Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “software differences”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 487 records · Page 27
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Large-scale application of free energy perturbation calculations for antibody design

Abstract Alchemical free energy perturbation (FEP) is a rigorous and powerful technique to calculate the free energy difference between distinct chemical systems. Here we report our implementation of automated large-scale FEP calculations, using the Amber software package, to facilitate antibody design and evaluation. In combination with Hamiltonian replica exchange, our FEP simulations aim to predict the effect of mutations on both the binding affinity and the structural stability. Importantly, we incorporate multiple strategies to faithfully estimate the statistical uncertainties in the FEP results. As a case study, we apply our protocols to systematically evaluate variants of the m396 antibody for their conformational stability and their binding affinity to the spike proteins of SARS-CoV-1 and SARS-CoV-2. By properly adjusting relevant parameters, the particle collapse problems in the FEP simulations are avoided. Furthermore, large statistical errors in a small fraction of the FEP calculations are effectively reduced by extending the sampling, such that acceptable statistical uncertainties are achieved for the vast majority of the cases with a modest total computational cost. Finally, our predicted conformational stability for the m396 variants is qualitatively consistent with the experimentally measured melting temperatures. Our work thus demonstrates the applicability of FEP in computational antibody design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Analyzing the Impact of System Reliability Events on Applications in the Titan Supercomputer

Extreme-scale computing systems employ Reliability, Availability and Serviceability (RAS) mechanisms and infrastructure to log events from multiple system components. In this paper, we analyze RAS logs in conjunction with the application placement and scheduling database, in order to understand the impact of common RAS events on application performance. This study conducted on the records of about 2 million applications executed on Titan supercomputer provides important insights for system users, operators and computer science researchers. Specifically, we investigate the impact of RAS events on application performance and its variability by comparing cases where events are recorded with corresponding cases where no events are recorded. Such a statistical investigation is possible since we observed that system users tend to execute their applications multiple times. Our analysis reveals that most RAS events do impact application performance, although not always. We also find that different system components affect application performance differently. In particular, our investigation includes the following components: parallel file system processor, memory, graphics processing units, system and user software issues. Our work establishes the importance of providing feedback to system users for increasing operational efficiency of extreme-scale systems.

Ashraf, Rizwan↗
DOE OSTI2018

Storage for Advanced Scientific Use-Cases and Beyond

The dCache project provides open-source storage software deployed internationally to satisfy ever more demanding scientific storage requirements. Its multifaceted approach provides an integrated way of supporting different use-cases with the same storage, from high throughput data ingest, through wide access and easy integration with existing systems. In this paper, we describe some of the recent features that facilitate the use of storage to maximise the gain from stored data, including quality-of-service management, heterogeneous systems - both through integrated tertiary storage support and geographical locality - the parallel NFS (pNFS) extension, and innovative delegated authorisation schemes.

43 PARTICLE ACCELERATORS↗
DOE OSTI2023

State of the Art of Molecular Visualization in Immersive Virtual Environments

Abstract Visualization plays a crucial role in molecular and structural biology. It has been successfully applied to a variety of tasks, including structural analysis and interactive drug design. While some of the challenges in this area can be overcome with more advanced visualization and interaction techniques, others are challenging primarily due to the limitations of the hardware devices used to interact with the visualized content. Consequently, visualization researchers are increasingly trying to take advantage of new technologies to facilitate the work of domain scientists. Some typical problems associated with classic 2D interfaces, such as regular desktop computers, are a lack of natural spatial understanding and interaction, and a limited field of view. These problems could be solved by immersive virtual environments and corresponding hardware, such as virtual reality head‐mounted displays. Thus, researchers are investigating the potential of immersive virtual environments in the field of molecular visualization. There is already a body of work ranging from educational approaches to protein visualization to applications for collaborative drug design. This review focuses on molecular visualization in immersive virtual environments as a whole, aiming to cover this area comprehensively. We divide the existing papers into different groups based on their application areas, and types of tasks performed. Furthermore, we also include a list of available software tools. We conclude the report with a discussion of potential future research on molecular visualization in immersive environments.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

DeconTools

DeconTools is a software package used for detecting features in MS data by using the isotopic signatures of expected components. The tool uses different algorithms for different parts of the deconvolution process: noise reduction, peak detection, prediction of theoretical isotopic envelope and scoring functions that quantitate the quality of signature observed in the data.

Crowell, Kevin↗
DOE OSTI2023

Reposcanner

SAND2023-05455O Reposcanner provides a highly modular, extensible framework for defining routines for mining data from software repositories and performing analyses on that data to yield valuable insights on team behaviors. Reposcanner features seamless support for different version control platforms like GitHub, Gitlab, and Bitbucket; smart parsing of URLs; intelligent credential management capabilities; and a comprehensive test suite. Reposcanner is connected to the Exascale Computing Project and is intended for research purposes.

Mundt, Miranda↗
DOE OSTI2024

2D Polyhedral Template Matching for Atomic Resolution Microscopy

SAND2024-13879O The 2D Polyhedral Template Matching for Atomic Resolution Microscopy is a suite of functions for analyzing atomic resolution electron microscopy images using the 2D polyhedral template matching (2D-PTM) method. This software analyzes atomic resolution microscopy data from electron microscopic imaging or scanning probe microscopies. The primary application is for identifying different crystal phases, crystal orientations, and defect structures obtained in such atomic resolution images. Written in MATLAB and starting from an atomic resolution image, the code identifies the positions of atomic intensity peaks. It then matches predefined structural templates to the local atomic environments. Outputs include the local structural identification, the template scaling factor and rotation angle, root-mean-squared deviation (RMSD), and centrosymmetry parameter.

Medlin, Douglas↗
DOE OSTI2018

Online Simulation Tools for Orbit Correction in the CBETA Machine (CBETA Note 029)

Control of beam trajectory is essential in particle accelerators. The trajectory of a beam is sensitive to various types of imperfections that cause it to deviate from its desired path along the accelerator. Orbit correction is hence fundamental for the control of beam trajectory. In this work we aim demonstrate orbit correction using singular value decomposition techniques applied to distorted orbits generated in the CBETA-V Virtual Machine. In particular we present two concrete examples of such correction in different sections of the CBETA Fractional Arc Test layout. Our goal is to construct the backbone of an orbit correction software toolkit to be tested in the CBETA-V Virtual Machine and eventually implemented in the completed CBETA control system.

43 PARTICLE ACCELERATORS↗
DOE OSTI2021

A Comprehensive Open-Source R Software For Statistical Metrology Calculations: From Uncertainty Evaluation To Risk Analysis

Whether calibrating equipment or inspecting products on the factory floor, metrology requires many complicated statistical calculations to achieve a full understanding and evaluation of measurement uncertainty and quality. In order to assist its workforce in performing these calculations in a consistent and rigorous way, the Primary Standards Lab at Sandia National Laboratories (SNL) has developed a free and open-source software package for computing various metrology calculations from uncertainty propagation to risk analysis. In addition to propagating uncertainty through a measurement model using the well-known Guide to Expression of Uncertainty in Measurement or Monte Carlo approaches, evaluating the individual Type A and Type B uncertainty components that go into the measurement model often requires other statistical methods such as analysis of variance or determining uncertainty in a fitted curve. Once the uncertainty in a measurement has been calculated, it is usually evaluated from a risk perspective to ensure the measurement is suitable for making a particular conformance decision. Finally, SNL’s software can perform all these calculations in a single application via an easy-to-use graphical interface, where the different functions are integrated so the results of one calculation can be used as inputs to another calculation.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

Risk perception and social representation on radioactive waste: a case study with students of IPEN

Proper management of radioactive waste in teaching and research laboratories involves not only techniques and procedures for the treatment, storage and disposal of these materials but also the responsibility of all those who handle them. Responsibility begins with with methods that generate less waste and with the correct segregation of contaminated materials prior to disposal, In this context, the present study aimed to know, identify, understand and analyze the perception of risk and social representations about radioactive waste and its management by students and researchers of the Nuclear and Energy Research Institute. According to Renn (1992), two of the approaches to risk perception are cultural and sociological, which served as the basis to the present study. Within this analysis, the concept of risk is understood as a phenomenon and, therefore, the phenomena experienced by the individuals are related to their life histories, social relations, religious beliefs and academic formation, elements that interfere in the perception of risk. The method used to collect data was free evocation, with participants receiving the following instructions: 'Please write five words that pop up into your mind when you listen to the words radioactive waste and, sequentially, write a sentence using these words'. All participants received instructions of the voluntary character of the participation and of the confidentiality of the data. A total of 73 students and researchers were interviewed, including scientific initiation, masters degree, doctorate and postdoctoral researchers. 353 words were mentioned, of which 209 were different from each other. After analyzing the sentences, the words were inserted in 12 categories and later analyzed in the software INVOCADO, which provides a diagram with the possible structure of the social representations of the group studied. The analysis of the four-quadrants and their categories, as well as the mentioned words that compose them, are therefore consistent with the universe of the public analyzed. While it is not the totality of students dealing with radioactive materials, in general these individuals understand the importance of technology and that the adoption of safe practices ensures the successful development of research. Future developments: Analyze quantitatively and qualitatively the other questions of the questionnaire. Analyze the data and information obtained from the participant observation, which consisted of a follow-up of three students in their laboratory practices. Propose to the institute a manual of good practices that can be used by the students in their laboratory practices.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2019

Research on the Corrosion Behavior of X70 Pipeline Steel Under Coupling Effect of AC + DC and Stress

The coupling effect of stray AC (alternating current) + DC (direct current) and tensile stress-induced X70 pipeline corrosion is complicated with its mechanism uncovered. In this work, the corrosion behavior of X70 pipeline steel under three different corrosion (including an individual AC corrosion, mixed AC + 150 MPa tensile stress corrosion, coupling effect of AC + a 30 A/m{sup 2} DC interference and 150 MPa tensile stress corrosion) conditions in Dagang soil simulated solution was investigated by COMSOL Multiphysics software simulation, electrochemical tests, scanning electron microscope and other techniques. The results indicated that with the increase in AC density, the open-circuit potential of the X70 steel samples was negatively shifted and corrosion rate increased in three different corrosion conditions. The corrosion rates of X70 steel samples under individual AC interference were almost unchanged when 150.9 MPa tensile stress was applied. When applying 30 A/m{sup 2} DC interference, the corrosion rate of X70 steel increases significantly. Therefore, the factors affecting corrosion performance of X70 pipeline steel were DC > AC > stress. Under individual AC interference, uniform corrosion occurred on the X70 steel at an AC current density of less than 30 A/m{sup 2}, while the pitting corrosion occurred at an AC current density of greater than 100 A/m{sup 2}. The application of tensile stress and DC had a certain inhibitory effect on pitting corrosion.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Evaluating the Impact of Price-Responsive Load on Power Systems Using Integrated T&D Simulation

This paper explores the differences between simulating price-responsive load (PRL) interactions with power systems using integrated transmission and distribution (T&D) models and transmission-only (T-only) models. This analysis uses the Integrated Grid Modeling System (IGMS) software to capture 'ISO-to-appliance' simulations using a synthetic T&D model built on the PJM 5-Bus transmission network with multiple full-scale taxonomy feeders that include physics-based models of thousands of customers and PRLs. The results show important differences in the impacts of PRLs between integrated T&D and T-only models. Experiments with the synthetic integrated T&D dataset demonstrated that integrated T&D simulation revealed notably larger differences between the PRL and no-PRL cases for load, and prices compared to T-only simulation. Similarly, differences are observed between the price response of individual buildings and distribution feeders and the corresponding transmission bus in the integrated T&D simulations, which are difficult to capture in traditional T-only simulations.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2021

Building envelope anomaly characterization and simulation using drone time-lapse thermography

Defects in building envelopes deteriorate over time without being visible to the human eye, while significantly impacting energy performance due to unaccounted heat transfer. Defects can be characterized in the infrared (IR) spectrum. However, IR readings are typically recorded at singular points in time, when in several cases anomalies can only be revealed at specific times of the day, possibly in different seasons of the year. This paper presents a novel workflow for 3D envelope defect characterization and modeling using aerial time-lapse IR data collection using drones. A comprehensive envelope thermal profile is developed for a case study building employing the photogrammetry software Agisoft Photoscan, which generates temporal IR inspections of building skins using multiple thermography orthomosaics. Point-cloud data is then translated into a CAD model and thermal zones for whole Building Energy Modeling (BEM) using Honeybee as a frontend to EnergyPlus to showcase the potential of inclusion of detailed 4D data. Envelope contributions in this case study’s anomalies showed heat losses of 6447.6 kWh, and Energy Use Intensity (EUI) differences of ~2 kWh/m 2 /year from the baseline. Finally, why there is currently little translation of this work in BEM software is discussed, while identifying limitations and future research in the employment of time-lapse thermography using drones for more accurate building envelope inspection and modeling.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2023

Hybrid Tandem Photovoltaics

Tandem solar cell structures are the only strategy demonstrated to surpass the detailed balance efficiency limit of high-quality single-junction solar cells. To continue to improve the efficiencies of cost-effective terrestrial solar power, hybrid tandems of dissimilar subcells are being considered by many around the world, especially designs that incorporate silicon solar cells as a bottom subcell. In this project, we studied a wide variety of tandem design possibilities including those with three-terminal (3T) and four-terminal (4T) configurations. The use of 3T and 4T designs could be useful for efficient and economical hybrid tandem designs that utilize the best available subcell materials such as emerging perovskite materials. Three-terminal configurations, in particular, have not been sufficiently studied previously. We have laid the foundational groundwork in this project for understanding the operation of 3T tandems: developing a taxonomy for naming, a methodology for measuring and interconnecting, and models for simply characterizing 3T tandems. Electrical and optical subcell coupling between the subcells was also measured and modeled. An important part of this work was the fabrication of novel example tandem structures, including 4T GaAs/Si, 3T GaInP/Si, 3T GaAs/Si, and 3T GaInP/GaAs devices. Using these high-quality tandem cells, we have been able to clearly demonstrate the achievability of high-efficiencies, and subtle physical effects such as photon recycling and luminescent coupling. We have developed and demonstrated essential building-block tools such as transparent conductive adhesives (TCA) and 3T silicon bottom cells with interdigitated back contacts (IBC) that can also be used in many other tandem designs. We have tested the reliability of these tools and devices under standardized testing and outdoor measurements. We have found 4T GaAs/Si tandems to be relatively straightforward to fabricate and robust in real-world outdoor conditions. While we have demonstrated working hybrid 3T III-V/TCA/Si IBC tandems, we experienced low yields even with our best process flows yet. Further work is still needed to improve the processing yield of these devices. We therefore also created tandem cells using an all-III-V 3T tandem process which was very robust with high yields, allowing for the creation of voltage-matched strings in many different configurations using 8 nearly identical 3T tandems. Using these robust 3T tandem examples, we were able measure and precisely characterize 3T tandem behaviors to predict their operation under changing spectrum and temperature. The optoelectronic equivalent-circuit model was shown to be very general and applicable to hybrid tandems, and encompassed the operation 3T Si IBC cells. This general model has been distributed to the public in as open-source Python-based software called PVcircuit. We have calculated the implications of these new tandem device designs on the real-world energy production and shown how the relative performance of different tandem configurations is situational and can be engineered using the tools developed here.

14 SOLAR ENERGY↗
DOE OSTI2022

Design and performance analysis of a Swirl Pintle injector for a 1 MW th pressurized oxy-coal combustor

Pressurized Oxy-coal combustion has the potential to achieve high thermal efficiency by recovering the latent heat of steam from flue gases and providing options for up to 95% carbon capture. Here, this study proposes a novel burner technology for pressurized oxy-coal combustion and investigates its operability. Three burner versions are designed and tested; no swirl, swirl numbers 0.9 and 1.2 to identify optimum design parameters and performance. A commercially available Dantec Dynamics software is used to conduct the shadowgraph experiments to observe burner performance. Coal water slurry is used as fuel with three different slurry ratios where the coal percentage by weights were 30, 40 and 50. Droplet size, distribution, spray angle and jet breakup lengths are measured and analyzed to quantify the performance. The study found that increasing the swirl number enhanced atomization. Implementing swirlers allowed the jet to spread through faster primary jet separation, thus improving atomization. In addition, higher slurry ratios improved the generation of smaller particles. However, it was also found that excessive increases in oxidizer momentums negatively impact the atomization process by jet shrinkage. The study concluded that operating a pintle burner at 1.2 swirl conditions with a 40/60 slurry ratio produces optimum performance.

42 ENGINEERING↗
DOE OSTI2023

Numerical modeling of hydrogen mixing in a direct-injection engine fueled with gaseous hydrogen

Hydrogen is considered as one of the most promising options to achieve effective decarbonization of the energy and transportation sectors. As such, it has recently been receiving increasing attention because of its promising potential as an energy carrier for advanced energy and propulsion systems. With a focus on internal combustion engines, direct injection (DI) of gaseous hydrogen during the compression stroke offers great potential for high engine efficiency and specific power while reducing the risk of backfiring and pre-ignition issues. Therefore, many experimental and numerical efforts have recently been dedicated to understanding the physical and chemical behaviors of hydrogen in engine during mixing and combustion. This study focuses on computational fluid dynamics (CFD) modeling of the hydrogen DI process in a hydrogen optical research engine. Under the conditions studied, gaseous hydrogen is injected into the combustion chamber via a centrally located single-hole injector at a pressure of 100 bar. Two configurations, namely low-and high-tumble, are investigated to understand the impact of different in-cylinder flow patterns on the fuel-air mixture preparation. Simulations are carried out using the commercial CFD software CONVERGE. Here, the in-cylinder turbulence is modeled with an unsteady Reynolds-averaged Navier-Stokes (URANS) formulation closed by the renormalization group (RNG) k-ε model. Several numerical methods and model constants, including but not limited to turbulent Schmidt number, are evaluated. The numerical results are systematically compared against experimental measurements of velocity and hydrogen concentration fields on the vertical center plane to assess the performance of the CFD model, unveil the physics of hydrogen mixing, and establish best practices for modeling hydrogen DI under relatively high injection pressure conditions.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2024

Spatial modeling algorithms for reactions and transport in biological cells

Biological cells rely on precise spatiotemporal coordination of biochemical reactions to control their functions. Such cell signaling networks have been a common focus for mathematical models, but they remain challenging to simulate, particularly in realistic cell geometries. Here we present Spatial Modeling Algorithms for Reactions and Transport (SMART), a software package that takes in high-level user specifications about cell signaling networks and then assembles and solves the associated mathematical systems. SMART uses state-of-the-art finite element analysis, via the FEniCS Project software, to efficiently and accurately resolve cell signaling events over discretized cellular and subcellular geometries. We demonstrate its application to several different biological systems, including yes-associated protein (YAP)/PDZ-binding motif (TAZ) mechanotransduction, calcium signaling in neurons and cardiomyocytes, and ATP generation in mitochondria. Throughout, we utilize experimentally derived realistic cellular geometries represented by well-conditioned tetrahedral meshes. These scenarios demonstrate the applicability, flexibility, accuracy and efficiency of SMART across a range of temporal and spatial scales.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Automated Metadata Extraction: Challenges and Opportunities

Proper application of the FAIR data principles is what separates a vibrant data ecosystem, in which research data are frequently shared and reused, from a lifeless data graveyard. Automated metadata extraction systems have been proposed as a means of bolstering the findability, interoperability, and reusabil- ity of data repositories with little or no human intervention. These extraction systems mine metadata by crawling a repository and applying lightweight extractors that, for various types of file (e.g., image, CSV file), extract or synthesize relevant attributes. In practice, however, the automated creation of generally useful metadata is fraught with challenges. Data consumers may have different perspectives as to what metadata representations are useful, the standards for recording metadata tend to change over time, and the software model for processing updates can introduce unnecessary human and computational effort. Thus, generalizing extraction for a broad audience of data consumers is a difficult and relatively unsolved problem.In this work, we explore these challenges faced by extraction systems in the context of constructing our own extraction system for science data. We first define the metadata extraction problem and provide context to the issues faced in generalizing metadata. Additionally, we identify potential research directions to help alleviate many of these challenges for all automated extraction systems. Ultimately, this work represents a first step in designing ubiquitous metadata extraction systems that can maximize the value of research data while minimizing the human efforts required in doing so.

Skluzacek, Tyler↗