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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.

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At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

A parallel discrete dislocation dynamics/kinetic Monte Carlo method to study non-conservative plastic processes

Non-conservative processes play a fundamental role in plasticity and are behind important macroscopic phenomena such as creep, dynamic strain aging, loop raft formation, etc. In the most general case, vacancy-induced dislocation climb is the operating unit mechanism. While dislocation/vacancy interactions have been modeled in the literature using a variety of methods, the approaches developed rely on continuum descriptions of both the vacancy population and its fluxes. However, there are numerous situations in physics where point defect populations display heterogeneous concentrations and/or non-smooth kinetics. Here, a kinetic Monte Carlo (kMC) approach for modeling vacancy transport in response to arbitrary stress fields is used. Vacancies are treated as point particles and are coupled to the dislocation substructure representing a deformed material via an advection term defined by the local stress gradients. The stress fields and the dislocation substructure are evolved using a discrete dislocation dynamics (DDD) module. To extend the coupled model to the treatment of large systems, we have implemented it in the massively-parallel DDD code ParaDiS. To avoid numerical incompatibilities associated with merging deterministic (DDD) and stochastic (kMC) integration algorithms, we cast the entire elasto-plastic-diffusive problem within a single stochastic framework, taking advantage of a parallel kMC algorithm to evolve the system as a single event-driven process. The large-scale implementation enables the study of the evolution of a variety of dislocation-defect scenarios governed by non-conservative transport kinetics. After carrying out an exhaustive numerical and computational analysis of our parallel algorithm, we show results that emphasize situations where inhomogeneous vacancy dynamics are of relevance, and compare discrete kinetics to continuum solutions for several cases.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Cross-Neutralization of a SARS-CoV-2 Antibody to a Functionally Conserved Site Is Mediated by Avidity

Most antibodies isolated from individuals with coronavirus disease 2019 (COVID-19) are specific to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, COVA1-16 is a relatively rare antibody that also cross-neutralizes SARS-CoV. Here, we determined a crystal structure of the COVA1-16 antibody fragment (Fab) with the SARS-CoV-2 receptor-binding domain (RBD) and negative-stain electron microscopy reconstructions with the spike glycoprotein trimer to elucidate the structural basis of its cross-reactivity. COVA1-16 binds a highly conserved epitope on the SARS-CoV-2 RBD, mainly through a long complementarity-determining region (CDR) H3, and competes with the angiotensin-converting enzyme 2 (ACE2) receptor because of steric hindrance rather than epitope overlap. COVA1-16 binds to a flexible up conformation of the RBD on the spike and relies on antibody avidity for neutralization. These findings, along with the structural and functional rationale for epitope conservation, provide insights for development of more universal SARS-like coronavirus vaccines and therapies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Neutralizing monoclonal antibodies elicited by mosaic RBD nanoparticles bind conserved sarbecovirus epitopes

Increased immune evasion by SARS-CoV-2 variants of concern highlights the need for new therapeutic neutralizing antibodies. Immunization with nanoparticles co-displaying spike receptor-binding domains (RBDs) from eight sarbecoviruses (mosaic-8 RBD-nanoparticles) efficiently elicits cross-reactive polyclonal antibodies against conserved sarbecovirus RBD epitopes. Here, we identified monoclonal antibodies (mAbs) capable of cross-reactive binding and neutralization of animal sarbecoviruses and SARS-CoV-2 variants by screening single mouse B cells secreting IgGs that bind two or more sarbecovirus RBDs. Single-particle cryo-EM structures of antibody-spike complexes, including a Fab-Omicron complex, mapped neutralizing mAbs to conserved class 1/4 RBD epitopes. Structural analyses revealed neutralization mechanisms, potentials for intra-spike trimer cross-linking by IgGs, and induced changes in trimer upon Fab binding. In addition, we identified a mAb-resembling Bebtelovimab, an EUA-approved human class 3 anti-RBD mAb. These results support using mosaic RBD-nanoparticle vaccination to generate and identify therapeutic pan-sarbecovirus and pan-variant mAbs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A conservative, consistent, and scalable meshfree mimetic method

Mimetic methods discretize divergence by restricting the Gauss theorem to mesh cells. Because point clouds lack such geometric entities, construction of a compatible meshfree divergence remains a challenge. In this work, we define an abstract Meshfree Mimetic Divergence (MMD) operator on point clouds by contraction of field and virtual face moments. This MMD satisfies a discrete divergence theorem, provides a discrete local conservation principle, and is first-order accurate. We consider two MMD instantiations. The first one assumes a background mesh and uses generalized moving least squares (GMLS) to obtain the necessary field and face moments. This MMD instance is appropriate for settings where a mesh is available but its quality is insufficient for a robust and accurate mesh-based discretization. The second MMD operator retains the GMLS field moments but defines virtual face moments using computationally efficient weighted graph-Laplacian equations. This MMD instance does not require a background grid and is appropriate for applications where mesh generation creates a computational bottleneck. It allows one to trade an expensive mesh generation problem for a scalable algebraic one, without sacrificing compatibility with the divergence operator. We demonstrate the approach by using the MMD operator to obtain a virtual finite-volume discretization of conservation laws on point clouds. Finally, numerical results in the paper confirm the mimetic properties of the method and show that it behaves similarly to standard finite volume methods.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Implicit fast sweeping method for hyperbolic systems of conservation laws

Implicit time-accurate methods are often used to integrate stiff problems where explicit schemes impose severe time step restrictions. This paper presents an efficient numerical framework based on the Fast Sweeping Method (FSM) for solving linear and nonlinear hyperbolic systems of conservation laws. The solution at each discrete location is computed by sweeping the numerical domain in several predetermined directions that follow the causality of the characteristic families. The use of a fractional step strategy eliminates the need for a solution selection criterion while one-sided stencils limit the number of sweeps to at most 2 d for d space dimensions. This work focuses on the first-order implicit upwind method since it constitutes the building block for high-order conservative schemes. For problems where the degree of stiffness evolves over time, implicit-explicit hybridization can be accomplished with the same algorithm by simply switching the stencil at each time level. As opposed to traditional implicit solvers, the sweeping method does not require a local time linearization of the fluxes thereby preserving the nonlinear stability properties of the original implicit scheme. It also avoids the large computational and memory requirements associated with solving large block-diagonal systems of equations. Here, a series of one- and two-dimensional test cases are presented for the inviscid Burgers' equation and the reactive Euler equations. The results indicate that the implicit FSM can allow a major reduction in the number of time steps even in the presence of discontinuous solution profiles.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

An explicitly solvable energy-conserving algorithm for pitch-angle scattering in magnetized plasmas

In this work, we develop an Explicitly Solvable Energy-Conserving (ESEC) algorithm for the Stochastic Differential Equation (SDE) describing the pitch-angle scattering process in magnetized plasmas. The Cayley transform is used to calculate both the deterministic gyromotion and stochastic scattering, affording the algorithm to be explicitly solvable and exactly energy conserving. An unusual property of the SDE for pitch-angle scattering is that its coefficients diverge at the zero velocity and do not satisfy the global Lipschitz condition. Consequently, when standard numerical methods, such as the Euler-Maruyama (EM), are applied, numerical convergence is difficult to establish. For the proposed ESEC algorithm, its energy-preserving property enables us to overcome this obstacle. We rigorously prove that the ESEC algorithm is order 1/2 strongly convergent. This result is confirmed by detailed numerical studies. For the case of pitch-angle scattering in a magnetized plasma with a constant magnetic field, the numerical solution is benchmarked against the analytical solution, and excellent agreements are found.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Fast nonlinear iterative solver for an implicit, energy-conserving, asymptotic-preserving charged-particle orbit integrator

Here recently, an asymptotic-preserving (AP) particle orbit integrator has been proposed with remarkable properties including exact energy conservation, the ability to capture of all first-order drifts (including the ∇B-drift), the ability to capture trapped-passing boundaries with parallel velocity extremely close to the critical velocity, and the ability to transition from strongly to weakly magnetized spatial regions. The new AP orbit integrator is implicit, employing a Crank-Nicolson (CN) temporal discretization to ensure exact energy conservation. This, in turn, requires a local nonlinear iteration involving particle velocities and positions, and the local electromagnetic fields, to obtain the new-time solution. Ref. [1] did not attempt to provide an efficient solver for this system, and employed a brute-force GMRES-driven Jacobian-free Newton-Krylov (JFNK) solver to invert the particle orbit equations at every timestep for expediency. While JFNK is robust and reliable, it is also expensive and very intrusive for practical implementations of the method (it requires having the JFNK machinery available and solving a 6 x 6 Jacobian system iteratively once per iteration per particle).

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

On the design of stable, consistent, and conservative high-order methods for multi-material hydrodynamics

Obtaining stable and high-order numerical solutions for multi-material hydrodynamics is an open challenge. Although slope limiters are widely used to maintain monotonicity near discontinuities, typical limiting procedures violate closure laws at the discrete level when applied to multi-material hydrodynamics equations. Due to this, the high-order expansions of quantities related by the closure laws are no longer consistent. The commonly observed symptom of this consistency-violation is that the numerical method fails to maintain constant pressure and velocity across material interfaces. This leads to sub-optimal convergence rates for smooth multi-material problems as well. Specialized limiting procedures that satisfy consistency while maintaining conservation need to be developed for such equations. A novel procedure that re-instates consistency into slope-limited high-order discretizations applied to the multi-material hydrodynamics equations is presented here. Using simple examples, it is demonstrated that the presented method satisfies closure laws at the discrete level, while maintaining conservative properties of the high-order method. Furthermore, this procedure involves a projection step which relies on the compact basis of the underlying spatial discretization, i.e. for discontinuous schemes (viz. DG and FV) the projection is local, and does not involve global matrix solves. Comparisons with conventional approaches emphasizes the necessity of the consistent closure-law preserving limiting approach, in order to maintain design order of accuracy for smooth multi-material problems.

36 MATERIALS SCIENCE↗
DOE OSTI2023

An implicit particle code with exact energy and charge conservation for electromagnetic studies of dense plasmas

A collisional particle code based on implicit energy- and charge-conserving methods is presented. A modified version of the particle-suppressed Jacobian-Free Newton-Krylov method that can enhance the solver efficiency is introduced. Mathematically, it is shown that this new approach can be viewed as a fixed-point iteration method for the particle positions. The model can exactly conserve global energy and local charge and can efficiently use time steps larger than the plasma period. In conclusion, the algorithm's ability to simulate dense plasmas accurately and efficiently is quantified by simulating the dynamic compression of a plasma slab via a magnetic piston in 1D planar geometry.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

An implicit particle code with exact energy and charge conservation for studies of dense plasmas in axisymmetric geometries

A collisional particle code based on implicit energy- and charge-conserving methods in axisymmetric geometries is presented. A new particle pusher for axisymmetric systems is introduced that is compatible with exact energy and charge conservation and yields improved accuracy compared to other methods. How to appropriately treat all aspects of the algorithm near the r = 0 axis of symmetry is described in detail. Here, the axisymmetric model is verified by simulating the free expansion of a plasma sphere in 2D cylindrical and 1D spherical geometries. The algorithm's ability to study the dynamic compression of a dense plasma is illustrated by simulating the dynamic Z-pinch in 1D cylindrical geometry.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2026

A conservative discontinuous Galerkin algorithm for particle kinetics on smooth manifolds

A novel, conservative discontinuous Galerkin algorithm is presented for particle kinetics on manifolds. The motion of particles on the manifold is represented using both canonical and non-canonical Hamiltonian formulations. Our schemes apply to both formulations, but the canonical formulation results in a particularly efficient scheme that also conserves particle density and energy exactly. The collisionless update is coupled to a Bhatnagar-Gross-Krook (BGK) collision operator that provides a simplified model for relaxation to local thermodynamic equilibrium. An iterative scheme is constructed to ensure collisional invariants (density, momentum and energy) are preserved numerically. Rotation of the manifold is incorporated by modifying the Hamiltonian while ensuring a canonical formulation. Several test problems, including a kinetic version of the classical Sod shock problem, Kelvin-Helmholtz instability on the surfaces of a sphere and a hyperboloid, with and without rotations, are presented. A prospectus for further development of this approach to simulation of kinetic theory in general relativity is presented.

Discontinuous Galerkin↗
DOE OSTI2025

Identifying Receptor Kinase Substrates Using an 8000 Peptide Kinase Client Library Enriched for Conserved Phosphorylation Sites

In eukaryotic organisms, protein kinases regulate diverse protein activities and signaling pathways through phosphorylation of specific protein substrates. Isolating and characterizing kinase substrates is vital for defining downstream signaling pathways. The kinase-client (KiC) assay is an in vitro synthetic peptide LC-MS/MS phosphorylation assay that has enabled identification of protein substrates (i.e., clients) for various protein kinases. For example, previous use of a 2100-member (2k) peptide library identified substrates for the extracellular ATP receptor-like kinase, P2K1. Many P2K1 clients were confirmed by additional in vitro and in planta studies, including integrin-linked kinase 4, for which we provide the evidence herein. In addition, we developed a new KiC peptide library containing 8000 (8k) peptides based on phosphorylation sites primarily from Arabidopsis thaliana datasets. The 8k peptides are enriched for sites with conservation in other angiosperm plants, with the paired goals of representing functionally conserved sites and usefulness for screening kinases from diverse plants. Screening the 8k library with the active P2K1 kinase domain identified 177 phosphopeptides, including calcineurin B–like protein and G protein alpha subunit 1, which functions in cellular calcium signaling. We confirmed that P2K1 directly phosphorylates calcineurin B–like protein and G protein alpha subunit 1 through in vitro kinase assays. This expanded 8k KiC assay will be a useful tool for identifying novel substrates across diverse plant protein kinases, ultimately facilitating the exploration of previously undiscovered signaling pathways.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Conserved role of ATP synthase in mammalian cilia

Highlights: • ATP synthase localizes to cilia in mammalian cells. • ATP synthase is involved in ciliogenesis. • ATP synthase probably participates in polycystin signalling pathway. We previously found that ATP synthases localize to male-specific sensory cilia and control the ciliary response by regulating polycystin signalling in Caenorhabditis elegans. Herein, we discovered that the ciliary localization of ATP synthase is evolutionarily conserved in mammals. We showed that the ATP synthase subunit F1β is colocalized with the cilia marker acetylated α-tubulin in both mammalian renal epithelial cells (MDCK) and normal mouse cholangiocytes (NMCs). Treatment with ATP synthase inhibitor oligomycin impaired ciliogenesis in MDCK cells, and F1β was co-immunoprecipitated with PKD2 in mammalian cells. Our study provides evidence for the evolutionarily conserved localization of ATP synthase in cilia from worm to mammals. Defects in ATP synthase can lead to ciliary dysfunction, which may be a potential mechanism of polycystic kidney disease.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Structural Conservation of the A 1 Binding Site in Photosystem I across Cyanobacteria and Green Algae

Time-resolved step-scan Fourier transform infrared (FTIR) difference spectroscopy was used to obtain (A 1 − − A 1 ) FTIR difference spectra from photosystem I (PSI) samples isolated from eight phylogenetically diverse cyanobacterial strains and one green alga, totaling 13 PSI preparations. These included samples from cells grown under farred light and PSI in monomeric, dimeric, trimeric, and tetrameric states. Spectral profiles were shown to be independent of oligomeric state. Remarkably, all (A 1 − − A 1 ) FTIR difference spectra exhibited high similarity, underscoring the robustness of the technique and indicating minimal experimental variability. This congruence reveals a highly conserved environment for the phylloquinone cofactor at the A 1 binding site across diverse taxa. Conserved bands associated with the A 0 pigment further suggest structural continuity from A 0 to A 1 . To leverage this consistency, we constructed a composite (A 1 − − A 1 ) FTIR difference spectrum by averaging all 13 spectra. This composite spectrum provides enhanced resolution, enabling unambiguous identification of previously unresolved bands. The fact that a highly resolved composite spectrum can be obtained by averaging demonstrates the similarity in the spectra from the different types of samples. Band assignments were refined using prior studies, yielding an improved spectral framework for future investigations of PSI electron transfer cofactors.

Charge transfer↗
DOE OSTI2024

A Mass‐Conserving‐Perceptron for Machine‐Learning‐Based Modeling of Geoscientific Systems

Although decades of effort have been devoted to building Physical-Conceptual (PC) models for predicting the time-series evolution of geoscientific systems, recent work shows that Machine Learning (ML) based Gated Recurrent Neural Network technology can be used to develop models that are much more accurate. However, the difficulty of extracting physical understanding from ML-based models complicates their utility for enhancing scientific knowledge regarding system structure and function. Here, we propose a physically interpretable Mass-Conserving-Perceptron (MCP) as a way to bridge the gap between PC-based and ML-based modeling approaches. The MCP exploits the inherent isomorphism between the directed graph structures underlying both PC models and GRNNs to explicitly represent the mass-conserving nature of physical processes while enabling the functional nature of such processes to be directly learned (in an interpretable manner) from available data using off-the-shelf ML technology. As a proof of concept, we investigate the functional expressivity (capacity) of the MCP, explore its ability to parsimoniously represent the rainfall-runoff (RR) dynamics of the Leaf River Basin, and demonstrate its utility for scientific hypothesis testing. To conclude, we discuss extensions of the concept to enable ML-based physical-conceptual representation of the coupled nature of mass-energy-information flows through geoscientific systems.

58 GEOSCIENCES↗
DOE OSTI2021

Conserved and reproducible bacterial communities associate with extraradical hyphae of arbuscular mycorrhizal fungi

Abstract Extraradical hyphae (ERH) of arbuscular mycorrhizal fungi (AMF) extend from plant roots into the soil environment and interact with soil microbial communities. Evidence of positive and negative interactions between AMF and soil bacteria point to functionally important ERH-associated communities. To characterize communities associated with ERH and test controls on their establishment and composition, we utilized an in-growth core system containing a live soil–sand mixture that allowed manual extraction of ERH for 16S rRNA gene amplicon profiling. Across experiments and soils, consistent enrichment of members of the Betaproteobacteriales, Myxococcales, Fibrobacterales, Cytophagales, Chloroflexales, and Cellvibrionales was observed on ERH samples, while variation among samples from different soils was observed primarily at lower taxonomic ranks. The ERH-associated community was conserved between two fungal species assayed, Glomus versiforme and Rhizophagus irregularis, though R. irregularis exerted a stronger selection and showed greater enrichment for taxa in the Alphaproteobacteria and Gammaproteobacteria. A distinct community established within 14 days of hyphal access to the soil, while temporal patterns of establishment and turnover varied between taxonomic groups. Identification of a conserved ERH-associated community is consistent with the concept of an AMF microbiome and can aid the characterization of facilitative and antagonistic interactions influencing the plant-fungal symbiosis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Conserved enhancers control notochord expression of vertebrate Brachyury

The cell type-specific expression of key transcription factors is central to development and disease. Brachyury/T/TBXT is a major transcription factor for gastrulation, tailbud patterning, and notochord formation; however, how its expression is controlled in the mammalian notochord has remained elusive. Here, we identify the complement of notochord-specific enhancers in the mammalian Brachyury/T/TBXT gene. Using transgenic assays in zebrafish, axolotl, and mouse, we discover three conserved Brachyury-controlling notochord enhancers, T3, C, and I, in human, mouse, and marsupial genomes. Acting as Brachyury-responsive, auto-regulatory shadow enhancers, in cis deletion of all three enhancers in mouse abolishes Brachyury/T/Tbxt expression selectively in the notochord, causing specific trunk and neural tube defects without gastrulation or tailbud defects. The three Brachyury-driving notochord enhancers are conserved beyond mammals in the brachyury/tbxtb loci of fishes, dating their origin to the last common ancestor of jawed vertebrates. Our data define the vertebrate enhancers for Brachyury/T/TBXTB notochord expression through an auto-regulatory mechanism that conveys robustness and adaptability as ancient basis for axis development.

59 BASIC BIOLOGICAL SCIENCES↗