An Automated Model Test System for Systematic Development and Improvement of Gene Expression Models
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Biochemistry & Molecular Biology↗
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Data-driven compact photocurrent models: A system identification approach for non-intrusive reduced order modeling of dose-rate induced photocurrents.
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Bochev, Pavel B.↗
Quantifying CanESM5 and EAMv1 sensitivities to Mt. Pinatubo volcanic forcing for the CMIP6 historical experiment
Large volcanic eruptions reaching the stratosphere have caused marked perturbations to the global climate including cooling at the Earth's surface, changes in large-scale circulation and precipitation patterns and marked temporary reductions in global ocean heat content. Many studies have investigated these effects using climate models; however, uncertainties remain in the modelled response to these eruptions. This is due in part to the diversity of forcing datasets that are used to prescribe the distribution of stratospheric aerosols resulting from these volcanic eruptions, as well as uncertainties in optical property derivations from these datasets. To improve this situation for the sixth phase of the Coupled Model Intercomparison Project (CMIP6), a two-step process was undertaken. First, a combined stratospheric aerosol dataset, the Global Space-based Stratospheric Aerosol Climatology (GloSSAC; 1979–2016), was constructed. Next, GloSSAC, along with information from ice cores and Sun photometers, was used to generate aerosol distributions, characteristics and optical properties to construct a more consistent stratospheric aerosol forcing dataset for models participating in CMIP6. This “version 3” of the stratospheric aerosol forcing has been endorsed for use in all contributing CMIP6 simulations. Recent updates to the underlying GloSSAC from version 1 to version 1.1 affected the 1991–1994 period and necessitated an update to the stratospheric aerosol forcing from version 3 to version 4. As version 3 remains the official CMIP6 input, quantification of the impact on radiative forcing and climate is both relevant and timely for interpreting results from experiments such as the CMIP6 historical simulations. This study uses two models, the Canadian Earth System Model version 5 (CanESM5) and the Energy Exascale Earth System Model (E3SM) Atmosphere Model version 1 (EAMv1), to estimate the difference in instantaneous radiative forcing in simulated post-Pinatubo climate response when using version 4 instead of version 3. Differences in temperature, precipitation and radiative forcings are generally found to be small compared to internal variability. An exception to this is differences in monthly temperature anomalies near 24 km altitude in the tropics, which can be as large as 3 °C following the eruption of Mt. Pinatubo.
58 GEOSCIENCES↗
Investigating coastal backwater effects and flooding in the coastal zone using a global river transport model on an unstructured mesh
Abstract. Coastal backwater effects are caused by the downstream water level increase as a result of elevated sea level, high river discharge and their compounding influence. Such effects have crucial impacts on floods in densely populated regions but have not been well represented in large-scale river models used in Earth system models (ESMs), partly due to model mesh deficiency and oversimplifications of river hydrodynamics. Using two mid-Atlantic river basins as a testbed, we perform the first attempt to simulate the backwater effects comprehensively over a coastal region using the MOSART river transport model under an ESM framework, i.e., Energy Exascale Earth System Model (E3SM) configured on a regionally refined unstructured mesh, with a focus on understanding the backwater drivers and their long-term variations. By including sea level variations at the river downstream boundary, the model performance in capturing backwaters is greatly improved. We also propose a new flood event selection scheme to facilitate the decomposition of backwater drivers into different components. Our results show that while storm surge is a key driver, the influence of extreme discharge cannot be neglected, particularly when the river drains to a narrow river-like estuary. Compound flooding, while not necessarily increasing the flood peaks, exacerbates the flood risk by extending the duration of multiple coastal and fluvial processes. Furthermore, our simulations and analysis highlight the increasing strength of backwater effects due to sea level rise and more frequent storm surge during 1990–2019. Thus, backwaters need to be properly represented in ESMs to improve the predictive understanding of coastal flooding.
54 ENVIRONMENTAL SCIENCES↗
Performance and Accuracy Implications of Parallel Split Physics-Dynamics Coupling in the Energy Exascale Earth System Atmosphere Model
Simultaneous calculation of atmospheric processes is faster than calculating processes one at a time. This type of parallelism is beneficial or perhaps even necessary to provide good performance on modern supercomputers, which achieve faster performance through increased processor count rather than improved clock speed. The scalability of the Energy Exascale Earth System Model (E3SM) Atmosphere Model (EAM) is limited by the fluid dynamics which scales up to the number of mesh cells in the global mesh. In contrast, the suite of physics parameterizations in EAM is scalable up to the total number of physics columns, which is an order of magnitude greater than the number of mesh cells. A proposed solution to unlocking the greater potential performance from the physics suite is to solve the physics and dynamics in parallel. This work represents a first attempt at parallel splitting of the grid-scale fluid dynamics model and the subgrid-scale physics parameterizations in a global atmosphere model. We will demonstrate that switching to parallel physics-dynamics coupling extends the scalability of the EAM to up to 3 times the previous peak scalability limit and is up to 20% faster than the sequentially split coupling at the highest core counts and the same time step. Decadal simulations of both coupling approaches show very little impact to the model climate. This improved performance does not come without drawbacks, however. Parallel splitting requires a shorter time step and other modifications which largely offset performance gains. A mass fixer is required for conservation. Techniques for mitigating these issues are also discussed.
97 MATHEMATICS AND COMPUTING↗
Tracking Improvement in Simulated Marine Biogeochemistry Between CMIP5 and CMIP6
The changes or updates in ocean biogeochemistry component have been mapped between CMIP5 and CMIP6 model versions, and an assessment made of how far these have led to improvements in the simulated mean state of marine biogeochemical models within the current generation of Earth system models (ESMs). The representation of marine biogeochemistry has progressed within the current generation of Earth system models. However, it remains difficult to identify which model updates are responsible for a given improvement. In addition, the full potential of marine biogeochemistry in terms of Earth system interactions and climate feedback remains poorly examined in the current generation of Earth system models. Increasing availability of ocean biogeochemical data, as well as an improved understanding of the underlying processes, allows advances in the marine biogeochemical components of the current generation of ESMs. The present study scrutinizes the extent to which marine biogeochemistry components of ESMs have progressed between the 5th and the 6th phases of the Coupled Model Intercomparison Project (CMIP).
54 ENVIRONMENTAL SCIENCES↗
The Polar System Analysis Package (Ver. 1 Specifications)
The Polar System Analysis Package (POLeSTAr) is a modern data fusion tool being designed to benchmark,evaluate and compare the polar physics and biogeochemistry of Earth System Models (ESMs). It is being written in Python to make use of libraries including Xarray, Matplotlib, SciPy, NumPy and PyTorch within algorithms developed specifically for polar system modeling. Initial POLeSTAr algorithms will be adapted from the MATLAB Ridgepack package that was designed to analyze the Model for Prediction Across Scales (MPAS) sea ice component of the Energy Exascale Earth System Model (E3SM) and sea ice model CICE within the Community Earth System Model (CESM).
97 MATHEMATICS AND COMPUTING↗
National Center for Airborne Laser Mapping (NCALM) LiDAR and DEM data from two NGEE Arctic Sites, Seward Peninsula, Alaska, Winter 2022
From April 3 through April 6 of 2022, airborne remote sensing data was collected by the National Center for Airborne Laser Mapping (NCALM) in collaboration with NGEE Arctic scientists. Snow-on data was collected around two NGEE Arctic study sites on the Seward Peninsula of Alaska: Teller mm 27 and Kougarok mm 64. A Robinson R44 II helicopter with a RIEGL VQ-580 II airborne laser scanner was used to collect the LiDAR point cloud data for each study site. This survey was conducted during expected peak snow cover at the end of the winter on the Seward Peninsula, and can be paired with data collected in 2021 during the snow-off campaign "National Center for Airborne Laser Mapping (NCALM) LiDAR, Imagery, and DEM data from five NGEE Arctic Sites, Seward Peninsula, Alaska, August 2021" (Singhania et al., 2023) (NGA270). This data package contains LiDAR point clouds (.las), Digital Elevation Models (.tif), and shapefiles of the .las tiling system (.shp). A project report detailing data collection details, GNSS stations and GNSS corrections, and processing steps is also included. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).
54 ENVIRONMENTAL SCIENCES↗
Simulation process and data flow for a large system dynamics model
This paper documents the workflow and supporting technologies that a large system dynamics model, the biomass scenario model, employs to streamline the data preparation, simulation, quality control, and analysis process at the National Renewable Energy Laboratory. The workflow centers on automation of routine aspects of the flow of data between data stores, simulations, and visualizations. It enforces quality checks on data, reproducibility of computations, and traceability of results, while maintaining complete archives of modeling and analysis artifacts. The resulting frictionless simulation/analysis environment supports large-scale sensitivity analysis, interactive creation of ensembles of simulations, and rapid visualization-based exploration of simulation results.
09 BIOMASS FUELS↗
Particle Receiver Models for Systems Analysis
Particle receivers are gaining importance in the field of Concentrating Solar Power (CSP) due to the high temperature that particles can achieve without degradation. Several researchers are studying the potential of this technology by means of system analyses, which need simple and light models of the system. This study presents two simple models for the particle receiver. The simplest model is a correlation obtained by fitting the results calculated with a more complex receiver model simulated in CFD. The other model is a 1D model, which is benchmarked against the same CFD results. Although both models achieve high coefficient of determination, R2, when compared to CFD results, the 1D model seems to provide more accurate results (especially during sunsets and sunrises). Both models are integrated into a tecno-economic model developed in previous work. The LCOE obtained with the 1D model is between 7% and 10% greater than the one obtained with the correlation.
González-Portillo, Luis F. (ORCID:0000000348643825↗
Capturing Historic Reliability Performance Through Graph Databases: A Model Based System Engineering Approach
With the goal of improving the performance and reliability of high dependable technological systems such as nuclear power plants, advanced monitoring and health management systems are employed to inform system engineers on observed degradation processes and anomalous behaviors of assets and components. This information is captured in the form of large amount of data which can be heterogenous in nature (e.g., numeric, textual). Such large data availability poses challenges when system engineers are required to parse and analyze them in order to track historic reliability performance of assets and components. This paper tackles directly this challenge by providing means to organize data in the form of a graph: a knowledge graph. The presented approach distinguish itself from current knowledge graph-based methods by the fact that model-based system engineering (MBSE) models are used to “put data into context”. In particular, MBSE models are used as skeleton of a knowledge graph; numeric and textual data elements, once processed, are associated to MBSE model elements. Thus, a knowledge graph captures both system architecture (though MBSE models) and health/performance data. Such feature opens the door to new data analytics methods designed to identify causal relations between observed phenomena.
97 - MATHEMATICS AND COMPUTING↗
Data-Enabled Predictive Control for Building HVAC Systems
Model predictive control is widely used as a control technology for the computation of optimal control inputs of building heating, ventilating, and air conditioning (HVAC) systems. However, both the benefits and widespread adoption of model predictive control (MPC) are hindered by the effort of model creation, calibration, and accuracy of the predictions. In this paper, we apply the data-enabled predictive control (DeePC) algorithm for designing controls for building HVAC systems. The algorithm solely depends on input/output data from the system to predict future state trajectories without the need for system identification. The algorithm relies on the idea that a vector space of all input–output trajectories of a discrete-time linear time-invariant (LTI) system is spanned by time-shifts of a single measured trajectory, given the input signal is persistently exciting. Closed-loop simulations using EnergyPlus are performed to demonstrate the approach. The simulated building modeled in EnergyPlus is a modified commercial large office prototype building served by an air handling unit-variable air volume HVAC system. Temperature setpoints of zones are used as control variables to minimize the HVAC energy cost of the building considering a time-of-use electricity rate structure. Furthermore, sensitivity analysis is conducted to gain insights into the effect of parameter tuning on DeePC performance. Simulation results are used to illustrate the performance of the algorithm and compare the algorithm with model-based MPC and occupancy-based setpoint controller. Overall, DeePC achieves similar performance compared to MPC for lower engineering effort.
32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
Disentangling the Effects of Vapor Pressure Deficit and Soil Water Availability on Canopy Conductance in a Seasonal Tropical Forest During the 2015 El Niño Drought
In land models used in Earth system models, vegetation water stress is heuristically related to soil water matric potential, and root water uptake in soil layers is simply proportional to root density to meet the transpiration demand. The efficiency of roots utilizing deeper soil water under water stress cannot be well represented, but it is of critical importance for transpiration regulation and carbon flux. To improve modeling of tropical forest response to drought, a plant hydrodynamic scheme (HYDRO), adapted from a trait-based model in the Functionally Assembled Terrestrial Ecosystem Simulator (FATES), has been implemented in the Energy Exascale Earth System Model (E3SM) Land Model (ELM) to represent the hydraulic dynamics and root water uptake strategy. The adapted model conforms to the big-leaf photosynthesis model in ELM. Vegetation water stress in the model is a function of prognostic leaf water potential and is used to regulate stomatal conductance. Point simulations were performed at two tropical forest sites in the Amazon and Panama. Model sensitivity to the numerical solver, plant hydraulic traits, soil properties, and atmospheric forcing has been evaluated. Our results showed that, even though water stress factors calculated at our study sites using HYDRO are comparable to that simulated by the heuristic water stress model, soil moisture prediction is improved with soil water redistributions through roots. Simulated results using HYDRO is not as sensitive to plant hydraulic traits measured for different tree species as to the soil properties and atmospheric forcing. Simplified numerical solver may cause inaccuracy as to where roots uptake water. This study suggests that plant hydrodynamic representation is critical for improved simulations of soil moisture under water stresses.
54 ENVIRONMENTAL SCIENCES↗
Targeted alpha therapy in a systemic mouse model of prostate cancer - a feasibility study
225 Ac-PSMA-617 targeted-therapy has demonstrated efficacy in 75-85% of patients; however, responses are not durable. We aimed to establish translatable mouse models of disseminated prostate cancer (PCa) to evaluate effectiveness of 225 Ac-PSMA-617 at various disease stages. Methods: C4-2, C4-2B, or 22Rv1 cells were injected into the left ventricle of male NSG mice. Disease progression was monitored using bioluminescence imaging (BLI). For treatment, mice were injected with 40 kBq 225 Ac-PSMA-617 at one (early treatment cohort) or three weeks (late treatment cohort) post-inoculation. Treatment efficacy was monitored by BLI of whole-body tumor burden. Mice were sacrificed based on body conditioning score. Results: C4-2 cells yielded metastases in liver, lungs, spleen, stomach, bones, and brain - achieving a clinically relevant model of widespread metastatic disease. The disease burden in the early treatment cohort was stable over 27 weeks in 5/9 mice and progressive in 4/9 mice. These mice were sacrificed due to brain metastases. Median survival of the late treatment cohort was superior to controls (13 vs. 7 weeks; p<0.0001) but inferior to that in the early treatment cohort (13 vs. 27 weeks; p<0.001). Late cohort mice succumbed to extensive liver involvement. The 22Rv1 and C4-2B systemic models were not used for treatment due to high kidney metastatic burden or low take rate, respectively. Conclusion: C4-2 cells reproduced metastatic cancer spread most relevantly. Early treatment with 225 Ac-PSMA-617 prevented liver metastases and led to significant survival benefit. Late treatment improved survival without reducing tumor burden in the liver, the main site of metastasis. The current findings suggest that early 225 Ac-PSMA-617 intervention is more efficacious in the setting of widespread metastatic PCa.
38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
Education for PV Modeling Professionals: Observations from the 2025 PVPMC Workshop
We surveyed professionals in the photovoltaic industry to understand interests in education and training for performance modeling of solar power systems. We found that most professionals are self-taught and rely on a variety of public sources of technical materials. Available formal education, such as courses or certification programs, either lacks detail or is focused on software user training. Responses indicate several opportunities to create public resources that would benefit professional learning for solar power system modeling: • Create a glossary of terms and common variable names. • Develop guidance on uncertainty analysis in the context of solar power systems modeling. • Assemble a catalog of available educational materials and data sources.
14 SOLAR ENERGY↗
Soft matter roadmap
Soft materials are usually defined as materials made of mesoscopic entities, often self-organised, sensitive to thermal fluctuations and to weak perturbations. Archetypal examples are colloids, polymers, amphiphiles, liquid crystals, foams. The importance of soft materials in everyday commodity products, as well as in technological applications, is enormous, and controlling or improving their properties is the focus of many efforts. From a fundamental perspective, the possibility of manipulating soft material properties, by tuning interactions between constituents and by applying external perturbations, gives rise to an almost unlimited variety in physical properties. Together with the relative ease to observe and characterise them, this renders soft matter systems powerful model systems to investigate statistical physics phenomena, many of them relevant as well to hard condensed matter systems. Understanding the emerging properties from mesoscale constituents still poses enormous challenges, which have stimulated a wealth of new experimental approaches, including the synthesis of new systems with, e.g. tailored self-assembling properties, or novel experimental techniques in imaging, scattering or rheology. Theoretical and numerical methods, and coarse-grained models, have become central to predict physical properties of soft materials, while computational approaches that also use machine learning tools are playing a progressively major role in many investigations. This Roadmap intends to give a broad overview of recent and possible future activities in the field of soft materials, with experts covering various developments and challenges in material synthesis and characterisation, instrumental, simulation and theoretical methods as well as general concepts.
36 MATERIALS SCIENCE↗
Data Files for Runoff Evaluation in an Earth System Land Model for Permafrost Regions
Modeling of hydrological runoff is essential for accurately capturing spatiotemporal feedbacks within the land–atmosphere system, particularly in sensitive regions such as permafrost landscapes. However, substantial uncertainties persist in the terrestrial runoff parameterization schemes used in Earth system and land surface models. This is particularly true in permafrost regions, where landscape heterogeneity is high and reliable observational data are scarce.This data set includes all files that were produced and applied in the paper Runoff Evaluation in an Earth System Land Model for Permafrost Regions [Xiang et al. in review]. The paper is in review as of July 1 2025 in Geoscientific Model Development (GMD). In this study, we evaluate the performance of runoff parameterization schemes in the Energy Exascale Earth System Model (E3SM) land model (ELM). Our proposed framework leverages simulation results from the Advanced Terrestrial Simulator (ATS), which is a physics-rich integrated surface/subsurface hydrologic model that has been successfully evaluated previously in Arctic tundra regions. We used ATS to simulate runoff from 22 representative hillslopes in the Sagavanirktok River basin, located on the North Slope of Alaska, then compared the output with ELM’s parameterized representation of total runoff. This dataset contains 2 figure image files (*.png, *jpg) that describe the study site and methods, as well as folders (Figure*.zip) that contain the associated data files (*.csv, *.dat) and python code notebooks (*.ipynb) for figures 3-7 in the paper. Jupyter notebook (*.ipynb) files that produce the figure files using the associated data files will run within a python environment configured with Jupyter Lab or Notebook packages.
54 ENVIRONMENTAL SCIENCES↗
A propagation-based fault detection and discrimination method and the optimization of sensor deployment
Industrial processes can be affected by faults having a serious impact on operation when not promptly detected and diagnosed. Here in this paper, a propagation-based fault detection and discrimination(PFDD) method is proposed to develop a strategy for fault diagnosis while in the design phase of a system. The PFDD method constructs the system model using the Integrated System Fault Analysis(ISFA) technique. Based on the system model, the propagation of hardware and software faults are simulated qualitatively. Given the results of the simulation, the process by which a fault propagates can be characterized using the qualitative features of system variables including the deviation of the system variables from their expected values, the variation of the system variables over time, and the order in which each variable is influenced during the propagation of the fault. The strategy by which a fault can be detected and discriminated is defined using those features. The PFDD method supports the detection and discrimination of faults in both steady states and transient states. Based on the PFDD method, the optimization of sensor deployment in a system is discussed. A brute force algorithm is developed to examine the system’s capability at diagnosing faults and the cost of sensor deployment for all possible configurations of sensors. The optimal sensor deployment strategy can be derived accordingly. However, the brute force method is only applicable to small-scale systems due to its high computational cost. A genetic algorithm is used to optimize sensor deployment in large-scale systems. The PFDD and sensor deployment optimization methods are applied to the Experimental Breeder Reactor II (EBR-II) for verification.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗