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At least 1,243 records · Page 69

A Tale from the Trenches: Applying Metamorphic and Differential Testing to Bioinformatics Software

Metamorphic and differential testing have been proposed as best practices for testing software that is difficult to test, such as for programs in scientific domains. An assumption is that these approaches can be easily customized and applied to almost any domain. However, scientific software is often data-driven, and metamorphic relations may require significant domain knowledge to develop. In addition, tools are often written for ad-hoc experimentation by the scientists and often embed many assumptions about the importance and representation of different natural phenomena. In this paper, we present our experience applying both metamorphic and differential testing to a set of four computational biology tools that predict the growth of an organism. While our original goal was to evaluate these techniques to improve our system-level testing, we encountered multiple roadblocks along the way. Although we did find faults (some confirmed by developers), we also uncovered a set of challenges, including the considerable manual effort required for (a) defining domain-specific tests, (b) validating correctness, and (c) distinguishing between issues stemming from poor data and those arising from incorrect software.

Marsh, Alexis L [Iowa State University/Ames Labora↗

Evaluating Recombination Mechanisms in RbF Treated Cu(In${}_\mathrm{x}$Ga$_\mathrm{1-x}$)Se$_{2}$ Solar Cells

Rubidium fluoride (RbF) postdeposition treatment (PDT) has been shown to improve the performance of Cu(In x Ga 1-x )Se 2 (CIGS) photovoltaic devices. Here, in this study, temperature-dependent current voltage (JVT) and time-resolved photoluminescence (TRPL) experiments were combined with modeling using the solar cell capacitance simulator (SCAPS) computer code to investigate the effect of the RbF PDT. Two devices, one as-deposited and one with RbF PDT, were deposited by a three stage coevaporation process. JVT measurements suggest the dominant recombination mechanism may be tunneling-enhanced recombination via bandtail states, but that defect states in the bandgap can also be important. RbF PDT is shown to decrease the characteristic energy of the bandtails. TRPL data show an increase in the minority carrier lifetime after RbF PDT, leading to an improved open-circuit voltage. SCAPS modeling indicates that the dominant recombination mechanism is dependent on the specific defect makeup of a device, suggesting that small changes in processing conditions can impact device behavior. This explains the observation that, for some devices, defect states in the gap dominate while others, as is the case here, appear to be dominated by bandtails.

14 SOLAR ENERGY↗

Numerical study of advanced compression ignition and combustion in a gasoline direct injection engine

Multi-mode combustion strategies may provide a considerable thermal efficiency improvement targeted at part-load operating conditions for light-duty spark-ignition (SI) engines. The extension from boosted SI mode at high loads to advanced compression ignition (ACI) mode at low loads can be achieved by increasing compression ratio and utilizing intake air heating. In order to enable an accurate control of intake charge condition for ACI control and rapid mode-switches, it is essential to gain fundamental insight into the autoignition process with regard to thermal and fuel-air mixture stratification in the combustion chamber. In this work, a computational fluid dynamics (CFD) study is carried out to reveal some degrees of correlation between the mixture and thermal stratifications induced by the cylinder wall temperature and combustion-phasing across varying engine load conditions. The computational analysis begins with a calibrated simulation setup best matching the engine experiments, and subsequently evaluates the baseline setup for an extended range of engine load conditions for two excess-air ratio cases. The present study emphasizes the dominance of thermal stratifications for autoignition process due to wall temperature effects depending on the engine load conditions of interest. In addition, this study also aims to provide insight into the impact of mixture stratification on cyclic variability, especially at colder wall engine conditions (e.g., cold start). Observations herein provide highlight of the propensity of autoignition in correlation with mixture reactivity space.

Advanced Compression Ignition (ACI) engine↗

Affine Approximation of Parametrized Kernels and Model Order Reduction for Nonlocal and Fractional Laplace Models

In this work, we consider parametrized problems driven by spatially nonlocal integral operators with parameter-dependent kernels. In particular, kernels with varying nonlocal interaction radius $\delta > 0$ and fractional Laplace kernels, parametrized by the fractional power $s\in(0,1)$, are studied. Furthermore, in order to provide an efficient and reliable approximation of the solution for different values of the parameters, we develop the reduced basis method as a parametric model order reduction approach. Major difficulties arise since the kernels are not affine in the parameters, singular, and discontinuous. Moreover, the spatial regularity of the solutions depends on the varying fractional power $s$. To address this, we derive regularity and differentiability results with respect to $\delta$ and $s$, which are of independent interest for other applications such as optimization and parameter identification. We then use these results to construct affine approximations of the kernels by local polynomials. Finally, we certify the method by providing reliable a posteriori error estimators, which account for all approximation errors, and support the theoretical findings by numerical experiments.

97 MATHEMATICS AND COMPUTING↗

Error Estimates for the Optimal Control of a Parabolic Fractional PDE

In this work, we consider the integral definition of the fractional Laplacian and analyze a linear-quadratic optimal control problem for the so-called fractional heat equation; control constraints are also considered. We derive existence and uniqueness results, first order optimality conditions, and regularity estimates for the optimal variables. To discretize the state equation we propose a fully discrete scheme that relies on an implicit finite difference discretization in time combined with a piecewise linear finite element discretization in space. We derive stability results and a novel $L^2(0,T;L^2(\Omega))$ a priori error estimate. On the basis of the aforementioned solution technique, we propose a fully discrete scheme for our optimal control problem that discretizes the control variable with piecewise constant functions, and we derive a priori error estimates for it. We illustrate the theory with one- and two-dimensional numerical experiments.

97 MATHEMATICS AND COMPUTING↗

Learning Functions Varying along a Central Subspace

Many functions of interest are in a high-dimensional space but exhibit low-dimensional structures. This paper studies regression of an s-Hölder function in $R^D$ which varies along a central subspace of dimension $d$ while $d \ll D$. A direct approximation of $f$ in $R^D$ with an accuracy $\varepsilon$ requires the number of samples in the order of $\varepsilon^{-(2s+D)/s}$. In this paper, we analyze the generalized contour regression (GCR) algorithm for the estimation of the central subspace and use piecewise polynomials for function approximation. GCR is among the best estimators for the central subspace, but its sample complexity is an open question. In this paper, we partially answer this questions by proving that if a variance quantity is exactly known, GCR leads to a mean squared estimation error of $O(n^{-1})$ for the central subspace. The estimation error of this variance quantity is also given in this paper. The mean squared regression error of $f$ is proved to be in the order of $(n/\log n)^{-\frac{2s}{2s+d}}$, where the exponent depends on the dimension of the central subspace instead of the ambient space . This result demonstrates that GCR is effective in learning the low-dimensional central subspace. We also propose a modified GCR with improved efficiency. Here, the convergence rate is validated through several numerical experiments.

97 MATHEMATICS AND COMPUTING↗

XRIPL

XRIPL is a library of tools for processing x-ray radiographs and extracting contours of interest within the image using computer vision techniques. Features include spatial calibration, denoising, background and attenuation correction through pseudo-flatfielding, watershed segmentation, contour processing, and visualization. The details of the XRIPL analysis pipeline are published in the Proceedings of the 23rd Topical Conference on High-Temperature Plasma Diagnostics Proceedings (LA-UR-20-30133) [1]. [1] P. M. Kozlowski, Y. Kim, B. M. Haines, H. F. Robey, T. J. Murphy, H. M. Johns, and T. S. Perry. Use of Computer Vision for analysis of image data sets from high temperature plasma experiments. Review of Scientific Instruments 92, 033532 (2021) https://doi.org/10.1063/5.0040285

Kozlowski, Pawel↗

ExaAM: Metal additive manufacturing simulation at the fidelity of the microstructure

Additive manufacturing (AM), or 3D printing, of metals is transforming the fabrication of components, in part by dramatically expanding the design space, allowing optimization of shape and topology. However, although the physical processes involved in AM are similar to those of welding, a field with decades of experimental, modeling, simulation, and characterization experience, qualification of AM parts remains a challenge. The availability of exascale computational systems, particularly when combined with data-driven approaches such as machine learning, enables topology and shape optimization as well as accelerated qualification by providing process-aware, locally accurate microstructure and mechanical property models. We describe the physics components comprising the Exascale Additive Manufacturing simulation environment and report progress using highly resolved melt pool simulations to inform part-scale finite element thermomechanics simulations, drive microstructure evolution, and determine constitutive mechanical property relationships based on those microstructures using polycrystal plasticity. We report on implementation of these components for exascale computing architectures, as well as the multi-stage simulation workflow that provides a unique high-fidelity model of process–structure–property relationships for AM parts. In addition, we discuss verification and validation through collaboration with efforts such as AM-Bench, a set of benchmark test problems under development by a team led by the National Institute of Standards and Technology.

3D printing↗

Numerical Experiments and Identification of Areas for Further Consideration (B639388 Subcontract Quarter II Report)

The second quarter of the project was spent carrying out numerical experiments on a variety of test matrices, using a combination of precisions, with the intent to study the numerical properties (namely, accuracy and convergence behavior) of the Conjugate Gradient (CG) method. We summarize our findings in the remainder of the document. Other activities include attending biweekly xSDK meetings. We are also currently collaborating with Steven Thomas (NREL) on the numerical stability analysis of “low-synch” Gram-Schmidt routines, for potential application within high-performance GMRES variants. This work is in progress. The subsequent quarter will be spent delving into the numerical analysis in order to provide theoretical explanation for the behavior observed in our experiments.

97 MATHEMATICS AND COMPUTING↗

Cathode to Target Simulations for Scorpius: I. Simulation Codes and Models

The new Scorpius linear induction electron accelerator is under development for multi-pulse flash radiography of large, explosively-driven hydrodynamic experiments. Beam physics from the cathode to the target was examined with computer simulations, including envelope, ray-trace, and particle-in cell (PIC) codes. Beam instabilities investigated included beam breakup (BBU), image displacement, diocotron, parametric envelope, ion hose, and the resistive wall instability. Beam corkscrew motion and emittance growth from beam mismatch were also studied. The results of these simulations is documented in a series of reports. In this report the computer codes and physical models used for these simulations are described. The conclusion of this study is that Scorpius will produce and accelerate a beam with radiographic quality equivalent to the present accelerators at Los Alamos National Laboratory if the same engineering standards and construction details are upheld.

43 PARTICLE ACCELERATORS↗

NMDQi Thermal-hydraulic Optimization, Analysis, and Scoping Tool (TOAST)

The Thermal-hydraulic Optimization, Analysis, and Scoping Tool (TOAST) is developed to support the thermal-hydraulic aspects for the design of optimal irradiation vehicles for the Nuclear Materials Discovery and Qualification initiative (NMDQi). TOAST is currently a MATLAB-based tool that utilizes a simplified steady-state analytical model where a radial thermal resistance circuit is utilized to account for conduction through up to 2 capsules, a gas gap, a thermal bond, a sample cladding, and a sample, as well as the convection from a water coolant outside the capsules. The geometry is discretized axially along the user-defined height of a basket with a user-defined number of points/nodes, essentially turning TOAST into a semi-2D heat transfer analysis utility for cylindrical irradiation vehicles with practically any configuration, solving for temperatures radially at multiple axial locations. TOAST utilizes a Graphical User Interface (GUI) in-which a user can define the geometrical layout, the materials utilized for each component, the coolant characteristics, and the required solution. The user can define the geometry by inputting the diameters, thicknesses, and heights for each component, whereas the materials are defined via the user-provided constant or variable thermal conductivities. The user can select the coolant's inlet temperature, pressure, and the pressure drop across the height of the problem (which is used to calculate the velocity of the flow). Finally, the user can choose to solve for a sample heat generation rate limit by inputting temperature limits for the sample and capsules or can choose to purely solve for the axial temperature distributions of each component by inputting a pre-selected heat generation rate. Either way, TOAST provides the user with axial temperature distributions of all the components including the coolant, and the heat generation rate limit as well as the maximum outlet coolant temperature. The user can also choose to do one of 6 sensitivity analyses in TOAST. The sensitivity analyses yield plots of the sensitivity of the heat generation rate limit, the maximum coolant temperature, and the pressure limit for the annular components due to perturbations in 1-2 unknown variables based on the selected sensitivity analysis. Benchmarks between computations in TOAST and equivalent 2D axis symmetric ABAQUS models are presented, showing that TOAST results are within less than 3% of ABAQUS results in most cases, and a maximum of 8% difference in some cases. The benchmarks also revealed that this uncertainty is tied to the selection of an appropriate Nusselt number correlation and appropriate thermal conductivities, which the user can do from the GUI. Regardless, TOAST is demonstrated as a computationally efficient, highly accessible, and accurate utility for optimization and scoping s of studies different irradiation vehicles.

42 ENGINEERING↗

Detector and Beamline Simulation for Next-Generation High Energy Physics Experiments

The success of high energy physics programs relies heavily on accurate detector simulations and beam interaction modeling. The increasingly complex detector geometries and beam dynamics require sophisticated techniques in order to meet the demands of current and future experiments. Common software tools used today are unable to fully utilize modern computational resources, while data-recording rates are often orders of magnitude larger than what can be produced via simulation. In this paper, we describe the state, current and future needs of high energy physics detector and beamline simulations and related challenges, and we propose a number of possible ways to address them.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Study of The Compression of an Imploding Plasma and the Magnetic- Field Flux Using Advanced, Non-Intrusive, Spectroscopic Techniques

The main motivation of the project was to measure the magnetic field in pulsed power driven plasma compression using advanced non-intrusive spectroscopic techniques. The strength of the project is that it encompasses a combination of laboratory experiments with diagnostics for both the magnetic field and plasma properties and computational modeling. The following issues were addressed: (1) Plasma and magnetic field dynamics, (2) Field compression and diffusion, (3) Energy balance in the system, (4) Onset of instabilities, and (5) Correlation of the plasma and field evolutions with the initial conditions. The unique feature of the research was the use of advanced spectroscopy to measure both the magnetic field and various plasma properties in multiple locations using both side-on and end-on views, simultaneously. The experimental system allowed for imploding different gas mixtures (which facilitated local measurements) and for flexibility in modifying the initial conditions. Two current generators were used with significantly different current rise times (200 ns and 1.6 µs) but at the same current level of 400 kA. The slower pulsed power generator (at rise time 1.6 µs) was based at the Weizmann Institute of Science (WIS) and imploded plasma into which an axial magnetic field (up to 1 T) was initially embedded. The faster current rise time generator (at rise time 200 ns) based at University of California San Diego (UCSD) was used for plasma parameter studies initially, with collaborative efforts we successfully implemented the advanced spectroscopy techniques at UC San Diego. One graduate student (Nick Aybar) and a postdoctoral scholar (Maylis Dozeries) were trained. They both are based at the Lawrence Livermore National Laboratory now.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

R-Matrix Analysis of the Neutron-Induced Cross Sections on 143 Nd Measured at LANSC [Slides]

An established use of R-Matrix codes is being implemented at LANSCE. There are unique features accessible with detectors at LANSCE that can be used to perform more complete R-Matrix analysis. Further, Spin separation is a powerful technique that can be applied in DANCE measurements. Additionally, a unique method to measure transmission with DICER is being undertaken. Transmission and capture data were analyzed in this work. The study can be extended to other channels. The results of the 143 Nd data are presented in this work. New resonances found in this work: 21 compared to ENDF/B-VIII.0 and JEFF-3.3, and 24 compared to JENDL-5. Wrong spin assignment in 23 resonances in ENDF/B-VIII.0, 25 in JEFF-3.3 and 26 in JENDL-5. The 143 Nd and 147,149 Sm have been analyzed. Exciting future for new measurements and analysis!

97 MATHEMATICS AND COMPUTING↗

Large Language Model Integration for Knowledge Retrieval and Interaction for the DUNE Experiment

The Deep Underground Neutrino Experiment (DUNE) is a next-generation neutrino experiment that will generate an unprecedented volume of heterogeneous information-from documentation and technical notes to experimental data and reconstruction pipelines. Efficient knowledge retrieval and contextual understanding are increasingly critical for collaboration-wide productivity and onboarding. In this work, we present DUNE-GPT, a prototype framework that leverages large language models (LLMs) and retrieval-augmented generation (RAG) to enable natural-language querying of DUNE's internal documentation and technical resources. The system provides an intelligent interface for DUNE collaborators to interact with experiment-specific knowledge while maintaining data privacy and infrastructure compliance within Fermilab computing resources.

Rafique, A. [Argonne (main)]↗

Multiparticle cumulant mapping for Coulomb explosion imaging: Calculations and algorithm

We present a versatile cumulant mapping algorithm for analyzing correlated particle emission, offering insights into complex electronic and nuclear dynamics. Recently, we have demonstrated the use of cumulant mapping to extract information-rich correlations between the momenta of multiple fragments produced in Coulomb explosion imaging experiments [C. Cheng et al., Phys. Rev. Lett. 130, 093001 (2023)]. We define cumulant mapping in terms of histograms, enabling fast computation of linear (additive) observables. However, applying the same algorithm to nonlinear (nonadditive) observables poses challenges, as the computation time of conventional estimators scales nonlinearly with data size. To overcome this, we develop estimators and an accompanying algorithm to enable computationally efficient estimation of the cumulant of interest. Comparisons of computation times and signal-to-noise ratios reveal the superior performance of our approach. This method is demonstrated on the (D+, D+, C+, O+) dissociation channel of CD 2 ⁢O 4+ produced in a strong-field ionization experiment. Additionally, Poisson statistics are used to simulate the two methods and provide insights into the efficiency of our algorithm. The proposed methodology unlocks efficient computation of cumulant mapping for a broader range of complex systems and observables, such as the laser pulse dependence of ionization dynamics.

74 ATOMIC AND MOLECULAR PHYSICS↗

Modeling SARS-CoV-2 proteins in the CASP-commons experiment

Critical Assessment of Structure Prediction (CASP) is an organization aimed at advancing the state of the art in computing protein structure from sequence. In the spring of 2020, CASP launched a community project to compute the structures of the most structurally challenging proteins coded for in the SARS-CoV-2 genome. Forty-seven research groups submitted over 3000 three-dimensional models and 700 sets of accuracy estimates on 10 proteins. The resulting models were released to the public. CASP community members also worked together to provide estimates of local and global accuracy and identify structure-based domain boundaries for some proteins. Subsequently, two of these structures (ORF3a and ORF8) have been solved experimentally, allowing assessment of both model quality and the accuracy estimates. Models from the AlphaFold2 group were found to have good agreement with the experimental structures, with main chain GDT_TS accuracy scores ranging from 63 (a correct topology) to 87 (competitive with experiment).

59 BASIC BIOLOGICAL SCIENCES↗

Development of Analysis Methods that Integrate Numeric and Textual Equipment Reliability Data

Within the Light Water Reactor Sustainability (LWRS) program, the Risk-Informed Systems Analysis (RISA) Pathway is performing collaborative research on the development and deployment of technologies designed to assist operating nuclear power plants (NPPs) to reduce operating costs improve plant reliability and availability. One of the RISA research areas is focusing on the development of methods and tools designed to optimize plant operations (e.g., maintenance/replacement schedules, optimal maintenance postures for plant structures, systems, and components [SSCs]) in a manner that is more cost effective than current approaches and makes better use of available SSC health data. The Risk-Informed Asset Management (RIAM) project targets this research area by creating a direct bridge between component equipment reliability (ER) data and system engineer decision making regarding maintenance activity scheduling and component aging management. In this respect, one challenge that NPP system engineers are facing is that the amount of ER data being continuously generated is not only extremely large in size, but it comes in different forms: textual (e.g., condition or maintenance reports) and numeric (e.g., generated by monitoring systems). All these data elements provide them with valuable insights and information regarding: 1) the discovery of anomalous behaviors or degradation trends, 2) the identification of the possible causes behind such behaviors/trends, and 3) the prediction of their direct consequences. However, several challenges have proved to be roadblocks to this process. While some of these challenges are technical in nature (i.e., data are often distributed over several physical servers/databases), others are conceptual in nature: data elements come in different formats (e.g., numeric or textual), and measured values have different scales (e.g., vibration spectra and oil temperature). The activities performed by the RIAM project during FY23 directly tackles the need to simultaneously integrate the analysis of ER data in all its forms, numeric and textual. Note that such task has never been performed before due to the complexity of the systems under consideration but, most importantly, because of the technical challenges behind the harmonization of ER data formats and the lack of adequate computational methods to analyze them. Our approach borrows ideas and concepts from the medical field where integration of several data sources is vital to assist medical practitioners to perform correct diagnosis and indicate optimal treatments. In our view a NPP asset is equivalent to a patient in a medical context. The main difference is the complexity of a human body is a magnitude more complex when compared to typical assets commonly present in NPPs (e.g., centrifugal pumps, or motor operated valves). This simplifies our first requirement when analyzing heterogenous ER data formats: to put data into “context”. Context is here intended as the additional piece of information that is needed by ER data analysis tools to understand what these data elements are referring to, i.e., which king of knowledge they are generating. In our context, this knowledge can be translated into models that capture the form and functional architecture of assets/systems, their dependencies, and how they interact. These models actually emulate the knowledge that that NPP system engineers possess about assets and systems; this is their key of success when analyzing ER data, their challenge is ability to handle large amount of data. Here, we employ model-based system engineering (MBSE) models of systems and assets to represent and capture their architecture and functional, i.e. cause-effect, relations. Then, ER data elements are processed by identifying first of all which elements of the developed MBSE elements they are referring to. For numeric ER data this task is fairly easy since it is possible to precisely pinpoint what MBSE elements the corresponding sensor are observing (e.g., bearing temperature of a centrifugal pump). Task is much harder for textual data since the information contained in issue or maintenance reports needs to “be understood” by a computational tool. Here we called this process as “knowledge extraction”. Once again, we borrow the experience in the medical field where methods to extract knowledge from textual data have been developed in the past decade. The missing element for us is the availability of a complete dictionary of NPP related concepts (in addition to the MBSE models presented earlier) that can put “text into context”. In FY23, such dictionary has been developed along with all the computational elements required for knowledge extraction. Lastly, once numeric and textual ER data elements have been processed and “understood”, then the last step is the discovery of possible cause-effect relations among them. This is performed by observing if a logical connection through the MBSE models exists, and if the

97 MATHEMATICS AND COMPUTING↗