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At least 19 records

Coarse-grained resource allocation modeling for decoding and rewiring microbial metabolism

Microbial metabolism is a complex, emergent system driven by the coordinated interplay of intricate and dynamic molecular processes. To elucidate cellular behavior and enable biotechnological applications, quantitative models that address the inherent complexity of metabolism have been developed from a resource allocation perspective. Here, we synthesize recent advances in coarse-grained resource allocation frameworks and their applications in understanding microbial physiology and guiding gene circuit design. Here, these frameworks reveal global regulatory constraints and predict cellular adaptation to nutrient and environmental changes. In addition, they enable the quantification of metabolic costs, the dissection of circuit–host interactions, and the development of strategies for burden mitigation. Collectively, these modeling frameworks provide a powerful platform for uncovering quantitative principles of microbial growth and engineering robust synthetic biological systems.

coarse-grained modeling

Recovery Simulator and Analysis Formulation: Mathematical Framework for Enhanced Resilience and Resource Allocation

This report introduces recovery simulator and analysis (RSA), a framework aimed at enhancing the resilience of electrical grids post-disruption. The RSA model leverages an optimization problem formulation that focuses on maximizing the load served (or optionally customers served) through a coordinated and cooptimized recovery of non-black start generation, transmission lines, feeders and substations subject to labor budget constraints. By integrating advanced linear programming techniques, the simulator selects efficient reocovery pathways, optimizing both short-term and long-term grid recovery strategies. The mathematical framework guides decision-making through a comprehensive evaluation of potential recovery actions, factoring in the trade-offs between labor constraints and load (or optionally customer) restoration efficacy. This enables grid operators to simulate diverse outage scenarios and delineate optimal recovery pathways, thereby prioritizing critical repair tasks and ensuring resource allocation is both economical and effective. The intended use case of RSA is to allow planners to explore many recovery scenarios quickly and determine assets most critical across a wide range of scenarios, and therefore strong candidates for hardening or additional investment. RSA might also be used in an operational setting, following a single event, for exploring efficient recovery pathways.

24 POWER TRANSMISSION AND DISTRIBUTION

The Myth of Fungible FTE: A Quantitative Assessment of Matrixed Resource Allocation

Matrix organizations allow scientific facilities to share specialized personnel across projects, operations, maintenance, and strategic initiatives. Nominal staffing allocations, however, may not capture the schedule consequences of fragmented individual commitments, limited access to specialist groups, and intermittent availability of key decision makers. We developed a stochas- tic, daily-time-step simulation of a hypothetical medium-sized accelerator-facility project com- prising sequential phases and parallel tasks. Each task requires role-specific work measured in FTE-days. Ordinary personnel may be unavailable because they contribute concurrently to other institutional activities, while designated key roles have independently specified daily un- availability probabilities. An organization-wide priority factor scales the number of people from each functional group who can effectively contribute to the project. It is interpreted as a composite proxy for project access and workforce fragmentation across competing commit- ments. We examined project completion time as a function of this factor and Project Lead unavailability using 100 Monte Carlo runs per condition. Increasing priority factor from 0.1 to 1.0 reduced median completion time from 1708.5 days (interquartile range 1681.5–1735.25) to 390 days (interquartile range 379–399). At priority factor = 0.1, increasing Project Lead unavailability from 0.5 to 0.9 increased median completion time from 1713.5 days (interquartile range 1691–1733.25) to 4,417 days (interquartile range 4271.75–4550.5). The model quantifies the commonly expected sensitivity of project schedules to fragmented resource commitments and limited coordination availability. Within this model, the results also indicate a possible threshold regime in which small increases in workforce availability yield only modest sched- ule improvements until sufficient capacity becomes accessible, after which project performance improves sharply. With further validation and calibration, this quantitative framework could support resource-allocation decisions during initial project planning and subsequent schedule rebaselining.

Bai, Mei [SLAC National Accelerator Laboratory (SL

Optimizing resource allocation in Miscanthus breeding via sparse testing designs for genomic prediction

Phenotyping high-biomass perennial crops is laborious and the rate of genetic gain in conventional perennial crop breeding programs is typically low. So, it is especially important to identify methods that produce efficiency gains in the breeding process. Miscanthus is a C4 perennial grass with favorable characteristics for producing biomass as a feedstock for biofuels and diverse bio-based products. Increasing biomass yield will increase profitability and environmental benefits, so it is a key target for Miscanthus breeding. In addition, the identification of well-adapted genotypes across a wide range of environmental conditions requires the establishment of multi-environment trials (METs). Sparse testing is a genomic prediction-based strategy that reduces the phenotyping costs in METs by selecting a subset of genotypes to evaluate in a subset of environments and then predicts the performance of the unobserved genotype-environment combinations. A Miscanthus sacchariflorus (MSA) population comprising 336 genotypes observed across three environments was analyzed implementing sparse testing designs. Three prediction models considering main effects (environments, genotypes, genomic) and interaction effects (genotype-by-environment; G×E interaction) were implemented for forecasting dry biomass yield (YDY), total culm (TCM), average internode length (AIL), and culm node number (CNN). Multiple calibration sets based on different compositions and sizes were considered to evaluate performance in terms of the predictive ability (PA) and the mean square error (MSE) for a fixed testing set size. The training set size ranged from 52 to 112 to predict a fixed set of 224 unobserved genotypes across all three environments. The results showed that the model accounting for G×E interaction consistently presented the highest PA and the lowest MSE: for CNN (PA: ~0.77, MSE: ~0.5) and YDY (PA: ~0.70, MSE: ~1.3) while for TCM and AIL these ranged from ~0.28 to 0.41 and ~1.3 to 4.3, respectively. Overall, varying training sets and allocation strategies did not affect PA and MSE, with 52 non-overlapping and 0 overlapping genotypes per environment as the optimal cost-effective allocation framework. This suggests that implementing sparse testing designs could significantly reduce phenotyping costs by fivefold, without compromising PA in breeding programs for perennial crops such as Miscanthus.

Miscanthus sacchariflorus (MSA)

Microbiome Adaptation Could Amplify Modeled Projections of Global Soil Carbon Loss With Climate Warming

Warming alters soil microbial traits through ecological and evolutionary processes, directly influencing the decomposition of organic matter, which significantly affects global soil carbon emissions. Yet, soil carbon models largely ignore these processes and their implications for global responses to warming. Here, we incorporate eco-evolutionary theory into a mechanistic model describing microbial soil carbon decomposition to address the question of whether such processes could have consequential effects on climate carbon feedbacks globally. We assume that a key trait of microbes, their resource allocation to production of exoenzymes (which facilitate decomposition of organic matter)—is optimized to environmental temperatures by natural selection. We find that eco-evolutionary optimization results in microbes allocating more resources to enzyme production under warming. When applied at the global scale, eco-evolutionary optimization enhances the biological realism of soil carbon models and significantly amplifies global soil carbon loss by 2100. Our results highlight the significant potential of microbial eco-evolutionary responses to influence carbon cycle feedbacks to climate change, and motivate an urgent need for more comprehensive data to accurately quantify the adaptive potential of microbiomes in response to climate change.

Biodiversity & Conservation

A sequential Attacker-Defender game for distribution systems resilience enhancement against extreme weather events

Improving distribution system resilience against frequent extreme weather events is important for reliable power system operations. Especially when dealing with events such as hurricanes that have short-term predictions, proactive pre-event preparedness plays a vital role in system resilience performance. In this paper, we propose a novel approach to construct pre-event resource allocation plans for system operators to cope with upcoming threats through a sequential attacker-defender game framework. The sequential attacker-defender game is designed to model the interaction between the extreme weather and the system operator. In each round of the game, the attacker and the defender sequentially update their current strategies by accounting for the opponent’s action set. The attacker model is formulated as a bi-level problem to identify the severe outage scenarios, and the defender model is formulated as a two-stage optimization problem to determine the allocation of restoration resources including mobile responsive resources and repair crews. Two scale-reduction strategies are proposed to ensure the scalability of the game scheme. Finally, case studies on the IEEE 33-bus and a 7149-node practical utility system validate the effectiveness of the proposed sequential game and the efficiency of the scale-reduction strategies.

24 POWER TRANSMISSION AND DISTRIBUTION

Decentralized Distributed Proximal Policy Optimization (DD-PPO) for High Performance Computing Scheduling on Multi-User Systems

Resource allocation in High Performance Computing (HPC) environments presents a complex and multifaceted challenge for job scheduling algorithms. Beyond the efficient allocation of system resources, schedulers must account for and optimize multiple performance metrics, including job wait time and system throughput. Traditional heuristic-based scheduling algorithms increasingly struggle and lack the efficiency needed to meet the demands and address the complexity and scale of modern HPC systems. Consequently, recent research efforts have focused on leveraging advancements in Artificial Intelligence (AI) and Deep Learning (DL), particularly Reinforcement Learning (RL), to develop more adaptable and intelligent scheduling strategies. Previous RL-based scheduling approaches have explored a range of algorithms, from Deep Q-Networks (DQN) to Proximal Policy Optimization (PPO), and more recently, hybrid methods that integrate Graph Neural Networks (GNNs) with RL techniques. However, a common limitation across these methods is their reliance on relatively small datasets, with few methods being evaluated using large-scale, multi-million-job trace datasets representative of real-world HPC workloads. Moreover, existing RL schedulers face scalability issues due to centralized policy updates, which hinder training efficiency and performance when applied to large datasets. This study introduces a novel RL-based scheduler utilizing Decentralized Distributed Proximal Policy Optimization (DD-PPO) algorithm, which supports large-scale distributed training across multiple workers without requiring parameter synchronization at every step. By eliminating reliance on centralized updates to a shared policy, the DD-PPO scheduler enhances scalability, training efficiency, and sample utilization. Experimental validation using a large real-world dataset containing over 11.5 million job traces collected from petascale HPC systems over six years assesses the influence of dataset scale on training effectiveness and compares DD-PPO performance to traditional and advanced scheduling approaches. The experimental results demonstrate improved scheduling performance in comparison to both heuristic-based schedulers and existing RL-based scheduling algorithms.

AI

Hybridization Assessment of Trybrid Pumped Storage Hydropower System—Part 1: A Case Study of Corral Summit

This report is a part of the deliverables for technical assistance provided to Cat Creek Energy for the Coral Summit Trybrid (Triple Hybrid-Pumped Storage Hydropower, Battery Energy Storage System, and photovoltaic solar energy) energy project. This report explores the operational benefits and challenges of hybridizing an open loop PSH (200MW) located at Mackay, Custer County, Idaho with solar PV (Ground mount 300MW and floating 40MW) and battery (720MWhr). This document reports two activities performed as a part of the hybridization assessment task 1) optimal resource allocation and energy management strategy, and 2) power quality and reliability assessment. From optimal resource allocation and energy management strategy (activity 1), the following key findings can be observed: • Conventional PSH (CPSH) with two reversible pump turbines and separate penstocks can provide required flexibility equivalent to that from two ternary PSH with separate penstock. With single unit CPSH, upper reservoir head cannot be maintained accurately, the variation of water level is rapid and pump mode flexibility is not available. These disadvantages can be overcome by single unit TPSH. However, using two CPSH units with separate penstocks also overcome these disadvantages with the formation of the hydraulic short circuit between two conventional units. • Flooding of the lower reservoir is a severe concern when considering continuous operation for black start. This limits the duration of continuous operation from PSH alone to around 50 hours. Due to the complementary PV and battery action, the duration of continuous operation and smooth power output can be extended. • An optimization problem is framed that maximizes the power output on an hourly basis while minimizing constraint violations and respecting seasonal variations of solar PV and load profiles . Two value streams, arbitrage and baseload generation are served by this profile. It was uncovered that for smooth power output during regular operation, PV curtailment will be required, or the battery capacity needs to be increased above 90MW to accommodate additional PV. From power quality and reliability assessment (activity 2) the following takeaway points can be observed: • The Trybrid, when integrated at the Lost River bus, and limited to 250MW in generation mode and -150MW in the pump mode, causes no violation of voltage or flow.

13 - HYDRO ENERGY

Queue wait time prediction in high performance computing (HPC) systems

High Performance Computing (HPC) systems are critical enablers for groundbreaking scientific research across various domains. Efficient resource allocation, facilitated by job scheduling, is paramount for maximizing the utilization of HPC systems. However, the variability in wait times for queued jobs poses challenges for users, necessitating accurate job wait time estimation. This paper explores the influence of job characteristics, including job size (the number of nodes requested and walltime), the queue to which the job is submitted and other resource requirements, on job wait times in leadership-class HPC systems. Focusing on the Theta Cray XC40 and Polaris machines at Argonne National Laboratory, the study evaluates the performance of different supervised learning algorithms in predicting job wait times. It also evaluates the impact of data preprocessing, including outlier detection, Principal Component Analysis (PCA), and feature selection, on the performance of wait time prediction models. The findings reveal insights into the relationship between job characteristics and wait times, offering a foundation for optimizing resource allocation and enhancing user experience. The methodologies and tools developed in this study are adaptable to other leadership-class HPC systems, providing a valuable contribution to the broader HPC community aiming to improve job scheduling efficiency and user satisfaction.

Okafor, Nwamaka

A Versatile Simulated Data Transport Layer for in Situ Workflows Performance Evaluation

In situ processing does not only allow scientific applications to face the explosion in data volume and velocity but also to address the time constraints of many simulation-analysis workflows by providing scientists with early insights about their applications at runtime. Multiple frameworks implement the concept of a data transport layer (DTL) to enable such in situ workflows. These tools are very versatile, directly or indirectly access the data generated on the same node, another node of the same compute cluster, or a completely distinct node, and allow data publishers and subscribers to run on the same computing resources or not. This versatility puts on researchers the onus of taking key decisions related to resource allocation and how to transport data to ensure the most efficient execution of their in situ workflows. However, domain scientists and workflow practitioners lack the appropriate tools to assess the respective performance of particular design and deployment options. In this paper we introduce a versatile simulated DTL designed to provide researchers with insights on the respective performance of different execution scenarios of in situ workflows. This open-source, standalone library builds on the SimGrid toolkit and can be linked to any SimGrid-based simulator. It facilitates the evaluation of the performance behavior, at scale, of different data transport configurations and the study of the effects of resource allocation strategies. We demonstrate the scalability, versatility, and accuracy of this simulated DTL by reproducing the execution of two synthetic benchmarks and of a real-world in situ workflow composed of an MPI application and a parallel data analysis. Results of simulations run on a single core show that the proposed library can simulate the interactions of tens of thousands of simulated processes deployed on two interconnected commodity clusters in a few seconds, and the execution by a thousand simulated processes of an in situ workflow in less than three minutes.

Suter, Fred [ORNL] (ORCID:0000000319021955)

Tactical Analysis for Calculating Contextual Risk at Boundaries: Summary of Laboratory Directed Research & Development Effort

The Tactical Analysis for Calculating Contextual Risk at Boundaries (TACCRAB) tool is an innovative digital twin (DT) platform and automated risk algorithm designed to transform operational decision-making in structured screening environments, with an initial focus on Southern Border Land Ports of Entry (POEs). The invention provides integration points for advanced artificial intelligence, predictive modeling, and real-time data analysis to produce a comprehensive risk management tool that enables proactive, data-informed security strategies. The core inventive features of TACCRAB center on its unique risk algorithm, which dynamically calculates contextual risk by synthesizing historical data, near real-time streaming data from the checkpoints themselves, and AI-generated predictions. Unlike traditional risk assessment methods, TACCRAB utilizes a DT to provide comprehensive operational insights, allowing stakeholders to visualize, simulate, and optimize checkpoint configurations with unprecedented speed and contextual awareness. TACCRAB's key innovation lies in its ability to combine multiple complex inputs - including technology detection probabilities, resource availability, screening pathway characteristics, and threat actor behavioral patterns - into a unified risk calculation and update these inputs based on changing operational and environmental conditions. By leveraging a DT that continuously updates and learns from linked data, TACCRAB can suggest adaptive mitigation strategies that minimize risk while maintaining operational efficiency. Particularly novel is the platform's approach to decision support, which goes beyond static risk assessment. The DT provides dynamic metrics such as wait times, resource allocation effectiveness, and potential emerging threat scenarios, enabling users to view sophisticated, relevant what-if simulations and optimize checkpoint operations in near real-time. The system's architecture allows for generalized application across different screening environments, such as secure facilities, ports of entry, and soft targets, making it a versatile tool for security and operational management. The invention distinguishes itself through its comprehensive integration of predictive modeling, AI-driven pattern discovery, and user-friendly interface design. By combining these elements, TACCRAB transforms complex risk data into actionable insights, supporting decision-makers at various organizational levels - from booth agents making split-second screening decisions to checkpoint managers optimizing the day's resource allocation to strategic planners managing long-term investments.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF

Data for 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. 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.

Miscanthus

From Bricks to Clicks: Mapping the White Space in Building Innovation

It is a critical national imperative to transform the buildings sector, yet innovation is impeded by deployment failures that leave promising technologies stranded. Conventional market reports and techno-economic analysis provide an insufficient understanding of markets and resource allocation for emerging building technologies. They omit crucial commercialization factors such as ecosystem maturity and adoption friction, where the coordinated participation of a network of suppliers, contractors, financiers, regulators, and integrators is required to scale solutions. This study addresses these gaps by introducing an evaluation framework grounded in front-line data from six years of the DOE's IMPEL incubator, comprising experience from 300 building-sector innovators and the adjacent, complex ecosystem. Our methodology synthesizes top-down market analysis with bottom-up, practitioner-level data across five megatrends: (M1) Affordable materials and industrialized construction; (M2) Healthy and efficient mechanical systems; (M3) Intelligent building operations; (M4) Buildings as grid assets; and (M5) High-density power and cooling for data centers and therein identify twelve "white space" technology opportunities. Next, we develop a multi-criteria scoring rubric to rank these opportunities based on parameters, i.e., Affordability, Quality of Life, Reliability, and Security, yielding composite ‘Demand’ and ‘Maturity’ indices. Our results indicate that the most significant white spaces may not be incremental products but a new class of ‘Ecosystem Enablers’, such as logistics platforms, orchestration layers, and automated compliance software that solve structural deployment gaps. This paper summarizes this transparent, evidence-based, practitioner-informed evaluation framework for policymakers and investors to re-evaluate policy and resource allocation and unlock scalable market transformation.

Singh, Reshma

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

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)