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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,513 records · Page 84
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Three-Dimensional Pore Networks in Miocene Stevens Sandstone of California: Implications for CO 2 Geologic Storage

The Miocene Stevens Sandstone in the San Joaquin Basin of California is increasingly recognized as a promising candidate for CO 2 geological storage due to the enormous storage capacity, proven sealing, and existing infrastructure. In this study, computed microtomography imaging and pore network modeling were employed to investigate the influence of pore geometry and wettability on the CO 2 injectivity and residual trapping. Image analysis revealed that a significant fraction of the cement and matrix consists of microporous regions. The microporosity can substantially increase the overall pore space, yet its contribution to permeability remains modest, particularly in samples with low permeability. The intrinsic heterogeneity of turbidite reservoirs further complicates the reservoir properties among different layers. Two-phase flow simulations under varying wettability conditions (water-wet, weak water-wet, and neutral-wet) demonstrated that the CO 2 injection is predominantly controlled by macropores. CO 2 invades microporous regions only after these larger pores are filled. The presence of microporosity leads to a decrease in both initial and residual CO 2 saturations, with the magnitude of the reduction being influenced by wettability. Neutral-wet scenarios exhibit higher CO 2 mobility and thus lower residual trapping than water-wet scenarios. The results imply that heterogeneity in pore geometry and cement distribution across different layers can result in stratified CO 2 flow pathways, complicating efforts to predict injection performance. Overall, the Stevens Sandstone shows considerable promise for CO 2 geologic storage, but effective implementation will require detailed characterization of the pore structure as well as the integration of reactive fluid flow to account for potential mineral dissolution and fines migration.

fluids↗
DOE OSTI2019

Biofilm Feedbacks Alter Hydrological Characteristics of Fractured Rock Impacting Sulfidogenesis and Treatment

Flow-through fractures dominate the movement of fluids in a variety of natural as well as engineered subsurface systems. Microbial activities in fractured rock impact subsurface energy recovery, storage, and waste disposal. It has been recognized that understanding how the contrasting permeability between fracture and matrix interacts with microbial metabolism under thermal and hydrological gradients is key to effective utilization of the subsurface, yet such studies are sparse. Microorganisms mediate the production of hydrogen sulfide (also known as souring) in oil-bearing geological formations. We conducted a comprehensive experimental study of a novel 2D fractured rock system to understand these complex interactions and demonstrated how biofilm development can impact fracture flow, which subsequently feedbacks to moderate sulfidogenesis. Elevated temperature relevant to reservoir conditions interacted with the injection of cold fluid and formed a thermal gradient away from fractures, creating thermal niches for microbial activities in the fractured rock. Finally, results showed that while fracture flows were dominant in the beginning, with time, growth of the biofilm in the fractures reduced permeability, effectively moderating the initial fracture-matrix contrast, and limited microbial accessibility to nutrients and subsequent reactions rates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Food–Energy–Water Crises in the United States and China: Commonalities and Asynchronous Experiences Support Integration of Global Efforts

Food, energy, and water (FEW) systems have been recognized as an issue of critical global importance. Understanding the mechanisms that govern the FEW nexus is essential to develop solutions and avoid humanitarian crises of displacement, famine, and disease. The U.S. and China are the world’s leading economies. Although the two nations are shaped by fundamentally different political and economic systems, they share FEW trajectories in several complementary ways. These realities place the U.S. and China in unique positions to engage in problem definition, dialogue, actions, and transdisciplinary convergence of research to achieve productive solutions addressing FEW challenges. By comparing the nexus and functions of the FEW systems in the two nations, this perspective aims to facilitate collaborative innovations that reduce disciplinary silos, mitigate FEW challenges, and enhance environmental sustainability. Finally, the review of experiences and challenges facing the U.S. and China also offers valuable insights for other nations seeking to achieve sustainable development goals.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Respiratory Vinyl Chloride Reductive Dechlorination to Ethene in TceA-Expressing Dehalococcoides mccartyi

Bioremediation of chlorinated ethenes in anoxic aquifers hinges on organohalide-respiring Dehalococcoidia expressing vinyl chloride (VC) reductive dehalogenase (RDase). The tceA gene encoding the trichloroethene-dechlorinating RDase TceA is frequently detected in contaminated groundwater but not recognized as a biomarker for VC detoxification. We demonstrate that tceA-carrying Dehalococcoides mccartyi (Dhc) strains FL2 and 195 grow with VC as an electron acceptor when sufficient vitamin B 12 (B 12 ) is provided. Strain FL2 cultures that received 50 μg L –1 B 12 completely dechlorinated VC to ethene at rates of 14.80 ± 1.30 μM day –1 and attained 1.64 ± 0.11 × 10 8 cells per μmol of VC consumed. Strain 195 attained similar growth yields of 1.80 ± 1.00 × 10 8 cells per μmol of VC consumed, and both strains could be consecutively transferred with VC as the electron acceptor. Proteomic analysis demonstrated TceA expression in VC-grown strain FL2 cultures. Resequencing of the strain FL2 and strain 195 tceA genes identified non-synonymous substitutions, although their consequences for TceA function are currently unknown. The finding that Dhc strains expressing TceA respire VC can explain ethene formation at chlorinated solvent sites, where quantitative polymerase chain reaction analysis indicates that tceA dominates the RDase gene pool.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Identification of Novel Microcystins Using High-Resolution MS and MS n with Python Code

Cyanotoxins called microcystins (MCs) are highly toxic and can be present in drinking water sources. Determining the structure of MCs is paramount because of its effect on toxicity. Though over 300 MC congeners have been discovered, many remain unidentified. In this work, a method is described for the putative identification of MCs using liquid chromatography (LC) coupled with high-resolution (HR) Orbitrap mass spectrometry (MS) and a new bottom-up sequencing strategy. Maumee River water samples were collected during a harmful algal bloom and analyzed by LC–MS with simultaneous HRMS and MS/MS. Unidentified ions with characteristic MC fragments (135 and 213 m/z) were recognized as possible novel MC congeners. An innovative workflow was developed for the putative identification of these ions. Python code was written to generate the potential structures of unidentified MCs and to assign ions after the fragmentation for structural confirmation. The workflow enabled the putative identification of eight previously reported MCs for which standards are not available and two newly discovered congeners, MC-HarR and MC-E(OMe)R.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Hexavalent Chromium Generation within Naturally Structured Soils and Sediments

Chromium(VI) produced from the oxidation of indigenous Cr(III) minerals is increasingly being recognized as a threat to groundwater quality. A critical determinant of Cr(VI) generation within soils and sediments is the necessary interaction of two low-solubility phases$-$Cr(III) silicates or (hydr)oxides and Mn(III/IV) oxides—that lead to its production. Here in this paper, we investigate the potential for Cr(III) oxidation by Mn oxides within fixed solid matrices common to soils and sediments. Artificial aggregates were constructed from Cr(OH) 3 - and Cr 0.25 Fe 0.75 (OH) 3 -coated quartz grains and either mixed with synthetic birnessite or inoculated with the Mn(II)-oxidizing bacterium Leptothrix cholodnii. In aggregates simulating low organic carbon environments, we observe Cr(VI) concentrations within advecting solutes at levels more than twenty-times the California drinking water standard. Chromium(VI) production is highly dependent on Cr-mineral solubility; increasing Fe-substitution (x = 0 to x = 0.75) decreases the solubility of the solid and concomitantly decreases total Cr(VI) generation by 37%. In environments with high organic carbon, reducing conditions within aggregate cores (microbially) generate sufficient Fe(II) to suppress Cr(VI) efflux. Our results illustrate Cr(VI) generation from reaction with Mn oxides within structured media simulating soils and sediments and provide insight into how fluctuating hydrologic and redox conditions impact coupled processes controlling Cr and Mn cycling.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Hypophosphite Is a Naturally Occurring Selective Inhibitor of Syntrophic Methanogenesis

Microbial methanogenesis is a major contributor to global warming, and methane fluxes represent a loss of energy and electrons from industrial ecosystems. The chemical space of methane control strategies is still underexplored. Most known methanogenesis inhibitors target methanogenic archaeal enzymes. However, interference with the exchange of syntrophic electron carriers (H 2 or formate) in methanogenic systems presents an additional target for methane control. Here, we show that hypophosphite (H 2 PO 2 − ), an inorganic formate analogue, is a potent and selective inhibitor of syntrophic methanogenesis versus primary fermentation in rice field sediments and cattle rumens. Hypophosphite is also generally recognized as safe and relatively nontoxic to plants and animals. Genetic screens and physiological assays in the model methanogen Methanococcus maripaludis S2 implicate formate metabolism as the target of hypophosphite inhibition. Currently, there is no known biological pathway for anaerobic hypophosphite oxidation, and hypophosphite is stable in anoxic sediments for weeks to months. Given its widespread natural occurrence, we propose that hypophosphite may modulate the carbon cycle in natural environments. Taken together, our results suggest that hypophosphite could be used as a safe, inexpensive strategy for methane control in syntrophic methanogenic ecosystems.

chemical inhibitor↗
DOE OSTI2018

Unraveling Microbial Communities Associated with Methylmercury Production in Paddy Soils

Here, we report rice consumption is now recognized as an important pathway of human exposure to the neurotoxin methylmercury (MeHg), particularly in countries where rice is a staple food. Although the discovery of a two-gene cluster hgcAB has linked Hg methylation to several phylogenetically diverse groups of anaerobic microorganisms converting inorganic mercury (Hg) to MeHg, the prevalence and diversity of Hg methylators in microbial communities of rice paddy soils remain unclear. We characterized the abundance and distribution of hgcAB genes using third-generation PacBio long-read sequencing and Illumina short-read metagenomic sequencing, in combination with quantitative PCR analyses in several mine-impacted paddy soils from southwest China. Both Illumina and PacBio sequencing analyses revealed that Hg methylating communities were dominated by iron-reducing bacteria (i.e., Geobacter ) and methanogens, with a relatively low abundance of hgcA + sulfate-reducing bacteria in the soil. A positive correlation was observed between the MeHg content in soil and the relative abundance of Geobacter carrying the hgcA gene. Phylogenetic analysis also uncovered some hgcAB sequences closely related to three novel Hg methylators, Geobacter anodireducens , Desulfuromonas sp. DDH964, and Desulfovibrio sp. J2, among which G. anodireducens was validated for its ability to methylate Hg. Lastly, these findings shed new light on microbial community composition and major clades likely driving Hg methylation in rice paddy soils.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Investigation of the Solution Chemistry of Hybrid Organic–Inorganic Indium Halides for New Material Discovery

Recently, metal halide perovskites (MHPs) have emerged as a new class of materials for optical and electronic applications such as solar cells and ionizing radiation detectors. Although the solution-processability of MHPs is among their greatest advantages, the solution chemistries of most metal halide systems and their relationship with the observed structural and chemical diversity are poorly understood. In this work, we study the solution chemistry of a model indium halide system, methylammonium (MA)–In–Br, using a combination of the UV–vis spectroscopy, electrospray ionization mass spectrometry (ESI-MS) measurements, small-angle X-ray scattering (SAXS), and density functional theory (DFT) calculations. Our results show that indium could form either octahedral [InBr 6 3– ] or tetrahedral [InBr 4 – ] anions in solution or a combination of both, depending on the loading ratios of MABr and InBr 3 reactants. Understanding the solution chemistry of this system and recognizing the optical fingerprints of these polyanions allow for targeted crystallization of two novel compounds: MAInBr 4 featuring tetrahedral [InBr 4 – ] anions and MA 2 InBr 5 containing both octahedral [InBr 6 3– ] and tetrahedral [InBr 4 – ] anions. Further increase of the MABr content leads to the formation of previously reported MA 4 InBr 7 , containing only octahedral [InBr 6 3– ] anions separated by Br – anions. Furthermore, our results suggest that understanding the solution chemistry of multinary metal halide systems could be a valuable tool for discovering functional materials for practical applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Engineered Recognition of Tetravalent Zirconium and Thorium by Chelator–Protein Systems: Toward Flexible Radiotherapy and Imaging Platforms

Targeted α therapy holds tremendous potential as a cancer treatment: it offers the possibility of delivering a highly cytotoxic dose to targeted cells while minimizing damage to surrounding healthy tissue. The metallic α-generating radioisotopes 225 Ac and 227 Th are promising radionuclides for therapeutic use, provided adequate chelation and targeting. In this work, we demonstrate a new chelating platform composed of a multidentate high-affinity oxygen-donating ligand 3,4,3-LI(CAM) bound to the mammalian protein siderocalin. Respective stability constants log β 110 = 29.65 ± 0.65, 57.26 ± 0.20, and 47.71 ± 0.08, determined for the Eu III (a lanthanide surrogate for Ac III ), Zr IV , and Th IV complexes of 3,4,3-LI(CAM) through spectrophotometric titrations, reveal this ligand to be one of the most powerful chelators for both trivalent and tetravalent metal ions at physiological pH. The resulting metal-ligand complexes are also recognized with extremely high affinity by the siderophore-binding protein siderocalin, with dissociation constants below 40 nM and tight electrostatic interactions, as evidenced by X-ray structures of the protein:ligand:metal adducts with Zr IV and Th IV . Finally, differences in biodistribution profiles between free and siderocalin-bound 238 Pu IV -3,4,3-LI(CAM) complexes confirm in vivo stability of the protein construct. The siderocalin:3,4,3-LI(CAM) assembly can therefore serve as a "lock" to consolidate binding to the therapeutic 225 Ac and 227 Th isotopes or to the positron emission tomography emitter 89 Zr, independent of metal valence state.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2019

X-ray Absorption Spectroscopy and Theoretical Investigation of the Reductive Protonation of Cyclopentadienyl Cobalt Compounds

Cobalt(III) hydrides, formed via protonation of basic cobalt(I) centers, have long been recognized as key intermediates in the electrocatalytic reduction of protons to hydrogen. An understanding of the structural and electronic factors that govern their formation is key to developing more efficient and potent catalysts. A combination of Co K-edge X-ray absorption spectroscopy, extended X-ray absorption fine structure, density functional theory (DFT), and time-dependent DFT methods have been used to investigate several cyclopentadienyl (Cp) Co(III)L (L = ligand) species and their two-electron reduced Co(I) analogues. The results reveal that when L is strongly π-accepting, the reduced species demonstrates strong backbonding between the electron-rich Co(I) center and the ligand L, resulting in a weakly basic Co center that does not protonate to form a Co(III)–H. In contrast, a weakly π-accepting or σ-donating ligand system results in an electron-rich Co(I) center, which is readily protonated to form a Co(III)–H. Here, this study reveals the strength of a combined X-ray spectroscopy/theory method in understanding the role of ligands in tuning the electronic structure and subsequent reactivity of the metal center.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Discovery of Novel Rhizoctonia solani DHFR Inhibitors as Fungicides Using Virtual Screening

Dihydrofolate reductase (DHFR) is an essential enzyme in the folate pathway and has been recognized as a well-known target for antibacterial and antifungal drugs. We discovered eight compounds from the ZINC database using virtual screening to inhibit Rhizoctonia solani (R. solani), a fungal pathogen in crops. These compounds were evaluated with in vitro assays for enzymatic and antifungal activity. Among these, compound Hit8 is the most active R. solani DHFR inhibitor, with the IC 50 of 10.2 μM. The selectivity of inhibition is 22.3 against human DHFR with the IC 50 of 227.7 μM. Moreover, Hit8 has higher antifungal activity against R. solani (EC 50 of 38.2 mg L –1 ) compared with validamycin A (EC 50 of 67.6 mg L –1 ), a well-documented fungicide. These results suggest that Hit8 may be a potential fungicide. Finally, our study exemplifies a computer-aided method to discover novel inhibitors that could target plant pathogenic fungi.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Safety moments in chemical safety education.

Chemical safety education is a critical aspect of an integrated culture of safety in academic research settings. Showcasing best practices and sharing practical solutions for recognizing hazards and minimizing risks represent one way of reinforcing a research community's actions, attitudes, and behavior toward safety. For goals of improving chemical safety education with nonformal endeavors, safety moments are similar to 1-2 slides that focus on raising awareness and knowledge for routine safety issues in research laboratories. Intended to catalyze brief discussions at the beginning of meetings and presentations, these materials provide a proactive way for students and faculty to engage in open communication on diverse research safety topics across science and engineering. This commentary provides an overview of designing effective safety moments and tailoring them to highlight practical safety needs and considerations. Key components of model safety moment slides are presented, alongside centralized resources assembled by student-led laboratory safety teams, which can also be extended to posters, social media platforms, online videos, and other forms of scientific communication. Combined with both top-down backing from institution leaders and bottom-up support from student researchers, safety moments remain a low-barrier risk reduction strategy that is easy to implement, encourages local dialogue on safety, combats complacency, and holds potential for facilitating long-term improvements to academic lab safety culture.

Communication/Writing↗
DOE OSTI2024

NCAP: Noncanonical Amino Acid Parameterization Software for CHARMM Potentials

Noncanonical Amino Acids (NCAAs) provide numerous avenues for introduction of novel functionality to peptides and proteins. NCAAs can be incorporated through solid phase synthesis or genetic code expansion in conjugation with heterologous expression of the encoded protein modification. Due to the difficulty of synthesis, wide chemical space and lack of empirically resolved structures modeling the effects of NCAA mutation is critical for rational protein design. To evaluate the structural and functional perturbations NCAAs introduce we utilize molecular potentials that describe the forces in protein structure. Most potentials such as CHARMM are designed to model canonical residues but can be parameterized in include novel NCAAs. Here, in this work, we introduce NCAP a software package to generate CHARMM compatible parameters from quantum chemical calculation. Unlike currently available tools NCAP is designed to recognize NCAA structure and automatically bridge the gap between DFT calculations and potential parameters. For our software we discuss workflow, validation against canonical parameter sets and comparison to published NCAA-protein structures.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis

The importance of incorporating solvent polarization effects into the modeling of solvation processes has been well-recognized, and therefore a new generation of hybrid quantum mechanics/molecular mechanics (QM/MM) approaches that accounts for this effect is desirable. We present a fully self-consistent, mutually polarizable QM/MM scheme using the AMOEBA force field, in which the total energy of the system is variationally minimized with respect to both the QM electronic density and the MM induced dipoles. This QM/AMOEBA model is implemented through the Q-Chem/LibEFP code interface and then applied to the evaluation of solute-solvent interaction energies for various systems ranging from the water dimer to neutral and ionic solutes (NH 3 , NH 4 + , CN - ) surrounded by increasing numbers of water molecules (up to 100). In order to analyze the resulting interaction energies, we also utilize an energy decomposition analysis (EDA) scheme which identifies contributions from permanent electrostatics, polarization, and van der Waals (vdW) interaction for the interaction between the QM solute and the solvent molecules described by AMOEBA. This facilitates a component-wise comparison against full QM calculations where the corresponding energy components are obtained via a modified version of the absolutely localized molecular orbitals (ALMO)-EDA. The results show that the present QM/AMOEBA model can yield reasonable solute-solvent interaction energies for neutral and cationic species, while further scrutiny reveals that this accuracy highly relies on the delicate balance between insufficiently favorable permanent electrostatics and softened vdW interaction. For anionic solutes where the charge penetration effect becomes more pronounced, the QM/MM interface turns out to be unbalanced. These results are consistent with and further elucidate our findings in a previous study using a slightly different QM/AMOEBA model (Dziedzic et al. J. Chem. Phys. 2016, 145, 124106). The implications of these results for further refinement of this model are also discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

String Method for Protein–Protein Binding Free-Energy Calculations

A powerful computational strategy to determine the equilibrium association constant of two macromolecules with explicit-solvent molecular dynamics (MD) simulations is the "geometric route", which considers the reversible physical separation of the bound complex in solution. Nonetheless, multiple challenges remain to render this type of methodology reliable and computationally efficient in practice. In particular, in one, formulation of the geometric route relies on the potential of mean force (PMF) for physically separating the two binding partners restrained along a straight axis, which must be selected prior to the calculation. However, practical applications indicate that the calculation of the separation PMF along the predefined rectilinear pathway may be suboptimal and slowly convergent. Recognizing that a rectilinear straight separation pathway is generally not representative of how the protein complex physically separates in solution, we put forth a novel theoretical framework for binding free-energy calculations, leaning on the optimal curvilinear minimum free-energy path (MFEP) determined from the string method. The proposed formalism is validated by comparing the results obtained using both rectilinear and curvilinear pathways for a prototypical host-guest complex formed by cucurbit[7]uril (CB[7]) binding benzene, and for the barnase-barstar protein complex. On the basis of multi-microsecond MD calculations, we find that the calculations following the traditional rectilinear pathway and the string-based curvilinear pathway agree quantitatively, but convergence is faster with the latter.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Is the Trotterized UCCSD Ansatz Chemically Well-Defined?

The variational quantum eigensolver (VQE) has emerged as one of the most enticing near-term quantum algorithms that can be used to simulate many-body systems such as molecular electronic structures. Serving as an attractive ansatz in the VQE algorithm, unitary coupled cluster (UCC) theory has seen a renewed interest in recent literature. Yet, unlike the original classical UCC theory, implementation on a quantum computer requires a finite-order Suzuki-Trotter decomposition to separate the exponentials of the large sum of Pauli operators. While previous literature has recognized the non-uniqueness of different orderings of the operators in the Trotterized form of UCC methods, the question of whether or not different orderings matter at the chemical scale has not been addressed. In this letter, we explore the effect of operator ordering on the Trotterized UCCSD ansatz, as well as the much more compact k-UpCCGSD ansatz recently proposed by Lee et al. We observe a significant, system-dependent variation in the energies of Trotterizations with different operator orderings. The energy variations occur on a chemical scale, sometimes on the order of hundreds of kcal/mol. This letter establishes the need to define not only the operators present in the ansatz, but also the order in which they appear. This is necessary for adhering to the quantum chemical notion of a ``model chemistry'', in addition to the general importance of scientific reproducibility. As a final note, we suggest a useful strategy to select out of the combinatorial number of possibilities, a single well-defined and effective ordering of the operators.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Discovery and Development of a Small-Molecule Inhibitor Targeting the GAS41 YEATS Domain in Nonsmall Cell Lung Cancer

Abstract GAS41 is frequently overexpressed in Non-Small Cell Lung Cancer (NSCLC). GAS41 contains a YEATS domain, which recognizes acetylated lysine residues on histones to recruit protein complexes and facilitate transcription. Suppression of GAS41 in NSCLC models inhibits cellular proliferation and markedly reduces tumor growth in mouse xenografts, justifying the development of small-molecule inhibitors. We have employed structure-based design and medicinal chemistry optimization to discover DLG-41, a submicromolar inhibitor binding to the GAS41 YEATS domain. DLG-41 potently disrupts the association of GAS41 YEATS with chromatin in mammalian cells and inhibits the proliferation of NSCLC cell lines with submicromolar potency without significantly affecting normal lung fibroblasts. DLG-41 induces more effective growth inhibition in A549 versus GAS41-knockout cells, demonstrating on-target activity. DLG-41 treatment upregulates the CDKN1A gene and downregulates pathways associated with lung cancer cell identity, tumor migration, and invasion. DLG-41 is a promising chemical probe for targeting GAS41 protein in NSCLC models and has potential for future development.

Listunov, Dymytrii [University of Michigan , , , ,↗