs) constitute ideal actuators for soft robots because their light-induced macroscopic shape changes can be harnessed to perform specific articulated motions. Conventional LCEs, however, do not typically exhibit complex modes of bending and twisting necessary to perform sophisticated maneuvers. Here, we model LCE microposts encompassing side-chain mesogens oriented along a magnetically programmed nematic director, and azobenzene cross-linkers, which determine the deformations of illuminated posts. On altering the nematic director orientation from vertical to horizontal, the post’s bending respectively changes from light-seeking to light-avoiding. Moreover, both modeling and subsequent experiments show that with the director tilted at 45°, the initially achiral post reversibly twists into a right- or left-handed chiral structure, controlled by the angle of incident light. We exploit this photoinduced chirality to design “chimera” posts (encompassing two regions with distinct director orientations) that exhibit simultaneous bending and twisting, mimicking motions exhibited by the human musculoskeletal system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Special Observing Period (SOP) data for the Year of Polar Prediction site Model Intercomparison Project (YOPPsiteMIP)

The rapid changes occurring in the polar regions require an improved understanding of the processes that are driving these changes. At the same time, increased human activities such as marine navigation, resource exploitation, aviation, commercial fishing, and tourism require reliable and relevant weather information. One of the primary goals of the World Meteorological Organization's Year of Polar Prediction (YOPP) project is to improve the accuracy of numerical weather prediction (NWP) at high latitudes. During YOPP, two Canadian “supersites” were commissioned and equipped with new ground-based instruments for enhanced meteorological and system process observations. Additional pre-existing supersites in Canada, the United States, Norway, Finland, and Russia also provided data from ongoing long-term observing programs. These supersites collected a wealth of observations that are well suited to address YOPP objectives. In order to increase data useability and station interoperability, novel Merged Observatory Data Files (MODFs) were created for the seven supersites over two Special Observing Periods (February to March 2018 and July to September 2018). All observations collected at the supersites were compiled into this standardized NetCDF MODF format, simplifying the process of conducting pan-Arctic NWP verification and process evaluation studies. This paper describes the seven Arctic YOPP supersites, their instrumentation, data collection and processing methods, the novel MODF format, and examples of the observations contained therein. MODFs comprise the observational contribution to the model intercomparison effort, termed YOPP site Model Intercomparison Project (YOPPsiteMIP). All YOPPsiteMIP MODFs are publicly accessible via the YOPP Data Portal (Whitehorse: https://doi.org/10.21343/a33e-j150, Huang et al., 2023a; Iqaluit: https://doi.org/10.21343/yrnf-ck57, Huang et al., 2023b; Sodankylä: https://doi.org/10.21343/m16p-pq17, O'Connor, 2023; Utqiagvik: https://doi.org/10.21343/a2dx-nq55, Akish and Morris, 2023c; Tiksi: https://doi.org/10.21343/5bwn-w881, Akish and Morris, 2023b; Ny-Ålesund: https://doi.org/10.21343/y89m-6393, Holt, 2023; and Eureka: https://doi.org/10.21343/r85j-tc61, Akish and Morris, 2023a), which is hosted by MET Norway, with corresponding output from NWP models.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

SNAPSHOT USA 2020: A second coordinated national camera trap survey of the United States during the COVID-19 pandemic

Managing wildlife populations in the face of global change requires regular data on the abundance and distribution of wild animals, but acquiring these over appropriate spatial scales in a sustainable way has proven challenging. Here, in this study, we present the data from Snapshot USA 2020, a second annual national mammal survey of the USA. This project involved 152 scientists setting camera traps in a standardized protocol at 1485 locations across 103 arrays in 43 states for a total of 52,710 trap-nights of survey effort. Most (58) of these arrays were also sampled during the same months (September and October) in 2019, providing a direct comparison of animal populations in 2 years that includes data from both during and before the COVID-19 pandemic. All data were managed by the eMammal system, with all species identifications checked by at least two reviewers. In total, we recorded 117,415 detections of 78 species of wild mammals, 9236 detections of at least 43 species of birds, 15,851 detections of six domestic animals and 23,825 detections of humans or their vehicles. Spatial differences across arrays explained more variation in the relative abundance than temporal variation across years for all 38 species modeled, although there are examples of significant site-level differences among years for many species. Temporal results show how species allocate their time and can be used to study species interactions, including between humans and wildlife. These data provide a snapshot of the mammal community of the USA for 2020 and will be useful for exploring the drivers of spatial and temporal changes in relative abundance and distribution, and the impacts of species interactions on daily activity patterns. There are no copyright restrictions, and please cite this paper when using these data, or a subset of these data, for publication.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Critical Literature Review of Quantitative Sustainability Assessment Methods for the Circular Economy

The circular economy (CE) has been proposed to be an operational framework for sustainable development that decouples economic growth from resource consumption. The CE ambition is to maximize the retention of value in products, materials, and resources in the economy over time with the help of CE strategies such as selling a service rather than a product, reusing and repairing products or their components, and recycling. The social, economic, and environmental performances of CE strategies need to be measured against their linear counterparts to avoid strategies that increase circularity but have other unintended externalities. However, there is currently no tool specifically designed to compare circular to linear systems and, thus, various methods from different fields have been applied. This session aims at reviewing, contrasting, and critiquing different methods that have been applied to assess the CE until now, along with an up to date state of the science in this field. Methods from the industrial ecology field have most often been applied to study the CE. However, the transition to CE involves both technological improvements as well as social changes. New business models such as collaborative consumption models (e.g., Uber or Airbnb) are examples of the new patterns of production and consumption of the CE, which may be difficult to analyze from a purely industrial ecology perspective. Methods from complexity science and humanities could therefore complement the industrial ecology perspective to extend the scope of the analysis. Such an approach could also answer a longstanding criticism of the CE which, in contrast with sustainability, solely focuses on the environment and the economy. Moreover, the hybridization of two or more existing methods can yield additional capabilities, which may enable the exploration of additional CE-related research questions. The 90 minutes session will have several presentations and conclude with a moderated, interactive panel discussion on how methods from different fields could be combined to harness their relative strengths.

circular economy↗

DOE OSTI2020

Hydrogen Risk Assessment Models (HyRAM) (Version 3.0 Technical Reference Manual)

The HyRAM software toolkit provides a basis for conducting quantitative risk assessment and consequence modeling for hydrogen infrastructure and transportation systems. HyRAM is designed to facilitate the use of state-of-the-art science and engineering models to conduct robust, repeatable assessments of hydrogen safety, hazards, and risk. HyRAM includes generic probabilities for hydrogen equipment failures, probabilistic models for the impact of heat flux on humans and structures, and computationally and experimentally validated first-order models of hydrogen release and flame physics. HyRAM integrates deterministic and probabilistic models for quantifying accident scenarios, predicting physical effects, and characterizing hydrogen hazards (thermal effects from jet fires, overpressure effects from deflagrations), and assessing impact on people and structures. HyRAM is developed at Sandia National Laboratories for the U.S. Department of Energy to increase access to technical data about hydrogen safety and to enable the use of that data to support development and revision of national and international codes and standards. HyRAM is a research software in active development and thus the models and data may change. This report will be updated at appropriate developmental intervals. This document provides a description of the methodology and models contained in the HyRAM version 3.0. HyRAM 3.0 includes the new ability to model cryogenic hydrogen releases from liquid hydrogen systems, using a different property calculation method and different equations of state. Other changes include modifications to the ignition probability calculations, component leak frequency calculations, and addition of default impulse data.

08 HYDROGEN↗

DOE OSTI2026

Ecosystems for Scientific Computing in the Age of AI

Scientific computing is at an inflection point. Artificial intelligence (AI) is reshaping how scientific software is developed, how teams collaborate, how projects are governed, and how the next generation is trained. Drawing on insights from a 2025 workshop report, this article argues that the future of discovery will depend on agile, robust ecosystems built through socio-technical co-design—the intentional integration of technical and human systems. This perspective is essential for ensuring that future scientific computing remains trustworthy, sustainable, and scalable. It combines advances in AI, high-performance computing, and software with new models for cross-disciplinary collaboration, education, and workforce development. Key recommendations include building modular, trustworthy AI-enabled software ecosystems; enabling teams to integrate AI into scientific workflows while preserving human creativity, integrity, and rigor; and developing adaptive training pathways that keep pace with rapid technological change. By sharing these perspectives, we hope to stimulate broader community dialogue and encourage coordinated action.

AI↗

DOE OSTI2020

Quantifying cover crop effects on soil health and productivity

The dataset presented here supports the research paper entitled “A calculator to quantify cover crop effects on soil health and productivity”. Soil health (sometimes used synonymously with soil quality) is a concept that describes soil as a living system to sustain plants, animals, and human. Soil physical, chemical, and biological properties, along with their interactions, are required to quantify soil health. The use of cover crops in agricultural rotations may enhance soil health, yet there has been little progress in understanding how external factors such as climate, soil type, and agronomic practices affect soil and cash crop responses. In response, this dataset compiles measurements from 281 studies and provides an analysis of field-measured changes in 38 soil health indicators due to cover crop usage. Environmental and background indicators were also compiled to assess how climatic and management practices affect soil and cash crop responses to cover crops, with specific categories including climate type (tropical, arid, temperate, and continental), soil texture (coarse, medium, and fine), cover crop type (legume, grass, multi-species mixture, and other), and cash crop type (corn, soybean, wheat, vegetable, corn-soybean rotation, corn-soybean-wheat rotation, and other). An unbalanced analysis of variation was used to determine the hierarchy of most to least important factors that affected responsiveness of each soil health indicator. Based on the hierarchy structure, a soil health calculator was then developed to quantify the response of 13 parameters – erosion, runoff, weed suppression, soil aggregate stability, leaching, infiltration, microbial biomass carbon, soil bulk density, soil organic carbon, soil nitrogen, microbial biomass nitrogen, cash crop yield, and saturated hydraulic conductivity – to cover crops. The presented data in the calculator report the mean change in parameter values based on all combinations of climate, soil texture, cover crop type, and cash crop type.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

MultiSector Dynamics: Advancing the Science of Complex Adaptive Human-Earth Systems

The field of MultiSector Dynamics (MSD) explores the dynamics and co-evolutionary pathways of human and Earth systems with a focus on critical goods, services, and amenities delivered to people through interdependent sectors. This commentary lays out core definitions and concepts, identifies MSD science questions in the context of the current state of knowledge, and describes ongoing activities to expand capacities for open science, leverage revolutions in data and computing, and grow and diversify the MSD workforce. Central to our vision is the ambition of advancing the next generation of complex adaptive human-Earth systems science to better address interconnected risks, increase resilience, and improve sustainability. This will require convergent research and the integration of ideas and methods from multiple disciplines. Understanding the tradeoffs, synergies, and complexities that exist in coupled human-Earth systems is particularly important in the context of energy transitions and increased future shocks.

Reed, Patrick↗

DOE OSTI2023

The need to operationalize climate modelling

We report climate models have changed the world. Starting out as simple globally averaged representations of vertical energy exchanges in the atmosphere in the 1950s, today’s climate models are highly complex numerical representations of the Earth system based on the fundamental laws of physics. Their development has largely been driven by scientific curiosity, with the many approximate virtual representations of Earth available today enabling the interrogation of the past and present climate system and the development of an understanding of the influence of human activity on its future. It is this understanding that underpins the climate mitigation targets enshrined in the Paris Agreement to limit global mean temperature increases.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI1995

Nuclear Safety [Vol. 36, No. 2, July-December 1995]

Nuclear Safety is a journal that covers significant issues in the field of nuclear safety. Its primary scope is safety in the design, construction, operation, and decommissioning of nuclear power reactors worldwide and the research and analysis activities that promote this goal, but it also encompasses the safety aspects of the entire nuclear fuel cycle, including fuel fabrication, spent-fuel processing and handling, and nuclear waste disposal, the handling of fissionable materials and radioisotopes, and the environmental effects of all these activities. Table of Contents for this issue follows. THE CHORNOBYL ACCIDENT: 195 The Chornobyl Accident Revisited, Part III: Chernobyl Source Term Release Dynamics and Reconstruction of Events During the Active Phase, A. R. Sich; GENERAL SAFETY CONSIDERATIONS: 218 Second ANS Workshop on the Safety of Soviet-Designed Nuclear Power Plants, R. A. Bari; 234 Elements of a Nuclear Criticality Safety Program, C. M. Hopper; 243 Rickover, Excellence, and Criticality Safety Programs, R. E. Wilson; ACCIDENT ANALYSIS: 249 Transient Analysis of the PIUS Advanced Reactor Design with the TRAC-PF1/MOD2 Code, B. E. Boyack, J. L Steiner, S. C. Harmony, H. J. Stumpf, and J. F. Lime; 278 The Hierarchy-By-Interval Approach to Identifying Important Models that Need Improvement in Severe-Accident Simulation Codes, T. J. Heames, M. Khatib-Rahbar, J. E. Kelly, R. P. Jenks-Johnson, and Y.-S. Chen; 290 RELAP5/MOD3 Code Coupling Model, R. P. Martin; 299 Missiles Caused by Severe Pressurized-Water Reactor Accidents, R. Krieg; DESIGN FEATURES: 310 Validation of COMMIX with Westinghouse AP-600 PCCS Test Data, J. G. Sun, T. H. Chien, J. Ding, and W T. Sha; ENVIRONMENTAL EFFECTS: 321 Spent Nuclear Fuel Characterization for a Bounding Reference Assembly for the Receiving Basin for Off-Site Fuel, S. D. Kahook, R. L. Garrett, L. R. Canas, and M J. Beckum; OPERATING EXPERIENCES: 332 Reactor Shutdown Experience, Compiled by J. W. Cletcher; U.S. NUCLEAR REGULATORY COMMISSION INFORMATION AND ANALYSES: 335 Reactor Coolant System Blowdown at Wolf Creek on September 17, 1994, J. V. Kauffman and S. L. Israel; RECENT DEVELOPMENTS: 344 Reports, Standards, and Safety Guides, D. S. Oueener; 349 Proposed Rule Changes as of June 30, 1995; ANNOUNCEMENTS: 320 Symposium on Acceptability of Risk From Radiation—Application to Manned Space Flight; 320 24th DOE/NRC Nuclear Air Cleaning and Treatment Conference; 361 Radiation Biology and Radiation Protection— Modern Developments and Tendencies in Radiation Biology; 362 1997 IEEE Sixth Conference on Human Factors and Power Plants; 354 The Authors; 360 Reviewers of Nuclear Safety, Vol. 36.

05 NUCLEAR FUELS↗

DOE OSTI1995

Nuclear Safety [Vol. 36, No. 2, July-December 1995]

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2022

NPP Simulators for Coupled Thermal and Electric Power Dispatch

The Light Water Reactor Sustainability (LWRS) program within the United States Department of Energy supports extending the operation of the U.S. commercial nuclear power plant (NPP) fleet. Within the LWRS program, the Flexible Plant Operation and Generation (FPOG) Pathway works to diversify the revenue streams of light water reactors (LWRs) by opening opportunities for the co-generation of non-electric products in addition to supplying electrical power to the grid. Recent events have added greater motivation to these efforts. For example, the recent Inflation Reduction Act (IRA) passed by the U.S. federal government offers substantial tax incentives for producing clean hydrogen, the technology readiness level of dispatchable and high-efficiency hydrogen production has dramatically increased in a short time, and societal response to world climate change is driving a transition away from fossil fuels. Producing hydrogen with maximum efficiency using nuclear power requires dispatching both electrical and thermal power from the nuclear plant to the hydrogen plant, so testing concepts of operations for combined electrical and thermal power dispatch (TPD) from an NNP to a hydrogen plant is of interest. This report documents achievement of the Light Water Reactor Sustainability (LWRS) program milestone “Install and demonstrate a vendor-developed simulator on the Human Systems Simulation Laboratory (HSS) for dispatch of LWR electrical power to a close-coupled electrolysis plant” with a due date of Dec. 22, 2022. Several factors provide motivation for this effort. Coupling the power generation deck of a nuclear power plant to a hydrogen production facility introduces new possibilities for operational transients that must be addressed. In particular, the performance of the integrated system during startup and shutdown of the hydrogen production facility, as well as offnormal conditions, need to be evaluated to ensure there are no adverse effects on the operation of the existing NPP. The concept of operations involving the NPP, the hydrogen plant, and the electric power grid must be tested using NPP simulators and operating procedures that have been modified for TPD operations. These tests must also include dynamic simulations of the coupled tertiary thermal and electric loads as well as coordinated activities with NPP operators, tertiary load operators and grid power coordinators. The report summarizes progress in developing and testing full-scope NPP simulators at the HSSL, including a generic BWR simulator from GSE Systems, Inc. and generic PWR simulator from Westinghouse. In the case of the TPD-GBWR Simulator from GSE Systems, Inc., a BWR is thermally coupled to a high temperature electrolysis (HTE) plant that produces hydrogen and oxygen from de-ionized water. The hydrogen plant is not explicitly simulated but only included as a transient heat sink. A thermal power dispatch (TPD) system transfers heat between the steam systems at the BWR and the hydrogen plant. Operational results from two versions of the modified simulator are presented. The first version uses synthetic oil as a heat transfer fluid in a closed delivery heat loop (DHL) that generates steam at the hydrogen plant. The second version uses steam as the heat transfer fluid in a delivery steam line (DSL) to provide steam to the hydrogen plant. For both versions, the estimated thermal power delivery distance is approximately one kilometer. The amount of thermal power dispatched in the simulators is 15% of the total reactor thermal power such that the simulators provide a tool to study the feasibility of coupling a BWR to industrial processes that benefit from a combination electrical and thermal power dispatch. Ongoing work within a CRADA is also developing a full-scope PWR simulator provided by Westinghouse for both thermal and electric power coupling. This simulator is based on a PWR plant with two three-loop Westinghouse reactors. Westinghouse PWRs are sufficiently similar that a simulator of a three-loop reactor is an appropriate representation for two-loop and four-loop PWR reactors. The three-loop simulator will initially be modified for close-coupling to a 100 MW HTE hydrogen production plant that will require approximately 25 MW of thermal power while operating at its maximum rated capacity. The simulator testing will include full coupling to dynamic simulations of a hydrogen production plant and a representative bulk electric grid. The simulator provided by Westinghouse is similar to the GPWR simulator that INL has already obtained from GSE Systems but has a few important added benefits. First, the Westinghouse simulator is based on digital controls and has additional screens that can be called up to show parameter trends to assist operators in decision-making. The Westinghouse simulator also has upgrades to the controls and hardware representations, such as valve actuators, that make it more realistic and flexible in terms of accurately sim

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2022

Machine Learning of All Mycobacterium tuberculosis H37Rv RNA-seq Data Reveals a Structured Interplay between Metabolism, Stress Response, and Infection

Mycobacterium tuberculosis is one of the most consequential human bacterial pathogens, posing a serious challenge to 21st century medicine. A key feature of its pathogenicity is its ability to adapt its transcriptional response to environmental stresses through its transcriptional regulatory network (TRN). While many studies have sought to characterize specific portions of the M. tuberculosis TRN, and some studies have performed system-level analysis, few have been able to provide a network-based model of the TRN that also provides the relative shifts in transcriptional regulator activity triggered by changing environments. Here, we compiled a compendium of nearly 650 publicly available, high quality M. tuberculosis RNA-sequencing data sets and applied an unsupervised machine learning method to obtain a quantitative, top-down TRN. It consists of 80 independently modulated gene sets known as “iModulons,” 41 of which correspond to known regulons. These iModulons explain 61% of the variance in the organism’s transcriptional response. We show that iModulons (i) reveal the function of poorly characterized regulons, (ii) describe the transcriptional shifts that occur during environmental changes such as shifting carbon sources, oxidative stress, and infection events, and (iii) identify intrinsic clusters of regulons that link several important metabolic systems, including lipid, cholesterol, and sulfur metabolism. This transcriptome-wide analysis of the M. tuberculosis TRN informs future research on effective ways to study and manipulate its transcriptional regulation and presents a knowledge-enhanced database of all published high-quality RNA-seq data for this organism to date.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Biosystems Design to Accelerate C 3 -to-CAM Progression

Global demand for food and bioenergy production has increased rapidly, while the area of arable land has been declining for decades due to damage caused by erosion, pollution, sea level rise, urban development, soil salinization, and water scarcity driven by global climate change. In order to overcome this conflict, there is an urgent need to adapt conventional agriculture to water-limited and hotter conditions with plant crop systems that display higher water-use efficiency (WUE). Crassulacean acid metabolism (CAM) species have substantially higher WUE than species performing C 3 or C 4 photosynthesis. CAM plants are derived from C 3 photosynthesis ancestors. However, it is extremely unlikely that the C 3 or C 4 crop plants would evolve rapidly into CAM photosynthesis without human intervention. Currently, there is growing interest in improving WUE through transferring CAM into C 3 crops. However, engineering a major metabolic plant pathway, like CAM, is challenging and requires a comprehensive deep understanding of the enzymatic reactions and regulatory networks in both C 3 and CAM photosynthesis, as well as overcoming physiometabolic limitations such as diurnal stomatal regulation. Recent advances in CAM evolutionary genomics research, genome editing, and synthetic biology have increased the likelihood of successful acceleration of C 3 -to-CAM progression. Here, we first summarize the systems biology-level understanding of the molecular processes in the CAM pathway. Then, we review the principles of CAM engineering in an evolutionary context. Lastly, we discuss the technical approaches to accelerate the C 3 -to-CAM transition in plants using synthetic biology toolboxes.

59 BASIC BIOLOGICAL SCIENCES↗