Multi-criteria spatial screening and uncertainty analysis applied to direct-use geothermal projects
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Computer Science↗
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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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UCB-GLOBES: An open-access mass spectral database of identified and unidentified atmospheric organic compounds
Chemical characterization of atmospheric organic aerosols using gas chromatography with 70 eV electron ionization mass spectrometry (GC/EI-MS) has been used for decades in advancing molecular marker detection and identification, though primarily through suspect screening and/or targeted analyses. To advance non-targeted analyses of environmental samples, we have catalogued approximately 27 000 mass spectra (MS) of the trimethylsilyl derivatives of semi-volatile organic aerosol (OA) analytes in the open-access University of California Berkeley Goldstein Library of Organic Biogenic Environmental Spectra (UCB-GLOBES). Analytes were observed in ambient samples from the U.S. and the Central Amazon and/or laboratory simulations of secondary OA (SOA) formation. These samples are representative of OA under urban and biomass burning influences as well as SOA derived from biogenic precursors (e.g., isoprene, monoterpenes, sesquiterpenes) and biomass burning intermediates. MS are documented in UCB-GLOBES without regard to known chemical identity, annotated with extensive metadata such as sample source/experimental conditions, any structural information gained from MS analyses, and predicted chemical properties such as average carbon oxidation state and carbon number. UCB-GLOBES MS are compatible for importing into the NIST MS Search program, and we have also provided a Jupyter Notebook for MS visualization and comparisons. We demonstrate the utility of UCB-GLOBES through MS reanalyses of prior analytes observed in ambient data, finding a 20 % reduction in the number of analytes assigned to OA source categories reliant solely on time series correlation and an overall 11 % increase in new MS-based OA source categorization for the Southeast U.S. For 1513 analytes observed previously in the Central Amazon, we found 375 MS matches using UCB-GLOBES vs. 136 MS matches during prior analyses, representing a 14 % gain in newly confirmed or newly categorized OA species. While OA from laboratory oxidation experiments in UCB-GLOBES are highly diverse chemically, on average only 29 % of UCB-GLOBES MS have a mass spectral match to another MS entry in UCB-GLOBES and/or in databases of known compounds (i.e. NIST MS Database, Adams Essential Oil, MANE Flavor and Fragrance Company). This indicates that roughly 70 % of UCB-GLOBES MS are unique thus far, not observed more than once among the laboratory oxidation samples and ambient data in UCB-GLOBES MS. Further, only 18 % can be positively identified using these databases or known authentic standards. This points to a large gap between these laboratory simulations and ambient OA. Overall, the UCB-GLOBES database can be utilized for improving confidence in OA source categorization and/or identification, novel chemical marker discovery, tracking chemical diversity, de novo structure and properties prediction, and improving MS search and matching algorithms. This can ultimately inform future research priorities for the chemical characterization of atmospheric organic samples.
Mass spectrometry↗
Ground Source Heat Pump Screening Tool and Related Resources
This archive contains both a link to Oak Ridge National Laboratory's Ground Source Heat Pump (GSHP) Screening Tool and related resources documenting its development, technical features, and applications. The web-based screening tool is a techno-economic analysis resource designed to evaluate the feasibility, costs, and benefits of implementing GSHP systems in buildings across various U.S. climate zones. It is intended for use by building owners, HVAC system designers, and installers to support decision-making in residential and commercial applications, incorporating advanced modeling capabilities such as ground heat exchanger design. The included resources detail the tool's creation and use, covering topics such as innovative ground heat exchanger design methodologies, the development of an open library of g-functions for borehole configurations, and studies on GSHP performance and economic viability in retrofitting single-family homes.
15 GEOTHERMAL ENERGY↗
High-throughput functional variant screens via in vivo production of single-stranded DNA
Significance We report a methodology for the pooled construction of mutants bearing precise genomic sequence variations and multiplex phenotypic characterization of these mutants using next-generation sequencing (NGS). Unlike existing techniques depending on CRISPR-Cas–directed genomic breaks for genome editing, this strategy instead uses single-stranded DNA produced by a retron element for recombineering. This enables libraries of millions of elements to be constructed and offers relaxed design constraints which permit natural DNA or random variation to be used as inputs.
59 BASIC BIOLOGICAL SCIENCES↗
Machine Learning-Guided Identification of PET Hydrolases from Natural Diversity
The enzymatic depolymerization of poly(ethylene terephthalate) (PET) is emerging as a leading chemical recycling technology for waste polyester. As part of this endeavor, new candidate enzymes identified from natural diversity can serve as useful starting points for enzyme evolution and engineering. In this study, we improved upon HMM searches by applying an iterative machine learning strategy to identify 400 putative PET-degrading enzymes (PET hydrolases) from naturally occurring homologs. Using high-throughput (HTP) experimental techniques, we successfully expressed and purified >200 enzyme candidates and assayed them for PET hydrolysis activity as a function of pH, temperature, and substrate crystallinity. From this library, we discovered 91 previously unknown PET hydrolases, 35 of which retain activity at pH 4.5 on crystalline material, which are conditions relevant to developing more efficient commercial processes. Notably, four enzymes showed equal to or higher activity than LCC-ICCG, a benchmark PET hydrolase, at this challenging condition in our screening assay, and 11 of which have pH optima <7. Using these data, we identified regions of PETases statistically correlated to activity at lower pH. We additionally investigated the effect of condition-specific activity data on trained machine learning predictors and found a precision (putative hit rate) improvement of up to 30% compared to a Hidden Markov Model alone. Our findings show that by pointing enzyme discovery toward conditions of interest with multiple rounds of experimental and machine learning, we can discover large sets of active enzymes and explore factors associated with activity at those conditions.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Cross-family and phage-specific gene requirements for Klebsiella infection revealed by scalable RB-TnSeq genetic screens.
Bacteriophages are being cataloged at an accelerating pace and are recognized as key players in nutrient and energy cycling across ecosystems. Yet the bacterial genetic determinants that govern phage-host specificity and infection success remain poorly understood, particularly in clinically and ecologically important genera such as Klebsiella where prior receptor characterization has been almost entirely limited to capsulated strains. Here we used a randomly barcoded, genome-wide, loss-of-function transposon mutant library (RB-TnSeq) of Klebsiella sp. M5al, a naturally acapsular, nitrogen-fixing rhizobacterium, to generate the first systematic, cross-family map of phage receptor gene dependencies in Klebsiella. Challenging the library against 25 double-stranded DNA phages spanning five families in 213 parallel assays, we identified 42 bacterial genes associated with phage infection, of which 15 had no prior association with phage infection in any bacterial system. Disruption of surface receptor biosynthesis genes conferred cross-resistance across multiple phage families, while intracellular gene disruptions had predominantly phage-specific effects. Clonal validation of eight genes confirmed LPS outer core biosynthesis genes as primary receptor determinants alongside additional host factors spanning outer membrane transport, cofactor biosynthesis, and two-component signaling. Comparative analysis across all 25 phages revealed that phage genus rather than family is the stronger predictor of host gene dependency profiles, a finding with direct implications for the functional annotation of uncharacterized phage isolates and rational phage cocktail design. Together, these findings provide a community resource for linking phage genomic diversity to functional host interaction space in this ecologically and clinically important genus.
Gittrich, Marissa R↗
LibERI—A portable and performant multi-GPU accelerated library for electron repulsion integrals via OpenMP offloading and standard language parallelism
A portable and performant graphics processing unit (GPU)-accelerated library for electron repulsion integral (ERI) evaluation, named LibERI, has been developed and implemented via directive-based (e.g., OpenMP and OpenACC) and standard language parallelism (e.g., Fortran DO CONCURRENT). Offloaded ERIs consist of integrals over low and high contraction s, p, and d functions using the rotated-axis and Rys quadrature methods. GPU codes are factorized based on previous developments with two layers of integral screening and quartet presorting. In this work, the density screening is moved to the GPU to enhance the computational efficacy for large molecular systems. Here, the L-shells in the Pople basis set are also separated into pure S and P shells to increase the ERI homogeneity and reduce atomic operations and the memory footprint. LibERI is compatible with any quantum chemistry drivers supporting the MolSSI Driver Interface. Benchmark calculations of LibERI interfaced with the GAMESS software package were carried out on various GPU architectures and molecular systems. The results show that the LibERI performance is comparable to other state-of-the-art GPU-accelerated codes (e.g., TeraChem and GMSHPC) and, in some cases, outperforms conventionally developed ERI CUDA kernels (e.g., QUICK) while fully maintaining portability.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Pathway complexity in fibre assembly: from liquid crystals to hyper-helical gelmorphs
Pathway complexity results in unique materials from the same components according to the assembly conditions. Here a chiral acyl-semicarbazide gelator forms three different gels of contrasting fibre morphology (termed ‘gelmorphs’) as well as lyotropic liquid crystalline droplets depending on the assembly pathway. The gels have morphologies that are either hyperhelical (HH-Gel), tape-fibre (TF-Gel) or thin fibril derived from the liquid crystalline phase (LC-Gels) and exhibit very different rheological properties. The gelator exists as three slowly interconverting conformers in solution. All three gels are comprised of an unsymmetrical, intramolecular hydrogen bonded conformer. The kinetics show that formation of the remarkable HH-Gel is cooperative and is postulated to involve association of the growing fibril with a non-gelling conformer. This single molecule dynamic conformational library shows how very different materials with different morphology and hence very contrasting materials properties can arise from pathway complexity as a result of emergent interactions during the assembly process.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Discovery of Innovative Polymers for Next-Generation Gas-Separation Membranes using Interpretable Machine Learning
Polymer membranes perform innumerable separations with far-reaching environmental implications. Despite decades of research on membrane technologies, design of new membrane materials remains a largely Edisonian process. To address this shortcoming, we demonstrate a generalizable, accurate machine-learning (ML) implementation for the discovery of innovative polymers with ideal separation performance. Specifically, multitask ML models are trained on available experimental data to link polymer chemistry to gas permeabilities of He, H2, O2, N2, CO2, and CH4. Here, we interpret the ML models and extract chemical heuristics for membrane design, through Shapley Additive exPlanations (SHAP) analysis. We then screen over nine million hypothetical polymers through our models and identify thousands of candidates that lie well above current performance upper bounds. Notably, we discover hundreds of never-before-seen ultrapermeable polymer membranes with O2 and CO2 permeability greater than 104 and 105 Barrer, respectively. These hypothetical polymers are capable of overcoming undesirable trade-off relationship between permeability and selectivity, thus significantly expanding the currently limited library of polymer membranes for highly efficient gas separations. High-fidelity molecular dynamics simulations confirm the ML-predicted gas permeabilities of the promising candidates, which suggests that many can be translated to reality.
Yang, Jason↗
Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2
The nonstructural protein 3 (NSP3) of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) contains a conserved macrodomain enzyme (Mac1) that is critical for pathogenesis and lethality. While small-molecule inhibitors of Mac1 have great therapeutic potential, at the outset of the COVID-19 pandemic, there were no well-validated inhibitors for this protein nor, indeed, the macrodomain enzyme family, making this target a pharmacological orphan. Here, we report the structure-based discovery and development of several different chemical scaffolds exhibiting low- to sub-micromolar affinity for Mac1 through iterations of computer-aided design, structural characterization by ultra-high-resolution protein crystallography, and binding evaluation. Potent scaffolds were designed with in silico fragment linkage and by ultra-large library docking of over 450 million molecules. Both techniques leverage the computational exploration of tangible chemical space and are applicable to other pharmacological orphans. Overall, 160 ligands in 119 different scaffolds were discovered, and 153 Mac1-ligand complex crystal structures were determined, typically to 1 Å resolution or better. Our analyses discovered selective and cell-permeable molecules, unexpected ligand-mediated conformational changes within the active site, and key inhibitor motifs that will template future drug development against Mac1.
60 APPLIED LIFE SCIENCES↗
Biosensor-driven strain engineering reveals key cellular processes for maximizing isoprenol production in Pseudomonas putida
Synthetic biology generates vast combinatorial designs, yet high-throughput analytical methods to screen them are poorly matched to interrogate this search space. We address this challenge by developing a biosensor-driven, growth-coupled selection strategy in Pseudomonas putida for isoprenol, a potential aviation fuel precursor. We found and characterized a noncanonical signaling pathway, revealing a functional and physical complex between a hybrid histidine kinase and an alcohol dehydrogenase, whose activity is tuned by heterodimerization. Leveraging this biosensor in a pooled CRISPRi library selection, we identified key host limitations. Iterative combinatorial strain engineering derived from these hits yielded a 36-fold titer increase to ~900 milligrams per liter. Integrated omics analysis revealed that metabolic rewiring toward amino acid catabolism was crucial for this improvement. This observation was found to be beneficial by technoeconomic analysis. Our modular workflow provides a powerful strategy for optimizing complex heterologous pathways and uncovering emergent host biology.
CRISPRi↗
Exploring phage–host interactions in Burkholderia cepacia complex bacterium to reveal host factors and phage resistance genes using CRISPRi functional genomics and transcriptomics
Complex interactions of bacteriophages with their bacterial hosts determine phage host range and infectivity. While phage defense systems and host factors have been identified in model bacteria, they remain challenging to predict in non-model bacteria. In this paper, we integrate functional genomics and transcriptomics to investigate phage–host interactions, revealing active phage resistance and host factor genes in Burkholderia cenocepacia K56-2. Burkholderia cepacia complex species are commonly found in soil and are opportunistic pathogens in immunocompromised patients. We studied infection of B. cenocepacia K56-2 with Bcep176, a temperate phage isolated from Burkholderia multivorans. A genome-wide dCas9 knockdown library targeting B. cenocepacia K56-2 was constructed, and a pooled infection experiment identified 63 novel genes or operons coding for candidate host factors or phage resistance genes. The activities of a subset of candidate host factor and resistance genes were validated via single-gene knockdowns. Transcriptomics of B. cenocepacia K56-2 during Bcep176 infection revealed that expression of genes coding for host factor and resistance candidates identified in this screen was significantly altered during infection by 4 h post-infection. Identifying which bacterial genes are involved in phage infection is important to understand the ecological niches of B. cenocepacia and its phages, and for designing phage therapies.
Bacterial Pathogenesis↗
High-throughput validation of phase formability and simulation accuracy of Cantor alloys
High-throughput methods enable accelerated discovery of novel materials in complex systems such as high-entropy alloys, which exhibit intricate phase stability across vast compositional spaces. Computational approaches, including Density Functional Theory (DFT) and calculation of phase diagrams (CALPHAD), facilitate screening of phase formability as a function of composition and temperature. However, the integration of computational predictions with experimental validation remains challenging in high-throughput studies. In this work, we introduce a quantitative confidence metric to assess the agreement between predictions and experimental observations, providing a quantitative measure of the confidence of machine learning models trained on either DFT or CALPHAD input in accounting for experimental evidence. The experimental dataset was generated via high-throughput in-situ synchrotron X-ray diffraction on compositionally varied FeNiMnCr alloy libraries, heated from room temperature to ~1000 °C. Agreement between the observed and predicted phases was evaluated using either temperature-independent phase classification or a model that incorporates a temperature-dependent probability of phase formation. This integrated approach demonstrates where strong overall agreement between computation and experiment exists, while also identifying key discrepancies, particularly in FCC/BCC predictions at Mn-rich regions to inform future model refinement.
36 - MATERIALS SCIENCE↗
Next generation experimental data access at NSLS-II
The NSLS-II network and computing infrastructure has been significantly updated recently. The re-IP process in 2020-2021 enabled the NSLS-II network to be routable to the rest of the BNL campus. Then, standardization of the operating systems and deployment procedures helped to deliver a consistent environment to workstations and servers used by all NSLS-II beamlines. In particular, the RedHat Enterprise Linux 8 was deployed to 700+ machines using the RedHat Satellite infrastructure management product, and all critical services (IOCs, databases, etc.) were migrated to the new OS. NFS users’ home directories are consistent across all of the machines, which eliminates the need for the individual configuration of the user environment on each host. The standard suite of software packages is available to the beamline staff and users, which includes the system packages (deployed via RPM) as well as the conda environments for data acquisition and analysis. Security measures were implemented to comply with the industry standards, which include multi-factor authentication (using Duo), secure screen lock for the beamline machines, and advanced access control to the experimental data that is stored in shared central storage available on all hosts. These major enhancements facilitated sharing the experimental data (currently for a number of selected beamlines, with a plan to extend it to the whole facility in the nearest future) with the users via an externally facing JupyterHub instance. The beamlines keep using the Bluesky data acquisition framework to orchestrate their experiments, and the new infrastructure enabled them to use a next-generation data access library called tiled.
36 MATERIALS SCIENCE↗
Ambient mechanosynthesis of flexible two-dimensional covalent organic frameworks
We present the first ambient mechanosynthesis of 16 flexible covalent organic frameworks (COFs) within an hour. Notably, one representative COF exhibited a high iodine uptake capacity of ∼4.3 g g −1 from aqueous solutions and 5.97 g g −1 from vapor. Flexible two-dimensional covalent organic frameworks (2D COFs) constructed from nonplanar building blocks represent an emerging paradigm in COF design. Nevertheless, the prevailing solvothermal synthesis suffers from low time efficiency, environmental unfriendliness, and cumbersome protocols. Here, we address these challenges by developing the first ambient mechanosynthesis of a diverse library of flexible 2D COFs. Sixteen distinct triazine-cored Schiff-base COFs, including five as-yet-unreported ones, were rapidly synthesized via ball milling using 2,4,6-tris(4-aminophenoxy)-1,3,5-triazine (TPT-NH 2 ) and 2,4,6-tris(4-formylphenoxy)-1,3,5-triazine (TPT-CHO) as building blocks. Notably, the representative COF, MC-flexible-COF-1, was synthesized in as little as one hour under mechanosynthesis conditions, whereas it remained unattainable via the traditional solvothermal method, despite prolonged heating and extensive solvent screening. The highly dynamic nature of the imine linkage was unequivocally demonstrated through mechanochemical “scrambling” experiments using molecular model compounds. Furthermore, MC-flexible-COF-1 exhibited a high iodine uptake capacity of ∼4.30 g g −1 from aqueous solutions and 5.97 g g −1 from the vapor phase. This work underscores the immense potential of mechanochemistry as a powerful and sustainable tool for the rapid synthesis of advanced 2D COFs, including those inaccessible via conventional solution-based methods.
Nailwal, Yogendra↗
Thermophilic site-specific recombination system for rapid insertion of heterologous DNA into the Clostridium thermocellum chromosome
Clostridium thermocellum is an anaerobic thermophile capable of producing ethanol and other commodity chemicals from lignocellulosic biomass. The insertion of heterologous DNA into the C. thermocellum chromosome is currently achieved via a time-consuming homologous recombination process, where a single stable insertion can take 2–4 weeks or more to construct. In this work, we developed a thermostable version of the Serine recombinase Assisted Genome Engineering (tSAGE) approach for gene insertion in C. thermocellum utilizing a site-specific recombinase from Geobacillus sp. Y412MC61, enabling quick and easy insertion of DNA into the chromosome for accelerated genetic tool screening and heterologous gene expression. Using tSAGE, chromosomal insertion of plasmid DNA occurred at a maximum transformation efficiency of 5 × 10 3 CFU/µg, which is comparable to the transformation efficiency of a replicating control plasmid in C. thermocellum. Using tSAGE, we chromosomally integrated and characterized 17 reporter genes, 15 homologous and 31 heterologous constitutive promoters of varying strengths, 4 inducible promoters, and 5 riboswitches in C. thermocellum. We also determined that a 6–7 nucleotide gap between the ribosome binding site (RBS) and the start codon is optimal for high expression by employing a library of superfolder green fluorescent protein expression constructs driven by our strongest tested promoter (P clo1313_1194 ) with different distances between the RBS and start codon. The tools developed here will aid in accelerating C. thermocellum strain engineering for producing sustainable fuels and chemicals directly from plant biomass.
Biofuels↗
Multi-objective parametrization of interatomic potentials for large deformation pathways and fracture of two-dimensional materials
Abstract This investigation presents a generally applicable framework for parameterizing interatomic potentials to accurately capture large deformation pathways. It incorporates a multi-objective genetic algorithm, training and screening property sets, and correlation and principal component analyses. The framework enables iterative definition of properties in the training and screening sets, guided by correlation relationships between properties, aiming to achieve optimal parametrizations for properties of interest. Specifically, the performance of increasingly complex potentials, Buckingham, Stillinger-Weber, Tersoff, and modified reactive empirical bond-order potentials are compared. Using MoSe 2 as a case study, we demonstrate good reproducibility of training/screening properties and superior transferability. For MoSe 2 , the best performance is achieved using the Tersoff potential, which is ascribed to its apparent higher flexibility embedded in its functional form. These results should facilitate the selection and parametrization of interatomic potentials for exploring mechanical and phononic properties of a large library of two-dimensional and bulk materials.
Zhang, Xu↗
Exploration of structure-activity relationships for the SARS-CoV-2 macrodomain from shape-based fragment linking and active learning
The macrodomain of severe acute respiratory syndrome coronavirus 2 nonstructural protein 3 is required for viral pathogenesis and is an emerging antiviral target. We previously performed an x-ray crystallography–based fragment screen and found submicromolar inhibitors by fragment linking. However, these compounds had poor membrane permeability and liabilities that complicated optimization. Here, we developed a shape-based virtual screening pipeline—FrankenROCS. We screened the Enamine high-throughput collection of 2.1 million compounds, selecting 39 compounds for testing, with the most potent binding with a 130 μM median inhibitory concentration (IC 50 ). We then paired FrankenROCS with an active learning algorithm (Thompson sampling) to efficiently search the Enamine REAL database of 22 billion molecules, testing 32 compounds with the most potent binding with a 220 μM IC 50 . Further optimization led to analogs with IC 50 values better than 10 μM. This lead series has improved membrane permeability and is poised for optimization. FrankenROCS is a scalable method for fragment linking to exploit synthesis-on-demand libraries.
Science & Technology - Other Topics↗