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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.

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At least 793 records · Page 44
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Formally Verified ZTA Requirements for OT/ICS Environments with Isabelle/HOL

The clean energy transformation includes the integration of distributed energy resources with the power grid, which has led to a substantial increase in the complexity of power grids infrastructure and the underlying operational technology environment. Power grids infrastructure represents an operational technology environment that has become a system of systems, integrating heterogeneous devices which are both software-and hardware-intensive; as a result, there are increasing demands to exploit advances in the commodity of software-hardware infrastructures to improve energy systems requirements such as cybersecurity and resilience. In such a setting, system requirements at different levels mix, which leads to vulnerabilities and undesirable outcomes. The use of formal methods to characterize and prove system requirements removes ambiguity, increases automation, and provides high levels of assurance and reliability. In this paper, we contribute a methodology and a framework for the system-level verification of zero trust architecture requirements in operational technology environments. We define a formal specification for the core functionalities of operational technology environments, the corresponding invariants, and security proofs. Of particular note is our modular approach for the formal verification of asynchronous interactions in operational technology environments. The formal specification and the proofs have been mechanized using the interactive theorem proving environment Isabelle/HOL.

formal methods↗
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 OSTI2016

Potential application of mono/bi-layer molybdenum disulfide (MoS{sub 2}) sheet as an efficient transparent conducting electrode in silicon heterojunction solar cells

In this paper, we have simulated the structure of n-type MoS{sub 2}/silicon heterojunction solar cell and studied its function under different conditions. The optimization of parameters of the cell's layer has been carried out by using AFORS-HET software. In the present study, MoS{sub 2} has been considered as 3-D in nature instead of the reported 2-D nature. In order to ensure the formation of Schottky junction, electric contact has been made along the c-axis to collect the minority charge carriers. After optimizing the various parameters of n-type single layer MoS{sub 2}, power efficiency of 12.44% has been achieved at the room temperature, which has further decreased to 9.042% as the layer number has increased up to 40. Furthermore, after optimizing the parameters of silicon wafer maximum efficiency of 16.4% has been achieved. Temperature dependence of the cell performance has also been studied and the maximum efficiency has been achieved at 300 K. In the present study, we have demonstrated that n-type ultrathin layer of MoS{sub 2} can be used as an excellent transparent conducting electrode.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Comparing generalized ensemble methods for sampling of systems with many degrees of freedom

Here, we compare two standard replica exchange methods using temperature and dielectric constant as the scaling variables for independent replicas against two new corresponding enhanced sampling methods based on non-equilibrium statistical cooling (temperature) or descreening (dielectric). We test the four methods on a rough 1D potential as well as for alanine dipeptide in water, for which their relatively small phase space allows for the ability to define quantitative convergence metrics. We show that both dielectric methods are inferior to the temperature enhanced sampling methods, and in turn show that temperature cool walking (TCW) systematically outperforms the standard temperature replica exchange (TREx) method. We extend our comparisons of the TCW and TREx methods to the 5 residue met-enkephalin peptide, in which we evaluate the Kullback-Leibler divergence metric to show that the rate of convergence between two independent trajectories is faster for TCW compared to TREx. Finally we apply the temperature methods to the 42 residue amyloid-β peptide in which we find non-negligible differences in the disordered ensemble using TCW compared to the standard TREx. All four methods have been made available as software through the OpenMM Omnia software consortium.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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 OSTI2015

SU-E-I-13: Evaluation of Metal Artifact Reduction (MAR) Software On Computed Tomography (CT) Images

Purpose: A new commercially available metal artifact reduction (MAR) software in computed tomography (CT) imaging was evaluated with phantoms in the presence of metals. The goal was to assess the ability of the software to restore the CT number in the vicinity of the metals without impacting the image quality. Methods: A Catphan 504 was scanned with a GE Optima RT 580 CT scanner (GE Healthcare, Milwaukee, WI) and the images were reconstructed with and without the MAR software. Both datasets were analyzed with Image Owl QA software (Image Owl Inc, Greenwich, NY). CT number sensitometry, MTF, low contrast, uniformity, noise and spatial accuracy were compared for scans with and without MAR software. In addition, an in-house made phantom was scanned with and without a stainless steel insert at three different locations. The accuracy of the CT number and metal insert dimension were investigated as well. Results: Comparisons between scans with and without MAR algorithm on the Catphan phantom demonstrate similar results for image quality. However, noise was slightly higher for the MAR algorithm. Evaluation of the CT number at various locations of the in-house made phantom was also performed. The baseline HU, obtained from the scan without metal insert, was compared to scans with the stainless steel insert at 3 different locations. The HU difference between the baseline scan versus metal scan was improved when the MAR algorithm was applied. In addition, the physical diameter of the stainless steel rod was over-estimated by the MAR algorithm by 0.9 mm. Conclusion: This work indicates with the presence of metal in CT scans, the MAR algorithm is capable of providing a more accurate CT number without compromising the overall image quality. Future work will include the dosimetric impact on the MAR algorithm.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

SU-E-T-355: Efficient Scatter Correction for Direct Ray-Tracing Based Dose Calculation

Purpose: To propose a scatter correction method with linear computational complexity for direct-ray-tracing (DRT) based dose calculation. Due to its speed and simplicity, DRT is widely used as a dose engine in the treatment planning system (TPS) and monitor unit (MU) verification software, where heterogeneity correction is applied by radiological distance scaling. However, such correction only accounts for attenuation but not scatter difference, causing the DRT algorithm less accurate than the model-based algorithms for small field size in heterogeneous media. Methods: Inspired by the convolution formula derived from an exponential kernel as is typically done in the collapsed-cone-convolution-superposition (CCCS) method, we redesigned the ray tracing component as the sum of TERMA scaled by a local deposition factor, which is linear with respect to density, and dose of the previous voxel scaled by a remote deposition factor, D(i)=aρ(i)T(i)+(b+c(ρ(i)-1))D(i-1),where T(i)=e(-αr(i)+β(r(i))2) and r(i)=Σ-(j=1,..,i)ρ(j).The two factors together with TERMA can be expressed in terms of 5 parameters, which are subsequently optimized by curve fitting using digital phantoms for each field size and each beam energy. Results: The proposed algorithm was implemented for the Fluence-Convolution-Broad-Beam (FCBB) dose engine and evaluated using digital slab phantoms and clinical CT data. Compared with the gold standard calculation, dose deviations were improved from 20% to 2% in the low density regions of the slab phantoms for the 1-cm field size, and within 2% for over 95% of the volume with the largest discrepancy at the interface for the clinical lung case. Conclusion: We developed a simple recursive formula for scatter correction for the DRT-based dose calculation with much improved accuracy, especially for small field size, while still keeping calculation to linear complexity. The proposed calculator is fast, yet accurate, which is crucial for dose updating in IMRT optimization.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

A method for evaluating image quality of monochrome and color displays based on luminance by use of a commercially available color digital camera

Purpose: The aim of this study is to propose a method for the quantitative evaluation of image quality of both monochrome and color liquid-crystal displays (LCDs) using a commercially available color digital camera. Methods: The intensities of the unprocessed red (R), green (G), and blue (B) signals of a camera vary depending on the spectral sensitivity of the image sensor used in the camera. For consistent evaluation of image quality for both monochrome and color LCDs, the unprocessed RGB signals of the camera were converted into gray scale signals that corresponded to the luminance of the LCD. Gray scale signals for the monochrome LCD were evaluated by using only the green channel signals of the camera. For the color LCD, the RGB signals of the camera were converted into gray scale signals by employing weighting factors (WFs) for each RGB channel. A line image displayed on the color LCD was simulated on the monochrome LCD by using a software application for subpixel driving in order to verify the WF-based conversion method. Furthermore, the results obtained by different types of commercially available color cameras and a photometric camera were compared to examine the consistency of the authors’ method. Finally, image quality for both the monochrome and color LCDs was assessed by measuring modulation transfer functions (MTFs) and Wiener spectra (WS). Results: The authors’ results demonstrated that the proposed method for calibrating the spectral sensitivity of the camera resulted in a consistent and reliable evaluation of the luminance of monochrome and color LCDs. The MTFs and WS showed different characteristics for the two LCD types owing to difference in the subpixel structure. The MTF in the vertical direction of the color LCD was superior to that of the monochrome LCD, although the WS in the vertical direction of the color LCD was inferior to that of the monochrome LCD as a result of luminance fluctuations in RGB subpixels. Conclusions: The authors’ method based on the use of a commercially available color camera is useful to evaluate and understand the display performances of both monochrome and color LCDs in radiology departments.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-F-T-300: Impact of Electron Density Modeling of ArcCHECK Cylindricaldiode Array On 3DVH Patient Specific QA Software Tool Analysis

Purpose: 3DVH software is a patient specific quality assurance tool which estimates the 3D dose to the patient specific geometry with the help of Planned Dose Perturbation algorithm. The purpose of this study is to evaluate the impact of HU value of ArcCHECK phantom entered in Eclipse TPS on 3D dose & DVH QA analysis. Methods: Manufacturer of ArcCHECK phantom provides CT data set of phantom & recommends considering it as a homogeneous phantom with electron density (1.19 gm/cc or 282 HU) close to PMMA. We performed this study on Eclipse TPS (V13, VMS) & trueBEAM STx VMS Linac & ArcCHECK phantom (SNC). Plans were generated for 6MV photon beam, 20cm×20cm field size at isocentre & SPD (Source to phantom distance) of 86.7 cm to deliver 100cGy at isocentre. 3DVH software requires patients DICOM data generated by TPS & plan delivered on ArcCHECK phantom. Plans were generated in TPS by assigning different HU values to phantom. We analyzed gamma index & the dose profile for all plans along vertical down direction of beam’s central axis for Entry, Exit & Isocentre dose. Results: The global gamma passing rate (2% & 2mm) for manufacturer recommended HU value 282 was 96.3%. Detector entry, Isocentre & detector exit Doses were 1.9048 (1.9270), 1.00(1.0199) & 0.5078(0.527) Gy for TPS (Measured) respectively.The global gamma passing rate for electron density 1.1302 gm/cc was 98.6%. Detector entry, Isocentre & detector exit Doses were 1.8714 (1.8873), 1.00(0.9988) & 0.5211(0.516) Gy for TPS (Measured) respectively. Conclusion: Electron density value assigned by manufacturer does not hold true for every user. Proper modeling of electron density of ArcCHECK in TPS is essential to avoid systematic error in dose calculation of patient specific QA.

60 APPLIED LIFE SCIENCES↗
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 OSTI2014

Poster — Thur Eve — 51: An analysis of the effectiveness of automated pre-, post- and intra-treatment auditing of electronic health records

We describe development of automated, web-based, electronic health record (EHR) auditing software for use within our paperless radiation oncology clinic. By facilitating access to multiple databases within the clinic, each patient's EHR is audited prior to treatment, regularly during treatment, and post treatment. Anomalies such as missing documentation, non-compliant workflow and treatment parameters that differ significantly from the norm may be monitored, flagged and brought to the attention of clinicians. By determining historical trends using existing patient data and by comparing new patient data with the historical, we expect our software to provide a measurable improvement in the quality of radiotherapy at our centre.

60 APPLIED LIFE SCIENCES↗