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DOE OSTI2024

Microbial DNA Database and Demonstration

2024 Annual Review meeting talk, "Microbial DNA Database and Demonstration." Description of the NETL's PW DNA Database that will be 1) curated to make it more useable, 20 include metadata linked to each sequencing set, such as qPCR and geochemistry, and 30 allow better filtering and visualization. The database is hosted on KBase so terabytes worth of data can be used directly on the program without having to download it to personal computers.

Schweitzer, Hannah↗

DOE OSTI2025

U.S. Solar Siting Regulation and Zoning Ordinances (2025)

A machine readable collection of documented solar siting ordinances at the state and local (e.g., county, township) level throughout the United States. The data were compiled using the Infrastructure Continuous Ordinance Mapping for Planning and Siting Systems (INFRA-COMPASS) tool, which leverages Large Language Models (LLMs) to automate the collection of local codes and ordinances applicable to energy infrastructure. URLs for the ordinance source documents are included in the Solar Ordinances spreadsheet. The GeoPackage file included below contains the jurisdiction shapes for each ordinance. Note that the GeoPackage file is formatted for ingestion by NLR's reVX setbacks tool and therefore does not contain any of the state-level regulations. NOTE: This data was collected with the help of generative AI. The Large Language Models used for this effort make mistakes. Always validate the data for critical use cases. This data is an update to a previously developed database of wind ordinances found in OEDI Submission 5734: see the "U.S. Solar Siting Regulation and Zoning Ordinances 2022" link below. INFRA-COMPASS version used for collection: v0.11.3 LLMs used for collection: GPT-4.1, GPT-4.1 mini, GPT-4.1 nano

14 SOLAR ENERGY↗

DOE OSTI2025

U.S. Wind Siting Regulation and Zoning Ordinances (2025)

A machine readable collection of documented wind siting ordinances at the state and local (e.g., county, township) level throughout the United States. The data were compiled using the Infrastructure Continuous Ordinance Mapping for Planning and Siting Systems (INFRA-COMPASS) tool, which leverages Large Language Models (LLMs) to automate the collection of local codes and ordinances applicable to energy infrastructure. URLs for the ordinance source documents are included in the Wind Ordinances spreadsheet. The GeoPackage file included below contains the jurisdiction shapes for each ordinance. Note that the GeoPackage file is formatted for ingestion by NREL's reVX setbacks tool and therefore does not contain any of the state-level regulations. NOTE: This data was collected with the help of generative AI. The Large Language Models used for this effort make mistakes. Always validate the data for critical use cases. This data is an update to a previously developed database of wind ordinances found in OEDI Submission 5733: see the "U.S. Wind Siting Regulation and Zoning Ordinances 2022" link below. INFRA-COMPASS version used for collection: v0.8.2 LLMs used for collection: GPT-4.1, GPT-4.1 mini, GPT-4.1 nano, GPT-4o mini

17 WIND ENERGY↗

DOE OSTI2020

Local measurements of the spatial magnetic field distribution in a z-pinch plasma during and near stagnation using polarization spectroscopy

We present here the detailed measurements of radial distribution of the magnetic field in a gas-puff z-pinch plasma at the final stages of the implosion phase and at stagnation. While the measurements are chordal, the radial distribution of different charge states was utilized to measure the magnetic field locally for certain radii, so that unlike chordal measurements in general, the magnetic field radial distribution was obtained with no need for the Abel inversion of the data. The distribution was measured using the Zeeman effect via a novel spectroscopic technique, at several axial locations, and demonstrates striking features such as the peak field remaining at a radius much larger than the stagnation radius at all times. Furthermore, while the distribution observed is sometimes monotonic with respect to the radius, it is often not, a behavior that can be linked to 2D features in the plasma column resulting from the Rayleigh–Taylor instability. The current flowing through the stagnating plasma was found to be a small fraction of the total current, resulting in clearly insufficient magnetic pressure to balance the plasma pressure at stagnation. The magnetic field data, taken over several axial positions, are used to obtain the true inductance in the imploding plasma for the first time; it is found that the data cannot explain the current turnover at stagnation. A simulation with the MACH2-Tabular Collisional-Radiative Equilibrium magnetohydrodynamics code in the r–z plane shows that the peak of the magnetic field pinches to a much smaller radius than is observed in the spectroscopic data. Furthermore, the depth of the computed current turnover at stagnation is smaller than the measured one. The two observed features of a radially extended magnetic field at stagnation together with a deep current turnover are a challenge to match in simulations. Various calculations and estimates of the inductive and resistive load voltages are examined to ascertain if they are responsible for the observed current notch. Lastly, the results demonstrate that the knowledge of the true inductance in the driven load requires such magnetic-field-distribution measurements and that imaging data or electrical measurements are insufficient.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

Evaluating the state-of-the-art in remote volcanic eruption characterization Part I: Raikoke volcano, Kuril Islands

Raikoke, a small, unmonitored volcano in the Kuril Islands, erupted in June 2019. We integrate data from satellites (including Sentinel-2, TROPOMI, MODIS, Himawari-8), the International Monitoring System (IMS) infrasound network, and global lightning detection network (GLD360) with information from local authorities and social media to retrospectively characterize the eruptive sequence and improve understanding of the pre-, syn- and post- eruptive behavior. In this work, we observe six infrasound pulses beginning on 21 June at 17:49:55 UTC as well as the main Plinian phase on 21 June at 22:29 UTC. Each pulse is tracked in space and time using lightning and satellite imagery as the plumes drift eastward. Post-eruption visible satellite imagery shows expansion of the island's surface area, an increase in crater size, and a possibly-linked algal bloom south of the island. We use thermal satellite imagery and plume modeling to estimate plume height at 10–12 km asl and 1.5–2 × 10 6 kg/s mass eruption rate. Remote infrasound data provide insight into syn-eruptive changes in eruption intensity. Our analysis illustrates the value of interdisciplinary analyses of remote data to illuminate eruptive processes. However, our inability to identify deformation, pre-eruptive outgassing, and thermal signals, which may reflect the relatively short duration (~12 h) of the eruption and minimal land area around the volcano and/or the character of closed-system eruptions, highlights current limitations in the application of remote sensing for eruption detection and characterization.

58 GEOSCIENCES↗

DOE OSTI2026

NGEE Arctic Integrated Modeling (IM2): Improved subgrid hillslope hydrologic connectivity

This data product represents the integration of new code capability for arctic tundra hillslope hydrologic processes into the Energy Exascale Earth System Model (E3SM), through the E3SM Land Model (ELM) component. This code integration is the result of collaborative effort between the NGEE Arctic project and the E3SM project. The current ELM represents water movement primarily through vertical processes, such as precipitation, canopy interception, evaporation, infiltration, and soil water movement. Lateral water movement—such as surface runoff, subsurface flow, and river transport—plays a significant role in the hydrological cycle, especially in regions with varied topography. While E3SM includes a runoff routing component representing water transport in the river network, the lateral transport of water at the subgrid scale within the land model has previously not been taken into account. With the recent development of topographic units within the ELM subgrid data structure, there is an opportunity to simulate hillslope hydrologic connectivity by introducing water transport along topographic gradients. We expect that more realistic representation of hillslope hydrologic processes will lead to improved predictions of both soil water content and river network flows. Lateral transport of water at and near the surface is represented as a sub-grid process in this new code development. Water is tracked as it moves from higher to lower elevations within a gridcell. This capability uses the nested hierarchical sub-grid scheme within ELM to connect water fluxes from sub-grid elements with higher elevation to those with lower elevation. This data record consists of a single document (pdf format) that describes the theoretical basis for the hillslope hydrology processes added to ELM, and describes the modifications made to the ELM code. The Methods section of this metadata record includes a link to the public E3SM code repository where the exact code modifications as integrated in E3SM can be accessed. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

Thornton, Peter E [ORNL] (ORCID:0000000247595158)↗

DOE OSTI2026

Data-driven particle dynamics: Structure-preserving coarse-graining for emergent behavior in non-equilibrium systems

Multiscale systems are ubiquitous in science and technology, but are notoriously challenging to simulate as short spatiotemporal scales must be appropriately linked to emergent bulk physics. When expensive high-dimensional dynamical systems are coarse-grained into low-dimensional models, the entropic loss of information leads to emergent physics which are dissipative, history-dependent, and stochastic. To machine learn coarse-grained dynamics from time-series observations of particle trajectories, we propose a framework using the metriplectic bracket formalism that preserves these properties by construction; most notably, the framework guarantees discrete notions of the first and second laws of thermodynamics, conservation of momentum, and a discrete fluctuation-dissipation balance crucial for capturing non-equilibrium statistics. We introduce the mathematical framework abstractly before specializing to a particle discretization. As labels are generally unavailable for entropic state variables, we introduce a novel self-supervised learning strategy to identify emergent structural variables. We validate the method on benchmark systems and demonstrate its utility on two challenging examples: (1) coarse-graining star polymers at challenging levels of coarse-graining while preserving non-equilibrium statistics, and (2) learning models from high-speed video of colloidal suspensions that capture coupling between local rearrangement events and emergent stochastic dynamics. We provide open-source implementations in both PyTorch and LAMMPS, enabling large-scale inference and extensibility to diverse particle-based systems.

Computational Engineering, Finance, and Science (c↗

DOE OSTI2024

National Climate Database (NCDB)

The National Climate Database (NCDB) is a high resolution, bias-corrected climate dataset consisting of the three most widely used variables of solar radiation- global horizontal (GHI), direct normal (DNI), and diffuse horizontal irradiance (DHI)- as well as other meteorological data. The goal of the NCDB is to provide unbiased high temporal and spatial resolution climate data needed for renewable energy modeling. The NCDB is modeled using a statistical downscaling approach with Regional Climate Model (RCM)-based climate projections obtained from the North American Coordinated Regional Climate Downscaling Experiment (NA-CORDEX; linked below). Daily climate projections simulated by the Canadian Regional Climate Model 4 (CanRCM4) forced by the second-generation Canadian Earth System Model (CanESM2) for two Representative Concentration Pathways (RCP4.5 or moderate emissions scenario and RCP8.5 or highest baseline emission scenario) are selected as inputs to the statistical downscaling models. The National Solar Radiation Database (NSRDB) is used to build and calibrate statistical models.

Array↗

DOE OSTI2022

Progress on Demonstration of a MOOSE-Based Coupled Capability for Hot Channel Factors in Fast Reactors

Hot channel factors (HCFs) are computed values that account for the impact on predicted peak fuel, cladding, and coolant temperatures due to uncertainties in the as-built reactor’s material properties and geometry as well as uncertainties due to modeling approximations. Reduction in computed HCF values via reduction or elimination of modeling approximations may translate to significant economic savings if the reactor power can be raised due to the extra temperature margin gained. While limited historical datasets exist for sodium-cooled fast reactors (SFRs), there are no available HCF data for lead-cooled fast reactors (LFRs) outside of work generated previously within NEAMS. The computation of HCFs involves insights from reactor physics, thermal fluids and heat conduction calculations to determine how the peak temperatures respond to various uncertainties in the design. Due to the significant advantages for multi-physics coupling offered by the MOOSE framework, Griffin (MOOSE-based reactor physics code), MOOSE Heat Conduction Module, and Cardinal (MOOSE-wrapped multi-physics application which includes the NekRS thermal fluids code) are being coupled together using the MOOSE MultiApp System to develop a highfidelity multi-physics modeling capability for HCF simulations. This high-fidelity coupling workflow may also be beneficial for other fast reactor applications in the future. In previous work, Griffin and NekRS were individually assessed to ensure the necessary capabilities were in place. This work describes initial efforts to couple the codes (including folding in the MOOSE Heat Conduction Module) and determining the workflow for the perturbed calculations which will leverage the Stochastic Tools Module (STM). To our knowledge, this is the first coupling of Griffin and NekRS as well as the first exploratory use of Stochastic Tools Module for Cardinal. In this report, the neutronics code Griffin, the heat conduction solver in MOOSE, and the MOOSE-wrapped application containing NekRS (Cardinal) are linked together to demonstrate the coupled capability. Griffin and Cardinal are linked dynamically by specifying shared libraries. Different coupling hierarchies are tested for selecting the most appropriate coupling strategy. A coupling scheme is selected based on the efficiency of calculation and ease of data communication. Multiple tests are performed to choose suitable mesh structure, model configurations, scheme setup and boundary conditions to avoid loss of energy due to data interpolation between different modules or weak imposition of fluxes in finite element codes. Computational experiments are performed to study the tolerance control of each type of iteration to avoid false convergence. The coupled capability is demonstrated in both single pin and 7-pin models based on LFR materials and geometry. The study finds that the use of too large a time step size in the heat conduction module can lead to temperature oscillation even though the heat conduction equation does not have a time-derivative kernel, but only the time-dependent boundary condition. A 7-pin model without duct region achieved good convergence in the coupled calculation while a 7 pin model with duct region experienced data communication issues which need to be resolved.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2020

Coupled methane and NO x conversion on Pt + Pd/Al 2 O 3 monolith: Conversion enhancement through feed modulation and Mn 0.5 Fe 2.5 O 4 spinel addition

The performance of a dual-layer Pt-Pd/Al 2 O 3 washcoated monolith promoted by an Al 2 O 3 -supported Mn 0.5 Fe 2.5 O 4 spinel base layer was evaluated with the objective to develop a catalyst with a lower loading of Platinum group metal (PGM) for stoichiometric natural gas vehicle (NGV) emission control. Flow reactor results show that a combination of a lean/rich modulated feed and spinel addition gives enhanced methane and NO conversions compared to a steady-state feed having the same overall composition. Washcoated catalysts – PGM-only, spinel-only, PGM + spinel – were compared over a wide range of operating conditions. The results show a decrease in the methane conversion light-off temperature of up to 85 °C for an application-relevant feed (CH 4 + NO + H 2 + CO + O 2 + H 2 O + CO 2 ) while a moderate 40 °C decrease was observed for a simple feed (CH 4 + O 2 + H 2 O + CO 2 ). In the absence of spinel the modulation enhancement is negatively impacted at high methane conversion (> 80 %). The data show that the O 2 storage and release property of the spinel is needed to fully exploit the modulation enhancement. The mechanism responsible for the enhancement is linked to suppression of O 2 inhibition on the methane oxidation rate near the stoichiometric neutral point (λ = 1). Sufficiently fast cycling achieves a balance between a metallic and oxidic precious metal crystallites favorable for methane activation. The addition of spinel moves this balance closer to the λ = 1 feed, enabling a high oxidation efficiency with lower byproduct NH 3 selectivity. Enhancement in the NO conversion follows the methane conversion due to an easier NO reduction under the slightly rich of stoichiometric feed. Comparison of the PGM + spinel catalysts to PGM-only catalysts shows that the addition of spinel in combination with modulation can achieve the same activity with a lower PGM loading.

03 NATURAL GAS↗

DOE OSTI2020

Uncovering DNA-PKcs ancient phylogeny, unique sequence motifs and insights for human disease

DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is a key member of the phosphatidylinositol-3 kinase-like (PIKK) family of protein kinases with critical roles in DNA-double strand break repair, transcription, metastasis, mitosis, RNA processing, and innate and adaptive immunity. The absence of DNA-PKcs from many model organisms has led to the assumption that DNA-PKcs is a vertebrate-specific PIKK. Here, we find that DNA-PKcs is widely distributed in invertebrates, fungi, plants, and protists, and that threonines 2609, 2638, and 2647 of the ABCDE cluster of phosphorylation sites are highly conserved amongst most Eukaryotes. Furthermore, we identify highly conserved amino acid sequence motifs and domains that are characteristic of DNA-PKcs relative to other PIKKs. These include residues in the Forehead domain and a novel motif we have termed YRPD, located in an α helix C-terminal to the ABCDE phosphorylation site loop. Combining sequence with biochemistry plus structural data on human DNA-PKcs unveils conserved sequence and conformational features with functional insights and implications. The defined generally progressive DNA-PKcs sequence diversification uncovers conserved functionality supported by Evolutionary Trace analysis, suggesting that for many organisms both functional sites and evolutionary pressures remain identical due to fundamental cell biology. The mining of cancer genomic data and germline mutations causing human inherited disease reveal that robust DNA-PKcs activity in tumors is detrimental to patient survival, whereas germline mutations compromising function are linked to severe immunodeficiency and neuronal degeneration. We anticipate that these collective results will enable ongoing DNA-PKcs functional analyses with biological and medical implications.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Simulations of activities, solubilities, transport properties, and nucleation rates for aqueous electrolyte solutions

This article reviews recent molecular simulation studies of "collective" properties of aqueous electrolyte solutions, specifically free energies and activity coefficients, solubilities, nucleation rates of crystals, and transport coefficients. These are important fundamental properties for biology and geoscience, but also relevant for many technological applications. Their determination from molecular-scale calculations requires large systems and long sampling times, as well as specialized sampling algorithms. As a result, such properties have not typically been taken into account during optimization of force field parameters; thus, they provide stringent tests for the transferability and range of applicability of proposed molecular models. There has been significant progress on simulation algorithms to enable the determination of these properties with good statistical uncertainties. Comparisons of simulation results to experimental data reveal deficiencies shared by many commonly used models. Moreover, there appear to exist specific tradeoffs within existing modeling frameworks, so that good prediction of some properties is linked to poor prediction for specific other properties. For example, non-polarizable models that utilize full charges on the ions generally fail to predict accurately both activity coefficients and solubilities; the concentration dependence of viscosity and diffusivity for these models is also incorrect. Scaled-charge models improve the dynamic properties and could also perform well for solubilities, but fail in the prediction of nucleation rates. Even models that do well at room temperature for some properties generally fail to capture their experimentally observed temperature dependence. Finally, the main conclusion from the present review is that qualitatively new physics will need to be incorporated in future models of electrolyte solutions to allow description of collective properties for broad ranges of concentrations, temperatures, and solvent conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Urban morphology and urban water demand: a case study in the land constrained Los Angeles region using urban growth modeling

The interactions between population growth, urban morphology, and water demand have important implications for water resources and supply in urban regions. Water use for irrigation comprises a significant fraction of urban water demand, and is potentially influenced by long-term changes in urban morphology. To investigate this, we used spatially explicit projections of urban land development intensity (fraction impervious area) generated from a 30 m resolution urban growth model for the Los Angeles (LA) region. Recent historical data on water use and high resolution landcover were used to establish relationships between green area, urban development intensity, and outdoor water demand. These relationships were then used to project outdoor and total water demand in 2100 using the urban growth model outputs. We considered two different population scenarios informed by the shared socioeconomic pathway (SSP) projections for the region (SSP3 and SSP5), and three scenarios of urban development intensification. Our analysis is resolved for over 80 water providers in the region, from the urban core to suburban fringe, and highlights diverse demand responses influenced by initial urban form and water demand attributes. Assumptions about outdoor water use factors based on recent water supply data were found to be nearly as influential on future outdoor demand as the urban growth scenario settings. Compared to previous studies, our work is unique in coherently linking high resolution SSP population scenarios, urban land cover evolution, and urban water demand projections, demonstrating the approach for the LA region—the largest population center in the western United States.

54 ENVIRONMENTAL SCIENCES↗

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 OSTI2020

Characterization of vacuum conductance in commercially available (sintered) and additively manufactured porous structures

This report documents the work performed in characterizing the vacuum conductance of porous structures made by conventional sintering (purchased as commercially available products from Mott Corporation ranging from 20 to 100 media grade) and additive manufacturing (powder bed fusion). The additively manufactured structures described in this report were originally intended to be the first iteration of several in an effort to produce desirable conductance characteristics. While resources were not available to link the experimental results to a modeling effort to better understand why certain characteristics were observed, the author hopes that this report may provide a useful set of data for future use, especially as sintered porous structures are not uncommonly procured from Mott corporation for research and development purposes. For that reason, all of the raw data is tabulated in the Appendix: it is possible to reproduce all of the figures shown in this report independently. For a quick order-of magnitude scan of the conductances, refer to Figures 5, 6, 8 and 9.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Finding the missing pieces: filling gaps that impede the translation of omics data into models

High-throughput omics technologies such as DNA sequencing have made the sequencing and computational assembly of microbial genomes recovered from the environment relatively routine. Computational inference of the protein products encoded by these genomes, and the associated biochemical functions, should enable the accurate prediction and modeling of microbial metabolism, organismal interactions, and ecosystem processes. However, a lack of scalable, probabilistic protein annotation tools limits the full potential of modeling for understanding the metabolism and biogeochemical cycles of microbial communities. Our approach to improve inference of protein annotations and metabolic models relied on learning from and emulating expert manual curation, leveraging software engineering and data science best practices to scale up the throughput and accuracy of annotations and metabolic model construction, building software to objectively evaluate different annotation strategies, and more closely linking the protein annotation and metabolic model inference process. Outcomes of this research include several improved or new computational tools, including DRAM (Distilled and Refined Annotation of Metabolism) for annotating microbial genomes with protein function and metabolic traits, CAMPER (Curated Annotations for Microbial Polyphenol Enzymes and Reactions) for annotating key polyphenol metabolisms, EC-Bench for comprehensive and unbiased benchmarking of annotation tools, and several apps available via the DOE Systems Biology Knowledgebase (KBase) for building genome-scale metabolic models. We demonstrate that these tools allow us to scalably annotate and understand thousands of genomes for microbial communities from a variety of systems and test cases, including rivers, thawing permafrost, and gut microbiomes. All of these computational tools are available as open-source software, with most broadly and easily accessible to the scientific community via KBase apps.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Covalently Linked, Two-Dimensional Quantum Dot Assemblies

Using nanoscale building blocks to construct hierarchical materials is a radical new branch point in materials discovery that promises new structures and emergent functionality. Understanding the design principles that govern nanoparticle assembly is critical to moving this field forward. By exploiting mixed ligand environments to target patchy nanoparticle surfaces, we have demonstrated a novel method of colloidal quantum dot (QD) assembly that gives rise to 2D structures. The equilibration of solutions of spherical and quasispherical QDs, including CdS, CdSe, and InP, with 2,2'-bipyridine-5,5'-diacrylic acid resulted in the preferential formation of 2D assemblies over the course of days as determined by transmission electron microscopy analysis. Small-angle X-ray scattering confirms the existence of the QD assemblies in solution. The dependence of the assembly on linker properties (length and rigidity), linker concentration, and total concentration was investigated, together with the data point to a mechanism involving ligand redistribution to create a patchy surface that maximizes the steric repulsion of neighboring QDs. By operating in an underexchanged regime, the arising patchiness results in enthalpically preferred directions of cross-linking that can be accessed by thermal equilibration.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

IsoForma: An R Package for Quantifying and Visualizing Positional Isomers in Top-Down LC-MS/MS Data

Proteoforms, the different forms of a protein with sequence variations including post-translational modifications (PTMs), execute vital functions in biological systems such as cell signaling and epigenetic regulation. Precisely defining the stoichiometry of PTMs has been challenging because, in the widely used bottom-up proteomics methods, the detection occurs at the peptide level and thus the link between peptides and their specific modification site is lost, resulting in proteoform ambiguity. Advances in top-down mass spectrometry (MS) technology have permitted the direct characterization of intact proteoforms and their exact number of modification sites, allowing for the relative quantification of positional isomers (PI). Proteins with positional isomers refers to proteoforms with identical total mass and set of modifications but varying PTM site combinations. The relative abundance of PI can be estimated by matching proteoform-specific fragment ions to top-down tandem MS (MS2) data to localize and quantify modifications. However, current approaches heavily rely on manual annotation. Here, we present IsoForma, an open-source R package for relative quantification of PI within a single tool. We benchmarked IsoForma’s performance against two existing workflows and highlight the similarity of the results and improvements in speed. Overall, IsoForma provides a streamlined process, reduces the time of conducting isoform-based analyses, and offers an essential framework for developing customized proteoform analysis workflows. Finally, the software is open source and available at https://github.com/EMSL-Computing/isoforma-lib.

59 BASIC BIOLOGICAL SCIENCES↗