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DOE OSTI2022

Image transformers for classifying acute lymphoblastic leukemia

Cancer is the leading cause of death by disease in American children. Each year, nearly 16,000 children in the United States and over 300,000 children globally are diagnosed with cancer. Leukemia is a form of blood cancer that originates in the bone marrow and accounts for one-third of pediatric cancers. This disease occurs when the bone marrow contains 20% or more immature white blood cell blasts. Acute lymphoblastic leukemia is the most prevalent leukemia type found in children, with half of all annual cases in the U.S. diagnosed for subjects under 20 years of age. To diagnose acute lymphoblastic leukemia, pathologists often conduct a morphological bone marrow assessment. This assessment determines whether the immature white blood cell blasts in bone marrow display the correct morphological characteristics, such as size and appearance of nuclei. Pathologists also use immunophenotyping via multi-channel flow cytometry to test whether certain antigens are present on the surface of blast cells; the antigens are used to identify the cell lineage of acute lymphoblastic leukemia. These manual processes require well-trained personnel and medical professionals, thus being costly in time and expenses. Computerized decision support via machine learning can accelerate the diagnosis process and reduce the cost. Training a reliable classification model to distinguish between mature and immature white blood cells is essential to the decision support system. Here, we adopted the Vision Transformer model to classify white blood cells. The Vision Transformer achieved superb classification performance compared to state-of-the-art convolutional neural networks while requiring less computational resources for training. Additionally, the latent self-attention architecture provided attention maps for a given image, providing clues as to which portion(s) of the image were significant in decision-making. We applied the Vision Transformer model and a convolutional neural network model to an acute lymphoblastic leukemia classification dataset of 12,528 samples and achieved accuracies of 88.4% and 86.2%.

Cho, Priscilla↗

DOE OSTI2023

Activation of human STING by a molecular glue-like compound

Stimulator of interferon genes (STING) is a dimeric transmembrane adapter protein that plays a key role in the human innate immune response to infection and has been therapeutically exploited for its antitumor activity. The activation of STING requires its high-order oligomerization, which could be induced by binding of the endogenous ligand, cGAMP, to the cytosolic ligand-binding domain. Here we report the discovery through functional screens of a class of compounds, named NVS-STGs, that activate human STING. Our cryo-EM structures show that NVS-STG2 induces the high-order oligomerization of human STING by binding to a pocket between the transmembrane domains of the neighboring STING dimers, effectively acting as a molecular glue. Our functional assays showed that NVS-STG2 could elicit potent STING-mediated immune responses in cells and antitumor activities in animal models.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Measurement of Local Magnetic Fields in Actinide Tetrafluorides

Fluorine-19 magnetic shielding tensors have been measured in a series of actinide tetrafluorides (AnF4) by solid state nuclear magnetic resonance (NMR) spectroscopy. Tetravalent actinide centers with 0 to 8 valence electrons can form tetrafluorides with the same unit cell, making these compounds an attractive choice for a systematic study of the variation in electronic structure across the 5f row of the Periodic Table. Pronounced deviations from predictions based on localized valence electron models have been detected by these experiments, which suggests that this approach may be used as a quantitative probe of electronic correlations.

Walter, Eric D.↗

DOE OSTI2022

An Investigation of Chemo-Mechanical Phenomena and Li Metal Penetration in All-Solid-State Lithium Metal Batteries Using In Situ Optical Curvature Measurements

Solid-electrolytes (SEs) can provide a pathway to increase energy-density in lithium metal batteries. However, lithium metal penetration through garnet based LLZO solid electrolytes has been identified as a critical failure process. This phenomenon is related to chemo-mechanical processes which are difficult to probe. In particular, characterizing the dynamic mechanical deformations that occur in electrode-SE structures is very challenging. Here study reports in situ curvature measurements that are thus designed to probe chemo-mechanical phenomena that occur during lithium plating. The novel experimental cell configuration created for this work shows that pressure builds up in the Li metal during plating, up until the point where short circuits occur. The resulting data are analyzed with a detailed finite element model (FEM) to quantitatively evaluate stress evolution. The results show that Li metal plating within a surface flaw can produce stress build-up prior to short-circuiting. The combined results from both the experiments and the FEM suggest that it is critical to minimize surface defects and flaws during the manufacturing processes.

25 ENERGY STORAGE↗

DOE OSTI2025

Delineating the Impact of Diluent on High-Concentration Electrolytes for Developing High-Voltage LiNi 0.5 Mn 1.5 O 4 Spinel Cathode

LiNi 0.5 Mn 1.5 O 4 (LNMO) is a high-voltage spinel cathode with low nickel content, making it an attractive candidate for next-generation lithium-ion batteries (LIBs). However, its application is limited by interfacial instability with conventional carbonate-based electrolytes at high voltages. In this work, a localized saturated electrolyte (LSE) capable of stably operating up to 4.85 V is investigated. Molecular dynamics simulations and Fourier transform infrared spectroscopy reveal that adding “non-solvating” 1,1,2,2-tetrafluoroethyl-2,2,3,3-tetrafluoropropyl ether diluent in the saturated electrolyte, more PF 6 − anions are present in the first solvation shell of Li + , at the expense of solvent molecules. This tailored solvation environment promotes the formation of a robust, LiF-rich cathode-electrolyte interphase that mitigates transition metal dissolution and parasitic side reactions. The optimized LSE enables excellent cycling performance, with 95% capacity retention in Li|LNMO half-cells after 100 cycles and 94% retention in Li 4 Ti 5 O 12 |LNMO full cells after 250 cycles, even at a practically relevant LNMO cathode loading of ≈15 mg cm −2 . In conclusion, these results highlight the benefits of electrolyte engineering and solvation structure control in advancing high-voltage LIB technologies.

LNMO cathode↗

DOE OSTI2022

A systematic exploration of boceprevir-based main protease inhibitors as SARS-CoV-2 antivirals

Boceprevir is an HCV NSP3 inhibitor that was explored as a repurposed drug for COVID-19. It inhibits the SARS-CoV-2 main protease (M Pro ) and contains an α-ketoamide warhead, a P1 β-cyclobutylalanyl moiety, a P2 dimethylcyclopropylproline, a P3 tert-butylglycine, and a P4 N-terminal tert-butylcarbamide. By introducing modifications at all four positions, we synthesized 20 boceprevir-based M Pro inhibitors including PF-07321332 and characterized their M Pro inhibition potency in test tubes (in vitro) and 293T cells (in cellulo). Crystal structures of M Pro bound with 10 inhibitors and cytotoxicity and antiviral potency of 4 inhibitors were characterized as well. Replacing the P1 site with a β-(S-2-oxopyrrolidin-3-yl)-alanyl (Opal) residue and the warhead with an aldehyde leads to high in vitro potency. The original moieties at P2, P3 and the P4 N-terminal cap positions in boceprevir are better than other tested chemical moieties for high in vitro potency. In crystal structures, all inhibitors form a covalent adduct with the M Pro active site cysteine. Here, the P1 Opal residue, P2 dimethylcyclopropylproline and P4 N-terminal tert-butylcarbamide make strong hydrophobic interactions with M Pro , explaining high in vitro potency of inhibitors that contain these moieties. A unique observation was made with an inhibitor that contains a P4 N-terminal isovaleramide. In its M Pro complex structure, the P4 N-terminal isovaleramide is tucked deep in a small pocket of M Pro that originally recognizes a P4 alanine side chain in a substrate. Although all inhibitors show high in vitro potency, they have drastically different in cellulo potency to inhibit ectopically expressed M Pro in human 293T cells. In general, inhibitors with a P4 N-terminal carbamide or amide have low in cellulo potency. This trend is reversed when the P4 N-terminal cap is changed to a carbamate. The installation of a P3 O-tert-butyl-threonine improves in cellulo potency. Three molecules that contain a P4 N-terminal carbamate were advanced to cytotoxicity tests on 293T cells and antiviral potency tests on three SARS-CoV-2 variants. They all have relatively low cytotoxicity and high antiviral potency with EC 50 values around 1 μM. A control compound with a nitrile warhead and a P4 N-terminal amide has undetectable antiviral potency. Based on all observations, we conclude that a P4 N-terminal carbamate in a boceprevir derivative is key for high antiviral potency against SARS-CoV-2.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Tumor-promoting UBR4 coordinates impaired mitophagy–associated senescence and lung adenocarcinoma pathogenesis

Cellular senescence, an irreversible cell cycle arrest, plays a pivotal role in development, aging, and tumor suppression. However, the fundamental pathway coordinating senescence and neoplastic transformation remains unclear. Here, we describe the tumorigenic involvement of ubiquitin protein ligase E3 component n-recognin 4 (UBR4), an E3 ubiquitin ligase of the N-degron pathway, in lung adenocarcinoma (LUAD). Public genome databases revealed high UBR4 expression in LUAD patients, associated with a dysregulated cell cycle and impaired mitochondrial homeostasis.UBR4knockout (ΔUBR4) in A549 lung cancer cells induced cellular senescence with defective mitochondria. Restoration of UBR4 or antioxidant treatment reversed the ΔUBR4 phenotypes caused by impaired mitophagy. Mitochondrial stress exacerbated mitochondrial dysfunction in ΔUBR4 cells, contributing to diverse cellular phenotypes. Additionally, ΔUBR4 cells exhibited substantially slow tumor growth in mouse xenograft models. In LUAD patients, UBR4 levels correlated with tumor stage, mitophagy markers, and poor survival. These findings suggest a tumor-promoting function of UBR4 in LUAD by regulating mitochondrial quality control. Further research into the pharmacological inhibition of UBR4 could open promising avenues for developing effective antitumor therapies targeting LUAD.

Science & Technology - Other Topics↗

DOE OSTI2024

A phosphorylation-deficient ribosomal protein eS6 is largely functional in Arabidopsis thaliana , rescuing mutant defects from global translation and gene expression to photosynthesis and growth

The eukaryote-specific ribosomal protein of the small subunit eS6 is phosphorylated through the target of rapamycin (TOR) kinase pathway. Although this phosphorylation event responds dynamically to environmental conditions and has been studied for over 50 years, its biochemical and physiological significance remains controversial and poorly understood. Here, we report data from Arabidopsis thaliana, which indicate that plants expressing only a phospho-deficient isoform of eS6 grow essentially normally under laboratory conditions. The eS6z (RPS6A) paralog of eS6 functionally rescued a double mutant in both rps6a and rps6b genes when expressed at approximately twice the wild-type dosage. A mutant isoform of eS6z lacking the major six phosphorylatable serine and threonine residues in its carboxyl-terminal tail also rescued the lethality, rosette growth, and polyribosome loading of the double mutant. This isoform also complemented many mutant phenotypes of rps6 that were newly characterized here, including photosynthetic efficiency, and most of the gene expression defects that were measured by transcriptomics and proteomics. However, compared with plants rescued with a phospho-enabled version of eS6z, the phospho-deficient seedlings retained a mild pointed-leaf phenotype, root growth was reduced, and certain cell cycle-related mRNAs and ribosome biogenesis proteins were misexpressed. The residual defects of the phospho-deficient seedlings could be understood as an incomplete rescue of the rps6 mutant defects. There was little or no evidence for gain-of-function defects. As previously published, the phospho-deficient eS6z also rescued the rps6a and rps6b single mutants; however, phosphorylation of the eS6y (RPS6B) paralog remained lower than predicted, further underscoring that plants can tolerate phospho-deficiency of eS6 well. Our data also yield new insights into how plants cope with mutations in essential, duplicated ribosomal protein isoforms.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Powder X-ray diffraction of fluorometholone, C 22 H 29 FO 4

Commercial fluorometholone, CAS #426-13-1, crystallizes in the monoclinic space group P 2 1 (#4) with a = 6.40648(2), b = 13.43260(5), c = 11.00060(8) Å, β = 92.8203(5)°, V = 945.517(5) Å 3 , and Z = 2. A reduced cell search in the Cambridge Structural Database yielded one previous structure determination, using single-crystal data at 292 K. In this work, the sample was ordered from the United States Pharmacopeial Convention (Lot # R032K0) and analyzed as-received. The room temperature (295 K) crystal structure was refined using synchrotron ( λ = 0.412826 Å) powder diffraction data and optimized using density functional theory (DFT) techniques. Hydrogen positions were included as a part of the structure and were re-calculated during the refinement. The diffraction data were collected on beamline 11-BM at the Advanced Photon Source, Argonne National Laboratory, and the powder X-ray diffraction pattern of the compound has been submitted to ICDD® for inclusion in the Powder Diffraction File™. The agreement of the Rietveld-refined and DFT-optimized structures is excellent; the root-mean-square Cartesian displacement is 0.060 Å. In addition to the O–H&ctdot;O hydrogen bonds observed by Park et al. (Park, Y. J., Lee, M. Y., and Cho, S. I. ( 1992 ). “Fluorometholone,” J. Korean Chem. Soc. 36 , 812–817), C–H&ctdot;O hydrogen bonds contribute to the crystal energy.

Gonzalez, Diana↗

DOE OSTI2021

Understanding the Selective Deposition of Li Metal on Nonuniform Electrode Surfaces Using Atomic Force Microscopy

The use of lithium metal in secondary batteries has been impeded by its tendency to form dendrites: branching conductive structures of metal that can lead to capacity loss and, ultimately, internal shorts in the battery. Patterned electrodes, in addition to artificially increasing the current density of cells by increasing the surface area available for reaction, also generate a nonuniform electric field in the vicinity of the electrode surface. This nonuniform electric field, though rapidly screened by the electrolyte, can promote inhomogeneous deposition and Solid Electrolyte Interphase formation. As the consequence of these effects is not theoretically apparent since Solid Electrolyte Interphase volume and conductivity changes can, in principle, offset variations in local current density, we have performed experiments to examine the deposition of Li on nonuniform electrode surfaces using Atomic Force Microscopy. In this work, we measure the local variations in topography, SEI thickness, and composition, and discuss their implications for the formation of dendrites in Li metal.

25 ENERGY STORAGE↗

DOE OSTI2020

Effect of Aluminum Oxide on the Performance of Ionic Liquid-Based Aluminum–Air Battery

The aluminum–air (or oxygen) battery has received intense attention in the past because of its excellent benefits such as low cost and high energy density, but due to the challenging issues such as hydrogen evolution and inactive oxide film formation on the Al surface, it could not be fully applied. In this study, 1-Ethyl 3-Methyl Imidazolium Chloride ([EmIm]Cl) and aluminum chloride (AlCl3) are applied to resolve the aforementioned issues. Ex situ component-level and in situ cell-level open circuit voltage (OCV) tests combined with the physics-based model analyses were conducted to investigate the electrochemical reaction behaviors of the Al–air cell. Especially, the effect of aluminum oxide formation on the anode- and cathode-side reactions were analyzed in detail. The oxide film formed at the Al surface strongly was found to significantly impede the electrochemical reaction at the surface, and the film growth was controlled by decreasing the surface tension by aggressive anions. In the cathode side, the aluminum oxide precipitated in the porous cathode electrode was found to decrease the porous reaction area and block reactant access into the reaction sites. The effects of O2 solubility in the electrolyte, initial porosity and thickness of the porous electrode are compared in detailed, and optimal thickness is suggested.

25 ENERGY STORAGE↗

DOE OSTI2022

Observation of Reentrant Correlated Insulators and Interaction-Driven Fermi-Surface Reconstructions at One Magnetic Flux Quantum per Moiré Unit Cell in Magic-Angle Twisted Bilayer Graphene

The discovery of flat bands with nontrivial band topology in magic-angle twisted bilayer graphene (MATBG) has provided a unique platform to study strongly correlated phenomena including superconductivity, correlated insulators, Chern insulators, and magnetism. A fundamental feature of the MATBG, so far unexplored, is its high magnetic field Hofstadter spectrum. Here, we report on a detailed magnetotransport study of a MATBG device in external magnetic fields of up to B = 3 1 T , corresponding to one magnetic flux quantum per moiré unit cell Φ 0 . At Φ 0 , we observe reentrant correlated insulators at a flat band filling factors of ν = + 2 and of ν = + 3 , and interaction-driven Fermi-surface reconstructions at other fillings, which are identified by new sets of Landau levels originating from these. These experimental observations are supplemented by theoretical work that predicts a new set of eight well-isolated flat bands at Φ 0 , of comparable band width, but with different topology than in zero field. Overall, our magnetotransport data reveal a qualitatively new Hofstadter spectrum in MATBG, which arises due to the strong electronic correlations in the reentrant flat bands.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2025

Strain-associated nanoscale fluctuating lithium transport within single-crystalline LiNi 1/3 Mn 1/3 Co 1/3 O 2 cathode particles

Solid-state lithium diffusion dynamics are critical for the rate capability and longevity of Li-ion batteries. Conventionally, nanoscale lithium diffusion within individual battery particles has been simplified as being primarily driven by concentration gradients, despite the associated processes inducing local lattice expansion, contraction, and strain fields. Using operando scanning transmission soft X-ray microscopy with high spatial resolution and chemical sensitivity to track nanoscale intraparticle lithium transport, and post-cycling Bragg coherent diffraction X-ray imaging to directly reveal three-dimensional intraparticle strain fields, we uncover strain-associated lithium transport dynamics within single-crystalline LiNi 1/3 Mn 1/3 Co 1/3 O 2 (scNMC) particles during cycling. Contrary to the expected thermodynamic solid-solution behavior of scNMC, our observations reveal near-uniform but fluctuating regions of lithium-dense and lithium-dilute areas during cycling. These fluctuations suggest that nanoscale lithium diffusion can proceed counter to concentration gradients. Additionally, we demonstrate that an increased presence of lithium-dilute regions near the surface enhances lithium surface insertion kinetics, emphasizing the importance of controlling surface lithium distribution to improve rate performance. Our study provides insights into nanoscale solid-state ion transport, with potential applications in batteries, solid-state fuel cells, and memristors.

Lee, Danwon [Seoul National Univ. (Korea, Republic↗

DOE OSTI2023

EMDB—the Electron Microscopy Data Bank

Abstract The Electron Microscopy Data Bank (EMDB) is the global public archive of three-dimensional electron microscopy (3DEM) maps of biological specimens derived from transmission electron microscopy experiments. As of 2021, EMDB is managed by the Worldwide Protein Data Bank consortium (wwPDB; wwpdb.org) as a wwPDB Core Archive, and the EMDB team is a core member of the consortium. Today, EMDB houses over 30 000 entries with maps containing macromolecules, complexes, viruses, organelles and cells. Herein, we provide an overview of the rapidly growing EMDB archive, including its current holdings, recent updates, and future plans.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Exploration of Nirmatrelvir Derivatives as Optimized SARS‐CoV‐2 Antivirals

Nirmatrelvir (NMV) is a SARS‐CoV‐2 antiviral component of the approved COVID‐19 therapeutic Paxlovid. It is a reversible covalent inhibitor of SARS‐CoV‐2 main protease (M Pro ) that is effluxed from human cells by P‐glycoprotein (P‐gp). To identify NMV analogs with improved potency and reduced P‐gp efflux, a structure–activity relationship campaign was conducted. Warheads alternative to nitrile for engaging the active site cysteine were tested showing aldehyde and dichloroacetamide with better enzyme inhibition potency. Crystal structure of MPI‐136−M Pro shows its aldehyde warhead forming a thiohemiacetal with active Cys145 of M Pro . Several S4 binders were explored revealing that an O‐to‐S shift at the N ‐terminal amide leads to better enzyme inhibition. By exploring different combinations of S2, S3, and S4 binders, two inhibitors with better enzyme inhibition potency than NMV were found. Crystal structure of MPI‐148, with ( S )‐2‐azaspiro[4,5]decane‐3‐carboxylate as an alternative S2 binder, shows extensive hydrogen‐bond networks for locking the inhibitor in active site, explaining high affinity of NMV analogs. Further characterization of cellular M Pro engagement and antiviral potency against SARS‐CoV‐2 revealed four inhibitors with greater potency than NMV in P‐gp‐expressing cells. Studies with the P‐gp inhibitor CP‐100356 showed that these compounds were less sensitive to P‐gp inhibition than NMV, consistent with reduced P‐gp‐mediated efflux.

Alugubelli, Yugendar R. [Texas A&M Drug Discovery ↗

DOE OSTI2022

Convective Heat Transfer Potential of Particles/Airflow Through Single Cell Thick Additively Manufactured Octet-Shaped Lattice Frame Material

Abstract Particle-to-Supercritical Carbon Dioxide (sCO2) heat exchangers are one of the most critical components of the next-generation Concentrating Solar Power (CSP) plants. There have been several efforts to enhance the overall heat exchanger performance which essentially comprises of thermal resistances offered by sCO2 channel, wall (separating sCO2 with particles) thickness, particle-wall contact resistance and particle-side effective heat transfer coefficient. This study is focused towards reducing the particle side thermal resistance by incorporating single unit cell thick reticulated Octet lattice frame structures on the falling particle side to enhance the effective thermal conductivity of the particle channel and to enhance convective heat transfer between the falling particles and the solid phase of the falling particle channel (endwalls and fibers). Steady-state experiments were conducted to measure the effective thermal conductivity of lattice frame material for two cases: a) when void space was occupied by air, b) when void space was occupied with particles. Further, convective heat transfer experiments have been conducted with both air (steady-state) and particles (quasi steady-state) as “working fluid” for panels sandwiching the Octet array. Three different lattice porosities ranging from 0.75 to 0.9 have been tested for a wide range of air flow rates and a fixed particle flow rate (highest potential).

Aider, Youssef↗

DOE OSTI2026

Air-Stable Room-Temperature Quasi-2D Tin Iodide Perovskite Microlasers

Quasi-2D tin iodide perovskites (TIPs) are promising lead-free alternatives for optoelectronic applications, but achieving stable lasing remains challenging due to their limited environmental stability. Here, we report air-stable, room-temperature lasing from quasi-2D TIP microcrystals as small as 4 μm. Incorporation of the organic spacer 5IPA3 significantly enhanced the stability of these materials compared with previously reported TIPs. Lasing was observed from both dielectric (n = 4) and plasmonic (n = 3 and n = 4) TIP microlasers. Under picosecond pumping, lasing was sustained for over 108 pump pulses in ambient conditions. These results represent a significant step toward practical photonic applications of tin-based perovskites.

crystals↗

DOE OSTI2022

Effect of the Selective Halogenation of Small Molecule Acceptors on the Blend Morphology and Voltage Loss of High-Performance Solar Cells

Herein, the impacts of the selective halogenation at two different positions of dicyanomethylene-3-indanone (IC) end groups and inner side chains of small molecular acceptors (SMAs) on the P D :SMA interfacial interactions, blend morphology, and resulting photovoltaic properties are described. In this study, four different SMAs (A1, A2, A3, and A4) with the same molecular backbone, but with different degrees of halogenation, are synthesized. The IC end groups on the backbones of the A1 and A3, and A2 and A4 SMAs are chlorinated and fluorinated, respectively; in addition, 6-phenoxyhexyl inner side chains of the A3 and A4 are chlorinated. The SMAs are paired with a chlorinated PBDT-Cl PD to construct organic solar cells (OSCs). The PBDT-Cl:A4-based OSC exhibits the highest power conversion efficiency of 17.2%, outperforming the PBDT-Cl:A1-(13.3%), PBDT-Cl:A2-(15.6%), and PBDT-Cl:A3-based OSC (16.5%). The Cl atoms on the side chains in the A3 and A4 SMAs enhance the molecular/energetic interactions at the P D :SMA interfaces and improve the blend morphology in terms of domain purity and spacing. These effects lead to the improved fill factors and reduced voltage loss of the PBDT-Cl:A3- and PBDT-Cl:A4-based OSCs. This study demonstrates the importance of appropriate halogenation of SMAs in optimizing the blend morphology, reducing voltage loss, and improving OSC performance.

36 MATERIALS SCIENCE↗