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At least 199 records · Page 11

Accelerating Climate Simulations Through Hybrid Computing

Unconventional multi-core processors (e.g., IBM Cell B/E and NYIDIDA GPU) have emerged as accelerators in climate simulation. However, climate models typically run on parallel computers with conventional processors (e.g., Intel and AMD) using MPI. Connecting accelerators to this architecture efficiently and easily becomes a critical issue. When using MPI for connection, we identified two challenges: (1) identical MPI implementation is required in both systems, and; (2) existing MPI code must be modified to accommodate the accelerators. In response, we have extended and deployed IBM Dynamic Application Virtualization (DAV) in a hybrid computing prototype system (one blade with two Intel quad-core processors, two IBM QS22 Cell blades, connected with Infiniband), allowing for seamlessly offloading compute-intensive functions to remote, heterogeneous accelerators in a scalable, load-balanced manner. Currently, a climate solar radiation model running with multiple MPI processes has been offloaded to multiple Cell blades with approx.10% network overhead.

Zhou, Shujia↗

Experimentally Modeling the Emergence of Prebiotically Plausible Phospholipid Vesicles

The prebiotic emergence of protocells is an important part of any origins of life scenario. Although fatty-acid-based vesicles are well studied, how they transitioned to phospholipid vesicles is uncertain. Herein, we show that cyclic-phospholipids formed from fatty acids and glycerol could have played a role by generating a heterogeneous library of vesicles with diverse morphologies and tolerance to a range of metal ions, temperature, and pH. The cyclic phosphate moiety facilitates the natural emergence of vesicles composed of diacyl-phospholipids to become part of the chemical evolutionary process. Competing emergent properties of the various systems (facilitated by additives) could have led to an early preference of the sn-1,2-acyl-substitution on the glycerol backbone coincidental with extant biology. Thus, cyclic-phospholipids could have played a significant role not only in early prebiotic protocellular chemistry but also in facilitating the chemical evolution of protocells from the structurally simple to the functionally more complex.

Sunil Pulletikurti↗

Implementation and Evaluation of Emission‐Driven Land‐Atmosphere Coupled Simulation in E3SMv2.1

Emissions-driven (prognostic CO 2 ) simulations are essential for representing two-way carbon-climate feedback in Earth System Models. We present an emissions-driven land–atmosphere coupled biogeochemistry (BGC) configuration (BGCLNDATM_progCO2) in version 2.1 of the Energy Exascale Earth System Model (E3SMv2.1). This is the first E3SM configuration that performs land-atmosphere emission-hindcasts. Here, we document its implementation, evaluate the model's performance against observations and other models, and propose a structured evaluation protocol for such emissions-driven simulations. We conducted transient historical simulations (1850–2014) with BGCLNDATM_progCO2 and compare them to reference simulations—a land-atmosphere coupled simulation without BGC and a standalone land simulation with BGC, both using prescribed CO 2 concentrations—and to observations. BGCLNDATM_progCO2 overestimates atmospheric CO 2 concentrations by 11–23 ppm yet stays within the 40-ppm spread CMIP6 emission-driven models and retains physical climate properties comparable to the reference runs. The CO 2 biases are partly attributed to underrepresented oceanic CO 2 uptake and inadequate representations of some terrestrial processes. In general, introducing prognostic CO 2 did not change physical climate metrics at the global scale but had larger regional effects, particularly over land where spatially heterogeneous CO 2 and prognostic leaf area index influenced surface energy balance. Finally, we propose a general evaluation protocol including spin-up assessment, atmospheric CO 2 benchmarking, physical climate evaluation, and land biogeochemical analysis to support scientific rigor and facilitate inter-model comparisons. The new configuration lays the groundwork for future enhancements, including improved terrestrial biogeochemical processes, integrated marine biogeochemistry, and additional human–Earth system interactions. These developments advance E3SM toward fully coupled emissions-driven simulations, enabling more accurate carbon–climate feedback projections and informing mitigation policy by providing physically consistent carbon-budget metrics for mitigation scenarios.

54 ENVIRONMENTAL SCIENCES↗

Using probability distribution function as a scaling approach to incorporate soil heterogeneity into biogeochemical models for greenhouse gas predictions (Final Technical Report)

The project investigated biogeochemical processes at terrestrial-aquatic interfaces (TAIs), focusing on soil microsite heterogeneity and its impact on greenhouse gas (GHG) fluxes. Using laboratory experiments, modeling, and data integration, researchers explored redox-driven microbial processes under fluctuating hydrological conditions. Key advancements included modifying the DAMM-GHG model to incorporateelectron acceptor availability and enhancing the AquaMEND model for improved microbial metabolism representation. Results highlighted microsite redox variability as a key driver of GHG fluxes, informing Earth system models. The project fostered interdisciplinary collaborations, student training, and the development of novel modeling frameworks to improve Earth'senergy budget.

54 ENVIRONMENTAL SCIENCES↗

Integrated Effects of Site Hydrology and Vegetation on Exchange Fluxes and Nutrient Cycling at a Coastal Terrestrial‐Aquatic Interface

Abstract The complex interactions among soil, vegetation, and site hydrologic conditions driven by precipitation and tidal cycles control the biogeochemical transformations and bi‐directional exchange of carbon and nutrients across the terrestrial–aquatic interfaces (TAIs) in coastal regions. This study uses a highly mechanistic model, Advanced Terrestrial Simulator (ATS)‐PFLOTRAN, to explore how these interactions affect exchanges of materials and carbon and nitrogen cycling. We used a transect in the Chesapeake Bay region that spans zones of open water, coastal wetland, transition, and upland forest. We designed several simulation scenarios to parse the effects of the individual controlling factors and the sensitivity of carbon cycling to reaction rate parameters derived from laboratory experiments. Our simulations reveal an active zone for carbon cycling under the transition zones between the wetland and the upland. Evapotranspiration is found to enhance the exchange fluxes between the surface and subsurface domains, resulting in a higher dissolved oxygen concentration in the TAIs. The transport of organic carbon derived from plant leaves and roots provide an additional source of organic carbon needed for the aerobic respiration and denitrification processes in the TAIs. The variability in reaction rate parameters associated with microbial activities is also found to play a dominant role in controlling the heterogeneity and dynamics of the simulated redox conditions. This modeling‐focused exploratory study enabled us to better understand the complex interactions among soil, water and microbes that govern the hydro‐biogeochemical processes at the TAIs, which is an important step toward representing coastal ecosystems in larger‐scale Earth system models.

54 ENVIRONMENTAL SCIENCES↗

Mechanisms of voids formation during cooldown and freezing of lithium in SP-100 type systems

The mechanisms of void formation during the cooldown and freezing of lithium coolant within the primary loop of SP-100 type systems are investigated. These mechanisms are: (a) homogeneous nucleation, (b) heterogeneous nucleation, (c) normal segregation of helium gas dissolved in liquid lithium, and (d) shrinkage of lithium during freezing. To evaluate the void formation potential due to segregation, a numerical scheme that couples the freezing and mass diffusion processes in both the solid and liquid regions is developed. The results indicated that the formation of He bubbles is unlikely by either homogeneous or heterogeneous nucleation during the cooldown process. However, homogeneous nucleation of He bubbles following the segregation of dissolved He in liquid Lithium ahead of the solid-liquid interface is likely to occur. Results also show that total volume of He void is insignificant when compared to that of shrinkage voids.

Yang, Jae Y.↗

Exploring Diverse Data Sets and Developing New Theories and Ideas With Project Integration Architecture

The development of new ideas is the essence of scientific research. This is frequently done by developing models of physical processes and comparing model predictions with results from experiments. With models becoming ever more complex and data acquisition systems becoming more powerful, the researcher is burdened with wading through data ranging in volume up to a level of many terabytes and beyond. These data often come from multiple, heterogeneous sources and usually the methods for searching through it are at or near the manual level. In addition, current documentation methods are generally limited to researchers pen-and-paper style notebooks. Researchers may want to form constraint-based queries on a body of existing knowledge that is, itself, distributed over many different machines and environments and from the results of such queries then spawn additional queries, simulations, and data analyses in order to discover new insights into the problem being investigated. Currently, researchers are restricted to working within the boundaries of tools that are inefficient at probing current and legacy data to extend the knowledge of the problem at hand and reveal innovative and efficient solutions. A framework called the Project Integration Architecture is discussed that can address these desired functionalities.

Benyo, Theresa L.↗

Spatial Heterogeneity in Cloud Condensation Nuclei (SHINE) Field Campaign Report

Multiple land-atmosphere coupling processes influence the spatial distribution of boundary-layer energy, moisture, aerosol, or cloud condensation nuclei (CCN) properties. Accurately quantifying the spatial and temporal distributions of CCN concentrations is essential for investigating aerosol-cloud interactions and reducing uncertainties in aerosol radiative forcing estimates of Earth's system.

54 ENVIRONMENTAL SCIENCES↗

Atomic Evolution of Hydrogen Intercalation Wave Dynamics in Palladium Nanocrystals Revealed by Liquid-Phase Transmission Electron Microscopy

Solute-intercalation-induced phase separation creates spatial heterogeneities in host materials, a phenomenon ubiquitous in batteries, hydrogen storage, and other energy devices. Despite many efforts, probing intercalation processes at the atomic scale has been a significant challenge. By utilizing liquid-phase transmission electron microscopy (TEM), we study hydrogen (de)intercalation in palladium nanocrystals as a model system and have achieved unprecedented atomic-resolution imaging of hydrogen intercalation wave dynamics. Our observations reveal that intercalation wave mechanisms, instead of shrinking-core mechanisms, prevail at ambient temperature for palladium nanocubes ranging from ∼60 nm down to ∼10 nm. Systematic image analysis uncovers the atomic evolution of the hydrogen intercalation wave, transitioning from nonplanar and inclined boundaries to those closely aligned with {100} planes. Our kinetic Monte Carlo simulations demonstrate that the observed intercalation wave dynamics correspond to sorption pathways minimizing the lattice mismatch strain at the phase boundary. In conclusion, unveiling the atomic intercalation pathways holds profound implications for engineering intercalation-mediated devices and advancements in energy sciences.

Lee, Daewon [Lawrence Berkeley National Laboratory↗

BULKI-Store v0.3.2

BULKI-Store is a distributed object storage system optimized for high-performance computing environments. Built with a Rust core and Python bindings, it efficiently manages scientific and machine learning datasets across HPC clusters. The system employs a client-server architecture with MPI integration, enabling seamless scaling on supercomputers like Perlmutter. BULKI-Store's object-oriented approach provides intuitive data organization with rich metadata support, contrasting with traditional file-based solutions. Key optimizations include selective checkpoint loading, unified checkpoint files, and object chunking for large data transfers. For machine learning workloads, BULKI-Store offers advantages through fine-grained access patterns, dynamic data sharing between training instances, and reduced memory pressure. Memory management features include strategic Python GC calls, minimized data copies, and batch processing capabilities. The system leverages Rayon's thread pool for asynchronous data prefetching and supports multiple CPU architectures (ARM64, x86, AMD, RISC-V). By combining performance optimizations with developer-friendly APIs, BULKI-Store addresses the complex data management challenges of modern HPC applications while maintaining compatibility across heterogeneous computing environments.

Zhang, Wei [Lawrence Berkeley National Laboratory ↗

HI and FIR emission from S0 galaxies

A large body of work has accumulated in recent years which throws into disarray the traditional assumption that S0 systems are inert, non-starforming galaxies with uniform, old stellar populations. The copious 21-cm data have been recently reviewed and assessed by Wardle and Knapp (1986). This work showed that roughly a third of the several hundred observed S0's contain detectable amounts of neutral hydrogen (HI). More recently, Pogge and Eskridge (1987) have shown that a significant fraction of HI-rich systems also exhibit H alpha emission. Thronson et al. (1989) report detection of CO line emission from two thirds of the S0's in their sample. Both of these last papers, however, report on fairly small data sets (approx. 20 objects each). From co-added Infrared Astronomy Satellite (IRAS) data, Knapp et al. (1989) report that roughly two thirds of a sample of several hundred S0's are detected at 60 and 100 microns. Work by Bally and Thronson (1989) and Walsh et al. (1989) has shown that, while a large number of S0's follow a relation between radio continuum and far infrared radiation (FIR) emission similar to that found for spirals, significant numbers of both radio-bright, and FIR-bright S0's exist. Clearly, a large number of factors are involved in determining the state of the interstellar medium in S0 galaxies. The class is probably heterogeneous, suggesting that large data samples are required to sort out various sorts of objects. The 21 cm and FIR samples are the two largest currently available. It is therefore of interest to compare the two and see where this leads. The following results are already clear: HI and FIR flux data can be used to isolate strong candidates for systems which have gained their HI gas via accretion; a rough power-law relationship exists for galaxies which are undergoing relatively normal star-forming activity; a heterogeneous class of galaxies with strong FIR emission compared to their HI emission exists. Further work is required to determine the various physical processes responsible for this last class.

Eskridge, Paul B.↗

The AI Bus architecture for distributed knowledge-based systems

The AI Bus architecture is layered, distributed object oriented framework developed to support the requirements of advanced technology programs for an order of magnitude improvement in software costs. The consequent need for highly autonomous computer systems, adaptable to new technology advances over a long lifespan, led to the design of an open architecture and toolbox for building large scale, robust, production quality systems. The AI Bus accommodates a mix of knowledge based and conventional components, running on heterogeneous, distributed real world and testbed environment. The concepts and design is described of the AI Bus architecture and its current implementation status as a Unix C++ library or reusable objects. Each high level semiautonomous agent process consists of a number of knowledge sources together with interagent communication mechanisms based on shared blackboards and message passing acquaintances. Standard interfaces and protocols are followed for combining and validating subsystems. Dynamic probes or demons provide an event driven means for providing active objects with shared access to resources, and each other, while not violating their security.

Schultz, Roger D.↗

Catalytic methods using molecular oxygen for treatment of PMMS and ECLSS waste streams, volume 2

Catalytic oxidation has proven to be an effective addition to the baseline sorption, ion exchange water reclamation technology which will be used on Space Station Freedom (SSF). Low molecular weight, polar organics such as alcohols, aldehydes, ketones, amides, and thiocarbamides which are poorly removed by the baseline multifiltration (MF) technology can be oxidized to carbon dioxide at low temperature (121 C). The catalytic oxidation process by itself can reduce the Total Organic Carbon (TOC) to below 500 ppb for solutions designed to model these waste waters. Individual challenges by selected contaminants have shown only moderate selectivity towards particular organic species. The combined technology is applicable to the more complex waste water generated in the Process Materials Management System (PMMS) and Environmental Control and Life Support System (ECLSS) aboard SSF. During the phase 3 Core Module Integrated Facility (CMIF) water recovery tests at NASA MSFC, real hygiene waste water and humidity condensate were processed to meet potable specifications by the combined technology. A kinetic study of catalytic oxidation demonstrates that the Langmuir-Hinshelwood rate equation for heterogeneous catalysts accurately represent the kinetic behavior. From this relationship, activation energy and rate constants for acetone were determined.

Akse, James R.↗

Web Based Prognostics and 24/7 Monitoring

We created a general framework for analysts to store and view data in a way that removes the boundaries created by operating systems, programming languages, and proximity. With the advent of HTML5 and CSS3 with JavaScript the distribution of information is limited to only those who lack a browser. We created a framework based on the methodology: one server, one web based application. Additional benefits are increased opportunities for collaboration. Today the idea of a group in a single room is antiquated. Groups will communicate and collaborate with others from other universities, organizations, as well as other continents across times zones. There are many varieties of data gathering and condition-monitoring software available as well as companies who specialize in customizing software to individual applications. One single group will depend on multiple languages, environments, and computers to oversee recording and collaborating with one another in a single lab. The heterogeneous nature of the system creates challenges for seamless exchange of data and ideas between members. To address these limitations we designed a framework to allow users seamless accessibility to their data. Our framework was deployed using the data feed on the NASA Ames' planetary rover testbed. Our paper demonstrates the process and implementation we followed on the rover.

CSS3↗

GeneLab Analysis Working Group Kick-Off Meeting

Goals to achieve for GeneLab AWG - GL vision - Review of GeneLab AWG charter Timeline and milestones for 2018 Logistics - Monthly Meeting - Workshop - Internship - ASGSR Introduction of team leads and goals of each group Introduction of all members Q/A Three-tier Client Strategy to Democratize Data Physiological changes, pathway enrichment, differential expression, normalization, processing metadata, reproducibility, Data federation/integration with heterogeneous bioinformatics external databases The GLDS currently serves over 100 omics investigations to the biomedical community via open access. In order to expand the scope of metadata record searches via the GLDS, we designed a metadata warehouse that collects and updates metadata records from external systems housing similar data. To demonstrate the capabilities of federated search and retrieval of these data, we imported metadata records from three open-access data systems into the GLDS metadata warehouse: NCBI's Gene Expression Omnibus (GEO), EBI's PRoteomics IDEntifications (PRIDE) repository, and the Metagenomics Analysis server (MG-RAST). Each of these systems defines metadata for omics data sets differently. One solution to bridge such differences is to employ a common object model (COM) to which each systems' representation of metadata can be mapped. Warehoused metadata records are then transformed at ETL to this single, common representation. Queries generated via the GLDS are then executed against the warehouse, and matching records are shown in the COM representation (Fig. 1). While this approach is relatively straightforward to implement, the volume of the data in the omics domain presents challenges in dealing with latency and currency of records. Furthermore, the lack of a coordinated has been federated data search for and retrieval of these kinds of data across other open-access systems, so that users are able to conduct biological meta-investigations using data from a variety of sources. Such meta-investigations are key to corroborating findings from many kinds of assays and translating them into systems biology knowledge and, eventually, therapeutics.

GeneLab↗

Radiation-induced transients on solid and molten Li and K iodides

The study, quantification, and monitoring of iodine in nuclear power generation systems have been paramount due to its environmental and health implications. Thorough speciation and transport studies strengthened the development and deployment of water reactors, which are now required for the new generation of Molten Salt Reactors (MSR), where the fuel and coolant are a complex liquid system of suitable halides. The speciation, radiation-induced chemistry, and transport of iodine (I-127, I-129 and I-131) under extreme conditions of temperature and ionizing radiation are among the challenges for the future implementation of MSR’s. In aqueous systems, the triiodide-iodine-iodide (I3--I2-I-) equilibrium is strongly dependent on the conditions of the medium. In molten iodides and chlorides, the triiodide detection (and its disproportionation) poses challenges due to the extreme conditions of temperature and radiation, but studies have shown a dependence on temperature, absorbed dose and salt composition. Through absorption spectroscopy techniques (diffuse reflectance and high-temperature UV-Vis), as well as resonance (Electron Paramagnetic Resonance) it is possible to identify primary transients induced by ionizing radiation trapped in the solid phase (Solid-state radiolysis), and steady-state main absorption components with a fast-acquisition real-time spectroscopy. The presence of heterogeneous phase (colloids), viscosity changes, and gas evolution are among the observed processes. A specific case of study is speciation in the presence of Ni. A corrosion product with magnetic properties due to unpaired electrons in its electronic structure. Ferromagnetic materials are monitored in solidified salts to identify aggregation and phase separation. Comparative studies of eutectic mixtures of LiI-KI and LiCl-KCl with known addition of dopants will be presented, with a perspective of radiation chemistry and its possible implications in complex systems.

36 - MATERIALS SCIENCE↗

A programming environment for distributed complex computing. An overview of the Framework for Interdisciplinary Design Optimization (FIDO) project. NASA Langley TOPS exhibit H120b

The Framework for Interdisciplinary Design Optimization (FIDO) is a general programming environment for automating the distribution of complex computing tasks over a networked system of heterogeneous computers. For example, instead of manually passing a complex design problem between its diverse specialty disciplines, the FIDO system provides for automatic interactions between the discipline tasks and facilitates their communications. The FIDO system networks all the computers involved into a distributed heterogeneous computing system, so they have access to centralized data and can work on their parts of the total computation simultaneously in parallel whenever possible. Thus, each computational task can be done by the most appropriate computer. Results can be viewed as they are produced and variables changed manually for steering the process. The software is modular in order to ease migration to new problems: different codes can be substituted for each of the current code modules with little or no effect on the others. The potential for commercial use of FIDO rests in the capability it provides for automatically coordinating diverse computations on a networked system of workstations and computers. For example, FIDO could provide the coordination required for the design of vehicles or electronics or for modeling complex systems.

Townsend, James C.↗

Development of Machine Learning Algorithms to Segment and Study Images of Astromaterial Samples

Introduction: Micrometer-scale chemical analyses of chondritic meteorites and mission-returned asteroid samples can reveal details of the physical and chemical processes operating in the early solar system, including processes that gave rise to planets, moons, and minor bodies. These primitive astromaterials are comprised of chondrules, calcium- and aluminum-rich inclusions (CAI), and many other silicates, oxides, metals, sulfides, and fine-grained materials. The chemical and mineralogical complexity of these samples, vast populations of different components, and heterogeneity across mm to km scales, all limit our understanding of the origin and evolution of these materials. Here, we describe recent efforts to use machine learning techniques to automate the segmentation of chemical maps of chondritic meteorites, designed to aid studies of asteroid samples returned by spacecraft. By automating the task of segmentation it will become possible to rapidly analyze and interpret the sizes, shapes, mineralogy, chemistry, and other properties of every chondrule, calcium- and aluminum-rich inclusion (CAI) and other clast within and between asteroid samples. Sample return missions significantly accelerate and heighten the need to develop such new data analysis techniques, and associated data repositories. Techniques: Neural networks require abundant training data, i.e. images which have been segmented by a human user. We have manually segmented data available from previous petrologic and chemical work at NASA Johnson Space Center and the American Museum of Natural History [1-4]. These data were derived from energy- and wavelength-dispersive X-ray spectroscopy (EDS, WDS) mapping of samples from many chondrite groups. The Deeplabv3+ [5] neural network architecture was trained on human-labeled masks and used to create machine-labeled masks. Several different algorithms were investigated, with inputs ranging from common RGB image formats through to hyperspectral datasets, with raw data comprising greyscale maps of Mg, Ca, and Al, with or without Si, Fe, Ti for both EDS and WDS data, and extending to other elements in EDS only. Each greyscale image was paired with a binary mask for each labelled particle type. Results: The trained algorithms can segment (Fig 1), classify, and measure the dimensions of thousands of particles in chemical maps of a standard 1-inch round petrographic section in seconds to minutes, rather than many hours needed by a human. Accuracy of the algorithms varied from chondrite to chondrite and across particle types. Further results and details of the algorithms will be presented at the workshop. Future directions: Machine learning has the potential to revolutionize our understanding of complex particle populations contained within primitive astromaterial, with segmentation being a critical first step. Example applications include better understanding of particle transport, nebular reservoirs, parent body accretion, and a deeper understanding of the relationships between particle populations and bulk rock elemental and isotopic compositions. In addition to benefits that machine learning can bring to individual researchers, building a community data repository of thousands to millions of particles across hundreds of samples will open up many other possibilities. For example, with a large enough dataset it will be possible to search for exceptionally closely matching particles across disparate samples. Such a capability would enable a single CAI from OSIRISREx or Hayabusa/II samples to be matched to chondritic CAIs that exhibit near-identical size, texture, and mineralogy, down to the level of similar core phenocrysts, zonation, and rim sequences. Such comparative analyses will help to disentangle precursor chemistry, chronology, gas/dust reservoirs during heating, and accretion. Such an endeavor would be impossible without machine learning and a large community data repository of astromaterial chemical/mineralogic maps.

Machine Learning↗