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At least 37 records · Page 2

How Does Escherichia coli Allocate Proteome?

Microorganisms are shown to actively partition their intracellular resources, such as pro- teins, for growth optimization. Recent experiments have begun to reveal molecular com- ponents unpinning the partition; however, it remains unclear quantitatively how individual parts orchestrate to yield precise resource allocation that is both robust and dynamic. Here we developed a coarse-grained mathematical framework that centers on guanosine pentaphosphate (ppGpp)-mediated regulation, and used it to systematically uncover the design principles of proteome allocation in Escherichia coli. Our results showed that cellular ability of resource partition lies in an ultrasensitive, negative feedback control- ling topology with the ultrasensitivity arising from zero-order amino acid kinetics and the negative feedback from ppGpp-controlled ribosome synthesis. In addition, together with the time-scale separation between slow ribosome kinetics and fast turnovers of ppGpp and amino acids, the network topology confers the organism an optimization mechanism which mimics sliding mode control, a nonlinear optimization strategy that is widely used in man-made systems. We further showed that such a controlling mechanism is robust against parameter variations and molecular fluctuations, and is also efficient for biomass production over time. Furthermore, this work elucidates the fundamental controlling mechanism of E. coli proteome allocation, thereby providing insights into quantitative microbial physiology as well as the design of synthetic gene networks.

59 BASIC BIOLOGICAL SCIENCES

Enabling HPC Scientific Workflows for Serverless

The convergence of edge computing, big data analytics, and AI with traditional scientific calculations is increasingly being adopted in HPC workflows. Workflow management systems are crucial for managing and orchestrating these complex computational tasks. However, it is difficult to identify patterns within the growing population of HPC workflows. Serverless has emerged as a novel computing paradigm, offering dynamic resource allocation, quick response time, fine-grained resource management and auto-scaling. In this paper, we propose a framework to enable HPC scientific workflows on serverless. Our approach integrates a widely used traditional HPC workflow generator with an HPC serverless workflow management system to create benchmark suites of scientific workflows with diverse characteristics. These workflows can be executed on different serverless platforms. We comprehensively compare executing workflows on traditional local containers and serverless computing platforms. Our results show that serverless can reduce CPU and memory usage respectively by 78.11% and 73.92% without compromising performance.

Andrei da silva, Anderson

Model of metabolism and gene expression predicts proteome allocation in Pseudomonas putida

Abstract The genome-scale model of metabolism and gene expression (ME-model) forPseudomonas putidaKT2440,iPpu1676-ME, provides a comprehensive representation of biosynthetic costs and proteome allocation. Compared to a metabolic-only model,iPpu1676-ME significantly expands on gene expression, macromolecular assembly, and cofactor utilization, enabling accurate growth predictions without additional constraints. Multi-omics analysis using RNA sequencing and ribosomal profiling data revealed translational prioritization inP. putida, with core pathways, such as nicotinamide biosynthesis and queuosine metabolism, exhibiting higher translational efficiency, while secondary pathways displayed lower priority. Notably, the ME-model significantly outperformed the M-model in alignment with multi-omics data, thereby validating its predictive capacity. Thus,iPpu1676-ME offers valuable insights intoP. putida’s proteome allocation and presents a powerful tool for understanding resource allocation in this industrially relevant microorganism.

Mathematical & Computational Biology

LandScan mosaic enables high-resolution gridded population estimates with explicit uncertainty

Gridded population datasets represent high-resolution distributions of human occupancy, enabling informed decision-making across a broad range of fields. These data products are valuable for assessing environmental risk, urban development, disaster preparedness and resource allocation—areas where accurate population estimates directly enhance policy effectiveness and optimize resource distribution. Despite the importance of gridded population datasets, traditional population modeling approaches often overlook inherent uncertainties in the estimation process. This limitation can create a false sense of certainty in population estimates, potentially leading to flawed decisions by those who rely on the data. To address this methodological gap, we introduce a probabilistic machine learning modeling framework, LandScan Mosaic, that explicitly incorporates uncertainty into the population modeling process. Our approach systematically quantifies uncertainty in three key modeling parameters of the LandScan HD gridded population dataset: building use types, floor counts, and occupancy rates. By employing Monte Carlo simulations, we propagate these uncertainties through the modeling process, yielding probability distributions of population counts in place of deterministic point estimates. We demonstrate the practical application of this framework in Iloilo City, Philippines, using structured decision-making techniques and our probabilistic estimates to identify and prioritize areas most affected by projected flooding, supporting targeted interventions that address both economic and social risks. In doing so, we propose a population-specific approach for incorporating confidence into structured decision making processes. Through a comparative analysis with conventional deterministic approaches and point estimate approaches, including LandScan HD and WorldPop, we evaluate how the incorporation of machine learning and uncertainty influences decision rankings. This research advances population distribution modeling by offering a robust, quantitative approach that explicitly accounts for uncertainty in the underlying data, along with guidance for how users can apply uncertainty in their decision-making.

Environmental sciences

DISTRI: Distributed Multi-Facility HPC Simulator (DISTRI) v2.1

DISTRI is an advanced network simulator designed for multi-facility computational infrastructures with agentic behavior. It simulates HPC facilities where computational resources act as autonomous agents, making intelligent decisions about job scheduling, load balancing, and resource allocation. The simulator focuses on developing and testing decentralized algorithms that promote resilience and efficiency in multi-facility environments. Key Features: - Agentic Resource Behavior: Processors and DTNs act as autonomous agents with decision-making capabilities - Pheromone-Based Load Balancing: Decentralized load balancing inspired by ant colony optimization - Dual Topology Support: Mesh (normal operations) and Dumbell (network testing) topologies - Comprehensive TCP Simulation: Realistic TCP implementations with multiple congestion control algorithms - Failure Resilience Testing: Processor failure simulation with automatic job reassignment - Extensive Visualization: Detailed performance analysis and metrics collection - Research-Ready: Designed for algorithm development and benchmarking

Bez, Jean Luca [Lawrence Berkeley National Laborat

Transforming Agricultural Productivity with AI-Driven Forecasting: Innovations in Food Security and Supply Chain Optimization

Global food security is under significant threat from climate change, population growth, and resource scarcity. This review examines how advanced AI-driven forecasting models, including machine learning (ML), deep learning (DL), and time-series forecasting models like SARIMA/ARIMA, are transforming regional agricultural practices and food supply chains. Through the integration of Internet of Things (IoT), remote sensing, and blockchain technologies, these models facilitate the real-time monitoring of crop growth, resource allocation, and market dynamics, enhancing decision making and sustainability. The study adopts a mixed-methods approach, including systematic literature analysis and regional case studies. Highlights include AI-driven yield forecasting in European hydroponic systems and resource optimization in southeast Asian aquaponics, showcasing localized efficiency gains. Furthermore, AI applications in food processing, such as plasma, ozone and Pulsed Electric Field (PEF) treatments, are shown to improve food preservation and reduce spoilage. Key challenges—such as data quality, model scalability, and prediction accuracy—are discussed, particularly in the context of data-poor environments, limiting broader model applicability. The paper concludes by outlining future directions, emphasizing context-specific AI implementations, the need for public–private collaboration, and policy interventions to enhance scalability and adoption in food security contexts.

99 GENERAL AND MISCELLANEOUS

Constrained variational optimization of counting-time allocation in sequential scattering measurements: Application to Bonse–Hart USANS

Sequential scattering measurements are often performed under a fixed experimental-time budget, even though the expected count rate varies strongly across the measured coordinate. When the dwell time at each measurement position can be controlled independently, this variation creates a general resource-allocation problem: how should the available time be distributed to minimize the uncertainty of the reconstructed profile? We formulate this problem as a constrained variational optimization for measurements governed by Poisson counting statistics. When each measurement is treated independently, minimizing the averaged squared relative uncertainty yields an inverse-square-root intensity allocation. The formulation is then generalized to include correlations between neighboring measurements and an instrumental resolution operator, leading to an allocation criterion that equalizes the marginal reduction in posterior uncertainty per unit measurement time. Bonse–Hart ultra-small-angle neutron scattering (USANS), in which reciprocal space is sampled sequentially through analyzer-angle stepping, provides an experimentally grounded application. Computational benchmarking shows that the optimized allocation outperforms uniform-time and constant-relative-error strategies, while application to an experimentally measured graphite USANS profile from the Spallation Neutron Source, using Poisson resampling under alternative schedules, demonstrates how counting time should be redistributed toward weak-intensity regions under an identical total duration. The resulting framework applies to sequential scattering and related scanning measurements whenever local dwell times are adjustable and directly determine the measurement uncertainties, and when the relevant correlation and instrumental-response models are available.

Tung, Chi-Huan [ORNL] (ORCID:0000000221972074)

A Performance Model of In-Situ Techniques

The computational capacity of High-Performance Computing (HPC) systems increases continuously with the rapid development of central processing units (CPUs) and graphic processing units (GPUs), while the in-/output (IO) subsystem develops relatively slowly and storage capacity is also limited. Data-intensive applications, which are designed to leverage the high computational capacity of HPC resources, typically generate a considerable amount of data for post-processing visualizations and data analytics. The limited IO speed and storage space could lead to constraints in the actual performance of these applications and, therefore, scientific discovery. In-situ techniques, where data is visualized/analysed while still in memory rather than through disk, can contribute to alleviating these problems as they can reduce or even fully avoid data writing/reading through the IO subsystem to/from storage. However, the overall efficiency of insitu techniques crucially depends on the characteristics of both the in-situ tasks and the applications, and the resource distribution among them. Therefore, choosing the right in-situ approach (synchronous, asynchronous, or hybrid) and resource allocation is essential to minimize overhead and maximize the benefits of concurrent execution. In this paper, we present a performance model of in-situ techniques to find the most beneficial in-situ approach and the preferred resource configuration. We verify the high accuracy of our approach with over 6800 measurements and provide use cases with different applications.

Ju, Yi [Max Planck Computing and Data Facility, Ga

Enhancing Security and Resiliency in Operational Technology Environments Through Network Slicing and Federated Learning

The growing convergence of Information Technology (IT) and Operational Technology (OT) within Industry 4.0 environments has introduced new demands on industrial network infrastructure. As cyber-physical systems become increasingly interconnected, ensuring the secure, timely, and efficient exchange of critical data is essential. This thesis explores how network slicing, a method of creating isolated virtual network segments, can be applied within OT environments to address challenges such as latency, security, and resource allocation. The first research question addressed in this thesis is: How can OT networks take advantage of NFV and SDN technology to become cyber resilient? This study examines the operational, security, and architectural implications of introducing network slicing into traditionally static OT infrastructures such as Industrial Control Systems (ICS) and SCADA. Through simulated deployments and case studies, the research demonstrates how slicing enables better isolation between critical and non-critical services, thereby improving response time, throughput, and security in sensitive environments. The second question considers: How to dynamically implement network slicing and take advantage of network resources towards integrating decentralized machine learning? In response, this thesis proposes a framework that combines Software-Defined Networking (SDN), Network Function Virtualization (NFV), and Federated Learning (FL) to enable real-time analytics while maintaining data locality. The proposed approach reduces the burden on centralized infrastructure and minimizes privacy risks by supporting on-site training of models across distributed OT nodes, coordinated through dynamically allocated network slices. The third focus explores: How slicing helps to increase the resiliency of OT networks through the orchestration of a dynamic DMZ? To answer this, the thesis presents a method for creating and managing Dynamic Demilitarized Zones (DMZs) using network slicing. This enables flexible and automated isolation of sensitive subsystems during threat scenarios or high-risk operations. Coupled with intelligent orchestration and containerized security services, the dynamic DMZ significantly enhances the system's ability to respond to cyber incidents without halting production. Ultimately, this thesis contributes a comprehensive architecture that blends network slicing with machine learning, secure segmentation, and automation, paving the way for resilient, adaptive, and intelligent OT environments. Performance evaluations across multiple scenarios show improvements in system reliability, threat response time, model accuracy, and resource utilization, providing a strong foundation for future industrial automation systems.

Rodiles Delgado, Brian G

VA EDH Advanced Software Pipeline Framework Report: Enhancing Automation and Scalability

The VA Environmental Determinants of Health (EDH) Advanced Software Pipeline Framework is designed to enhance the efficiency, scalability, and security of geospatial data processing workflows. This framework integrates modern data orchestration and containerization technologies, including Prefect for workflow automation, Docker for containerization, and PostgreSQL/PostGIS for geospatial data storage and analysis. It ensures standardized, reproducible, and automated data processing, supporting VA objectives related to substance use risk assessment and recovery research. The pipeline addresses key scalability and performance challenges through horizontal and vertical scaling, high-performance computing (HPC) integration, parallel processing, task caching, and dynamic resource allocation. These optimizations improve throughput and reduce latency, allowing the system to efficiently manage large and complex datasets. Additionally, security and compliance measures—such as data encryption (SSL), Role-Based Access Control (RBAC), and adherence to GDPR and HIPAA standards—safeguard sensitive information throughout data transmission and storage. A key implementation of this framework includes the automation of shelter list geolocation workflows, ensuring that up-to-date data is readily available for VA decision-making. Lessons learned from this project include the transition from in-memory processing to incremental storage writes, improving resource management and reliability. Future enhancements aim to expand automation, integrate AI-driven anomaly detection, and incorporate high-performance computing resources. This framework provides a scalable, secure, and adaptable solution for managing geospatial datasets, reinforcing the VA’s ability to support clinical and strategic initiatives through data-driven decision-making.

97 MATHEMATICS AND COMPUTING

Pavement condition and climatic data in southeast Texas: A dataset for evaluating flood impacts on pavement performance

Effective pavement maintenance is essential for economic stability, optimal network performance, and roadway safety. Achieving this requires thorough evaluation of pavement conditions, including structural integrity, surface roughness, and distress characteristics. Pavement performance indicators play a critical role in influencing vehicle safety and ride quality. Recent advances have emphasized the use of data-driven modeling to anticipate pavement behavior, with the goal of optimizing resource allocation and refining Maintenance and Rehabilitation (M&R) strategies through accurate condition assessment. A foundational requirement for these modeling efforts is the availability of standardized, high-quality datasets that can support robust and reproducible infrastructure analysis. This data article presents a comprehensive dataset assembled to facilitate pavement performance prediction, with a geographic focus on Southeast Texas, particularly the flood-vulnerable area of Beaumont. The dataset encompasses pavement and traffic attributes, meteorological records, flood simulation outputs, ground deformation measurements, and topographic indices, enabling detailed examination of both load-associated and non-load-associated degradation mechanisms. Data preprocessing was performed using ArcGIS Pro, Microsoft Excel, and Python to ensure consistency and usability in data-driven modeling applications, including machine learning workflows. Key contributions of this dataset include its utility in analyzing the climatic and environmental factors affecting pavement conditions, identifying critical predictive features, and enabling in-depth correlation analysis across diverse variables. By filling existing gaps in input variable selection resources, this dataset supports the development of predictive tools for estimating future maintenance demand and enhancing the resilience of pavement networks in flood-impacted areas. The resource highlights the importance of standardized datasets for advancing pavement management practices and provides a robust foundation for ongoing infrastructure performance modeling.

42 ENGINEERING

Evaluating advanced nuclear fission technologies for future decarbonized power grids

Advanced nuclear fission, which encompasses various innovative nuclear reactor designs, could contribute to the decarbonization of the United States electricity sector. However, little is known about how cost-competitive these reactors would be compared to other technologies, or about which aspects of their designs offer the most value to a decarbonized power grid. We employ an electricity system optimization model and a case study of a decarbonized U.S. Eastern Interconnection circa 2050 to generate initial indicators of future economic value for advanced reactors and the sensitivity of future value to various design parameters, the availability of competing technologies, and the underlying policy environment. These results can inform long-term cost targets and guide near-term innovation priorities, investments, and reactor design decisions. We find that advanced reactors should cost $\$5.7$–$\$7.3$/W to gain an initial market share (assuming 30 year asset life and 3.5 %–6.5 % real weighted average cost of capital), while those that include thermal storage in their designs can cost up to $\$6.0$/W–$\$7.7$/W (not including cost of storage). Since the marginal value of advanced fission reactors declines as market penetration increases, break-even costs fall ~32 % at 100 GW of cumulative capacity and ~51 % at 300 GW. Additionally, policies that provide investment tax credits for nuclear energy create the most favorable environment for advanced nuclear fission. In conclusion, these findings can inform near-term resource allocation decisions by stakeholders, innovators and investors working in the energy technology sector.

Capacity expansion

Intercomparison of flood inundation models across land use types and hydrological flood stages

Flood Inundation Mapping (FIM) model selection is a key operational decision because accurate, rapid mapping underpins early warning and resource allocation. FIM performance is context-dependent and can vary with hydrograph phase, land-use/land-cover (LULC), and the evaluation benchmark. Intercomparison studies typically assess a single near-peak snapshot against one reference dataset. Here, we provide a context-stratified intercomparison across (i) multiple hydrograph phases, (ii) LULC classes, and (iii) benchmark types, for five FIM approaches spanning a wide range of physical complexity and operational cost (TRITON, LISFLOOD-FP, HEC-RAS 2D, ARC-Curve2Flood, and OWP HAND-FIM). We use the Hurricane Matthew flood (2016) in the Neuse River Basin, North Carolina, USA, as a case study. Using high-resolution remote sensing-derived flood inundation maps, hand-labeled points, and building footprints, we assess model skill across two rising and two falling hydrograph limbs and across major LULC types. Results show that model rankings shift systematically across contexts: LISFLOOD-FP ranks highest in three of four flood phases, while TRITON leads during one rising limb phase; LISFLOOD-FP performs best in vegetated areas, whereas HEC-RAS improves relative performance in agricultural and urban areas; and benchmark choice influences conclusions, with LISFLOOD-FP performing best for flooded-building detection in the late falling limb, while TRITON ranks highest against hand-labeled points. We also report representative wall-clock runtimes for each workflow to provide use-case context for operational feasibility. Together, these results offer transferable guidance for model selection and for designing large-scale, benchmark-aware FIM intercomparison studies.

Nikrou, Parvaneh [University of Alabama]

Greenhouse Gas Accounting Procedures in Low Carbon Fuel Policies Overlook the Spatial Variability of Miscanthus-Derived Sustainable Aviation Fuel

Low carbon fuel policies such as the U.S. Renewable Fuel Standard (RFS), Canada Clean Fuel Regulations (CFR), and California Low Carbon Fuel Standard (LCFS) as well as the 45Z tax credit are intended to reduce greenhouse gas (GHG) emissions from transportation. Cellulosic feedstocks, optimized biorefineries, and favorable farming locations can significantly reduce biofuel carbon intensity (CI). Despite advances in field-to-fuel GHG monitoring and flexibility in resource allocation within biorefineries (e.g., governing net electricity production), rigid CI accounting procedures in current policies may limit CI responsiveness across candidate sites and processing facilities. Here, this work examines a hypothetical biomass-to-sustainable aviation fuel (SAF) pathway using miscanthus and alcohol-to-jet (i) to demonstrate how GHG accounting requirements drive estimates of biofuel CIs and (ii) to explore potential CI and financial implications of scenario-specific life cycle assessment (LCA). Results demonstrate that GHG accounting using the CFR/LCFS can reasonably account for distinct levels of net electricity production by a biorefinery, but only the CFR yields similar CI sensitivity to spatially explicit factors (feedstock CI, grid electricity CI) as scenario-specific LCA: most GHG accounting frameworks do not capture CI variation across candidate sites in the United States. Ultimately, this work demonstrates the importance of LCA methodological specifications in low carbon fuel policies and tax credits.

29 ENERGY PLANNING, POLICY, AND ECONOMY

Simulating Global Terrestrial Carbon and Nitrogen Biogeochemical Cycles With Implicit and Explicit Representations of Soil Microbial Activity

Abstract Nutrient limitation is widespread in terrestrial ecosystems. Accordingly, representations of nitrogen (N) limitation in land models typically dampen rates of terrestrial carbon (C) accrual, compared with C‐only simulations. These previous findings, however, rely on soil biogeochemical models that implicitly represent microbial activity and physiology. Here we present results from a biogeochemical model testbed that allows us to investigate how an explicit versus implicit representation of soil microbial activity, as represented in the MIcrobial‐MIneral Carbon Stabilization (MIMICS) and Carnegie‐Ames‐Stanford Approach (CASA) soil biogeochemical models, respectively, influence plant productivity, and terrestrial C and N fluxes at initialization and over the historical period. When forced with common boundary conditions, larger soil C pools simulated by the MIMICS model reflect longer inferred soil organic matter (SOM) turnover times than those simulated by CASA. At steady state, terrestrial ecosystems experience greater N limitation when using the MIMICS‐CN model, which also increases the inferred SOM turnover time. Over the historical period, however, warming‐induced acceleration of SOM decomposition over high latitude ecosystems increases rates of N mineralization in MIMICS‐CN. This reduces N limitation and results in faster rates of vegetation C accrual. Moreover, as SOM stoichiometry is an emergent property of MIMICS‐CN, we highlight opportunities to deepen understanding of sources of persistent SOM and explore its potential sensitivity to environmental change. Our findings underscore the need to improve understanding and representation of plant and microbial resource allocation and competition in land models that represent coupled biogeochemical cycles under global change scenarios.

54 ENVIRONMENTAL SCIENCES

Informed Investments in Clean Energy Technologies

Governments and companies face consequential decisions about allocating resources to the research, development, demonstration and deployment of energy technologies to meet environmental, economic and social goals. Here we discuss how research insights can inform and potentially improve these decisions to make effective use of limited resources and time in shaping the next-generation energy infrastructure. We outline three key research steps: forecasting technological change, relating investments to economic, social and environmental outcomes and informing decision-making processes. We recommend advances to address uncertainty as well as to make methods and results more practicable, emphasizing the importance of model validation, streamlining and interactivity. Progress has been made, yet further work is needed-for example, in the development of reduced-order, testable models and more comprehensive data collection. Overall, this research is beginning to inform decisions but could be adopted more widely by governments and the private sector to help support technological progress for energy affordability, equitable climate change mitigation, health benefits and other objectives.

29 ENERGY PLANNING, POLICY, AND ECONOMY

Used Nuclear Fuel Management Using the Next Generation System Analysis Model

The U.S. Department of Energy (DOE) is leading the National effort to manage the back end of the nuclear fuel cycle, encompassing the safe transportation, storage/staging, and/or eventual disposal of used nuclear fuel (UNF) and high-level radioactive waste. The Next Generation System Analysis Model (NGSAM) is DOE’s discrete-event, agent-based simulation tool designed to model the full life cycle of UNF from reactor discharge to final disposal. NGSAM supports the DOE Office of Spent Fuel and High-Level Waste Disposition by enabling a detailed, scenario-based analysis of logistics, infrastructure, and shipping strategies. NGSAM replaces legacy models with a modern, flexible platform built on Repast Simphony and enhanced by the Process Analysis Tool. NGSAM simulates the movement and interaction of individual fuel assemblies with system components such as canisters, casks, railcars, and facilities. The model integrates with the Java Transportation Operations Model to plan and execute transportation scenarios, supporting both constrained and unconstrained resource allocation. Key features include customizable allocation and acceptance algorithms, detailed facility-level operations, and a Quick Edit tool for rapid scenario adjustments. NGSAM supports multimodal transportation modeling (e.g. rail, road, barge) and provides comprehensive cost, schedule, and infrastructure data. NGSAM utilizes data from sources such as DOE’s STANDARDS UNF database and DOE’s Stakeholder Tool for Assessing Radioactive Transportation, while also allowing user-defined inputs for scenario customization. NGSAM enables stakeholders to evaluate complex UNF management strategies, assess system performance under varying assumptions, and inform decision making for future infrastructure investments. Its modular architecture and integration with other Integrated Waste Management System tools make it a critical asset for planning the safe and efficient disposition of the Nation’s growing UNF inventory.

Craig, Brian [Argonne National Laboratory (ANL)]

Popnet : computer vision based deep learning model for forecasting gridded population

Here, this study introduces Popnet, a deep learning model for forecasting 1 km-gridded populations, integrating U-Net, ConvLSTM, a Spatial Autocorrelation module and deep ensemble methods. Using spatial variables and population data from 2000 to 2020, Popnet predicts South Korea’s population trends by age groups (under 14, 15-64 and over 65) up to 2040. In validation, it outperforms traditional machine learning and state-of-the-art computer vision models. The output of this model discovered significant polarisation: population growth in urban areas, especially the capital region, and severe depopulation in rural areas. Popnet is a robust tool for offering significant insights to policymakers and related stakeholders about the detailed future population, which allows them to establish detailed, localised planning and resource allocations.

computer vision