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At least 865 records · Page 48

Biosystems Design by Machine Learning

Biosystems such as enzymes, pathways, and whole cells have been increasingly explored for biotechnological applications. Yet, the intricate connectivity and complexity of biosystems pose a major hurdle in designing biosystems with desired features. As -omics and other high throughput technologies have been rapidly developed, the promise of applying machine learning (ML) techniques in biosystems design has started to become a reality. ML models enable the identification of patterns within complicated biological data across multiple scales of analysis and can augment biosystems design applications by predicting new candidates for optimized performance. ML is being used at every stage of biosystems design to help find non-obvious engineering solutions with fewer design iterations. In this review, we first describe commonly used models and modeling paradigms within ML. We then discuss some applications of these models that have already shown success in biotechnological applications. Moreover, we discuss successful applications at all scales of biosystems design, including nucleic acids, genetic circuits, proteins, pathways, genomes, and bioprocess. Lastly, we discuss some limitations of these methods and potential solutions as well as prospects of the combination of ML and biosystems design.

59 BASIC BIOLOGICAL SCIENCES↗

The Power of Many: An Ensemble Approach to Spectral Similarity

Quantifying the similarity between two mass spectra─a known reference mass spectrum and an unidentified sample mass spectrum─is at the heart of compound identification workflows in gas chromatography–mass spectrometry (GC-MS). The reference spectrum most like the sample is assigned as its identification (provided some quantitative similarity threshold is met, e.g., 80%) and thus accurately measuring similarity is essential. Significant research has gone toward developing metrics for this purpose, each of which has attempted to improve upon existing methods by incorporating GC-MS-specific information (e.g., peak ratios or retention times) or adopting various statistical and algorithmic frameworks. While this active development has led to a plethora of similarity metrics with demonstrated value across different contexts, the unfortunate consequence has been confusion surrounding which metric should be used as a global standard. No such metric is currently accepted as the standard method because different metrics have demonstrated optimal performance in different contexts. In this work, we propose an ensemble approach to spectral similarity scoring that combines the collective information from across existing similarity metrics to form an improved, globally representative similarity metric as a step toward establishing a global standard method. In conclusion, the resulting ensemble metrics are evaluated on over 88,000 spectra of varying complexity and demonstrate improved abilities to accurately rank the correct reference spectrum as the top-matching candidate for a sample relative to the rankings generated by individual similarity scores.

Carbohydrates↗

A Scalable Semi-Implicit Barotropic Mode Solver for the MPAS-Ocean

A scalable semi-implicit barotropic mode solver for the ocean component of the model for prediction across scales has been implemented as a competitor to an existing explicit-subcycling scheme to allow faster and more stable simulations while not sacrificing accuracy. The semi-implicit solver adopts the pipelined preconditioned bi-conjugate gradient stabilization algorithm as an iterative solver in conjunction with the restricted additive Schwarz preconditioner that accelerates the convergence rate of the iterative solver. The preconditioner is constructed from a linearized barotropic system that also reorders the system for optimal performance, while the semi-implicit solver deals with the fully nonlinear barotropic system that requires reassembly of the coefficient matrix for every time step. Several numerical experiments, from simple one-dimensional tests to three-dimensional real-world tests, demonstrate that the semi-implicit solver has almost the same accuracy and better parallel scalability compared with the existing scheme while allowing faster and more stable simulations. Furthermore, the semi-implicit solver accelerates the barotropic mode up to 2.9 times faster than the existing scheme on 16,320 processors, leading to an overall runtime speedup of 1.9.

97 MATHEMATICS AND COMPUTING↗

Electron transport and visible light absorption in a plasmonic photocatalyst based on strontium niobate

Semiconductor compounds are widely used for photocatalytic hydrogen production applications, where photogenerated electron–hole pairs are exploited to induce catalysis. Recently, powders of a metallic oxide (Sr 1-x NbO 3 , 0.03$<$x$<$0.20) were reported to show competitive photocatalytic efficiencies under visible light, which was attributed to interband absorption. This discovery expanded the range of materials available for optimized performance as photocatalysts. Here we study epitaxial thin films of SrNbO 3+δ and find that their bandgaps are ~4.1 eV. Surprisingly, the carrier density of the conducting phase exceeds 10 22 cm -3 and the carrier mobility is only 2.47 cm 2 V -1 s -1 . Contrary to earlier reports, the visible light absorption at 1.8 eV (~688 nm) is due to the plasmon resonance, arising from the large carrier density. We propose that the hot electron and hole carriers excited via Landau damping (during the plasmon decay) are responsible for the photocatalytic property of this material under visible light irradiation.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Bright and durable scintillation from colloidal quantum shells

Abstract Efficient, fast, and robust scintillators for ionizing radiation detection are crucial in various fields, including medical diagnostics, defense, and particle physics. However, traditional scintillator technologies face challenges in simultaneously achieving optimal performance and high-speed operation. Herein we introduce colloidal quantum shell heterostructures as X-ray and electron scintillators, combining efficiency, speed, and durability. Quantum shells exhibit light yields up to 70,000 photons MeV −1 at room temperature, enabled by their high multiexciton radiative efficiency thanks to long Auger-Meitner lifetimes (>10 ns). Radioluminescence is fast, with lifetimes of 2.5 ns and sub-100 ps rise times. Additionally, quantum shells do not exhibit afterglow and maintain stable scintillation even under high X-ray doses (>10 9 Gy). Furthermore, we showcase quantum shells for X-ray imaging achieving a spatial resolution as high as 28 line pairs per millimeter. Overall, efficient, fast, and durable scintillation make quantum shells appealing in applications ranging from ultrafast radiation detection to high-resolution imaging.

47 OTHER INSTRUMENTATION↗

The northeast materials database for magnetic materials

The discovery of magnetic materials with high operating temperature ranges and optimized performance is essential for advanced applications. Current data-driven approaches are limited by the lack of accurate, comprehensive, and feature-rich databases. This study aims to address this challenge by using Large Language Models (LLMs) to create a comprehensive, experiment-based, magnetic materials database named the Northeast Materials Database (NEMAD), which consists of 67,573 magnetic materials entries (www.nemad.org). The database incorporates chemical composition, magnetic phase transition temperatures, structural details, and magnetic properties. Enabled by NEMAD, we trained machine learning models to classify materials and predict transition temperatures. Our classification model achieved an accuracy of 90% in categorizing materials as ferromagnetic (FM), antiferromagnetic (AFM), and non-magnetic (NM). The regression models predict Curie (Néel) temperature with a coefficient of determination (R 2 ) of 0.87 (0.83) and a mean absolute error (MAE) of 56K (38K). These models identified 25 (13) FM (AFM) candidates with a predicted Curie (Néel) temperature above 500K (100K) from the Materials Project. This work shows the feasibility of combining LLMs for automated data extraction and machine learning models to accelerate the discovery of magnetic materials.

Ferromagnetism↗

Adaptive stretching of representations across brain regions and deep learning model layers

Prefrontal cortex (PFC) is known to modulate the visual system to favor goal-relevant information by accentuating task-relevant stimulus dimensions. Does the brain broadly re-configures itself to optimize performance by stretching visual representations along task-relevant dimensions? We considered a task that required monkeys to selectively attend on a trial-by-trial basis to one of two dimensions (color or motion direction) to make a decision. Although effects were most prominent in frontal areas, representations stretched along task-relevant dimensions in all sites considered: V4, MT, lateral PFC, frontal eye fields (FEF), lateral intraparietal cortex (LIP), and inferotemporal cortex (IT). Spike timing was crucial to this code. A deep learning model was trained on the same visual input and rewards as the monkeys. Despite lacking an explicit selective attention or other control mechanism, by minimizing error during learning, the model’s representations stretched along task-relevant dimensions, indicating that stretching is an adaptive strategy.

59 BASIC BIOLOGICAL SCIENCES↗

Modulating coordinate site occupancy in high-entropy spinel electrocatalysts

High entropy spinel oxides provide a versatile platform for electrocatalysis because multiple metal cations can be incorporated into a single crystalline lattice, enabling tunable electronic structures. However, controlling how these cations distribute between tetrahedral and octahedral coordination sites remains a major challenge, limiting rational catalyst design. Here, we modulate cation coordination site occupancy between tetrahedral and octahedral sites in a Co–Fe–Cr–Mn–Ni framework by introducing a sixth cation (Zn, Ga, Mg, or Al) with distinct site preference energies. Using density functional theory, synchrotron X-ray absorption spectroscopy, and magnetic circular dichroism, we demonstrate that Zn preferentially occupies tetrahedral sites, driving increased octahedral occupancy of cobalt. This redistribution increases the population of octahedrally coordinated cobalt in mixed oxidation states, enhances electrical conductivity, and improves oxygen evolution reaction activity. Our findings establish coordination site occupancy as a critical design parameter, providing a strategic pathway for tailoring multicomponent spinel electrocatalysts with optimized performance.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Understanding important features of deep learning models for segmentation of high-resolution transmission electron microscopy images

Cutting edge deep learning techniques allow for image segmentation with great speed and accuracy. However, application to problems in materials science is often difficult since these complex models may have difficultly learning meaningful image features that would enable extension to new datasets. In situ electron microscopy provides a clear platform for utilizing automated image analysis. In this work, we consider the case of studying coarsening dynamics in supported nanoparticles, which is important for understanding, for example, the degradation of industrial catalysts. By systematically studying dataset preparation, neural network architecture, and accuracy evaluation, we describe important considerations in applying deep learning to physical applications, where generalizable and convincing models are required. With a focus on unique challenges that arise in high-resolution images, we propose methods for optimizing performance of image segmentation using convolutional neural networks, critically examining the application of complex deep learning models in favor of motivating intentional process design.

36 MATERIALS SCIENCE↗

Machine Learning Augmented Predictive and Generative Model for Rupture Life in Ferritic and Austenitic Steels

The Larson-Miller parameter (LMP) offers an efficient and fast scheme to estimate the creep rupture life of alloy materials for high temperature applications. However, owing to poor generalizability and dependence on the constant C, which is typically not known a-priori, estimations using the Larson-Miller parameter often result in suboptimal performance for a wide range of materials. At best it is useful in comparing alloys of similar composition. In this work, three machine learning (ML) schemes were developed for rupture life prediction for 9-12% Cr ferritic-martensitic steels and austenitic stainless steels, i.e., a hierarchical model to parameterize LMP using the LMP constant C to compute rupture life, a hierarchical model to parameterize both C and LMP to compute rupture life, and a direct prediction of rupture life. Specifically, we show that the third scheme, using a gradient boosting algorithm, can be used to train ML models for very accurate prediction of rupture life in a variety of alloys (Pear-son Correlation Coefficient > 0.9 for 9-12% Cr and > 0.8 for austenitic stainless steels). In addition, the Shapley value was used to quantify feature importance, making the model interpretable by identifying the effect of various features on the model performance. Furthermore, a variational autoencoder-based generative model was built by conditioning on the experimental dataset to sample hypothetical synthetic candidate alloys from the learnt joint distribution not existing in both 9-12 % Cr ferritic-martensitic steel and austenitic stainless steel datasets. Finally, based on the predictive and generative model, a reinforcement learning strategy has been proposed to guide experimentalists into designing better heat resistant alloys.

Mamun, Md Osman G.↗

Ultimate precision limit of noise sensing and dark matter search

Abstract The nature of dark matter is unknown and calls for a systematical search. For axion dark matter, such a search relies on finding feeble random noise arising from the weak coupling between dark matter and microwave haloscopes. We model such process as a quantum channel and derive the fundamental precision limit of noise sensing. An entanglement-assisted strategy based on two-mode squeezed vacuum is thereby demonstrated optimal, while the optimality of a single-mode squeezed vacuum is found limited to the lossless case. We propose a “nulling” measurement (squeezing and photon counting) to achieve the optimal performances. In terms of the scan rate, even with 20-decibel of strength, single-mode squeezing still underperforms the vacuum limit which is achieved by photon counting on vacuum input; while the two-mode squeezed vacuum provides large and close-to-optimum advantage over the vacuum limit, thus more exotic quantum resources are no longer required. Our results highlight the necessity of entanglement assistance and microwave photon counting in dark matter search.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Liquid-like thermal conduction in intercalated layered crystalline solids

As a generic property, all substances transfer heat through microscopic collisions of constituent particles. A solid conducts heat through both transverse and longitudinal acoustic phonons, but a liquid employs only longitudinal vibrations. As a result, a solid is usually thermally more conductive than a liquid. In canonical viewpoints, such a difference also serves as the dynamic signature distinguishing a solid from a liquid. Here in this work, we report liquid-like thermal conduction observed in the crystalline AgCrSe 2 . The transverse acoustic phonons are completely suppressed by the ultrafast dynamic disorder while the longitudinal acoustic phonons are strongly scattered but survive, and are thus responsible for the intrinsically ultralow thermal conductivity. This scenario is applicable to a wide variety of layered compounds with heavy intercalants in the van der Waals gaps, manifesting a broad implication on suppressing thermal conduction. Finally, these microscopic insights might reshape the fundamental understanding on thermal transport properties of matter and open up a general opportunity to optimize performances of thermoelectrics.

36 MATERIALS SCIENCE↗

Elemental zoning enhances mass transport in zeolite catalysts for methanol to hydrocarbons

Mass transport limitations in zeolite catalysts pose major hurdles for their optimal performance in diverse chemical reactions. Most approaches to reduce these restrictions focus on the synthesis of either hierarchical or nanosized zeolites. Here we demonstrate that the existence of a siliceous, catalytically inactive exterior rim on ZSM-5 particles dramatically reduces the diffusion limitations, which leads to an enhanced catalyst lifetime for the methanol-to-hydrocarbon reaction. In this study, our findings reveal that binary inorganic and organic structure-directing agents enable a one-pot synthesis of Si-zoned ZSM-5 catalysts with diffusion properties that are characteristic of particles with a much smaller size. Operando ultraviolet–visible light diffuse reflectance spectroscopy reveals a marked reduction in external coking among Si-zoned samples. Molecular dynamics simulations to assess the diffusion of methanol and benzene in siliceous pores and in those with Brønsted acids reveal substantially reduced transport limitations in zoned regions, consistent with the improved catalyst activity of Si-zoned zeolites relative to that of ZSM-5 with a homogeneous acid-site distribution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Sub-10 nm Ta Channel Responsible for Superior Performance of a HfO 2 Memristor

Memristive devices are promising candidates for the next generation non-volatile memory and neuromorphic computing. It has been widely accepted that the motion of oxygen anions leads to the resistance changes for valence-change-memory (VCM) type of materials. Only very recently it was speculated that metal cations could also play an important role, but no direct physical characterizations have been reported yet. We report a Ta/HfO 2 /Pt memristor with fast switching speed, record high endurance (120 billion cycles) and reliable retention. We also programmed the device to 24 discrete resistance levels, and also demonstrated over a million (220) epochs of potentiation and depression, suggesting that our devices can be used for both multi-level non-volatile memory and neuromorphic computing applications. More importantly, we directly observed a sub-10 nm Ta-rich and O-deficient conduction channel within the HfO 2 layer that is responsible for the switching. Our work deepens our understanding of the resistance switching mechanism behind oxide-based memristive devices and paves the way for further device performance optimization for a broad spectrum of applications.

36 MATERIALS SCIENCE↗

A surface plasmon enabled liquid-junction photovoltaic cell

Plasmonic nanosystems have recently been shown to be capable of functioning as photovoltaics and of carrying out redox photochemistry, purportedly using the energetic electrons and holes created following plasmonic decay as charge carriers. Although such devices currently have low efficiency, they already manifest a number of favorable characteristics, such as their tunability over the entire solar spectrum and a remarkable resistance to photocorrosion. Here, we report a plasmonic photovoltaic using a 25 μm thick electrolytic liquid junction which supports the iodide/triiodide (I - /I 3 - ) redox couple. The device produces photocurrent densities in excess of 40 μA cm -2 , an open circuit voltage ( V oc ) of ~0.24 V and a fill factor of ~0.5 using AM 1.5 G solar radiation at 100 mW cm -2 . The photocurrent and the power conversion efficiency are primarily limited by the low light absorption in the 2-D gold nanoparticle arrays. The use of a liquid junction greatly reduces dielectric breakdown in the oxide layers utilized, which must be very thin for optimal performance, leading to a great improvement in the long-term stability of the cell's performance.

Lee, Woo-ram↗

Uranium recovery from seawater: development of fiber adsorbents prepared via atom-transfer radical polymerization

We developed a novel adsorbent preparation method using atom-transfer radical polymerization (ATRP) combined with radiation-induced graft polymerization (RIGP) in order to synthesize an adsorbent for uranium recovery from seawater. Furthermore, the ATRP method allowed a much higher degree of grafting on the adsorbent fibers (595 2818%) than that allowed by RIGP alone. The adsorbents were prepared with varied composition of amidoxime groups and hydrophilic acrylate groups. The successful preparation revealed that both ligand density and hydrophilicity were critical for optimal performance of the adsorbents. Adsorbents synthesized in this study showed a relatively high performance (141 179 mg/g at 49 62 % adsorption) in laboratory screening tests using a uranium concentration of ~6 ppm. This performance is much higher than that of known commercial adsorbents. However, actual seawater experiment showed impeded performance compared to the recently reported high-surface-area-fiber adsorbents, due to slow adsorption kinetics. The impeded performance motivated an investigation of the effect of hydrophilic block addition on the graft chain terminus. The addition of hydrophilic block on the graft chain terminus nearly doubled the uranium adsorption capacity in seawater, from 1.56 mg/g to 3.02 mg/g. Our investigation revealed the importance of polymer chain conformation, in addition to ligand and hydrophilic group ratio, for advanced adsorbent synthesis for uranium recovery from seawater.

07 ISOTOPE AND RADIATION SOURCES↗

Atomic/molecular layer deposition for energy storage and conversion

Energy storage and conversion systems, including batteries, supercapacitors, fuel cells, solar cells, and photoelectrochemical water splitting, have played vital roles in the reduction of fossil fuel usage, addressing environmental issues and the development of electric vehicles. The fabrication and surface/interface engineering of electrode materials with refined structures are indispensable for achieving optimal performances for the different energy-related devices. Atomic layer deposition (ALD) and molecular layer deposition (MLD) techniques, the gas-phase thin film deposition processes with self-limiting and saturated surface reactions, have emerged as powerful techniques for surface and interface engineering in energy-related devices due to their exceptional capability of precise thickness control, excellent uniformity and conformity, tunable composition and relatively low deposition temperature. In the past few decades, ALD and MLD have been intensively studied for energy storage and conversion applications with remarkable progress. In this work, we give a comprehensive summary of the development and achievements of ALD and MLD and their applications for energy storage and conversion, including batteries, supercapacitors, fuel cells, solar cells, and photoelectrochemical water splitting. Moreover, the fundamental understanding of the mechanisms involved in different devices will be deeply reviewed. Furthermore, the large-scale potential of ALD and MLD techniques is discussed and predicted. Finally, we will provide insightful perspectives on future directions for new material design by ALD and MLD and untapped opportunities in energy storage and conversion.

25 ENERGY STORAGE↗