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At least 1,189 records · Page 66

Development of Prototypical District-Scale Models: Preprint

The U.S. has set the climate goal to achieve net-zero greenhouse gas emissions by 2050. District-scale solutions, which include scale-specific opportunities for energy and emissions savings, can be investigated and implemented to help accelerate decarbonization and progress toward this goal. However, there is currently a lack of district-scale models of buildings and community energy systems that can be used to evaluate potential district-scale technologies and strategies across a range of representative community types. This initial work aims to define and develop prototype district models that can be adapted to support the planning, design, and operation of buildings and energy systems in districts considering the complexity and interactions of diverse building loads, weather impacts, distributed energy resources (e.g., PV, EV, electric and thermal energy storage), electric and thermal grid systems, and pricing signals. An overall workflow for developing these prototype district models is established. Stakeholders and potential users of the prototype district models provided technical feedback. The specifications of the selected high priority districts were defined and documented in a scorecard format. An example prototype district model was implemented with the URBANoptTM platform workflows. A case study was performed to demonstrate the model application.

district↗

Knowledge Oriented Graph Unified Transformer (KOGUT) v0.1

KOGUT — Knowledge Oriented Graph Unified Transformer KOGUT implements the Relational Graph Transformer (RelGT) architecture for knowledge graph link prediction in biological domains, with a primary focus on microbial growth media prediction. While the original RelGT (arXiv:2505.10960) targets relational tables, time series, and multi-table databases, KOGUT adapts this architecture for heterogeneous biological knowledge graphs, providing first-in-class AI predictive models for microbial cultivation. Key Adaptations Beyond Original RelGT: - Knowledge Graph Focus: Applied to biological KGs with semantic node types (taxa, chemicals, media, phenotypes, environments) versus generic relational database tables, trained on the KG-Microbe knowledge graph (1.3M entities, 2.9M edges, 24 relation types). - Multimodal Node Encoding: Integrates node labels, categories, descriptions, and synonyms from KG metadata through learned embedding layers—adapting relational column features to graph node attributes with textual semantics. - Extended K-Hop Subgraph Strategy: Optimized neighborhood sampling (3-hop default, configurable up to 200 nodes) tuned for sparse biological networks, building on the original local-global attention framework with biological relation preservation. - Biolink Predicate Preservation: Type-specific transformations for 24 biological edge semantics (occurs_in, consumes, produces, has_phenotype, subclass_of) beyond standard relational foreign keys, enabling multi-relation link prediction. - Inductive Learning Support: Enables zero-shot predictions for novel taxa through feature-based embeddings (temperature, oxygen requirements, gram stain, cell shape), extending the original transductive relational benchmark scope to uncultured microorganisms. CheapSOTA Performance Optimizations (This Distribution): - VQ-EMA Centroid Attention: Vector quantization with exponential moving average for improved global context modeling (+5-10% MRR improvement). - HDF5 Precomputed Data Loading: One-time preprocessing of k-hop subgraphs to eliminate redundant graph traversals (2-5× training speedup). - Distributed Data Parallel Training: Multi-GPU support for scaling to larger knowledge graphs (tested on 4× NVIDIA A100 GPUs at NERSC Perlmutter). - Mixed Precision Training: Automatic mixed precision (AMP) for memory efficiency and faster training. Advantages Over Standard Knowledge Graph Embedding Models: Combines RelGT's proven multi-element tokenization (features, type, hop, structure) with graph-native biological representations, enabling interpretable link prediction across heterogeneous entities that standard embedding models (TransE, RotatE, ComplEx) and table-based transformers cannot directly model. Achieves near-perfect performance on microbial growth media prediction (MRR: 0.9966, Precision@1: 0.9932, Hit@10: 1.0000) while maintaining explainability through attention-based reasoning over biological pathways. Training Data: - KG-Microbe merged knowledge graph: 1,379,337 nodes, 2,960,472 edges - 24 biological relation types including taxonomic hierarchies, metabolic interactions, phenotype associations, and environmental relationships - Primary prediction task: Growth media suitability for microbial taxa (biolink:occurs_in, 50K edges) - Multi-relation capability: Predicts links for any of the 24 relation types, including chemical consumption/production, phenotype associations, and taxonomic classification Citation: Original RelGT Architecture: Dwivedi et al., "Relational Graph Transformer", arXiv:2505.10960, 2025 KOGUT Implementation: Knowledge Oriented Graph Unified Transformer for Microbial Growth Media Prediction Developed at Lawrence Berkeley National Laboratory (LBNL) Trained on NERSC Perlmutter supercomputer

Joachimiak, Marcin [Lawrence Berkeley National Lab↗

Propagule Pressure in Microbial Introductions

The use of potentially beneficial microorganisms in agriculture (microbial inoculants) has rapidly accelerated in recent years. For microbial inoculants to be effective as agricultural tools, these organisms must be able to survive and persist in novel environments while not destabilizing the resident community or spilling over into adjacent natural ecosystems. Here, we adapt a macroecological propagule pressure model to a microbial scale and present an experimental approach for testing the role of propagule pressure in microbial inoculant introductions. We experimentally determined the risk-release relationship for an IAA-expressing Pseudomonas simiae inoculant in a model monocot system. We then used this relationship to simulate establishment outcomes under a range of application frequencies (propagule number) and inoculant concentrations (propagule size). Our simulations show that repeated inoculant applications may increase establishment, even when increased inoculant concentration does not alter establishment probabilities. The dataset filed here includes the experimemtal datafile, and a RMarkdown file that includes all the code used in in both the modeling and anaylsis.

agriculture↗

Modeling of topographic effects on Antarctic sea ice using multivariate adaptive regression splines

The role of seafloor topography in the spatial variations of the southern ocean sea ice cover as observed (every other day) by the Nimbus 7 scanning multichannel microwave radiometer satellite in the years 1980, 1983, and 1984 is studied. Bottom bathymetry can affect sea ice surface characteristics because of the basically barotropic circulation of the ocean south of the Antarctic Circumpolar current. The main statistical tool used to quantify this effect is a local nonparametric regression model of sea ice concentration as a function of the depth and its first two derivatives in both meridional and zonal directions. First, we model the relationship of bathymetry to sea ice concentration in two sudy areas, one over the Maud Rise and the other over the Ross Sea shelf region. The multiple correlation coefficient is found to average 44% in the Maud Rise study area and 62% in the Ross Sea study area over the years 1980, 1983, and 1984. Second, a strategy of dividing the entire Antarctic region into an overlapping mosaic of small areas, or windows is considered. Keeping the windows small reduces the correlation of bathymetry with other factors such as wind, sea temperature, and distance to the continent. We find that although the form of the model varies from window to window due to the changing role of other relevant environmental variables, we are left with a spatially consistent ordering of the relative importance of the topographic predictors. For a set of three representative days in the Austral winter of 1980, the analysis shows that an average of 54% of the spatial variation in sea ice concentration over the entire ice cover can be attributed to topographic variables. The results thus support the hypothesis that there is a sea ice to bottom bathymetry link. However this should not undermine the considerable influence of wind, current, and temperature which affect the ice distribution directly and are partly responsible for the observed bathymetric effects.

De Veaux, Richard D.↗

REBOUND: Reverse Engineering Bidirectional Outflow Under Non-Equilibrium Diffusion

Rare-earth elements (REEs) are essential for electronics, renewable energy, and defense technologies. However, the current supply of REEs relies on mining concentrated in a few countries and energy-intensive separations. DOE’s Basic Energy Sciences (BES) program has launched a grand challenge which aims to ensure a sustainable supply of critical REEs by developing innovative and environmentally friendly separation methods. As an alternative to costly and harmful traditional methods, the Non-Equilibrium Transport Driven Separations (NETS) initiative has created a microfluidic Y-channel co-flow method that applies external fields to exploit magneto- and electrohydrodynamic effects for separating dilute REE ions from complex feedstocks. Computational fluid dynamics (CFD) studies have identified a few operating conditions with promising ion selectivity and separation efficiency. However, challenges remain regarding Y-channel versatility across feedstocks and accurate incorporation of physical phenomena into CFD models. In this work, we develop a multi-fidelity modelling approach which integrates experimental results with CFD simulation to build a surrogate model for the dependence of separation efficiency to variation of design parameters. The surrogate model enables a reinforcement learning (RL) method to adaptively launch CFD and experimental runs, improving model fidelity around optimal Y-channel parameters.

36 MATERIALS SCIENCE↗

The Integrated Medical Model

The goals of the Integrated Medical Model (IMM) are to develop an integrated, quantified, evidence-based decision support tool useful to crew health and mission planners and to help align science, technology, and operational activities intended to optimize crew health, safety, and mission success. Presentation slides address scope and approach, beneficiaries of IMM capabilities, history, risk components, conceptual models, development steps, and the evidence base. Space adaptation syndrome is used to demonstrate the model's capabilities.

Kerstman, Eric↗

Mass Inferencing Model Creation and Deployment to the RASSOR Lunar Excavation Robot

The Regolith Advanced Surface Systems Operations Robot (RASSOR) Excavator is a teleoperated mobile robotic platform with a unique space regolith excavation capability. The Intelligent Capabilities Enhanced RASSOR research project developed functionality for inferencing regolith mass ingested during RASSOR operation, enhancing RASSOR’s ability to successfully complete ISRU missions. To teleoperate or run autonomously, it is crucial for the quantity of regolith mass ingested by RASSOR to be available as a system state for efficient operation. For example, during autonomous operation, RASSOR should navigate and move to a processing plant to offload the collected regolith when the drums are full; without knowledge of how much mass is in the drums, this type of high-level planning is not possible. Four distinct modeling approaches were employed in developing a mass inferencing approach that could work on RASSOR. All take in system states, such as arm/drum positions, velocities, currents, voltages, and robot pose, and output a mass prediction for each set of the robot’s bucket drums.1) A neural network model that takes a vector of normalized system states; 2) A model that uses the integrated power consumption of an arm-raise (normalized by velocity); 3) A model that uses average drum current over a variable length interval of the drum disengaged from the surface; and 4) A real-time estimation model that aggregates excavation drum current. The developed models run in real time, outputting predictions for the front and rear drums, timestamp of the last prediction, and total mass in RASSOR’s drums. Further testing is required to validate the arm-raise model (2), though initial tests indicate reasonable performance (<10% mean error) on the hardware. The linear fit of average drum-current model (3) had a front value of r^2=0.99 and a rear value of r^2=0.98 on the validation dataset. This model currently has the best performance on unseen data. The real time model (4) is still in development, though initial results on a small subset of the training data show that it has high accuracy in predicting the increase in mass during excavation. Though work remains to be done with deploying a high-fidelity model to the physical system that makes predictions with error below the desired threshold, the modular architecture for model development allows quick adjustment of parameters to increase model fidelity. This architecture can also be adapted to use lunar excavation data to create models that are reflective of RASSOR’s dynamics when operating on the lunar surface. The results are promising as it has been shown that models can be developed that accurately estimate excavated regolith mass.

rassor↗

Enabling energy‐efficient manufacturing of pharmaceutical solid oral dosage forms via integrated techno‐economic analysis and advanced process modeling

Abstract The global pharmaceutical industry is a trillion‐dollar market. However, the pharmaceutical sector often lags in manufacturing innovation and automation which limits its potential to maximize energy efficiency. The integration of techno‐economic analysis (TEA) with advanced process models as part of an overarching smart manufacturing platform, can help industries create business models, which can be adapted for manufacturing to reduce energy consumption and operating costs while ensuring product quality which can further enable a more sustainable process operation. In this study, a rational design of experiment on three unit‐operations (wet granulation, drying, and milling) was performed on a batch (case 1) and continuous (case 2) pharmaceutical process to obtain experimental data. Process models for predicting product quality and energy efficiency of each of the three‐unit operations were developed. The experimental data were used to validate the models and good agreement was observed. The energy consumption of each unit operation was calculated using statistical models relating the power consumption and the process parameters. The developed process models and energy models were further integrated into a TEA framework, which quantified the energy and monetary cost of manufacturing for both batch and continuous manufacturing cases. With this integrated framework, energy costs savings of ~33% was obtained in the continuous manufacturing process (case 2) over the batch process (case 1).

Sampat, Chaitanya↗

Multimodal Deep Learning for Flaw Detection in Software Programs

We explore the use of multiple deep learning models for detecting flaws in software programs. Current, standard approaches for flaw detection rely on a single representation of a software program (e.g., source code or a program binary). We illustrate that, by using techniques from multimodal deep learning, we can simultaneously leverage multiple representations of software programs to improve flaw detection over single representation analyses. Specifically, we adapt three deep learning models from the multimodal learning literature for use in flaw detection and demonstrate how these models outperform traditional deep learning models. We present results on detecting software flaws using the Juliet Test Suite and Linux Kernel.

97 MATHEMATICS AND COMPUTING↗

Joint Analysis of Program Data Representations using Machine Learning for Improved Software Assurance and Development Capabilities

We explore the use of multiple deep learning models for detecting flaws in software programs. Current, standard approaches for flaw detection rely on a single representation of a software program (e.g., source code or a program binary). We illustrate that, by using techniques from multimodal deep learning, we can simultaneously leverage multiple representations of software programs to improve flaw detection over single representation analyses. Specifically, we adapt three deep learning models from the multimodal learning literature for use in flaw detection and demonstrate how these models outperform traditional deep learning models. We present results on detecting software flaws using the Juliet Test Suite and Linux Kernel.

97 MATHEMATICS AND COMPUTING↗

Using Adaptive Mesh Refinement to Study Grid Resolution Effects for Shock-Boundary Layer Interactions

Adaptive Mesh Refinement (AMR) promises a much more computationally efficient means to obtain a discrete approximation to a continuous boundary value problem of a specified accuracy than classic isotropic grid refinement. The AMR capability of OVERFLOW (a computational fluid dynamics (CFD) code) is utilized to provide estimates of the exact analytical solutions to problems of interest to turbulence modeling. Predictions of surface pressure and skin friction, essentially the state of stress at the surface, shows little difference with grids believed to be "grid resolved." Velocity profiles, on the other hand, show marked differences in flows with shocks. The AMR method, as implemented in OVERFLOW 2.2k, appears to provide the ability to produce arbitrarily accurate solutions at a predictable cost much smaller than classic uniform mesh refinement.

Turbulence Modeling↗

Solar Ion Processing of Itokawa Grains: Reconciling Model Predictions with Sample Observations

Analytical TEM observations of Itokawa grains reported to date show complex solar wind ion processing effects in the outer 30-100 nm of pyroxene and olivine grains. The effects include loss of long-range structural order, formation of isolated interval cavities or "bubbles", and other nanoscale compositional/microstructural variations. None of the effects so far described have, however, included complete ion-induced amorphization. To link the array of observed relationships to grain surface exposure times, we have adapted our previous numerical model for progressive solar ion processing effects in lunar regolith grains to the Itokawa samples. The model uses SRIM ion collision damage and implantation calculations within a framework of a constant-deposited-energy model for amorphization. Inputs include experimentally-measured amorphization fluences, a Pi steradian variable ion incidence geometry required for a rotating asteroid, and a numerical flux-versus-velocity solar wind spectrum.

Christoffersen, Roy↗

Forecasting fluid-injection induced seismicity to choose the best injection strategy for safety and efficiency

Induced seismicity poses a challenge to the development of Enhanced Geothermal Systems (EGS). Improving monitoring and forecasting techniques is essential to mitigate induced seismicity and thereby fostering a positive perception of EGS projects among local authorities and population. Induced seismicity is the result of complex and coupled thermo-hydro-mechanical-chemical mechanisms. Injection flux and pressure are crucial controlling parameters for both hydraulic stimulation and circulation protocols. We develop a methodology combining a hydro-mechanical model with a seismicity rate model to estimate the magnitude and frequency of mainshocks and aftershocks induced by fluid injection. We apply the methodology to the case of the Basel EGS (2006, Switzerland) to compare the effects of progressive, cyclic and constant injections on the mechanical response of discrete faults. Results from the coupled hydro-mechanical models show that the pore pressure diffusion and consequent enhancement of fault permeability are limited to the vicinity of the injection well during cyclic injection. Additionally, constant injection induces seismicity from the start of the injection but enhances the permeability of most of the faults within a shorter duration, inducing less post-injection seismicity. The methodology can be adapted to any numerical model and allows new projects to be developed by anticipating the safest injection protocol. This article is part of the theme issue ‘Induced seismicity in coupled subsurface systems’.

58 GEOSCIENCES↗

Near-Body Mesh Adaption for Transitional Flows Using OVERFLOW

Accurate modeling of boundary-layer transition is an important aspect of developing greener air transport technologies. In that regard, transition models based on auxiliary transport equations offer a robust approach that is easily integrated into the Reynolds-averaged Navier-Stokes (RANS) solvers. Recent workshops under NATO and AIAA have identified the verification of transport-equations-based transition modeling as a critical aspect of reducing the scatter between the predictions of different CFD codes. Follow-on work has highlighted the need for highly dense grids to achieve an asymptotic convergence of transition related flow metrics. The present work examines the role of automatic near-body mesh adaptation capability in the NASA OVERFLOW CFD solver to enable verification studies in an efficient manner, and for establishing best practices for designing grids for the RANS-based transition models. A sensor function relevant to the Langtry-Menter \gamma-Re_{\theta t}\ transition model has been identified and used for error-based mesh adaptation for canonical configurations comprising a flat plate, and the S809 and NLR-7301 airfoils. The efficacy of the mesh adaptation approach is assessed for flow conditions involving multiple transition scenarios such as natural transition, separation-induced transition, and shock-induced transition. The results from this exploratory study indicate that the meshes adapted using the proposed sensor provide solutions that approach the references solutions obtained with uniformly refined hand-crafted meshes, in terms of the chosen metrics, and yield modest yet significant savings in grid count. We also highlight areas for improvement in the grid adaptation methodology within OVERFLOW.

CFD↗

Journal of Gravitational Physiology, Volume 12, Number 1

The following topics were covered: System Specificity in Responsiveness to Intermittent -Gx Gravitation during Simulated Microgravity in Rats; A Brief Overview of Animal Hypergravity Studies; Neurovestibular Adaptation to Short Radius Centrifugation; Effect of Artificial Gravity with Exercise Load by Using Short-Arm Centrifuge with Bicycle Ergometer as a Countermeasure Against Disused Osteoporosis; Perception of Body Vertical in Microgravity during Parabolic Flight; Virtual Environment a Behavioral and Countermeasure Tool for Assisted Gesture in Weightlessness: Experiments during Parabolic Flight; Artificial Gravity: Physiological Perspectives for Long-Term Space Exploration; Comparison of the Effects of DL-threo-Beta-Benzyloxyaspartate on the Glutamate Release from Synaptosomes before and after Exposure of Rats to Artificial Gravity; Do Perception and Postrotatory Vestibulo-Ocular Reflex Share the Same Gravity Reference?; Vestibular Adaptation to Changing Gravity Levels and the Orientation of Listing's Plane; Compound Mechanism Hypothesis on +Gz - Induced Brain Injury and Dysfunction of Learning and Memory; Environmental Challenge Impairs Prefrontal Brain Functions; Effect of 6-Days of Support Withdrawal on Characteristics of Balance Function; Hypergravity-Induced Changes of Neuronal Activities in CA1 Region of Rat Hippocampus; Audiological Findings in Antiorthostatic Position Modelling Microgravitation; Investigating Human Cognitive Performance during Spaceflight; The Relevance of the Minimization of Torque Exchange with the Environment in Weightlessness is Confirmed by Asimulation Study; Characteristics of the Eyes Pursuit Function during Readaptation to Terrestrial Gravity after Prolonged Flights Aboard the International Space Station; Comparison of Cognitive Performance Tests for Promethazine Pharmacodynamics in Human Subjects; Structural Reappraisal of Dendritic Tree of Cerebellar Purkinje Cell for Novel Functional Modeling of Elementary Sensorimotor Adaptive Processes; Orpheus 0 G or Ear in Microgravity to Establish Symptoms Concomittant of Inner and Middle Ear and Osteoporosis in Microgravity; Understanding Visual Perception in the Perspective of Gravity; Cortical Regions Associated with Orthostatic Stress in Conscious Humans; Restoration of Central Blood Volume: Application of a Simple Concept and Simple Device to Counteract Cardiovascular Instability in Syncope and Hemorrhage; WISE-2005: Integrative Cardiovascular Responses with LBNP during 60-Day Bed Rest in Women; Intracranial Pressure Increases during Weightlessness. A Parabolic Flights Study; Lower Limb & Portal Veins Echography for Predicting Risk of Thrombosis during a 90-D Bed Rest; Calf Tissue Liquid Stowage and Muscular and Deep Vein Distension in Orthostatic Tests after a 90-Day Head Down Bed Rest; Morphology of Brain Vessels in the Tail Suspended Rats Exposed to Intermittent 2 G; Alterations in Vasoreactivity of Femoral Artery Induced by Hindlimb Unweighting are Related to the Changes of Contractile Protein in Rats; and Respiratory Sinus Arrhythmia: A Marker of Decreased Parasympathetic Modulation after Short Duration.

Fuller, Charles A.↗

Dual-loop model of the human controller

A dual-loop model of the human controller in single-axis compensatory tracking tasks is introduced. This model possesses an inner-loop closure that involves feeding back that portion of controlled element output rate that is due to control activity. A novel feature of the model is the explicit appearance of the human's internal representation of the manipulator-controlled element dynamics in the inner loop. The sensor inputs to the human controller are assumed to be system error and control force. The former can be sensed via visual, aural, or tactile displays, whereas the latter is assumed to be sensed in kinesthetic fashion. A set of general adaptive characteristics for the model is hypothesized, including a method for selecting simplified internal models of the manipulator-controlled element dynamics. It is demonstrated that the model can produce controller describing functions that closely approximate those measured in four laboratory tracking tasks in which the controlled element dynamics vary considerably in terms of ease of control. An empirically derived expression for the normalized injected error remnant spectrum is introduced.

Hess, R. A.↗

The Artificial Scientist: in-Transit Machine Learning of Plasma Simulations

Large-scale simulations or scientific experiments produce petabytes of data per run. This poses massive challenges for I/O and storage when scientific analysis workflows are run manually offline. Unsupervised deep learning-based techniques to extract patterns and non-linear relations from these large amounts of data provide a way to build scientific understanding from raw data, reducing the need for manual pre-selection of analysis steps, but require exascale compute and memory to process the full dataset available. In this paper, we demonstrate a heterogeneous streaming workflow in which plasma simulation data is streamed directly to a Machine Learning (ML) application training a model on the simulation data in-transit, completely circumventing the capacity-constrained filesystem bottleneck. This workflow employs openPMD to provide a high level interface to describe scientific data and also uses ADIOS2, to transfer volumes of data that exceed the capabilities of the filesystem. We employ experience replay to avoid catastrophic forgetting in learning from this non-steady state process in a continual manner and adapt it to improve model convergence while learning in-transit. As a proof-of-concept, we approach the ill-posed inverse problem of predicting particle dynamics from radiation in a particle-incell (PIConGPU) simulation of the Kelvin-Helmholtz instability (KHI). We detail hardware-software co-design challenges as we scale PIConGPU to full Frontier, the Top-1 system as of June 2024 Top500 list.

Kelling, Jeffrey [Helmholtz-Zentrum Dresden Rossen↗

REDOTHERM: a thermodynamic modeling framework for redox-based thermochemical processes

Two-step thermochemical redox cycles are being developed as a potential pathway for the production of hydrogen and syngas. While there are many possible reactor and system configurations, moving oxide systems are considered promising in terms of the redox thermodynamics, due to the potential implementation of a countercurrent system that can achieve higher performance compared to other configurations. There is a lack of a robust thermodynamic modeling framework in the field, with multiple models incorporating incorrect thermodynamic assumptions that violate the second law of thermodynamics. We present in this work REDOTHERM, an open-source system model for moving oxides that incorporates the correct thermodynamic limits, as well as various options for the system auxiliary units including product separation, heat recovery, and oxygen removal. The model is agnostic to the energy source, and could be used for solar thermal or other configurations. We highlight the uses of this model, presenting some of the tradeoffs and challenges in redox-active material selection and how they affect the entire thermochemical hydrogen production process. This model could be easily adapted and used for material exploration, system/reactor design, and technoeconomic analysis.

08 HYDROGEN↗