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At least 73 records · Page 4

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DOE OSTI2016

SU-F-J-72: A Clinical Usable Integrated Contouring Quality Evaluation Software for Radiotherapy

Purpose: To introduce the Auto Contour Evaluation (ACE) software, which is the clinical usable, user friendly, efficient and all-in-one toolbox for automatically identify common contouring errors in radiotherapy treatment planning using supervised machine learning techniques. Methods: ACE is developed with C# using Microsoft .Net framework and Windows Presentation Foundation (WPF) for elegant GUI design and smooth GUI transition animations through the integration of graphics engines and high dots per inch (DPI) settings on modern high resolution monitors. The industrial standard software design pattern, Model-View-ViewModel (MVVM) pattern, is chosen to be the major architecture of ACE for neat coding structure, deep modularization, easy maintainability and seamless communication with other clinical software. ACE consists of 1) a patient data importing module integrated with clinical patient database server, 2) a 2D DICOM image and RT structure simultaneously displaying module, 3) a 3D RT structure visualization module using Visualization Toolkit or VTK library and 4) a contour evaluation module using supervised pattern recognition algorithms to detect contouring errors and display detection results. ACE relies on supervised learning algorithms to handle all image processing and data processing jobs. Implementations of related algorithms are powered by Accord.Net scientific computing library for better efficiency and effectiveness. Results: ACE can take patient’s CT images and RT structures from commercial treatment planning software via direct user input or from patients’ database. All functionalities including 2D and 3D image visualization and RT contours error detection have been demonstrated with real clinical patient cases. Conclusion: ACE implements supervised learning algorithms and combines image processing and graphical visualization modules for RT contours verification. ACE has great potential for automated radiotherapy contouring quality verification. Structured with MVVM pattern, it is highly maintainable and extensible, and support smooth connections with other clinical software tools.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2026

CAHS: Context-Aware Homology Search

Protein homology search is foundational to bioinformatics: it supports annotation transfer, structure/function inference, and evolutionary analysis over rapidly expanding sequence repositories (e.g., UniProtKB). Profile hidden Markov models (pHMMs), as implemented in HMMER, remain the most widely trusted approach because they provide statistically calibrated E-values; however, their gap behavior is fixed once a profile is trained, despite biological evidence that insertion/deletion tolerance varies across flexible loops and intrinsically disordered regions. We present CAHS (Context-Aware Homology Search), a lightweight query-time adapter for pHMM search that incorporates learned and biologically motivated signals without changing HMMER's downstream search pipeline or its calibrated E-value reporting. Given a query sequence, CAHS computes per-residue representations from a protein language model and a disorder predictor, maps these to profile coordinates, and modulates only match-state transition rows (gap-open and gap-extension probabilities) while preserving Plan7 constraints. We comprehensively evaluate CAHS across six structurally diverse protein families and multi-domain architectures against a 570k-sequence target corpus. CAHS expands detection capability, retrieving thousands of additional remote homologs at relaxed thresholds by maintaining alignment quality through flexible regions. For multi-domain proteins, context-aware modulation resolves 94% of fragmented alignments. Crucially, CAHS preserves hit-set invariance at stringent operating points (E<10-10), demonstrating increased statistical confidence without inflating false positives. Furthermore, sharper statistical distinction between homologs and background noise during early filter stages yields up to a 3.87× acceleration in end-to-end wall-clock time on high-performance computing clusters. Overall, CAHS illustrates a practical AI-for-science design pattern: augmenting a trusted probabilistic model with query-specific learned signals to improve interpretable, reproducible inference in data-rich biology.

Bhattaram, Swethasree [Georgia Institute of Techno↗

DOE OSTI2016

Flexible Computer Science Infrastructure (FleCSI)

FleCSI is a compile-time configurable framework designed to support multi-physics application development. As such, FleCSI attempts to provide a very general set of infrastructure design patterns that can be specialized and extended to suit the needs of a broad variety of solver and data requirements. Current support includes multi-dimensional mesh topology, mesh geometry, and mesh adjacency information, n-dimensional hashed-tree data structures, graph partitioning interfaces, and dependency closures. FleCSI also introduces a functional programming model with control, execution, and data abstractions that are consistent with both MPI and state-of-the-art task-based runtimes such as Legion and Charm++. The FleCSI abstraction layer provides the developer with insulation from the underlying runtime, while allowing support for multiple runtime systems, including conventional models like asynchronous MPI. The intent is to give developers a concrete set of user-friendly programming tools that can be used now, while allowing flexibility in choosing runtime implementations and optimizations that can be applied to architectures and runtimes that arise in the future. The control and execution models in FleCSI also provide formal nomenclature for describing poorly understood concepts like kernels and tasks.

Moss, Nicholas↗

DOE OSTI2025

solposx: A Python package for determining solar position and atmospheric refraction

solposx is a Python package of reference algorithms for calculating the sun’s position and atmospheric refraction. The package includes 11 solar position algorithms and 6 refraction models from the past 50 years. All functions follow a standardized design pattern, making it easy to compare different algorithms. The provided algorithm implementations have been thoroughly vetted, making the package a valuable research tool and a reliable reference for implementing solar position algorithms in other programming languages or applications.

Jensen, Adam R. [Technical University of Denmark, ↗

DOE OSTI2017

FleCSPH notes

FleCSI is a compile-time con gurable framework designed to support multi-physics application development. As such, FleCSI provides a very general set of infrastructure design patterns that can be specialized and extended to suit the needs of a broad variety of solver and data requirements. FleCSI currently supports multi-dimensional mesh topology, geometry, and adjacency information, as well as n-dimensional hashed-tree data structures, graph partitioning interfaces, and dependency closures. FleCSI introduces a functional programming model with control, execution, and data abstractions that are consistent both with MPI and with state-of-the-art, task-based runtimes such as Legion and Charm++. The abstraction layer insulates developers from the underlying runtime, while allowing support for multiple runtime systems including conventional models like asynchronous MPI. The intent is to provide developers with a concrete set of user-friendly programming tools that can be used now, while allowing exibility in choosing runtime implementations and optimization that can be applied to future architectures and runtimes. FleCSI's control and execution models provide formal nomenclature for describing poorly understood concepts such as kernels and tasks. FleCSI's data model provides a low-buy-in approach that makes it an attractive option for many application projects, as developers are not locked into particular layouts or data structure representations. FleCSI currently provides a parallel but not distributed implementation of Binary, Quad and Oct-tree topology. This implementation is base on space lling curves domain decomposition, the Morton order. The current FleCSI version requires the implementation of a driver and a specialization driver. The role of the specialization driver is to provide the data distribution. This feature is not complete in FleCSI code and we provide it. The next step will be to incorporate it directly from FleCSPH to FleCSI as we reach a good level of performance. Then the driver represent the general execution of the resolution without worrying of the data locality and communications. As FleCSI is an On-Development code the structure may change in the future and we keep track of these changes in FleCSPH.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2020

Petronius Offshore Oil Field Case Study

This document is one of three offshore post-primary CO 2 enhanced oil recovery project case studies that compares the modeling results from an industry standard compositional simulator (“GEM”) and a variant of the FE/NETL CO 2 Prophet Model (CO 2 Prophet Model), which determined the CO 2 Prophet Model was able to reasonably represent the performance of the CO 2 flood modeled using the more sophisticated GEM. This case study uses the Petronius oil field J-2 Sand using a quarter of a five-spot pattern design (one CO 2 injector well and five production wells), for a 40-year injection scenario. A version of the CO 2 Prophet Model is available on NETL’s website under the Collection Name: FE/NETL CO 2 Prophet Model.

02 PETROLEUM↗

DOE OSTI2020

Cognac Offshore Oil Field Case Study

This document is one of three offshore post-primary CO 2 enhanced oil recovery project case studies that compares the modeling results from an industry standard compositional simulator (“GEM”) and a variant of the FE/NETL CO 2 Prophet Model (CO 2 Prophet Model), which determined the CO 2 Prophet Model was able to reasonably represent the performance of the CO 2 flood modeled using the more sophisticated GEM. This case study uses the Cognac oil field J Sand, in the field’s Northeast fault block, using a line drive pattern design (one CO 2 injector and two production wells), for 10-year and 20-year injection scenarios. A version of the CO 2 Prophet Model is available on NETL’s website under the Collection Name: FE/NETL CO 2 Prophet Model.

02 PETROLEUM↗

DOE OSTI2020

Horn Mountain Offshore Oil Field Case Study

This document is one of three offshore post-primary CO 2 enhanced oil recovery project case studies that compares the modeling results from an industry standard compositional simulator (“GEM”) and a variant of the FE/NETL CO 2 Prophet Model (CO 2 Prophet Model), which determined the CO 2 Prophet Model was able to reasonably represent the performance of the CO 2 flood modeled using the more sophisticated GEM. This case study uses the Horn Mountain oil field NFB M Sand, in the field's North fault block, using three pairs of wells. Each pair of wells is a line drive pattern design (one CO 2 injector and one production well). Four 20-year injection scenarios were assessed, varying CO 2 injector well placements. A version of the CO 2 Prophet Model is available on NETL’s website under the Collection Name: FE/NETL CO 2 Prophet Model.

02 PETROLEUM↗

DOE OSTI2025

Idiomatic Correctness-Checking via Julienne in Fortran 2023

This paper presents a unified approach to unit testing and runtime assertion checking using Fortran 2023. The paper describes the support for our approach in the Julienne framework. Julienne leverages recent Fortran standards to implement object-oriented design patterns, support testing parallel programs, and implement functional programming patterns in order to craft idioms inspired by natural-language expressions. The presented idioms employ novel operators to write expressions that evaluate to a test-diagnosis object encapsulating two components: (1) the test outcome or assertion outcome and (2) an automatically generated diagnostic string. Two other novel aspects of the approach include (1) the ability to enforce assertions inside pure procedures and (2) the ability to output rich diagnostic information inside pure procedures during error termination when assertions fail. The latter capability mitigates against a reason that Fortran programmers commonly cite for not writing pure procedures: difficulty obtaining useful program output inside pure procedures when debugging code. This paper demonstrates how the adoption of the proposed idioms leads naturally to a unifying theme across two otherwise disparate technologies: unit testing and runtime assertion checking. Finally, this paper describes the usage of the Julienne testing framework for writing unit tests and assertions in the Matcha high-performance computing application and the Fiats deep learning library.

Rouson, Damian↗

DOE OSTI2016

Flexible Computer Science Infrastructure (FleCSI)

Bergen, Ben↗

DOE OSTI2023

Enabling Interconnected Science Workflows through an Adapter Approach

The INTERSECT Software framework project aims to create an open federated library that connects, coordinates, and controls systems in the scientific domain. It features the Adapter, a flexible and extensible interface inspired by the Adapter design pattern in object-oriented programming. By utilizing Adapters, the INTERSECT SDK enables effective communication and coordination within a diverse ecosystem of systems. This adaptability facilitates the execution of complex operations within the framework, promoting collaboration and efficient workflow management in scientific research. Additionally, the generalizability of Adapters and their patterns enhances their utility in other scientific software projects and challenges.

McGaha, Jesse↗

DOE OSTI2019

Rosette-scan video-rate atomic force microscopy: Trajectory patterning and control design

We introduce an analysis and a systematic design methodology for a novel nonraster scan method based on a rosette pattern and demonstrate its application in video-rate atomic force microscopy. This pattern is traced when the lateral axes of a parallel kinematic scanner are commanded to follow a combination of two sinusoids with identical amplitudes and different frequencies. We create an internal-model-based controller to enhance the tracking performance of this pattern and implement the scheme on a microelectromechanical system scanner. The conclusions reveal high-precision tracking of the rosette pattern in order to acquire time-lapsed atomic force microscope images at the rate of 10 frames/s.

42 ENGINEERING↗

DOE OSTI2024

Patterned dielectric back contact design for GaAs thermophotovoltaic devices

-Patterned-dielectric back contact structures in optoelectronic devices are designed to boost the reflectance of light from the device back surface while retaining a low-resistance pathway for electrical conductance. Their reduced light absorption at near- and sub-bandgap photon energies leads to improved luminescence in light-emitting diodes, greater photon recycling, voltage, and efficiency in photovoltaic cells, and greater recuperation of unabsorbed sub-bandgap light in thermophotovoltaic (TPV) systems. However, diffraction from the patterned features can deflect incident light in propagation directions that lead to light trapping and parasitic absorption in the cell. Here, in this article, we use rigorous coupled-wave analysis (RCWA) to study three-dimensional diffractive scattering of electromagnetic waves by periodic metal point-contact gratings on 1.42-eV GaAs TPV cells, to analyze their effect on unwanted sub-bandgap absorption in order to achieve higher TPV system efficiency. Solutions of Maxwell's equations calculated using RCWA are compared to measured sub-bandgap reflectance in experimental GaAs TPV devices with varying metal point-contact diameters and spacing. Modeling and experiments indicate decreased total reflectance due to these diffractive effects for a small point contact diameter of 1 μm, and this effect is much stronger at higher contact coverage fractions.

14 SOLAR ENERGY↗

DOE OSTI2017

Established patterns of animal study design undermine translation of disease-modifying therapies for Parkinson’s disease

Translation of disease-modifying therapies in neurodegenerative disease has been disappointing. Parkinson’s disease (PD) was used to compare patterns of preclinical study design for symptomatic and potentially disease-modifying interventions. We examined the relationship of model, intervention type and timing, outcomes and outcome measures in 543 animal and human studies (1973–2015) across a contemporary cohort of animal and human interventional studies (n = 445), animal studies for approved interventions (n = 28), animal and human studies for those that failed to translate (n = 70). Detailed study design data were collected for 216 studies in non-human primate (NHP) and rodent toxin-induced models. Species-specific patterns of study design prevailed regardless of whether interventions were symptomatic or potentially disease-modifying. In humans and NHPs, interventions were typically given to both sexes well after the PD phenotype was established, and clinical outcome measures were collected at single (symptomatic) or multiple (disease-modifying) time-points. In rodents, interventions often preceded induction of the model, acute toxic protocols were common, usually given to young males, clinical outcome measures were used less commonly, and outcomes were less commonly assessed at multiple time points. These patterns were more prevalent in mice than rats. In contrast, study design factors such as randomization and blinding did not differ appreciably across symptomatic and disease-modifying intervention categories. The translational gap for potentially disease-modifying interventions in PD in part results from study designs, particularly in mice, that fail to model the progressive nature and relatively late intervention characteristic of PD, or that anchor mechanistic and neuropathologic data to longitudinal clinical outcomes. Even if measures to improve reproducibility are broadly adopted, perpetuation of these norms will continue to impede effective translation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Extracting Grain Orientations from EBSD Patterns of Polycrystalline Materials Using Convolutional Neural Networks

Abstract We present a deep learning approach to the indexing of electron backscatter diffraction (EBSD) patterns. We design and implement a deep convolutional neural network architecture to predict crystal orientation from the EBSD patterns. We design a differentiable approximation to the disorientation function between the predicted crystal orientation and the ground truth; the deep learning model optimizes for the mean disorientation error between the predicted crystal orientation and the ground truth using stochastic gradient descent. The deep learning model is trained using 374,852 EBSD patterns of polycrystalline nickel from simulation and evaluated using 1,000 experimental EBSD patterns of polycrystalline nickel. The deep learning model results in a mean disorientation error of 0.548° compared to 0.652° using dictionary based indexing.

Materials Science↗

DOE OSTI2016

Design and investigation of planar technology based ultra-wideband antenna with directional radiation patterns

A novel design technique based on planar technology for ultra-wideband (UWB) antennas with different ground shape having directional radiation pattern is being presented here. Firstly, the L-shape corner reflector ground plane antenna is designed with microstrip feed line in order to achieve large bandwidth and directivity. Thereafter, for the further improvement in the directivity as well as for better impedance matching the parabolic-shape ground plane has been introduced. The coaxial feed line is given for the proposed directional antenna in order to achieve better impedance matching with 50 ohm transmission line. The simulation analysis of the antenna is done on CST Microwave Studio software using FR-4 substrate having thickness of 1.6 mm and dielectric constant of 4.4. The simulated result shows a good return loss (S11) with respect to -10 dB. The radiation pattern characteristic, angular width, directivity and bandwidth performance of the antenna have also been compared at different resonant frequencies. The designed antennas exhibit low cost, low reflection coefficient and better directivity in the UWB frequency band.

42 ENGINEERING↗

DOE OSTI2017

An Integrated Design Approach for Infill Patterning of Fused Deposition Modeling and its Application to an Airfoil

We present a new approach to incorporate an internal stress distribution into the design of infill via fused deposition modeling of additive manufacturing (AM). This design approach differs from topology optimization, since the topology optimization of AM focuses on changing the overall shape of the product, whereas the approach we propose in this research focuses on the porous infill and remains the overall shape of the product intact. The approach presented here is effective if the overall shape is an important functioning aspect of a product and the stress is applied to the entire body, not to given localized points. As an application, we demonstrate an airfoil with its infill densities optimized based on the pressure applied during operation. Specifically, the stress of an airfoil is analyzed with operational loading conditions. The local density of the infill pattern is determined based on the computational stress analysis. The infill geometry is mathematically generated using a circle packing algorithm. Test results show that the airfoil with the optimized infill outperforms the same shape with the traditional uniform infill pattern of an airfoil having the same weight.

Kim, Pum↗

DOE OSTI2022

Lithium-Ion Batteries with Safer Current Collectors

The US Department of Energy’s Oak Ridge National Laboratory and Soteria Battery Innovation Group collaborated to develop a metallized polymer film as a current collector for lithium-ion batteries and design slit patterns for electrodes to improve battery safety. The metallized polymer film serves as a fuse that will break under high temperature resulting from a short circuit. Consequently, the short circuit will be broken and the heat generated from the short circuit will be alleviated to avoid thermal runaway. The electrodes with slit patterns are expected to be broken into small segments upon mechanical impact, which can isolate the damaged electrodes from the rest. Thus, the heat generation associated with the mechanical impact will be reduced, along with the likelihood of thermal runaway. This effort aimed to improve lithium-ion battery safety by replacing traditional metal foils with metallized polymer films as current collector and introducing slit patterns to battery electrodes. The metallized polymer films were polyethylene terephthalate with a thin metal (aluminum for cathodes and copper for anodes) coating on both sides. Slit patterns with various geometries and dimensions were designed via simulation. Temperature distribution on cells with electrodes with and without slit patterns was also simulated via nemerical modeling. Electrodes on traditional metal foils and metallized polymer films were coated via a pilot-scale slot-die coater at the US Department of Energy Battery Manufacturing Facility at Oak Ridge National Laboratory. The electrodes were calendered to 35% porosity and punched out with and without slit patterns. Pouch cells were assembed with the electrodes inside a dry room for electrochemical and safety testing. Electrodes coated on metallized polymer films exhibited comparable electrochemical performance to their counterparts coated on traditional metal foils. They also showed improved safety in nail penetration and indentation tests.

25 ENERGY STORAGE↗