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DOE OSTI2023

Renewable Energy Potential Model: Geothermal Supply Curves

The Renewable Energy Potential (reV) model is a geospatial platform for estimating technical potential and developing renewable energy supply curves, initially developed for wind and solar technologies. The model evaluates deployment constraints, considering land use, environmental, and cultural factors, and estimates the distance to existing grid features to connect future plants (Maclaurin et al., 2021). A pressing deficiency in the reV model, however, is representation of geothermal electricity generation technologies. To address this gap, we developed a novel geothermal generation module for reV that allows for representation and analysis at the same level of detail as other renewable technologies. The included paper describes our process for evaluating data sources for the modeling, and presents five preliminary reV geothermal results. More specifically, we present two sets of resource data that represent upper and lower bounds for geothermal potential. We then present several sensitivity runs using the upper bound resource data; the results are encouraging that levelized cost of electricity (LCOE) can be reduced by optimizing the location and estimated capacity of the spatially diverse geothermal resource while considering the distance to existing grid infrastructure. Our preliminary supply curves and levelized cost of electricity (LCOE) results provided here should be considered with care due to the high uncertainty in geothermal resource potential data. We present median LCOE values for the conterminous U.S. for three scenarios: two hydrothermal (3.5km depth, USGS heat flow & SMU temperatures respectively) and one EGS (4.5km depth, SMU temperatures). The capital and operating costs for each respective technology are modeled. We also compare results using two different resource data sources.

15 GEOTHERMAL ENERGY↗

DOE OSTI2023

A Genome-Scale Atlas Reveals Complex Interplay of Transcription and Translation in an Archaeon

The scale of post-transcriptional regulation and the implications of its interplay with other forms of regulation in environmental acclimation are underexplored for organisms of the domain Archaea. Here, we have investigated the scale of post-transcriptional regulation in the extremely halophilic archaeon Halobacterium salinarum NRC-1 by integrating the transcriptome-wide locations of transcript processing sites (TPSs) and SmAP1 binding, the genome-wide locations of antisense RNAs (asRNAs), and the consequences of RNase_2099C knockout on the differential expression of all genes. This integrated analysis has discovered that 54% of all protein-coding genes in the genome of this haloarchaeon are likely targeted by multiple mechanisms for putative post-transcriptional processing and regulation, with about 20% of genes likely being regulated by combinatorial schemes involving SmAP1, asRNAs, and RNase_2099C. Comparative analysis of mRNA levels (transcriptome sequencing [RNA-Seq]) and protein levels (sequential window acquisition of all theoretical fragment ion spectra mass spectrometry [SWATH-MS]) for 2,579 genes over four phases of batch culture growth in complex medium generated additional evidence for the conditional post-transcriptional regulation of 7% of all protein-coding genes. We demonstrate that post-transcriptional regulation may act to fine-tune specialized and rapid acclimation to stressful environments, e.g., as a switch to turn on gas vesicle biogenesis to promote vertical relocation under anoxic conditions and modulate the frequency of transposition by insertion sequence (IS) elements of the IS200/IS605, IS4, and ISH3 families. Findings from this study are provided as an atlas in a public Web resource (https://halodata.systemsbiology.net).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Renewable biohydrogen production from lignocellulosic biomass using fermentation and integration of systems with other energy generation technologies

Biohydrogen is a clean and renewable source of energy. It can be produced by using technologies such as thermochemical, electrolysis, photoelectrochemical and biological, etc. Among these technologies, the biological method (dark fermentation) is considered more sustainable and ecofriendly. Dark fermentation involves anaerobic microbes which degrade carbohydrate rich substrate and produce hydrogen. Lignocellulosic biomass is an abundantly available raw material and can be utilized as an economic and renewable substrate for biohydrogen production. Although there are many hurdles, continuous advancements in lignocellulosic biomass pretreatment technology, microbial fermentation (mixed substrate and co-culture fermentation), the involvement of molecular biology techniques, and understanding of various factors (pH, T, addition of nanomaterials) effect on biohydrogen productivity and yield render this technology efficient and capable to meet future energy demands. Further integration of biohydrogen production technology with other products such as bio-alcohol, volatile fatty acids (VFAs), and methane have the potential to improve the efficiency and economics of the overall process. In this study, various methods used for lignocellulosic biomass pretreatment, technologies in trends to produce and improve biohydrogen production, a coproduction of other energy resources, and techno-economic analysis of biohydrogen production from lignocellulosic biomass are reviewed.

09 BIOMASS FUELS↗

DOE OSTI2020

Single Amino Acid Mutations Affect Zika Virus Replication In Vitro and Virulence In Vivo

The 2014–2016 Zika virus (ZIKV) epidemic in the Americas resulted in large deposits of next-generation sequencing data from clinical samples. This resource was mined to identify emerging mutations and trends in mutations as the outbreak progressed over time. Information on transmission dynamics, prevalence, and persistence of intra-host mutants, and the position of a mutation on a protein were then used to prioritize 544 reported mutations based on their ability to impact ZIKV phenotype. Using this criteria, six mutants (representing naturally occurring mutations) were generated as synthetic infectious clones using a 2015 Puerto Rican epidemic strain PRVABC59 as the parental backbone. The phenotypes of these naturally occurring variants were examined using both cell culture and murine model systems. Mutants had distinct phenotypes, including changes in replication rate, embryo death, and decreased head size. In particular, a NS2B mutant previously detected during in vivo studies in rhesus macaques was found to cause lethal infections in adult mice, abortions in pregnant females, and increased viral genome copies in both brain tissue and blood of female mice. Additionally, mutants with changes in the region of NS3 that interfaces with NS5 during replication displayed reduced replication in the blood of adult mice. This analytical pathway, integrating both bioinformatic and wet lab experiments, provides a foundation for understanding how naturally occurring single mutations affect disease outcome and can be used to predict the of severity of future ZIKV outbreaks. To determine if naturally occurring individual mutations in the Zika virus epidemic genotype affect viral virulence or replication rate in vitro or in vivo, we generated an infectious clone representing the epidemic genotype of stain Puerto Rico, 2015. Using this clone, six mutants were created by changing nucleotides in the genome to cause one to two amino acid substitutions in the encoded proteins. The six mutants we generated represent mutations that differentiated the early epidemic genotype from genotypes that were either ancestral or that occurred later in the epidemic. We assayed each mutant for changes in growth rate, and for virulence in adult mice and pregnant mice. Three of the mutants caused catastrophic embryo effects including increased embryonic death or significant decrease in head diameter. Three other mutants that had mutations in a genome region associated with replication resulted in changes in in vitro and in vivo replication rates. These results illustrate the potential impact of individual mutations in viral phenotype.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Converged Computing: A Best of Both Worlds of High-Performance Computing and Cloud

Collaboration between Cloud and High Performance Computing (HPC) communities has accelerated in the last half decade. A common goal to run batch workloads combined with a desire for reproducibility, automation, and optimization has led to successful projects that range from container technologies to workload management and security. This span of current and future work defines a novel “Converged Computing” paradigm that aims to combine the best of both worlds, both from a technological and cultural standpoint. Furthermore, in this Special Issue, we review common themes in the space, showcasing current work and encouraging a continued effort toward innovative ideas that will enable the next generations of scientific discovery.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Humming Trains in Seismology: An Opportune Source for Probing the Shallow Crust

Abstract Seismologists are eagerly seeking new and preferably low-cost ways to map and track changes in the complex structure of the top few kilometers of the crust. By understanding it better, they can build on what is known regarding important, practical issues. These include telling us whether imminent earthquakes and volcanic eruptions are generating telltale underground signs of hazard, about mitigation of induced seismicity such as from deep injection of wastewater, how the Earth and its atmosphere couple, and where accessible natural resources are. Passive seismic imaging usually relies on blind correlations within extended recordings of Earth’s ceaseless “hum” or coda of well-mixed, small vibrations. In this article, we propose a complementary approach. It is seismic interferometry using opportune sources—specifically ones not stationary in time and moving in a well-understood configuration. Its interpretation relies on an accurate understanding of how these sources radiate seismic waves, precise timing, careful placement of pairs of listening stations, and seismic phase differentiation (surface and body waves). Massive freight trains were only recently recognized as such a persistent, powerful cultural (human activity-caused) seismic source. One train passage may generate a tremor with an energy output of a magnitude 1 earthquake and be detectable for up to 100 km from the track. We discuss the source mechanisms of train tremors and review the basic theory on sources. Finally, we present case studies of body- and surface-wave retrieval as an aid to mineral exploration in Canada and to monitoring of a southern California fault zone. We believe noise recovery from this new signal source, together with dense data acquisition technologies such as nodes or distributed acoustic sensing, will deeply transform our ability to monitor activity in the shallow crust at sharpened resolution in time and space.

Geochemistry & Geophysics↗

DOE OSTI2023

Waste-to-Energy Pipeline through Consolidated Fermentation–Microbial Fuel Cell (MFC) System

The rise in population, urbanization, and industrial developments have led to a substantial increase in waste generation and energy demand, posing significant challenges for waste management as well as energy conservation and production. Bioenergy conversions have been merged as advanced, sustainable, and integrated solutions for these issues, encompassing energy generation and waste upcycling of different types of organic waste. Municipal solid waste (MSW) and agricultural residues (AR) are two main resources for bioenergy conversions. Bioenergy production involves feedstock deconstruction and the conversion of platform chemicals to energy products. This review provides a detailed overview of waste sources, biofuel, and bioelectricity production from fermentation and microbial fuel cell (MFC) technology, and their economic and environmental perspectives. Fermentation plays a critical role in liquid biofuel production, while MFCs demonstrate promising potential for simultaneous production of electricity and hydrogen. Fermentation and MFCs hold a significant potential to be integrated into a single pipeline, enabling the conversion of organic matter, including a variety of waste material and effluent, into diverse forms of bioenergy via microbial cultures under mild conditions. Furthermore, MFCs are deemed a promising technology for pollutant remediation, reducing COD levels while producing bioenergy. Importantly, the consolidated fermentation–MFC system is projected to produce approximately 7.17 trillion L of bioethanol and 6.12 × 10 4 MW/m 2 of bioelectricity from MSW and AR annually, contributing over USD 465 billion to the global energy market. Such an integrated system has the potential to initiate a circular economy, foster waste reduction, and improve waste management practices. This advancement could play a crucial role in promoting sustainability across the environmental and energy sectors.

09 BIOMASS FUELS↗

DOE OSTI2024

How Earth System Models Can Inform Key Dimensions of Marine Food Security in the Alaskan Arctic

The Arctic is home to several groups of Indigenous Peoples, each with distinct ways of interacting with their environment and ways of life. Arctic, Indigenous Peoples’ food sovereignty is tightly linked with food security. Subsistence harvesting activities provide nutritious and culturally vital foods for Alaska Native households and communities. Climate change is causing rapid and more unpredictable shifts in environmental conditions that impact three of the key aspects of food security, availability, stability, and accessibility. While communities monitor the abundance and health of food webs and environments as part of subsistence harvest practices, anticipating major transformations and changes in these systems is challenging. We explored the potential of Earth System Model output in helping anticipate or project physical or ecosystem changes relevant to Alaska Indigenous peoples’ food security needs. Through examples of model products, that provide measures of accessibility and availability of marine resources, we show that modern models, such as the Energy Exascale Earth System Model presented here, can provide estimates of a broad suite of variables relevant to food security. We investigate how Earth System Model output could contribute to exploring questions related to aspects of Arctic food security such as accessibility and availability and highlight present model shortcomings that, if addressed, would move Earth System Models closer to being a useful tool for understanding environmentally driven changes to the availability and accessibility of harvestable food resources. Our example model-derived food security indicators illustrate how Earth System Model output could be combined with relevant, non-model, information sources; These model products are meant only as a starting point and a tool for engaging community members and to present, in an accessible way, the model’s potential utility, or current lack thereof, to rights holders and stakeholders concerned about food security. We are hopeful that with example products in hand, additional model development efforts will have a higher likelihood of success in achieving an iterative discussion with stakeholders regarding feasible and desired products.

Gibson, Georgina A.↗

DOE OSTI2024

Building and Sustaining a Community Resource for Best Practices in Scientific Software: The Story of BSSw.io

The development of scientific software—a cornerstone of long-term collaboration and scientific progress—parallels the development of other types of software but still poses distinct challenges, especially in high-performance computing. Although web searches yield numerous resources on software engineering, there is still a scarcity specifically for scientific software development. Here, this article introduces the Better Scientific Software site (https://bssw.io), a platform that hosts a community of researchers, developers, and practitioners who share their experiences and insights on scientific software development. Since 2017, this collaborative hub has gained traction within the scientific computing community, attracting a growing number of readers and contributors eager to share ideas and elevate their software development practices. In sharing the BSSw.io site’s story, we hope to encourage further growth of the BSSw.io community through both readership and contributors, with a long-term goal of fostering culture change by increasing emphasis on best practices in scientific software.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Branched-chain amino acid specialization drove diversification within Calditenuaceae ( Caldarchaeia ) and enables their cultivation

Many thermophiles that are abundant in high-temperature geothermal systems have never been cultivated and are poorly understood, including deeply branching members of the archaeal phylum Thermoproteota. Here, we describe the genome-guided cultivation of one such organism, Calditenuis ramacidaminiphagus, and show that it has evolved a heterotrophic metabolism focused on branched-chain amino acids (BCAAs). Initially, fluorescence in situ hybridization and nanoscale secondary ion mass spectrometry (FISH-nanoSIMS) showed that Cal. ramacidaminiphagus assimilated amino acids rapidly in casamino acid-amended enrichment cultures. Metagenome and metaproteome analyses showed a high abundance and expression of BCAA transporter genes, suggesting a BCAA-focused metabolism. This inference was supported by the subsequent enrichment of Cal. ramacidaminiphagus in BCAA-fed cultures, reaching 2.66×10 6 cells/mL and 48.7% of the community, whereas it was outcompeted when polar amino acids were included. Metabolic reconstruction and metaproteomics suggest that BCAAs are channeled into the mevalonate pathway for lipid biosynthesis and fuel ATP production through the TCA cycle coupled with aerobic respiration and through production of branched-chain organic acids by overflow metabolism. Ancestral state reconstructions and phylogenetic analyses of 62 Caldarchaeales genomes revealed multiple horizontal transfers of BCAA transporters to the ancestor of the genus Calditenuis. Our study highlights the crucial role of BCAAs in the early evolution and niche of this genus, and suggests a high degree of resource partitioning even within low-diversity thermophilic communities.

Biological and medical sciences↗

DOE OSTI2021

The Value of Diversity in the Renewable Energy Industry and Research Community

Part of creating a successful solar industry is developing a capable workforce. It has been repeatedly shown that organizations and companies are more productive when they have diverse and inclusive cultures. The solar industry in the U.S. performs well in some aspects (non-white workforce, positive work environment) but drastically under-performs in many others. We discuss these metrics and how this impacts the renewable energy industry and the solar research community. We highlight some initial actions which are necessary to begin to remediate these deficiencies, such as demographic tracking, recruiting strategies, and mentoring. We also present the historical and ongoing efforts to improve the diversity and inclusion of the Photovoltaic Specialists Conference, particularly through the work of this year’s Diversity and Inclusion (D&I) oversight committee. This year’s D&I committee is implementing diversity tracking, a women’s lunch, a diversity lunch, childcare resources, pronouns on badges, gender-neutral restrooms, addressing accessibility issues, and publishing a diversity statement and code of conduct to the PVSC website.

diversity↗

DOE OSTI2023

Moderate high temperature is beneficial or detrimental depending on carbon availability in the green alga Chlamydomonas reinhardtii

High temperatures impair plant growth and reduce agricultural yields, but the underlying mechanisms remain elusive. The unicellular green alga Chlamydomonas reinhardtii is an excellent model to study heat responses in photosynthetic cells due to its fast growth rate, many similarities in cellular processes to land plants, simple and sequenced genome, and ample genetic and genomics resources. Chlamydomonas grows in light by photosynthesis and with externally supplied acetate as an organic carbon source. Understanding how organic carbon sources affect heat responses is important for the algal industry but remains understudied. We cultivated wild-type Chlamydomonas under highly controlled conditions in photobioreactors at 25 °C (control), 35 °C (moderate high temperature), or 40 °C (acute high temperature) with or without constant acetate supply for 1 or 4 day. Treatment at 35 °C increased algal growth with constant acetate supply but reduced algal growth without sufficient acetate. The overlooked and dynamic effects of 35 °C could be explained by induced acetate uptake and metabolism. Heat treatment at 40 °C for more than 2 day was lethal to algal cultures with or without constant acetate supply. Furthermore, our findings provide insights to understand algal heat responses and help improve thermotolerance in photosynthetic cells.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Genomic characterization of three marine fungi, including Emericellopsis atlantica sp. nov. with signatures of a generalist lifestyle and marine biomass degradation

ABSTRACT Marine fungi remain poorly covered in global genome sequencing campaigns; the 1000 fungal genomes (1KFG) project attempts to shed light on the diversity, ecology and potential industrial use of overlooked and poorly resolved fungal taxa. This study characterizes the genomes of three marine fungi: Emericellopsis sp. TS7, wood-associated Amylocarpus encephaloides and algae-associated Calycina marina. These species were genome sequenced to study their genomic features, biosynthetic potential and phylogenetic placement using multilocus data. Amylocarpus encephaloides and C. marina were placed in the Helotiaceae and Pezizellaceae (Helotiales) , respectively, based on a 15-gene phylogenetic analysis. These two genomes had fewer biosynthetic gene clusters (BGCs) and carbohydrate active enzymes (CAZymes) than Emericellopsis sp. TS7 isolate. Emericellopsis sp. TS7 ( Hypocreales , Ascomycota ) was isolated from the sponge Stelletta normani . A six-gene phylogenetic analysis placed the isolate in the marine Emericellopsis clade and morphological examination confirmed that the isolate represents a new species, which is described here as E. atlantica . Analysis of its CAZyme repertoire and a culturing experiment on three marine and one terrestrial substrates indicated that E. atlantica is a psychrotrophic generalist fungus that is able to degrade several types of marine biomass. FungiSMASH analysis revealed the presence of 35 BGCs including, eight non-ribosomal peptide synthases (NRPSs), six NRPS-like, six polyketide synthases, nine terpenes and six hybrid, mixed or other clusters. Of these BGCs, only five were homologous with characterized BGCs. The presence of unknown BGCs sets and large CAZyme repertoire set stage for further investigations of E. atlantica . The Pezizellaceae genome and the genome of the monotypic Amylocarpus genus represent the first published genomes of filamentous fungi that are restricted in their occurrence to the marine habitat and form thus a valuable resource for the community that can be used in studying ecological adaptions of fungi using comparative genomics.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

One-Step Regeneration of Hairy Roots to Induce High Tanshinone Plants in Salvia miltiorrhiza

Salvia miltiorrhiza is a traditional Chinese medicinal plant of Labiatae, which has been widely utilized to treat a variety of cardiovascular and cerebrovascular diseases. However, due to the long growth cycle, low content of active ingredients, and serious quality deterioration of S. miltiorrhiza , the use of biotechnology to improve S. miltiorrhiza to meet the growing demand for clinical applications has become a research hotspot. In this study, a novel one-step hairy root regeneration method was developed, which could rapidly obtain hairy roots and regenerated plants with high tanshinone content. By optimizing the parameters of Agrobacterium rhizogenes transformation in S. miltiorrhiza , it was finally established that the explants were infected in Ar.qual (OD 600 = 0.6) for 10 min, co-cultured for 3 days, and then screened on the screening medium containing 7.5 mg/l hygromycin, the maximum transformation frequency can reach 73.85%. GFP and PCR detection yielded a total of 9 positive transgenic hairy root lines and 11 positive transgenic regenerated plants. SmGGPPS1 was successfully overexpressed in positive transgenic regenerated plants, according to the results of qRT-PCR. The content of tanshinone IIA and cryptotanshinone were dramatically enhanced in transgenic regenerated plants and hairy roots by Ultra Performance Liquid Chromatography analysis. Based on the Agrobacterium-mediated transformation of S. miltiorrhiza , this study developed a new method for regenerating plants with transgenic hairy roots. This method provides a foundation for the breeding of S. miltiorrhiza and the sustainable development of medicinal plant resources, as well as provides a useful reference for the application of other species.

Su, Yuekai↗

DOE OSTI2023

Agent-based modeling and simulation for the circular economy: Lessons learned and path forward

Circular economy aims at decoupling human activities from resource use and creating wealth. However, many have questioned the link between increased circularity and sustainability, resulting in several methodological approaches being developed to answer that question. This article analyzes and discusses the insights gained from applying agent-based modeling and simulation to study the techno-economic and social conditions promoting circularity and sustainability. This article analyzes the benefits and limitations of this technology and discusses future methodology developments within the circular economy context. Moreover, six limits of the circular economy concept are used to interpret insights from the literature: thermodynamic limits, system boundary limits, limits posed by the physical scale of the economy, limits posed by path dependencies and lock-in, limits of governance and management, and limits of social and cultural definitions. Promising research avenues are to use this methodology with machine learning, industrial ecology methods, and detailed geographic information.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2025

Cyber-Informed Engineering (CIE) Guide for States

The Cyber-Informed Engineering (CIE) Guide for States provides state energy offices, public utility commissions, and partner organizations with a structured framework for integrating cyber-resilient engineering practices into energy planning, grantmaking, interconnection processes, and workforce development. As grid digitalization and the adoption of distributed energy resources accelerate, states face expanding cyber-physical risks that traditional cybersecurity measures alone cannot fully address. CIE offers a proactive, consequence-focused engineering methodology that emphasizes eliminating or mitigating high-impact failure modes through design, physical controls, and operational safeguards. The guide outlines the 12 core CIE principles, demonstrates their application through state-focused use cases—including grant evaluation rubrics, interconnection reviews, allow-list development, and training programs—and provides practical tools such as scoring frameworks, impact assessment methods, and implementation checklists. It also highlights pathways for state–utility collaboration and opportunities for technical assistance from national laboratories. By adopting CIE, states can enhance grid reliability, reduce lifecycle costs, strengthen supply-chain assurance, and foster a security-aware engineering culture that aligns with broader resilience and modernization goals. November 2025

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2025

Cyber-Informed Engineering (CIE) Guide for States

29 - ENERGY PLANNING, POLICY AND ECONOMY↗

DOE OSTI2025

Low-Cost Screening of Algae for Extreme Tolerance to pH, Temperature, Salinity, and Light

AbstractBioprospecting algae strains with tolerance to extreme conditions such as pH, temperature, salinity, and light is crucial for advancing biotechnology and environmental applications. However, traditional screening methods often involve significant costs and labor, restricting their accessibility and practical use. In this study, we developed and validated low-cost, high-throughput screening techniques, predominantly employing agar plates and liquid culture assays, to effectively differentiate tolerance levels among various algae strains. The methodologies were optimized using the model microalgaChlamydomonas reinhardtiiand its closely related speciesChlamydomonas incertaand the recently discovered extremophilicChlamydomonas pacifica. We systematically evaluated the algae for tolerance to extremes by establishing precise gradients of pH (acidic to alkaline conditions), salinity (0 to 5 M NaCl), temperature (34–42°C), and light intensity (40 to 2977 μE·m⁻²·s⁻¹). Our results demonstrated that these cost-effective, agar plate-based methods effectively distinguished algae strains exhibiting superior tolerance to extreme environmental conditions. These screening techniques not only provided clear differentiation among the closely related strains but also delivered reproducible outcomes suitable for scaling up to larger bioprospecting efforts. Furthermore, the affordability and simplicity of these methods facilitate their implementation in resource-limited laboratories, thereby broadening participation in algae bioprospecting endeavors. This study highlights the potential of low-cost, accessible screening techniques to significantly enhance the discovery and characterization of algal strains with extreme traits. Ultimately, these methods support the development of robust algae-based resources, driving innovation in diverse industrial processes and environmental solutions.Graphical Abstract

Saucedo, Barbara (ORCID:0009000008860839)↗