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At least 721 records · Page 40

Automated Nanocrystal Synthesis: Lessons from 25 Years of Robots, Microfluidics, and Machine Learning

Here, this perspective highlights the evolution of techniques for automating the synthesis of colloidal nanocrystals. Over the past 25 years, microfluidic reactors and robotic workflows have been developed to enhance the reproducibility of nanocrystal synthesis, facilitate rapid screening of reaction conditions, optimize material properties, and perform multistep syntheses of high-quality nanoparticles with complex heterostructures. Modern automated systems are now valued for their ability to generate robust data sets for validating physical models, supporting chemical mechanisms, training machine learning models, and for directing autonomous experimentation. We discuss the early challenges and limitations of these technologies and present key lessons for effectively utilizing automated and ML-guided tools to accelerate nanocrystal discovery for the next 25 years.

Nanocrystals↗

Accurate and Rapid Forecasts for Geologic Carbon Storage via Learning-Based Inversion-Free Prediction

Carbon capture and storage (CCS) is one approach being studied by the U.S. Department of Energy to help mitigate global warming. The process involves capturing CO 2 emissions from industrial sources and permanently storing them in deep geologic formations (storage reservoirs). However, CCS projects generally target “green field sites,” where there is often little characterization data and therefore large uncertainty about the petrophysical properties and other geologic attributes of the storage reservoir. Consequently, ensemble-based approaches are often used to forecast multiple realizations prior to CO 2 injection to visualize a range of potential outcomes. In addition, monitoring data during injection operations are used to update the pre-injection forecasts and thereby improve agreement between forecasted and observed behavior. Thus, a system for generating accurate, timely forecasts of pressure buildup and CO 2 movement and distribution within the storage reservoir and for updating those forecasts via monitoring measurements becomes crucial. This study proposes a learning-based prediction method that can accurately and rapidly forecast spatial distribution of CO 2 concentration and pressure with uncertainty quantification without relying on traditional inverse modeling. The machine learning techniques include dimension reduction, multivariate data analysis, and Bayesian learning. The outcome is expected to provide CO 2 storage site operators with an effective tool for timely and informative decision making based on limited simulation and monitoring data.

58 GEOSCIENCES↗

Sparse Data Machine Learning Integration with Theory, Experiment and Uncertainty Quantification: Process-Structure-Property-Performance of Friction Deformation Processing

Computer vision and deep learning tools that advance the ability to establish processing-structure-property-performance (PSPP) relations are presented. The Bayesian binning method for image segmentation enables quantitative analysis of microstructural features in an automated way, while the analysis of shapes and relative orientation of these features reveals local deformation maps indicative of both, material flow and residual stresses due to materials processing. The deep learning method leads to the previous knowledge agnostic mapping of empirically observed microstructural zones in friction stir welding (FSW) process and synthetic microstructure generation capability that is statistically equivalent to experimentally collected data.

97 MATHEMATICS AND COMPUTING↗

Evaluating the factors influencing accuracy, interpretability, and reproducibility in the use of machine learning classifiers in biology to enable standardization

The complexity and variability of biological data has promoted the increased use of machine learning methods to understand processes and predict outcomes. These same features complicate reliable, reproducible, interpretable, and responsible use of such methods, resulting in questionable relevance of the derived. outcomes. Here we systematically explore challenges associated with applying machine learning to predict and understand biological processes using a well- characterized in vitro experimental system. We evaluated factors that vary while applying machine learning classifers: (1) type of biochemical signature (transcripts vs. proteins), (2) data curation methods (pre- and post-processing), and (3) choice of machine learning classifier. Using accuracy, generalizability, interpretability, and reproducibility as metrics, we found that the above factors significantly mod- ulate outcomes even within a simple model system. Our results caution against the unregulated use of machine learning methods in the biological sciences, and strongly advocate the need for data standards and validation tool-kits for such studies.

59 BASIC BIOLOGICAL SCIENCES↗

The design space of E(3)-equivariant atom-centred interatomic potentials

Abstract Molecular dynamics simulation is an important tool in computational materials science and chemistry, and in the past decade it has been revolutionized by machine learning. This rapid progress in machine learning interatomic potentials has produced a number of new architectures in just the past few years. Particularly notable among these are the atomic cluster expansion, which unified many of the earlier ideas around atom-density-based descriptors, and Neural Equivariant Interatomic Potentials (NequIP), a message-passing neural network with equivariant features that exhibited state-of-the-art accuracy at the time. Here we construct a mathematical framework that unifies these models: atomic cluster expansion is extended and recast as one layer of a multi-layer architecture, while the linearized version of NequIP is understood as a particular sparsification of a much larger polynomial model. Our framework also provides a practical tool for systematically probing different choices in this unified design space. An ablation study of NequIP, via a set of experiments looking at in- and out-of-domain accuracy and smooth extrapolation very far from the training data, sheds some light on which design choices are critical to achieving high accuracy. A much-simplified version of NequIP, which we call BOTnet (for body-ordered tensor network), has an interpretable architecture and maintains its accuracy on benchmark datasets.

Computer Science↗

Machine-Learned Force Field for Molecular Dynamics Simulations of Nonequilibrium Ammonia Synthesis on Iron Catalysts

Ammonia (NH 3 ) is one of the most important industrial chemicals. The conventional NH 3 synthesis method-the Haber–Bosch process-converts atmospheric nitrogen (N 2 ) into NH 3 using H 2 with an iron (Fe) catalyst. However, this process requires high pressures (100–200 atm) and temperatures (700–800 K) near thermal equilibrium. Recently, Fe-based nanocatalysts have been reported to produce promising NH 3 yields under atmospheric pressures and temperature-modulated nonequilibrium conditions. Understanding the mechanism of nonequilibrium catalysis with programmed temperature variation could help to optimize this fully electrified and less energy-intensive process. Although reactive molecular dynamics (RMD) simulations can be a useful tool to model nonequilibrium catalytic processes, they require the development of accurate force fields (i.e., interatomic potentials). Here, we present a machine-learned (ML) force field within the Deep Potential MD (DPMD) framework, trained using periodic density functional theory (DFT) calculations, to model NH 3 synthesis on Fe catalysts with various surface adsorbates such as *N, *H, *N 2 , *H 2 , *NH, *NH 2 , and *NH 3 . Here, we generated the DFT data from static models of elementary reactions on the most stable (110) surface of body-centered cubic Fe, which then were augmented by data from constant number of particles–volume–temperature (NVT) DFT-MD trajectories at various temperatures. Finally, we utilized the fully optimized ML force field to investigate reaction dynamics at an Fe(110) surface at linearly increasing temperatures using NVT-DPMD simulations. Our simulations indicate that pulsed temperature ramping could prove favorable for NH3 synthesis. For example, we conducted ramping under multiple sets of conditions: (i) from 900 to 1200 K over periods of 0.1–0.3 ns for Fe surfaces precovered with N or NH along with H; and (ii) from 300 to 600 K over 0.1–0.3 ns for Fe surfaces precovered with NH 3 . While our simulations so far are limited to short time scales (very rapid heating), these observations shed light on the mechanism of the high NH 3 synthesis rate achieved in a novel temperature-modulated nonequilibrium catalytic reactor using pulsed heating and cooling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Striving to translate shale physics across ten orders of magnitude: What have we learned?

Shales will play an important role in the successful transition of energy from fossil-based resources to renewables in the coming decades. Aside from being a significant source of low-carbon intensity fuels, like natural gas, they also serve as geologic seals of subsurface formations that may be used to isolate nuclear waste, sequester CO 2 , or store intermittent energy (e.g., solar hydrogen). Despite their importance, shales pose significant engineering and environmental challenges due to their nanoporous structure and extreme heterogeneity that spans at least ~10 orders of magnitude in spatial scale. Two challenges inhibit a system-level understanding: (1) the physics of fluid flow and phase behavior in shales are poorly understood due to the dominant molecular interactions between minerals and fluids under confinement, and (2) the apparent lack of scale separation that prevents a reliable (closed) description of the physics at any single scale of observation. In this review, we focus on the latter issue and discuss scale translation, which in its broadest sense is transforming data or simulations from one spatiotemporal scale to another. While effective scale translation is not exclusive to shales, but all geologic porous media, the need for it is especially acute in shales given their high degree of heterogeneity. Classical theories like homogenization, while indispensable, fail when scales are not separated. Other methods, like numerical upscaling, scale-translate in only one direction: small to large, but not the reverse, called downscaling. However, the confluence of advances in three areas are bringing challenging problems such as shales within reach: increased computational power and scalable algorithms; high-resolution imaging and multi-modal data acquisition; and machine learning to process massive amounts of data. While these advances equip geoscientists with a wide array of experimental and computational tools, no individual tool can probe the entire gamut of heterogeneity in shales. Their effective use, therefore, requires an ability to bridge between various data types obtained at different scales. The aim of this review is to present a coherent account of computational and experimental methods that may be used to achieve just that, i.e., to perform scale translation. We provide a broader definition of scale translation, one that transcends classical homogenization and upscaling methods, but is consistent with them and accommodates notions like downscaling and data translation. After a brief introduction to homogenization, we review hybrid methods, numerical upscaling and its recent extensions, multiscale computing, high-resolution imaging, and machine learning. We place particular emphasis on multiscale computing and propose an algorithmic framework to bridge between the pore (micro) and Darcy (macro) scales. Throughout the paper, we draw comparisons between the various methods and highlight their (often hidden) similarities, differences, benefits, and pitfalls. We finally conclude with two case studies on shales that exemplify some of the methods presented.

58 GEOSCIENCES↗

NASA Earth Systems Digital Twins (ESDT)

"Similarly to artificial intelligence, which is now revolutionizing many aspects of our daily lives, Earth system digital twin technologies have the potential to revolutionize the way Earth Science research will be conducted in the future, and how results and knowledge from this research will provide information to support decision making and yield impactful societal benefits. An Earth System Digital Twin or ESDT is a dynamic and interactive information system that first provides a digital replica of the past and current states of the Earth or Earth system as accurately and timely as possible; second, allows for computing forecasts of future states under nominal assumptions and based on the current replica; and third, offers the capability to investigate many hypothetical scenarios under varying impact assumptions. In other words, an ESDT provides the integrated What-Now, What-Next, and What-If pictures of the Earth or Earth system, by continuously ingesting newly observed data and by leveraging multiple interconnected models, machine learning as well advanced computing and visualization capabilities. Digital twins have been developed in engineering since 2002, but the interest in digital twins for the Earth domain is more recent and stems from the convergence of several developments: - The huge amount of diverse data that has now been collected continuously for more than 50 years, and that is becoming more and more difficult to access, understand, and utilize. - At the same time, because of climate change and its impacts the information produced by all of this data is becoming of interest to many new non-traditional users for analyzing and predicting various phenomena. - Because of advances in computational and visualization capabilities and the parallel unprecedented development of machine learning (ML), extracting relevant information from these large amounts of data and running complex models faster has become possible. As a result, it is becoming necessary and possible to build intuitive and interactive frameworks that will enable users with various skill levels and/or organizational hierarchy levels to easily access large amounts of targeted information along with the relevant tools and models (Earth system and human activity models), to support them in analyzing and visualizing this information, to help them understand interactions among models, to visualize the potential outcomes of various impacts, and to support decision or policy making. The full power of digital twins is that, through an integrated representation and standardized tools and software technologies, the same digital replica can address the needs of multiple users at various resolutions (spatial and temporal) and for various applications (science, economic, policy, etc.) – “from farmer to scientist”. With all these interests at stake, the challenges of building optimal digital twins are many and complex. The first challenge is to determine if a Digital Twin should be global or local, and multi-domain or thematic. For example, some domains such as Climate or Weather will require a global Digital Twin or Digital Twin capabilities while science areas such as Biodiversity might be more local. We can also envision that multiple thematic ESDTs, e.g., Air Quality, Wildfires, Hydrology could be federated or provide input to other ESDTs, either on a regional level or to a more global ESDT. Overall, we can imagine a future “web” of Digital Twins co-existing in a hierarchy or in a network, and capable of being connected or federated depending on the needs. This last point brings up the very important challenge of interoperability, including standards and protocols that will need to be built into these systems from the beginning. Each individual digital twin would have full flexibility in internal construction but would need standards-based interfaces (input and output) or hooks to make it compatible with others. Another challenge when building digital twins will be to decide how to organize each digital replica. Based on the applications targeted by the DT under implementation, various amounts and types of raw data, Analysis Ready Data (ARD) and information will need to be incorporated. Depending on the required latencies and needs of the users, various solutions can be considered, including Data Cubes, Data Lakes, pointers, or computing information on demand. We envision that each ESDT will choose a solution adapted to its specific objectives. Another important challenge is the type(s) of visualization that will be used, as well as the level of interactivity and refresh rate that will be required. Again, this will depend on the objectives of the ESDT, but also on the various users’ needs. In most cases, several types of visualizations and human interfaces will need to be offered depending on the projected users of that system. In parallel to the challenges highlighted above, there are also many tools and technologies that will need to be developed or improved for all types of digital twins. Among those are improved machine learning technologies, for example providing explainability, but also ML techniques for causality and providing a better integration of physics models. Additionally, reliable uncertainty quantification methods will be needed for all ESDT components, from validating data fusion and assimilation to assessing the accuracy of ML models and weighing the values of decisions supported by those systems. This presentation introduces the ESDT concept, presents several ESDT use cases, and a proposed ESDT architecture framework, as well as various technologies being developed by the Advanced Information Systems Technology (AIST) Program."

Earth Science Remote Sensing; Information Systems↗

DeePKS-kit: A package for developing machine learning-based chemically accurate energy and density functional models

We introduce DeePKS-kit, an open-source software package for developing machine learning based energy and density functional models. DeePKS-kit is interfaced with PyTorch, an open-source machine learning library, and PySCF, an ab initio computational chemistry program that provides simple and customized tools for developing quantum chemistry codes. It supports the DeePHF and DeePKS methods. In addition to explaining the details in the methodology and the software, we also provide an example of developing a chemically accurate model for water clusters.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

MACAW v1.0

The ability to embed molecules in a numeric space is essential in order to build mathematical and machine-learning models describing molecular properties or other processes affected by molecules. MACAW is a cheminformatic tool that allows embedding small molecules into a multidimensional numeric space. In the embedding, each molecule is assigned a numeric vector that captures information of the molecule in relation to other molecules, and that vector can be used as input to mathematical models. Molecules that are more similar to each other are embedded closer in this numeric space, whereas molecules that are more different are embedded further away. One advantage of the MACAW embedding technology compared to established alterantives is that it is fast and does not require extensive computational resources or expertise. In particular, MACAW embeddings can be used as input to mathematical models without the need for variable cleaning or feature selection, saving time and simplifying their use. On the other hand, MACAW also contains methods to generate new molecules and to recommend new molecules satisfying a desired molecular property. The generation of new molecules can be biased based on an input set of molecules, effectively generating molecular diversity around it. In its turn, MACAW's molecular recommendation tool is a novel method for evolving molecules in silico towards a desired molecular specification. In this method, the biased molecular generator tool is applied iteratively in combination with a molecular selection step. As a result, in each iteration the molecules selected by the software are increasingly closer to the desired specification. Both the molecular generation and the molecular recommendation tools are very fast, efficient, and intuitive to use.

Roger, VincentBlay↗

Computational Modeling to Advance Novel Medical Isotopes for Radiotheranostics: A DOE-NIH Joint Workshop Executive Summary

The DOE-NIH Joint Workshop on Computational Modeling to Advance Novel Medical Isotopes for Radiotheranostics, held on September 27, 2024, brought together experts from government, academia, and industry to address critical challenges in radionuclide production and clinical translation. Here, the workshop emphasized interdisciplinary collaboration, particularly between the Department of Energy (DOE) and the National Institutes of Health (NIH), to strengthen the domestic isotope supply, streamline regulatory pathways, and further integrate computational tools into radiopharmaceutical therapy (RPT). Key discussions explored the role of AI-driven modeling, machine learning, and digital twin technologies in optimizing dosimetry, dynamically personalizing treatments, and reducing time to clinical adoption. Advances in predictive computational modeling were highlighted as essential for improving radionuclide yield, purity, and synthesis efficiency. Regulatory considerations and equitable access were central themes, with participants advocating for harmonized global standards, adaptive trial designs, and expanded infrastructure for clinical implementation. DOE computational and production infrastructure was emphasized. Future priorities identified include increased investment in radionuclide production infrastructure, expanded workforce development in radiopharmaceutical sciences and computational modeling, and the creation of robust public-private partnerships. The workshop concluded that continued strategic collaboration and sustained resources will be vital for advancing next-generation radiotheranostics, ensuring safe and effective therapies accessible to all patients.

digital twins↗

Representing the Unrepresented Impact of River Ice on Hydrology, Biogeochemistry, Vegetation, and Geomorphology: A Hybrid Physics-Machine Learning Approach

Focal areas include: Predictive modeling through the use of AI techniques and AI-derived model components; the use of AI and other tools to design a prediction system composed of a hierarchy of models (e.g., AI driven model/component/parameterization selection). Insight gleaned from complex data (both observed and simulated) using AI, big data analytics, and other advanced methods, including explainable AI and physics- or knowledge-guided AI.

54 ENVIRONMENTAL SCIENCES↗

Earth Science Deep Learning: Applications and Lessons Learned

Deep Learning: A subfield of machine learning; Algorithms inspired by function of the brain; Scales with amount of training data; Powerful tool without the need for feature engineering; Suitable for Earth Science applications. Deep Learning for Earth science at MSFC (Marshall Space Flight Center): Phenomena identification; Hurricane intensity (wind speed) estimation; Severe storm (hailstorm) detection; Transverse bands detection; Entity extraction for knowledge graph creation; Ephemeral water detection.

Labeled Data↗

Deploying E3’s RESERVE Tool to Enable Advanced Operation of Clean Grids

Energy and Environmental Economics, Inc. (E3) developed an open-source machine learning model, RESERVE, for deriving ancillary services timeseries in deeply decarbonized electricity grids. E3 used a bespoke PLEXOS production simulation model of the California Independent System Operator’s (CAISO) balancing area to validate RESERVE’s ability to enable production cost, greenhouse gas emissions (GHG), and renewable energy curtailment savings. These savings were modeled by comparing PLEXOS cases with RESERVE’s outputs to PLEXOS cases with CAISO’s incumbent reserve product in the Western Energy Imbalance Market (EIM)’s 15-minute market. E3 also tested cases with solar operating flexibly to provide reserves. E3 found that, in a 2030 modeling year, using RESERVE and flexible solar enabled significant production cost, GHG and curtailment savings versus the incumbent CAISO method in cases with low penetrations of lithium-ion batteries. However, with the full 14 gigawatts (about 30% of peak CAISO demand) of 4-hour lithium-ion batteries that are expected to be installed by 2030, these savings approach zero due to batteries saturating ancillary services markets. E3 also found significant savings under a 2019 benchmarking year.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

SimNet: Accurate and High-Performance Computer Architecture Simulation using Deep Learning

While cycle-accurate simulators are essential tools for architecture research, design, and development, their practicality is limited by an extremely long time-to-solution for realistic applications under investigation. This work describes a concerted effort, where machine learning (ML) is used to accelerate microarchitecture simulation. First, an ML-based instruction latency prediction framework that accounts for both static instruction properties and dynamic processor states is constructed. Then, a GPU-accelerated parallel simulator is implemented based on the proposed instruction latency predictor, and its simulation accuracy and throughput are validated and evaluated against a state-of-the-art simulator. Leveraging modern GPUs, the ML-based simulator outperforms traditional CPU-based simulators significantly.

97 MATHEMATICS AND COMPUTING↗

Tackling Climate Change with Machine Learning

Climate change is one of the greatest challenges facing humanity, and we, as machine learning (ML) experts, may wonder how we can help. Here we describe how ML can be a powerful tool in reducing greenhouse gas emissions and helping society adapt to a changing climate. From smart grids to disaster management, we identify high impact problems where existing gaps can be filled by ML, in collaboration with other fields. Our recommendations encompass exciting research questions as well as promising business opportunities. We call on the ML community to join the global effort against climate change.

54 ENVIRONMENTAL SCIENCES↗

Understanding Machine Learning in Earth Science: A Natural Language Processing Approach

Machine learning (ML) is being increasingly utilized in Earth science research. Benefits of ML include efficiency, reduction of human error, and ability to extract hidden patterns within data. However, the mutual lack of each other’s domain knowledge by ML and Earth science stands as a barrier to timely and effective implementation. Earth science, in particular, faces challenges in generating sample data, compared to those of traditional ML problems such as face recognition or stock predictions, where data is abundant and not lacking in ground truth, which is necessary for labeling. Earth science data are more varying in formats, such as HDF5 and image resolutions, and are not standardized across instruments, even within a given Earth science discipline. Previous studies have been done to outline the specific challenges that Earth science faces with ML, while others have focused on using existing publications to mine information efficiently. Other resources such as Scikit-Learn have developed decision trees for choosing appropriate machine learning algorithms, but application within Earth science subjects becomes much more complex. For the current study, we propose a methodology and tool that aids in implementation of ML in Earth science using natural language processing (NLP). Our work comprises three main parts: (1) analyzing existing publications related to ML and Earth science, using natural language processing: (2) extracting from the publications information on ML models subjects in Earth Science: and (3) visualizing the extracted relationships as a network graph. The resulting network graph should aid the Earth science communities in applying optimal ML algorithms and guiding data preparation through visualization of similar studies. The network graph and analysis of document similarity will be the basis of our next step, which is to develop a decision tree for selecting optimal machine learning methodologies for specified Earth science applications.

Zheng, Laura↗