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At least 451 records · Page 25

Antiviral discovery using sparse datasets by integrating experiments, molecular simulations, and machine learning

Computational methods have demonstrated success in identifying virucidal agents, effectively contributing to the discovery of novel virucidal molecules. In this study, we developed a machine learning (ML) model, trained on a small dataset, to predict inhibitors of human enterovirus 71 (EV71), a pathological agent that causes severe disease in children and immunocompromised adults. Despite the dataset’s limitation, comprising of only 36 compounds tested, our ML framework demonstrated significant predictive capability. Notably, experimental validation revealed that five out of the eight compounds predicted by our model from the Chinese cosmetic material list exhibited virucidal activity. The inhibitor effects displayed by the main active compounds were further confirmed by molecular dynamics simulation. This underscores the potential of our AI-driven approach to bypass data constraints in identifying active molecules against viral pathogens.

60 APPLIED LIFE SCIENCES↗

exRNA-eCLIP intersection analysis reveals a map of extracellular RNA binding proteins and associated RNAs across major human biofluids and carriers

Although the role of RNA binding proteins (RBPs) in extracellular RNA (exRNA) biology is well established, their exRNA cargo and distribution across biofluids are largely unknown. To address this gap, we extend the exRNA Atlas resource by mapping exRNAs carried by extracellular RBPs (exRBPs). This map was developed through an integrative analysis of ENCODE enhanced crosslinking and immunoprecipitation (eCLIP) data (150 RBPs) and human exRNA profiles (6,930 samples). Computational analysis and experimental validation identified exRBPs in plasma, serum, saliva, urine, cerebrospinal fluid, and cell-culture-conditioned medium. exRBPs carry exRNA transcripts from small non-coding RNA biotypes, including microRNA (miRNA), piRNA, tRNA, small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), Y RNA, and lncRNA, as well as protein-coding mRNA fragments. Computational deconvolution of exRBP RNA cargo reveals associations of exRBPs with extracellular vesicles, lipoproteins, and ribonucleoproteins across human biofluids. Overall, we mapped the distribution of exRBPs across human biofluids, presenting a resource for the community.

59 BASIC BIOLOGICAL SCIENCES↗

13 C-metabolic flux analysis of Clostridium ljungdahlii illuminates its core metabolism under mixotrophic culture conditions

Carbon dioxide-fixing acetogenic bacteria (acetogens) utilizing the Wood-Ljungdahl Pathway (WLP) play an important role in CO 2 fixation in the biosphere and in the development of biological processes – alone or in cocultures, under both autotrophic and mixotrophic conditions – for production of chemicals and fuels. To date, limited work has been reported in experimentally validating and quantifying reaction fluxes of their core metabolic pathways. Here, the core metabolic model of the acetogen Clostridium ljungdahlii was interrogated using 13 C-metabolic flux analysis ( 13 C-MFA), which required the development of a new defined culture medium. Autotrophic, heterotrophic, and mixotrophic growth in defined medium was possible by adding 1 mM methionine to replace yeast extract. Our 13 C-MFA found an incomplete TCA cycle and inactive core pathways/reactions, notably those of the oxidative pentose phosphate pathway, Entner-Doudoroff pathway, and malate dehydrogenase. 13 C-MFA during mixotrophic growth using the parallel tracers [1– 13 C]fructose, [1,2– 13 C]fructose, [1,2,3– 13 C]fructose, and [U– 13 C]asparagine found that externally supplied CO 2 contributed the majority of carbon consumed. All internally-produced CO 2 from the catabolism of asparagine and fructose was consumed by the WLP. While glycolysis of fructose was active, it was not a major contributor to overall production of ATP, NADH, and acetyl-CoA. Gluconeogenic reactions were active despite the availability of organic carbon. Asparagine was catabolized equally via conversion to threonine and subsequent cleavage to produce acetaldehyde and glycine, and via deamination to fumarate and then the anaplerotic conversion of malate to pyruvate. Both pathways for asparagine catabolism produced acetyl-CoA, either directly via pyruvate or indirectly via the WLP. Cofactor stoichiometry based on our data predicted an essentially zero flux through the ferredoxin-dependent transhydrogenase (Nfn) reaction. Instead, nearly all of NADPH generated from the hydrogenase reaction was consumed by the WLP. Reduced ferredoxin produced by the hydrogenase reaction and glycolysis was mostly used for ATP generation via the RNF/ATPase system, with the remainder consumed by the WLP. NADH produced by RNF/ATPase was entirely consumed via the WLP.

13C metabolic flux analysis↗

Tunable Atomic Layer Deposition into Ultra-High-Aspect-Ratio (>60000:1) Aerogel Monoliths Enabled by Transport Modeling

Atomic layer deposition (ALD) modification of ultra-high-aspect-ratio structures (>10,000:1) is a powerful platform with applications in catalysis, filtration, and energy conversion. However, the deposition of conformal and tunable ALD coatings at these aspect ratios remains challenging, resulting in empirical tradeoffs between precursor utilization and reaction time. Here, we demonstrate tunable control of the ALD infiltration depth into an aerogel monolith (AM) and develop a reaction-diffusion model to accurately describe the coating process. Specifically, we investigate the ALD exposure time and precursor dose needed to conformally coat a silica AM with pore sizes of ~20 nm, a monolith thickness of ~2.5 mm, and aspect ratios exceeding 60,000:1. We demonstrate complete infiltration into the AM, which is quantified by elemental mapping. A reaction-diffusion model is developed, which accounts for multiple doses and precursor depletion in the ALD chamber during an exposure step. The experimentally validated model enables the prediction and tuning of infiltration depth into a tortuous, high-aspect-ratio structure such as an AM, allowing for the synthesis of rationally designed material architectures. Additionally, the model allows for co-optimization of the total deposition time and percentage of unreacted precursor, which are important for the manufacturability and sustainability of ALD processing. Lastly, we demonstrate that ultra-thin ALD Al 2 O 3 coatings can be used to stabilize silica AMs against structural degradation under high-temperature annealing conditions (700-800 °C), by limiting changes in surface area and monolith volume. As a result, this improved high-temperature stability has implications for numerous aerogel applications, including catalysis and thermal insulation.

14 SOLAR ENERGY↗

Physics-Informed Machine-Learning Prediction of Curie Temperatures and Its Promise for Guiding the Discovery of Functional Magnetic Materials

High-performance permanent magnets with a high Curie temperature, containing less critical materials, are integral to zero-carbon energy solutions. We built a machine-learning model trained over available experimentally measured Curie temperature values to predict the T C of multicomponent magnetic materials. We chose two compositions from a pseudo-binary (Zr 1–x Ce x )Fe 2 system, namely, (Zr 0.16 Ce 0.84 )Fe 2 and (Zr 0.94 Ce 0.06 )Fe 2 , to experimentally validate the ability of our model to predict the Curie temperature of novel compounds. We also provided a detailed discussion on the correlation of the Curie temperature with the de Gennes scaling factor in rare-earth intermetallic compounds and its breakdown below a certain rare-earth content. The electronic structure calculations (density of states and Fermi surface) were performed using the density functional theory on selected compounds (Zr 0.16 Ce 0.84 )Fe 2 and (Zr 0.94 Ce 0.06 )Fe 2 to understand the electronic origin of a strong magnetic exchange. We found that the change in the electronic density of states and electron/hole fillings at the Fermi level directly correlate with the Curie temperature. Notably, our model was able to capture these key electronic structure trends, which show that physics-informed machine learning can play a crucial role in designing new high-performance magnets with improved properties for environmentally sustainable applications.

36 MATERIALS SCIENCE↗

Discovery of Ternary Antimonides A–Al–Sb (A = Rb or Cs) with Desired Structural Motifs Guided by Machine Learning

Specific structural motifs in inorganic solids are often related to their targeted physical properties. For many classes of solids, such as Zintl phases and polar intermetallics, the crystal structures are diverse and not easy to predict. Various antimonides that are potential thermoelectric materials were proposed to be synthesizable on the basis of their estimated formation energies. Their structures were broadly classified as clathrate, channel, layered, or network through a machine learning model trained on existing ternary phases and features based on elemental properties using the sure independence screening and sparsifying operator algorithm. Through experimental validation, three new ternary antimonides were synthesized and confirmed to form layered structures: tetragonal RbAlSb 2 and CsAlSb 2 , which are isopointal but not isotypic to LiBSi 2 ; and monoclinic Rb 2 Al 2 Sb 3 , which adopts the Na 2 Al 2 Sb 3 -type structure. Finally, reinvestigation of the related compound Cs 2 In 2 Sb 3 revealed a low thermal conductivity and p-type semiconducting behavior.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Defect Diffusion Graph Neural Networks for Materials Discovery in High-Temperature Energy Applications

Here, the migration of crystallographic defects dictates material properties and performance for a plethora of technological applications. Density functional theory (DFT)-based nudged elastic band (NEB) calculations are a powerful computational technique for predicting defect migration activation energy barriers, yet they become prohibitively expensive for high-throughput screening of defect diffusivities. Without introducing hand-crafted (i.e., chemistry- or structure-specific) descriptors, we propose a generalized deep learning approach to train surrogate models for NEB energies of vacancy migration by hybridizing graph neural networks with transformer encoders and simply using pristine host structures as input. With sufficient training data, computationally efficient and simultaneous inference of vacancy defect thermodynamics and migration activation energies can be obtained to compute temperature-dependent vacancy diffusivities and to down-select candidates for more thorough DFT analysis or experiments. Thus, as we specifically demonstrate for potential water-splitting materials, candidates with desired defect thermodynamics, kinetics, and host stability properties can be more rapidly targeted from open-source databases of experimentally validated or hypothetical materials.

14 SOLAR ENERGY↗

Deciphering the Scattering of Mechanically Driven Polymers Using Deep Learning

Here, we present a deep learning approach for analyzing two-dimensional scattering data of semiflexible polymers under external forces. In our framework, scattering functions are compressed into a three-dimensional latent space using a Variational Autoencoder (VAE), and two converter networks establish a bidirectional mapping between the polymer parameters (bending modulus, stretching force, and steady shear) and the scattering functions. The training data are generated using off-lattice Monte Carlo simulations to avoid the orientational bias inherent in lattice models, ensuring robust sampling of polymer conformations. The feasibility of this bidirectional mapping is demonstrated by the organized distribution of polymer parameters in the latent space. By integrating the converter networks with the VAE, we obtain a generator that produces scattering functions from given polymer parameters and an inferrer that directly extracts polymer parameters from scattering data. While the generator can be utilized in a traditional least-squares fitting procedure, the inferrer produces comparable results in a single pass and operates 3 orders of magnitude faster. This approach offers a scalable automated tool for polymer scattering analysis and provides a promising foundation for extending the method to other scattering models, experimental validation, and the study of time-dependent scattering data.

Ding, Lijie [Oak Ridge National Laboratory (ORNL),↗

Benchmarking the Performance of the ReaxFF Reactive Force Field on Hydrogen Combustion Systems

A thorough understanding of the kinetics and dynamics of combusting mixtures is of considerable interest, especially in regimes beyond the reach of current experimental validation. The ReaxFF reactive force field method has provided a way to simulate large-scale systems of hydrogen combustion via a parametrized potential that can simulate bond breaking. This modeling approach has been applied to hydrogen combustion, as well as myriad other reactive chemical systems. In this work, we benchmark the performance of several common parametrizations of this potential against higher-level quantum mechanical (QM) approaches. We demonstrate instances where these parametrizations of the ReaxFF potential fail both quantitatively and qualitatively to describe reactive events relevant for hydrogen combustion systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Automated Development of Molten Salt Machine Learning Potentials: Application to LiCl

The in silico modeling of molten salts is critical for emerging "carbon-free" energy applications but is inhibited by the cost of quantum mechanically treating the high polarizabilities of molten salts. Here, we integrate configurational sampling using classical force fields with active learning to automate and accelerate the generation of Gaussian approximation potentials (GAP) for molten salts. This methodology reduces the number of expensive ab initio evaluations required for training set generation to O(100), enabling the facile parametrization of a molten LiCl GAP model that exhibits a 19 000-fold speedup relative to AIMD. The developed molten LiCl GAP model is applied to sample extended spatiotemporal scales, permitting new physical insights into molten LiCl's coordination structure as well as experimentally validated predictions of structures, densities, self-diffusion constants, and ionic conductivities. The developed methodology significantly lowers the barrier to the in silico understanding and design of molten salts across the periodic table.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Coaxial Ceramic Direct Ink Writing on Heterogenous and Rough Surfaces: Investigation of Core–Shell Interactions

In this work, coaxial conductor–ceramic direct ink writing enables the printing of sensitive or encapsulated materials onto heterogeneous and rough substrates. While encasing the core fluid within a stiff ceramic shell, continuity may be maintained, even while printing onto conventionally challenging substrates. Here, we report the development of a coaxial ceramic direct ink writing suite and explore coflow interrelationships based on microfluidic principles. A coaxial nozzle is designed to facilitate the coextrusion of an alumina shell, whereas indium–tin-oxide inks constitute the core. In this manner, a core–shell ceramic element may be printed onto rough substrates for future high-temperature applications. Colloidal inks are engineered to provide the required rheological and sintering performance. Moreover, flow simulations in conjunction with microfluidic coflow principles are used to explore the coaxial printing processing space, thus controlling the core–shell architectures. Physical modeling is further used to analyze core deformations and eccentricity. As a result, simulations are validated experimentally, and the analyses are used to deposit coaxial ceramic features onto heterogeneous, high-temperature ceramic substrates.

20 FOSSIL-FUELED POWER PLANTS↗

Control of Permanent Porosity in Type 3 Porous Liquids via Solvent Clustering

Porous liquids (PLs) are an exciting new class of materials for carbon capture due to their high gas adsorption capacity and ease of industrial implementation. They are composed of sorbent particles suspended in a nonadsorbed solvent, forming a liquid with permanent porosity. While PLs have a vast number of potential compositions based on the number of solvents and sorbent materials available, most of the research has been focused on the selection of the sorbent rather than the solvent. Therefore, PL design criteria on the supramolecular structures of the solvent are explored to create a fundamental understanding of how the solvent enables PL formation for rapid discovery of new PL compositions. Atomistic molecular dynamics simulation of eight solvents with a range of molecular sizes, shapes, and intramolecular bonding was performed, identifying that the shape and size of molecular clusters formed in the solvent are the driving predictor of PL formation rather than the size of the individual solvent molecule. The results demonstrate a significant departure from common approaches to PL formation based on the steric exclusion of solvent molecules from the sorbent via the size of the pore aperture. A modeling and experimental validation study further supports these findings. In conclusion, through this computational material design study, a previously unexplored mechanism in PL formation, solvent–solvent clustering, is identified as a critical factor for the accelerated discovery of liquid phase carbon capture materials.

Carbon capture↗

Raman Digital Twin of Monolayer Janus Transition Metal Dichalcogenides

Monolayer transition metal dichalcogenides (TMDs) are a key class of two-dimensional (2D) materials with broad technological potential. Their Janus counterparts exhibit unique properties due to broken out-of-plane symmetry and further enrich the functionalities of TMDs. However, experimental synthesis and identification of Janus TMDs remain challenging. It is thus highly desirable to have a rapid, simple, and in situ characterization technique to monitor, in real time, the conversion process from the parent to Janus structure. Raman spectroscopy stands out for such a task as it is a powerful, nondestructive, and very commonly used tool to characterize 2D materials both in situ and ex situ. To realize the full potential of Raman spectroscopy on rapid characterization of Janus TMDs, we present a computational “Raman digital twin” library for various monolayer Janus TMDs in both 2H and Td phases. We focus on group-6 TMDs: MoS 2 , WS 2 , MoSe 2 , WSe 2 , MoTe 2 , WTe 2 and their Janus variants: MoSSe, MoSTe, MoSeTe, WSSe, WSTe, and WSeTe. Using first-principles density functional theory (DFT), we calculate their vibrational properties and predict distinct Raman fingerprints. These phonon and Raman signatures reflect each material’s structural symmetry and atomic composition, enabling clear identification via Raman spectroscopy. Our theoretical work supports experimental efforts by providing benchmarks for material identification, structural analysis, and quality control. In conclusion, the computational library expedites the discovery and development of Janus 2D materials, facilitating tighter integration between theoretical predictions and experimental validation.

Chalcogenides↗

Tuning the Functionalities of Porous Liquids for Emergent Gas-Capture Properties

Type 3 Porous Liquids (PLs) are a class of materials with the potential to revolutionize gas capture, storage, and utilization. These PLs are formed by suspending sorbent nanoparticles (e.g., metal−organic frameworks) in sterically excluded solvents, creating permanent porosity for gas capture in a processable, low-viscosity phase. Herein, a computational study revealed sorbent surface functionalization strategies to enhance CO 2 sorption, and the molecular structural signatures underpinning the enhancements in gas uptake. PLs composed of a ZIF-8 surface functionalized with 3-amino-1,2,4-triazole (Atz) in glyceryl triacetate were targeted for emergent CO 2 capture, exceeding that of the unfunctionalized ZIF-8 PL. ZIF-8 was surface functionalized with Atz at various surface coverage fractions (f), and classical molecular dynamics simulations predicted an increase in CO 2 sorption capacity with increasing f, up to f = 0.75. Additionally, detailed structural analyses revealed that solvent orientational order, derived from the solvent triplet-angle distribution, can identify the gas-capture potential of a PL without requiring computationally expensive direct modeling of the CO 2 sorption. Combined with experimental validation, initial computational screening of PL compositions promises to accelerate the discovery of PL compositions for novel gas separation materials platforms.

gas capture↗

Shining a Light on Some Fundamental Research Opportunities in Semiconductor Photoelectrochemistry

Decades of research in semiconductor photoelectrochemistry have yielded a deep understanding of charge transfer, energetics, and stability at solid−liquid interfaces. Theoretical frameworks developed by Gerischer and contemporaries, together with extensive experimental validation, have clarified the key principles affecting the interfacial kinetics and energetics of semiconductor photoelectrodes. Nevertheless, significant opportunities remain for advances in fundamental understanding of semiconductor photoelectrochemistry. Exciting opportunities include exploiting advances in theory, synthesis, and instrumentation to determine the chemical identity and reactivity of surface states; exerting control of band-edge energetics through molecular-level surface modification processes; and systematically improving emerging photoelectrode protection strategies to enable long-term photoelectrode operation under both oxidative and reductive conditions. Advanced morphologies, such as nanowire and microwire arrays, present new pathways to combine efficient light absorption with effective charge collection and catalyst integration. Unique light−matter interactions during photoelectrochemical deposition of p-type semiconductors readily allow preparation at scale of complex 3D morphologies that are difficult, if not impossible, to access by other methods. Continued exploration of these avenues will expand the fundamental understanding of semiconductor−liquid interfaces and could additionally advance the realization of efficient, stable, and scalable systems for solar fuel generation and other emerging photoelectrochemical applications.

Bean, Paul J. L. [California Institute of Technolo↗

Continuum Model to Define the Chemistry and Mass Transfer in a Bicarbonate Electrolyzer

Bicarbonate electrolyzers are devices designed to convert CO 2 captured from point sources or the atmosphere into chemicals and fuels without needing to first isolate pure CO 2 gas. In this work, we report here an experimentally validated model that quantifies the reaction chemistry and mass transfer processes within the catalyst layer and cation exchange membrane layer of a bicarbonate electrolyzer. Our results demonstrate that two distinct chemical microenvironments are key to forming CO at high rates: an acidic membrane layer that promotes in situ CO 2 formation and a basic catalyst layer that suppresses the hydrogen evolution reaction. We show that the rate of CO product formation can be increased by modulating the catalyst and membrane layer properties to increase the rate of in situ CO 2 generation and transport to the cathode. These insights serve to inform the design of bicarbonate and BPM-based CO 2 electrolyzers while demonstrating the value of modeling for resolving rate-determining processes in electrochemical systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Lithium–Sulfur Batteries Enabled by Fluorine-Free Electrolytes with a Compressed Solvation Structure

In this paper, a fluorine-free aromatic cosolvent strategy is presented to regulate electrolyte solvation chemistry in Li-S batteries with sulfurized polyacrylonitrile (SPAN) cathodes. Assisted by the Uni-ELF AI tool and experimental validation, toluene is identified as an optimal weakly solvating cosolvent. Its incorporation compresses the Li⁺ solvation sheath and induces an anion-dominated solvation structure, thereby enhancing interfacial ion transport and sulfur redox kinetics through controlled π-π interactions with polysulfides. Consequently, Li || Li symmetric cells exhibit stable cycling for over 1,000 cycles at a current density of 1 mA cm⁻². Meanwhile, Li-S cells employing high-loading SPAN cathodes retain more than 75% of their initial capacity after 250 cycles at -10 °C. Additionally, a practical pouch cell with high SPAN loading and a low electrolyte-to-SPAN ratio of 3 µL mg⁻¹ delivers an initial capacity of around 600 mAh gSPAN⁻¹, underscoring the potential of fluorine-free electrolytes for practical metal-sulfur batteries.

25 ENERGY STORAGE↗

Accelerated Discovery of Cost-Effective Photoabsorber Materials for Near-Infrared (λ = 1600 nm) Photodetector Applications

Current infrared sensing devices are based on costly materials with relatively few viable alternatives known. To identify promising candidate materials for infrared photodetection, we have developed a high-throughput screening methodology based on high-accuracy r 2 SCAN and HSE calculations in density functional theory. Using this method, we identify ten already synthesized materials between the inverse perovskite family, the barium silver pnictide family, the alkaline pnictide family, and ZnSnAs 2 as top candidates. Among these, ZnSnAs 2 emerges as the most promising candidate due to its experimentally verified band gap of 0.74 eV at 0 K and its cost-effective synthesis through Bridgman growth. BaAgP also shows potential with an HSE-calculated band gap of 0.64 eV, although further experimental validation is required. Lastly, we discover an additional material, Ca 3 BiP, which has not been previously synthesized, but exhibits a promising optical spectra and a band gap of 0.56 eV. The method applied in this work is sufficiently general to screen wider bandgap materials in high-throughput and now extended to narrow-band gap materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗