Results for “Completeness” — Page 7

DOE OSTI2025

Combining genome-wide association studies and expression quantitative trait nucleotide mapping with molecular and genetic validations to identify transcriptional networks regulating drought tolerance in Populus

Objectives: (i). To deploy a large-scale experimental drought trial for up to 1000 unique genotypes of Populus equipping the sites with controlled irrigation and drought treatments that are fully automated and monitored. FULLY COMPLETED (ii) To test the hypothesis that a suite of traits identified for drought tolerance in P. nigra can be measured in drought and control treatments in the wide germplasm collection of P. trichocarpa. FULLY COMPLETED (iii) To use established and novel GWAS model approaches to identify gene loci linked to drought tolerance traits on interest in P. trichocarpa. FULLY COMPLETED (iv) To undertake comparative analysis of GWAS results for drought tolerance traits in P. nigra and P. trichocarpa. PARTIALLY COMPLETED – remains active (v) Using RNAseq in P. trichocarpa, in droughted and control treatments to identify cis- and trans-regulated eQTN. FULLY COMPLETED (vi) Validate up to 50 cis-QTNs, from network hubs using transient protoplast assays. FULLY COMPLETED (vii) To establish Agrobacterium-based gene editing protocols in Populus. FULLY COMPLETED (viii) To utilize early leads from previous research to investigate at least 6 candidate genes for drought tolerance in Populus. FULLY COMPLETED (ix) To validate up to 20 candidate genes for drought tolerance in P. trichocarpa refined from the long-list tested in the transient assays for cis-acting hub gene targets. PARTIALLY COMPLETED- remains active.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Flexible Fuel Electric Hybrid Glass Furnace Demonstration

The furnace contractor completed General Arrangement (GA) layouts and Piping and Instrumentation Diagrams (P&ID) for both furnaces during this reporting period. Preliminary equipment lists accompanied this work. Control system architecture in progress. Key furnace design elements and deliverables on track to be complete by end of phase. The facilities design and integration contractor completed a 3D scan and modeling of the facility. The work during this period focused on preliminary design with a focus on overall project scope and feasibility. This key work supports the overall project deliverables for 30% preliminary engineering and Preliminary Design Report (PDR) which are on track to be complete by the end of the phase. These deliverables are approximately 50% complete through the end of this reporting period. The batch house operations design contractor continues development of site plan and General Arrangement (GA) layout to support the 30% preliminary engineering and design package. This work is 60% complete by the end of this reporting period and is on track to be complete by the end of the phase.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2024

Measuring Thread Timing to Assess the Feasibility of Early-Bird Message Delivery Across Systems and Scales

Early-bird communication is a communication/computation overlap technique that leverages fine-grained communication to improve application run-time. Communication is divided such that each individual thread can initiate transmission of its portion of the data upon completion rather than waiting for a dedicated communication phase. The benefit of early-bird communication depends on the completion timing of the individual threads: On the one hand, if all threads are complete at nearly the same time, the overheads of sending multiple messages will accumulate, leading to performance that is worse than if a single message had been sent. On the other hand, if thread completions are spread out in time, those that complete earlier can send data while others continue working, leading to performance that is better than if a single message had been sent. The challenge is that the completion times are currently unknown and can vary based on application, problem size, system software, and underlying hardware. In this paper, we address this lacuna by measuring and evaluating the potential overlap afforded by early-bird communication for a selection of proxy applications. These measurements help us understand whether a given application could benefit from early-bird communication. Here, we present our technique for gathering this data and evaluate data collected from three proxy applications: MiniFE, MiniMD, and MiniQMC. Each application is run on three systems with distinct CPU architectures and strong scales across three run sizes. To characterize the behavior of these workloads, we study the trends of thread timings at both a macro level, across all threads across all runs of an application, and a micro level, that is, within a single process of a single run. We observe that our tested applications exhibit significantly different thread arrival distributions. The machine used had a significant impact, with the window of potential overlap varying by as much as an order of magnitude.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Decomposing a San Francisco estuary microbiome using long-read metagenomics reveals species- and strain-level dominance from picoeukaryotes to viruses

ABSTRACT Although long-read sequencing has enabled obtaining high-quality and complete genomes from metagenomes, many challenges still remain to completely decompose a metagenome into its constituent prokaryotic and viral genomes. This study focuses on decomposing an estuarine metagenome to obtain a more accurate estimate of microbial diversity. To achieve this, we developed a new bead-based DNA extraction method, a novel bin refinement method, and obtained 150 Gbp of Nanopore sequencing. We estimate that there are ~500 bacterial and archaeal species in our sample and obtained 68 high-quality bins (>90% complete, <5% contamination, ≤5 contigs, contig length of >100 kbp, and all ribosomal and tRNA genes). We also obtained many contigs of picoeukaryotes, environmental DNA of larger eukaryotes such as mammals, and complete mitochondrial and chloroplast genomes and detected ~40,000 viral populations. Our analysis indicates that there are only a few strains that comprise most of the species abundances. IMPORTANCE Ocean and estuarine microbiomes play critical roles in global element cycling and ecosystem function. Despite the importance of these microbial communities, many species still have not been cultured in the lab. Environmental sequencing is the primary way the function and population dynamics of these communities can be studied. Long-read sequencing provides an avenue to overcome limitations of short-read technologies to obtain complete microbial genomes but comes with its own technical challenges, such as needed sequencing depth and obtaining high-quality DNA. We present here new sampling and bioinformatics methods to attempt decomposing an estuarine microbiome into its constituent genomes. Our results suggest there are only a few strains that comprise most of the species abundances from viruses to picoeukaryotes, and to fully decompose a metagenome of this diversity requires 1 Tbp of long-read sequencing. We anticipate that as long-read sequencing technologies continue to improve, less sequencing will be needed.

Lui, Lauren M.↗

DOE OSTI2024

Low Purge and Mercury Recovery Testing with Sludge Batch 10 Tank 40 Simulant

Researchers at the Savannah River National Laboratory (SRNL) have completed testing as requested by Savannah River Mission Completion (SRMC) to perform experiments to determine the impact of using a lower or inert purge in Sludge Batch (SB) 10 processing under the Nitric-Glycolic Acid (NGA) flowsheet. A key objective of this testing was also to determine the mercury speciation and recovery during each experiment. The testing was performed as part of the SB10 Technical Task Request (TTR) and Task Technical and Quality Assurance Plan (TTQAP). Two sets of tests were performed, and a Run Plan was approved prior to each set of experiments to document the planned testing. Three initial experiments were completed to determine whether a low air purge would be beneficial to CPC processing at higher acid stoichiometry (110%) based on the Koopman minimum acid (KMA) equation (116% Hsu). One of the tests, an inert nitrogen purge experiment, was also completed to demonstrate that excluding oxygen did not introduce any new hazards. The experiments were designed to be identical except for the change in purge gas and purge flowrate from run to run. After reviewing the results from the initial three experiments, six additional tests were proposed by SRNL to support the lower purge study and to look for processing alternatives for improving mercury recovery. These additional six tests were all completed at a very low acid stoichiometry to mimic the pH experienced during processing in DWPF (~7). DWPF is processing SB10 sludge at an acid stoichiometry of 90% based on the Hsu equation. The additional SRNL experiments were performed at an acid stoichiometry of 62.5% KMA stoichiometry (66.3% Hsu) to produce a Sludge Receipt and Adjustment Tank (SRAT) product with a pH of about 7. All experiments used simulants of both SWPF streams, although no entrained solvent was added during any of the experiments

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2024

Process–Property–Performance Mapping of Additively Manufactured 316H Stainless Steel Components

The Advanced Materials and Manufacturing Technologies Program is focused on accelerating the development of advanced materials and components fabricated via additive manufacturing, and is using laser powder bed fusion (LPBF) of 316H stainless steel as an initial case study. In the previous fiscal year, miniature high-throughput specimens were printed on multiple LPBF systems to provide initial processing windows to minimize porosity and limit epitaxial grain growth during prints. This fiscal year, scaled builds were completed on three different LPBF systems at ORNL: a GE Concept Laser M2, a Renishaw AM400, and an EOS M290. Builds on the Concept Laser were conducted on multiple powder lots and processing parameter ranges to provide microstructure effects on time-independent and time-dependent mechanical properties. Builds on the Renishaw were produced using Oak Ridge National Laboratory (ORNL)-optimized printing parameters and Argonne National Laboratory (ANL)-optimized printing parameters to compare outcomes of parallel process optimization efforts at different national laboratories on the same LPBF system. Similarly, the build completed on the EOS M290 replicated the processing parameters of builds completed at Los Alamos National Laboratory (LANL). Optical microscopy and electron backscatter diffraction characterization was completed on all builds. In addition to the general round robin characterization, this work-package generated time-independent data, including tensile and fracture toughness test data on scaled Concept Laser builds as a function of processing parameters and post-build heat treatment. This analysis is complimentary to work in parallel work packages aiming to establish heat treatment and processing effects on time-dependent properties. It was found that although the stress-relief heat treatment provides the highest strength at lower-temperatures, tensile strength begins to converge at higher temperatures regardless of heat treatment condition. In addition, the more rigorous solution annealing and hot-isostatic pressing post-build heat treatments result in higher fracture toughness than the stress-relieved condition. The root-causes of the lower fracture toughness of the stress-relieved LPBF 316H material was informed via a stress-relief optimization study on a scaled concept laser print, where it was found that although dislocation recovery was largely complete after only a couple hours at 650°C, the extended hold of the current 24h heat treatment employed on scaled builds likely caused increased carbide volume fractions along the LPBF 316H grain boundaries, thereby deteriorating crack propagation resistance. This trend was seen to become more deleterious with additional increases of stress-relief temperature to 750°C or 850°C. These results have helped inform a new optimal stress-relief annealing condition for LPBF 316H for future campaign testing (650°C for 2h).

36 MATERIALS SCIENCE↗

DOE OSTI2025

Fiscal Year 2025 Software Quality Assurance Activities for the ARC Software

The continued goal of the ARC SQA project in the Advanced Reactor Technologies program of DOE is to resolve the QA gaps for the ARC software that limit, or prevent, commercialization of the software for industry users. This project started in earnest in fiscal year 2023 which saw the entire code system moved from a SVN repository to a GitLab repository and an associated software quality assurance plan (SQAP) developed and ratified. Most of the QA gaps in the ARC software were identified in collaboration with industry partners and work begin in fiscal year 2023 and continued through 2024 and 2025. The continuous integration testing was extended to RCT, DASSH, and SE2ANL. Minor changes were required to the original continuous integration methodology to make this happen. When full confidence in the methodology is complete, a report will be created to detail the automated regression testing methodology and minor reports will be created to detail the tolerance settings that have been applied to the output for each ARC code. The primary documentation that is missing includes user manuals, user guides, software verification reports, and code coverage assessments. The DASSH, SE2ANL, and SE2RCT manuals were completed this fiscal year. A review of the SE2ANL software identified that it is unrealistic to include updated correlations or different geometry models and it was scheduled for deprecation in favor of DASSH. The SE2ANL manual is essential for SE2RCT as they are similar but quite different in purpose. The only piece of software missing a manual consistent with the source code is NUBOW-3D which is a focus of the coming year. The code coverage report for DIF3D was updated and code coverage reports were created for REBUS, RCT, PERSENT, GAMSRC, and DASSH. Minor coverage issues were identified for all of these pieces of software which did not prevent the work done to transition them to the OneAPI compiler. Because SE2ANL was scheduled for deprecation, it was not transitioned, but it was successfully tested with the OneAPI compiler. This leaves SE2RCT and NUBOW-3D as the only pieces of software not transitioned to OneAPI and further work is required to get SE2RCT to work properly. The SE2RCT software transition will begin early next year while the NUBOW-3D software requires a manual before it can begin. Software verification work has been completed for DIF3D, REBUS, GAMSOR, GAMSRC, VARPOW, EvaluateFlux, and SUMMAR. The PERSENT software verification work was completed this year which was somewhat delayed because of unexpected bugs in the software. The PERSENT manual was updated to detail some of the issues and discuss the bowing reactivity worth feature added in the previous fiscal year. The RCT, DASSH, SE2RCT, and NUBOW-3D software are the only maintained pieces of software without verification reports. The software verification work for DASSH will be a focus in the upcoming fiscal year and it is hoped that some of the test cases created can serve as verification tests for SE2RCT. The NUBOW-3D work will begin when the manual and requirements report are completed. Only minor industry partner software development funds were provided this year. The DASSH software was updated to handle general axial geometry for each assembly and the NUBOW-3D software was updated to incorporate a new input format and better output. Overall progress on resolving the QA gaps has been good this year.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2025

Fiscal Year 2025 Software Quality Assurance Activities for the ARC Software

The continued goal of the ARC SQA project in the Advanced Reactor Technologies program of DOE is to resolve the QA gaps for the ARC software that limit, or prevent, commercialization of the software for industry users. This project started in earnest in fiscal year 2023 which saw the entire code system moved from a SVN repository to a GitLab repository and an associated software quality assurance plan (SQAP) developed and ratified. Most of the QA gaps in the ARC software were identified in collaboration with industry partners and work begin in fiscal year 2023 and continued through 2024 and 2025. The continuous integration testing was extended to RCT, DASSH, and SE2ANL. Minor changes were required to the original continuous integration methodology to make this happen. When full confidence in the methodology is complete, a report will be created to detail the automated regression testing methodology and minor reports will be created to detail the tolerance settings that have been applied to the output for each ARC code. The primary documentation that is missing includes user manuals, user guides, software verification reports, and code coverage assessments. The DASSH, SE2ANL, and SE2RCT manuals were completed this fiscal year. A review of the SE2ANL software identified that it is unrealistic to include updated correlations or different geometry models and it was scheduled for deprecation in favor of DASSH. The SE2ANL manual is essential for SE2RCT as they are similar but quite different in purpose. The only piece of software missing a manual consistent with the source code is NUBOW-3D which is a focus of the coming year. The code coverage report for DIF3D was updated and code coverage reports were created for REBUS, RCT, PERSENT, GAMSRC, and DASSH. Minor coverage issues were identified for all of these pieces of software which did not prevent the work done to transition them to the OneAPI compiler. Because SE2ANL was scheduled for deprecation, it was not transitioned, but it was successfully tested with the OneAPI compiler. This leaves SE2RCT and NUBOW-3D as the only pieces of software not transitioned to OneAPI and further work is required to get SE2RCT to work properly. The SE2RCT software transition will begin early next year while the NUBOW-3D software requires a manual before it can begin. Software verification work has been completed for DIF3D, REBUS, GAMSOR, GAMSRC, VARPOW, EvaluateFlux, and SUMMAR. The PERSENT software verification work was completed this year which was somewhat delayed because of unexpected bugs in the software. The PERSENT manual was updated to detail some of the issues and discuss the bowing reactivity worth feature added in the previous fiscal year. The RCT, DASSH, SE2RCT, and NUBOW-3D software are the only maintained pieces of software without verification reports. The software verification work for DASSH will be a focus in the upcoming fiscal year and it is hoped that some of the test cases created can serve as verification tests for SE2RCT. The NUBOW-3D work will begin when the manual and requirements report are completed. Only minor industry partner software development funds were provided this year. The DASSH software was updated to handle general axial geometry for each assembly and the NUBOW-3D software was updated to incorporate a new input format and better output. Overall progress on resolving the QA gaps has been good this year.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Process–Property–Performance Mapping of Additively Manufactured 316H Stainless Steel Components

The Advanced Materials and Manufacturing Technologies Program is focused on accelerating the development of advanced materials and components fabricated via additive manufacturing, and is using laser powder bed fusion (LPBF) of 316H stainless steel as an initial case study. In the previous fiscal year, miniature high-throughput specimens were printed on multiple LPBF systems to provide initial processing windows to minimize porosity and limit epitaxial grain growth during prints. This fiscal year, scaled builds were completed on three different LPBF systems at ORNL: a GE Concept Laser M2, a Renishaw AM400, and an EOS M290. Builds on the Concept Laser were conducted on multiple powder lots and processing parameter ranges to provide microstructure effects on time-independent and time-dependent mechanical properties. Builds on the Renishaw were produced using Oak Ridge National Laboratory (ORNL)-optimized printing parameters and Argonne National Laboratory (ANL)-optimized printing parameters to compare outcomes of parallel process optimization efforts at different national laboratories on the same LPBF system. Similarly, the build completed on the EOS M290 replicated the processing parameters of builds completed at Los Alamos National Laboratory (LANL). Optical microscopy and electron backscatter diffraction characterization was completed on all builds. In addition to the general round robin characterization, this work-package generated time-independent data, including tensile and fracture toughness test data on scaled Concept Laser builds as a function of processing parameters and post-build heat treatment. This analysis is complimentary to work in parallel work packages aiming to establish heat treatment and processing effects on time-dependent properties. It was found that although the stress-relief heat treatment provides the highest strength at lower-temperatures, tensile strength begins to converge at higher temperatures regardless of heat treatment condition. In addition, the more rigorous solution annealing and hot-isostatic pressing post-build heat treatments result in higher fracture toughness than the stress-relieved condition. The root-causes of the lower fracture toughness of the stress-relieved LPBF 316H material was informed via a stress-relief optimization study on a scaled concept laser print, where it was found that although dislocation recovery was largely complete after only a couple hours at 650°C, the extended hold of the current 24h heat treatment employed on scaled builds likely caused increased carbide volume fractions along the LPBF 316H grain boundaries, thereby deteriorating crack propagation resistance. This trend was seen to become more deleterious with additional increases of stress-relief temperature to 750°C or 850°C. These results have helped inform a new optimal stress-relief annealing condition for LPBF 316H for future campaign testing (650°C for 2h).

36 MATERIALS SCIENCE↗

DOE OSTI2025

Surrogate models for development of unconventional shale reservoirs by an integrated numerical approach of hydraulic fracturing, flow and geomechanics, and machine learning

We develop well-completion surrogate models by taking an integrated workflow of hydraulic fracturing, flow, geomechanics, and machine learning simulation. There are three steps in the proposed workflow. First, history-matching processes are conducted with the field data including pumping and production data for characterization. Second, full-physics simulation is performed with various parameters of the field development (e.g., cluster spacing, clusters per stage, pumping rates and times, amount of proppant, and well spacing) to generate multiple simulation results by changing the parameters of the completion design with well-known hydraulic fracturing, reservoir, geomechanics simulators to calculate fracture geometry, reservoir depressurization, induced stress changes. The workflow is demonstrated over a field in the Southern Midland Basin. Here, we take two completion scenarios: a single well case followed by a multi-well case. Finally, a Long Short-Term Memory (LSTM) machine learning algorithm is employed to create surrogate models that can replicate the full-physics simulation results. Furthermore, results show that the trained models applied in the single well and multi-well cases for a particular geological system can provide good accuracy close to those provided by full-physics simulations. Specifically, the site-specific surrogate models can predict fracture parameters (length, height, and surface area) and cumulative production accurately with computational efficiency, suggesting our proposed workflow can be used as a pragmatic tool for expediting the well completion optimization process.

Geomechanics↗

DOE OSTI2024

Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires

Borgs are huge extrachromosomal elements (ECE) of anaerobic methane-consuming “Candidatus Methanoperedens” archaea. Here, we used nanopore sequencing to validate published complete genomes curated from short reads and to reconstruct new genomes. 13 complete and four near-complete linear genomes share 40 genes that define a largely syntenous genome backbone. We use these conserved genes to identify new Borgs from peatland soil and to delineate Borg phylogeny, revealing two major clades. Remarkably, Borg genes encoding nanowire-like electron-transferring cytochromes and cell surface proteins are more highly expressed than those of host Methanoperedens, indicating that Borgs augment the Methanoperedens activity in situ. We reconstructed the first complete 4.00 Mbp genome for a Methanoperedens that is inferred to be a Borg host and predicted its methylation motifs, which differ from pervasive TC and CC methylation motifs of the Borgs. Thus, methylation may enable Methanoperedens to distinguish their genomes from those of Borgs. Very high Borg to Methanoperedens ratios and structural predictions suggest that Borgs may be capable of encapsulation. The findings clearly define Borgs as a distinct class of ECE with shared genomic signatures, establish their diversification from a common ancestor with genetic inheritance, and raise the possibility of periodic existence outside of host cells.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Addressing genome scale design tradeoffs in Pseudomonas putida for bioconversion of an aromatic carbon source

Genome-scale metabolic models (GSMM) are commonly used to identify gene deletion sets that result in growth coupling and pairing product formation with substrate utilization and can improve strain performance beyond levels typically accessible using traditional strain engineering approaches. However, sustainable feedstocks pose a challenge due to incomplete high-resolution metabolic data for non-canonical carbon sources required to curate GSMM and identify implementable designs. Here we address a four-gene deletion design in the Pseudomonas putida KT2440 strain for the lignin-derived non-sugar carbon source, p-coumarate (p-CA), that proved challenging to implement. We examine the performance of the fully implemented design for p-coumarate to glutamine, a useful biomanufacturing intermediate. In this study glutamine is then converted to indigoidine, an alternative sustainable pigment and a model heterologous product that is commonly used to colorimetrically quantify glutamine concentration. Through proteomics, promoter-variation, and growth characterization of a fully implemented gene deletion design, we provide evidence that aromatic catabolism in the completed design is rate-limited by fumarase hydratase (FUM) enzyme activity in the citrate cycle and requires careful optimization of another fumarate hydratase protein (PP_0897) expression to achieve growth and production. A double sensitivity analysis also confirmed a strict requirement for fumarate hydratase activity in the strain where all genes in the growth coupling design have been implemented. Metabolic cross-feeding experiments were used to examine the impact of complete removal of the fumarase hydratase reaction and revealed an unanticipated nutrient requirement, suggesting additional functions for this enzyme. While a complete implementation of the design was achieved, this study highlights the challenge of completely inactivating metabolic reactions encoded by under-characterized proteins, especially in the context of multi-gene edits.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

SPT-SZ MCMF: an extension of the SPT-SZ catalogue over the DES region

We present an extension to a Sunyaev–Zel’dovich Effect (SZE) selected cluster catalogue based on observations from the South Pole Telescope (SPT); this catalogue extends to lower signal to noise than the previous SPT–SZ catalogue and therefore includes lower mass clusters. Optically derived redshifts, centres, richnesses, and morphological parameters together with catalogue contamination and completeness statistics are extracted using the multicomponent matched filter (MCMF) algorithm applied to the S/N > 4 SPT–SZ candidate list and the Dark Energy Survey (DES) photometric galaxy catalogue. The main catalogue contains 811 sources above S/N = 4, has 91 per cent purity, and is 95 per cent complete with respect to the original SZE selection. It contains in total 50 per cent more clusters and twice as many clusters above z = 0.8 in comparison to the original SPT-SZ sample. The MCMF algorithm allows us to define subsamples of the desired purity with traceable impact on catalogue completeness. As an example, we provide two subsamples with S/N > 4.25 and S/N > 4.5 for which the sample contamination and cleaning-induced incompleteness are both as low as the expected Poisson noise for samples of their size. The subsample with S/N > 4.5 has 98 per cent purity and 96 per cent completeness and is part of our new combined SPT cluster and DES weak-lensing cosmological analysis. We measure the number of false detections in the SPT-SZ candidate list as function of S/N, finding that it follows that expected from assuming Gaussian noise, but with a lower amplitude compared to previous estimates from simulations.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2026

Contrasting effects of glutamate and branched-chain amino acid metabolism on acid tolerance in a Castellaniella isolate from acidic groundwater

Groundwater acidification co-occurring with nitrate pollution is a common, global environmental health hazard. Denitrifying bacteria have been leveraged for the in situ removal of nitrate in groundwater. However, co-existing stressors—such as low pH—reduce the efficacy of biological removal processes. Castellaniella sp. str. MT123 is a complete denitrifier that was isolated from acidic, nitrate-contaminated groundwater. The strain grows robustly by nitrate respiration at pH < 6.0, completely reducing nitrate to dinitrogen gas. Genomic analyses of MT123 revealed few previously characterized acid tolerance genes. Thus, we utilized a combination of proteomics, metabolomics, and competitive mutant fitness to characterize the genetic mechanisms of MT123 acclimation to growth under mildly acidic conditions. We found that glutamate accumulation is critical in the acid acclimation of MT123, possibly through consumption of intracellular protons via glutamate decarboxylation to GABA. This is despite the fact that MT123 lacks the canonical glutamate decarboxylase-glutamate/GABA antiporter system implicated in acid tolerance in other bacteria. In contrast, branched-chain amino acid (BCAA) accumulation was detrimental to cell growth at lower pHs, possibly through indirect mechanisms impacting the cellular glutamate pool. Genetic analysis previously linked MT123 to a population of Castellaniella that bloomed—concurrent to nitrate removal—during a biostimulation effort to reduce groundwater nitrate concentrations at MT123’s location of origin. Thus, our analyses provide novel insight into mechanisms of acclimation to acidic conditions in a strain with significant potential for nitrate bioremediation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Chemical Recommender System: Replacement Suggestions for Small Molecules

The Chemical Recommender System (CRS) is an open-source, high-performance toolkit that enables real-time similarity searches across the complete PubChem database (over 50 million molecules) using commodity hardware. The CRS addresses critical limitations in existing chemical informatics platforms through a novel vector database infrastructure, extensible model integration capabilities, and complete algorithmic transparency. The system implements a vector database deployment with partitioned indexing that achieves a ~60x speedup over traditional approaches. A containerized model integration framework allows researchers to seamlessly incorporate custom predictive models into the full-scale search and scoring pipeline, while complete configurability of search parameters, filtering logic, and scoring functions provides capabilities not available in existing black-box solutions. Beyond structural similarity, the CRS integrates OPERA QSAR models for thermophysical and toxicity predictions, RDKit synthetic accessibility scoring, and user-defined models to compute weighted final replacement scores. The complete system is accessible through an interactive web application supporting real-time progress monitoring, post-processing score re-weighting, automated PDF reporting, and batch processing capabilities.

Nair, Parthiv Anand [Sandia National Laboratories ↗

DOE OSTI2024

Retrofitting Holcim Ste. Genevieve Cement Plant with CO2 Capture Plant Using Air Liquide Cryocap™ FG Technology

The global cement manufacturing industry is a major contributor to carbon dioxide emissions. The International Energy Agency's "Net Zero Emissions by 2050 Scenario" identifies CCS as a major strategy for meeting that goal. This project is among the first attempts to transfer capture technology developed at coal-fired power plants to the cement industry. The main objective of the project is to execute and complete a front-end engineering and design (FEED) studies for commercial-scale, carbon capture projects that separates 95% of the total CO2 emissions at the Holcim (US) Ste. Genevieve cement manufacturing facility using Air Liquide’s Pressure Swing Adsorption system (PSA) assisted Cryocap™ technology. The Holcim Ste. Genevieve cement plant in Missouri, US, boasts one of the largest single cement production lines in the world, with a capacity of approximately 12,000 t/day. The plant currently uses traditional fuels, namely coal and petcoke. The captured CO2 will be pipeline and geological storage grade. The industrial host site emits approximately 3.0 million tonne CO2/yr. Air Liquide’s Cryocap™ technology has been developed over the last 18+ years for CO2 capture applications. It has been shown to be applicable to a variety of industrial applications (e.g., steel, cement, SMR, Fluidized Catalytic Crackers (FCCs)). Cryocap™ FG consists of a Pressure Swing Adsorption (PSA) unit coupled with a Cryogenic System. The PSA pre-concentrates the CO2 from the flue gas, while the cryogenic unit enables the CO2 purity to be increased to the desired level. The project team is led by the Prairie Research Institute at the University of Illinois at Urbana-Champaign. The tasks include: complete FEED study for retrofitting the industrial facility with a carbon capture system to support developing a detailed cost estimate; business case analysis outlining the anticipated revenue and credits if projects was built and operated; technoeconomic analysis (TEA) outlining how capture system achieves DOE capture goals; and life cycle (LCA) analysis demonstrating zero net carbon emissions. The FEED study was successfully completed. This includes completing the process basis of design; preliminary engineering; outside battery limits (OSBL) detailed engineering including a Zero Liquid Discharge (ZLD) wastewater treatment system; inside battery limits (ISBL) detailed engineering [1]. An overall project capital cost estimate within a -20%/+30% accuracy was developed. The major contributors to the Total Plant Cost (TPC), by system, are the costs associated with the Outside Battery Limit (OSBL) section of the plant which includes a new river water intake structure and a Zero Liquid Discharge (ZLD) system. By cost category, the major contributors to the TPC are equipment and subcontractor costs, followed closely by engineering, construction management, home office and contractor fees. The TEA has been created to reflect the findings of the project. It analyzes the economic performance of the Cryocap™ technology by reviewing the estimated capital costs, operating cost, and revenue. The Cost of Capture (COC) associated with the Cryocap™ technology for 95% CO2 capture, when considering NETL 2018 economic assumptions (42/58 debt/equity ratio, 5.15% interest on debt and 1.42% return on equity in real dollars) and 2022 economic assumptions (42/58 debt/equity ratio, 8.82% interest on debt and 4.90% return on equity in real dollars) was found to be much lower than that for the DOE-NETL’s base-line cases. The highest contributors to the COC are annualized capital expenditures (CAPEX) and electricity consumption which can be offset by using lower cost renewable sources. The LCA was conducted using OpenLCA which is an open-source software that is recommended by NETL. The database utilized for this study was a modified version of TRACI 2.1 (developed by the US. Environmental Protection Agency’s National Risk Management Research Laboratory and modified by NETL). The Cryocap™ FG technology does not consume fuels in significant quantities and does not utilize specialized chemical solvents subject to decomposition, such as those utilized in amine-based carbon capture systems. The Cryocap™ FG technology mainly utilizes electricity as its energy input; hence, its calculated emissions are mainly associated with the generation of electricity offsite and are dependent on the energy matrix of the grid at the time of project implementation. The water consumption impact of the Cryocap™ FG is mostly for makeup of the water lost by evaporation in the cooling tower; however, the carbon capture plant will be equipped with a ZLD system to avoid effluent streams and minimize water consumption. The successful construction and operation of this plant based on this study results will provide a means to demonstrate an economically attractive and transformational capture technology that can be used to retrofit existing plants and be deployed at new plants.

01 COAL, LIGNITE, AND PEAT↗

DOE OSTI2024

Enhanced Resistance Pines for Improved Renewable Biofuel and Chemical Production (Technical Report)

We completed phenotyping constitutive and inducible oleoresin flow across two seasons, constitutive resin canal number and density and wood terpene content in our ADEPT2 and CCLONES populations. We completed genetic association between 19 oleoresin phenotypes and a total of 523,192 SNP markers from ADEPT2 and 13,883 SNP markers in CCLONES using four mixed linear models. A total of 293 significant SNPs (FDR = 0.20) were identified. We used the MENTOR tool to mine mechanistic connections from a multiplex network constructed from poplar multi-omic data to construct a conceptual model for a subset of these significant SNPs. Our model contains 6 transcriptional regulators in addition to 3 monoterpene synthases. To generate more lines of evidence for these significant SNPs, we completed a time course RNAseq experiment after inducing vascular zone cells to differentiate into new resin canals with a methyl jasmonate treatment, a single nuclei RNAseq that identified differentiating resin canal epithelial cells and are completing analysis for a QTL study in a hybrid pine population. The time course identified 4634 significantly down and 1890 significantly up regulated transcripts after treatment with methyl jasmonate, an inducer of new resin canal formation in the vascular cambial meristem. To analyze this large set of differentially regulated genes, we created a predictive expression network and analyzed it with random walk restart using 6 seed genes coding for transcription factors regulating xylem differentiation in poplar. Of the top ranked 200 transcripts, 119 transcripts were significant differentially expressed supporting these transcripts as potential candidates regulating resin canal formation. Analysis of single nuclei sequencing of shoot tips that contain differentiating resin canals, identified 10 clusters. One cluster was highly enriched in transcripts coding for 9 of the enzymes in the MEP pathway 3 prenyl synthetases, and 3 monoterpene synthases strongly suggesting that this cluster represents resin canal epithelial cells. We are mining the additional transcripts to create a trajectory analysis. In summary, we have identified > 10 novel genes that are strongly supported candidates for further analysis in breeding lines and for genetic engineering over- and under- expressing lines to increase wood terpene content to improve resistance to insect and fungal pathogens while simultaneously increasing terpene supplies for renewable chemicals and biofuels.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Water Resource Assessment In The New Mexico Permian Basin: BLM 2023 Assessment Report

The Permian Basin is the highest producing oil field in the United States and is comprised of three component basins including; the Midland Basin, Delaware Basin and the Marfa Basin. This report describes the work conducted by Sandia National Laboratories (SNL) for the Bureau of Land Management (BLM) to investigate the occurrence of usable water (quality, and depth to water) in the Delaware Sub-basin of the Permian Basin. High Production Areas (HPAs) were identified for the region based on Reasonable Foreseeable Development Scenario (RFD) published by New Mexico Tech University. HPAs were established based on potential for future development of oil reserves. The study was initiated by the BLM-Carlsbad Field Office (CFO) based on concerns that special protections for groundwater in these HPAs may be warranted. A combination of analysis of existing data and field work to collect new data for analysis were used to complete the investigation objectives. This study summarizes the most recent analyses in an ongoing project and builds on previously completed work as listed in Table 1. Advancements in directional drilling and well completion technologies have resulted in an exponential growth in the use of hydraulic fracturing for oil and gas extraction in the Permian Basin. Within the New Mexico portion of the Delaware Sub-basin, water demand to complete each hydraulically fractured well is estimated to average 7.3 acre-feet (2.4 million gallons), resulting in 30 billion barrels of water over the life of the plan or 1.5 billion barrels per year. This rising demand is creating concern for the regions ability to provide the necessary water in a manner that fulfills BLM’s role of protecting human health and the environment while sustainably meeting the needs of various water users in the region. This report documents water-level and water chemistry baselines to aid the BLM in understanding the regional water supply dynamics under various management, policy, and growth scenarios and to pre-emptively identify risks to water sustainability.

54 ENVIRONMENTAL SCIENCES↗