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DOE OSTI2026

Finding the missing pieces: filling gaps that impede the translation of omics data into models

High-throughput omics technologies such as DNA sequencing have made the sequencing and computational assembly of microbial genomes recovered from the environment relatively routine. Computational inference of the protein products encoded by these genomes, and the associated biochemical functions, should enable the accurate prediction and modeling of microbial metabolism, organismal interactions, and ecosystem processes. However, a lack of scalable, probabilistic protein annotation tools limits the full potential of modeling for understanding the metabolism and biogeochemical cycles of microbial communities. Our approach to improve inference of protein annotations and metabolic models relied on learning from and emulating expert manual curation, leveraging software engineering and data science best practices to scale up the throughput and accuracy of annotations and metabolic model construction, building software to objectively evaluate different annotation strategies, and more closely linking the protein annotation and metabolic model inference process. Outcomes of this research include several improved or new computational tools, including DRAM (Distilled and Refined Annotation of Metabolism) for annotating microbial genomes with protein function and metabolic traits, CAMPER (Curated Annotations for Microbial Polyphenol Enzymes and Reactions) for annotating key polyphenol metabolisms, EC-Bench for comprehensive and unbiased benchmarking of annotation tools, and several apps available via the DOE Systems Biology Knowledgebase (KBase) for building genome-scale metabolic models. We demonstrate that these tools allow us to scalably annotate and understand thousands of genomes for microbial communities from a variety of systems and test cases, including rivers, thawing permafrost, and gut microbiomes. All of these computational tools are available as open-source software, with most broadly and easily accessible to the scientific community via KBase apps.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1991

A model for the three-dimensional spacecraft control laboratory experiment

A model for the three-dimensional Spacecraft Control Laboratory Experiment (SCOLE) is developed. The objective behind this method of modelling is to utilize the basic partial differential equations of motion for this distributed parameter system and not to use the modal expansion in developing the model. The final model obtained is in terms of a transfer function matrix which relates the flexible mast parameters like displacement, slope, shear stress, etc. to external forces and moments.

Kakad, Yogendra P.↗

NASA NTRS2015

Impact and Penetration of Thin Aluminum 2024 Flat Panels at Oblique Angles of Incidence

The U.S. Federal Aviation Administration (FAA) and the National Aeronautics and Space Administration (NASA) are actively involved in improving the predictive capabilities of transient finite element computational methods for application to safety issues involving unintended impacts on aircraft and aircraft engine structures. One aspect of this work involves the development of an improved deformation and failure model for metallic materials, known as the Tabulated Johnson-Cook model, or MAT224, which has been implemented in the LS-DYNA commercial transient finite element analysis code (LSTC Corp., Livermore, CA) (Ref. 1). In this model the yield stress is a function of strain, strain rate and temperature and the plastic failure strain is a function of the state of stress, temperature and strain rate. The failure criterion is based on the accumulation of plastic strain in an element. The model also incorporates a regularization scheme to account for the dependency of plastic failure strain on mesh size. For a given material the model requires a significant amount of testing to determine the yield stress and failure strain as a function of the three-dimensional state of stress, strain rate and temperature. In addition, experiments are required to validate the model. Currently the model has been developed for Aluminum 2024 and validated against a series of ballistic impact tests on flat plates of various thicknesses (Refs. 1 to 3). Full development of the model for Titanium 6Al-4V is being completed, and mechanical testing for Inconel 718 has begun. The validation testing for the models involves ballistic impact tests using cylindrical projectiles impacting flat plates at a normal incidence (Ref. 2). By varying the thickness of the plates, different stress states and resulting failure modes are induced, providing a range of conditions over which the model can be validated. The objective of the study reported here was to provide experimental data to evaluate the model under more extreme conditions, using a projectile with a more complex shape and sharp contacts, impacting flat panels at oblique angles of incidence.

Ruggeri, Charles R.↗

DOE OSTI2023

Operation Optimization Using Reinforcement Learning with Integrated Artificial Reasoning Framework

In large and complex systems, operational decision-making requires a systematic analysis with a vast amount of data from both process parameters and component status monitoring. In this paper, we present an integrated artificial reasoning approach for system state transition models that can help operational decision-making with explainable and traceable reasoning. The integrated artificial reasoning framework is a physics-based approach of defining the system structure in a Bayesian network, so we leveraged it in a Markov decision process (MDP) for finding optimal operational solutions. In our proposed framework, the MDP is implemented on a dynamic Bayesian network (DBN), which represents causalities in a system. The multilevel flow modeling was utilized in order to extract these causalities in a more efficient and objective manner. Since multilevel flow modeling is based on the fundamental energy and mass conservation laws, the target system is decomposed into several mass, energy, and information structures, which serve as the basis for a DBN. The MDP consists of the processes of finding a solution for the Bellman equation, which can be derived from the conditional probability equations of the constructed DBN. System operators can capture stochastic system dynamics as multiple subsystem state transitions based on their physical relations and uncertainties coming from the component degradation process or random failures. We analyzed a simplified example system to illustrate finding an optimal operational policy with this approach.

Kim, Junyung↗

NASA NTRS1992

Pressure measurements on a rectangular wing with a NACA0012 airfoil during conventional flutter

The Structural Dynamics Division at NASA LaRC has started a wind tunnel activity referred to as the Benchmark Models Program. The primary objective of the program is to acquire measured dynamic instability and corresponding pressure data that will be useful for developing and evaluating aeroelastic type CFD codes currently in use or under development. The program is a multi-year activity that will involve testing of several different models to investigate various aeroelastic phenomena. The first model consisted of a rigid semispan wing having a rectangular planform and a NACA 0012 airfoil shape which was mounted on a flexible two degree-of-freedom mount system. Two wind-tunnel tests were conducted with the first model. Several dynamic instability boundaries were investigated such as a conventional flutter boundary, a transonic plunge instability region near Mach = 0.90, and stall flutter. In addition, wing surface unsteady pressure data were acquired along two model chords located at the 60 to 95-percent span stations during these instabilities. At this time, only the pressure data for the conventional flutter boundary is presented. The conventional flutter boundary and the wing surface unsteady pressure measurements obtained at the conventional flutter boundary test conditions in pressure coefficient form are presented. Wing surface steady pressure measurements obtained with the model mount system rigidized are also presented. These steady pressure data were acquired at essentially the same dynamic pressure at which conventional flutter had been encountered with the mount system flexible.

Rivera, Jose A., Jr.↗

NASA NTRS1992

NACA 0012 benchmark model experimental flutter results with unsteady pressure distributions

The Structural Dynamics Division at NASA Langley Research Center has started a wind tunnel activity referred to as the Benchmark Models Program. The primary objective of the program is to acquire measured dynamic instability and corresponding pressure data that will be useful for developing and evaluating aeroelastic type CFD codes currently in use or under development. The program is a multi-year activity that will involve testing of several different models to investigate various aeroelastic phenomena. This paper describes results obtained from a second wind tunnel test of the first model in the Benchmark Models Program. This first model consisted of a rigid semispan wing having a rectangular planform and a NACA 0012 airfoil shape which was mounted on a flexible two degree-of-freedom mount system. Experimental flutter boundaries and corresponding unsteady pressure distribution data acquired over two model chords located at the 60 and 95 percent span stations are presented.

Rivera, Jose A., Jr.↗

DOE OSTI2021

A Binomial Stochastic Framework for Efficiently Modeling Discrete Statistics of Convective Populations

Abstract Understanding the coupling between convective clouds and the general circulation, as well as addressing the gray zone problem in convective parameterization, requires insight into the genesis and maintenance of spatial patterns in cumulus cloud populations. In this study, a simple toy model for recreating populations of interacting convective objects as distributed over a two‐dimensional Eulerian grid is formulated to this purpose. Key elements at the foundation of the model include i) a fully discrete formulation for capturing discrete behavior in convective properties at small population sample sizes, ii) object age‐dependence for representing life‐cycle effects, and iii) a prognostic number budget allowing for object interactions and co‐existence of multiple species. A primary goal is to optimize the computational efficiency of this system. To this purpose the object birth rate is represented stochastically through a spatially aware Bernoulli process. The same binomial stochastic operator is applied to horizontal advection of objects, conserving discreteness in object number. The applicability to atmospheric convection as well as behavior implied by the formulation is assessed. Various simple applications of the BiOMi model (Binomial Objects on Microgrids) are explored, suggesting that important convective behavior can be captured at low computational cost. This includes i) subsampling effects and associated powerlaw scaling in the convective gray zone, ii) stochastic predator‐prey behavior, iii) the downscale turbulent energy cascade, and iv) simple forms of spatial organization and convective memory. Consequences and opportunities for convective parameterization in next‐generation weather and climate models are discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2019

Estimating physics models and quantifying their uncertainty using optimization with a Bayesian objective function

This paper reports a verification study for a method that fits functions to sets of data from several experiments simultaneously. The method finds a maximum a posteriori probability (MAP) estimate of a function subject to constraints (e. g., convexity in the study), uncertainty about the estimate, and a quantitative characterization of how data from each experiment constrains that uncertainty. While the present work focuses on a model of the Equation Of State (EOS) of gasses produced by detonating a high explosive, the method can be applied to a wide range of physics processes with either parametric or semi-parametric models. As a verification exercise, a reference EOS is used and artificial experimental data sets are created using numerical integration of ordinary differential equations and pseudo-random noise. The method yields an estimate of the EOS that is close to the reference, and identifies how each experiment most constrains the result.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

NASA NTRS2008

Testing the Paradigm that Ultra-Luminous X-Ray Sources as a Class Represent Accreting Intermediate

To test the idea that ultraluminous X-ray sources (ULXs) in external galaxies represent a class of accreting Intermediate-Mass Black Holes (IMBHs), we have undertaken a program to identify ULXs and a lower luminosity X-ray comparison sample with the highest quality data in the Chandra archive. We establish a general property of ULXs that the most X-ray luminous objects possess the fattest X-ray spectra (in the Chandra band pass). No prior sample studies have established the general hardening of ULX spectra with luminosity. This hardening occurs at the highest luminosities (absorbed luminosity > or equals 5x10(exp 39) ergs/s) and is in line with recent models arguing that ULXs are actually stellar-mass black holes. From spectral modeling, we show that the evidence originally taken to mean that ULXs are IMBHs - i.e., the "simple IMBH model" - is nowhere near as compelling when a large sample of ULXs is looked at properly. During the last couple of years, XMM-Newton spectroscopy of ULXs has to some large extent begun to negate the simple IMBH model based on fewer objects. We confirm and expand these results, which validates the XMM-Newton work in a broader sense with independent X-ray data. We find (1) that cool disk components are present with roughly equal probability and total flux fraction for any given ULX, regardless of luminosity, and (2) that cool disk components extend below the standard ULX luminosity cutoff of 10(exp 39) ergs/s, down to our sample limit of 10(exp 38:3) ergs/s. The fact that cool disk components are not correlated with luminosity damages the argument that cool disks indicate IMBHs in ULXs, for which a strong statistical support was never made.

Berghea, C. T.↗

NASA NTRS1985

Robot environment expert system

The Robot Environment Expert System uses a hexidecimal tree data structure to model a complex robot environment where not only the robot arm moves, but also the robot itself and other objects may move. The hextree model allows dynamic updating, collision avoidance and path planning over time, to avoid moving objects.

Potter, J. L.↗

NASA NTRSDate not supplied

Estimation With Range Depended Sensor Model

This paper focuses on the improvement of object detection accuracy taking into account the sensor’s reading degradation as the relative range increases. The approach is based on the assumption that range measurement error depends on the actual range. Specifically, we model the measurement error as a proportional to the actual range term plus a zero-mean, Gaussian distributed, and uncorrelated process. The tracking problem is considered in a mixed continuous-discrete time domain, where the target dynamics is in continuous-time and the measurements are in discrete-time, which is an optimal choice in many tracking and navigation applications. We adopt a commonly used continuous time coordinate-uncoupled white-noise acceleration model for a point object to describe the target motion, and use Extended Kalman Filter (EKF) framework to estimate the target's state and the unknown proportionality coefficient.

Vahram Stepanyan↗

DOE OSTI2020

Mixed-Mechanism Stimulation Enabled Enhanced Geothermal Systems (CRADA FP00007509 Final Report)

In this project, we aimed to develop a robust, novel EGS design that would enable broad deployment of geothermal energy at costs competitive with other sources of renewable energy. The technical objectives included developing reservoir models for synthetic geothermal systems that meet target reservoir performance characteristics, performing a quantitative assessment of selection criteria for candidate geothermal sites, perform proppant studies under relevant geothermal conditions, and complete an induced seismicity risk analysis for potential geothermal development sites. The project team made significant progress towards these objectives. Specifically, we developed a prioritization to rank candidate sites for suitability of our technology based on 10 separate technical, operational, logistic, regulatory, and commercial criteria. The team performed laboratory testing at Lawrence Berkeley National Laboratory to characterize the functionality of several different types of proppant materials at temperatures of up to 200 C for durations of up to 9 weeks. We also created an Induced Seismicity Mitigation Plan for the top two sites selected for our future field demonstrations.

58 GEOSCIENCES↗

NASA NTRS1992

C-Language Integrated Production System, Version 5.1

CLIPS 5.1 provides cohesive software tool for handling wide variety of knowledge with support for three different programming paradigms: rule-based, object-oriented, and procedural. Rule-based programming provides representation of knowledge by use of heuristics. Object-oriented programming enables modeling of complex systems as modular components. Procedural programming enables CLIPS to represent knowledge in ways similar to those allowed in such languages as C, Pascal, Ada, and LISP. Working with CLIPS 5.1, one can develop expert-system software by use of rule-based programming only, object-oriented programming only, procedural programming only, or combinations of the three.

Riley, Gary↗

NASA NTRS1992

NACA0012 benchmark model experimental flutter results with unsteady pressure distributions

The Structural Dynamics Division at NASA Langley Research Center has started a wind tunnel activity referred to as the Benchmark Models Program. The primary objective of this program is to acquire measured dynamic instability and corresponding pressure data that will be useful for developing and evaluating aeroelastic type computational fluid dynamics codes currently in use or under development. The program is a multi-year activity that will involve testing of several different models to investigate various aeroelastic phenomena. This paper describes results obtained from a second wind tunnel test of the first model in the Benchmark Models Program. This first model consisted of a rigid semispan wing having a rectangular planform and a NACA 0012 airfoil shape which was mounted on a flexible two degree of freedom mount system. Experimental flutter boundaries and corresponding unsteady pressure distribution data acquired over two model chords located at the 60 and 95 percent span stations are presented.

Rivera, Jose A., Jr.↗

NASA NTRS1992

A vision architecture for the extravehicular activity retriever

The Extravehicular Activity Retriever (EVAR) is a robotic device currently being developed by the Automation and Robotics Division at the NASA Johnson Space Center to support activities in the neighborhood of the Space Shuttle or Space Station Freedom. As the name implies, the Retriever's primary function will be to provide the capability to retrieve tools, equipment or other objects which have become detached from the spacecraft, but it will also be able to rescue a crew member who may have become inadvertently de-tethered. Later goals will include cooperative operations between a crew member and the Retriever such as fetching a tool that is required for servicing or maintenance operations. This report documents a preliminary design for a Vision System Planner (VSP) for the EVAR that is capable of achieving visual objectives provided to it by a high level task planner. Typical commands which the task planner might issue to the VSP relate to object recognition, object location determination, and obstacle detection. Upon receiving a command from the task planner, the VSP then plans a sequence of actions to achieve the specified objective using a model-based reasoning approach. This sequence may involve choosing an appropriate sensor, selecting an algorithm to process the data, reorienting the sensor, adjusting the effective resolution of the image using lens zooming capability, and/or requesting the task planner to reposition the EVAR to obtain a different view of the object. An initial version of the Vision System Planner which realizes the above capabilities using simulated images has been implemented and tested. The remaining sections describe the architecture and capabilities of the VSP and its relationship to the high level task planner. In addition, typical plans that are generated to achieve visual goals for various scenarios will be discussed. Specific topics to be addressed will include object search strategies, repositioning of the EVAR to improve the quality of information obtained from the sensors, complementary usage of the sensors and redundant capabilities.

Magee, Michael↗

NASA NTRS1993

A vision system planner for increasing the autonomy of the Extravehicular Activity Helper/Retriever

The Extravehicular Activity Retriever (EVAR) is a robotic device currently being developed by the Automation and Robotics Division at the NASA Johnson Space Center to support activities in the neighborhood of the Space Shuttle or Space Station Freedom. As the name implies, the Retriever's primary function will be to provide the capability to retrieve tools and equipment or other objects which have become detached from the spacecraft, but it will also be able to rescue a crew member who may have become inadvertently de-tethered. Later goals will include cooperative operations between a crew member and the Retriever such as fetching a tool that is required for servicing or maintenance operations. This paper documents a preliminary design for a Vision System Planner (VSP) for the EVAR that is capable of achieving visual objectives provided to it by a high level task planner. Typical commands which the task planner might issue to the VSP relate to object recognition, object location determination, and obstacle detection. Upon receiving a command from the task planner, the VSP then plans a sequence of actions to achieve the specified objective using a model-based reasoning approach. This sequence may involve choosing an appropriate sensor, selecting an algorithm to process the data, reorienting the sensor, adjusting the effective resolution of the image using lens zooming capability, and/or requesting the task planner to reposition the EVAR to obtain a different view of the object. An initial version of the Vision System Planner which realizes the above capabilities using simulated images has been implemented and tested. The remaining sections describe the architecture and capabilities of the VSP and its relationship to the high level task planner. In addition, typical plans that are generated to achieve visual goals for various scenarios are discussed. Specific topics to be addressed will include object search strategies, repositioning of the EVAR to improve the quality of information obtained from the sensors, and complementary usage of the sensors and redundant capabilities.

Magee, Michael↗

DOE OSTI2017

Marine Corps Base Camp Lejeune Geospatial Marsh Model: French Output

Critical military training and testing on lands along the nation’s coastal and estuarine shorelines are increasingly placed at risk because of encroachment pressures in surrounding areas, impairments due to other anthropogenic disturbances, and changes in climate and sea level. The U.S. Department of Defense (DoD) intends to enhance and sustain its training and testing assets and also optimize its stewardship of natural resources through the development and application of an ecosystem-based management approach on DoD installations. To accomplish this goal, particularly for installations in estuarine/coastal environments, the Strategic Environmental Research and Development Program (SERDP) launched the Defense Coastal/Estuarine Research Program (DCERP) as a 10-year effort at Marine Corps Base Camp Lejeune (MCBCL) in North Carolina. The results of the second 5 years of the program (DCERP2) are presented in the DCERP2 Final Report.There were four overarching objectives of DCERP2. The first objective was to understand the effects of climate change impacts, including warming temperatures, variability in the hydrological cycle, storm events, and sea level rise on the coastal ecosystems at MCBCL from observations and measurements made over the 10-year program. The second objective was to understand the carbon cycle of the coastal and terrestrial ecosystems at MCBCL through a highly integrated sampling program. The third objective was to develop models, tools, and indicators to evaluate current and projected future ecosystem state changes and translate scientific findings into actionable information for installation managers. The last objective was to recommend adaptive management strategies to sustain ecosystem natural resources within the context of an active military installation.This data package contains geospatial data of habitat and elevation as ascii and tabular output (.xlxs) for each site under each SLR scenario for the years 2013 (initial), 2035, 2065, & 2100.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2017

Marine Corps Base Camp Lejeune Geospatial Marsh Model: Trap's Bay Output

54 ENVIRONMENTAL SCIENCES↗