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Discovery of AG-270, a First-in-Class Oral MAT2A Inhibitor for the Treatment of Tumors with Homozygous MTAP Deletion
The metabolic enzyme methionine adenosyltransferase 2A (MAT2A) was recently implicated as a synthetic lethal target in cancers with deletion of the methylthioadenosine phosphorylase (MTAP) gene, which is adjacent to the CDKN2A tumor suppressor and codeleted with CDKN2A in approximately 15% of all cancers. Previous attempts to target MAT2A with small-molecule inhibitors identified cellular adaptations that blunted their efficacy. Here, we report the discovery of highly potent, selective, orally bioavailable MAT2A inhibitors that overcome these challenges. Fragment screening followed by iterative structure-guided design enabled >10 000-fold improvement in potency of a family of allosteric MAT2A inhibitors that are substrate noncompetitive and inhibit release of the product, S-adenosyl methionine (SAM), from the enzyme’s active site. We demonstrate that potent MAT2A inhibitors substantially reduce SAM levels in cancer cells and selectively block proliferation of MTAP-null cells both in tissue culture and xenograft tumors. These data supported progressing AG-270 into current clinical studies (ClinicalTrials.gov NCT03435250).
Investigations into Spin- and Unpolarized Secondary Electron-Induced Reactions in Self-Assembled Monolayers of Cysteine
Cysteine is the simplest thiolated, chiral amino acid and is often used as the anchor for studies of self-assembled monolayers (SAMs) of complex biomolecules such as peptides. Understanding the interaction of SAMs of cysteine with low-energy secondary electrons (SEs) produced by X-rays can further our understanding of radiation damage in biomolecules. In particular, if the electrons are polarized, chiral-selective chemistry could have bearing on the origin of homochirality in nature. In the present paper, we use synchrotron radiation-based X-ray photoelectron spectroscopy to determine the changes that occur in the bonding of self-assembled layers of cysteine on gold as a result of soft X-ray irradiation. To investigate the possibility of chiral selectivity resulting from the interaction of low-energy, spin-polarized SEs (SPSEs), measurements were conducted on cysteine adsorbed on a 3 nm-thick gold layer deposited on a CoPt thin-film multilayer with perpendicular magnetic anisotropy. Time-dependent measurements of the C 1s, N 1s, O 1s, S 2p, and Au 4f core levels are used to follow the changes in surface chemistry and determine reaction cross-sections as a function of SE exposure. Analysis of the data results in cross-sections in the range of 5-7 Mb and suggests possible reaction pathways. Changing the magnetization direction of the CoPt multilayer produces SPSEs with opposite polarity. Some evidence of spin-dependent reactions is indicated but is inconclusive. Possible reasons for the discrepancy are posited.
Toward Lithium Recovery Using Modular (and Membraneless) Phase Separation and Extraction (MPSE) Technology with Ionic Liquid (IL) Solvents: Effect of Coatings
In this work, a single-channel slope-plate Modular and Membrane-less Phase Separation and Extraction (MPSE) device was fabricated using 3D printing. The slope-plate was designed with an insertable glass slide to enable surface modification with coatings. Self-assembled monolayers (SAMs) and perfluoropolyether (Zdol) coatings were applied to tailor surface wettability and enhance phase separation. Using a model biphasic system of water and hexadecane, both coatings significantly improved the separation efficiency compared to the uncoated device by promoting selective wetting. Building on these results, lithium extraction from a simulated saline solution was investigated using 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([EMIM][NTf₂]) as the ionic liquid (IL) extractant. The IL effectively extracted Li⁺ from the aqueous phase in bulk extraction, demonstrating its potential for lithium recovery. However, the low interfacial tension between the IL and aqueous phases posed challenges for phase separation. The application of SAM and Zdol coatings effectively mitigated this issue. Overall, integrating tailored surface chemistry with the slope-plate MPSE design shows great promise as an efficient and scalable platform for studying liquid–liquid separation and optimizing ionic liquid–based extraction processes for lithium recovery from saline sources.
Additive Lithography–Organic Monolayer Patterning Coupled with an Area-Selective Deposition
The combination of area-selective deposition (ASD) with a patternable organic monolayer provides a versatile additive lithography platform, enabling the generation of a variety of nanoscale feature geometries. Stearate hydroxamic acid self-assembled monolayers (SAMs) were patterned with extreme ultraviolet (λ = 13.5 nm) or electron beam irradiation and developed with ASD to achieve line space patterns as small as 50 nm. Density functional theory was employed to aid in the synthesis of hydroxamic acid derivatives with optimized packing density to enhance the imaging contrast and improve dose sensitivity. Near-edge X-ray absorption fine structure spectroscopy and infrared spectroscopy reveal that the imaging mechanism is based on improved deposition inhibition provided by the cross-linking of the SAM to produce a more effective barrier during a subsequent deposition step. With patterned substrates composed of coplanar copper lines and silicon spacers, hydroxamic acids selectively formed monolayers on the metal portions and could undergo a pattern-wise exposure followed by ASD in the first combination of a patternable monolayer with ASD. This material system presents an additional capability compared to traditional ASD approaches that generally reflect a starting patterned surface. Finally, this bottoms-up additive approach to lithography may be a viable alternative to subtractive nanoscale feature generation.
Amino Acid Sequence Controls Enhanced Electron Transport in Heme-Binding Peptide Monolayers
Metal-binding proteins have the exceptional ability to facilitate long-range electron transport in nature. Despite recent progress, the sequence-structure–function relationships governing electron transport in heme-binding peptides and protein assemblies are not yet fully understood. In this work, the electronic properties of a series of heme-binding peptides inspired by cytochrome bc1 are studied using a combination of molecular electronics experiments, molecular modeling, and simulation. Self-assembled monolayers (SAMs) are prepared using sequence-defined heme-binding peptides capable of forming helical secondary structures. Following monolayer formation, the structural properties and chemical composition of assembled peptides are determined using atomic force microscopy and X-ray photoelectron spectroscopy, and the electronic properties (current density–voltage response) are characterized using a soft contact liquid metal electrode method based on eutectic gallium–indium alloys (EGaIn). Our results show a substantial 1000-fold increase in current density across SAM junctions upon addition of heme compared to identical peptide sequences in the absence of heme, while maintaining a constant junction thickness. These findings show that amino acid composition and sequence directly control enhancements in electron transport in heme-binding peptides. Overall, this study demonstrates the potential of using sequence-defined synthetic peptides inspired by nature as functional bioelectronic materials.
Connecting Interfacial Mechanical Adhesion, Efficiency, and Operational Stability in High Performance Inverted Perovskite Solar Cells
Carbazole-based self-assembled monolayers (SAMs) at the interface between the metal-halide perovskite (MHP) and the transparent conducting oxide (TCO) serve the function of hole-transport layers in p-i-n "inverted" perovskite solar cells (PSCs). In this report we show that the use of an iodine-terminated carbazole-based SAM increases the interfacial mechanical adhesion dramatically (2.6-fold) and that this is responsible for substantial improvements in the interfacial morphology, photocarrier transport, and operational stability. While the improved morphology and optoelectronic properties impart high efficiency (up to 25.39%) to the PSCs, the enhanced adhesion suppresses nucleation and propagation of pores/cracks during PSC operation, resulting in the retention of 96% of the initial efficiency after 1000 h of continuous-illumination testing at the maximum power-point. This demonstrates the strong connection between judicious interfacial adhesion toughening and simultaneous enhancement in the efficiency and operational stability of p-i-n PSCs, with broader implications for the reliability and durability of perovskite photovoltaics before they can be commercialized.
Sub-Diurnal Methane Variations on Mars Driven by Barometric Pumping and Planetary Boundary Layer Evolution
In recent years, the Tunable Laser Spectrometer within the Sample Analysis at Mars (TLS-SAM) instrument on board the Mars Science Laboratory (MSL) Curiosity rover has detected methane variations in the atmosphere at Gale crater. Methane concentrations appear to fluctuate seasonally as well as sub-diurnally, which is difficult to reconcile with an as-yet-unknown transport mechanism delivering the gas from underground to the atmosphere. To potentially explain the fluctuations, we consider barometrically induced transport of methane from an underground source to the surface, modulated by temperature-dependent adsorption. The subsurface fractured-rock seepage model is coupled to a simplified 1-D atmospheric mixing model to provide insights on the pattern of atmospheric methane concentrations in response to transient surface methane emissions, as well as to predict sub-diurnal variation in methane abundance for the northern summer period, which is a candidate time frame for a MSL Curiosity sampling campaign. Our analysis suggests that there is a lower limit to the subsurface fracture density that can produce the observed methane patterns, below which the atmospheric methane variations would be out of phase with the observations. The best-performing model scenarios indicate a significant, short-lived methane pulse just prior to sunrise, the detection of which by TLS-SAM would be a potential indicator of the contribution of barometric pumping to Mars' atmospheric methane variations.
Molecular bridge-mediated ultralow-power gas sensing
Abstract We report the electrical detection of captured gases through measurement of the quantum tunneling characteristics of gas-mediated molecular junctions formed across nanogaps. The gas-sensing nanogap device consists of a pair of vertically stacked gold electrodes separated by an insulating 6 nm spacer (~1.5 nm of sputtered α-Si and ~4.5 nm ALD SiO 2 ), which is notched ~10 nm into the stack between the gold electrodes. The exposed gold surface is functionalized with a self-assembled monolayer (SAM) of conjugated thiol linker molecules. When the device is exposed to a target gas (1,5-diaminopentane), the SAM layer electrostatically captures the target gas molecules, forming a molecular bridge across the nanogap. The gas capture lowers the barrier potential for electron tunneling across the notched edge region, from ~5 eV to ~0.9 eV and establishes additional conducting paths for charge transport between the gold electrodes, leading to a substantial decrease in junction resistance. We demonstrated an output resistance change of >10 8 times upon exposure to 80 ppm diamine target gas as well as ultralow standby power consumption of <15 pW, confirming electron tunneling through molecular bridges for ultralow-power gas sensing.
Structural basis of RNA cap modification by SARS-CoV-2
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of COVID-19 illness, has caused millions of infections worldwide. In SARS coronaviruses, the non-structural protein 16 (nsp16), in conjunction with nsp10, methylates the 5'-end of virally encoded mRNAs to mimic cellular mRNAs, thus protecting the virus from host innate immune restriction. We report here the high-resolution structure of a ternary complex of SARS-CoV-2 nsp16 and nsp10 in the presence of cognate RNA substrate analogue and methyl donor, S-adenosyl methionine (SAM). The nsp16/nsp10 heterodimer is captured in the act of 2'-O methylation of the ribose sugar of the first nucleotide of SARS-CoV-2 mRNA. We observe large conformational changes associated with substrate binding as the enzyme transitions from a binary to a ternary state. This induced fit model provides mechanistic insights into the 2'-O methylation of the viral mRNA cap. We also discover a distant (25 Å) ligand-binding site unique to SARS-CoV-2, which can alternatively be targeted, in addition to RNA cap and SAM pockets, for antiviral development.
Towards linking lab and field lifetimes of perovskite solar cells
Metal halide perovskite solar cells (PSCs) represent a promising low-cost, thin-film photovoltaic (PV) technology, with unprecedented power conversion efficiencies (PCEs) obtained for both single-junction and tandem applications. To push PSCs toward commercialization, it is critical, albeit challenging, to understand device reliability under real-world outdoor conditions where multiple stress factors (e.g., light, heat, humidity) coexist, generating complicated degradation behaviors. It is necessary to identify accelerated indoor testing protocols - which can correlate specific stressors with observed degradation modes in fielded devices - to quickly guide PSC development. Here, we use a state-of-the-art p-i-n PSC stack (with PCE up to ~25.5%) to show that indoor accelerated stability tests can predict our 6-month outdoor aging tests. Device degradation rates under illumination and at elevated temperatures are most instructive for understanding outdoor device reliability. Further, we also find that the indium tin oxide (ITO)/self-assembled monolayer (SAM)-based hole transport layer (HTL)/perovskite interface most strongly affects our device operation stability. Improving the ion-blocking properties of the SAM HTL increases averaged device operational stability at 50 degree C-85 °C by a factor of ~2.8, reaching over 1000 h at 85 °C and to near 8200 h at 50 °C with a projected 20% degradation, which is among the best to date for high-efficiency p-i-n PSCs.
Patch-Based Convolutional Neural Networks for Multiple Microstructural Features Detection in FIB-SEM Micrographs of Irradiated Nuclear Fuel
Focused ion beam scanning electron microscopy (FIB-SEM) tomography has increasingly been utilized for acquiring three-dimensional (3D) microstructure features at the sub-micron scale in irradiated nuclear materials. This technique involves sequential ion beam slicing followed by electron beam imaging and compositional mapping using energy dispersive spectroscopy (EDS). Despite its growing use, several challenges persist. These include the time-intensive nature of data collection of EDS data, difficulties in distinguishing between various microstructures, and issues with image alignment. These challenges currently limit the broader application of FIB-SEM tomography in the field. To overcome these limitations, we propose using convolutional neural networks (CNNs) to automate microstructure identification in SEM images. Our study introduces a new framework for identifying microstructures in irradiated U-10Zr (wt. %) metallic fuel with limited annotated data. The framework includes the creation of a reliable annotated dataset with paired SEM and ground truth data from EDS maps, the applications of CNNs for microstructure identification, and the validation of model performance. Specifically, we employed the Segment Anything Model (SAM) to align SEM images with corresponding EDS maps and focused ion beam (FIB) tomography SEM data. We evaluate several models, including Patch-based U-Net, Attention U-Net, and Residual U-Net, finding that patch-based U-Net exhibits superior segmentation performance and consistency. This approach reduces reliance on EDS detectors and aids in accelerating nuclear material analysis process, highlighting the potential of advanced deep learning techniques to improve microstructural understanding in nuclear material. This is the first framework to integrate SAM and Patch-based CNN models for semantic segmentation of irradiated nuclear materials, with potential applicability to other tomography datasets.
Efficient generation and amplification of intense vortex and vector laser pulses via strongly-coupled stimulated Brillouin scattering in plasmas
The past decade has seen tremendous progress in the production and utilization of vortex and vector laser pulses. Although both are considered as structured light beams, the vortex lasers have helical phase fronts and phase singularities, while the vector lasers have spatially variable polarization states and polarization singularities. In contrast to the vortex pulses that carry orbital angular momentum (OAM), the vector laser pulses have a complex spin angular momentum (SAM) and OAM coupling. Despite many potential applications enabled by such pulses, the generation of high-power/-intensity vortex and vector beams remains challenging. Here, we demonstrate using theory and three-dimensional simulations that the strongly-coupled stimulated Brillouin scattering (SC-SBS) process in plasmas can be used as a promising amplification technique with up to 65% energy transfer efficiency from the pump beam to the seed beam for both vortex and vector pulses. We also show that SC-SBS is strongly polarization-dependent in plasmas, enabling an all-optical polarization control of the amplified seed beam. Additionally, the interaction of such structured lasers with plasmas leads to various angular momentum couplings and decouplings that produce intense new light structures with controllable OAM and SAM. This scheme paves the way for novel optical devices such as plasma-based amplifiers and light field manipulators.
Phonon-mediated ultrafast dynamics in self-assembled monolayers of 4-mercaptobenzoic acid on gold
Non-equilibrium interactions between plasmonic metals and adsorbed molecules lie at the heart of emerging applications such as plasmonic photocatalysis and sensing, though the ultrafast charge and energy transfer mechanisms arising from these interactions are not well understood. Herein, we investigate the ultrafast dynamics of Au nano-islands tethered with a self-assembled monolayer (SAM) of electron-withdrawing 4-mercaptobenzoic acid (4MBA) molecules. Ultrafast UV-visible transient absorption spectroscopy following excitation of the interband transition in Au reveals three well-known, characteristic time constants that quantify electron–electron (el–el), electron–phonon (el–ph) and phonon–phonon (ph–ph) scattering lifetimes. When comparing the dynamics of bare Au and 4MBA-Au, we find that the el–ph and ph–ph scattering lifetimes are notably longer in 4MBA-Au. Density functional perturbation theory calculations ascribe the elongation in el–ph lifetimes in 4MBA-Au to the significant coupling of acoustic phonon modes of Au with certain molecular vibrations of 4MBA, leading to decreased spatial overlap between carrier electronic states and the acoustic modes. We speculate that the elongation of ph–ph scattering lifetimes in 4MBA-Au arises due to poor thermal conductivity of the SAM which disrupts efficient energy dissipation from Au to the environment, thus slowing down the thermalization of phonons. This work provides a glimpse into how molecular adsorbates modify the charge carrier and phonon dynamics of Au and sets the stage for further systematic exploration of plasmonic metal–molecule interactions.
Production Operations Management System (POMS) for Fermilab Experiments
The Production Operations Management System (POMS) software allows production teams and analysis groups across multiple Fermilab experiments to launch, modify and monitor large scale campaigns of related Monte Carlo or data processing jobs, and currently manages the majority of production computing of experiments at Fermilab.POMS provides a web service interface that enables automated job submission on distributed resources according to customers’ requests, as well as subsequent monitoring of those submissions as well as recovery of failed submissions, debugging and record keeping.POMS interfaces with existing HEP data access, processing, movement and monitoring tools at Fermilab, including Jobsub (for job submission), SAM (for data management), and Landscape (for monitoring), and in combination with them handles the creation of intermediate datasets of files for multistage campaigns.POMS visualizes these campaigns with an interactive GUI interface. An important feature of POMS is a one-to-one connection between the GUI campaign visualizer and a text based representation of the complete campaign configuration. An extensible library of template campaign configurations is available. The templates are user modifiable and map cleanly to and from the GUI description of the campaign.This paper will discuss the current usage, history, and some technical details of POMS, as well as planned future extensions, particularly interfacing with Rucio as well as SAM for file movement.
S-adenosyl-L-methionine is the unexpected methyl donor for the methylation of mercury by the membrane-associated HgcAB complex
Mercury (Hg) is a heavy metal that exhibits high biological toxicity. Monomethylmercury and dimethylmercury are neurotoxins and a significant environmental concern as they bioaccumulate and biomagnify within the aquatic food web. Microbial Hg methylation involves two proteins, HgcA and HgcB. Here, we show that HgcA and HgcB can be heterologously coexpressed, and the HgcAB complex can be purified. We demonstrated that HgcA is a membrane-associated cobalamin-dependent methyltransferase and HgcB is a ferredoxin-like protein containing two [4Fe-4S] clusters. Further, spectroscopic and kinetic results demonstrate that S-adenosyl-L-methionine (SAM) donates the methyl group to Hg in a two-step reaction involving a methylcob(III)alamin intermediate including Co-thiolate ligation from a conserved Cys residue. Our findings uncover a biological role for SAM in microbial Hg methylation.
Numerical Simulation and Experimental Comparison of System Analysis Module 1D Mixing Model for Cold Shock Transients in the Gallium Thermal-Hydraulic Mixing Facility
Abstract Liquid metals are being investigated as coolants in many advanced reactor designs because of their high thermal conductivity and effectiveness at high temperatures. However, they often pose challenges to reactor operation and safety because of the complex thermal mixing and stratification in the plenum of pool-type reactor designs. The advanced system analysis code System Analysis Module (SAM) currently under development at Argonne National Laboratory aims to develop and implement thermal mixing models to accurately capture these complex thermal fluid behaviors. In this study, the SAM thermal mixing model was compared against experimental data from the Gallium Thermal-Hydraulic Experiment facility, a scaled liquid metal test facility that uses gallium as a surrogate fluid to investigate the stratification and thermal mixing of low-Prandtl-number fluids in the upper plenum of a liquid metal-cooled reactor. Two cold shock transient cases were used: one with stable stratified flow (Ri = 32) and one with stronger thermal mixing (Ri = 0.5). The resultant temperatures were then compared with the experimental temperatures over the entire plenum to assess the ability of the mixing models to capture the thermal behavior and to better correspond mixing parameters to various flow scenarios. Generally, the zero-dimensional mixing model was more capable of capturing the bulk temperature of the component modeled assuming that an accurate mass flow rate was provided, but it was inherently unable to capture thermal gradients in space. The one-dimensional mixing model was capable of capturing that the thermal gradients provided accurate selection of the mixing coefficients. Further, the temperature at the outlet junction was compared over time for each of the mixing models with the recorded experimental temperature. The implemented mixing models demonstrated the ability to effectively capture the overall thermal behavior for stronger mixing scenarios but struggled with more stably stratified flows. It was found that a system analysis code's covering of the entire range of different operating conditions still remains a challenging task, and it is suggested that further model and closure improvements are necessary to accurately capture complex thermal mixing and stratification phenomena.
Development and Experimental Validation of a Heat Transfer Model for Spilled Molten Salt Pools
A spill of radionuclide-bearing molten salt is one of the major postulated events that needs to be analyzed for liquid fluorine salt-cooled high-temperature reactor (FHR) or molten salt reactor licensing purposes. In this postulated event, radioactive source term materials (RSTMs) in the molten salt are discharged from the reactor vessel to the reactor building. The release of RSTMs from the spilled salt pool to the gas space in the reactor building is expected to be controlled by the cooling behavior of the spilled salt, including the growth and shrinkage of the solid crust on the surface of the spilled salt pool. This paper presents a simulation model for spilled salt pool heat transfer and validation efforts. The validation data come from two molten salt spill tests that were performed recently: the PELE2 test by the Rapid Experimental Laboratory of Kairos Power LLC (KP) and the Argonne salt cooling test conducted by Argonne National Laboratory. The former was a large-scale test involving kilograms of molten spilled FLiNaK salt, and the latter was a relatively smaller-scale test targeting various processes associated with a salt spill event. Both tests generated valuable data sets that can be used to assess salt cooling and validate evaluation models. This paper provides a new one-dimensional model that can simulate the cooling process of a spilled salt pool as well as the thermal responses of heat structures, such as the stainless steel liner and the concrete below the salt. The model has been implemented as part of KP-SAM code, which is a branch of the systems code SAM specific to KP FHR. In conclusion, the simulation results of the model are compared with the data of the PELE2 and Argonne tests, and reasonable agreements are observed between the model and test data.