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DOE OSTI2024

Did the exposure of coacervate droplets to rain make them the first stable protocells?

Membraneless coacervate microdroplets have long been proposed as model protocells as they can grow, divide, and concentrate RNA by natural partitioning. However, the rapid exchange of RNA between these compartments, along with their rapid fusion, both within minutes, means that individual droplets would be unable to maintain their separate genetic identities. Hence, Darwinian evolution would not be possible, and the population would be vulnerable to collapse due to the rapid spread of parasitic RNAs. In this study, we show that distilled water, mimicking rain/freshwater, leads to the formation of electrostatic crosslinks on the interface of coacervate droplets that not only suppress droplet fusion indefinitely but also allow the spatiotemporal compartmentalization of RNA on a timescale of days depending on the length and structure of RNA. We suggest that these nonfusing membraneless droplets could potentially act as protocells with the capacity to evolve compartmentalized ribozymes in prebiotic environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

From 2D to 4D: a containerized workflow and browser to explore dynamic chromatin architecture

Background Characterizing the physical organization of the genome is essential for understanding long-range gene regulation, chromatin compartmentalization, and epigenetic accessibility. Hi-C experiments generate two-dimensional (2D) genome-wide contact maps of chromatin interactions by capturing the spatial proximity between genomic loci, which reveal interaction frequencies but lack the spatial resolution needed to interpret the three-dimensional (3D) genome structure(s). Emerging evidence suggests that epigenetic regulation is closely linked to 3D genome architecture, and that structural changes over time (4D) drive key biological processes in development, disease, and environmental response. Thus, integrating 3D structure with functional data is critical for a more complete understanding of genome regulation. Previous work, most notably the 4DHiC chromosome modeling framework, has shown that physical multi-dimensional modeling approaches rooted in polymer physics and molecular dynamics can resolve these structures at biologically meaningful resolutions by integrating temporal Hi-C data with physical constraints to uncover dynamic chromosome reorganization. Thus, molecular dynamics simulations, constrained by Hi-C contact matrices, can resolve fine-scale structural changes and reveal functionally significant transitions in chromatin conformation. Results Herein, we present the 4D Genome Browser Workflow (4DGBWorkflow) and the 4D Genome Browser (4DGB). The algorithm is based on the 4DHiC method, and the containerized tool is an end-to-end workflow that can transform, filter, and view 4D epigenomics and chromatin datasets, allowing non-specialists to apply three-dimensional modeling principles to diverse datasets and experimental conditions. The software executes on a laptop running macOS, Linux or Windows. From input Hi-C files (.hic), the 4DGBWorkflow produces 3D reconstructions of chromosomes, integrates the reconstruction with track data (e.g., epigenetic marks, transcriptome profiles), and provides comparative visualization of the results in a single workflow. Conclusions The 4DGBWorkflow and 4D Genome Browser are open-source tools for comparative analysis and visualization of 4D chromosome datasets, including chromatin architecture and epigenomic signals. Automatic integration of Hi-C data with molecular dynamics democratizes the construction of time resolved 3D genome structures, simplifying complex simulations and data integration schemes.

3D Genome Browser↗

DOE OSTI2024

Data for "Design of Diverse, Functional Mitochondrial Targeting Sequences Across Eukaryotic Organisms Using Variational Autoencoder"

Mitochondria play a key role in energy production and metabolism, making them a promising target for metabolic engineering and disease treatment. However, despite the known influence of passenger proteins on localization efficiency, only a few protein-localization tags have been characterized for mitochondrial targeting. To address this limitation, we leverage a Variational Autoencoder to design novel mitochondrial targeting sequences. In silico analysis reveals that a high fraction of the generated peptides (90.14%) are functional and possess features important for mitochondrial targeting. We characterize artificial peptides in four eukaryotic organisms and, as a proof-of-concept, demonstrate their utility in increasing 3-hydroxypropionic acid titers through pathway compartmentalization and improving 5-aminolevulinate synthase delivery by 1.62-fold and 4.76-fold, respectively. Moreover, we employ latent space interpolation to shed light on the evolutionary origins of dual-targeting sequences. Overall, our work demonstrates the potential of generative artificial intelligence for both fundamental research and practical applications in mitochondrial biology.

AI/ML↗

DOE OSTI2022

NRAP-Open-IAM: NRAP Open Source Integrated Assessment Model

Note: This is the last version (a2.6.1) of NRAP-Open-IAM released during NRAP Phase II in 2022. The latest version of NRAP-Open-IAM is available here: https://edx.netl.doe.gov/dataset/phase-iii-nrap-open-iam NRAP-Open-IAM is an open-source software product that enables quantification of containment effectiveness and leakage risk at storage sites in the context of system uncertainties and variability. NRAP-Open-IAM represents the next-generation in a line of systems-based computational models developed for quantitative geological carbon storage (GCS) risk assessment. The model comprises a set of reduced-order and analytical models of various components of the GCS system, potential leakage pathways, receptors of concern including impact to groundwater resources and the atmosphere, a framework to support stochastic simulation, time stepping, uncertainty quantification, other analytical functionality for scenario and risk-performance evaluation, and a basic graphical user interface to support scenario development, data input simulation definition, and basic post-processing and results display. As the NRAP Open-IAM functionality continues to evolve, we continue to add to its capability to develop quantitative, probabilistic, and time-dependent profiles of the evolution of risk at a GCS site and evaluate the influence of uncertain parameters on uncertainty in predicted risk. It can be used to quantify the dynamics of reservoir saturation plume and pressure-affected area, for evaluation of the area of potential groundwater impact (i.e., Area of Review) and monitoring requirements to support cost and regulatory analysis, and for consideration of different post-injection site care and closure scenarios. This submission contains the current version of NRAP-Open-IAM available for evaluation and testing. To use the NRAP-Open-IAM, download the source code (https://edx.netl.doe.gov/dataset/08f396c8-bc5f-44ad-a028-6e98a6ea6d70/resource/4c24a3da-3b40-4ffe-9892-c807ae9f8760) then open the NRAP-Open-IAM user's guide (https://edx.netl.doe.gov/dataset/08f396c8-bc5f-44ad-a028-6e98a6ea6d70/resource/8b27335a-343c-4836-b8a3-3ad0bdc9e669) to read more about the tool. Installation instructions for Windows, Mac, and Linux can be found in the "installers" folder of the extracted NRAP-Open-IAM folder and describe setup of environment (e.g., Python libraries) needed for proper work of the tool. Test of installation can be done by running "python openiam_setup_tests.py" in the "setup" folder. The installation test also runs a test suite to see if the NRAP-Open-IAM has been installed correctly. To run the test suite separately, run "python iam_test.py" in the "test" folder. User's guide: https://edx.netl.doe.gov/dataset/08f396c8-bc5f-44ad-a028-6e98a6ea6d70/resource/8b27335a-343c-4836-b8a3-3ad0bdc9e669 Developer's guide: https://edx.netl.doe.gov/dataset/08f396c8-bc5f-44ad-a028-6e98a6ea6d70/resource/3bc6ee7d-609d-4eb6-80ba-fa6130ee0313 Reservoir simulation data used in some examples distributed with NRAP-Open-IAM: - Kimberlina: https://edx.netl.doe.gov/dataset/08f396c8-bc5f-44ad-a028-6e98a6ea6d70/resource/eb62cece-61b2-4037-9b6d-32407dde2ab8 - Kimberlina (compartmentalized): https://edx.netl.doe.gov/dataset/08f396c8-bc5f-44ad-a028-6e98a6ea6d70/resource/366f9530-3b32-4b84-affe-ab2df1d9a8b5 - FutureGen 2.0: https://edx.netl.doe.gov/dataset/futuregen-2-0-1008-simulation-reservoir-lookup-table NRAP-Open-IAM GitLab repository: https://gitlab.com/NRAP/OpenIAM Related publications: - Bacon, D., Yonkofski, C., Brown, C., Demirkanli, D. and Whiting, J., 2019. Risk-based post injection site care and monitoring for commercial-scale carbon storage: Reevaluation of the FutureGen 2.0 site using NRAP-Open-IAM and DREAM. International Journal of Greenhouse Gas Control 90: 102784. - Bacon, D. Demirkanli, D., and White, S., 2020. Probabilistic risk-based Area of Review (AoR) determination for a deep-saline carbon storage site. International Journal of Greenhouse Gas Control 102: 103153. - Harp, D., Oldenburg, C., and Pawar, R., 2019. A metric for evaluating conformance robustness during geologic CO2 sequestration operations. International Journal of Greenhouse Gas Control 85: 100-108. - Lackey, G., Vasylkivska, V., Huerta, N., King, S., and Dilmore, R., 2019. Managing well leakage risks at a geologic carbon storage site with many wells, International Journal of Greenhouse Gas Control, 88 :182-194. - Vasylkivska, V., Dilmore, R., Lackey, G., Zhang, Y., King, S., Bacon, D., Chen, B., Mansoor, K., and Harp, D., 2021. NRAP-Open-IAM: A flexible open-source integrated assessment model for geologic carbon storage risk assessment and management, Environmental Modelling & Software, 143: 105114. Presentations: - Chen, B., Harp, D., and Pawar, R., A data assimilation approach (ES-MDA) coupling with NRAP-Open-IAM for quantifying uncertainty reduction in geological CO2 sequestration. AGUFM 2019: T44A-02. - Chen, B., and Harp, D., Improving risk analysis precision for geologic CO2 sequestration by quantifying the uncertainty reduction before and after acquiring monitoring data. 14th Greenhouse Gas Control Technologies Conference, Melbourne, Australia, 2018, pp. 21-26. - Harp, D., National Risk Assessment Partnership Task 2: Containment Assurance. No. LA-UR-19-28654, Los Alamos National Laboratory (LANL), Los Alamos, NM (United States), 2019. - Vasylkivska, V., King, S., Bacon, D., Harp, D., Chen, B., Mansoor, K., Onishi, T., Yang, Y., Zhang, Y., and Keating, E., NRAP-Open-IAM: An open-source integrated assessment model, poster, Mastering the Subsurface Through Technology Innovation, Partnerships and Collaboration: Carbon Storage and Oil and Natural Gas Technologies Review Meeting, Pittsburgh, PA, August 13-16, 2018. - Vasylkivska, V., Lackey, G., King, S., Wentworth, A., Huerta, N., Creason, C., DiGiulio, J., Yang, Y., and Dilmore, R., Long-term risk analysis of a geologic CO2 storage project during the post-injection period, SIAM Conference on Computational Science and Engineering, Spokane, WA, February 25-March 1, 2019. - Vasylkivska, V., Overview of the NRAP-Open-IAM tool for carbon storage (beta release), 2019 Annual NRAP Tool Users Meeting, Pittsburgh, PA, August 27, 2019. - Vasylkivska, V., Bacon, D., Chen, B., Dilmore, R., Harp, D., King, S., Lackey, G., Lindner, E., Liu, G., Mansoor, K. and Zhang, Y., NRAP-Open-IAM: A new, open-source code for integrated assessment of geologic carbon storage containment effectiveness and leakage risk, poster, American Geophysical Union Fall Meeting 2020 (virtual meeting), December 2020. - Vasylkivska, V., NRAP open-source integrated assessment model and relevant application, oral presentation, NRAP workshop "NRAP Tools for Geologic Carbon Storage Risk-Based Decision Making" held in conjunction with Groundwater Protection Council (GWPC) 2021 Annual Forum (virtual meeting), Salt Lake City, UT, September 2021. - Vasylkivska, V., NRAP-Open-IAM: open-source integrated assessment model, digital poster/demonstration, software demonstration session, 2022 Carbon Management Project Review Meeting, August 16, 2022

AoR↗

DOE OSTI2022

Comparative genomic and transcriptomic analyses of trans-kingdom pathogen Fusarium solani species complex reveal degrees of compartmentalization

Background: The Fusarium solani species complex (FSSC) comprises fungal pathogens responsible for mortality in a diverse range of animals and plants, but their genome diversity and transcriptome responses in animal pathogenicity remain to be elucidated. We sequenced, assembled and annotated six chromosome-level FSSC clade 3 genomes of aquatic animal and plant host origins. We established a pathosystem and investigated the expression data of F. falciforme and F. keratoplasticum in Chinese softshell turtle (Pelodiscus sinensis) host. Results: Comparative analyses between the FSSC genomes revealed a spectrum of conservation patterns in chromosomes categorised into three compartments: core, fast-core (FC), and lineage-specific (LS). LS chromosomes contribute to variations in genomes size, with up to 42.2% of variations between F. vanettenii strains. Each chromosome compartment varied in structural architectures, with FC and LS chromosomes contain higher proportions of repetitive elements with genes enriched in functions related to pathogenicity and niche expansion. We identified differences in both selection in the coding sequences and DNA methylation levels between genome features and chromosome compartments which suggest a multi-speed evolution that can be traced back to the last common ancestor of Fusarium. We further demonstrated that F. falciforme and F. keratoplasticum are opportunistic pathogens by inoculating P. sinensis eggs and identified differentially expressed genes also associated with plant pathogenicity. These included the most upregulated genes encoding the CFEM (Common in Fungal Extracellular Membrane) domain. Conclusions: The high-quality genome assemblies provided new insights into the evolution of FSSC chromosomes, which also serve as a resource for studies of fungal genome evolution and pathogenesis. This study also establishes an animal model for fungal pathogens of trans-kingdom hosts.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Design of diverse, functional mitochondrial targeting sequences across eukaryotic organisms using variational autoencoder

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

EV Charging Infrastructure Energization An Overview of Approaches for Simplifying and Accelerating Timelines to Processing EV Charging Load Service Requests

The United States has seen significant growth in electric vehicle (EV) adoption, leading to increased demand for EV charging infrastructure. Over the past decade, EV charging infrastructure site developers, site hosts, and electric distribution utilities have navigated the process to integrate chargers onto the electric grid. Site developers and site hosts have raised the alarm that the integration process for high-powered EV charging projects does not meet the needs of the EV market for timeliness or cost. High-powered charging stations typically require a load service request or an agreement with the local utility to connect to the grid. The process of energizing a new high-powered charging site can be complex and time-consuming, often taking up to 2 years. This timeline is the result of current utility energization processes having been designed for construction projects that take longer to build (i.e., buildings). The specific challenges stem from various factors, including compartmentalization in application processes, the integration of EV charging process approvals with other distributed energy resources (DERs), and the need to ensure grid reliability. The energization process needs to evolve to meet the growing demand for high-powered EV charging. This white paper compiles information gathered through various conversations with key stakeholders, including utilities, utility regulators, EV charging operators, site developers, and authorities having jurisdiction (AHJ) as well as through an extensive literature review. This document identifies the challenges and provides potential solutions to streamline the process of connecting EV charging infrastructure to the power grid in the United States, serving as a starting point for future conversations around these solutions. The solutions noted in this white paper require collaborative efforts among utilities, regulators, and EV charging infrastructure developers to streamline the grid connection process for EV charging infrastructure. They are broadly organized into four areas: 1. Increase data access and transparency: Develop automated load service request tools, integrate hosting capacity and load service request analyses, incorporate EV adoption forecasts, and provide transparency on the processing queue. 2. Improve energization processes and timing: Create fast-track options based on prescreening criteria, provide flexibility or phased approvals in the load service request/interconnection process, build internal knowledge within utilities about EV charging technologies, and provide standardized workforce training. 3. Promote economic efficiency: Right size distribution components to accurately reflect the load requirements of EV charging infrastructure, make proactive investments in grid infrastructure based on EV adoption forecasts and growth projections, and consider energy equity and environmental justice factors such as equitable access to EV charging when planning infrastructure. 4. Improve grid reliability and resilience: Use load management/power control systems (PCS) at EV charging stations, adopt and implement harmonized standards for communication protocols and information models between the EV charging and grid control infrastructure, and address cybersecurity considerations by implementing robust security measures and standards for EV charging infrastructure—with particular emphasis on clarifying the security requirements for the interface to the grid. The objective of the solutions proposed in this white paper is to accelerate the timeline and decrease costs associated with connecting EV charging infrastructure to the grid. Electric utilities, utility regulators, EV charging infrastructure developers, and site hosts will first need to understand which solutions are available in their service territory, and if warranted, which combination of solutions would support their specific needs. Through the successful implementations of solutions at scale detailed here, industry will demonstrate a new and innovative ecosystem where timely deployment and energization of EV charging infrastructure with greater grid resiliency and reliability is a reality.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2021

3-D Geologic Controls of Hydrothermal Fluid Flow at Brady Geothermal Field, Nevada using PCA

In many hydrothermal systems, fracture permeability along faults provides pathways for groundwater to transport heat from depth. Faulting generates a range of deformation styles that cross-cut heterogeneous geology, resulting in complex patterns of permeability, porosity, and hydraulic conductivity. Vertical connectivity (a through going network of permeable areas that allows advection of heat from depth to the shallow subsurface) is rare and is confined to relatively small volumes that have highly variable spatial distribution. This local compartmentalization of connectivity represents a significant challenge to understanding hydrothermal circulation and for exploring, developing, and managing hydrothermal resources. Here, we present an evaluation of the geologic characteristics that control this compartmentalization in hydrothermal systems through 3-D analysis of the Brady geothermal field in western Nevada. A published 3-D geologic map of the Brady area is used as a basis to develop structural and geological variables that are hypothesized to control or effect permeability or connectivity. The 3-D distribution of these variables is compared to the distribution of productive and non-productive fluid flow intervals along production wells and non-productive wells via principal component analysis (PCA). This comparison elucidates which geologic and structural variables are most closely associated with productive fluid flow intervals. Results indicate that production intervals at Brady are located: (1) within or near to known and stress-loaded macro-scale faults, and (2) in areas of high fault and fracture density. This submission includes the published journal article detailing this work, the published 3-D geologic map of the Brady Geothermal Area used as a basis to develop structural and geological variables that are hypothesized to control or effect permeability or connectivity, 3-D well data, along which geologic data were sampled for PCA analyses, and associated metadata file. This work was done using existing R programs.

15 GEOTHERMAL ENERGY↗

DOE OSTI2024

Identifying recharge sources and their impacts on a North Central New Mexico shallow aquifer using unsupervised machine learning

In this article, shallow aquifers are important but highly variable resources in arid to semi-arid regions. Limited shallow aquifer volume results in high sensitivity to recharge fluctuations, which can impact the local fauna and flora, and transport of contaminants in the aquifer or vadose zone. Aquifer response to external forcing (e.g., precipitation) is usually solved by estimating aquifer parameters and running physics-based models to match known fluctuations of hydraulic head. However, this technique is time and computationally expensive. Furthermore, high aquifer complexity decreases precision in physics-based models. Alternatively supervised machine learning is used to predict aquifer dynamics. However, these techniques rely on input data and struggle to interpret aquifer response for missing sources (i.e., snowpack data). To counter these problems, we propose an unsupervised machine learning technique (NMFk) to estimate the impact of different sources on aquifer recharge. NMFk is used to understand the influence of external forcing on shallow aquifer recharge in the Pajarito Plateau (Los Alamos, NM, USA). The results show how NMFk can be used to reduce the data dimension in a complex field dataset to three recharge signals that cause fluctuations within the field data. Here, the source signals are interpreted as rainfall, snowmelt, and a delayed aquifer response to the previous two signals. These results evidence how heterogeneous aquifers delimited by canyons incised into the Pajarito Plateau respond in similar ways to the source signals identified by NMFk. Furthermore, results show the importance of the local geology where faults act as sinks, and anthropogenic disturbances can facilitate infiltration amplifying the interpreted signal.

54 ENVIRONMENTAL SCIENCES↗