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Adaptive laboratory evolution and metabolic engineering of Cupriavidus necator for improved catabolism of volatile fatty acids

Bioconversion of high-volume waste streams into value-added products will be an integral component of the growing bioeconomy. Volatile fatty acids (VFAs) (e.g., butyrate, valerate, and hexanoate) are an emerging and promising waste-derived feedstock for microbial carbon upcycling. Cupriavidus necator H16 is a favorable host for conversion of VFAs into various bioproducts due to its diverse carbon metabolism, ease of metabolic engineering, and use at industrial scales. Here, in this study, we report that a common strategy to improve product titers in C. necator, deletion of the polyhydroxybutyrate (PHB) biosynthetic operon, results in a significant growth defect on VFA substrates. Using adaptive laboratory evolution, we identify mutations to the regulator gene phaR, the two-component response regulator-histidine kinase pair encoded by H16_A1372/H16_A1373, and the tripartite transporter assembly encoded by H16_A2296-A2298 as causative for improved growth on VFA substrates. Deletion of phaR and H16_A1373 led to significantly reduced NADH abundance accompanied by large changes to expression of genes involved in carbon metabolism, balance of electron carriers, and oxidative stress tolerance that may be responsible for improved growth of these engineered strains. These results provide insight into the role of PHB biosynthesis in carbon and energy metabolism and highlight a key role for the regulator PhaR in global regulatory networks. By combining mutations, we generated platform strains with significant growth improvements on VFAs, which can enable improved conversion of waste-derived VFA substrates to target bioproducts.

09 BIOMASS FUELS↗

Biogeochemical and community ecology responses to the wetting of non-perennial streams

Transitions between dry and wet hydrologic states are the defining characteristic of non-perennial rivers and streams, which constitute the majority of the global river network. Although past work has focused on stream drying characteristics, there has been less focus on how hydrology, ecology and biogeochemistry respond and interact during stream wetting. Wetting mechanisms are highly variable and can range from dramatic floods and debris flows to gradual saturation by upwelling groundwater. This variation in wetting affects ecological and biogeochemical functions, including nutrient processing, sediment transport and the assembly of biotic communities. Here, in this work, we synthesize evidence describing the hydrological mechanisms underpinning different types of wetting regimes, the associated biogeochemical and organismal responses, and the potential scientific and management implications for downstream ecosystems. This combined multidisciplinary understanding of wetting dynamics in non-perennial streams will be key to predicting and managing for the effects of climate change on non-perennial ecosystems.

54 ENVIRONMENTAL SCIENCES↗

Unifying thermochemistry concepts in computational heterogeneous catalysis

Thermophysical properties of adsorbates and gas-phase species define the free energy landscape of heterogeneously catalyzed processes and are pivotal for an atomistic understanding of the catalyst performance. These thermophysical properties, such as the free energy or the enthalpy, are typically derived from density functional theory (DFT) calculations. Enthalpies are species-interdependent properties that are only meaningful when referenced to other species. The widespread use of DFT has led to a proliferation of new energetic data in the literature and databases. However, there is a lack of consistency in how DFT data is referenced and how the associated enthalpies or free energies are stored and reported, leading to challenges in reproducing or utilizing the results of prior work. Additionally, DFT suffers from exchange–correlation errors that often require corrections to align the data with other global thermochemical networks, which are not always clearly documented or explained. In this review, we introduce a set of consistent terminology and definitions, review existing approaches, and unify the techniques using the framework of linear algebra. This set of terminology and tools facilitates the correction and alignment of energies between different data formats and sources, promoting the sharing and reuse of ab initio data. Standardization of thermochemistry concepts in computational heterogeneous catalysis reduces computational cost and enhances fundamental understanding of catalytic processes, which will accelerate the computational design of optimally performing catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Anomaly Detection in Seismic Data with Deep Learning: Application for Instrument Failure Detection and Forecasting

Seismic data quality assessment (QA) is the first and one of the most important steps before conducting any further data analysis. Traditional methods involve checking various metrics, such as spike detection and power spectral density, by setting strict thresholds or comparing data against synthetic benchmarks. However, these approaches often rely on pre-existing knowledge and assumptions about data anomalies, leading to potential misclassification of unusual cases. Here, in this study, we propose a deep autoencoder model, an unsupervised learning approach that evaluates data quality without making assumptions about normal and anomalous data, which can be used to identify deviations in recorded data that may indicate nascent instrument failure. We test the model with the U.S. International Monitoring System (IMS) seismic stations and demonstrate the capability of detecting anomalies on a monthly scale. This could prompt station operators to examine potential problems early, allowing sufficient time for instrument maintenance to prevent data outages. In addition, we use a new manually selected testing dataset to compare our model performance against two supervised machine learning (ML) approaches and a standard QA package, as baseline models. When applied to the dataset containing known data anomalies, performance of the supervised and unsupervised ML approaches is similar, with an accuracy of 88.1% for our model compared to ∼90% for the supervised ML approach and 78.2% for the standard QA package. Our model outperforms the baseline models when applied to new stations, where new types of data anomalies can be station-specific and not included in the training dataset. Finally, we show model transferability by training the model with data from the Global Seismograph Network only and applying it to the IMS network data. The results suggest that our model is generalizable and can be applied to new stations with good accuracy.

Lin, Jiun-Ting [Lawrence Livermore National Labora↗

Hybrid classical-quantum communication networks

Over the past several decades, the proliferation of global classical communication networks has transformed various facets of human society. Concurrently, quantum networking has emerged as a dynamic field of research, driven by its potential applications in distributed quantum computing, quantum sensor networks, and secure communications. This prompts a fundamental question: rather than constructing quantum networks from scratch, can we harness the widely available classical fiber-optic infrastructure to establish hybrid quantum–classical networks? This paper aims to provide a comprehensive review of ongoing research endeavors aimed at integrating quantum communication protocols, such as quantum key distribution, into existing lightwave networks. This approach offers the substantial advantage of reducing implementation costs by allowing classical and quantum communication protocols to share optical fibers, communication hardware, and other network control resources—arguably the most pragmatic solution in the near term. In the long run, classical communication will also reap the rewards of innovative quantum communication technologies, such as quantum memories and repeaters. Accordingly, our vision for the future of the Internet is that of heterogeneous communication networks thoughtfully designed for the seamless support of both classical and quantum communications.

Fiber-optic communication↗

Enabling Real-Time Communication in Multi-Agent Systems: A Graph Neural Network Based Approach

Global connectivity enables effective coordination in Multi-Agent Systems (MAS). Solving these connection problems under hardware constraints is an NP-hard non-Euclidean Degree Constrained Minimum Spanning Tree (DCMST) problem. Prior MAS controllers coordinate team movement for task completion and collision avoidance; some considering Line-of-Sight (LOS) maintenance but prioritizing flexibility over guarantees. Evolutionary Algorithms (EA) have been shown to find good solutions for DCMST, but their performance degrades with larger populations required to support a large MAS. We present a method based on edge graph attention networks, trained offline to reduce online computation times. Empirical comparisons with greedy polynomial-time solvers and EA show that our method leverages latent graph information to consistently find constraint-satisfying solutions in less time.

connectivity maintenance↗

Explosion Detection Using Smartphones: Ensemble Learning with the Smartphone High-Explosive Audio Recordings Dataset and the ESC-50 Dataset

Explosion monitoring is performed by infrasound and seismoacoustic sensor networks that are distributed globally, regionally, and locally. However, these networks are unevenly and sparsely distributed, especially at the local scale, as maintaining and deploying networks is costly. With increasing interest in smaller-yield explosions, the need for more dense networks has increased. To address this issue, we propose using smartphone sensors for explosion detection as they are cost-effective and easy to deploy. Although there are studies using smartphone sensors for explosion detection, the field is still in its infancy and new technologies need to be developed. We applied a machine learning model for explosion detection using smartphone microphones. The data used were from the Smartphone High-explosive Audio Recordings Dataset (SHAReD), a collection of 326 waveforms from 70 high-explosive (HE) events recorded on smartphones, and the ESC-50 dataset, a benchmarking dataset commonly used for environmental sound classification. Two machine learning models were trained and combined into an ensemble model for explosion detection. The resulting ensemble model classified audio signals as either “explosion”, “ambient”, or “other” with true positive rates (recall) greater than 96% for all three categories.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

Powers of magnetic graph matrix: Fourier spectrum, walk compression, and applications

Magnetic graphs, originally developed to model quantum systems under magnetic fields, have recently emerged as a powerful framework for analyzing complex directed networks. Existing research has primarily used the spectral properties of the magnetic graph matrix to study global and stationary network features. However, their capacity to model local, nonequilibrium behaviors, often described by matrix powers, remains largely unexplored. We present a combinatorial interpretation of the magnetic graph matrix powers through directed walk profiles—counts of graph walks indexed by the number of edge reversals. Crucially, we establish that walk profiles correspond to a Fourier transform of magnetic matrix powers. The connection allows exact reconstruction of walk profiles from magnetic matrix powers at multiple discrete potentials, and more importantly, an even smaller number of potentials often suffices for accurate approximate reconstruction in real networks. This shows the empirical compressibility of the information captured by the magnetic matrix. This fresh perspective suggests further applications; for example, we illustrate how powers of the magnetic matrix can identify frustrated directed cycles (e.g., feedforward loops) and can be effectively employed for link prediction by encoding local structural details in directed graphs.

complex networks↗

Soybean rust‐resistant and tolerant varieties identified through the Pan‐African Trial Network

Abstract BACKGROUND The global demand for soybeans is increasing rapidly, with projections indicating an escalation of 70–80 million metric tons over the next decade. Sub‐Saharan Africa (SSA) contributes significantly to this growth, with soybean production increasing by 6.8% per year, outpacing the global average increase of 4.7%. Despite the expansion, soybean productivity in Africa remains less than half of the global average. This yield gap is largely due to diseases and pests, such as soybean rust, which can be particularly severe. Effective management of soybean rust depends on several factors, including resistant cultivars. However, there has been limited information on the rust‐resistance levels of African cultivars. To address this gap, the Pan‐African Trial network conducted soybean varietal trials across diverse locations. RESULT Analyzing data from 370 individual trials conducted between 2015–2022, the network identified 81 cultivars with sufficient rust‐resistance data. Six cultivars including, Black Hawk, Dundee, Egret, Heron, Ibis, and Peka 06 were found to be resistant, and 12 were classified as tolerant. CONCLUSION This research is a significant step forward in improving soybean productivity in Africa, and further assessments are being undertaken to address other crop production challenges in the region. © 2025 Society of Chemical Industry.

Favoretto, Vitor Rampazzo [Cenex Harvest States (C↗

Introducing Molecular Hypernetworks for Discovery in Multidimensional Metabolomics Data

Orthogonal separations of data from high-resolution mass spectrometry can provide insight into sample composition and address challenges of complete annotation of molecules in untargeted metabolomics. “Molecular networks” (MNs), as used in the Global Natural Products Social Molecular Networking platform, are a prominent strategy for exploring and visualizing molecular relationships and improving annotation. MNs are mathematical graphs showing the relationships between measured multidimensional data features. MNs also show promise for using network science algorithms to automatically identify targets for annotation candidates and to dereplicate features associated with a single molecular identity. Here, this paper introduces “molecular hypernetworks” (MHNs) as more complex MN models able to natively represent multiway relationships among observations. Compared to MNs, MHNs can more parsimoniously represent the inherent complexity present among groups of observations, initially supporting improved exploratory data analysis and visualization. MHNs also promise to increase confidence in annotation propagation, for both human and analytical processing. We first illustrate MHNs with simple examples, and build them from liquid chromatography- and ion mobility spectrometry-separated MS data. We then describe a method to construct MHNs directly from existing MNs as their “clique reconstructions”, demonstrating their utility by comparing examples of previously published graph-based MNs to their respective MHNs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

SoS-SDQN: System of Systems Software-defined Quantum Networking

Quantum networks are needed for quantum domain applications that may run across different network deployments - point-to-point, multi-node networks, and possibly across inter-domain quantum networks, like the quantum internet. Unlike classical computing networks, quantum networks involve heterogeneous systems nodes that currently require local and manual control. This needs a unified control approach to help them integrate, work seamlessly, and have global knowledge. Software-defined Networking (SDN) has been successfully leveraged in classical networking for seamless and software-driven control of network infrastructure and packet switching, but not in management of quantum network applications across heterogeneous systems. In this paper, we review the current state of the art and present early developments of a System-of-Systems Software-defined Quantum Networking architecture (SoS-SDQN), a generic architecture that supports software-driven quantum network experiments across heterogeneous quantum systems. The architecture modifies the generic SDN to address the domain requirements of quantum networks and proposes a multilevel SDQN to provide a global view of network status, running applications, and control of incorporated heterogeneous quantum systems. We also design and implement a SoS SouthBound Quantum Interface (SoS-SBQI), a quantum infrastructure protocol that abstracts automation of applications across the network.

Alnajjar, Anees [ORNL] (ORCID:0000000237101601)↗

SPARTAN and IMPROVE Comparison Experiment (SPICE) Interim Campaign Report

SPICE (the SPARTAN and IMPROVE Comparison Experiment) aims to obtain and quantify comparisons between aerosol PM 2.5 mass concentration measurements from the University of Oklahoma (OU) Surface Particulate Matter Network (SPARTAN) station and the U.S. Environmental Protection Agency (EPA) Interagency Monitoring of Protected Visual Environments (IMPROVE) station hosted by the U.S. Department of Energy Atmospheric Radiation Measurement (ARM) User Facility at ARM’s Southern Great Plains (SGP) observatory in Oklahoma. Aerosols—both natural and anthropogenic—affect human populations in multiple ways. Much of ARM’s research focuses on how aerosols influence weather and climate through their optical and radiative effects, as well as their impacts on clouds and precipitation. However, aerosols also pose direct risks to humans and other organisms through inhalation, with the severity of health impacts depending on particle size, chemical composition, and duration of exposure. The IMPROVE network was established by the U.S. EPA to monitor air quality, including visible clarity as well as total and chemically speciated aerosol mass concentrations. The ARM SGP site hosts the IMPROVE SOGP station. Separately, the SPARTAN network operates a globally distributed set of stations similar to IMPROVE but with an emphasis on remote deployment and semi-autonomous operation for use beyond the borders of the United States (IMPROVE only operates within the U.S.). The University of Oklahoma operates a SPARTAN station. To establish confidence in the OU SPARTAN instrumentation and measurement protocol relative to the EPA-certified IMPROVE station, the OU SPARTAN station is currently deployed at SGP in close proximity to the IMPROVE SOGP station. The SPICE campaign was envisioned as a contiguous calendar-year effort for 2025 to capture seasonal variation in mass loading as well as composition. However, independent of the SPICE campaign, the SPARTAN network adopted a new filter construction part-way through the year, interrupting our contiguous data set. Thus, to obtain a contiguous data set with a uniform consistent configuration, SPICE desires an extension through 2026.

54 ENVIRONMENTAL SCIENCES↗

Quantum Wrapper Networking for Entanglement Management and Control in Transparent Optical Quantum Networks

The overarching goal of this three-year project was to design and experimentally demonstrate a quantum wrapper networking (QWN) protocol and architecture for entanglement management and control in coexisted classical-quantum networks, facilitating a global quantum Internet. In QWN, the quantum payload (qubits) is wrapped with classical bits as a header. The classical bits facilitate end-to-end transport of the quantum payload without having to read or alter the quantum data payload at intermediate switches and routers.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Kinetic model development for single step ethanol to butene rich olefin process over Cu-Y/Beta catalysts

Here, this study presents the first intrinsic kinetic model for the single-step conversion of ethanol to butene-rich olefins over bifunctional Cu-Y/Beta catalysts, addressing a critical gap in the design and scale-up of Sustainable Aviation Fuel (SAF) processes. The reaction network comprises ten global steps involving dehydrogenation, aldol condensation, hydrogenation, and dehydration reactions, distributed across Cu and rare-earth (Y) active sites. The model incorporates dual-site functionality (Cu and Y site) and explicitly accounts for key intermediates such as crotonaldehyde and butanal. Reaction rates are formulated using Langmuir–Hinshelwood–Hougen–Watson (LHHW) kinetics. Kinetic parameters are extracted by fitting the model to lab-scale packed-bed reactor data across a wide range of temperatures and space velocities, demonstrating strong agreement in ethanol conversion and product selectivity. The reaction kinetics developed in this work provide a foundational basis for constructing reactor models that enable process optimization and scale-up of ethanol-to-jet fuel technologies.

Cu-Y/Beta catalyst↗

Bioorthogonal Click Chemistry for Antibody-Free Profiling of Acetylation, Propionylation, and Butyrylation in Pseudomonas aeruginosa and Methicillin-Resistant Staphylococcus aureus

Lysine acylation is a posttranslational modification (PTM) conserved in all domains of life and is essential for regulating diverse biological processes. Traditional methods for investigating acylation rely on anti-acyl-lysine antibodies, which are costly and time-consuming and often exhibit variable affinity. To remedy these pitfalls, we developed an antibody-free method for bacterial acylome enrichment using bioorthogonal click chemistry coupled with tandem mass spectrometry. We applied this approach to the pathogens Pseudomonas aeruginosa and methicillin-resistant Staphylococcus aureus (MRSA) to explore the biological significance of acylation in each organism. We characterized the acetylome, propionylome, and butyrylome in P. aeruginosa UCBPP-PA14 and the acetylome and propionylome in MRSA. Comparative analyses revealed unique PTM dynamics showing that acylation regulated a wide range of cellular functions, including metabolism, antibiotic resistance, virulence, and stress response. This work establishes the first antibody-free enrichment method for defining bacterial acylomes and provides new insight into global lysine acylation networks in pathogenic bacteria.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Abstraction hierarchy to define biofoundry workflows and operations for interoperable synthetic biology research and applications

Lack of standardization in biofoundries limits the scalability and efficiency of synthetic biology research. Here, we propose an abstraction hierarchy that organizes biofoundry activities into four interoperable levels: Project, Service/Capability, Workflow, and Unit Operation, effectively streamlining the Design‑Build‑Test‑Learn (DBTL) cycle. This framework enables more modular, flexible, and automated experimental workflows. It improves communication between researchers and systems, supports reproducibility, and facilitates better integration of software tools and artificial intelligence. Our approach lays the foundation for a globally interoperable biofoundry network, advancing collaborative synthetic biology and accelerating innovation in response to scientific and societal challenges.

Kim, Haseong↗

How Frequent Will the Rarest Daily Rainfall Records of Hurricane Ida’s Remnants Be in the Future?

Abstract Gaining continued insights into the impact of global warming on the occurrence of hurricane-associated intense record downpours is essential for building climate resilient communities. This study investigates projected future changes in extreme rainfall over the Northeast United States, as represented by extreme daily amounts during Hurricane Ida in 2021. We used historical control simulations of Weather Research and Forecasting (WRF) Model generated from 40 years of weather events (1980–2014, 12 km) forced by the fifth generation European Centre for Medium-Range Weather Forecasts atmospheric reanalysis. These simulations are thermodynamically modified (2060–2100) via an imposed warming for the high-emission scenario of shared socioeconomic pathway (SSP585) from a range of general circulation models. Ground observations from the Global Historical Climatology Network (1950–2014) and WRF simulations (historical, 1980–2014, and future, 2060–2100) are integrated into a nonstationary generalized extreme value (GEV) framework to assess the frequency of Ida’s heaviest daily rain rates under the SSP585 scenario. Results show that Ida’s daily maximum rainfall recorded at different observation locations was higher than the single highest September daily maximum observed (1950–2014) for 5 out of 17 stations (∼30% of the stations). Ida-like extreme daily rain rates are projected to be, on average, more than 2 times more likely to occur at the end of the century in the simulations (with some regions as high as 5 times). This work demonstrates that integrating a high-resolution atmospheric model’s present-day and thermodynamically modified future simulations along with ground observations, within a nonstationary statistical framework, is crucial for understanding changing characteristics of extreme weather events. Significance Statement Daily scale extreme precipitation is expected to become more frequent and severe, as evidenced by observations and model simulations. While it is important to investigate how these intensifying heavy rainfall events affect current engineering standards, fewer studies have contextualized how warming impacts the most extreme rainfall from a single storm event relative to historical heavy downpours. In this study, we focused on the daily extreme rainfall associated with the extratropical transition of Hurricane Ida (2021), particularly over the northeastern United States—some of which exceeded the commonly used hydrologic design criteria for a 100-yr storm. Using a high-resolution atmospheric model simulation, we investigated how continued warming may influence the frequency of such daily rain rates. Under a high-emission scenario, these events are projected to become up to 5 times more likely at the end of the twenty-first century.

Dollan, Ishrat J↗

CaloTrilogy: Toward a Breakthrough in One-Step, End-to-End, Physics-Guided Shower Generation for Modern Calorimeters

High-precision calorimeter simulation at current and future colliders imposes rapidly growing computational demands, motivating the development of machine-learning surrogates for traditional Monte Carlo tools such as Geant4. Flow matching and diffusion-based generative models have become leading approaches for high-dimensional fast simulation because of their sample quality, but typically require ${\cal O}(100)$ function evaluations at inference and often rely on auxiliary networks to constrain global observables, compromising streamlined end-to-end generation. We introduce a unified framework that improves the balance between speed, shower quality, and physics fidelity. The method combines: (i) an average velocity field integrator that enables sampling in one or a few evaluations; (ii) a learned generative prior in shower space, constructed from data rather than random noise; and (iii) physics-guided loss terms that impose inductive biases on key observables during training. These elements are training time regularizers, preserving end-to-end inference with no additional cost. With only one or a few evaluation steps, the model achieves shower quality competitive with state-of-the-art flow and diffusion approaches, tested on several public high granularity calorimeter datasets. The results demonstrate inter-layer shower structure consistent with the underlying physics, providing a strong candidate for future fast simulation workflows.

Jiang, Cheng [Edinburgh U.]↗