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All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Aggregation Methods for Quantifying PTM and Structural Changes in Bottom-Up Proteomics

Bottom-up proteomic workflows rely on sequential preprocessing steps, commonly including peptide-to-protein aggregation (“roll-up”), to enhance data reliability and interpretability. While roll-up is effective for protein-centered analyses, it may be suboptimal for applications focused on post-translational modifications (PTMs) or protein structural changes, such as limited proteolysis–mass spectrometry (LiP-MS). Here, we investigate how different roll-up strategies influence site-level quantification in PTM differential analysis. Moreover, we introduce a novel site-centric roll-up approach tailored for LiP-MS, which quantifies proteolytic fragments rather than solely tryptic peptides. We benchmark these methods through simulation studies, comparing their sensitivity and specificity in detecting structural and PTM-driven changes. We found that the median and mean roll-up methods outperform the sum method in both PTM and LiP proteomics, and site-level quantification in LiP outperforms peptide-level quantification. Our findings offer the first systematic, data-driven guidance for selecting roll-up techniques in site-level proteomic analyses, with implications for both PTM-focused and structural proteomics studies.

aggregation↗
DOE OSTI2020

Real-time Intrusion Detection for High-bandwidth Research Networks using Unsupervised Deep Learning

Nowadays, data generated by large-scale scientific experiments are on the scale of petabytes per month. These data are transferred through dedicated high-bandwidth networks across distributed collaboration sites for processing, storage, and analysis. Like general purpose networks, research networks experience attacks. However, monitoring traffic in such high-bandwidth network environments is challenging with conventional deep packet inspection (DPI)- based network intrusion detection systems (NIDS). Recently, machine learning (ML) algorithms have shown potential in detecting anomalous patterns with better generalizability and faster speed. Compared to the general purpose networks, traffic movement in research network is less volatile and more likely to benefit from the ML-based anomaly analysis. We present ThunderSecure, an efficient AI-powered system for detecting anomalies in 100G research networks. ThunderSecure implements a high-throughput packet processing infrastructure using multi-cores and GPUs. It takes time-series statistics from a variety of network measurements and uses 2D Convolutional Neural Network (CNN) to explore both spatial and temporal dependencies in network data stream. Patterns of science data traffic are learned with a one-class neural network, which blends an Adversarial Autoencoder (AAE) with Gaussian mixture density estimation. Testing traffic flows exhibiting significant deviations from the learned baseline of normality are marked as anomalies. We trained ThunderSecure on hundreds of billions of science data packets recorded from a 100G research network at Fermi National Accelerator Laboratory. The detection performance was evaluated on traffic captured from the same research network days and weeks after the training with different types of attack flows injected. To the best of our knowledge, this is the first ML work in the area of network anomaly detection that has been validated on such extreme scale datasets. Results show that ThunderSecure can recognize science data traffic that are captured long after the training and make nearly certain detection on those with anomalous flows injected, even in the case when the anomaly-to-normal mixing ratio is 0.1%.

Gong, Qian↗
DOE OSTI2020

Low Count and Background Radionuclides Analysis - 20488

The US Department of Energy (DOE) is often faced with the need to evaluate radionuclides at low concentrations. When site sample data are likely to be close to threshold activity concentrations of interest, then the means by which the radiochemical analysis is performed and reported is critical. This situation can occur when differentiating from zero (presence/absence) for radionuclides that do not occur naturally, close comparison with environmental background for naturally occurring radionuclides, close comparison with a risk- or dose-based threshold concentrations of interest, or even comparisons across studies. There are several analytical issues that are of concern, but the two that appear to cause incorrect decisions to be made most often involve establishing detection limits and subtracting ambient background conditions in the laboratory. These issues are not critical when radionuclide activity concentrations are large relative to thresholds of concern, but they seem to be poorly understood when it matters. When the comparisons are important and are likely to be close to a threshold of interest, then the general contract with the analytical laboratories needs to be changed so that the right or appropriate data are obtained. The concern is that important decisions are made incorrectly more often as greater scrutiny is placed on DoE's radionuclide cleanup or monitoring decisions by the public and other stakeholders. Examples are presented of problems that have been observed for different projects, both within and outside the realm of DOE and NRC remediation and radioactive waste disposal problems, and solutions are offered that should lead to better data from which important decisions need to be made. The first example is from Los Alamos National Laboratory (LANL) and involves radionuclide concentrations in soil and rock beneath LANL's Material Disposal Area (MDA) G. An initial review of the data led to a conclusion that americium and plutonium are a long way present beneath MDA G. A more thorough review of the data that accounted properly for ambient background and the detection limits that had been established led to the opposite conclusion. Another example is from the Nevada National Security Site where tritium results from one of the wells were unexpectedly high. Proper understanding and analysis of ambient background led to the conclusion that the increased concentrations were not so obvious, and that a different contract with the analytical laboratory was needed to provide more appropriate data to support a better determination. Other examples are used from regulatory review of projects in Nevada, where background levels and secular equilibrium for naturally occurring radionuclides are not established correctly because of analytical issues. The same basic issues have also been found to create difficulties analyzing historical data from the West Valley Demonstration Project. There is evidence in the data that the apparent lack of secular equilibrium where it is expected to exist is related to ambient background subtraction or other analytical issues. A final example is presented for analysis of Tc-99 in samples of depleted uranium. In this case, two different studies that were performed only three months apart provide quite different results. The US Environmental Protection Agency (EPA) established the data quality objectives (DQO) process in the mid-1980's to establish decision performance criteria for data collection. EPA guidance (EPA G-4, for example) clearly distinguishes between DQOs and measurement performance objectives (MQOs) that should be addressed for laboratory analysis of samples. The language of DQOs and MQOs has become confused over time it seems, and the subsequent effects seem to include a lack of attention to decision performance and a routine approach to measurement quality. In order to better address radionuclide sample analysis when the concentrations are close to thresholds of concern, which might be zero for some radionuclides, background for others, and risk-based thresholds for yet others, it is important that routine laboratory analysis methods are adjusted, and that the project team and the laboratory work closely together to ensure that the data meets the MQO requirements of laboratory analysis and reporting of results, and that the MQOs effectively support project-specific DQOs. This basic approach will be applied in Los Alamos in the coming year to the collection of moisture data from underneath MDA T that will be analyzed for americium and neptunium isotopes. Proper understanding of the radiochemistry methods and reporting, and of appropriate statistical methods is critical to the success of such projects, ensuring that the right decisions are made. (authors)

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2026

Wind and Temperature Consensus at Horn Point, HU-Beltsville, Piney Run (Maryland) in support of CoURAGE

The Maryland Department of the Environment (MDE) operates a ground-based atmospheric profiling network consisting of collocated radar wind profilers (RWP) and radio acoustic sounding systems (RASS) as part of its Ambient Air Monitoring Program. This network provides continuous observations of wind and temperature structure in the lower troposphere to support air quality forecasting, regulatory analysis, and atmospheric research. The network currently includes three fixed sites across Maryland: Horn Point (HP, lower eastern shore) [38.587525°,-76.141006°], Howard University-Beltsville (HUB, central Maryland) [39.055277°, -76.878632°], and Piney Run (PR, western Maryland) [39.705950°, -79.012000°] The network is designed to capture regional variability in atmospheric transport and boundary-layer processes. These systems measure vertical profiles of horizontal wind speed and direction using Doppler radar techniques, with observations typically spanning from ~100 m above ground level up to approximately 2.5–4 km. Measurements are derived from the Doppler shift of backscattered electromagnetic signals, enabling retrieval of wind vectors at multiple altitudes with high temporal resolution (e.g., 30-minute averages reported every 6 minutes). Each radar wind profiler is paired with a Radio Acoustic Sounding System (RASS) to provide profiles of virtual temperature in the lower atmosphere (~100–200 m AGL) by measuring the propagation speed of acoustic waves. Together, the RWP/RASS system yields a coupled data set of thermodynamic and kinematic atmospheric structure, including additional parameters such as vertical velocity, radial velocity, signal-to-noise ratio, and spectral width for advanced analysis. There are two types of files for each station: wind data (files with a "w" prefix) and virtual temperature RASS data (files with a "t" prefix). The wind data files are in the format wYYDDD.cns, where YY is the 2-digit year and DDD is the day of the year. The RASS virtual temperature data files are in the format tYYDDD.cns. Each record has the following header structure: Line 1 : Station Name RASS files Line 2 : RASS rev DeTect_2.0, WINDS files Line 2 : WINDS rev ATI 5.1 Line 3 : N latitude, W longitude, and site elevation (m) Line 4 : Date and begin time of consensus: yy mm dd hh mn ss plus # minutes to add to get UTC Line 5 : Consensus averaging time (minutes); number of beams; number of range gates Line 6 : Number of records required to make consensus (num) total number of records (tot) and the consensus window size (m/s) in the format: num:tot (window) RASS files Line 7 : no. of coded cells, no. of spec, pulse width (ns), and inter-pulse period (µs), WINDS files Line 7 : No. of coded cells, no. of spectra, pulse width (ns), and inter-pulse period (µs), each with a pair of values: first value is for oblique beams, second for vertical RASS files Line 8 : Full scale Doppler value (m/s) Delay to first gate (ns) Number of gates Spacing of gates (ns), WINDS files Line 8 : Full scale Doppler velocity (m/s), oblique and vertical Vertical correction applied to oblique beams? (0 = no, 1 = yes) Delay to first gate (ns), oblique and vertical Number of gates, oblique and vertical Spacing of gates (ns), oblique and vertical Line 9 : Azimuth and elevation (9s indicate vertical beam not used) RASS files Line 10, values : HT = Height above ground (km), T = Uncorrected virtual temperature consensus (deg C), Tc = Corrected virtual temperature consensus (deg C), W = Vertical wind consensus (9s indicate vertical beam not used, w-component, positive upward, m/s), CNT = Number of records that made consensus (for the 3 values in same order), SNR = Average signal to noise ratio (dB) of records in consensus (same order) WINDS files Line 10, values : HT = Height above ground (km), SPD = Wind speed (m/s), DIR = Wind direction (deg E of N from N), RAD = Radial velocities for each beam (m/s) in order given in azimuth and elevation line (positive toward radar; 9s indicate vertical beam not used, CNT = Number of records that made consensus, SNR = Average signal to noise ratio (dB) of records in consensus

{"wind speed and direction",temperature}↗
DOE OSTI2022

CO 2 hydrogenation: Selectivity control of CO versus CH 4 achieved using Na doping over Ru/m-ZrO 2 at low pressure

By doping 1%Ru/m-ZrO 2 with sodium, selectivity tuning between CO and CH 4 during CO 2 hydrogenation was achieved by controlling the relative rates of reverse water-gas shift and CO methanation. By increasing basicity through Na loading: (1) the formate C-H bond is weakened in DRIFTS of adsorbed CO, accelerating C-H bond formation of formate and promoting CO formation at the Ru/m-ZrO 2 interface; and (2) the coverage of Na increases on ensembles of Ru atoms responsible for methanation. Increasing Na content shifts selectivity from CH 4 (useful for synthetic natural gas) to CO, which can be used for Fischer-Tropsch synthesis or methanol-to-gasoline. Electronic modification of formate is likely due to enhanced basicity (strengthening bonding between catalyst and the-CO 2 function of formate and weakening C-H). In conclusion, no electron transfer from Na to Ru was detected in XANES. DRIFTS as a function of time and XPS results showed that Na exacerbates site blocking and deactivation.

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↗
DOE OSTI2022

Evaluating the Physisorption and Chemisorption of Iodine on Bismuth-Functionalized Carbon Foams

Bismuth-containing carbon materials have been shown to be highly promising sorbents for the capture of radioiodine. However, there is still a need to understand the effects of carbon and bismuth on the iodine sorption mechanism. In this study, we show the relationship between the physical and chemical sorption of iodine under different bismuth loading conditions. Here, highly porous and non-friable conductive carbon foams were prepared and bismuth was electrodeposited to provide strong iodine binding sites. For pure carbon foams, equal ratios of physisorbed and chemisorbed iodine-carbon phases were detected before desorption. As the concentration of bismuth increased, the chemisorption between bismuth and iodine dominated the total capture mechanism and physisorption was almost completely eliminated. Additionally, chemisorption of iodine depended upon the size and specific surface area of the bismuth particles present within the framework of the foam.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Galactic chemical evolution with the short-lived isotopes 53 Mn, 60 Fe, 182 Hf, and 244 Pu

We run a three-dimensional Galactic chemical evolution (GCE) model to follow the propagation of 53 Mn from supernovae of type Ia (SNIa), 60 Fe from core-collapse supernovae (CCSNe), 182 Hf from intermediate mass stars (IMSs), and 244 Pu from neutron star mergers (NSMs) in the Galaxy. We compare the GCE of these short-lived radioactive isotopes (SLRs) to recent detections on the deep-sea floor. We find that although these SLRs originate from different sites, they often arrive conjointly on Earth.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Novel application of neutrinos to evaluate U.S. nuclear weapons performance

There is a growing realization that neutrinos can be used as a diagnostic tool to better understand the inner workings of a nuclear weapon. Robust estimates demonstrate that an Inverse Beta Decay (IBD) neutrino scintillation detector built at the Nevada Test Site with a 1000-ton active target mass at a standoff distance of 500 m would detect thousands of antineutrino events per nuclear test. This would provide less than 4% statistical error on the measured antineutrino rate and 5% error on antineutrino energy. Extrapolating this to an error on the test device explosive yield requires knowledge from evaluated nuclear databases, non-equilibrium fission rates, and assumptions on internal neutron fluxes. Initial calculations demonstrate that the total number of neutrinos emitted per fission in the first 10 3 s after a short pulse of 239 Pu fission is about a factor of two less than that from Pu fissioning under steady state conditions. Furthermore, there are significant energy spectral differences as a function of time after the pulse that must be considered. These and other model dependencies will be discussed in the paper. In the absence of nuclear weapons testing, many of the technical and theoretical challenges of a full nuclear test could be mitigated with a low cost smaller scale 20 ton fiducial mass IBD demonstration detector placed near a pulsed reactor. Potential reactors include the Texas A&M University TRIGA 1 GW–10 ms pulsed facility or the Sandia Annular Core Research Reactor. The short duty cycle and repeatability of pulses would provide critical real environment testing and measurements, which would be valuable for planning a possible real test shot in the future. Furthermore, the antineutrino rate as a function of time data would provide unique constraints on fission databases and model assumptions. Finally, there are impactful science drivers such as sensitive searches for ∼1 eV 2 sterile neutrinos and ∼MeV scale axions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Lightning strike prediction at the Savannah River Site

At the Savannah River Site, employees receive warnings about lightning only after three strikes have already occurred near the site. In order to increase employee safety, it is preferential to warn employees of a lightning threat much sooner. We used data from an on-site Electric Field Mill to measure values of the atmospheric electric charge. We also used lightning detection data from the National Lightning Detection Network and the Geostationary Lightning Mapper. By comparing the data of each, we can determine how long before or after a lightning strike did the Electric Field Mill first measure within our lightning detection threshold. If the detection threshold occurs before the strike does, this provides a lead time for knowing about lightning risks before they happen. Our findings conclude that 95% of lightning strikes have a lead time in the electric field where we can predict the lightning before it occurs and warn employees of the potential lightning threat. However, our lightning detection threshold can occur even without lightning or precipitation. Finding how these false lightning alarms affect our data is necessary to improving the lightning warning system.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Abstract for CRADA between NETL and Louisiana State University

The National Energy Technology Laboratory (NETL) and Louisiana State University (PARTICIPANT) will collaborate in developing and testing distributed optical fiber CO 2 sensors for CO 2 storage site monitoring. Safe and reliable monitoring of CO 2 storage sites and transport infrastructure is critical for ensuring the long-term effectiveness and integrity of carbon capture and storage (CCS). In this project, the objective is to develop a novel optical fiber-based distributed CO 2 sensor for long-term monitoring of CCS sites and CO 2 pipelines and also implement machine learning to automate leak and structural anomaly detection. This effort aligns with NETL’s mission in reliable and sustainable energy and decarbonization.

47 OTHER INSTRUMENTATION↗
DOE OSTI2026

Stereo-vision thermal imaging system for tracking flying animals in wind farm areas (CRADA #763) Abstract

CRADA 763: abstract ThermalTracker-3D (TT3D) is a stereo vision thermal imaging system that provides 3D flight information on detected birds, bats, and other flying targets. The system was initially developed for use in the siting and monitoring of offshore wind projects to establish pre-construction and operation collision risk data but can be applied to terrestrial wind energy projects as well as national security monitoring. This technology will reduce monitoring cost, decrease processing time, and provide more accurate data for wind energy developers/operators and regulatory agencies. While the current technology is at a high level of readiness, Technology Readiness Level (TRL) 7, there remain several barriers to commercialization, particularly around ease-of-use, that result in a low Adoption Readiness Level (ARL). The proposed work will advance commercialization readiness by streamlining calibration methods for built systems. This work will:1. 1. develop a software package for factory and dynamic calibration processes 2. test that package with existing prototype TT3D systems, and 3. conduct outreach with industry end-users.

ThermalTracker↗
DOE OSTI2023

An Architectural Survey of the Pluto Test Bunker Facility, Nevada National Security Site, Nye County, Nevada

The U.S. Department of Energy (DOE), in conjunction with the National Nuclear Security Administration Nevada Field Office (NNSA/NFO), proposes to reactivate Building 26-2205 as part of a project to detect foundry-type operations with remote sensing. The project is known as the Signals Exploration Testbed, or SET for short. Building 26-2205 (State Historic Preservation Office [SHPO] Resource No. B11558) is the former Compressor Building for the Pluto Program in Area 26 of the Nevada National Security Site (NNSS). Proposed actions at Building 26-2205 include removal of exterior building and site features, such as fencing, concrete pads, a large steel tank, and visible utilities, as well as interior changes to the building’s floor plan. These activities constitute an undertaking subject to review under Section 106 of the National Historic Preservation Act (NHPA) (54 United States Code [USC] § 306101) and its implementing regulations, 36 Code of Federal Regulations (CFR) Part 800.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Source Physics Experiment: Rock Valley Interferometric Synthetic Aperture RADAR Earthquake Detection Study

Seismic signals from 1993 show a series of magnitude (Mw) 3.7 or less seismic events in Rock Valley on the Nevada National Security Site (NNSS). Historic synthetic aperture radar images of that location were found that could provide interferometric synthetic aperture radar (InSAR) measures of the ground height during 1993. Given this historic SAR imagery, we explore answering the question if ground movement from the 1993 Rock Valley earthquake activity could be sensed by remote sensing means. Finding earthquake surface movement would assist in locating the Rock Valley fault and the 1993 earthquake hypocenter where the Source Physics Experiment Phase III series of experiments will be conducted. In this report, we show that InSAR can sense very small height differences, and for the European Radar Satellite-1 InSAR collections during 1992 and 1993 over Rock Valley earth surface movements were measured with 8 mm uplift and 12.5 mm subsidence over isolated areas. One of these earth movement areas coincides with an InSAR image pair coherence drop between March 5, 1993 and June 18, 1993. The coherence drop is over an approximately 13 square km area south southeast of Skull Mountain centered at 36° 43' 30" N latitude and 116° 05' 00" W longitude. Measured small surface movement and a loss of InSAR coherence may be caused by the series of earthquakes. The location of these InSAR detections may also coincide with water drainage or erosion displacement. There are no records to disambiguate the earthquake and erosion earth surface motion possibilities. Therefore, the InSAR findings of earth surface movement by InSAR are inconclusive.

58 GEOSCIENCES↗
DOE OSTI2024

Time-lapse seismic inversion for CO 2 saturation with SeisCO2Net: An application to Frio-II site

Seismic monitoring of geological CO 2 storage (GCS) involves highly nonlinear seismic inversion and petrophysical inversion, making it challenging to estimate CO 2 volume efficiently and detect possible early CO 2 leakages. Deep learning (DL) using convolutional neural networks (CNNs) has shown promise in solving highly nonlinear seismic inversion problems. However, direct estimation of CO 2 plume extent/saturation from time-lapse seismic gathers using DL is still underexplored, with no reported field applications to date. The investigation of field data is primarily hindered by scarcity of field data for neural network training. Other obstacles include highly nonlinear seismic-petrophysics inverse relationship, and presence of noise in field seismic data. We introduce SeisCO2Net, a deep CNN that predicts CO 2 saturation maps directly from time-lapse full waveform shot gathers. For training, we use site-specific geological information, fluid flow physics, rock physics, and seismic modeling to generate synthetic datasets that closely resemble the CO 2 storage site. Synthetic tests show promising results, inspiring us to apply SeisCO2Net's trained weights on field data collected at Frio-II GCS site by leveraging transfer learning principles. As reference, we compare SeisCO2Net's predicted CO 2 saturation maps with results obtained from physics-based inversion. Our analyses show both methods display similar CO 2 plume shapes, reasonable CO 2 plume characteristics, and comparable saturation values. Our results suggest pre-training CNNs on physics-informed synthetic datasets and then applying the learned weights to field data is a viable approach to estimating field CO 2 saturation. This method effectively addresses the scarcity of field training data, thus encouraging the feasibility of long-term GCS monitoring.

58 GEOSCIENCES↗
DOE OSTI2022

Detecting impacts of surface development near weather stations since 1895 in the San Joaquin Valley of California

Abstract Temperature readings observed at surface weather stations have been used for detecting changes in climate due to their long period of observations. The most common temperature metrics recorded are the daily maximum (TMax) and minimum (TMin) extremes. Unfortunately, influences besides background climate variations impact these measurements such as changes in (1) instruments, (2) location, (3) time of observation, and (4) the surrounding artifacts of human civilization (buildings, farms, streets, etc.) Quantifying (4) is difficult because the surrounding infrastructure, unique to each site, often changes slowly and variably and is thus resistant to general algorithms for adjustment. We explore a direct method of detecting this impact by comparing a single station that experienced significant development from 1895 to 2019, and especially since 1970, relative to several other stations with lesser degrees of such development (after adjustments for the (1) to (3) are applied). The target station is Fresno, California (metro population ~ 15,000 in 1900 and ~ 1 million in 2019) situated on the eastern side of the broad, flat San Joaquin Valley in which several other stations reside. A unique component of this study is the use of pentad (5-day averages) as the test metric. Results indicate that Fresno experienced + 0.4 °C decade −1 more nighttime warming (TMin) since 1970 than its neighbors—a time when population grew almost 300%. There was little difference seen in TMax trends between Fresno and non-Fresno stations since 1895 with TMax trends being near zero. A case is made for the use of TMax as the preferred climate metric relative to TMin for a variety of physical reasons. Additionally, temperatures measured at systematic times of the day (i.e., hourly) show promise as climate indicators as compared with TMax and especially TMin (and thus TAvg) due to several complicating factors involved with daily high and low measurements.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Search for active and inactive ion insertion sites in organic crystalline materials

The position of mobile active and inactive ions, specifically ion insertion sites, within organic crystals, significantly affects the properties of organic materials used for energy storage and ionic transport. Identifying the positions of these atomic (and ionic) sites in an organic crystal is challenging, especially when the element has low X-ray scattering power, such as lithium (Li) and hydrogen, which are difficult to detect by powder X-ray diffraction. First-principles calculations, exemplified by density functional theory (DFT), are very practical for confirming the relative stability of ion positions in materials. However, the lack of effective strategies to identify ion sites in these organic crystalline frameworks renders this task extremely challenging. This work presents two algorithms: the (i) efficient location of ion insertion sites from extrema in electrostatic local potential and charge density (ELIISE), and the (ii) ElectRostatic InsertioN (ERIN), which leverage charge density and electrostatic potential fields accessed from first-principles calculations, combined with the Simultaneous Ion Insertion and Evaluation (SIIE) workflow. SIIE inserts all ions simultaneously—to determine ion positions in organic crystals. We demonstrate that these methods accurately reproduce known ion positions in 16 organic materials and identify previously overlooked low-energy sites in tetralithium 2,6-naphthalenedicarboxylate (Li4NDC), an organic electrode material, highlighting the importance of inserting all ions simultaneously, as in the SIIE workflow. These algorithms are also integrated with off-the-shelf machine learning potentials, yielding promising results comparable to first-principles findings.

Gopidi, Harshan Reddy [Argonne National Laboratory↗