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At least 1,495 records · Page 83

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DOE OSTI2013

DBSI: DNA-binding site identifier

In this study, we present the DNA-Binding Site Identifier (DBSI), a new structure-based method for predicting protein interaction sites for DNA binding. DBSI was trained and validated on a data set of 263 proteins (TRAIN-263), tested on an independent set of protein-DNA complexes (TEST-206) and data sets of 29 unbound (APO-29) and 30 bound (HOLO-30) protein structures distinct from the training data. We computed 480 candidate features for identifying protein residues that bind DNA, including new features that capture the electrostatic microenvironment within shells near the protein surface. Our iterative feature selection process identified features important in other models, as well as features unique to the DBSI model, such as a banded electrostatic feature with spatial separation comparable with the canonical width of the DNA minor groove. Validations and comparisons with established methods using a range of performance metrics clearly demonstrate the predictive advantage of DBSI, and its comparable performance on unbound (APO-29) and bound (HOLO-30) conformations demonstrates robustness to binding-induced protein conformational changes. Finally, we offer our feature data table to others for integration into their own models or for testing improved feature selection and model training strategies based on DBSI.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Extension and Validation of NEMA-Style Dual-Ring Controller in SUMO

Until recently, SUMO users could not model the behavior of a ring-and-barrier traffic signal via existing signal types, which left North American SUMO users without the direct ability to capture traffic dynamics of their local networks. This work presents the methods, implementation overview, and validation of a 'dual-ring' NEMA style traffic controller which has recently been added to the main SUMO code base. A brief explanation of the 'dual-ring' implementation is also provided as context for those new to this type of traffic controller. The foundation for this work was presented at the SUMO User Conference 2021 by researchers at the US Department of Energy's National Renewable Energy Laboratory, but was not integrated into SUMO code base at the time. Following the initial inclusion of the controller to SUMO, the authors began validation of the SUMO controller against an Econolite software-in-the-loop (SIL) traffic signal controller configured with actual setup parameters from controllers in a real-world three-intersection corridor in Tuscaloosa, Alabama, USA. This paper documents the process of adding new features to the controller code as well as validating their implementation through simulation-based and automated grey-box testing is presented in this paper. Key features such as fully-actuated operation, various timing offset plans, proper next-phase fit algorithms and more, have been added and validated against this SIL system. Though not an exhaustive demonstration of features, this work is intended make more users aware of this extension of SUMO capabilities.

MATHEMATICS AND COMPUTING↗

DOE OSTI2019

Instrumentation Plan for the OSU High Temperature Test Facility, Revision 4

This instrumentation plan describes the instrumentation requirements and design for the Oregon State University (OSU) High Temperature Test Facility (HTTF). This report outlines HTTF instrumentation design specifications, data acquisition and control system (DACS) design specifications as well as a brief description of the instrumentation to be used in the HTTF. The HTTF is an integral test facility, which has been designed to model the behavior of interest for a Very High Temperature Gas Reactor (VHTR) during the Depressurized Conduction Cooldown (DCC) event. It also has the potential to conduct limited explorations into the progression of the Pressurized Conduction Cooldown (PCC) event and phenomena during normal operations. The facility is scaled 1:4 by height and 1:64 by volume. The maximum core power for the facility is approximately 2.2MW. The core region is of a modular design to allow for both the prismatic block core and the pebble bed core designs to be tested. However, only the prismatic block design is discussed in this report. A correctly scaled integral facility modeling the VHTR that can be used to examine the thermal hydraulic system behavior of the design basis and beyond design basis transients is of significant value. The experimental results obtained in such a program could be used to validate analytical tools and methods being proposed for use with the VHTR. Therefore, it is of importance that the HTTF be instrumented in such a way that the required data is collected to meet its overall goals of phenomena examination and code validation. In addition to the instrumentation used to collect data to achieve the overall goals of the HTTF test program, there is instrumentation in the HTTF, which is primarily used to ensure the safe operation of the test facility. This type of instrumentation shall be termed “Control Instrumentation” and is discussed in this report. This report discusses the DACS, which is a personal computer controlled system that is used to control both the collection and storage of the test matrix and control system data as well as electrical and mechanical operation of the test facility.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2018

A hybrid of fractal image coding and fractal dimension for an efficient retrieval method

Fractal image coding (FIC) based on the inverse problem of an iterated function system plays an essential role in several areas of computer graphics and in many other interesting applications. Through FIC, an image can be transformed to compressed representative parameters and be expressed in a simple geometric way. Dealing with digital images requires storing a large number of images in databases, where searching such databases is time consuming. Therefore, finding a new technique that facilitates this task is a challenge that has received increasing attention from many researchers. In this study, a new method that combines fractal dimension (FD) which is an indicator of image complexity with the FIC scheme is proposed. Classifying images in databases according to their texture by using FD helps reduce the retrieval time of query images. The validity of the proposed method is evaluated using geosciences images. Result shows that the method is computationally attractive.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2014

Large-eddy simulation of turbulent cavitating flow in a micro channel

Large-eddy simulations (LES) of cavitating flow of a Diesel-fuel-like fluid in a generic throttle geometry are presented. Two-phase regions are modeled by a parameter-free thermodynamic equilibrium mixture model, and compressibility of the liquid and the liquid-vapor mixture is taken into account. The Adaptive Local Deconvolution Method (ALDM), adapted for cavitating flows, is employed for discretizing the convective terms of the Navier-Stokes equations for the homogeneous mixture. ALDM is a finite-volume-based implicit LES approach that merges physically motivated turbulence modeling and numerical discretization. Validation of the numerical method is performed for a cavitating turbulent mixing layer. Comparisons with experimental data of the throttle flow at two different operating conditions are presented. The LES with the employed cavitation modeling predicts relevant flow and cavitation features accurately within the uncertainty range of the experiment. The turbulence structure of the flow is further analyzed with an emphasis on the interaction between cavitation and coherent motion, and on the statistically averaged-flow evolution.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2025

Reassessing the Origins and Contemporary Relevance of ck Acceptability Parameters: Evolving Perspectives on Similarity

“Sensitivity and Uncertainty Analyses Applied to Criticality Safety Validation,” introduces sensitivity and uncertainty methods to address challenges in defining and extending areas of applicability for criticality safety validation. These areas are traditionally defined by the bounds or limits on key parameters, but establishing valid ranges and managing complex parameter variations remain challenging. NUREG/CR-6655 introduces ck and other integral indices, as well as concepts such as the completeness of benchmark coverage, to better quantify system similarities. The work proposed herein seeks to evaluate these foundational concepts to ensure that the bounds remain effective in guiding the assessment of similarity and applicability in modern applications. The concept of completeness, along with other parameters envisioned within the framework, serves as an example of the foundational ideas that have been established, though their effectiveness in practice may not be fully understood. Advancements in scripting tools, coupled with the speed and efficiency of modern computing and statistical models, now allow for faster and more thorough assessments than previously possible. These advancements also enable the identification of trends within the data, which could provide additional insight into system behavior and further broaden the scope of previously performed benchmarks. By leveraging these capabilities, we will revisit and expand the scope of these foundational methods to determine whether the necessary elements for robust similarity evaluation are already embedded, partially realized, or remain untapped.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

A stable potential-based time-domain method for wideband elec- tromagnetic analysis

In previous research, the frequency-domain A-ϕ formulation has been validated using the finite element method for electromagnetic simulations of low-frequency and multi- scale problems, demonstrating excellent numerical accuracy, good matrix condition, and high computational efficiency. Time- domain simulations provide significant advantages for modeling wideband problems and are crucial for multiphysics applications. In this paper, the frequency-domain A-ϕ formulation is extended to the time domain. The central difference scheme is employed for temporal discretization to ensure both accuracy and stability. A numerical example is presented to demonstrate the capability of the proposed time-domain method in wideband electromagnetic analysis.

Mekonnen, Minyichil↗

DOE OSTI2015

An Implicit Correlation Method for Cross-Correlation Sampling, with MCNPX-PoliMi Validation

Monte Carlo particle transport codes used to model detector response are traditionally run in analog mode. However, analog simulations of cross-correlation measurements are extremely time-consuming because the probability of coincident detection is small, approximately equal to the product of the probabilities of a single detection in each detector. The new “implicit correlation” method described here increases the number of correlated event scores, thereby reducing variance and required computation times. The cost of the implicit correlation method is comparable to the cost of simulating single-event detection for the lowest absolute detector efficiency in the problem. The new method is especially useful in the nuclear nonproliferation and safeguards fields for simulating correlation measurements of shielded special nuclear material. The new method was implemented in MCNPX-PoliMi for neutron-neutron cross-correlations with a Cf-252 spontaneous fission source measured by 14 detectors at various angles. The method demonstrated good agreement with analog simulation and reference measurement results. Small differences between nonanalog and analog cross-correlation distributions are attributed to discretization errors that are often not present in practical applications. Improvement in the figure of merit was greater than a factor of 100 in all tested cases.

Marcath, Matthew J.↗

DOE OSTI2020

A Simple Space Vector Modulation of High-Frequency AC Linked Three-Phase-to-Single-Phase/DC Converter

High frequency (HF) ac linked converter functions well to interface between buses with different voltage types. Using a three-phase-to-single-phase matrix converter, a single-phase cyclo converter, and a HF transformer, we can compose a HF ac linked converter to interface between three-phase ac grids and single-phase ac or dc distributed generations (DGs). In this paper, a novel space vector modulation (SVM) method is proposed for such kind of converter. The proposed SVM method converts the mains three-phase ac voltage to a HF ac voltage at the primary side of transformer, and then unfolds the HF ac voltage to a single-phase ac or dc voltage at the secondary side of transformer. Without need to compute separate switching signals for the primary and secondary converters and then coordinate their operations elaborately, the proposed SVM method can be easily implemented by incorporating the HF chopping into the SVM of traditional indirect matrix converter. Therefore, no complicated duty cycle computation or elaborate switching states combination is required. Simulation and hardware-in-loop implementation demonstrate the validity of the proposed method.

42 ENGINEERING↗

DOE OSTI2016

Novel Nano-Size Oxide Dispersion Strengthened Steels Development through Computational and Experimental Study

This report summarizes our recent works of theoretical modeling, simulation and experimental validation of the simulation results on the ferritic oxide dispersion strengthened (ODS) alloy research. The simulation of the stability and thermal dynamics simulation on potential thermal stable candidates were performed and related ODS samples were synthesized and characterized. The simulation methods and experimental texture validation techniques development, achievements already reached, course work development, students and postdoc training, and future improvement are briefly introduced.

01 COAL, LIGNITE, AND PEAT↗

DOE OSTI2016

TH-CD-BRA-02: 3D Remote Dosimetry for MRI-Guided Radiation Therapy: A Hybrid Approach

Purpose: To validate the dosimetric accuracy of a commercially available MR-IGRT system using a combination of 3D dosimetry measurements (with PRESAGE(R) radiochromic plastic and optical-CT readout) and an in-house developed GPU-accelerated PENELOPE Monte-Carlo dose calculation system. Methods: {sup 60}Co IMRT subject to a 0.35T lateral magnetic field has recently been commissioned in our institution following AAPM’s TG-119 recommendations. We performed PRESAGE(R) sensitivity studies in 4ml cuvettes to verify linearity, MR-compatibility, and energy-independence. Using 10cm diameter PRESAGE(R), we delivered an open calibration field to examine the percent depth dose and a symmetrical 3-field plan with three adjacent regions of varying dose to determine uniformity within the dosimeter under a magnetic field. After initial testing, TG-119 plans were created in the TPS and then delivered to 14.5cm 2kg PRESAGE(R) dosimeters. Dose readout was performed via optical-CT at a second institution specializing in remote 3D dosimetry. Absolute dose was measured using an IBA CC01 ion chamber and the institution standard patient-specific QA methods were used to validate plan delivery. Calculated TG-119 plans were then compared with an independent Monte Carlo dose calculation (gPENELOPE). Results: PRESAGE(R) responds linearly (R{sup 2}=0.9996) to {sup 60}Co irradiation, in the presence of a 0.35T magnetic field, with a sensitivity of 0.0305(±0.003)cm{sup −1}Gy{sup −1}, within 1% of a 6MV non-MR linac irradiation (R{sup 2}=0.9991) with a sensitivity of 0.0302(±0.003)cm{sup −1}Gy{sup −1}. Analysis of TG-119 clinical plans using 3D-gamma (3%/3mm, 10% threshold) give passing rates of: HN 99.1%, prostate 98.0%, C-shape 90.8%, and multi-target 98.5%. The TPS agreed with gPENELOPE with a mean gamma passing rate of 98.4±1.5% (2%/2mm) with the z-score distributions following a standard normal distribution. Conclusion: We demonstrate for the first time that 3D remote dosimetry using both experimental and computational methods is a feasible and reliable approach to commissioning MR-IMRT, which is particularly useful for less specialized clinics in adopting this new treatment modality.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2018

Multi-Timescale Three-Phase Unbalanced Distribution System Operation With Variable Renewable Generations

This paper proposes a multi-timescale operational approach for a three-phase unbalanced distribution system, which contains hourly scheduling at substation level and minutes power flow operation at feeder level. In the substation scheduling model, the objective is to minimize the system cost with variable renewable generations. The given error distribution model of renewable generation is formulated as a chance constraint, and derived into a deterministic form by Gaussian mixture model (GMM) with genetic algorithm-based expectation-maximization (GAEM). In the feeder scheduling model, the system cost is further reduced with the optimal power flow (OPF) at a timescale of minutes. Considering the nonconvexity of the three-phase unbalanced OPF problem in distribution systems, the semidefinite programming (SDP) is used to relax the problem into a convex problem, and a distributed computation approach is built based on alternating direction method of multiplier (ADMM). The IEEE 123-bus distribution system, DU (University of Denver) campus distribution system, and the IEEE 8500-bus distribution system are used as the test bench for the proposed approach. And the numerical results demonstrate the effectiveness and validity of the proposed method.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2018

Development of a characterization methodology for post-irradiation examination of miniature fuel specimens

The miniature fuel (MiniFuel) irradiation experimental design at Oak Ridge National Laboratory (ORNL) enables benchmark testing and separate effects testing of novel fuel types in the High Flux Isotope Reactor (HFIR) in support of the Advanced Fuels Campaign (AFC). The first round of MiniFuel sub-capsules will be available for post-irradiation examination at the end of 2018. This report establishes the procedure for disassembly, fuel retrieval, post-irradiation analysis of the fission product behavior (fission gas release and fuel swelling), and microstructural characterization of the irradiated MiniFuel specimens. All methods were tested and validated out-of-cell and are ready to be implemented in-cell for use on the first set of irradiated MiniFuel specimens. The path forward regarding further characterization techniques is presented, which will involve analyzing other specimen geometries using the methods presented in this report and expanding the post-irradiation analysis of MiniFuel specimens to include additional properties.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2016

Cone-Beam Computed Tomography Internal Motion Tracking Should Be Used to Validate 4-Dimensional Computed Tomography for Abdominal Radiation Therapy Patients

Purpose: To demonstrate that fiducial tracking during pretreatment Cone-Beam CT (CBCT) can accurately measure tumor motion and that this method should be used to validate 4-dimensional CT (4DCT) margins before each treatment fraction. Methods and Materials: For 31 patients with abdominal tumors and implanted fiducial markers, tumor motion was measured daily with CBCT and fluoroscopy for 202 treatment fractions. Fiducial tracking and maximum-likelihood algorithms extracted 3-dimensional fiducial trajectories from CBCT projections. The daily internal margin (IM) (ie, range of fiducial motion) was calculated for CBCT and fluoroscopy as the 5th-95th percentiles of displacement in each cardinal direction. The planning IM from simulation 4DCT (IM{sub 4DCT}) was considered adequate when within ±1.2 mm (anterior–posterior, left–right) and ±3 mm (superior–inferior) of the daily measured IM. We validated CBCT fiducial tracking as an accurate predictive measure of intrafraction motion by comparing the daily measured IM{sub CBCT} with the daily IM measured by pretreatment fluoroscopy (IM{sub pre-fluoro}); these were compared with pre- and posttreatment fluoroscopy (IM{sub fluoro}) to identify those patients who could benefit from imaging during treatment. Results: Four-dimensional CT could not accurately predict intrafractional tumor motion for ≥80% of fractions in 94% (IM{sub CBCT}), 97% (IM{sub pre-fluoro}), and 100% (IM{sub fluoro}) of patients. The IM{sub CBCT} was significantly closer to IM{sub pre-fluoro} than IM{sub 4DCT} (P<.01). For patients with median treatment time t < 7.5 minutes, IM{sub CBCT} was in agreement with IM{sub fluoro} for 93% of fractions (superior–inferior), compared with 63% for the t > 7.5 minutes group, demonstrating the need for patient-specific intratreatment imaging. Conclusions: Tumor motion determined from 4DCT simulation does not accurately predict the daily motion observed on CBCT or fluoroscopy. Cone-beam CT could replace fluoroscopy for pretreatment verification of simulation IM{sub 4DCT}, reducing patient setup time and imaging dose. Patients with treatment time t > 7.5 minutes could benefit from the addition of intratreatment imaging.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2015

Two-body potential model based on cosine series expansion for ionic materials

There is a method to construct a two-body potential model for ionic materials with a Fourier series basis and we examine it. For this method, the coefficients of cosine basis functions are uniquely determined by solving simultaneous linear equations to minimize the sum of weighted mean square errors in energy, force and stress, where first-principles calculation results are used as the reference data. As a validation test of the method, potential models for magnesium oxide are constructed. The mean square errors appropriately converge with respect to the truncation of the cosine series. This result mathematically indicates that the constructed potential model is sufficiently close to the one that is achieved with the non-truncated Fourier series and demonstrates that this potential virtually provides minimum error from the reference data within the two-body representation. The constructed potential models work appropriately in both molecular statics and dynamics simulations, especially if a two-step correction to revise errors expected in the reference data is performed, and the models clearly outperform two existing Buckingham potential models that were tested. Moreover, the good agreement over a broad range of energies and forces with first-principles calculations should enable the prediction of materials behavior away from equilibrium conditions, such as a system under irradiation.

36 MATERIALS SCIENCE↗

DOE OSTI2011

Semi-analytic stellar structure in scalar-tensor gravity

Precision tests of gravity can be used to constrain the properties of hypothetical very light scalar fields, but these tests depend crucially on how macroscopic astrophysical objects couple to the new scalar field. We study the equations of stellar structure using scalar-tensor gravity, with the goal of seeing how stellar properties depend on assumptions made about the scalar coupling at a microscopic level. In order to make the study relatively easy for different assumptions about microscopic couplings, we develop quasi-analytic approximate methods for solving the stellar-structure equations rather than simply integrating them numerically. (The approximation involved assumes the dimensionless scalar coupling at the stellar center is weak, and we compare our results with numerical integration in order to establish its domain of validity.) We illustrate these methods by applying them to Brans-Dicke scalars, and their generalization in which the scalar-matter coupling slowly runs — or 'walks' — as a function of the scalar field: a(φ) ≅ a{sub s}+b{sub s}φ. (Such couplings can arise in extra-dimensional applications, for instance.) The four observable parameters that characterize the fields external to a spherically symmetric star are the stellar radius, R, mass, M, scalar 'charge', Q, and the scalar's asymptotic value, φ{sub ∞}. These are subject to two relations because of the matching to the interior solution, generalizing the usual mass-radius, M(R), relation of General Relativity. Since φ{sub ∞} is common to different stars in a given region (such as a binary pulsar), all quantities can be computed locally in terms of the stellar masses. We identify how these relations depend on the microscopic scalar couplings, agreeing with earlier workers when comparisons are possible. Explicit analytical solutions are obtained for the instructive toy model of constant-density stars, whose properties we compare to more realistic equations of state for neutron star models.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Deep-learning-guided high-resolution subsurface reflectivity imaging with application to ground-penetrating radar data

Subsurface reflectivity imaging is one of the most important geophysical characterization methods for revealing subsurface structures. In many cases, accurate subsurface reflectivity imaging is challenging because of, for example, random or coherent noise in the data and sparse source-receiver observation geometry. Here, we develop a deep-learning-guided iterative imaging method to improve subsurface structure imaging. Specifically, we train a supervised neural network to infer a noise-free, high-resolution image from a noisy, low-resolution image and use this estimated image as guidance to regularize least-squares imaging. We develop a systematic method to generate high-quality synthetic training data (data-label pairs) to train the guidance neural network. The trained neural network can provide high-fidelity predictions even for field-data images that are not in the training data. We validate our new imaging method using one synthetic and two field ground-penetrating radar data examples, and find that our method can produce clean, high-resolution subsurface reflectivity images where existing single-pass and least-squares imaging methods fail due to noise and insufficient data coverage.

58 GEOSCIENCES↗

DOE OSTI2025

Learning-Based Quantum Compilation: Translating QASM to QIR with CodeBERT

We propose a learning-based approach to quantum compilation by translating OpenQASM to Quantum Intermediate Representation (QIR) using a fine-tuned CodeBERT model. Trained on 10,000 synthetic QASM-QIR pairs, the model captures code semantics while addressing QIR verbosity and the 512-token limit via a custom token compression scheme. Finetuning was performed on the Frontier supercomputer, with results showing syntactic correctness and stable validation loss reduction. Our method moves toward enabling flexible, language-modeldriven quantum software tools. It also introduces syntax error handling and the possibility of incorporating classical control constructs, addressing limitations in existing rule-based compilers like qBraid-QIR. While the current model has been validated on quantum-only circuits, we propose future evaluations on hybrid quantum-classical examples. This poster will provide architecture insights, compression examples, training loss plots, and QIR outputs. Our work highlights the potential for scalable, adaptable compilation in future quantum toolchains.

Afrose, Sharmin [ORNL]↗