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This code performs a simulation experiment that involves (i) drawing random numbers from the normal distribution, (ii) resampling elements from arrays with replacement, and (iii) computing various quantities like mean, standard deviation, etc. Further information is available in section 4 of FERMILAB-FN-1273-ETD [https://inspirehep.net/literature/2925453].
In January 2019, the US Department of Energy, Office of Science program in Advanced Scientific Computing Research, convened a workshop to identify priority research directions (PRDs) for in situ data management (ISDM). A fundamental finding of this workshop is that the methodologies used to manage data among a variety of tasks in situ can be used to facilitate scientific discovery from many different data sources—simulation, experiment, and sensors, for example—and that being able to do so at numerous computing scales will benefit real-time decision-making, design optimization, and data-driven scientific discovery. This article describes six PRDs identified by the workshop, which highlight the components and capabilities needed for ISDM to be successful for a wide variety of applications—making ISDM capabilities more pervasive, controllable, composable, and transparent, with a focus on greater coordination with the software stack and a diversity of fundamentally new data algorithms.
Abstract Neurodegenerative diseases involve progressive neuronal death. Traditional treatments often struggle due to solubility, bioavailability, and crossing the Blood-Brain Barrier (BBB). Nanoparticles (NPs) in biomedical field are garnering growing attention as neurodegenerative disease drugs (NDDs) carrier to the central nervous system. Here, we introduced computational and experimental analysis. In the computational study, a specific IFPTML technique was used, which combined Information Fusion (IF) + Perturbation Theory (PT) + Machine Learning (ML) to select the most promising Nanoparticle Neuronal Disease Drug Delivery (N2D3) systems. For the application of IFPTML model in the nanoscience, NANO.PTML is used. IF-process was carried out between 4403 NDDs assays and 260 cytotoxicity NP assays conducting a dataset of 500,000 cases. The optimal IFPTML was the Decision Tree (DT) algorithm which shown satisfactory performance with specificity values of 96.4% and 96.2%, and sensitivity values of 79.3% and 75.7% in the training (375k/75%) and validation (125k/25%) set. Moreover, the DT model obtained Area Under Receiver Operating Characteristic (AUROC) scores of 0.97 and 0.96 in the training and validation series, highlighting its effectiveness in classification tasks. In the experimental part, two samples of NPs (Fe 3 O 4 _A and Fe 3 O 4 _B) were synthesized by thermal decomposition of an iron(III) oleate (FeOl) precursor and structurally characterized by different methods. Additionally, in order to make the as-synthesized hydrophobic NPs (Fe 3 O 4 _A and Fe 3 O 4 _B) soluble in water the amphiphilic CTAB (Cetyl Trimethyl Ammonium Bromide) molecule was employed. Therefore, to conduct a study with a wider range of NP system variants, an experimental illustrative simulation experiment was performed using the IFPTML-DT model. For this, a set of 500,000 prediction dataset was created. The outcome of this experiment highlighted certain NANO.PTML systems as promising candidates for further investigation. The NANO.PTML approach holds potential to accelerate experimental investigations and offer initial insights into various NP and NDDs compounds, serving as an efficient alternative to time-consuming trial-and-error procedures.
Studying the biology of sleep requires the accurate assessment of the state of experimental subjects, and manual analysis of relevant data is a major bottleneck. Recently, deep learning applied to electroencephalogram and electromyogram data has shown great promise as a sleep scoring method, approaching the limits of inter-rater reliability. As with any machine learning algorithm, the inputs to a sleep scoring classifier are typically standardized in order to remove distributional shift caused by variability in the signal collection process. However, in scientific data, experimental manipulations introduce variability that should not be removed. For example, in sleep scoring, the fraction of time spent in each arousal state can vary between control and experimental subjects. We introduce a standardization method, mixture z-scoring, that preserves this crucial form of distributional shift. Using both a simulated experiment and mouse in vivo data, we demonstrate that a common standardization method used by state-of-the-art sleep scoring algorithms introduces systematic bias, but that mixture z-scoring does not. We present a free, open-source user interface that uses a compact neural network and mixture z-scoring to allow for rapid sleep scoring with accuracy that compares well to contemporary methods. This work provides a set of computational tools for the robust automation of sleep scoring.
This dataset provides a set of experimental data on the performance of lost circulation materials (LCMs) used in geothermal drilling operations. It includes results from four distinct tests: thermal degradation, viscosity measurements, compression tests, and high-temperature flow loop experiments. The materials tested, such as cedar fiber, cotton seed hulls, magma fiber, microcellulose, and sawdust, were analyzed under a range of conditions to assess their effectiveness in mitigating fluid losses in geothermal wells. Data on thermal degradation explores mass loss, water loss, and gas release for each material when subjected to temperatures between 90C and 250C. Viscosity measurements capture the behavior of LCM mixtures under different temperatures, while compression tests investigate the structural integrity of both undegraded and thermally degraded materials. The high-temperature flow loop experiments simulate geothermal well conditions, analyzing how different materials and mixtures affect fluid flow and sealing performance in a fractured reservoir environment. In addition to the experimental data, the dataset includes photos documenting the materials, schematics of test setups, and several published manuscripts that provide detailed insights into the experimental methods and findings.
Thanks to decades of tireless efforts, nanoparticle assemblies have reached at an extremely high level of controllability, sophistication, and complexity, with new insights provided by integration with graph theory, cutting-edge characterization, and machine learning (ML)-based computation and modeling, as well as with ever-diversifying applications in energy, catalysis, biomedicine, optics, electronics, magnetics, organic biosynthesis, and quantum technology. Nanoparticle assemblies can be crystalline, known as superlattices or supracrystals. Their assembly entails a transition from disorder—dispersed nanoparticles—to order, which can be achieved through classical nucleation pathways or nonclassical pathways via prenucleation precursors or particle aggregation. Further, the periodic lattices allow facile manipulations of electrons, phonons, photons, and even spins, leading to advanced device components and metamaterials. Meanwhile, aperiodic assemblies out of nanoparticles, such as gels, networks, and amorphous solids, also start to attract attentions. Despite the loss of periodicity, symmetry-lowering or symmetry-breaking three-dimensional (3D) structures emerge with unique properties, such as chiroptical activity, topological mechanical strength, and quantum entanglement. Real-space imaging such as electron microscopy and X-ray based tomography methods are utilized to characterize these complex structures, while mathematical tools such as graph theories are in need to describe such complex structures. This issue aims to provide a timely review of the efforts in this greatly broadened materials design space including experiment, simulation, theory, and applications. Nine top experts (and their teams) from four countries deliver six review papers, summarizing fundamental mechanistic understandings of nanoparticle assemblies, highlighted with the developments of state-of-the-art in situ characterization tools and ML-assisted reverse engineering, and newly emergent applications of nanoarchitectures.
Summary There has been substantial controversy concerning the role of geological carbon storage (GCS) in sequestering anthropogenic carbon emissions to mitigate climate change and global warming. Arguments center on the inability to monitor a geological storage site precisely and continuously, especially highlighting the associated costs and spatiotemporal trade-offs when using conventional subsurface monitoring techniques (well logs, core samples, chemical tracers, and 4D seismics). Active surveillance of GCS sites is essential for managing and mitigating potential leaks but is also required by regulation. With the goal of enhancing the monitoring capability at GCS sites, we present a rock physics-based joint data assimilation model to study a popular GCS site at Cranfield, Mississippi, USA. Synthetic continuous active-source seismic monitoring (CASSM) data (in the form of Vp and Qp measurements) and wellbore pressure monitoring data are assimilated with an ensemble of reservoir realizations to monitor gas saturation and reservoir pressure changes over a period of 100 years. Synthetic seismic attributes are generated using rock physics models (RPMs) and wellbore pressure monitoring data are extracted from the ground truth. Two assimilation methods, ensemble Kalman filter (EnKF) and ensemble Kalman smoother (EnKS), are tested in an observation system simulation experiment (OSSE) environment to assess the prediction accuracy of the individual and composite observation systems. The joint monitoring system achieves more accurate estimates of gas saturation and pressure, across the time span from start of injection to end of forecast, as compared to a single type of monitoring tool and irrespective of data assimilation algorithm choice. These results indicate that jointly assimilated data from two types of sensors (in this case, crosswell seismic and downhole pressure) may lead to a more risk-reducing monitoring design. One would expect that more data, vis-à-vis inclusion of a new sensor type, will improve the accuracy of any GCS monitoring system. However, from a practical standpoint, one important question is whether such a gain in accuracy is worth the additional cost associated with the new sensor. This paper focuses on quantifying the gain in accuracy, such that a practitioner can answer this question.
This report discusses the progress on the collaboration between Sandia National Laboratories (Sandia) and Japan Atomic Energy Agency (JAEA) on the sodium fire research in fiscal year 2019. First, the current sodium pool fire model in MELCOR, which is adapted from CONTAIN-LMR code, is discussed. The associated sodium fire input requirements are also presented. A proposed model improvement developed at Sandia is discussed. Finally, the validation study of the sodium pool fire model in MELCOR carried out by a JAEA's staff is described. To validate this model, a JAEA sodium pool fire experiment (F7-1 test) is used. A preliminary calculation is performed using a modified MELCOR model from a previous experiment simulation. The results of the calculation are discussed as well as suggestions for improvement. Finally, recommendations are made for new MELCOR simulations for next fiscal year, 2020.
This report summarizes findings and discussion from the Fossil Energy Workshop on Quantum Information Science & Technology which took place on November 19-21, 2019. Quantum Information Science (QIS) is expected to profoundly change the practice of science and engineering in the coming decades. It is a rapidly progressing field, fueled by large investments from the private sector and governments. Its importance to the U.S. economy and national security is underscored by the National Quantum Initiative Act passed in December 2018. QIS includes quantum sensing, quantum communications, quantum simulation experiments, and quantum computation. QIS technology exploits quantum phenomena for performing tasks that are impossible to do today, such as finding prime factors of large numbers or elucidating reaction mechanisms in complex chemical systems. The opportunities for applying QIS to problems encountered in fossil energy technology development are not known today. This workshop brought together, for the first time, experts in these fields to exchange information and explore potential research opportunities for QIS to advance fossil energy. The goal of the workshop was to develop a set of priority research opportunities that can inform future research efforts in QIS and build a community of next-generation researchers at the intersection of QIS and fossil energy.
The U.S. Department of Energy (DOE) established a need to understand the thermal-hydraulic properties of dry storage systems for commercial spent nuclear fuel (SNF) in response to a shift towards the storage of high-burnup (HBU) fuel (> 45 gigawatt days per metric ton of uranium, or GWd/MTU). This shift raises concerns regarding cladding integrity, which faces increased risk at the higher temperatures within spent fuel assemblies present within HBU fuel compared to low-burnup fuel (≤ 45 GWd/MTU). A dry cask simulator (DCS) was built at Sandia National Laboratories (SNL) in Albuquerque, New Mexico to produce validation-quality data that can be used to test the accuracy of the modeling used to predict cladding temperatures. These temperatures are critical to evaluating cladding integrity throughout the storage cycle of commercial spent nuclear fuel. A model validation exercise was previously carried out for the DCS in a vertical configuration. Lessons learned during the previous validation exercise have been applied to a new, blind study using a horizontal dry cask simulator (HDCS). Three modeling institutions – the Nuclear Regulatory Commission (NRC), Pacific Northwest National Laboratory (PNNL), and Empresa Nacional del Uranio, S.A., S.M.E. (ENUSA) – were granted access to the input parameters from the DCS Handbook, SAND2017-13058R, and results from a limited data set from the horizontal BWR dry cask simulator tests reported in the HDCS update report, SAND2019-11688R. With this information, each institution was tasked to calculate peak cladding temperatures and air mass flow rates for ten HDCS test cases. Axial as well as vertical and horizontal transverse temperature profiles were also calculated. These calculations were done using modeling codes (ANSYS/Fluent, STAR-CCM+, or COBRA-SFS), each with their own unique combination of modeling assumptions and boundary conditions. For this validation study, the ten test cases of the horizontal dry cask simulator were defined by three independent variables – fuel assembly decay heat (0.5 kW, 1 kW, 2.5 W, and 5 kW), internal backfill pressure (100 kPa and 800 kPa), and backfill gas (helium and air). The plots provided in Chapter 3 of this report show the axial, vertical, and horizontal temperature profiles obtained from the dry cask simulator experiments in the horizontal configuration and the corresponding models used to describe the thermal-hydraulic behavior of this system. The tables provided in Chapter 3 illustrate the closeness of fit of the model data to the experiment data through root mean square (RMS) calculations of the error in peak cladding temperatures (PCTs), PCT axial locations, axial temperature profiles, vertical and horizontal temperature profiles at two different axial locations, and air mass flow rates for the ten test cases, normalized by the experimental results. The model results are assigned arbitrary model numbers to retain anonymity. Due to the relatively flat axial temperature profiles, small temperature gradients resulted in large deviations of all models’ PCT axial location from the experimental PCT axial location. When the PCT axial location error is excluded in the calculation of the combined RMS of the normalized errors that considers PCT, the temperature profiles, and the air mass flow rates, the model data fits the experimental data to within 5%. When the vault information is excluded, the model data fits the experimental data to within 2.5%. An error analysis was developed further for one model, using the model and experimental uncertainties in each validation parameter to calculate validation uncertainties. The uncertainties for each parameter were used to define quantifiable validation criteria. For this analysis, the model was considered validated for a given comparison metric if the normalized error in that metric divided by the validation uncertainty was less than or equal to 1. When considering the combined RMS of the normalized errors of all metrics divided by their validation uncertainties, the model was found to have satisfied the criterion for model validation.
High-power lasers require enormous beam sizes to avoid optics damage; without plasma control of light, future higher-power systems will have prohibitive costs. The laser-induced formation of ionization patterns in gases provides an opportunity to manipulate the spatial and temporal properties of femtosecond to picosecond beams with precise control at high intensity, providing a path towards compact multi-petawatt lasers. In this project, we proposed new concepts of diffractive optics elements relying on ionization-based structures, including a holographic lens and a compression grating. The theoretical characterization of these optical elements was supported by particle-in-cell simulations. Experiments have been carried out to achieve reflective elements (i.e., plasma-based gratings) that demonstrated high robustness and efficiencies on the order of 50%, which validates the feasibility of our new concepts and paves the way for future plasma-based high-power laser systems.
The Fusion of Simulation, Experiment, and Data (FuSED) team provides a set of tools for solving inverse problems in structural dynamics and thermal physics, and also sensor placement optimization via Optimal Experimental Design (OED). These methods are used for designing experiments, model calibration, and verification/validation analysis of systems. This document provides a user’s guide to the input for the three apps that are supported for these methods. Details of input specifications, output options, and optimization parameters are included.
The Fusion of Simulation, Experiment, and Data (FuSED) team provides a set of tools for solving inverse problems in structural dynamics (InverseSD) and thermal physics (InverseAria), a sensor placement optimization tool via Optimal Experimental Design (OED), and a decision boundary tool using SVMs (TRACE). These methods are used for designing experiments, model calibration, and verification/validation analysis of systems. This document provides a user’s guide.
Extreme weather and natural hazards can disrupt the energy sector, affecting demand, generation, transmission, distribution, consumption and operational planning at regional and national scales. These disruptions stem from a broad range of atmospheric phenomena, including winter storms, freezing rain, wet snow loading, severe convection, flooding and landslides, wildfires, prolonged heat, and drought. Many of these same phenomena can also affect national security through impacts to transportation and infrastructure. To support the U.S. Department of Energy (DOE) focus on energy resilience and national security, the Atmospheric Radiation Measurement (ARM) User Facility is uniquely positioned to contribute measurement data, analyses, and modeling frameworks that can significantly improve predictive understanding of these hazards to mitigate their effects. To explore this opportunity, ARM convened a two-part virtual workshop in November 2025. The workshop engaged interdisciplinary experts in atmospheric science, energy systems, modeling, and operations. The goal of the meeting was to engage with these interdisciplinary experts to address three questions: • What are examples of atmospheric processes that represent significant risks to energy security or national security and where are those risks greatest? • What measurements or measurement strategies would improve ARM’s capacity to address these issues? • How can ARM and users of the ARM facility better work with the Energy Exascale Earth System Model (E3SM) and multi-sector modeling communities to apply ARM data to improving E3SM simulations of these phenomena? Participants were asked to submit white papers ahead of the meeting to initiate thinking on these themes and to help organize discussions. Workshop sessions were then organized around themes identified in the white papers. First from the white papers and then through subsequent discussions, workshop participants identified many examples that address the three questions listed above. Participants called out energy system vulnerabilities to weather phenomena such as the impact of freezing rain, strong winds, and excessive heat on power grids. They also noted the effects that weather phenomena could have on energy demand or supply (e.g., through effects of extreme temperatures). They called out security vulnerabilities such as impacts to crops from aerosol-borne pathogens and risks to industry due to melting permafrost in the Arctic. In all, over a dozen meteorological phenomena were linked to energy or security vulnerabilities. For many of the identified phenomena, participants pointed out where ARM was well poised to address issues (e.g., through measurements of cloud microphysics to inform studies of freezing rain) but also noted needs for additional measurements or modified measurement strategies. For example, adaptive scanning of severe weather would be valuable for probing winter storms or severe convection. Participants pointed out the value in integrating external observations with ARM measurements and with applying artificial intelligence (AI) to ARM observation analysis and they advocated for using model simulations to help optimize measurement strategies through Observing System Simulation Experiments (OSSEs). It was clear from the workshop that there are many ways that ARM observations can be used to mitigate energy and security concerns, but meeting participants were also asked to identify what they considered to be the greatest opportunities by ranking issues pertaining to the three workshop questions. This was accomplished through a survey administered to participants between the two virtual sessions. The highest-priority phenomena identified were winter storms, severe convection, and arctic processes. Discussion in the second session, therefore, focused primarily on these three areas, which were most fully developed in exploring ARM opportunities. Nevertheless, it was also clear that ARM has opportunities to contribute to all the identified topics. This report describes the workshop, including input from discussion and white papers (Sections 2 and 3) and a list of priority recommendations (section 4). Many other ideas for ARM contributions are discussed in individual white papers (Appendix D).
Several unknowns remain surrounding marine Carbon Dioxide Removal (mCDR) monitoring, reporting, and verification (MRV) practices and capabilities. Current in-situ sensor technology is limited (primarily pH and pCO 2 ), requiring calculations and assumptions to estimate changes in carbonate chemistry parameters, including total alkalinity (TA). Considering that cost, energy consumption, and accuracy of commercial sensors can vary by orders of magnitude, understanding how well existing sensors perform in an mCDR context is important for this emerging community. Likewise, documenting sensor limitations and how relatively simple models can optimize sensor deployments will improve MRV efforts and support protocol development. Here we (1) compare performance a variety of commercially available sensors in a blind mesocosm experiment simulating ocean alkalinity enhancement (OAE), and how sensor performance impacted carbonate chemistry estimates; (2) evaluate if sensors can distinguish the OAE signal from natural variability during a small scale OAE field test in Sequim Bay, WA, USA, and (3) use an idealized ocean biogeochemistry model to explore optimal sensor network design based on (1) and (2). Our mesocosm results indicate that correctly constraining pH uncertainty will be critical for accurate TA estimates with current sensor technology compared to the less impactful variation caused by uncertainty in pCO 2 (pH data that are presented throughout are reported on the total scale (pH T ) unless otherwise noted). Our pilot field test demonstrated that sensors were capable of distinguishing mCDR signatures from natural variability under optimal real-world conditions. Idealized modeling simulations of the field test showed that a range of sparse and dense (3 to 100) sensors sampling areas of detectable increases will underestimate the net change in surface pH by at least 35–55%, at both realistic and highly elevated alkalinity input levels. We also highlight the limitations of current sensing technology for MRV, and the importance of ocean biogeochemistry models as critical tools for predicting when and where mCDR signals will be detectable using available sensors. Overall, our findings suggest that commercially available pCO 2 sensors and some pH sensors will form an important backbone for mCDR MRV tasks, though complete MRV characterization will require these data to be used in combination with other tools.
Acute releases of hydrogen sulfide (H2S) are of serious concern in agriculture, especially when farmers agitate manure to empty storage pits before land application. Agitation can cause the release of dangerously high H2S concentrations, resulting in human and animal fatalities. To date, there is no proven technology to mitigate these short-term releases of toxic gas from manure. In our previous research, we have shown that biochar, a highly porous carbonaceous material, can float on manure and mitigate gaseous emissions over extended periods (days–weeks). In this research, we aim to test the hypothesis that biochar can mitigate H2S emissions over short periods (minutes–hours) during and shortly after manure agitation. The objective was to conduct proof-of-the-concept experiments simulating the treatment of agitated manure. Two biochars, highly alkaline and porous (HAP, pH 9.2) made from corn stover and red oak (RO, pH 7.5), were tested. Three scenarios (setups): Control (no biochar), 6 mm, and 12 mm thick layers of biochar were surficially-applied to the manure. Each setup experienced 3 min of manure agitation. Real-time concentrations of H2S were measured immediately before, during, and after agitation until the concentration returned to the initial state. The results were compared with those of the Control using the following three metrics: (1) the maximum (peak) flux, (2) total emission from the start of agitation until the concentration stabilized, and (3) the total emission during the 3 min of agitation. The Gompertz’s model for determination of the cumulative H2S emission kinetics was developed. Here, 12 mm HAP biochar treatment reduced the peak (1) by 42.5% (p = 0.125), reduced overall total emission (2) by 17.9% (p = 0.290), and significantly reduced the total emission during 3 min agitation (3) by 70.4%. Further, 6 mm HAP treatment reduced the peak (1) by 60.6%, and significantly reduced overall (2) and 3 min agitation’s (3) total emission by 64.4% and 66.6%, respectively. Moreover, 12 mm RO biochar treatment reduced the peak (1) by 23.6%, and significantly reduced overall (2) and 3 min total (3) emission by 39.3% and 62.4%, respectively. Finally, 6 mm RO treatment significantly reduced the peak (1) by 63%, overall total emission (2) by 84.7%, and total emission during 3 min agitation (3) by 67.4%. Biochar treatments have the potential to reduce the risk of inhalation exposure to H2S. Both 6 and 12 mm biochar treatments reduced the peak H2S concentrations below the General Industrial Peak Limit (OSHA PEL, 50 ppm). The 6 mm biochar treatments reduced the H2S concentrations below the General Industry Ceiling Limit (OSHA PEL, 20 ppm). Research scaling up to larger manure volumes and longer agitation is warranted.
Remote detection of radioactive materials in mixtures using handheld or portal detectors remains a challenge because of factors such as low concentration, environmental interference, sensor noise, and other complications. This work introduces a fast framework for generating realistic mixture spectra. Moreover, we present mixture isotope identification using data generated by the fast framework. Researchers have examined a range of conventional and recent algorithms within the fields of machine learning and deep learning. An application to uranium enrichment-level prediction has been included. Extensive simulation experiments validated the efficacy of the proposed framework.
In crystals, lattice defects, such as dislocations, control mechanical deformation. Similarly, it is widely believed that even in glasses and liquids some kinds of defects, strongly disordered regions, play a major role in deformation. To identify defects researchers focused on the nature of the short-range order (SRO) in the nearest neighbor cage of atoms. However, recent results by experiment, simulation and theory raise serious questions about this assumption. They suggest that the atomic medium-range order (MRO) provides resistance against flow at the atomic level. Because the MRO is a bulk property, it implies that defects play only a limited role. This new insight is supported by the density wave theory which shows that the MRO is driven by a top-down global force, rather than being a consequence of the SRO in the bottom-up manner, and the MRO provides stiffness to resist deformation. We briefly summarize the density wave theory, show that the MRO is related to ductility of metallic glasses, and discuss the implications on the role of the MRO in the atomic-level mechanism of deformation.