Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “numerical differentiation”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 631 records · Page 35
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Multi-Scale Integrated Monitoring System for Enhancing Methane Emission Detection, Quantification & Prediction

This report details the progress and findings of a comprehensive study on reviewing existing solutions, identifying technology gaps, and formulating an “all-in-one” integrated strategy for developing the next-generation multiscale methane monitoring and modeling platform, conducted under grant number DE-FE0032292. Co-led by Dr. David Ebert, Dr. Binbin Weng, and Dr. Chenghao Wang at the University of Oklahoma, the project’s goal was to develop an integrated approach for building this engineering platform to detect, quantify, and mitigate methane emissions across various temporal scale, spatial scales, and sectors. The planning grant study began with an extensive review of various methane sensing and monitoring technologies and systems, surveying over 100 technology providers globally. This review revealed the prevalence of optical methods over chemical methods in commercially available sensors, with Non-Dispersive Infrared (NDIR), Tunable Diode Laser Absorption Spectroscopy (TDLAS), and Optical Gas Imaging (OGI) cameras being the most prevalent options. A trend towards more advanced optical techniques was observed, driven by increased regulatory focus and technological advancements. The technical evaluation of these sensing technologies provided crucial insights into their capabilities and limitations. The study examined emerging technologies such as Differential Absorption LiDAR (DIAL), which show promise for high-precision and long-range detection. The team then investigated the features and application bandwidth of various sensing platforms, including handheld, fixed/stationary, mobile, aerials, and spaceborne monitors. Pilot field studies were conducted to assess the capabilities of solutions for different emission scenarios. Field work with sensor deployments was conducted at three distinct site types: an oil & gas industry site, a cattle ranching operation, and a waste processing facility. The team also conducted a thorough review of methane flux inverse modeling approaches, focused on physically based methods. These approaches were categorized into simple, intermediate, and advanced methods. A realtime WRF-GHG (Weather Research and Forecasting-Greenhouse Gas) modeling system was developed and applied, incorporating multiple data sources to guide field experiments and inform methane plume detection. The project identified and analyzed numerous categories of methane data sources, including satellite measurements, ground-based sensors, and inventory databases. Key platforms examined include EDGAR, EPA GHGI, NASA TROPOMI, Carbon Mapper, and Climate TRACE, among others. The team proposed an architecture for a comprehensive methane monitoring platform. This system incorporates multi-source data acquisition, advanced data processing and assimilation, interactive visualization tools, and analytical capabilities for emissions forecasting and scenario analysis. The proposed platform aims to provide a user-friendly interface catering to various stakeholders, from researchers to policymakers. The architecture includes sophisticated data ingestion methods, a centralized data warehouse, and advanced analytical tools for data fusion and interpretation. To ensure the relevance and effectiveness of the proposed system, a comprehensive survey was conducted to gather stakeholder input on system requirements. Key findings include a strong need for integrating various data types and formats, a preference for real-time data updates and advanced visualization tools, and a demand for user-friendly interfaces catering to different expertise levels.

03 NATURAL GAS↗
DOE OSTI2022

A survey of unsupervised learning methods for high-dimensional uncertainty quantification in black-box-type problems

Constructing surrogate models for uncertainty quantification (UQ) on complex partial differential equations (PDEs) having inherently high-dimensional O(10 n ), n ≥ 2, stochastic inputs (e.g., forcing terms, boundary conditions, initial conditions) poses tremendous challenges. The “curse of dimensionality” can be addressed with suitable unsupervised learning techniques used as a pre-processing tool to encode inputs onto lower-dimensional subspaces while retaining its structural information and meaningful properties. In this work, we review and investigate thirteen dimension reduction methods including linear and nonlinear, spectral, blind source separation, convex and non-convex methods and utilize the resulting embeddings to construct a mapping to quantities of interest via polynomial chaos expansions (PCE). Here, we refer to the general proposed approach as manifold PCE (m-PCE), where manifold corresponds to the latent space resulting from any of the studied dimension reduction methods. To investigate the capabilities and limitations of these methods we conduct numerical tests for three physics-based systems (treated as black-boxes) having high-dimensional stochastic inputs of varying complexity modeled as both Gaussian and non-Gaussian random fields to investigate the effect of the intrinsic dimensionality of input data. We demonstrate both the advantages and limitations of the unsupervised learning methods and we conclude that a suitable m-PCE model provides a cost-effective approach compared to alternative algorithms proposed in the literature, including recently proposed expensive deep neural network-based surrogates and can be readily applied for high-dimensional UQ in stochastic PDEs.

42 ENGINEERING↗
DOE OSTI2023

A short account of thermoelectric film characterization techniques

Thermoelectric films and periodic structures have particularly intriguing electrical and thermal transport features due to their low dimensionality. As a result, they have piqued the attention of researchers from across the spectrum of disciplines. Their applications span from cooling fast CPUs to providing energy for wearable devices. The progress in the techniques for synthesizing TE materials and fabricating thin films has facilitated the emergence of a flourishing research domain in the field of electrical and thermal transport at the nanoscale. Further, a significant proportion of contemporary electronic, opto-electronic, and solar energy components are composed of materials featuring numerous interfaces and nanoscale contacts. Consequently, it is imperative to explore the thermal energy transfer and charge carrier transport across the films with thickness dimensions in the nanometer range. The development of cutting-edge approaches for grasping complicated processes at the nanoscale is critical. This review provides a concise overview of the prevalent methodologies developed over the last two decades and employed for the characterization of the Seebeck coefficient and electrical and thermal conductivity of thermoelectric films.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Material Compatibility of 3D Printed Polymer Composites with Low GWP Refrigerants

The recent development of 3D printing brings numerous opportunities to develop polymer heat exchangers with desired configurations and allows access to the new complex engineering design for better performance. To be used in the HVAC&R system, the compatibility of these materials to refrigerants needs to be thoroughly investigated and understood. This study tested the material compatibility of the printed polymer composites according to the ASHRAE Guideline 38 using metal pressure vessels. These printed parts were tested with R-134A, R-1234YF, R-1234ZE, R-1233ZD(E), and 32-3 MAF POE (10 wt.%) was used as the lubricants. The change in volume, mass, hardness, and mechanical properties was studied in detail. Different compatibility of the composites with refrigerants was observed when the composition of the composite changed. After exposure to refrigerants, the morphological and thermal properties were studied with the scanning electron microscope, thermogravimetric analysis, and differential scanning calorimetry to further reveal the influence of these refrigerants.

Li, Kai↗
DOE OSTI2021

Medium-induced radiative kernel with the Improved Opacity Expansion

We calculate the fully differential medium-induced radiative spectrum at next-to-leading order (NLO) accuracy within the Improved Opacity Expansion (IOE) framework. This scheme allows us to gain analytical control of the radiative spectrum at low and high gluon frequencies simultaneously. The high frequency regime can be obtained in the standard opacity expansion framework in which the resulting power series diverges at the characteristic frequency ω c ~ q^L 2 . In the IOE, all orders in opacity are resumed systematically below ωc yielding an asymptotic series controlled by logarithmically suppressed remainders down to the thermal scale T « ω c , while matching the opacity expansion at high frequency. Furthermore, we demonstrate that the IOE at NLO accuracy reproduces the characteristic Coulomb tail of the single hard scattering contribution as well as the Gaussian distribution resulting from multiple soft momentum exchanges. Finally, we compare our analytic scheme with a recent numerical solution, that includes a full resummation of multiple scatterings, for LHC-inspired medium parameters. Furthermore, we find a very good agreement both at low and high frequencies showcasing the performance of the IOE which provides for the first time accurate analytic formulas for radiative energy loss in the relevant perturbative kinematic regimes for dense media.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2026

Estimating and Evaluating Roughness Length and Displacement Height in Heterogeneous Urban Environments

The roughness length (z 0 ) and displacement height (z d ) are essential surface-layer parameters in numerical models (e.g., weather, climate, wall-modeled LES, etc.). This work evaluates the consistency of z 0 and z d estimates from morphometric and anemometric methods using data from two eddy-covariance flux towers (AmeriFlux US-INg and US-INc) in Indianapolis, IN. Results show inconsistencies in estimated z 0 and z d values depending on the chosen method. The two evaluated anemometric methods estimate non-physical values of z d when compared to roughness elements surrounding both towers. Additionally, predictions of mean wind speed using surface-layer similarity theory with morphometric estimates exhibit a bias during near-neutral and stable conditions relative to observations. The overestimation of mean wind speed by surface layer similarity theory is consistent with previous observational and modeling studies in urban areas, suggesting that the application of similarity theories to urban environments may have limitations. Differentiation of vegetation from built structures appears to impact morphometric z 0 and z d estimates, particularly where vegetation is abundant; however, it has little impact on correcting biases in the similarity theory. Specifically, we find that existing similarity theories using morphometric estimates underestimate integral velocity and length scales, and the degree of underestimation depends on the stability conditions. Accounting for the degree of anisotropy in surface-layer turbulence helps reduce the biases between similarity theories and observations during unstable conditions, but not in near-neutral cases. Future work is needed to identify the cause of such biases for near-neutral conditions.

Aerodynamic roughness length↗
DOE OSTI2021

End-exclusion zones in strongly stretched, molten polymer brushes of arbitrary shape

Theories of strongly stretched polymer brushes, particularly the parabolic brush theory, are valuable for providing analytically tractable predictions for the thermodynamic behavior of surface-grafted polymers in a wide range of settings. Furthermore, the parabolic brush limit fails to describe polymers grafted to convex curved substrates, such as the surfaces of spherical nanoparticles or the interfaces of strongly segregated block copolymers. It has previously been shown that strongly stretched curved brushes require a boundary layer devoid of free chain ends, requiring modifications of the theoretical analysis. While this “end-exclusion zone” has been successfully incorporated into the descriptions of brushes grafted onto the outer surfaces of cylinders and spheres, the behavior of brushes on surfaces of arbitrary curvature has not yet been studied. We present a formulation of the strong-stretching theory for molten brushes on the surfaces of arbitrary curvature and identify four distinct regimes of interest for which brushes are predicted to possess end-exclusion zones, notably including regimes of positive mean curvature but negative Gaussian curvature. Through numerical solutions of the strong-stretching brush equations, we report predicted scaling of the size of the end-exclusion zone, the chain end distribution, the chain polarization, and the free energy of stretching with mean and Gaussian surface curvatures. Through these results, we present a comprehensive picture of how the brush geometry influences the end-exclusion zones and exact strong-stretching free energies, which can be applied, for example, to model the full spectrum of brush geometries encountered in block copolymer melt assembly.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Unitary Bethe-Salpeter Methods in Two- and Three-Body Systems

The study of resonances, unstable particles formed in particle scattering, is motivated by the questions about the strong interaction and the composition of hadrons. In order to advance this study in the intermediate energy region, a variety of techniques are used. In this thesis, we present work done on two different analyses that use the principle of unitarity and the Bethe-Salpeter equation to study the resonances Lambda(1405), Sigma(1385), and a1(1260). Firstly, we perform a simultaneous analysis of Sand P-waves of the Strangeness = -1 two-body meson-baryon scattering amplitude using all low-energy data. For the first time, differential cross section data are included for chiral unitary coupled-channel models. From this model, S- and P-wave amplitudes are extracted and we observe both well-known I(JP)=0(1/2^-) S-wave states as well as a new I(JP)=1(1/2^+) state absent in quark models and lattice QCD results. Multiple statistical and phenomenological tests suggest that, while the data clearly require an I =1 P-wave resonance, the new state just accounts for the absence of the decuplet Sigma(1385)3/2+ in the model which is subsequently included in the parameterization. Secondly, we formulate the final state interaction of the a1(1260) resonance decay in a manifestly three-body-unitary parameterization and fit it to the a1(1260) lineshape measured by the ALEPH experiment. Dalitz plots calculated from this fit are presented. The work demonstrates the feasibility to numerically solve a previously derived amplitude and its generalization to isobars with spin and coupled channels. The model is a good test case because it can also be applied to other meson decays including exotic states and modified for the finite-volume problem as it arises in lattice QCD due to its manifest unitarity. The understanding of the resonances being analyzed in both the two-body work and the three-body work gives a better understanding of intermediate energy QCD.

Sadasivan, Daniel↗
DOE OSTI2023

(U) A General-Purpose Code for Correlated Sampling Using Batch Statistics with MCNP6 for Fixed-Source Problems

Correlated sampling can be used to reduce the uncertainty of a difference of tallies by taking advantage of the negative covariance term in the sandwich formula. Booth first showed how correlated sampling can be applied with batch statistics using MCNP’s tally fluctuation chart (TFC) to reduce the uncertainty of a difference of tallies in fixed-source problems. Booth presented a problem in which a 1273% uncertainty in a difference was reduced to 8% by accounting for correlations. Researchers He and Su recently studied correlated sampling using the TFC in MCNP version 5. They determined that the code did not print enough digits in the TFC tally means for accurate batch statistics in some cases. After modifying the source code, they concluded that “correlated sampling can yield a standard deviation of about one magnitude smaller than that predicted by the direct, un-correlated simulation when the changes in system response are small (say about 1%), which is equivalent to saving in CPU time by a factor of 100. Such saving [sic] becomes less significant as the change in system response becomes larger.” He and Su provided the formulas needed to apply batch statistics to compute the correlated uncertainty of a difference of tallies. In this report, we follow up on their work by providing the formulas needed to apply batch statistics to compute the correlated uncertainty of a ratio of tallies and of a difference of two tallies divided by a third tally. We extend these formulas to differences and ratios of ratios. These formulas are applied to reduce the uncertainty associated with calculating a relative sensitivity. He and Su did not investigate the accuracy of their correlated sampling uncertainty estimates. We use their test problems and evaluate the accuracy of the uncertainty estimates by comparing with results obtained from random sampling, and, in simple cases, with theoretical values of the “exact” uncertainties. We find that the uncertainties obtained from batch statistics are accurate as long as at least 100 batches are used. We present a new computer code, COSUBS (COrrelated Sampling Using Batch Statistics), that reads MCNP6 TFCs and applies correlated sampling using batch statistics for the tally combinations that the user specifies. COSUBS is a very general tool that compares all TFCs for a base case and one or two perturbed cases. It computes uncertainties for ratios if given only a base case. This report is organized as follows. The equations to apply batch statistics to the difference of random tallies are reviewed in Sec. II. Section III presents the equations for applying batch statistics to a ratio of random tallies; this is useful for computing relative sensitivities using a one-sided finite difference and the relative sensitivity using the differential operator method. Section IV presents the equations for applying batch statistics to a difference of two random tallies divided by a third; this is useful for computing a relative sensitivities using a central difference. Section V presents the equations for applying batch statistics to a difference of two ratios with four random tallies. Section VI presents the equations for applying batch statistics to a one-sided finite difference estimate of the relative sensitivity of a ratio (this uses four random tallies). Section VII presents the equations for applying batch statistics to a central difference estimate of the relative sensitivity of a ratio (this uses six random tallies). Section VIII presents the equations for applying batch statistics to a sum of random tallies. Section IX discusses how to apply batch statistics using MCNP6. Section X presents COSUBS, describing its command-line options and logic. Sections XI through XVI present numerical results for various test problems. Section XVII is a summary and conclusions. Appendix A derives the theoretical Monte Carlo tally variance given certain assumptions; these variances are used to verify the batch statistics for some of the problems. Appendix B lists the MCNP6 input for the unperturbed example problem. Appendix C presents modifications made to MCNP6.3 to support this work.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Structural Manipulation of Phase Transitions by Self‐Induced Strain in Geometrically Confined Thin Films

Strain engineering is a well-known method often used to tune material properties in thin films. The most studied sources of strain are lattice mismatch and differential thermal contraction between the substrate and film. However, in materials which undergo a structural phase transition (SPT), a third and often overlooked source of strain may play a very significant role. If the substrate confines the area of the film, the SPT may induce stress which changes the evolution of the transition. This is a 2D analog of the isochoric phase transition between water and ice, where the freezing point drops below 0 °C. To illustrate this, the prototypical Mott insulator V 2 O 3 which has an SPT coupled to a metal–insulator transition is used to show how self-induced strain can drastically alter structural and electronic properties. This effect provides an elegant approach for mapping the phase diagram of the SPT and the transitions coupled to it. Moreover, the magnitude of self-straining is tunable by modifying the substrate morphology. Furthermore, this effect may be important for numerous materials which exhibit an SPT and are subjected to geometrical constraints.

Kalcheim, Yoav↗
DOE OSTI2025

Neural Active Manifolds: Nonlinear Dimensionality Reduction for Uncertainty Quantification

We present a new approach for nonlinear dimensionality reduction, specifically designed for computationally expensive mathematical models. We leverage autoencoders to discover a one-dimensional neural active manifold (NeurAM) capturing the model output variability, through the aid of a simultaneously learnt surrogate model with inputs on this manifold. Our method only relies on model evaluations and does not require the knowledge of gradients. The proposed dimensionality reduction framework can then be applied to assist outer loop many-query tasks in scientific computing, like sensitivity analysis and multifidelity uncertainty propagation. In particular, we prove, both theoretically under idealized conditions, and numerically in challenging test cases, how NeurAM can be used to obtain multifidelity sampling estimators with reduced variance by sampling the models on the discovered low-dimensional and shared manifold among models. Several numerical examples illustrate the main features of the proposed dimensionality reduction strategy and highlight its advantages with respect to existing approaches in the literature.

Autoencoders↗
DOE OSTI2023

A general non-Fourier Stefan problem formulation that accounts for memory effects

The Stefan problem is the classical model of a melting phase change. In heterogeneous systems, such phase changes can exhibit non-Fourier (anomalous) behaviors, where the advance of the melt interface does not follow the expected time scaling. These situations can be modeled by replacing the derivatives, in the governing partial differential equations, with fractional order derivatives. In particular, replacing the time derivatives leads to non-Fourier models that account for memory effects in the system. In this work, by using appropriate time convolution integrals, a general thermodynamic balance statement for melting phase problems, explicitly accounting for memory effects, is developed. From this balance, a general model formulation applicable to problems involving melting over a temperature range (i.e., a mushy region) is derived. A key component in this model is the representation of memory effects through the use of fractional derivative based constitutive models of the enthalpy and heat flux. Further, on shrinking the mushy region to a single isotherm, a general sharp interface melting model is obtained. Here, in contrast to the classic Stefan problem, the fractional derivatives induce a natural regularization, such that the constitutive models for enthalpy and heat flux are continuous at the melt interface; a result confirmed through numerical simulation. To further support the theoretical findings, a physical example of a non-Fourier Stefan problem is presented. Overall the development and results in this paper underscore the importance of explicitly relating the development of fractional calculus models to the appropriate thermodynamic balance statements.

42 ENGINEERING↗
DOE OSTI2024

D2NO: Efficient handling of heterogeneous input function spaces with distributed deep neural operators

Neural operators have been applied in various scientific fields, such as solving parametric partial differential equations, dynamical systems with control, and inverse problems. However, challenges arise when dealing with input functions that exhibit heterogeneous properties, requiring multiple sensors to handle functions with minimal regularity. To address this issue, discretization-invariant neural operators have been used, allowing the sampling of diverse input functions with different sensor locations. However, existing frameworks still require an equal number of sensors for all functions. We propose a novel distributed approach to further relax the discretization requirements and solve the heterogeneous dataset challenges. Our method involves partitioning the input function space and processing individual input functions using independent and separate neural networks. A centralized neural network is used to handle shared information across all output functions. This distributed methodology reduces the number of gradient descent back-propagation steps, improving efficiency while maintaining accuracy. Here, we demonstrate that the corresponding neural network is a universal approximator of continuous nonlinear operators and present three numerical examples to validate its performance.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Physics-driven learning of Wasserstein GAN for density reconstruction in dynamic tomography

Object density reconstruction from projections containing scattered radiation and noise is of critical importance in many applications. Existing scatter correction and density reconstruction methods may not provide the high accuracy needed in many applications and can break down in the presence of unmodeled or anomalous scatter and other experimental artifacts. Incorporating machine-learning models could prove beneficial for accurate density reconstruction, particularly in dynamic imaging, where the time evolution of the density fields could be captured by partial differential equations or by learning from hydrodynamics simulations. In this work, we demonstrate the ability of learned deep neural networks to perform artifact removal in noisy density reconstructions, where the noise is imperfectly characterized. Here, we use a Wasserstein generative adversarial network (WGAN), where the generator serves as a denoiser that removes artifacts in densities obtained from traditional reconstruction algorithms. We train the networks from large density time-series datasets, with noise simulated according to parametric random distributions that may mimic noise in experiments. The WGAN is trained with noisy density frames as generator inputs, to match the generator outputs to the distribution of clean densities (time series) from simulations. A supervised loss is also included in the training, which leads to an improved density restoration performance. In addition, we employ physics-based constraints such as mass conservation during the network training and application to further enable highly accurate density reconstructions. Our preliminary numerical results show that the models trained in our frameworks can remove significant portions of unknown noise in density time-series data.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Physics Guided Simulation of Electrostatic Discharge: Technical Report

Triboelectrically-charged objects may create threshold sparks, electrostatic discharge (ESD) events, to equilibrate charge between themselves and other relatively charged objects. ESD events exhibit many complex physical phenomena. They are a nexus of several fields of physics with disparate characteristic scales: plasma physics, chemical kinetics, hydrodynamics, circuit models, etc. These scales can span many orders of magnitude from the varied collisions thermalizing information within a plasma on the $\mathcal{O}(fs/ps)$ to the physical size of the plasma channel on the $\mathcal{O}(100µm)$, to the speed of a nonlinear hydrodynamic wave propagating at $\mathcal{O}(µm, ns)$. These threshold ESD events may occur in situations of programmatic importance, delivering energy and power profiles to a “victim load” generating deleterious consequences. To predict and mitigate these consequences we must answer questions about the spark’s energy budget: how much energy goes into producing the spark channel; how much gets radiated away; how much energy is advected away into the hydrodynamics; and how much energy is delivered to a victim load. An ESD simulation toolset has been created and evolved in order to answer these questions. An appropriate, physics guided implementation for simulation can be done by gaining insight into its constituent physics and leveraging that intuition to choose a suitable numerical operator. We examine in detail the chemical kinetics, circuit discharge, and hydrodynamics to deter mine dominant regimes, values, timescales, and interactions to uncover the underlying physical dynamics. We also examine and propose model reduction schemes for high-dimensional chemical kinetics. We use past and current work with experimentally validated and theoretically-verified hydrodynamics to calculate applicability limits of the non-ionizing strong shock limit. We quantify the energy budget from a hydrodynamic perspective and demonstrate that a significant fraction of the stored energy is “earmarked” for hydrodynamic advection as an energy terminus. Lastly, we combine the constituent physics of an ESD event (chemical kinetics, circuit model, and hydrodynamics) into a cohesive, actionable toolset and obtain promising results from an isothermal test case. We then propose a viable, modular evolution of the ESD toolset based upon the performed examination of the physics uncovering dominant physical scales and the stiffness of the compositional differential system.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Generalized moving least squares vs. radial basis function finite difference methods for approximating surface derivatives

Approximating differential operators defined on two-dimensional surfaces is an important problem that arises in many areas of science and engineering. Over the past ten years, localized meshfree methods based on generalized moving least squares (GMLS) and radial basis function finite differences (RBF-FD) have been shown to be effective for this task as they can give high orders of accuracy at low computational cost, and they can be applied to surfaces defined only by point clouds. However, there have yet to be any studies that perform a direct comparison of these methods for approximating surface differential operators (SDOs). The first purpose of this work is to fill that gap. For this comparison, we focus on an RBF-FD method based on polyharmonic spline kernels and polynomials (PHS+Poly) since they are most closely related to the GMLS method. Additionally, we use a relatively new technique for approximating SDOs with RBF-FD called the tangent plane method since it is simpler than previous techniques and natural to use with PHS+Poly RBF-FD. Further, the second purpose of this work is to relate the tangent plane formulation of SDOs to the local coordinate formulation used in GMLS and to show that they are equivalent when the tangent space to the surface is known exactly. The final purpose is to use ideas from the GMLS SDO formulation to derive a new RBF-FD method for approximating the tangent space for a point cloud surface when it is unknown. For the numerical comparisons of the methods, we examine their convergence rates for approximating the surface gradient, divergence, and Laplacian as the point clouds are refined for various parameter choices. We also compare their efficiency in terms of accuracy per computational cost, both when including and excluding setup costs.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

3′ RNA-seq is superior to standard RNA-seq in cases of sparse data but inferior at identifying toxicity pathways in a model organism

The application of RNA-sequencing has led to numerous breakthroughs related to investigating gene expression levels in complex biological systems. Among these are knowledge of how organisms, such as the vertebrate model organism zebrafish (Danio rerio), respond to toxicant exposure. Recently, the development of 3' RNA-seq has allowed for the determination of gene expression levels with a fraction of the required reads compared to standard RNA-seq. While 3' RNA-seq has many advantages, a comparison to standard RNA-seq has not been performed in the context of whole organism toxicity and sparse data. Here, we examined samples from zebrafish exposed to perfluorobutane sulfonamide (FBSA) with either 3' or standard RNA-seq to determine the advantages of each with regards to the identification of functionally enriched pathways. We found that 3' and standard RNA-seq showed specific advantages when focusing on annotated or unannotated regions of the genome. We also found that standard RNA-seq identified more differentially expressed genes (DEGs), but that this advantage disappeared under conditions of sparse data. We also found that standard RNA-seq had a significant advantage in identifying functionally enriched pathways via analysis of DEG lists but that this advantage was minimal when identifying pathways via gene set enrichment analysis of all genes. These results show that each approach has experimental conditions where they may be advantageous. Our observations can help guide others in the choice of 3' RNA-seq vs standard RNA sequencing to query gene expression levels in a range of biological systems.

3’ RNA-seq↗
DOE OSTI2024

On the force exerted on a non-spherical asymmetric dust grain from homogeneous, stationary, isotropic, non-magnetized plasma

Whereas the conventional wisdom suggests that the force between non-magnetized homogeneous, stationary, isotropic plasma, and the dust grain is only possible for the case of relative plasma–grain velocity, it is shown that stationary non-spherical asymmetric dust grain immersed in stationary, non-magnetized, isotropic plasma can experience a force caused by the grain–plasma interactions. The component of the force due to scattering of plasma particles in the limit of infinite Debye length is considered analytically. Both the particle scattering and absorption force components are modeled numerically in the limits of infinite and finite Debye length using a newly developed 2D3V Aspherical Particle-in-Cell code. The code simulates interactions of dust grain of selected non-spherical asymmetric shape with plasmas using dust shape conforming coordinates. Here, the simulations confirm the existence of the force on non-spherical asymmetric grain in stationary non-magnetized plasma and show that the plasma screening effects can lead to reversal of the force direction.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗