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At least 883 records · Page 49

Geometrical analysis of Cys-Cys bridges in proteins and their prediction from incomplete structural information

Analysis of C-alpha atom positions from cysteines involved in disulphide bridges in protein crystals shows that their geometric characteristics are unique with respect to other Cys-Cys, non-bridging pairs. They may be used for predicting disulphide connections in incompletely determined protein structures, such as low resolution crystallography or theoretical folding experiments. The basic unit for analysis and prediction is the 3 x 3 distance matrix for Cx positions of residues (i - 1), Cys(i), (i +1) with (j - 1), Cys(j), (j + 1). In each of its columns, row and diagonal vector--outer distances are larger than the central distance. This analysis is compared with some analytical models.

NASA Discipline Exobiology↗

NEAMS Thermal-Fluids Test Stand for Fluoride-Slat Cooled, High Temperature Reactor Development (Final CRADA Report)

The work performed in this CRADA resulted in significant progress toward the development of a Thermal-fluid test-stand based on NEAMS tools. Significant work has been achieved in this area with simulations performed in Nek5000 of the heat and fluid flow in twisted tube heat exchangers and various software and modeling improvements in SAM geared toward heat exchanger simulations. In particular a set of simulations of flow and heat transfer in twisted elliptical tube geometries has been performed with Nek5000. The method was validated by simulating a case at a moderate Reynolds number and relatively high Froude number. This case was demonstrated to predict a Nusselt number in excellent agreement with the applicable correlation found in literature. It was further shown that at lower Froude numbers, this agreement becomes much worse. Additional cases were then simulated with low Froude numbers for both a square and a triangular unit cell to test the effect of pitch-to-maximum diameter ratio for the purposes of future CFD modeling. The results have proven invaluable to understand the flow physics in twisted tubes and provide reference data for design. Results have been summarized in a conference article. Moreover, work in SAM has led to significant improvement of software quality, the creation of a set of benchmarks for natural circulation and other significant software improvement.

97 MATHEMATICS AND COMPUTING↗

Lessons learned in transitioning to an open systems environment

Software development organizations, both commercial and governmental, are undergoing rapid change spurred by developments in the computing industry. To stay competitive, these organizations must adopt new technologies, skills, and practices quickly. Yet even for an organization with a well-developed set of software engineering models and processes, transitioning to a new technology can be expensive and risky. Current industry trends are leading away from traditional mainframe environments and toward the workstation-based, open systems world. This paper presents the experiences of software engineers on three recent projects that pioneered open systems development for NASA's Flight Dynamics Division of the Goddard Space Flight Center (GSFC).

Boland, Dillard E.↗

Empirical Validation of UBEM: An Assessment of Bias in Urban Building Energy Modeling for Chicago

Residential and commercial buildings currently account for 30% of total global final energy consumption. Urban-scale building energy modeling (UBEM) can enable scalable investments and unlock building improvements by quantifying energy, demand, emissions, and cost reductions of specific measures or packages for building-specific technologies in large geographic regions. While the sophistication of UBEM data sources and technologies have increased dramatically in the past decade, there remains a knowledge gap for empirical validation and sources of bias between building-specific energy models and measured data at varying geographic scales.As UBEM continues to develop, systemic analysis of accuracy, bias, and limitations of the resulting models is necessary to inform best practices and move toward standardization. These are characterized for the Automatic Building Energy Modeling (AutoBEM) software suite with an initial case study involving metered electricity consumption data from 247,188 buildings in Chicago, Illinois, USA - averaged across years 2019-2021 - compared to the following datasets: (1) the AutoBEM-generated nation-scale Model America version 2 (MAv2) data for 596,064 buildings, (2) tax assessor data for 579,829 buildings, (3) tax assessor data filled with MAv2, and (4) 102 representative dynamic archetypes. The accuracy is reported for every building type and vintage combination, along with multiple sources of bias for unique building descriptors. The AutoBEM simulation workflow produced energy consumption estimates that closely match aggregated metered electricity consumption data for different types of buildings constructed during various time periods at the city scale - with initial normalized mean bias error of 10.9%, and 1.1% after removing outliers. Contribution of statistically significant factors including building type, land use, age, and size to variance in UBEM bias is quantified.

Garg, Ankur↗

PHASM: A Toolkit for Creating AI Surrogate Models within Legacy Codebases

PHASM (“Parallel Hardware viA Surrogate Models”) is a software toolkit for creating AI-based surrogate models of scientific code. AI-based surrogate models are widely used for creating fast and inverse simulations. PHASM anticipates an additional future use case: adapting legacy code to modern hardware. While data centers are investing in heterogeneous hardware such as GPUs and FPGAs, many established scientific codebases remain unable to take advantage of the hardware’s higher parallelism without undergoing a costly rewrite. An alternative is to train a AI-based surrogate model to mimic computationally intensive functions in the code, and run the surrogate instead. PHASM formalizes a development lifecycle for such surrogate models, including discovering functions amenable to replacement with a surrogate model, predicting the resulting performance, identifying the function’s space of inputs and outputs, binding the model to the code, and managing model versions. A suite of software tools for facilitating these steps was written and validated against a set of model problems.

97 MATHEMATICS AND COMPUTING↗

Optical Thin Film Modeling: Using FTG's FilmStar Software

Every material has basic optical properties that define its interaction with light: The index of refraction (n) and extinction coefficient (k) vary for the material as a function of the wavelength of the incident light. Also significant are the phase velocity and polarization of the incident light These inherent properties allow for the accurate modeling of light s behavior upon contact with a surface: Reflectance, Transmittance, Absorptance.

Freese, Scott↗

CHMMPP: A c++ library for constrained Hidden Markov Models

SAND2024-13027O The CHMMPP: A c++ Library for Constrained Hidden Markov Models (HMM) software supports the analysis of multivariate time series data to detect patterns using HMM. Many applications involve the detection and characterization of hidden or latent states in a complex system using observable states and variables. This software supports inference of latent states integrating both an HMM and application-specific constraints that reflect known relationships in hidden states. The CHMMPP software supports application-specific and generic methods for constrained inference. This includes a framework for customized Viterbi methods, constrained inference of hidden states with A* and integer programming methods, and various constraint-informed methods for learning HMM model parameters. CHMMPP focuses on supporting generic methods that enable the agile expression of complex sets of constraints that naturally arise in many real-world applications.

Hart, William↗

Next-Generation Marine Energy Software Needs Assessment

Over the past decade the marine energy industry has continued to grow and evolve, with new concepts and technologies constantly being pursued. Additionally, the field of computing is vastly different today than it was five or ten years ago. By utilizing advanced software and hardware architectures, like graphics processing units as well as parallelization and high-performance computing resources, software can produce higher quality outputs and a higher volume of outputs. These software and hardware resources can enable the marine energy community to exploit computational advancements from other research fields, which can include machine learning, differentiable programming, and controls co-design. Better integration of existing software and development of potential new software is necessary to take advantage of trends in modern computing and respond to the current and future needs of the marine energy community. In order to better understand the existing marine energy software landscape and industry needs, DOE's Water Power Technologies Office (WPTO) tasked Sandia National Laboratories and the National Renewable Energy Laboratory to update the needs assessment by identifying existing software gaps and software needs, and assisting WPTO in planning the next wave of marine energy software development. The proposed effort involved cataloguing and analyzing the available data on existing software related to marine energy. The marine energy software landscape has vastly changed in the last ten years. There are now nearly 230 different software packages utilized by the marine energy sector, compared to a decade ago when the Cardinal Engineering survey identified approximately 40 software packages. In 2012, the marine energy software landscape was captured in two tables, whereas the current marine energy software landscape required development of a software database to collect and categorize software.

16 TIDAL AND WAVE POWER↗

Controls/CFD Interdisciplinary Research Software Generates Low-Order Linear Models for Control Design From Steady-State CFD Results

The NASA Lewis Research Center is developing analytical methods and software tools to create a bridge between the controls and computational fluid dynamics (CFD) disciplines. Traditionally, control design engineers have used coarse nonlinear simulations to generate information for the design of new propulsion system controls. However, such traditional methods are not adequate for modeling the propulsion systems of complex, high-speed vehicles like the High Speed Civil Transport. To properly model the relevant flow physics of high-speed propulsion systems, one must use simulations based on CFD methods. Such CFD simulations have become useful tools for engineers that are designing propulsion system components. The analysis techniques and software being developed as part of this effort are an attempt to evolve CFD into a useful tool for control design as well. One major aspect of this research is the generation of linear models from steady-state CFD results. CFD simulations, often used during the design of high-speed inlets, yield high resolution operating point data. Under a NASA grant, the University of Akron has developed analytical techniques and software tools that use these data to generate linear models for control design. The resulting linear models have the same number of states as the original CFD simulation, so they are still very large and computationally cumbersome. Model reduction techniques have been successfully applied to reduce these large linear models by several orders of magnitude without significantly changing the dynamic response. The result is an accurate, easy to use, low-order linear model that takes less time to generate than those generated by traditional means. The development of methods for generating low-order linear models from steady-state CFD is most complete at the one-dimensional level, where software is available to generate models with different kinds of input and output variables. One-dimensional methods have been extended somewhat so that linear models can also be generated from two- and three-dimensional steady-state results. Standard techniques are adequate for reducing the order of one-dimensional CFD-based linear models. However, reduction of linear models based on two- and three-dimensional CFD results is complicated by very sparse, ill-conditioned matrices. Some novel approaches are being investigated to solve this problem.

Melcher, Kevin J.↗

Repurposing Drilling Control Diagnostics for Subsurface Edge Detection and Boundary Advisement During Planetary Drilling

Informed decision-making during lunar drilling and sampling missions will require data monitoring tools and specialized ground data systems. Accurate and updated situational awareness, with ongoing data monitoring, is critical for timely responses by to incoming science data. Traverse plans and scheduled activities may need to be flexibly changed in order to react to unexpected data or situations. Unlike (for example) Mars missions, the relative lightspeed closeness of the Moon allows for near-real-time ground processing of incoming mission and instrument data. An Apollo-class lunar regolith drill will in a sense “travel” a meter or two vertically at a given subsurface characterization site. As the drill penetrates into lunar regolith, it is likely to encounter a range of material densities, orientations, fracture toughness, and (perhaps) ice percentages. Lunar drill telemetry can provide science teams with a valuable first look into the subsurface structure, the regolith bulk properties, and constituents at each drilled site. Real-time AI-based recognition and reaction to downhole situations has been developed for automated deeper drilling on Mars and beyond. We can leverage the same knowledge bases and pattern-matching as areal-time interpreter of the subsurface, a situational awareness tool during drilling operations. We recently (Sept. 2019) demonstrated this AI drilling monitoring and analysis capability, in control of in-situ drilling and sampling operations, mounted on a KREX-2 rover in Chile’s Atacama Desert. Terrestrial automated drilling log analyses in oil exploration have used similar machine learning techniques in classifying and identifying features in drilling logs –but these typically are designed assuming a drilling fluid influencing downhole measurements and data (permeability, resistivity). Drilling models and existing AI software designed to detect and respond to drilling faults and hard materials can be repurposed, for near-real-time (ground-based) interpretation of drilling telemetry –a potentially valuable advisory tool for strata boundaries and changes in drilling parameters. On the Moon, this approach could be used to study the structure and to some extent the composition of lunar regolith vs. borehole depth, based on recognizable variations in fracture hardness, drilling energy and penetration rates while actively drilling. Since the early 2000s, a series of increasingly-capable real-time drilling telemetry interpretation and characterization software tools have been developed. These subsurface models and software tools have monitored the real-time drilling data received, and automatically identified changes in drill behavior (e.g., encountering a harder target layer, bit inclusions, drill choking due to infall downhole, and others) correlating these with subsurface structures and features. We discuss the mappings between drill borehole parameters, faults or events detected, and modeled changes in rock layer boundaries, in examples drawn from field testing at analog sites in an Arctic impact crater, Rio Tinto, and Chile’s Atacama Desert. These demonstrate how subsurface structural boundaries led to fault detections and responses by the software.

drilling advisor↗

Model-Driven Development For PDS4 Software And Services

Software and services that access Planetary Data System (PDS) PDS4 data products need to parse product labels to retrieve, interpret, and process the referenced digital objects. Under PDS4 a driving principle is that the product label provide all of the information necessary for these functions to be performed accurately. However, significantly more information is available in the PDS4 Information Model (IM)[1], the controlling document used to define, create, and syntactically and semantically verify the product labels. This additional information in the IM is made available for use, by both software and services, to configure, promote resiliency, and improve interoperability.

Padams, Jordan↗

Making machine learning a useful tool in the accelerated discovery of transition metal complexes

Abstract As machine learning (ML) has matured, it has opened a new frontier in theoretical and computational chemistry by offering the promise of simultaneous paradigm shifts in accuracy and efficiency. Nowhere is this advance more needed, but also more challenging to achieve, than in the discovery of open‐shell transition metal complexes. Here, localized d or f electrons exhibit variable bonding that is challenging to capture even with the most computationally demanding methods. Thus, despite great promise, clear obstacles remain in constructing ML models that can supplement or even replace explicit electronic structure calculations. In this article, I outline the recent advances in building ML models in transition metal chemistry, including the ability to approach sub‐kcal/mol accuracy on a range of properties with tailored representations, to discover and enumerate complexes in large chemical spaces, and to reveal opportunities for design through analysis of feature importance. I discuss unique considerations that have been essential to enabling ML in open‐shell transition metal chemistry, including (a) the relationship of data set size/diversity, model complexity, and representation choice, (b) the importance of quantitative assessments of both theory and model domain of applicability, and (c) the need to enable autonomous generation of reliable, large data sets both for ML model training and in active learning or discovery contexts. Finally, I summarize the next steps toward making ML a mainstream tool in the accelerated discovery of transition metal complexes. This article is categorized under: Electronic Structure Theory > Density Functional Theory Software > Molecular Modeling Computer and Information Science > Chemoinformatics

Kulik, Heather J.↗

Pennsylvania Department of Environmental Protection (PA DEP) 26r Detailed Produced Water Compositions (version 1.0)

A database of geochemical compositions of aqueous species in produced water reported to the PA DEP. Samples were collected between mid-2012 to early-2020. Data from publicly-available PA DEP 26r reports were scraped from pdf files and cumulated into tabular spreadsheet format for >1000 produced water streams from Marcellus wells in Pennsylvania. In addition to providing the original values, the NETL NEWTS team has reformatted the dataset to allow sample streams to be easily copied into OLI Studio and Geochemist WorkBench (GWB) software for modeling the geochemistry and the recovery of critical minerals, such as lithium, from these produced water streams. In addition, a version of the dataset has been included with predictions for some missing values in the original dataset using machine learning techniques within CoDaRT software, a public ML software developed by the Nation Energy Technology Laboratory. We have made the Input into CoDaRT and one example output from CoDaRT available in this dataset.

Aqueous Chemistry↗

Vehicle Shield Optimization and Risk Assessment for Future Human Space Missions

As the focus of future human space missions shifts to destinations beyond low Earth orbit such as Near Earth Objects (NEO), the moon, or Mars, risks associated with extended stay in hostile radiation environment need to be well understood and assessed. Since future spacecrafts designs and shapes are evolving continuous assessments of shielding and radiation risks are needed. In this study, we use a predictive software capability that calculates risks to humans inside a spacecraft prototype that builds on previous designs. The software uses CAD software Pro/Engineer and Fishbowl tool kit to quantify radiation shielding provided by the spacecraft geometry by calculating the areal density seen at a certain point, dose point, inside the spacecraft. Shielding results are used by NASA-developed software, BRYNTRN, to quantify organ doses received in a human body located in the vehicle in case of solar particle event (SPE) during such prolonged space missions. Organ doses are used to quantify risks on astronauts health and life using NASA Space Cancer Model. The software can also locate shielding weak points-hotspots-on the spacecraft s outer surface. This capability is used to reinforce weak areas in the design. Results of shielding optimization and risk calculation on an exploration vehicle design for missions of 6 months and 30 months are provided in this study. Vehicle capsule is made of aluminum shell that includes main cabin and airlock. The capsule contains 5 sets of racks that surround working and living areas. Water shelter is provided in the main cabin of the vehicle to enhance shielding in case of SPE.

Nounu, Hatem N.↗

DUNE Software and High Performance Computing

DUNE, like other HEP experiments, faces a challenge related to matching execution patterns of our production simulation and data processing software to the limitations imposed by modern high-performance computing facilities. In order to efficiently exploit these new architectures, particularly those with high CPU core counts and GPU accelerators, our existing software execution models require adaptation. In addition, the large size of individual units of raw data from the far detector modules pose an additional challenge somewhat unique to DUNE. Here we describe some of these problems and how we begin to solve them today with existing software frameworks and toolkits. We also describe ways we may leverage these existing software architectures to attack remaining problems going forward. This whitepaper is a contribution to the Computational Frontier of Snowmass21.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Hypersonic Navier Stokes Comparisons to Orbiter Flight Data

Hypersonic chemical nonequilibrium simulations of low earth orbit entry flow fields are becoming increasingly commonplace as software and computational capabilities become more capable. However, development of robust and accurate software to model these environments will always encounter a significant barrier in developing a suite of high quality calibration cases. The US3D hypersonic nonequilibrium Navier Stokes analysis capability has been favorably compared to a number of wind tunnel test cases. Extension of the calibration basis for this software to Orbiter flight conditions will provide an incremental increase in confidence. As part of the Orbiter Boundary Layer Transition Flight Experiment and the Hypersonic Thermodynamic Infrared Measurements project, NASA is performing entry flight testing on the Orbiter to provide valuable aerothermodynamic heating data. An increase in interest related to orbiter entry environments is resulting from this activity. With the advent of this new data, comparisons of the US3D software to the new flight testing data is warranted. This paper will provide information regarding the framework of analyses that will be applied with the US3D analysis tool. In addition, comparisons will be made to entry flight testing data provided by the Orbiter BLT Flight Experiment and HYTHIRM projects. If data from digital scans of the Orbiter windward surface become available, simulations will also be performed to characterize the difference in surface heating between the CAD reference OML and the digitized surface provided by the surface scans.

Campbell, Charles H.↗

A model for a knowledge-based system's life cycle

The American Institute of Aeronautics and Astronautics has initiated a Committee on Standards for Artificial Intelligence. Presented here are the initial efforts of one of the working groups of that committee. The purpose here is to present a candidate model for the development life cycle of Knowledge Based Systems (KBS). The intent is for the model to be used by the Aerospace Community and eventually be evolved into a standard. The model is rooted in the evolutionary model, borrows from the spiral model, and is embedded in the standard Waterfall model for software development. Its intent is to satisfy the development of both stand-alone and embedded KBSs. The phases of the life cycle are detailed as are and the review points that constitute the key milestones throughout the development process. The applicability and strengths of the model are discussed along with areas needing further development and refinement by the aerospace community.

Kiss, Peter A.↗

Assessment of Crustal Leg Uncertainties for RSTT Path-dependent Uncertainty

The Regional Seismic Travel Time (RSTT) model and software were recently updated to allow for path-dependent uncertainty (PDU) estimates for travel-time (Begnaud et al. 2021; Begnaud et al. 2020). Begnaud et al. (2021) describes the process of improving the current distance-dependent uncertainty parameterization for RSTT using a random effects model (REM) to estimate slowness (inverse velocity) uncertainty as a mean squared error for each model parameter. The REM separates the error between observed slowness and model predicted slowness into bias and random components. The PDU is calculated by integrating these mean squared errors along a seismic-phase ray path.

58 GEOSCIENCES↗