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DOE OSTI2020

Similarity of capacitive radio-frequency discharges in nonlocal regimes

Similarity transformations are essential for correlating discharges at different scales, which are mostly utilized with local field or local energy approximations. In this work, we report the fully kinetic results from particle-in-cell/Monte Carlo collision simulations that unambiguously demonstrate the similarity of radio frequency (rf) discharges in nonlocal regimes where the electron energy relaxation length is much larger than the gap dimension. It is found that at a constant rf voltage amplitude, discharges will be similar if the gas pressure, inverse of gap distance, and rf driving frequency are all changed by the same scaling factor. The scaling relations of fundamental parameters are illustrated for rf discharges in the alpha-mode with secondary electron emission ignored, and the temporal electron kinetics are shown to have invariance in similar discharges. The results explicitly validate the scaling laws in nonlocal kinetic regimes, indicating promising application potentials of the similarity transformations across a wide range of kinetic regimes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2021

Similarity properties in capacitive radio frequency plasmas with nonlinear collision processes

Abstract Similarity laws (SL) are essential for correlating the characteristics of plasmas at different dimensional scales, which have been validated for radio frequency (rf) discharges at low pressure but under limited conditions. In this work, we evaluate the effects of nonlinear collisions (e.g. stepwise ionization) on the similarity properties in capacitive rf discharges in argon across a wide range of pressure regimes via fully kinetic particle-in-cell simulations. The SL scalings of fundamental discharge parameters, e.g. the electron power absorption and electron energy probability function, are examined with and without nonlinear collisions, respectively. Without the nonlinear collisions, the similarity scalings are found to be rigorously valid. When the nonlinear collisions are considered, the similarity properties in rf discharges still exist approximately, which indicates that the violations caused by the nonlinear collisions are still minor in the studied cases. The reasons for the effectiveness of SL scalings with nonlinear collision processes are also discussed. The results from this study confirmed the validity of similarity transformations with more complex reaction kinetics, which may promote the applicability of the SL scalings for the design and fabrications of plasma devices.

Physics↗

DOE OSTI2025

miss-SNF: a multimodal patient similarity network integration approach to handle completely missing data sources

Abstract Motivation Precision medicine leverages patient-specific multimodal data to improve prevention, diagnosis, prognosis, and treatment of diseases. Advancing precision medicine requires the non-trivial integration of complex, heterogeneous, and potentially high-dimensional data sources, such as multi-omics and clinical data. In the literature, several approaches have been proposed to manage missing data, but are usually limited to the recovery of subsets of features for a subset of patients. A largely overlooked problem is the integration of multiple sources of data when one or more of them are completely missing for a subset of patients, a relatively common condition in clinical practice. Results We propose miss-Similarity Network Fusion (miss-SNF), a novel general-purpose data integration approach designed to manage completely missing data in the context of patient similarity networks. miss-SNF integrates incomplete unimodal patient similarity networks by leveraging a non-linear message-passing strategy borrowed from the SNF algorithm. miss-SNF is able to recover missing patient similarities and is “task agnostic”, in the sense that can integrate partial data for both unsupervised and supervised prediction tasks. Experimental analyses on nine cancer datasets from The Cancer Genome Atlas (TCGA) demonstrate that miss-SNF achieves state-of-the-art results in recovering similarities and in identifying patients subgroups enriched in clinically relevant variables and having differential survival. Moreover, amputation experiments show that miss-SNF supervised prediction of cancer clinical outcomes and Alzheimer’s disease diagnosis with completely missing data achieves results comparable to those obtained when all the data are available. Availability and implementation miss-SNF code, implemented in R, is available at https://github.com/AnacletoLAB/missSNF.

Biochemistry & Molecular Biology↗

DOE OSTI2021

Sensitivity-based Similarity Metrics for New Experiment Design Optimization

The nuclear data used in advanced reactor simulations requires validation. Data from nuclear criticality experiments can provide this validation. New nuclear criticality experiment design requires extensive knowledge and expert judgement such that the experimental design parameters are selected in such a way to keep the experiment subcritical. To aide in this experimental design process, professionals can utilize sensitivity and uncertainty analysis. Sensitivity and uncertainty analysis relies on matching new application experiments with currently existing benchmark experiments. Currently, there is functionality in the Whisper 1.1 software package to calculate a similarity metric based on neutron multiplication factor sensitivity coefficients between a new application designed by the user and existing International Criticality Safety Benchmark Experiment Project (ICSBEP) benchmarks. The Whisper 1.1 software package is included in Monte Carlo N-Particle ® Code Version 6.21 (MCNP ® 6.2). This work is geared toward expanding this capability to new similarity metrics based on beta-effective sensitivity coefficients and reactivity coefficient sensitivity coefficients. While the investigation of these sensitivity coefficients is presented in detail in separate works at this same conference, this work will be primarily focused on studying the similarity metrics in more detail. These similarity metrics will then be incorporated into the optimization algorithms used for experiment design in EUCLID (Experiments Underpinned by Computational Learning for Improvements in nuclear Data), which is a Los Alamos National Laboratory (LANL) project designed to constrain nuclear data of interest, such that adjustments can be made to possible inaccuracies. A more detailed optimization can be subsequently performed by breaking down these similarity metrics by isotope, reaction, and energy.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2020

Gaussian Process Optimization of Sensitivity-Based Similarity Metrics between New Nuclear Applications and New/Existing Benchmarks [Slides]

This presentation discusses Nuclear Criticality Safety (NCS) and how designing safe, new nuclear criticality experiments requires expert judgement, which could take years of experience. Sensitivity/uncertainty (S/U) analysis can be utilized by less experienced individuals to conservatively estimate uncertainties in important parameters, such as k eff , in newly proposed nuclear experiments. The presentation poses the question of how this analysis can be performed and states that the answer lies in matching new nuclear experiments with existing benchmark experiments using similarity metrics. By increasing the criticality safety of the application in this work, higher mass limits could be used in PF-4 operations. Additionally, the presentation discusses MCNP6.2®, Whisper-1.1, the software that can be used in this analysis. Also discussed is the fact that International Criticality Safety Benchmark Evaluation Project (ICSBEP) benchmarks rarely match new nuclear applications and that there are significant differences in given set of materials and/or geometry. If there are no benchmarks that match the application, the presentation discusses the possibility of creating new benchmarks. In conclusion, this work presents a Gaussian process (GP) optimization scheme that was used to generate new benchmarks with the highest sensitivity-based similarity metrics to user-defined nuclear applications. The Gaussian process optimization successfully designed 3 new experimental benchmarks that were highly correlated to the application of interest and had k eff values near critical. Optimization over c k,i-r has shown that investigating specific isotope reactions for different applications is crucial to designing benchmark experiments. Partial contribution from Pu dominates c k similarity metric. Future work includes testing new stand-alone similarity metrics or new combinations of similarity metrics as the design criterion of this optimization – design criterion is application dependent.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2023

Characterizing Families of Spectral Similarity Scores and Their Use Cases for Gas Chromatography–Mass Spectrometry Small Molecule Identification

Metabolomics provides a unique snapshot into the world of small molecules and the complex biological processes that govern the human, animal, plant, and environmental ecosystems encapsulated by the One Health modeling framework. However, this “molecular snapshot” is only as informative as the number of metabolites confidently identified within it. The spectral similarity (SS) score is traditionally used to identify compound(s) in mass spectrometry approaches to metabolomics, where spectra are matched to reference libraries of candidate spectra. Unfortunately, there is little consensus on which of the dozens of available SS metrics should be used. This lack of standard SS score creates analytic uncertainty and potentially leads to issues in reproducibility, especially as these data are integrated across other domains. In this work, we use metabolomic spectral similarity as a case study to showcase the challenges in consistency within just one piece of the One Health framework that must be addressed to enable data science approaches for One Health problems. Here, using a large cohort of datasets comprising both standard and complex datasets with expert-verified truth annotations, we evaluated the effectiveness of 66 similarity metrics to delineate between correct matches (true positives) and incorrect matches (true negatives). We additionally characterize the families of these metrics to make informed recommendations for their use. Our results indicate that specific families of metrics (the Inner Product, Correlative, and Intersection families of scores) tend to perform better than others, with no single similarity metric performing optimally for all queried spectra. This work and its findings provide an empirically-based resource for researchers to use in their selection of similarity metrics for GC-MS identification, increasing scientific reproducibility through taking steps towards standardizing identification workflows.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1975

A similarity solution of the Navier-Stokes equations with wall catalysis and slip for hypersonic, low Reynolds number flow over spheres

The slip conditions for a multicomponent mixture with diffusion, wall-catalyzed atom recombination and thermal radiation are derived. The more realistic multicomponent species slip conditions are shown to be necessary for accurate merged shock layer solutions on a sphere. These slip conditions are used in a first-order similarity solution of the Navier-Stokes equations with nonequilibrium chemistry for the merged shock layer. Results of this quick numerical solution are compared with a time dependent solution around the sphere and with measured arc jet results at low Reynolds numbers. The similarity solution, unlike the time dependent solution, shows smooth radial profiles of the pressure and smooth variations of velocity slip, skin friction, temperature slip and heat transfer around the body. The present first-order similarity solution is valid up to 25 deg from the stagnation point and takes less than 1% of the computer time to run a time dependent scheme. The smaller stand-off distance obtained from the similarity solution is supported by experimental data. The measured heat flux is closer to the similarity solution than the time dependent method at the stagnation point and shows the proper variation with circumferential angle up to at least 40 deg.

Hendricks, W. L.↗

NASA NTRS1989

The evolution of cooling flows - Self-similar cooling waves

Similarity solutions are presented for the time-dependent evolution of cooling flows. A cooling flow expands when the cooling time computed from the initial gas distribution increases with radius. If certain simplifying conditions are met, the evolution of the resulting cooling wave becomes self-similar. The similarity solutions obtained here assumed subsonic flow, which is valid in the outer parts of observed cooling flows; they are matched to transonic accretion solutions valid in the central parts. The models are applied to the cooling flow onto M87, with unsatisfactory agreement at small radius. A local linear stability analysis shows that the similarity solution suffers isobaric thermal instability, suggesting that the neglect of star formation may be responsible for the poor agreement. The similarity solution suggests that the cooling flow around M87 was more vigorous in the past.

Bertschinger, Edmund↗

NASA NTRS1994

McIntosh active-region class similarities and suggestions for mergers

McIntosh active-region classifications reported during a five-year period were examined to determine similarities among the classes. Two methods were used extensively to determine these similarities. The number of transitions among classes were used to determine the most frequent transitions out of each class, and the alternative classes reported for the same region by different sites were used to establish which classes were neighboring classes. These transition frequencies and neighboring classes were used to identify classes that could be eliminated or merged with other classes. Class similarities were used to investigate the relative importance of several pairs of decisions that occur within a single McIntosh parameter. In particular, the redundancy of parameters in some classes was examined, and the class similarities were used to identify which of these parameters could be eliminated. Infrequently reported classes were also considered, and suggestions for mergers were made when similarities between classes could be identified.

Bornmann, P. L.↗

NASA NTRS1998

Self-Similar Compressible Free Vortices

Lie group methods are used to find both exact and numerical similarity solutions for compressible perturbations to all incompressible, two-dimensional, axisymmetric vortex reference flow. The reference flow vorticity satisfies an eigenvalue problem for which the solutions are a set of two-dimensional, self-similar, incompressible vortices. These solutions are augmented by deriving a conserved quantity for each eigenvalue, and identifying a Lie group which leaves the reference flow equations invariant. The partial differential equations governing the compressible perturbations to these reference flows are also invariant under the action of the same group. The similarity variables found with this group are used to determine the decay rates of the velocities and thermodynamic variables in the self-similar flows, and to reduce the governing partial differential equations to a set of ordinary differential equations. The ODE's are solved analytically and numerically for a Taylor vortex reference flow, and numerically for an Oseen vortex reference flow. The solutions are used to examine the dependencies of the temperature, density, entropy, dissipation and radial velocity on the Prandtl number. Also, experimental data on compressible free vortex flow are compared to the analytical results, the evolution of vortices from initial states which are not self-similar is discussed, and the energy transfer in a slightly-compressible vortex is considered.

vonEllenrieder, Karl↗

DOE OSTI2024

On the Departure from Monin–Obukhov Surface Similarity and Transition to the Convective Mixed Layer

Large-eddy simulations are used to evaluate mean profile similarity in the convective boundary layer (CBL). Particular care is taken regarding the grid sensitivity of the profiles and the mitigation of inertial oscillations in the simulation spin-up. The nondimensional gradients Φ for wind speed and air temperature generally align with Monin–Obukhov similarity across cases but have a steeper slope than predicted within each profile. The same trend has been noted in several other recent studies. The Businger-Dyer relations are modified here with an exponential cutoff term to account for the decay in Φ to first-order approximation, yielding improved similarity from approximately 0.05z i to above 0.3z i , where z i is the CBL depth. The necessity for the exponential correction is attributed to an extended transition from surface scaling to zero gradient in the mixed layer, where the departure from Monin–Obukhov similarity may be negligible at the surface but becomes substantial well below the conventional surface layer height of 0.1 z i .

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Alluvial fan morphology: A self-similar free boundary problem description

In this work, we examine approximate geometrically self-similar solutions to a parabolic free boundary value problem applied to alluvial fan surface morphology and growth. Alluvial fans are fan- or cone-shaped sedimentary deposits caused by the rapid deposition of sediment from a canyon discharging onto a flatter plain. Longitudinal, topographic profiles of fans can be readily described by a seemingly time independent dimensionless profile (DeChant et al., 1999). However, because an alluvial fan can be expected to grow over time, it is clear that this “steady” profile is certainly time dependent and can be described using a space-time self-similar solution. In an experimental and theory-based study, Guerit et al. (2014) developed a self-similar (or as they describe it a self-affine) linear solution based upon an approximate first order small parameter expansion solution for a 1-d homogeneous nonlinear diffusion equation. Direct substitution of this result into a linear diffusion equation suggests that this first order expression may not fully satisfy the associated governing equation. In contrast, we develop a more complete solution based upon a modeled approximation for the axi-symmetric formulation such that the associated temporal behavior is consistent with a 1/3 time power-law as described by Reitz and Jerolmack (2014). The resulting expression is an exact solution to a linear heat equation. Furthermore, we emphasize that a small parameter is not inherent to the resulting profile result and is not included in our model development. Though developed using rather different approaches, the formal solution developed here is in good agreement with the simple polynomial described by DeChant et al. (1999) suggesting that this self-similar solution is a suitable time dependent representation of alluvial fan longitudinal profile form and improves on earlier work.

58 GEOSCIENCES↗

DOE OSTI2024

Scaling methodologies and similarity analysis for thermal hydraulics test facility development for water-cooled small modular reactor

Small modular reactors (SMRs) represent a promising option for providing clean and sustainable energy due to their potential for enhanced safety, reduced capital costs, and increased siting flexibility. However, new reactor systems require the development and operation of representative scaled-down test facilities to support the verification and validation of system computer codes and models. Here this study reviews the research on scaling methodologies and similarity principles pivotal in developing non-nuclear integral effects test and separate effects test facilities for water-cooled SMRs. The study focuses on a review of the scaling methods, similarity approaches, and possible challenges posed by the unique and compact design features of integral-pressurized water reactor-type SMRs, and their representative test facilities. This study also reviews previous research related to scaling and similarity methodologies and provides insights into design considerations for achieving prototypic conditions in test facilities. The findings and recommendations emphasize the broader impact of appropriate scaling and similarity principles to ensure meaningful and transferable results from non-nuclear test facilities to accelerate the safe and efficient deployment of next-generation water-cooled SMRs.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2026

Optimization techniques in self-similar compressible flow

We investigate the one-dimensional (1D) inviscid compressible flow equations for an ideal gas through the lens of optimization techniques. It is the case that, to our knowledge, optimization analysis applied to the so-called “linear velocity” solutions of the Euler compressible flow equations has not been previously conducted. Through both gradient-based and variational techniques, new variants of well-studied flow scenarios, i.e., self-similar, 1D, linear velocity solution class to idealized inviscid compressible flow equations, are determined, as encoded in both the kinematic and thermodynamic properties of this self-similar solution class. With the kinematics of the said solutions being driven by a self-similar “scale radius” and the thermodynamics being driven separately through the appearance of an arbitrary function, a myriad of new solution classes is possible. Acting as a guide to more realistic physical circumstances as well as discovery, it is the hope that the presented cases serve as the framework for future investigations into the intersection of self-similarity and optimization techniques. Fields of study that may find this work to be of interest include aerodynamic design, flow control, inertial confinement fusion, physics-informed neural networks, and other related areas of interest.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2020

Planar Self-similar Antennas for Broadband Millimeter-Wave Measurements

Self-similar antennas offer extremely broadband functionality and easily scalable designs. Self-similar designs with a four-arm layout are also suited for dual polarization through excitations of opposing arms, although there has only been limited use of them for millimeter-wave detectors. These antennas have been used for measurements of the cosmic microwave background (CMB), which encompass a wide frequency range and are now actively focusing more on polarization anisotropies. Here, we analyze multiple planar self-similar antenna designs with simulations in high-frequency structure simulator and ongoing physical testing. They all exhibit broadband operation between 130 and 230 GHz and can couple to both linear polarizations through the previously mentioned four-arm symmetry. Furthermore, simulations include each antenna design coupled to an extended hemispherical, AR-coated lenslet. From these, a basic bowtie-like arm design produced minimal polarization wobble with moderate beam efficiency, while a hybrid trapezoidal design provided high beam efficiency with small polarization wobble. Current fabrication versions of each are being tested, coupled to multichroic microwave kinetic inductance detectors. These planar self-similar antennas, when implemented in CMB and other detectors, could improve observations while simultaneously simplifying fabrication and detector layout.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2020

Similarity of Precursors in Solid-State Synthesis as Text-Mined from Scientific Literature

Collecting and analyzing the vast amount of information available in the solid-state chemistry literature may accelerate our understanding of materials synthesis. However, one major problem is the difficulty of identifying which materials from a synthesis paragraph are precursors or are target materials. In this study, we developed a two-step chemical named entity recognition model to identify precursors and targets, based on information from the context around material entities. Using the extracted data, we conducted a meta-analysis to study the similarities and differences between precursors in the context of solid-state synthesis. To quantify precursor similarity, we built a substitution model to calculate the viability of substituting one precursor with another while retaining the target. From a hierarchical clustering of the precursors, we demonstrate that the “chemical similarity” of precursors can be extracted from text data. Quantifying the similarity of precursors helps provide a foundation for suggesting candidate reactants in a predictive synthesis model.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Self-similar Reynolds-averaged mechanical–scalar turbulence models for Rayleigh–Taylor mixing induced by power-law accelerations in the small Atwood number limit

Analytical self-similar solutions to two-, three-, and four-equation Reynolds-averaged mechanical–scalar turbulence models describing turbulent Rayleigh–Taylor mixing driven by a temporal power-law acceleration are derived in the small Atwood number (Boussinesq) limit. The solutions generalize those previously derived for constant acceleration Rayleigh–Taylor mixing for models based on the turbulent kinetic energy K and its dissipation rate ε, together with the scalar variance S and its dissipation rate χ [O. Schilling, “Self-similar Reynolds-averaged mechanical–scalar turbulence models for Rayleigh–Taylor, Richtmyer–Meshkov, and Kelvin–Helmholtz instability-induced mixing in the small Atwood number limit,” Phys. Fluids 33, 085129 (2021)]. The turbulent fields are expressed in terms of the model coefficients and power-law exponent, with their temporal power-law scalings obtained by requiring that the self-similar equations are explicitly time-independent. Mixing layer growth parameters and other physical observables are obtained explicitly as functions of the model coefficients and parameterized by the exponent of the power-law acceleration. Values for physical observables in the constant acceleration case are used to calibrate the two-, three-, and four-equation models, such that the self-similar solutions are consistent with experimental and numerical simulation data corresponding to a canonical (i.e., constant acceleration) Rayleigh–Taylor turbulent flow. The calibrated four-equation model is then used to numerically reconstruct the mean and turbulent fields, and turbulent equation budgets across the mixing layer for several values of the power-law exponent. Finally, the reference solutions derived here can be used to understand the model predictions for strongly accelerated or decelerated Rayleigh–Taylor mixing in the large Reynolds number limit.

42 ENGINEERING↗

DOE OSTI2022

PDBspheres: a method for finding 3D similarities in local regions in proteins

Abstract We present a structure-based method for finding and evaluating structural similarities in protein regions relevant to ligand binding. PDBspheres comprises an exhaustive library of protein structure regions (‘spheres’) adjacent to complexed ligands derived from the Protein Data Bank (PDB), along with methods to find and evaluate structural matches between a protein of interest and spheres in the library. PDBspheres uses the LGA (Local–Global Alignment) structure alignment algorithm as the main engine for detecting structural similarities between the protein of interest and template spheres from the library, which currently contains >2 million spheres. To assess confidence in structural matches, an all-atom-based similarity metric takes side chain placement into account. Here, we describe the PDBspheres method, demonstrate its ability to detect and characterize binding sites in protein structures, show how PDBspheres—a strictly structure-based method—performs on a curated dataset of 2528 ligand-bound and ligand-free crystal structures, and use PDBspheres to cluster pockets and assess structural similarities among protein binding sites of 4876 structures in the ‘refined set’ of the PDBbind 2019 dataset.

59 BASIC BIOLOGICAL SCIENCES↗