Search NASA⌕ Search

SEARCH · Search NASA

Results for “spatial variability”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,207 records · Page 67
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Urban morphology from a landscape perspective: How building morphology distribution land models (BMDLM) emulate pattern and process

Urban form (e.g., building morphology such as height or footprint) can be used to predict environmental footprints, such as energy/water consumption and carbon emissions. Although progress has been made in predicting building characteristics to fill gaps in observation or derive 3-D representations, the relationships between morphology and other variables such as land use and population are poorly understood. Understanding these relationships may enable projections for how cities will evolve with landscapes in the future. A suite of random forest models, the Building Morphology Distribution Land Models (BMDLM), was developed to determine how well building morphology for two distinct statistical measures (central tendency and frequency) can be predicted using land use (e.g., zoning) and population at different resolutions. Clark County, Nevada and Los Angeles County, California are explored as case studies. Generally, 1-km models outperformed 30-m models. Frequency distribution models had the best performance, especially in LA County. Frequency models significantly outperformed spatial autocorrelative models using inverse distance weighting (IDW). BMDLM offers a new take on modeling urban form in which generalized landscape patterns are characterized to understand the influence of population and zoning on urban development, as described by urban scaling theory.

Sturtevant, Jillian [Baylor Univ., Waco, TX (Unite↗
DOE OSTI2021

Explore Spatio‐Temporal Learning of Large Sample Hydrology Using Graph Neural Networks

Abstract Streamflow forecasting over gauged and ungauged basins play a vital role in water resources planning, especially under the changing climate. Increased availability of large sample hydrology data sets, together with recent advances in deep learning techniques, has presented new opportunities to explore temporal and spatial patterns in hydrological signatures for improving streamflow forecasting. The purpose of this study is to adapt and benchmark several state‐of‐the‐art graph neural network (GNN) architectures, including ChebNet, Graph Convolutional Network (GCN), and GraphWaveNet, for end‐to‐end graph learning. We explicitly represent river basins as nodes in a graph, learn the spatiotemporal nodal dependencies, and then use the learned relations to predict streamflow simultaneously across all nodes in the graph. The efficacy of the developed GNN models is investigated using the Catchment Attributes and MEteorology for Large‐sample Studies (CAMELS) data set under two settings, fixed graph topology (transductive learning), and variable graph topology (inductive learning), with the latter applicable to prediction in ungauged basins (PUB). Results indicate that GNNs are generally robust and computationally efficient, achieving similar or better performance than a baseline model trained using the long short‐term memory (LSTM) network. Further analyses are conducted to interpret the graph learning process at the edge and node levels and to investigate the effect of different model configurations. We conclude that graph learning constitutes a viable machine learning‐based method for aggregating spatiotemporal information from a multitude of sources for streamflow forecasting

Sun, Alexander Y.↗
DOE OSTI2024

Cosmic topology. Part IIa. Eigenmodes, correlation matrices, and detectability of orientable Euclidean manifolds

Abstract If the Universe has non-trivial spatial topology, observables depend on both the parameters of the spatial manifold and the position and orientation of the observer. In infinite Euclidean space, most cosmological observables arise from the amplitudes of Fourier modes of primordial scalar curvature perturbations. Topological boundary conditions replace the full set of Fourier modes with specific linear combinations of selected Fourier modes as the eigenmodes of the scalar Laplacian. We present formulas for eigenmodes in orientable Euclidean manifolds with the topologiesE 1 –E 6 ,E 11 ,E 12 ,E 16 , andE 18 that encompass the full range of manifold parameters and observer positions, generalizing previous treatments. Under the assumption that the amplitudes of primordial scalar curvature eigenmodes are independent random variables, for each topology we obtain the correlation matrices of Fourier-mode amplitudes (of scalar fields linearly related to the scalar curvature) and the correlation matrices of spherical-harmonic coefficients of such fields sampled on a sphere, such as the temperature of the cosmic microwave background (CMB). We evaluate the detectability of these correlations given the cosmic variance of the observed CMB sky. We find that topologies where the distance to our nearest clone is less than about 1.2 times the diameter of the last scattering surface of the CMB give a correlation signal that is larger than cosmic variance noise in the CMB. This implies that if cosmic topology is the explanation of large-angle anomalies in the CMB, then the distance to our nearest clone is not much larger than the diameter of the last scattering surface. We argue that the topological information is likely to be better preserved in three-dimensional data, such as will eventually be available from large-scale structure surveys.

Astronomy & Astrophysics↗
DOE OSTI2023

Investigating the impact of environmental factors on West Nile virus human case prediction in Ontario, Canada

West Nile virus is the most common mosquito borne disease in North America and the leading cause of viral encephalitis. West Nile virus is primarily transmitted between birds and mosquitoes while humans are incidental, dead-end hosts. Climate change may increase the risk of human infections as climatic variables have been shown to affect the mosquito life cycle, biting rate, incubation period of the disease in mosquitoes, and bird migration patterns. We develop a zero-inflated Poisson model to investigate how human West Nile virus case counts vary with respect to mosquito abundance and infection rates, bird abundance, and other environmental covariates. We use a Bayesian paradigm to fit our model to data from 2010–2019 in Ontario, Canada. Our results show mosquito infection rate, temperature, precipitation, and crow abundance are positively correlated with human cases while NDVI and robin abundance are negatively correlated with human cases. We find the inclusion of spatial random effects allows for more accurate predictions, particularly in years where cases are higher. Our model is able to accurately predict the magnitude and timing of yearly West Nile virus outbreaks and could be a valuable tool for public health officials to implement prevention strategies to mitigate these outbreaks.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Long-term hydro-economic analysis tool for evaluating global groundwater cost and supply: Superwell v1.1

Abstract. Groundwater plays a key role in meeting water demands, supplying over 40 % of irrigation water globally, with this role likely to grow as water demands and surface water variability increase. A better understanding of the future role of groundwater in meeting sectoral demands requires an integrated hydro-economic evaluation of its cost and availability. Yet substantial gaps remain in our knowledge and modeling capabilities related to groundwater availability, recharge, feasible locations for extraction, extractable volumes, and associated extraction costs, which are essential for large-scale analyses of integrated human–water system scenarios, particularly at the global scale. To address these needs, we developed Superwell, a physics-based groundwater extraction and cost accounting model that operates at sub-annual temporal and at the coarsest 0.5° (≈50 km × 50 km) gridded spatial resolution with global coverage. The model produces location-specific groundwater supply–cost curves that provide the levelized cost to access different quantities of available groundwater. The inputs to Superwell include recent high-resolution hydrogeologic datasets of permeability, porosity, aquifer thickness, depth to water table, recharge, and hydrogeological complexity zones. It also accounts for well capital and maintenance costs, as well as the energy costs required to lift water to the surface. The model employs a Theis-based scheme coupled with an amortization-based cost accounting formulation to simulate groundwater extraction and quantify the cost of groundwater pumping. The result is a spatiotemporally flexible, physically realistic, economics-based model that produces groundwater supply–cost curves. We show examples of these supply–cost curves and the insights that can be derived from them across a set of scenarios designed to explore model outcomes. The supply–cost curves produced by the model show that most (90 %) nonrenewable groundwater in storage globally is extractable at costs lower than USD 0.57 m−3, while half of the volume remains extractable at under USD 0.108 m−3. The global unit cost is estimated to range from a minimum of USD 0.004 m−3 to a maximum of USD 3.971 m−3. We also demonstrate and discuss examples of how these cost curves could be used by linking Superwell's outputs with other models to explore coupled human–environmental system challenges, such as water resources planning and management, or broader analyses of multisectoral feedbacks.

Global Change Analysis Model (GCAM)↗
DOE OSTI2021

Probabilistic Day-Ahead Forecasting Using an Analog Ensemble Approach for Wind Farm Grid Services

Wind resource assessment and wind power forecasting are used in research and industry to anticipate future power output at scales ranging from individual wind turbines to entire wind farms. Probabilistic day-ahead wind forecasting is useful for anticipating how a wind farm could potentially participate in the day-ahead market by providing upper and lower bounds for expected power generation, thus informing grid operators of its uncertainty. Understanding this uncertainty is part of a larger project focused on building a platform that combines efforts in weather forecasting, aerodynamic and economic modeling to create maximum value of a wind plant to better provide services to the grid. This effort is also known as the Atmosphere to Electrons to Grid (A2E2G) project. One method for producing a probabilistic forecast is through the analog ensemble approach (Delle Monache et al., 2011). This method leverages historical forecasts and their corresponding observations as a training data set from which future forecasts can be made. For some future forecast, the most similar historical forecasts (analogs) are identified on a regular time basis such as once per a 3-hour window. The most similar analogs, based on a metric such as root mean square error (RMSE), are recorded and their corresponding verifying observations are used as an ensemble member for this future forecast. Prior work in this area demonstrates improvements over raw Numerical Weather Prediction (NWP) forecasts and shows skill similar to techniques such as logistic regression and machine learning (Delle Monache et al., 2013; Alessandrini et al., 2015). Here, we take the High-Resolution Rapid Refresh model (HRRR) day-ahead forecast (0-36 hours) to create a probabilistic day-ahead forecast using an analog ensemble approach. The HRRR has an hourly temporal resolution, with a spatial resolution of 3 km. The 12 UTC HRRR model run is downloaded every day for one year from August 2019 - July 2020, with the first 11 months serving as a bank of analogs from which the forecasting algorithm can create a probabilistic forecast. Once downloaded, the original HRRR forecast is temporally interpolated to 5-minutes, aligning with both the temporal resolution of the observations as well as the timescale relevant for day-ahead power forecasts. The forecast is validated at the M2 tower at the Flatirons Campus of the National Renewable Energy Laboratory (NREL) at a typical wind turbine height of 80 m. Variables such as wind speed, wind direction, and turbulence intensity are incorporated into the probabilistic forecast model and weighted according to their relative importance to the forecast. Based on metrics such as mean bias error (MBE), mean absolute error (MAE), and root mean square error, the analog ensemble forecast outperforms the raw HRRR forecast during the testing period of July 2020. Figure 1 illustrates an example day-ahead forecast compared against the verifying observations. The general variability and ramps are captured throughout the day, with potential to further improve the analog ensemble model through machine learning techniques.

numerical weather prediction↗
DOE OSTI2024

Estimating irrigation water use from remotely sensed evapotranspiration data: Accuracy and uncertainties at field, water right, and regional scales

Irrigated agriculture is the dominant user of water globally, but most water withdrawals are not monitored or reported. As a result, it is largely unknown when, where, and how much water is used for irrigation. Here, we evaluated the ability of remotely sensed evapotranspiration (ET) data, integrated with other datasets, to calculate irrigation water withdrawals and applications in an intensively irrigated portion of the United States. We compared irrigation calculations based on an ensemble of satellite-driven ET models from OpenET with reported groundwater withdrawals from hundreds of farmer irrigation application records and a statewide flowmeter database at three spatial scales (field, water right group, and management area). At the field scale, we found that ET-based calculations of irrigation agreed best with reported irrigation when the OpenET ensemble mean was aggregated to the growing season timescale (bias = 1.6–4.9%, R 2 = 0.53–0.74), and agreement between calculated and reported irrigation was better for multi-year averages than for individual years. At the water right group scale, linking pumping wells to specific irrigated fields was the primary source of uncertainty. At the management area scale, calculated irrigation exhibited similar temporal patterns as flowmeter data but tended to be positively biased with more interannual variability. Disagreement between calculated and reported irrigation was strongly correlated with annual precipitation, and calculated and reported irrigation agreed more closely after statistically adjusting for annual precipitation. The selection of an ET model was also an important consideration, as variability across ET models was larger than the potential impacts of conservation measures employed in the region. From these results, we suggest key practices for working with ET-based irrigation data that include accurately accounting for changes in soil moisture, deep percolation, and runoff; careful verification of irrigated area and well-field linkages; and conducting application-specific evaluations of uncertainty.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Observations of Ocean Surface Wave Attenuation in Sea Ice Using Seafloor Cables

Abstract The attenuation of ocean surface waves during seasonal ice cover is an important control on the evolution of Arctic coastlines. The spatial and temporal variations in this process have been challenging to resolve with conventional sampling using sparse arrays of moorings or buoys. We demonstrate a novel method for persistent observation of wave‐ice interactions using distributed acoustic sensing (DAS) along existing seafloor fiber optic telecommunications cables. DAS measurements span a 36‐km cross‐shore cable on the Beaufort Shelf from Oliktok Point, Alaska. DAS optical sensing of fiber strain‐rate provides a proxy for seafloor pressure, which we calibrate with wave buoy measurements during the ice‐free season (August 2022). We apply this calibration during the ice formation season (November 2021) to obtain unprecedented resolution of variable wave attenuation rates in new, partial ice cover. The location and strength of wave attenuation serve as proxies for ice coverage and thickness, especially during rapidly evolving events.

Smith, Madison M.↗
DOE OSTI2021

Observations of Aerosol, Cloud, Turbulence, and Radiation Properties at the Top of the Marine Boundary Layer over the Eastern North Atlantic Ocean: The ACORES Campaign

We report on the Azores Stratocumulus Measurements of Radiation, Turbulence and Aerosols (ACORES) campaign, which took place around Graciosa and Pico Islands/Azores in July 2017. The main objective was to investigate the vertical distribution of aerosol particles, stratocumulus microphysical and radiative properties, and turbulence parameters in the eastern North Atlantic. The vertical exchange of mass, momentum, and energy between the free troposphere (FT) and the cloudy marine boundary layer (MBL) was explored over a range of scales from submeters to kilometers. To cover these spatial scales with appropriate measurements, helicopter-borne observations with unprecedented high resolution were realized using the Airborne Cloud Turbulence Observation System (ACTOS) and Spectral Modular Airborne Radiation Measurement System–Helicopter-Borne Observations (SMART-HELIOS) instrumental payloads. Here, the helicopter-borne observations were combined with ground-based aerosol measurements collected at two continuously running field stations on Pico Mountain (2,225 m above sea level, in the FT), and at the Atmospheric Radiation Measurement (ARM) station on Graciosa (at sea level). First findings from the ACORES observations we are discussing in the paper are as follows: (i) we have observed a high variability of the turbulent cloud-top structure on horizontal scales below 100 m with local temperature gradients of up to 4 K over less than 1 m vertical distance, (ii) we have collected strictly collocated radiation measurements supporting the relevance of small-scale processes by revealing significant inhomogeneities in cloud-top brightness temperature to scales well below 100 m, and (iii) we have concluded that aerosol properties are completely different in the MBL and FT with often-complex stratification and frequently observed burst-like new particle formation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Seasonal Variability in Local Carbon Dioxide Biomass Burning Sources Over Central and Eastern US Using Airborne In Situ Enhancement Ratios

We present observations of local enhancements in carbon dioxide (CO 2 ) from local emissions sources over three eastern US regions during four deployments of the Atmospheric Carbon Transport-America (ACT-America) campaign between summer 2016 and spring 2018. Local CO 2 emissions were characterized by carbon monoxide (CO) to CO 2 enhancement ratios (i.e., ΔCO/ΔCO 2 ) in air mass mixing observed during aircraft transects within the planetary boundary layer. By analyzing regional-scale variability of CO 2 enhancements as a function of ΔCO/ΔCO 2 enhancement ratios, observed relative contributions to CO 2 emissions were separated into fossil fuel and biomass burning (BB) regimes across regions and seasons. CO 2 emission contributions attributed to biomass burning (ΔCO/ΔCO 2 > 4%) were negligible during summer and fall in all regions but climbed to ∼9%–11% of observed combustion contributions in the South during winter and spring. Relative CO 2 fire emission trends matched observed winter and spring BB contributions, but conflictingly predicted similar levels of BB during the fall. Satellite fire data from MODIS and VIIRS suggested the use of higher spatial resolution fire data that might improve modeled BB emissions but were not able to explain the bulk of the discrepancy.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

National serosurvey and risk mapping reveal widespread distribution of Coxiella burnetii in Kenya

Coxiella burnetii, the causative agent of Q fever, is an emerging pathogen that has the potential to cause severe chronic infections in animals and humans worldwide. The detrimental impact on public health is projected to be higher in the low- and middle-income countries given their lower capacity to sustain effective surveillance and response measures. We implemented a national serosurvey of cattle in Kenya to map the spatial distribution of the pathogen. The study used serum samples that were collected from randomly selected cattle in different ago-ecological zones across the country. These samples were screened for the pathogen using PrioCHECK Ruminant Q Fever AB Plate ELISA kit. The laboratory findings were analyzed using INLA package to identify risk factors for C. burnetii exposure from herd- and animal-level factors, area, and bioclimatic datasets accessed from online databases. A total of 6,593 cattle were recruited for the study; of these, 7.9% (95% CI; 7.2–8.5) were seropositive. Outputs from the multivariable analysis revealed that the animal age and some of the geographical variables including wind speed, area under shrubs and “petric calcisols” type of soil were significantly associated with C. burnetii seropositivity. Being a calf, weaner or subadult was associated with lower odds of exposure compared to being an adult by 0.24 (credibility interval: 2.5% and 97.5%), 0.41 (0.30–0.55) and 0.51 (0.38–0.69), respectively. In addition, a unit increase in the wind speed increased the odds of C. burnetii seropositivity by 1.27 (1.05–1.52) while an increase on the land area under shrubs was associated with lower odds of exposure (0.67 [0.47–0.69]). The effect of petric calcisols was non-linear; an increase of the land area with this soil type was associated with an exponential increase in C. burnetii seropositivity. This study provides new data on C. burnetii seroprevalence, information of its risk factors and a prevalence map that can be used for C. burnetii risk surveillance and control. The identification of environmental risk factors for C. burnetii exposure, and the increasing awareness of the zoonotic potential of the pathogen, calls for the need to enhance the existing collaborations for the surveillance and control of C. burnetii in line with the One Health framework. The evidence generated on the potential role of environmental factors can also be used to design nature-based interventions, such as replacement of vegetation in denuded areas, to reduce potential for the aerosolization of the pathogen. Livestock vaccination in the hotspots would also reduce animal infections and hence the contamination of the environment.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Multiwavelength analysis of Fermi -LAT blazars with high-significance periodicity: detection of a long-term rising emission in PG 1553+113

ABSTRACT Blazars display variable emission across the entire electromagnetic spectrum, with time-scales that can range from a few minutes to several years. Our recent work has shown that a sample of five blazars exhibit hints of periodicity with a global significance ${\gtrsim}2\, \sigma$ at γ-ray energies, in the range of 0.1 GeV < E < 800 GeV. In this work, we study their multiwavelength emission, covering the X-ray, ultraviolet, optical, and radio bands. We show that three of these blazars present similar periodic patterns in the optical and radio bands. Additionally, fluxes in the different bands of the five blazars are correlated, suggesting a co-spatial origin. Moreover, we detect a long-term (≈10 yr) rising trend in the light curves of PG 1553+113, and we use it to infer possible constraints on the binary black hole hypothesis.

Astronomy & Astrophysics↗
DOE OSTI2020

Simulating coupled surface–subsurface flows with ParFlow v3.5.0: capabilities, applications, and ongoing development of an open-source, massively parallel, integrated hydrologic model

Surface flow and subsurface flow constitute a naturally linked hydrologic continuum that has not traditionally been simulated in an integrated fashion. Recognizing the interactions between these systems has encouraged the development of integrated hydrologic models (IHMs) capable of treating surface and subsurface systems as a single integrated resource. IHMs are dynamically evolving with improvements in technology, and the extent of their current capabilities are often only known to the developers and not general users. This article provides an overview of the core functionality, capability, applications, and ongoing development of one open-source IHM, ParFlow. ParFlow is a parallel, integrated, hydrologic model that simulates surface and subsurface flows. ParFlow solves the Richards equation for three-dimensional variably saturated groundwater flow and the two-dimensional kinematic wave approximation of the shallow water equations for overland flow. The model employs a conservative centered finite-difference scheme and a conservative finite-volume method for subsurface flow and transport, respectively. ParFlow uses multigrid-preconditioned Krylov and Newton–Krylov methods to solve the linear and nonlinear systems within each time step of the flow simulations. The code has demonstrated very efficient parallel solution capabilities. ParFlow has been coupled to geochemical reaction, land surface (e.g., the Common Land Model), and atmospheric models to study the interactions among the subsurface, land surface, and atmosphere systems across different spatial scales. This overview focuses on the current capabilities of the code, the core simulation engine, and the primary couplings of the subsurface model to other codes, taking a high-level perspective.

58 GEOSCIENCES↗
DOE OSTI2025

Stable Machine‐Learning Parameterization of Subgrid Processes in a Comprehensive Atmospheric Model Learned From Embedded Convection‐Permitting Simulations

Modern climate projections often suffer from inadequate spatial and temporal resolution due to computational limitations, resulting in inaccurate representations of sub-grid processes. A promising technique to address this is the multiscale modeling framework (MMF), which embeds a kilometer-resolution cloud-resolving model (CRM) within each atmospheric column of a host climate model to replace traditional convection and cloud parameterizations. Machine learning offers a unique opportunity to make MMF more accessible by emulating the embedded CRM and reducing its substantial computational cost. Although many studies have demonstrated proof-of-concept success of achieving stable hybrid simulations, it remains a challenge to achieve near operational-level success with real geography and comprehensive variable emulation that includes, for example, explicit cloud condensate coupling. In this study, we present a stable hybrid model capable of integrating for at least 5 years with near operational-level complexity, including coarse-grid geography, seasonality, explicit cloud condensate and wind predictions, and land coupling. Our model demonstrates skillful online performance, achieving a 5-year zonal mean tropospheric temperature bias within 2 K, water vapor bias within 1 g/kg, and a precipitation root mean square error of 0.96 mm/day. Key factors contributing to our online performance include an expressive U-Net architecture and physical thermodynamic constraints for microphysics. With microphysical constraints mitigating unrealistic cloud formation, our work is the first to demonstrate realistic multi-year cloud condensate climatology under the MMF framework. Despite these advances, online diagnostics reveal persistent biases in certain regions, highlighting the need for innovative strategies to further optimize online performance.

Hu, Zeyuan [NVIDIA Corporation, Santa Clara, CA (U↗
DOE OSTI2023

The Peculiar Variable X-Ray Spectrum of the Active Galactic Nucleus PKS 2005–489

PKS 2005-489 is a well-known, bright southern BL Lac object that has been detected up to TeV energies. In a low-flux state it exhibits the expected multiwavelength double-peaked spectrum in the radio- γ -ray band. The high-flux state shows extreme flux variations in the X-ray band with a hardening as well as a peculiar curved feature in the spectrum. Thus far, PKS 2005-489 is the only source to exhibit such a feature. To study the X-ray variability further, we obtained the first hard X-ray spectrum of the source with the Nuclear Spectroscopic Telescope Array. We compare quasi-simultaneous radio, optical, UV, soft and hard X-ray, and γ -ray data of PKS 2005-489 to archival data in order to study its broadband behavior. We find a very consistent quiet state in the spectral energy distribution, with little variation in spectral shape or flux between the 2012 and 2020 data. A possible explanation for the peculiar X-ray spectrum in the flaring state is an additional component in the jet, possibly accelerated via magnetic reconnection, that is not co-spatial to the low-flux state emission region.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Nonlinearity of the post-spinel transition and its expression in slabs and plumes worldwide

Phase transitions in the mantle control its internal dynamics and structure. The post-spinel transition marks the upper–lower mantle boundary, where ringwoodite dissociates into bridgmanite plus ferropericlase, and its Clapeyron slope regulates mantle flow across it. This interaction has previously been assumed to have no lateral spatial variations, based on the assumption of a linear post-spinel boundary in pressure and temperature. Here we present laser-heated diamond anvil cell experiments with synchrotron X-ray diffraction to better constrain this boundary, especially at higher temperatures. Combining our data with results from the literature, and using a global analysis based on machine learning, we find a pronounced nonlinearity in the post-spinel boundary, with its slope ranging from –4 MPa/K at 2100 K, to –2 MPa/K at 1950 K, and to 0 MPa/K at 1600 K. Changes in temperature over time and space can therefore cause the post-spinel transition to have variable effects on mantle convection and the movement of subducting slabs and upwelling plumes.

58 GEOSCIENCES↗
DOE OSTI2021

Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami

Wireframe DNA origami assemblies can now be programmed automatically from the top-down using simple wireframe target geometries, or meshes, in 2D and 3D, using either rigid, six-helix bundle (6HB) or more compliant, two-helix bundle (DX) edges. While these assemblies have numerous applications in nanoscale materials fabrication due to their nanoscale spatial addressability and high degree of customization, no easy-to-use graphical user interface software yet exists to deploy these algorithmic approaches within a single, standalone interface. Further, top-down sequence design of 3D DX-based objects previously enabled by DAEDALUS was limited to discrete edge lengths and uniform vertex angles, limiting the scope of objects that can be designed. Here, we introduce the open-source software package ATHENA with a graphical user interface that automatically renders single-stranded DNA scaffold routing and staple strand sequences for any target wireframe DNA origami using DX or 6HB edges, including irregular, asymmetric DX-based polyhedra with variable edge lengths and vertices demonstrated experimentally, which significantly expands the set of possible 3D DNA-based assemblies that can be designed. ATHENA also enables external editing of sequences using caDNAno, demonstrated using asymmetric nanoscale positioning of gold nanoparticles, as well as providing atomic-level models for molecular dynamics, coarse-grained dynamics with oxDNA, and other computational chemistry simulation approaches.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Probabilistic neural networks for fluid flow surrogate modeling and data recovery

We consider the use of probabilistic neural networks for fluid flow surrogate modeling and data recovery. This framework is constructed by assuming that the target variables are sampled from a Gaussian distribution conditioned on the inputs. Consequently, the overall formulation sets up a procedure to predict the hyperparameters of this distribution which are then used to compute an objective function given training data. We demonstrate that this framework has the ability to provide for prediction confidence intervals based on the assumption of a probabilistic posterior, given an appropriate model architecture and adequate training data. The applicability of the present framework to cases with noisy measurements and limited observations is also assessed. To demonstrate the capabilities of this framework, we consider canonical regression problems of fluid dynamics from the viewpoint of reduced-order modeling and spatial data recovery for four canonical data sets. The examples considered in this study arise from (i) the shallow-water equations, (ii) a two-dimensional cylinder flow, (iii) the wake of a NACA0012 airfoil with a Gurney flap, and (iv) the NOAA sea surface temperature data set. Furthermore, the present results indicate that the probabilistic neural network not only produces a machine-learning-based fluid flow surrogate model but also systematically quantifies the uncertainty therein to assist with model interpretability.

42 ENGINEERING↗