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DOE OSTI2024

Current State, Challenges, and Opportunities in Genome-Scale Resource Allocation Models: A Mathematical Perspective

Stoichiometric genome-scale metabolic models (generally abbreviated GSM, GSMM, or GEM) have had many applications in exploring phenotypes and guiding metabolic engineering interventions. Nevertheless, these models and predictions thereof can become limited as they do not directly account for protein cost, enzyme kinetics, and cell surface or volume proteome limitations. Lack of such mechanistic detail could lead to overly optimistic predictions and engineered strains. Initial efforts to correct these deficiencies were by the application of precursor tools for GSMs, such as flux balance analysis with molecular crowding. In the past decade, several frameworks have been introduced to incorporate proteome-related limitations using a genome-scale stoichiometric model as the reconstruction basis, which herein are called resource allocation models (RAMs). This review provides a broad overview of representative or commonly used existing RAM frameworks. This review discusses increasingly complex models, beginning with stoichiometric models to precursor to RAM frameworks to existing RAM frameworks. RAM frameworks are broadly divided into two categories: coarse-grained and fine-grained, with different strengths and challenges. Discussion includes pinpointing their utility, data needs, highlighting framework strengths and limitations, and appropriateness to various research endeavors, largely through contrasting their mathematical frameworks. Finally, promising future applications of RAMs are discussed.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

In Vivo Thermodynamic Analysis of Glycolysis in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum Using 13 C and 2 H Tracers

Clostridium thermocellum and Thermoanaerobacterium saccharolyticum are thermophilic anaerobic bacteria with complementary metabolic capabilities that utilize distinct glycolytic pathways for the conversion of cellulosic sugars to biofuels. We integrated quantitative metabolomics with 2 H and 13 C metabolic flux analysis to investigate the in vivo reversibility and thermodynamics of the central metabolic networks of these two microbes. We found that the glycolytic pathway in C. thermocellum operates remarkably close to thermodynamic equilibrium, with an overall drop in Gibbs free energy 5-fold lower than that of T. saccharolyticum or anaerobically grown Escherichia coli . The limited thermodynamic driving force of glycolysis in C. thermocellum could be attributed in large part to the small free energy of the phosphofructokinase reaction producing fructose bisphosphate. The ethanol fermentation pathway was also substantially more reversible in C. thermocellummthan in T. saccharolyticum. These observations help explain the comparatively low ethanol titers of C. thermocellum and suggest engineering interventions that can be used to increase its ethanol productivity and glycolytic rate. In addition to thermodynamic analysis, we used our isotope tracer data to reconstruct the T. saccharolyticum central metabolic network, revealing exclusive use of the Embden-Meyerhof-Parnas (EMP) pathway for glycolysis, a bifurcated tricarboxylic acid (TCA) cycle, and a sedoheptulose bisphosphate bypass active within the pentose phosphate pathway. Thermodynamics constitutes a key determinant of flux and enzyme efficiency in metabolic networks. Here, we provide new insights into the divergent thermodynamics of the glycolytic pathways of C. thermocellum and T. saccharolyticum, two industrially relevant thermophilic bacteria whose metabolism still is not well understood. We report that while the glycolytic pathway in T. saccharolyticum is as thermodynamically favorable as that found in model organisms, such as E. coli or Saccharomyces cerevisiae , the glycolytic pathway of C. thermocellum operates near equilibrium. The use of a near-equilibrium glycolytic pathway, with potentially increased ATP yield, by this cellulolytic microbe may represent an evolutionary adaptation to growth on cellulose, but it has the drawback of being highly susceptible to product feedback inhibition. The results of this study will facilitate future engineering of high-performance strains capable of transforming cellulosic biomass to biofuels at high yields and titers.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Considerations for Microbial Production of Oleochemicals

Fatty acids and their derivatives have a wide variety of uses in industrial and consumer products. While these compounds are traditionally derived from petrochemicals or natural lipids, microbes offer an alternate route for production. This chapter provides an overview of the highly conserved fatty acid biosynthetic pathway. Though highly conserved, key differences among organisms in how the pathway is realized and how it interacts within metabolism are also addressed. Finally, this chapter details engineering interventions aimed at increasing production of and upgrading fatty acids.

Hubbard, Susan C↗

DOE OSTI2023

Let’s Unleash the Network Judgment: A Self-Supervised Approach for Cloud Image Analysis

Accurate cloud type identification and coverage analysis are crucial in understanding the Earth’s radiative budget. Traditional computer vision methods rely on low-level visual features of clouds for estimating cloud coverage or sky conditions. Several handcrafted approaches have been proposed; however, scope for improvement still exists. Newer deep neural networks (DNNs) have demonstrated superior performance for cloud segmentation and categorization. These methods, however, need expert engineering intervention in the preprocessing steps—in the traditional methods—or human assistance in assigning cloud or clear sky labels to a pixel for training DNNs. Such human mediation imposes considerable time and labor costs. We present the application of a new self-supervised learning approach to autonomously extract relevant features from sky images captured by ground-based cameras, for the classification and segmentation of clouds. We evaluate a joint embedding architecture that uses self-knowledge distillation plus regularization. We use two datasets to demonstrate the network’s ability to classify and segment sky images—one with ~85,000 images collected from our ground-based camera and another with 400 labeled images from the WSISEG database. We find that this approach can discriminate full-sky images based on cloud coverage, diurnal variation, and cloud base height. Additionally, it semantically segments the cloud areas without labels. The approach shows competitive performance in all tested tasks, suggesting a new alternative for cloud characterization.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Lab Home Testing of Residential Isolation Space Control to Minimize Infectious Disease Transmission in Existing Single-Family Homes

Existing evidence strongly suggests that viral infectious diseases can be transmitted via an airborne route across distances in indoor environments. Accordingly, the risk of airborne transmission within homes should be managed. The public health emergency associated with SARS-CoV-2 makes controlling airborne transmission of respired viruses in indoor environments critical, especially in poorly ventilated indoor environments. The effectiveness of engineering interventions requiring minor efforts that create a negative-pressure isolation zone (IZ) for a contagious person has yet to be tested for existing residential homes. To mitigate the risk of airborne virus transmission and maximize health protection for the population in existing single-family homes, the relative effectiveness of several control strategies are investigated in this report. While very high-efficiency MERV filtration, high ventilation rates, and other controls can help be effective, most occupants are not likely to have the time or means for advanced measures found in hospitals. This project focused on testing relatively simple efforts that utilize existing or easy to acquire materials and simple processes.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2021

Lab Home Testing of Residential Isolation Space Control to Minimize Infectious Disease Transmission in Existing Single-Family Homes

30 DIRECT ENERGY CONVERSION↗

DOE OSTI2020

New Frontiers in Geoengineering Research

In late summer 2019, the ninth annual workshop of the Geoengineering Model Intercomparison Project (GeoMIP; http://climate.envsci.rutgers.edu/GeoMIP) convened at Beijing Normal University (Fig. 1). This meeting was held in conjunction with a summer school in which 89 participants from five continents learned about climate modeling of solar geoengineering, also known as climate engineering or climate intervention. Solar geoengineering refers to “radiation management” methods, which involve deliberate manipulations of the radiation budget through potential technologies such as stratospheric sulfate aerosols, marine cloud brightening, and cirrus thinning, but not CO2 removal. The students at the summer school were mainly physical science majors, with many from China, but also included some social science people. The summer school was focused on impact modeling (e.g., on agriculture and the cryosphere) and consideration of extremes, rather than just looking at climate modeloutput. There were also lectures on governance and economics. This event signifies the first major international geoengineering meeting held in Asia.

Kravitz, Benjamin S.↗

DOE OSTI2021

Engineering integration in elementary science classrooms: Effects of disciplinary language scaffolds on English learners' content learning and engineering identity

Abstract Background Limited research examines the effects of integrated science and engineering (SE) instruction emphasizing disciplinary literacy and language activities on engineering identity and content understanding. Far fewer studies target English learners (ELs). Purpose The impact of an SE intervention on the development of science, engineering, and technology knowledge as well as engineering identity was examined. To address ELs' learning needs, the curricular design was built on a validated SE model by integrating (1) developmental, (2) language scaffolds, and (3) culturally based accommodations. Design/Method Separate analysis of variance examined the effects of the intervention on science, engineering, and technology knowledge as well as engineering identity. The relationship among engineering identity and content outcomes was also examined. ELs from kindergarten to second grade classrooms were randomly assigned to the integrated SE group or control group. Results Integrated SE instruction significantly increased ELs' science, engineering, and technology knowledge as well as a substantially developed engineering identity. Overall, ELs' engineering identity is associated with an increase in science, engineering, and technology content knowledge. However, second grade girls' identity development was not associated with learning measures. These correlations suggest the context of the engineering activity may have reinforced gendered stereotypes and reduced the effects for girls' engineering attitudes. Conclusions Integrated SE instruction emphasizing disciplinary literacy and cultural accommodations increases early elementary ELs' learning and engineering identity. Future studies should examine the unique effects of language scaffolds and cultural modifications on student learning and the impact of gender stereotypes on girls' engineering attitudes.

Aguirre‐Muñoz, Zenaida↗

DOE OSTI2020

Understanding the Effects of Vehicle Platoons on Crash Type and Severity

Crash type is an informative indicator to infer driving behaviors and conditions that cause a crash. For example, rear-end and side-swipe crashes are typically caused by improper vehicle interaction such as sudden lane-changing or speed control while hit-object crashes are likely the result of a single driver’s mistake. This study investigated the impact of vehicles travelling as a group (platoon) and its configuration (i.e., types of vehicles consisting of the platoon) on crash type and severity since the vehicles could affect each other when travelling in close proximity. This study applied Generalized Structure Equation Modeling (GSEM) to capture the complex relationships among the various crash factors such as traffic condition, driver characteristics, environmental conditions, and vehicle interaction to the crash attributes including type and severity. This study collected over 3 million individual vehicle data from 39 traffic count sites in California to estimate the vehicle interactions and driving behaviors. The microscopic traffic data are matched to 1417 crash reports. Results showed that vehicles traveling in platoons are associated with more rear-end and side-swipe crashes. Speed difference in the platoon had a positive effect on hit-object crashes if the platoon comprises vehicles of homogeneous type – either trucks or non-trucks. In addition, human factors such as age and gender were identified as significant influential factors in all type of crashes, however truck involvement particularly played an important role amongst side-swipe crashes. Crash severity was negatively affected by total flow, and rear-end crashes were more likely to be severe compared with hit-object crashes. Based on findings, this study suggests practical operational strategies to reduce traffic instability associated with platooned vehicle patterns. Understanding the high-risk factors for different crash types and severities would provide valuable insights for decision-makers and transportation engineers to develop targeted intervention strategies in consideration of road users and traffic conditions such as fleet mix and speed.

ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2020

Systems Analysis of NADH Dehydrogenase Mutants Reveals Flexibility and Limits of Pseudomonas taiwanensis VLB120’s Metabolism

Obligate aerobic organisms rely on a functional electron transport chain for energy conservation and NADH oxidation. Because of this essential requirement, the genes of this pathway are likely constitutively and highly expressed to avoid a cofactor imbalance and energy shortage under fluctuating environmental conditions. In this work, we investigated the essentiality of the three NADH dehydrogenases of the respiratory chain of the obligate aerobe Pseudomonas taiwanensis VLB120 and the impact of the knockouts of corresponding genes on its physiology and metabolism. While a mutant lacking all three NADH dehydrogenases seemed to be nonviable, the single or double knockout mutant strains displayed no, or only a weak, phenotype. Only the mutant deficient in both type 2 dehydrogenases showed a clear phenotype with biphasic growth behavior and a strongly reduced growth rate in the second phase. In-depth analyses of the metabolism of the generated mutants, including quantitative physiological experiments, transcript analysis, proteomics, and enzyme activity assays revealed distinct responses to type 2 and type 1 dehydrogenase deletions. An overall high metabolic flexibility enables P. taiwanensis to cope with the introduced genetic perturbations and maintain stable phenotypes, likely by rerouting of metabolic fluxes. This metabolic adaptability has implications for biotechnological applications. While the phenotypic robustness is favorable in large-scale applications with inhomogeneous conditions, the possible versatile redirecting of carbon fluxes upon genetic interventions can thwart metabolic engineering efforts. While Pseudomonas has the capability for high metabolic activity and the provision of reduced redox cofactors important for biocatalytic applications, exploitation of this characteristic might be hindered by high, constitutive activity of and, consequently, competition with the NADH dehydrogenases of the respiratory chain. The in-depth analysis of NADH dehydrogenase mutants of Pseudomonas taiwanensis VLB120 presented here provides insight into the phenotypic and metabolic response of this strain to these redox metabolism perturbations. This high degree of metabolic flexibility needs to be taken into account for rational engineering of this promising biotechnological workhorse toward a host with a controlled and efficient supply of redox cofactors for product synthesis.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Metabolic and evolutionary responses of Clostridium thermocellum to genetic interventions aimed at improving ethanol production

Engineering efforts targeted at increasing ethanol by modifying the central fermentative metabolism of Clostridium thermocellum have been variably successful. Here, we aim to understand this variation by a multifaceted approach including genomic and transcriptomic analysis combined with chemostat cultivation and high solids cellulose fermentation. Three strain lineages comprising 16 strains total were examined. Two strain lineages in which genes involved in pathways leading to organic acids and/or sporulation had been knocked out resulted in four end-strains after adaptive laboratory evolution (ALE). A third strain lineage recapitulated mutations involving adhE that occurred spontaneously in some of the engineered strains.

Biotechnology & Applied Microbiology↗

DOE OSTI2022

DOE-NOAA Marine Cloud Brightening (Workshop Report 2022)

Marine Cloud Brightening (MCB) refers to the deliberate injection of aerosol particles into marine clouds to increase their reflection of solar radiation to temporarily cool the planet while decarbonization efforts are pursued. A workshop was conducted to assess the state of knowledge in the field of MCB, and to provide a possible research path toward reducing unknowns in key components of the underlying physical science. This three-day workshop took place in April 2022 and was jointly sponsored by Department of Energy (DOE)’s Atmospheric System Research (ASR) program and the National Oceanic and Atmospheric Administration (NOAA). The workshop focused on identifying key physical science knowledge gaps necessary to answer the following driving questions: 1) Is MCB feasible over sufficiently large regions and is implementation practicable for long-enough durations to avert the worst impacts of global warming? 2) If practicable, what will be the regional impacts of such MCB interventions? 3) Do we have adequate systems in place to detect and quantify the effects of such interventions? 4) What physical and engineering science challenges must be resolved satisfactorily before we can consider embarking on MCB?

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

DOE-NOAA Marine Cloud Brightening Workshop

Marine Cloud Brightening (MCB) refers to the deliberate injection of aerosol particles into marine clouds to increase their reflection of solar radiation to temporarily cool the planet while decarbonization efforts are pursued. A workshop was conducted to assess the state of knowledge in the field of MCB, and to provide a possible research path toward reducing unknowns in key components of the underlying physical science. This three-day workshop took place in April 2022 and was jointly sponsored by Department of Energy (DOE)’s Atmospheric System Research (ASR) program and the National Oceanic and Atmospheric Administration (NOAA). The workshop focused on identifying key physical science knowledge gaps necessary to answer the following driving questions: 1. Is MCB feasible over sufficiently large regions and is implementation practicable for long-enough durations to avert the worst impacts of global warming? 2. If practicable, what will be the regional impacts of such MCB interventions? 3. Do we have adequate systems in place to detect and quantify the effects of such interventions? 4. What physical and engineering science challenges must be resolved satisfactorily before we can consider embarking on MCB?

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Case studies of robots and automation as health/safety interventions in small manufacturing enterprises

This article reviews the experiences of 63 case studies of small businesses (<250 employees) with manufacturing automation equipment acquired through a health/safety intervention grant program. The review scope included equipment technologies classified as industrial robots (n = 17), computer numerical control (CNC) machining (n = 29), or other programmable automation systems (n = 17). Descriptions of workers' compensation (WC) claim injuries and identified risk factors that motivated the acquisition of the equipment were extracted from grant applications. Other aspects of the employer experiences, including qualitative and quantitative assessment of effects on risk factors for musculoskeletal disorders (MSD), effects on productivity, and employee acceptance of the intervention were summarized from the case study reports. Case studies associated with a combination of large reduction in risk factors, lower cost per affected employee, and reported increases in productivity were CNC stone cutting system, CNC/vertical machining system, automated system for bottling, CNC/routing system for plastics products manufacturing, and a CNC/Cutting system for vinyl/carpet. Six case studies of industrial robots reported quantitative reductions in MSD risk factors in these diverse manufacturing industries: snack foods; photographic film, paper, plate, and chemical; machine shops; leather goods and allied products; plastic products; and iron and steel forging. Furthermore, this review of health/safety intervention case studies indicates that advanced (programmable) manufacturing automation, including industrial robots, reduced workplace musculoskeletal risk factors, and improved process productivity in most cases.

42 ENGINEERING↗

DOE OSTI2021

In Situ Machine Learning for Intelligent Data Capture on Exascale Platforms. Final Report

In many dynamic systems, interesting events occur locally in time and space. Examples of such systems include ignition events in combustion simulations, material fractures in mechanics simulations, and extreme weather events in climate simulations. Due to memory constraints and data I/O costs, current simulation workflows save data at regularly spaced time-steps, at a fixed rate determined before the start of the simulation. Often this mode of operation results in missed events of interest, necessitating a simulation restart from before an event occurred with more frequent data saves. This data saving workflow is grossly inefficient and is already a bottleneck in the computing process. We propose to develop machine learning algorithms that can detect when interesting dynamical events are occurring, triggering data saves. These machine learning algorithms will perform in situ anomaly detection to flag regions with different dynamical properties than those previously recorded. The adaptive data saves would be local in time and space to match the event of interest, thereby enabling a much more efficient workflow that will reduce data I/O costs and data storage memory requirements. The algorithms will be tested on two applications: auto-ignition simulations and climate simulations. A critical component of this project will be developing machine learning algorithms that can be deployed efficiently in situ on HPC platforms with out-of-the-box functionality. The development of in situ machine learning methods to detect anomalous events would enable a more efficient and effective workflow, in which all the relevant data are saved in a single simulation run, without re-starts or scientist intervention.

42 ENGINEERING↗

DOE OSTI2020

Investigating the interconnectedness of active transportation and public transit usage as a primer for Mobility-as-a-Service adoption and deployment

With the advent of Mobility-as-a-Service packages to reduce car usage and (by extension) greenhouse gas emissions, it is crucial that researchers and practitioners consider mutual determinants and outcomes that link the adoption of multiple alternative modes. This study therefore investigates the joint usage of active travel (walking, cycling, bike-sharing) and public transit (bus, rail) modes with respect to personal and situational contexts. Online survey data (n = 826) were collected across six Midwestern U.S. states using Amazon MTurk. Respondents indicated their average weekly usage of eight travel modes across three trip purposes so that multimodality could be assessed. Several psychological constructs were extracted via (a) the stages of change framework, used to indicate willingness to adopt new behavior, and (b) confirmatory factor analysis conducted on Likert scales rooted in theories of community, identity, norms, personality, and well-being. A multiple-indicators multiple-causes structural equation model is then employed to investigate the process of adopting a modality style that incorporates active and transit modes. The model confirms that compatible physical and social contexts, as well as navigational skills and openness to learning, are key primers of multimodalism. However, a path juncture stemming from neighborhood support for mobility innovation illustrates a potential polarity in outcomes between individuals and communities. In addition, the stage of active mobility adoption is linked to identity and norm activation, offering further guidance on what influences readiness for change. The seamless integration of mobility services is critical to matching the convenience and comfort of the private vehicle; understanding potential pathways to sustainable mobility, though, requires analyses and interventions that are driven by well-being outcomes and grounded in rigorous psychological frameworks. Here, the research findings offer practical guidance for identifying intervention opportunities to be linked with MaaS enrollment while demonstrating the need to illuminate how mobility might relate to social cohesion, identity expression, and various sources of satisfaction.

42 ENGINEERING↗

DOE OSTI2022

Association of Diet and Antimicrobial Resistance in Healthy U.S. Adults

Antimicrobial resistance (AMR) represents a significant source of morbidity and mortality worldwide, with expectations that AMR-associated consequences will continue to worsen throughout the coming decades. Since resistance to antibiotics is encoded in the microbiome, interventions aimed at altering the taxonomic composition of the gut might allow us to prophylactically engineer microbiomes that harbor fewer antibiotic resistant genes (ARGs). Diet is one method of intervention, and yet little is known about the association between diet and antimicrobial resistance. To address this knowledge gap, we examined diet using the food frequency questionnaire (FFQ; habitual diet) and 24-h dietary recalls (Automated Self-Administered 24-h [ASA24 ® ] tool) coupled with an analysis of the microbiome using shotgun metagenome sequencing in 290 healthy adult participants of the United States Department of Agriculture (USDA) Nutritional Phenotyping Study. We found that aminoglycosides were the most abundant and prevalent mechanism of AMR in these healthy adults and that aminoglycoside-O-phosphotransferases (aph3-dprime) correlated negatively with total calories and soluble fiber intake. Individuals in the lowest quartile of ARGs (low-ARG) consumed significantly more fiber in their diets than medium- and high-ARG individuals, which was concomitant with increased abundances of obligate anaerobes, especially from the family Clostridiaceae, in their gut microbiota. Finally, we applied machine learning to examine 387 dietary, physiological, and lifestyle features for associations with antimicrobial resistance, finding that increased phylogenetic diversity of diet was associated with low-ARG individuals. These data suggest diet may be a potential method for reducing the burden of AMR.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Prediction of non-intuitive metabolic targets with bayesian metabolic control analysis to improve 3-hydroxypropionic acid production in Aspergillus niger

Development of efficient bioconversion processes is limited by the ability to predictably improve metabolic flux. Here we deployed Bayesian Metabolic Control Analysis as a platform to integrate multi-omics data with metabolic modeling and evaluated its ability to predict genetic interventions that improve metabolic flux. Global Metabolomics and proteomics data was collected from 17 Aspergillus niger strains engineered to produce the platform biochemical 3-hydroxypropionic acid from which seven actional genetic interventions were predicted from significant flux control coefficients. Of the suggested genetic interventions, two were present within the intuitively designed strains used for training (malonic semialdehyde dehydrogenase and pyruvate carboxylase) while five predicted targets were present within non-intuitive areas of the metabolic network including 5-formyltetrahydrofolate deformylase and four mitochondrial enzymes, alcohol dehydrogenase, succinyl-CoA ligase, aspartate aminotransferase, and malate dehydrogenase. Six of the targets were validated in the highest performing 3-HP strain used for multi-omics data generation which contained a prior disruption of the highest scoring target malonic semialdehyde dehydrogenase. Predicted directional perturbation of five of the six tested targets significantly improved titer and rate of 3-HP production and two significantly improved yield. The greatest improvements were observed following disruption of the non-intuitive target succinyl-CoA ligase which increased titer by 39% and yield by 29% (to 20.4 g/L 3-HP and 0.31 g 3-HP/g glucose) over the strains used for training. This study demonstrates the utility of Bayesian Metabolic Control Analysis and highlights the ability to predict meaningful genetic targets in unexpected areas of metabolism to improve engineered strains for bioconversion.

3-hydroxypropionic acid↗