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At least 757 records · Page 42
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Bottom-Up Meets Top-Down: The Crossroads of Multiscale Chromatin Modeling

Chromatin can be viewed as a hierarchically structured fiber that regulates gene expression. It consists of a complex network of DNA and proteins whose characteristic dynamical modes facilitate compaction and rearrangement in the cell nucleus. These modes stem from chromatin's fundamental unit, the nucleosome, and their effects are propagated across length scales. Understanding the effects of nucleosome dynamics on the chromatin fiber, primarily through post-translational modifications that occur on the histones, is of central importance to epigenetics. Within the last decade, imaging and chromosome conformation capture techniques have revealed a number of structural and statistical features of the packaged chromatin fiber at a hitherto unavailable level of resolution. Such experiments have led to increased efforts to develop polymer models that aim to reproduce, explain, and predict the contact probability scaling and density heterogeneity. At nanometer scales, available models have focused on the role of the nucleosome and epigenetic marks on local chromatin structure. At micrometer scales, existing models have sought to explain scaling laws and density heterogeneity. Less work, however, has been done to reconcile these two approaches: bottom-up and top-down models of chromatin. Here, we highlight the multiscale simulation models that are driving toward an understanding of chromatin structure and function, from the nanometer to the micron scale, and we highlight areas of opportunity and some of the prospects for new frameworks that bridge these two scales. Taken together, experimental and modeling advances over the last few years have established a robust platform for the study of chromatin fiber structure and dynamics, which will be of considerable use to the chromatin community in developing an understanding of the interplay between epigenomic regulation and molecular structure.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Performance of sweeping gas membrane distillation for treating produced water: Modeling and experiments

Membrane distillation (MD) has shown promise for desalination of produced water (PW), but there are very few studies reported on the performance of MD with real PW and the characteristics of the fouling and scaling in MD. Among different MD configurations, sweeping gas MD (SGMD) is the least studied configuration. Here we report the application of SGMD for treating high-salinity PW (123 g L -1 ). The SGMD operating conditions were first carefully optimized through pure water MD experiments by varying operating conditions. The flux evaluation was accompanied by a detailed Aspen Custom Modeler simulation based on the electrolyte-NRTL thermodynamic model to better understand the heat and mass transfer in the feed and permeate channel. Supported by experiments, modeling results confirmed the partial condensation of the vapor in the permeate channel. Furthermore, it was concluded that the saturation of the sweeping gas is controlling the overall mass transfer through the membrane. Selected membranes and optimized conditions were then used to conduct short-term and long-term performance tests with PW. In long-term MD test, the concentration of the PW increased by a factor of two (50% water recovery), while the membrane exhibited small flux decline. Elemental analysis showed that strontium and sodium were the major scalant compounds.

42 ENGINEERING↗
DOE OSTI2024

Automated Calibration of Parallel and Distributed Computing Simulators: A Case Study

Many parallel and distributed computing research results are obtained in simulation, using simulators that mimic real-world executions on some target system. Each such simulator is configured by picking values for parameters that define the behavior of the underlying simulation models it implements. The main concern for a simulator is accuracy: simulated behaviors should be as close as possible to those observed in the real-world target system. This requires that values for each of the simulator's parameters be carefully picked, or “calibrated,” based on ground-truth real-world executions. Examining the current state of the art shows that simulator calibration, at least in the field of parallel and distributed computing, is often undocumented (and thus perhaps often not performed) and, when documented, is described as a labor-intensive, manual process. In this work we evaluate the benefit of automating simulation calibration using simple algorithms. Specifically, we use a real-world case study from the field of High Energy Physics and compare automated calibration to calibration performed by a domain scientist. Our main finding is that automated calibration is on par with or significantly outperforms the calibration performed by the domain scientist. Furthermore, automated calibration makes it straightforward to operate desirable tradeoffs between simulation accuracy and simulation speed.

Mc donald, Jesse↗
DOE OSTI2022

Multi-modelling predictions show high uncertainty of required carbon input changes to reach a 4‰ target

Soils store vast amounts of carbon (C) on land, and increasing soil organic carbon (SOC) stocks in already managed soils such as croplands may be one way to remove C from the atmosphere, thereby limiting subsequent warming. The main objective of this study was to estimate the amount of additional C input needed to annually increase SOC stocks by 4‰ at 16 long-term agricultural experiments in Europe, including exogenous organic matter (EOM) additions. We used an ensemble of six SOC models and ran them under two configurations: (1) with default parametrization and (2) with parameters calibrated site-by-site to fit the evolution of SOC stocks in the control treatments (without EOM). We compared model simulations and analysed the factors generating variability across models. The calibrated ensemble was able to reproduce the SOC stock evolution in the unfertilised control treatments. We found that, on average, the experimental sites needed an additional 1.5 ± 1.2 Mg C ha -1 year -1 to increase SOC stocks by 4‰ per year over 30 years, compared to the C input in the control treatments (multi-model median ± median standard deviation across sites). That is, a 119% increase compared to the control. While mean annual temperature, initial SOC stocks and initial C input had a significant effect on the variability of the predicted C input in the default configuration (i.e., the relative standard deviation of the predicted C input from the mean), only water-related variables (i.e., mean annual precipitation and potential evapotranspiration) explained the divergence between models when calibrated. Here, our work highlights the challenge of increasing SOC stocks in agriculture and accentuates the need to increasingly lean on multi-model ensembles when predicting SOC stock trends and related processes. To increase the reliability of SOC models under future climate change, we suggest model developers to better constrain the effect of water-related variables on SOC decomposition.

4 per 1000 initiative↗
DOE OSTI2025

Snow Depth Datasets for Snodgrass Catchment, Colorado, Water Year 2022-2023

This data package presents snow depths data from distributed temperature probes at 18 locations near Snodgrass catchment, Colorado. These data show that snow melt-out dates are approximately one or two weeks later under evergreen forests compared to other vegetation types even at the same elevation. These data were collected to understand how snowmelt heterogeneity impacts headwater hydrology, including streamflow and groundwater levels. They were also used to compare with process-based model simulations of snow depth to evaluate whether the model accurately represents snowmelt dynamics and their effects on headwater hydrology. Snow_DTPs_locations.csv includes all probes locations and their associated elevation and vegetation types. Snow_Depth_Snodgrass_WY2022_2023.csv includes processed snow depths datasets for Water Year (WY) 2022 and 2023. This dataset also includes a file-level metadata (flmd.csv) file that lists each file contained in the dataset with associated metadata and a data dictionary (dd.csv) file that contains column/row headers used throughout the files along with a definition, units, and data type. Several probes have recordings for WY 2021.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Wabash CarbonSAFE Static and Dynamic Modeling: Task 9.0 (Technical Report)

The objective of the Wabash CarbonSAFE project’s static and dynamic modeling task is to assess the feasibility of storing 50 million tonnes (1.67 million metric tonnes annually; MMTA) of industrially-sourced carbon dioxide (CO 2 ) in a commercial-scale geological storage complex at Wabash Valley Resources LLC (WVR) gasification facility near Terre Haute, Indiana over a period of 30 years. The targeted formations for storing CO 2 are: 1) Mt. Simon Sandstone (MSS) and the 2) Potosi Dolomite (Knox Group). All of the available data from the recently drilled Wabash #1 stratigraphic test well (now plugged and abandoned) were used in the construction of both the static and dynamic models. Geologic models were constructed to characterize both the Mt. Simon Sandstone and Potosi Dolomite storage complexes. Dynamic simulation models were constructed and used to assess the feasibility of injecting CO 2 into the Mt. Simon and Potosi formations. The geocellular models for the Potosi Dolomite and Mt. Simon Sandstone were built using Petrel™, Schlumberger’s reservoir modeling software. The dynamic simulations were run using Landmark’s Nexus ® reservoir simulation software.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2025

A simulation pipeline for fast neutron imaging and spectroscopy using quantified detector attributes

Radiation imaging capabilities, essential in the nuclear nonproliferation regime, facilitate source localization and, in certain cases, spectroscopy. Scatter-based neutron cameras, which can measure the neutron signatures from special nuclear material, hold particular interest. Systems incorporating organic scintillators can extract neutron energy spectra, potentially distinguishing fission neutron sources from others, such as alpha-neutron sources. The development and testing of a scatter-based neutron imager, however, can be challenging without having an accurate simulation model or first constructing a prototype. This work describes a simulation pipeline that takes output from MCNPX-PoliMi simulations and creates the expected back-projection neutron images and neutron energy spectra. This pipeline was developed to improve the modeling of fast neutron imagers and bridge the current gap in literature, which predominantly focuses on gamma-ray Compton imager models. This work also reports on the significance of various real-world system considerations and their effects on the simulated detector responses. The pipeline was verified and validated with experimental data collected using a 252 Cf spontaneous fission source using a fast neutron scattering imager developed at the University of Michigan.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2020

Development and Evaluation of Occupancy-Aware Model Predictive Control for Residential Building Energy Efficiency and Occupant Comfort

The residential sector accounts for 25% of global primary energy consumption. Two methods have previously been proposed to reduce residential energy use associated with the provision of occupant thermal comfort: 1. Occupancy-based HVAC control, operating systems only during confirmed occupancy, and 2. model predictive control (MPC), harnessing a mathematical model and forecasts to find optimal operating strategies. Previous studies estimate the average energy savings of the two methods individually in the range of 21% and 16%, respectively. The research presented herein was carried out to evaluate the energy savings potential in residential buildings by combining both approaches across different climates, house vintages, and occupancy patterns. Occupancy and eight different physical modalities (e.g. CO2 and VOC) data were collected from five homes for time periods of 4–9 weeks. Collected data sets were used to train occupancy prediction models suggested by an extensive literature survey of occupancy model types. The trained prediction models were combined with MPC and detailed EnergyPlus building simulation models to evaluate residential building performance in terms of annual energy savings and thermal comfort, along with discomfort exceedance metrics. Multiple home types and regions were analyzed to understand regional and climate-dependent potential. Based on actual field data, the occupancy models had a prediction inaccuracy between 8% and 35% across the investigated homes. Average occupancy for the collected data ranged from 56% to 86%, a typical range reported in the literature. Building simulations were conducted for three control scenarios: conventional thermostatic control, occupancy-based, and occupancy-based MPC. The results indicate that all advanced strategies improve upon the conventional control, with some scenarios cutting energy use in half with only occasional incurrence of discomfort. The findings indicate that occupancy-aware model predictive residential building control has the potential to drastically reduce energy use and associated emissions while maintaining occupant comfort for both new and existing buildings.

ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATION↗
DOE OSTI2021

Effects of nanoconfinement and surface charge on iron adsorption on mesoporous silica

Here, we present a combined molecular dynamics (MD) simulation and X-ray absorption fine structure (XAFS) spectroscopic investigation of aqueous iron adsorption on nanoconfined amorphous silica surfaces. The simulation models examine the effects of pore size, pH (surface charge), iron valency, and counter-ion (chloride or hydroxide). The simulation methods were validated by comparing the coordination environment of adsorbed iron with coordination numbers and bond lengths derived from XAFS. In the MD models, nanoconfinement effects on local iron coordination were investigated by comparing results for unconfined silica surfaces and in confined domains within 2 nm, 4 nm, and 8 nm pores. Experimentally, coordination environments of iron adsorbed onto mesoporous silica with 4 nm and 8 nm pores at pH 7.5 were investigated. The effect of pH in the MD models was included by simulating Fe(II) adsorption onto negatively charged SiO 2 surfaces and Fe(III) adsorption on neutral surfaces. The simulation results show that iron adsorption depends significantly on silica surface charge, as expected based on electrostatic interactions. Adsorption on a negatively charged surface is an order of magnitude greater than on the neutral surface, and simulated surface coverages are consistent with experimental results. Pore size effects from the MD simulations were most notable in the adsorption of Fe(II) at deprotonated surface sites (SiO - ), but adsorption trends varied with concentration and aqueous Fe speciation. The coordination environment of adsorbed iron varied significantly with the type of anion. Considerable ion pairing with hydroxide anions led to the formation of oligomeric surface complexes and aqueous species, resulting in larger iron hydroxide clusters at higher surface loadings.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

A Shallow-Water Model for Convective Self-Aggregation

Randomly distributed convective storms can self-aggregate in the absence of large-scale forcings. Here we present a 1D shallow-water model to study the convective self-aggregation. This model simulates the dynamics of the planetary boundary layer and represents convection as a triggered process. Once triggered, convection lasts for finite time and occupies finite length. Here we show that the model can successfully simulate self-aggregation, and that the results are robust to a wide range of parameter values. In the simulations, convection excites gravity waves. The gravity waves then form a standing wave pattern, separating the domain into convectively active and inactive regions. We analyze the available potential energy (APE) budget and show that convection generates APE, providing energy for self-aggregation. By performing dimensional analysis, we develop a scaling theory for the size of convective aggregation, which is set by the gravity wave speed, damping time scale, and number density of convective storms. This paper provides a simple modeling framework to further study convective self-aggregation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

V1G Frequency Regulation: Algorithm Development, Validation & Analysis at Scale

Researchers at Argonne National Laboratory developed and validated a high-fidelity digital twin of a smart charging (V1G) ecosystem to model the participation of up to 1,000 unique electric vehicles (EVs) in the PJM frequency regulation market. Utilizing a discrete-event framework, the simulation models complex interactions, from dynamic grid signals (updated every 2 seconds) to individual EV charging dynamics. The simulation incorporates multiple EV models created from real-world lab test data. Researchers tested multiple control algorithms to balance the dual objectives of maximizing aggregator’s revenue and driver charging needs. Results demonstrate that aggregated EVs function as a controllable, highly effective grid resource, achieving high PJM Performance Scores (80–90%). Additionally, an optimized, market-aware bidding strategy was identified as key to profitability. The platform was shown to provide drivers with an average charging discount of nearly 50%. The algorithm was further validated in the lab using production EVs and charging stations to compare simulation results with real-world performance.

Manne, Nithin↗
DOE OSTI2024

Bimodality in simulated precipitation frequency distributions and its relationship with convective parameterizations

Abstract Bimodality in precipitation frequency distributions is often evident in atmospheric models, but rarely in observations. This study i) proposes a metric to objectively quantify the bimodality in precipitation distributions, ii) evaluates model simulations contributed to the Coupled Model Intercomparison Project (CMIP) phase 5 (CMIP5), phase 6 (CMIP6), and the DYnamics of the Atmospheric general circulation Modeled On Non-hydrostatic Domains (DYAMOND) project by comparing them to satellite-based and reanalysis precipitation products, and iii) investigates possible origins of bimodal precipitation distributions. Our results reveal that about 83% (20 out of 24) of CMIP5 and 70% (21 out of 30) of CMIP6 models used in this study exhibit bimodal distributions. The few DYAMOND models that use a deep convective parameterization also show bimodal distributions, while most DYAMOND models do not. Predictably, the bimodality originates from the separation of precipitation process between resolved grid-scale and parameterized subgrid-scale. However, in a larger number of models bimodality arises from the parameterized subgrid-scale convective precipitation alone.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

A Non‐Intrusive Machine Learning Framework for Debiasing Long‐Time Coarse Resolution Climate Simulations and Quantifying Rare Events Statistics

Abstract Due to the rapidly changing climate, the frequency and severity of extreme weather is expected to increase over the coming decades. As fully‐resolved climate simulations remain computationally intractable, policy makers must rely on coarse‐models to quantify risk for extremes. However, coarse models suffer from inherent bias due to the ignored “sub‐grid” scales. We propose a framework to non‐intrusively debias coarse‐resolution climate predictions using neural‐network (NN) correction operators. Previous efforts have attempted to train such operators using loss functions that match statistics. However, this approach falls short with events that have longer return period than that of the training data, since the reference statistics have not converged. Here, the scope is to formulate a learning method that allows for correction of dynamics and quantification of extreme events with longer return period than the training data. The key obstacle is the chaotic nature of the underlying dynamics. To overcome this challenge, we introduce a dynamical systems approach where the correction operator is trained using reference data and a coarse model simulation nudged toward that reference. The method is demonstrated on debiasing an under‐resolved quasi‐geostrophic model and the Energy Exascale Earth System Model (E3SM). For the former, our method enables the quantification of events that have return period two orders longer than the training data. For the latter, when trained on 8 years of ERA5 data, our approach is able to correct the coarse E3SM output to closely reflect the 36‐year ERA5 statistics for all prognostic variables and significantly reduce their spatial biases.

Barthel Sorensen, B.↗
DOE OSTI2025

A dynamic 2D Borehole Thermal Energy Storage (BTES) model for enhanced computational efficiency

Progressing toward a future increasingly reliant on renewable energy sources, the development of effective, durable energy storage solutions becomes essential to balance supply and demand fluctuations. Borehole Thermal Energy Storage (BTES) is a long-duration thermal energy storage technology that captures excess heat generated from renewable energy sources and stores it underground for later use, enabling the efficient utilization of sustainable energy. This approach is particularly valuable in district energy networks when integrated with Ground Source Heat Pumps (GSHP) to provide stable heating and cooling. However, traditional three-dimensional (3D) numerical models of BTES systems demand extensive computational resources, limiting their practicality for real-time and large-scale applications. This study introduces a novel two-dimensional (2D) modeling approach that reduces computational costs while maintaining high accuracy. By employing a radial ring-based discretization method, the model simulates heat injection, retention, and retrieval dynamics over seasonal cycles. A new thermal-mass weighted-average temperature parameter is introduced to evaluate the performance of BTES systems. Model validation against FEFLOW simulations demonstrates a 17-fold improvement in computational speed compared to traditional Computational Fluid Dynamics (CFD) models while achieving a mean absolute percentage error (MAPE) of 2 % during charging and 4 % during discharging. Additionally, a trade-off analysis between computational efficiency and accuracy is conducted, ensuring the model's applicability for real-world scenarios. The findings of this research contribute to the development of computationally efficient BTES models, facilitating better optimization, control, and integration into renewable energy systems. This work provides a foundation for further studies in techno-economic analysis, multi-year performance evaluation, and real-time operational strategies for BTES applications, supporting a more sustainable energy future.

2D modeling↗
DOE OSTI2024

Explicit Consideration of Plant Xylem Hydraulic Transport Improves the Simulation of Crop Response to Atmospheric Dryness in the U.S. Corn Belt

Abstract Atmospheric dryness (i.e., high vapor pressure deficit, VPD), together with soil moisture stress, limits plant photosynthesis and threatens ecosystem functioning. Regions where rainfall and soil moisture are relatively sufficient, such as the rainfed part of the U.S. Corn Belt, are especially prone to high VPD stress. With globally projected rising VPD under climate change, it is crucial to understand, simulate, and manage its negative impacts on agricultural ecosystems. However, most existing models simulating crop response to VPD are highly empirical and insufficient in capturing plant response to high VPD, and improved modeling approaches are urgently required. In this study, by leveraging recent advances in plant hydraulic theory, we demonstrate that the VPD constraints in the widely used coupled photosynthesis‐stomatal conductance models alone are inadequate to fully capture VPD stress effects. Incorporating plant xylem hydraulic transport significantly improves the simulation of transpiration under high VPD, even when soil moisture is sufficient. Our results indicate that the limited water transport capability from the plant root to the leaf stoma could be a major mechanism of plant response to high VPD stress. We then introduce a Demand‐side Hydraulic Limitation Factor (DHLF) that simplifies the xylem and the leaf segments of the plant hydraulic model to only one parameter yet captures the effect of plant hydraulic transport on transpiration response to high VPD with similar accuracy. We expect the improved understanding and modeling of crop response to high VPD to help contribute to better management and adaptation of agricultural systems in a changing climate.

Environmental Sciences & Ecology↗
DOE OSTI2022

Integration of Large-Scale Electrical Imaging into Geological Framework Development and Refinement

Geologic framework models (GFMs) are critical to the construction of reliable simulation models of groundwater flow and contaminant transport. To support GFM development, direct information (e.g., core samples, fluid samples, hydraulic testing) tends to be sparse and separated by large distances relative to the spatial scales of aquifer heterogeneity. There are additional challenges associated with highly contaminated legacy waste sites, where drilling is particularly costly, and invasive sampling requires specialized handling and disposal of hazardous materials. At these sites in particular, non-invasive geophysical imaging can play an important role in filling spatial gaps between boreholes and reducing characterization costs by optimizing and minimizing the number of necessary boreholes. Here this paper presents a case study demonstrating the use of large-scale (> 30 km 2 ) electrical mapping to identify hydrostratigraphy and potential paleochannels at the Hanford Site, located in Washington State, USA. In two field campaigns, over 36 line-kilometers of electrical resistivity tomography (ERT) data were collected along 14 transects. ERT surveys were sited and performed to image critical aspects (e.g., paleochannels, stratigraphic contacts) of the subsurface, demonstrating a general workflow for integrating ERT with GFM development. Inconsistencies between the GFM and ERT were catalogued to provide a basis for future site characterization using complementary geophysical methods and (or) direct sampling.

58 GEOSCIENCES↗
DOE OSTI2022

Impacts of climate change on estuarine stratification and implications for hypoxia within a shallow subtropical system

Vertical density stratification often plays an important role in the formation and expansion of coastal hypoxic zones through its effect on near-bed circulation and vertical oxygen flux. However, the impact of future climate change on estuarine circulation is widely unknown. Here, we developed and calibrated a three-dimensional hydrodynamic model for Pensacola Bay, a shallow subtropical estuary in the northeastern Gulf of Mexico. Model simulations based on years 2013–2017 were applied to examine changes in salinity, temperature, and density under future climate scenarios, including increased radiative forcing (IR) and temperature (T), increased freshwater discharge (D), sea level rise (SLR), and wind intensification (W). Simulations showed that the impacts of climate change on modeled state variables varied over time with external forcing conditions. The model demonstrated the potential for sea level rise and increased freshwater discharge to episodically increase vertical density gradients in the Bay. However, increased wind forcing destabilized vertical gradients, at times reducing the spatial extent and duration of stable stratification. For time periods with low freshwater discharge, moderate increases in wind speed (10%) can destabilize density gradients strengthened by increased discharge (10%) and sea level rise (0.48 m). In contrast, destruction of strong density gradients that form near the mid-Bay channel following flood events requires stronger wind forcing. Furthermore, these results highlight the importance of considering natural variability in freshwater and wind forcing, as well as local phenomena that are generally unresolved by global climate models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Impact of Rainfall on Tropical Cyclone-Induced Sea Surface Cooling

Tropical cyclones (TCs) are often accompanied by strong winds and torrential rains. While the winds associated with TCs tend to enhance mixing in the upper-ocean, the freshwater input from rain can stratify the water column and limit mixing. However, the extent to which the stabilizing effect of rainfall can compete with wind-induced mixing, and to what degree it modulates TC-induced sea surface cooling, remains unknown. Here we show, using a suite of observations, that heavy rains under weak TCs can significantly reduce the magnitude of cold wakes induced by them. Additionally, when compared to storms with low rain rates, the ocean surface under TCs with high rain rates freshens significantly and cools less. High-resolution climate model simulations and idealized experiments with an ocean mixed layer model support these results and reveal that oceanic mixing processes are primarily responsible for the reduced cooling under TCs, with a lesser role for surface fluxes.

54 ENVIRONMENTAL SCIENCES↗