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At least 37 records · Page 2

Looking through model medieval green glasses: From color to recipe

Abstract The colors of medieval stained glasses depend on their chemical composition. The redox interactions in glass between iron and copper and their influence on the color were investigated in two soda‐lime silicate model glasses. Both glasses have close iron and copper redox ratios and copper oxidizes iron when the iron content is smaller than the copper content. The redox speciation of iron and copper was determined using combining x‐ray and optical absorption spectroscopies in relation with the resulting color. The molar extinction coefficient of Cu 2+ was estimated from the combined analysis to be 32 mol/L/cm. The glass color change from green to blue‐green color is assigned to the decrease of the total iron content, confirming that ancient glassmakers could control the final color with the glass recipe. These results provide reference data for further spectroscopic investigations of medieval stained glasses. Comparison with ancient copper‐colored green glass compositions suggests that the higher ratio of copper to iron total contents was imposed by the more reducing melting conditions in medieval furnaces.

Hunault, Myrtille O. J. Y.↗

A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling

Mechanistic models of how single cells respond to different perturbations can help integrate disparate big data sets or predict response to varied drug combinations. However, the construction and simulation of such models have proved challenging. Here, we developed a python-based model creation and simulation pipeline that converts a few structured text files into an SBML standard and is high-performance- and cloud-computing ready. We applied this pipeline to our large-scale, mechanistic pan-cancer signaling model (named SPARCED) and demonstrate it by adding an IFNγ pathway submodel. We then investigated whether a putative crosstalk mechanism could be consistent with experimental observations from the LINCS MCF10A Data Cube that IFNγ acts as an anti-proliferative factor. The analyses suggested this observation can be explained by IFNγ-induced SOCS1 sequestering activated EGF receptors. This work forms a foundational recipe for increased mechanistic model-based data integration on a single-cell level, an important building block for clinically-predictive mechanistic models.

60 APPLIED LIFE SCIENCES↗

Work measurement for estimating food preparation time of a bioregenerative diet

During space missions, such as the prospective Mars mission, crew labor time is a strictly limited resource. The diet for such a mission (based on crops grown in a bioregenerative life support system) will require astronauts to prepare their meals essentially from raw ingredients. Time spent on food processing and preparation is time lost for other purposes. Recipe design and diet planning for a space mission should therefore incorporate the time required to prepare the recipes as a critical factor. In this study, videotape analysis of an experienced chef was used to develop a database of recipe preparation time. The measurements were highly consistent among different measurement teams. Data analysis revealed a wide variation between the active times of different recipes, underscoring the need for optimization of diet planning. Potential uses of the database developed in this study are discussed and illustrated in this work.

NASA Discipline Life Support Systems↗

MicroBooNE BNB Electron Neutrino Overlay Sample (No Wire Info)

MicroBooNE samples are provided for collaborative development in two different formats: HDF5, targeting the broadest audience, and artroot, targeting users that are familiar with the software infrastructure of Fermilab neutrino experiments and more in general of HEP experiments. The HDF5 files are stored on Zenodo, together with a list of artroot files accessible with xrootd.This sample includes simulated interactions of neutrinos from the Booster Neutrino Beam (BNB), overlaid on top of cosmic ray data. The sample is restricted to charged-current electron neutrino interactions within the argon active volume of the time projection chamber.The HDF5 files in this sample do not include the information at the wire waveform level ("NoWire" label), allowing for larger number of events to be included in the data set.More documentation, including detailed description of content, recipes, and example usage, at https://github.com/uboone/OpenSamples.Suggested text for acknowledgment is the following:We acknowledge the MicroBooNE Collaboration for making publicly available the data sets [data set DOIs] employed in this work. These data sets consist of simulated neutrino interactions from the Booster Neutrino Beamline overlaid on top of cosmic data collected with the MicroBooNE detector [2017 JINST 12 P02017].In addition, we request that software products resulting from the usage of the datasets are also made publicly available.

Abratenko, Polina↗

MicroBooNE BNB Inclusive Overlay Sample (No Wire Info)

MicroBooNE samples are provided for collaborative development in two different formats: HDF5, targeting the broadest audience, and artroot, targeting users that are familiar with the software infrastructure of Fermilab neutrino experiments and more in general of HEP experiments. The HDF5 files are stored on Zenodo, together with a list of artroot files accessible with xrootd.This sample includes simulated interactions of neutrinos from the Booster Neutrino Beam (BNB), overlaid on top of cosmic ray data. The sample is inclusive, i.e. it includes all types of neutrinos and interactions, with relative abundance matching our nominal flux and cross section models. Interactions are simulated in in the whole cryostat volume.The HDF5 files in this sample do not include the information at the wire waveform level ("NoWire" label), allowing for larger number of events to be included in the data set.More documentation, including detailed description of content, recipes, and example usage, at https://github.com/uboone/OpenSamples.Suggested text for acknowledgment is the following:We acknowledge the MicroBooNE Collaboration for making publicly available the data sets [data set DOIs] employed in this work. These data sets consist of simulated neutrino interactions from the Booster Neutrino Beamline overlaid on top of cosmic data collected with the MicroBooNE detector [2017 JINST 12 P02017].In addition, we request that software products resulting from the usage of the datasets are also made publicly available.

Abratenko, Polina↗

Recent progress in atomic-scale controlled plasma processing

Atomic-scale control in plasma processing is becoming increasingly critical for fabricating of advanced semiconductor devices, particularly as the industry shifts toward three-dimensional (3D) architectures and high-aspect-ratio (HAR) structures. This review presents a comprehensive overview of recent developments in atomic-scale controlled plasma processes, organized along two key directions: the hierarchical structure of plasma–surface interactions and the generational evolution of atomic layer processing (ALP) technologies. We examined the gas phase, where molecular design enables selective generation of ions and radicals; the boundary layer, where transport phenomena govern species delivery into nanoscale features, and the surface, where temperature-dependent reactions and cyclic processing determine etching selectivity and precision. Building on this foundation, we outline five generations of ALP—from thermal atomic layer deposition to transport-aware, temporally and structurally decoupled processes—highlighting the increasing sophistication of process control. The review further explores the transition from empirical recipe development to science-based, data-driven methodologies. By integrating quantum-chemical modeling, advanced diagnostics, and machine learning, we demonstrated how predictive models can link plasma species composition to process outcomes, enabling autonomous and adaptive control strategies. Finally, this review discusses the broader societal implications of plasma process innovation through the E4 quartet: energy and resource efficiency, environmental sustainability, evolutionary advancement, and educational promotion. These principles guide the development of sustainable and intelligent atomic-scale manufacturing technologies that are not only technically advanced but also socially responsible.

Ishikawa, Kenji [Nagoya Univ. (Japan)] (ORCID:0000↗

Processing Spacecraft Data Without Confusion

Producing multiple versions of the same data product for the same time frame with the same remotely sensed inputs can be a recipe for disaster. Yet, amidst the commotion of satellite launch and early operations (LEO), such data processing is needed. After LEO, the situation gets worse. Processing newly arriving data ("forward processing") is augmented with reprocessing and algorithm development, comparison, evaluation, and testing -- often happening all at the same time. The problem can be analyzed in three main parts -- maintaining multiple versions of algorithms and data so that end-product users are not overwhelmed,allocating computer resources efficiently, and simplifying production operations so that va st amounts of data can be processed with minimal staff and fewer errors. OMIDAPS provides a framework for execution of algorithms that transform lower level data acquired by OMI on NASA's Aura satellite into higher level science data products. In contrast to traditional science data processing systems, we address all parts of the problem with an innovative approach allowing multiple data processing to run within a single physical system. The data products, imports, exports, and execution planning are all segregated into distinct "ArchiveSets." This paper describes reasons for multiple concurrent productions on a typical satellite data processing project using OMI as an example. It describes the virtual data processing system concept and its advantages over separate physical processing strings. It explores the specific implementation of the virtual systems within OMIDAPS and discusses some of the implications of our approach and describes how virtual processing is used to accomplish the overall mission of OMI data processing.

Tilmes, Curt↗

Community-Driven Methods for Open and Reproducible Software Tools for Analyzing Datasets from Atom Probe Microscopy

Atom probe tomography, and related methods, probe the three-dimensional architecture of a material. The software tools that microscopists use, and how these tools are connected into workflows, makes a substantial contribution to the accuracy and precision of such a material characterization experiment. Typically, we adapt methods from other communities like mathematics, data science, computational geometry, artificial intelligence, or scientific computing. We also realize that improving on research data management is a challenge when it comes to align with the FAIR data stewardship principles. Faced with this global challenge, we are convinced that collaborating is useful. Here, we report the results and challenges with an inter-laboratory call for developing test cases for several types of atom probe software tools. The results support why defining detailed recipes of software workflows and sharing these recipes is necessary and rewarding: Open source tools and (meta)data exchange can help to make our day-to-day data processing tasks become more efficient, the training of new users and knowledge transfer become easier, and assist us with automated quantification of uncertainties to gain access to substantiated results.

36 MATERIALS SCIENCE↗

An autonomous laboratory for the accelerated synthesis of novel materials

To close the gap between the rates of computational screening and experimental realization of novel materials, we introduce the A-Lab, an autonomous laboratory for the solid-state synthesis of inorganic powders. This platform uses computations, historical data from the literature, machine learning (ML) and active learning to plan and interpret the outcomes of experiments performed using robotics. Over 17 days of continuous operation, the A-Lab realized 41 novel compounds from a set of 58 targets including a variety of oxides and phosphates that were identified using large-scale ab initio phase-stability data from the Materials Project and Google DeepMind. Synthesis recipes were proposed by natural-language models trained on the literature and optimized using an active-learning approach grounded in thermodynamics. Analysis of the failed syntheses provides direct and actionable suggestions to improve current techniques for materials screening and synthesis design. The high success rate demonstrates the effectiveness of artificial-intelligence-driven platforms for autonomous materials discovery and motivates further integration of computations, historical knowledge and robotics.

36 MATERIALS SCIENCE↗

Towards scanning nanostructure X-ray microscopy

This article demonstrates spatial mapping of the local and nanoscale structure of thin film objects using spatially resolved pair distribution function (PDF) analysis of synchrotron X-ray diffraction data. This is exemplified in a lab-on-chip combinatorial array of sample spots containing catalytically interesting nanoparticles deposited from liquid precursors using an ink-jet liquid-handling system. A software implementation is presented of the whole protocol, including an approach for automated data acquisition and analysis using the atomic PDF method. The protocol software can handle semi-automated data reduction, normalization and modeling, with user-defined recipes generating a comprehensive collection of metadata and analysis results. By slicing the collection using included functions, it is possible to build images of different contrast features chosen by the user, giving insights into different aspects of the local structure.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

A Collaborative Analysis Tool for Thermal Protection Systems for Single Stage to Orbit Launch Vehicles

Presented is a design tool and process that connects several disciplines which are needed in the complex and integrated design of high performance reusable single stage to orbit (SSTO) vehicles. Every system is linked to every other system and in the case of SSTO vehicles with air breathing propulsion, which is currently being studied by the National Aeronautics and Space Administration (NASA); the thermal protection system (TPS) is linked directly to almost every major system. The propulsion system pushes the vehicle to velocities on the order of 15 times the speed of sound in the atmosphere before pulling up to go to orbit which results high temperatures on the external surfaces of the vehicle. Thermal protection systems to maintain the structural integrity of the vehicle must be able to mitigate the heat transfer to the structure and be lightweight. Herein lies the interdependency, in that as the vehicle's speed increases, the TPS requirements are increased. And as TPS masses increase the effect on the propulsion system and all other systems is compounded. To adequately determine insulation masses for a vehicle such as the one described above, the aeroheating loads must be calculated and the TPS thicknesses must be calculated for the entire vehicle. To accomplish this an ascent or reentry trajectory is obtained using the computer code Program to Optimize Simulated Trajectories (POST). The trajectory is then used to calculate the convective heat rates on several locations on the vehicles using the Miniature Version of the JA70 Aerodynamic Heating Computer Program (MINIVER). Once the heat rates are defined for each body point on the vehicle, then insulation thicknesses that are required to maintain the vehicle within structural limits are calculated using Systems Improved Numerical Differencing Analyzer (SINDA) models. If the TPS masses are too heavy for the performance of the vehicle the process may be repeated altering the trajectory or some other input to reduce the TPS mass. The problem described is an example of the need for collaborative design and analysis. Analysis tools are being developed to facilitate these collaborative efforts. RECIPE is a cross-platform application capable of hosting a number of engineers and designers across the Internet for distributed and collaborative engineering environments. Such integrated system design environments allow for collaborative team design analysis for performing individual or reduced team studies. The analysis tools mentioned earlier are commonly run on different platforms and are usually run by different people. To facilitate the larger number of potential runs that may need to be made, RECIPE connects the computer codes that calculate the trajectory data, heat rate data, and TPS masses so that the output from each tool is easily transferred to the model input files that need it. This methodology is being applied to solve launch vehicle thermal design problems to shorten the design cycle, and enable the project team to evaluate design options. Results will be presented indicating the effectiveness of this as a collaborative design tool.

Alexander, Reginald A.↗

A Collaborative Analysis Tool for Integrated Hypersonic Aerodynamics, Thermal Protection Systems, and RBCC Engine Performance for Single Stage to Orbit Vehicles

Presented is a computer-based tool that connects several disciplines that are needed in the complex and integrated design of high performance reusable single stage to orbit (SSTO) vehicles. Every system is linked to every other system, as is the case of SSTO vehicles with air breathing propulsion, which is currently being studied by NASA. An RBCC propulsion system integrates airbreathing and rocket propulsion into a single engine assembly enclosed within a cowl or duct. A typical RBCC propulsion system operates as a ducted rocket up to approximately Mach 3. Then there is a transition to a ramjet mode for supersonic-to-hypersonic acceleration. Around Mach 8 the engine transitions to a scramjet mode. During the ramjet and scramjet modes, the integral rockets operate as fuel injectors. Around Mach 10-12 (the actual value depends on vehicle and mission requirements), the inlet is physically closed and the engine transitions to an integral rocket mode for orbit insertion. A common feature of RBCC propelled vehicles is the high degree of integration between the propulsion system and airframe. At high speeds the vehicle forebody is fundamentally part of the engine inlet, providing a compression surface for air flowing into the engine. The compressed air is mixed with fuel and burned. The combusted mixture must be expanded to an area larger than the incoming stream to provide thrust. Since a conventional nozzle would be too large, the entire lower after body of the vehicle is used as an expansion surface. Because of the high external temperatures seen during atmospheric flight, the design of an airbreathing SSTO vehicle requires delicate tradeoffs between engine design, vehicle shape, and thermal protection system (TPS) sizing in order to produce an optimum system in terms of weight (and cost) and maximum performance. To adequately determine the performance of the engine/vehicle, the Hypersonic Flight Inlet Model (HYFIM) module was designed to interface with the RBCC engine model. HYFIM performs the aerodynamic analysis of forebodies and inlet characteristics of RBCC powered SSTO launch vehicles. HYFIM is applicable to the analysis of the ramjet/scramjet engine operations modes (Mach 3-12), and provides estimates of parameters such as air capture area, shock-on-lip Mach number, design Mach number, compression ratio, etc., based on a basic geometry routine for modeling axisymmetric cones, 2-D wedge geometries. HYFIM also estimates the variation of shock layer properties normal to the forebody surface. The thermal protection system (TPS) is directly linked to determination of the vehicle moldline and the shaping of the trajectory. Thermal protection systems to maintain the structural integrity of the vehicle must be able to mitigate the heat transfer to the structure and be lightweight. Herein lies the interdependency, in that as the vehicle's speed increases, the TPS requirements are increased. And as TPS masses increase the effect on the propulsion system and all other systems is compounded. The need to analyze vehicle forebody and engine inlet is critical to be able to design the RBCC vehicle. To adequately determine insulation masses for an RBCC vehicle, the hypersonic aerodynamic environment and aeroheating loads must be calculated and the TPS thicknesses must be calculated for the entire vehicle. To accomplish this an ascent or reentry trajectory is obtained using the computer code Program to Optimize Simulated Trajectories (POST). The trajectory is then used to calculate the convective heat rates on several locations on the vehicles using the Miniature Version of the JA70 Aerodynamic Heating Computer Program (MINIVER). Once the heat rates are defined for each body point on the vehicle, then insulation thicknesses that are required to maintain the vehicle within structural limits are calculated using Systems Improved Numerical Differencing Analyzer (SINDA) models. If the TPS masses are too heavy for the performance of the vehicle the process may be repeated altering the trajectory or some other input to reduce the TPS mass. E-PSURBCC is an "engine performance" model and requires the specification of inlet air static temperature and pressure as well as Mach number (which it pulls from the HYFIM and POST trajectory files), and calculates the corresponding stagnation properties. The engine air flow path geometry includes inlet, a constant area section where the rocket is positioned, a subsonic diffuser, a constant area afterburner, and either a converging nozzle or a converging-diverging nozzle. The current capabilities of E-PSURBCC ejector and ramjet mode treatment indicated that various complex flow phenomena including multiple choking and internal shocks can occur for combinations of geometry/flow conditions. For a given input deck defining geometry/flow conditions, the program first goes through a series of checks to establish whether the input parameters are sound in terms of a solution path. If the vehicle/engine performance fails mission goals, the engineer is able to collaboratively alter the vehicle moldline to change aerodynamics, or trajectory, or some other input to achieve orbit. The problem described is an example of the need for collaborative design and analysis. RECIPE is a cross-platform application capable of hosting a number of engineers and designers across the Internet for distributed and collaborative engineering environments. Such integrated system design environments allow for collaborative team design analysis for performing individual or reduced team studies. To facilitate the larger number of potential runs that may need to be made, RECIPE connects the computer codes that calculate the trajectory data, aerodynamic data based on vehicle geometry, heat rate data, TPS masses, and vehicle and engine performance, so that the output from each tool is easily transferred to the model input files that need it.

Stanley, Thomas Troy↗

Comparison of MERRA-2 and ECCO-V4 Ocean Surface Heat Fluxes: Consequences of Different Forcing Feedbacks on Ocean Circulation and Implications for Climate Data Assimilation

Forcing ocean models with reanalysis data is a common practice in ocean modeling. As part of this practice, prescribed atmospheric state variables and interactive ocean SST (Sea Surface Temperature) are used to calculate fluxes between the ocean and the atmosphere. When forcing an ocean model with reanalysis fields, errors in the reanalysis data, errors in the ocean model and errors in the forcing formulation will generate a different solution compared to other ocean reanalysis solutions (which also have their own errors). As a first step towards a consistent coupled ocean-atmosphere reanalysis, we compare surface heat fluxes from a state-of-the-art atmospheric reanalysis, the Modern-Era Retrospective analysis for Research and Applications, Version 2 (MERRA-2), to heat fluxes from a state-of-the-art oceanic reanalysis, the Estimating the Circulation and Climate of the Ocean Version 4, Release 2 (ECCO-v4). Then, we investigate the errors associated with the MITgcm (Massachusetts Institute of Technology general circulation model) ocean model in its ECCO-v4 ocean reanalysis configuration (1992-2011) when it is forced with MERRA- 2 atmospheric reanalysis fields instead of with the ECCO-v4 adjoint optimized ERA-interim state variables. This is done by forcing ECCO-v4 ocean with and without feedbacks from MERRA-2 related to turbulent fluxes of heat and moisture and the outgoing long wave radiation. In addition, we introduce an intermediate forcing method that includes only the feedback from the interactive outgoing long wave radiation. The resulting ocean circulation is compared with ECCO-v4 reanalysis and in-situ observations. We show that, without feedbacks, imbalances in the energy and the hydrological cycles of MERRA-2 (which are directly related to the fact it was created without interactive ocean) result in considerable SST drifts and a large reduction in sea level. The bulk formulae and interactive outgoing long wave radiation, although providing air-sea feedbacks and reducing model-data misfit, strongly relax the ocean to observed SST and may result in unwanted features such as large change in the water budget. These features have implications in a desired forcing recipe to be used. The results strongly and unambiguously argue for next generation data assimilation climate studies to involve fully coupled systems.

MERRA-2↗

Alanna Conners and the Origins of Principled Data Analysis

Alanna was one of the most important pioneers in the development of not just sophisticated algorithms for analyzing astronomical data but more importantly an overall viewpoint emphasizing the use of statistically sound principles in place of blind application of cook-book recipes, or black boxes. I will outline some of the threads of this viewpoint, emphasizing time series data, with a focus on the importance of these developments for the Age of Digital Astronomy that we are entering.

age of digital astronomy↗

Dynamic Rupture Modeling of the M7.1, 2019 Ridgecrest, California, Earthquake

An important part of the simulation technique implemented in the strong motion prediction recipe developed in Japan, originally proposed by Irikura and Miyake (2011) is the earthquake rupture characterization that is based on established empirical scaling relationships between source parameters and seismic moment. These scaling relationships and rupture characterization are derived from recorded data and are tested by simulations. Recent analysis of results obtained with the Recipe for the 2016 M7.1 Kumamoto earthquake performed by several researchers, indicate that in order to reproduce near-fault long-period ground motions with permanent displacements, typical for earthquakes with surface rupturing, the recipe needs modifications. In particular, improvements are required in characterizing the rupture kinematics at shallow depths, above the seismogenic zone (Irikura et al., 2019). Modeling of rupture dynamics for recorded earthquakes, and numerical simulations for different rupture scenarios, provides physical constrains on slip evolution in time and space, which can be used in adjustments of empirical source scaling relationships for large crustal earthquakes. In this study we mainly focused on rupture dynamics modeling of the 2019 M7 Ridgecrest, California earthquake. The characterization of the kinematic rupture model derived from the dynamic rupture models of this earthquake can inform further refinements of rupture modeling proposed by the Recipe. Through different rupture scenarios we investigated potential relationships between characteristics of Long Period Ground Motion Generation Area (LMGA), used in the Recipe, and asperity depth and rupture initiation.

58 GEOSCIENCES↗

Learning to Predict and Improve Build Successes in Package Ecosystems

Software has become increasingly complex, with a typical application depending on tens or hundreds of packages. Finding compatible versions and build configurations of these packages is challenging. This paper presents a method to learn the likelihood of software build success, and techniques for leveraging this information to guide dependency solvers to better software configurations. We leverage the heavily parameterized package recipes from the Spack package manager to produce a training data set of builds, and we use Graph Neural Networks to learn whether a given package configuration will build successfully or not. We apply our tool to the U.S. Exascale Computing Project’s software stack. We demonstrate its effectiveness in predicting whether a given package will build successfully. We show that our technique can be used to improve the solutions generated by dependency solvers, reducing the need for developers to find working builds by trial and error.

97 MATHEMATICS AND COMPUTING↗

ORCHA: A performance portability system for extreme heterogeneity

Heterogeneity is the prevalent trend in the rapidly evolving high-performance computing (HPC) landscape in both hardware and application software. The diversity in hardware platforms, currently comprising various accelerators and a future possibility of specializable chiplets, poses a significant challenge for scientific software developers aiming to harness optimal performance across different computing platforms while maintaining the quality of solutions when their applications are simultaneously growing more complex. Code synthesis and code generation can provide mechanisms to mitigate this challenge. We have developed a divide and conquer approach where different aspects of performance are handled by different stand-alone tools that are interfaced with the application through generated code. This portability system, ORCHA, enables users to configure and orchestrate their computations among available resources on a platform by specifying a high-level recipe, thereby permitting a many-to-many paradigm where each recipe results in a different variant of the application. The core design goal is to let users decide the application’s hardware mapping and orchestration by editing only the high-level recipe—without modifying the maintained source code or binding the application to a particular runtime system. Tools in ORCHA distribution are: CG-Kit for translating the recipe into an execution graph; Milhoja to execute the graph by orchestrating data and task movement among hardware resources; and Macroprocessor that enables users to define their own code-shorthand for higher composability and easier management of code variants. Additionally, the design of ORCHA permits tools to work in a plug-and-play mode where the application can build and run without CG-Kit and Milhoja, and either tool can be swapped out for other tools with similar capabilities by modifying the code generation portion of ORCHA. In this paper, we describe the design of ORCHA and the role that code-generation plays in isolating applications from tools. We demonstrate the breadth of configurations ORCHA enables with a case study in which an application configuration is realized on three distinct hardware mappings—a GPU-centric, a CPU/GPU balanced, and a CPU/GPU concurrent layouts by using different recipes.

Lee, Youngjun↗