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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 OSTI2023

Broadening a SARS-CoV-1–neutralizing antibody for potent SARS-CoV-2 neutralization through directed evolution

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) underscores the need for strategies to rapidly develop neutralizing monoclonal antibodies that can function as prophylactic and therapeutic agents and to help guide vaccine design. Here, we demonstrate that engineering approaches can be used to refocus an existing antibody that neutralizes one virus but not a related virus. Through a rapid affinity maturation strategy, we engineered CR3022, a SARS-CoV-1–neutralizing antibody, to bind to the receptor binding domain of SARS-CoV-2 with >1000-fold increased affinity. The engineered CR3022 neutralized SARS-CoV-2 and provided prophylactic protection from viral challenge in a small animal model of SARS-CoV-2 infection. Deep sequencing throughout the engineering process paired with crystallographic analysis of engineered CR3022 elucidated the molecular mechanisms by which the antibody can accommodate sequence differences in the epitopes between SARS-CoV-1 and SARS-CoV-2. This workflow provides a blueprint for the rapid broadening of neutralization of an antibody from one virus to closely related but resistant viruses.

Biochemistry & Molecular Biology↗
DOE OSTI2021

Nonlinear Interface Reduction for Time-Domain Analysis of Hurty/Craig-Bampton Superelements with Frictional Contact

Virtual prototyping in engineering design relies today on modern numerical models of contacting structures with accurate resolution of interface mechanics, which strongly affect the system-level stiffness and energy dissipation due to frictional losses. High-fidelity modeling within the localized interfaces is required to resolve local quantities of interest that may drive design decisions. The high-resolution finite element meshes necessary to resolve inter-component stresses tend to be computationally expensive, particularly when the analyst is interested in response time histories. The Hurty/Craig-Bampton (HCB) transformation is a widely used method in structural dynamics for reducing the interior portion of a finite element model while having the ability to retain all nonlinear contact degrees of freedom (DOF) in physical coordinates. These models may still require many DOF to adequately resolve the kinematics of the interface, leading to inadequate reduction and computational savings. This study proposes a novel interface reduction method to overcome these challenges by means of system-level characteristic constraint (SCC) modes and properly orthogonal interface modal derivatives (POIMDs) for transient dynamic analyses. Both SCC modes and POIMDs are computed using the reduced HCB mass and stiffness matrices, which can be directly computed from many commercial finite element analysis software. Comparison of time history responses to an impulse-type load in a mechanical beam assembly indicate that the interface-reduced model correlates well with the HCB truth model. Localized features like slip and contact area are well-represented in the time domain when the beam assembly is loaded with a broadband excitation. The proposed method also yields reduced-order models with greater critical timestep lengths for explicit integration schemes.

42 ENGINEERING↗
DOE OSTI2025

Data and Code for Understanding Generative AI Content with Embedding Models

This repository contains code for the experiments in the paper "Understanding Generative AI Content with Embedding Models". Constructing high-quality features is critical to any quantitative data analysis. While feature engineering was historically addressed by carefully hand-crafting data representations based on domain expertise, deep neural networks (DNNs) now offer a radically different approach. DNNs implicitly engineer features by transforming their input data into hidden feature vectors called embeddings. For embedding vectors produced by foundation models -- which are trained to be useful across many contexts -- we demonstrate that simple and well-studied dimensionality-reduction techniques such as Principal Component Analysis uncover inherent heterogeneity in input data concordant with human-understandable explanations. Of the many applications for this framework, we find empirical evidence that there is intrinsic separability between real samples and those generated by artificial intelligence (AI).

Vargas, Max [Pacific Northwest National Laboratory↗
DOE OSTI2021

Inhibition of Pyruvate Kinase From Thermoanaerobacterium saccharolyticum by IMP Is Independent of the Extra-C Domain

The pyruvate kinase (PYK) isozyme from Thermoanaerobacterium saccharolyticum (TsPYK) has previously been used in metabolic engineering for improved ethanol production. This isozyme belongs to a subclass of PYK isozymes that include an extra C-domain. Like other isozymes that include this extra C-domain, we found that TsPYK is activated by AMP and ribose-5-phosphate (R5P). Our use of sugar-phosphate analogs generated a surprising result in that IMP and GMP are allosteric inhibitors (rather than activators) of TsPYK. We believe this to be the first report of any PYK isozyme being inhibited by IMP and GMP. A truncated protein that lacks the extra C-domain is also inhibited by IMP. A screen of several other bacterial PYK enzymes (include several that have the extra-C domain) indicates that the inhibition by IMP is specific to only a subset of those isozymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural basis for inhibition of coagulation factor VIII reveals a shared antigenic hotspot on the C1 domain

Hemophilia A arises from dysfunctional or deficient coagulation factor (F)VIII and leads to inefficient fibrin clot formation and uncontrolled bleeding events. The development of antibody inhibitors is a clinical complication in hemophilia A patients receiving FVIII replacement therapy. LE2E9 is an anti-C1 domain inhibitor previously isolated from a mild/moderate hemophilia A patient and disrupts FVIII interactions with von Willebrand factor and FIXa, though the intermolecular contacts that underpin LE2E9-mediated FVIII neutralization are undefined. To determine the structure of the complex between FVIII and LE2E9 and characterize its mechanism of inhibition. FVIII was bound to the antigen binding fragment (Fab) of NB2E9, a recombinant construct of LE2E9, and its structure was determined by cryogenic electron microscopy. Here, this report communicates the 3.46 Å structure of FVIII bound to NB2E9, with its epitope comprising FVIII residues S2040 to Y2043, K2065 to W2070, and R2150 to H2155. Structural analysis reveals that the LE2E9 epitope overlaps with portions of the epitope for 2A9, a murine-derived inhibitor, suggesting that these residues represent a shared antigenic region on the C1 domain between FVIII –/– mice and hemophilia A patients. Furthermore, the FVIII:NB2E9 structure elucidates the orientation of the LE2E9 glycan, illustrating how the glycan sterically blocks interactions between the FVIII C1 domain and the von Willebrand factor D' domain. A putative model of the FVIIIa:FIXa complex suggests potential clashing between the NB2E9 glycan and FIXa light chain. These results describe an antigenic “hotspot” on the FVIII C1 domain and provide a structural basis for engineering FVIII replacement therapeutics with reduced antigenicity.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Light-Modulated Self-Assembly of Synthetic Nanotubes

Artificial biomolecular polymers with the capacity to respond to stimuli are emerging as a key component to the development of living materials and synthetic cells. Here, in this work, we demonstrate artificial DNA tubular nanostructures that form in response to light in a dose-dependent manner. These nanotubes assemble from programmable DNA tile motifs that are engineered to include a UV-responsive domain so that UV irradiation activates nanotube self-assembly. We demonstrate that the nanotube formation speed can be tuned by adjusting the UV dose. We then couple the light-dependent activation of tiles with RNA transcription, making it possible to control nanotube formation via concurrent physical and biochemical stimuli. Finally, we illustrate how UV activation effectively controls nanotube assembly in confinement as a rudimentary stimulus-responsive cytoskeletal system that can achieve various conformations in a minimal synthetic cell. This study contributes new tile designs that are immediately useful to building biomolecular scaffolds with controllable dynamics in response to multiple stimuli.

DNA nanotechnology↗
DOE OSTI2021

Driving magnetic domains at the nanoscale by interfacial strain-induced proximity

Here, we investigate the local nanoscale changes of the magnetic anisotropy of a Ni film subject to an inverse magnetostrictive effect by proximity to a V 2 O 3 layer. Using temperature-dependent photoemission electron microscopy (PEEM) combined with X-ray magnetic circular dichroism (XMCD), direct images of the Ni spin alignment across the first-order structural phase transition (SPT) of V 2 O 3 were obtained. We find an abrupt temperature-driven reorientation of the Ni magnetic domains across the SPT, which is associated with a large increase of the coercive field. Moreover, angular dependent ferromagnetic resonance (FMR) shows a remarkable change in the magnetic anisotropy of the Ni film across the SPT of V 2 O 3 . Micromagnetic simulations based on these results are in quantitative agreement with the PEEM data. Direct measurements of the lateral correlation length of the Ni domains from XMCD images show an increase of almost one order of magnitude at the SPT compared to room temperature, as well as a broad spatial distribution of the local transition temperatures, thus corroborating the phase coexistence of Ni anisotropies caused by the V 2 O 3 SPT. We show that the rearrangement of the Ni domains is due to strain induced by the oxide layers’ structural domains across the SPT. Our results illustrate the use of alternative hybrid systems to manipulate magnetic domains at the nanoscale, which allows for engineering of coercive fields for novel data storage architectures.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Interlayer engineering of Fe 3 GeTe 2 : From 3D superlattice to 2D monolayer

The discoveries of ferromagnetism down to the atomically thin limit in van der Waals (vdW) crystals by mechanical exfoliation have enriched the family of magnetic thin films [C. Gong et al., Nature 546 , 265–269 (2017) and B. Huang et al., Nature 546 , 270–273 (2017)]. However, compared to the study of traditional magnetic thin films by physical deposition methods, the toolbox of the vdW crystals based on mechanical exfoliation and transfer suffers from low yield and ambient corrosion problem and now is facing new challenges to study magnetism. For example, the formation of magnetic superlattice is difficult in vdW crystals, which limits the study of the interlayer interaction in vdW crystals [M. Gibertini, M. Koperski, A. F. Morpurgo, K. S. Novoselov, Nat. Nanotechnol. 14 , 408–419 (2019)]. Here, we report a strategy of interlayer engineering of the magnetic vdW crystal Fe 3 GeTe 2 (FGT) by intercalating quaternary ammonium cations into the vdW spacing. Both three-dimensional (3D) vdW superlattice and two-dimensional (2D) vdW monolayer can be formed by using this method based on the amount of intercalant. On the one hand, the FGT superlattice shows a strong 3D critical behavior with a decreased coercivity and increased domain wall size, attributed to the co-engineering of the anisotropy, exchange interaction, and electron doping by intercalation. On the other hand, the 2D vdW few layers obtained by over-intercalation are capped with organic molecules from the bulk crystal, which not only enhances the ferromagnetic transition temperature ( T C ), but also substantially protects the thin samples from degradation, thus allowing the preparation of large-scale FGT ink in ambient environment.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Interface learning of multiphysics and multiscale systems

Complex natural or engineered systems comprise multiple characteristic scales, multiple spatiotemporal domains, and even multiple physical closure laws. To address such challenges, we introduce an interface learning paradigm and put forth a data-driven closure approach based on memory embedding to provide physically correct boundary conditions at the interface. To enable the interface learning for hyperbolic systems by considering the domain of influence and wave structures into account, we put forth the concept of upwind learning toward a physics-informed domain decomposition. The promise of the proposed approach is shown for a set of canonical illustrative problems. Here, we highlight that high-performance computing environments can benefit from this methodology to reduce communication costs among processing units in emerging machine-learning-ready heterogeneous platforms toward exascale era.

42 ENGINEERING↗
DOE OSTI2020

Improved Frequency-Domain Steady-State Modeling of the Dual-Active-Bridge Converter Considering Finite ZVS Transition Time Effects

This article presents an improved analytical modeling (IAM) approach for the dual-active-bridge (DAB) converter in the frequency-domain. Specifically, finite transition times are incorporated into the improved modeling that are significant in DAB converters operated at high frequency. The IAM approach is first motivated by comparing traditional frequency-domain modeling against realistic simulation results in LTspice. Next, the IAM approach is mathematically developed in an iterative fashion, where the conventional frequency-domain approach is used as the initialization of the operational behavior of the converter. Subsequent iterations of the IAM algorithm incorporate finite rise- and falltimes of device output capacitances based on detailed switching behavior analyses, which may considerably perturb the desired modulation parameters (i.e., phase shift and zero states). While the initially proposed IAM approach demonstrates advantages over ideal modeling, it is still shown to exhibit errors when applied to device transitions with significant nonlinearity in parasitic output capacitance. To account for this, a three-slope approximation to the switching transition is then motivated and developed, which enables significantly improved steady-state prediction accuracy. Simulation and experimental results confirm unacceptable inaccuracies associated with the conventional frequency-domain modeling across a wide range of operating conditions, alongside enhanced accuracy provided by the proposed modeling approach.

14 SOLAR ENERGY↗
DOE OSTI2020

Atomic-Scale Imaging of Polarization Switching in an (Anti-)Ferroelectric Memory Material: Zirconia (ZrO2)

Direct, atomic-scale visualization of polarization switching in a functional, polycrystalline, binary oxide via in-situ high-resolution transmission electron microscopy (HRTEM) biasing is reported for the first time. Antiferroelectric (AFE) ZrO2 was used as the model system, which is important for commercial DRAMs and as emerging NVMs (through work-function engineering). We observed (1) clear shifting and coalescing of domains within a single grain, and (2) dramatic changes of the atomic arrangements and crystalline phases—both at voltages above the critical voltage measured for AFE switching. Similar synergistic in-situ structural-electrical characterization can pave the way to understand and engineer microscopic mechanisms for retention, fatigue, variability, sub-coercive switching and analog states in ferroelectric and AFE-based memory devices.

Lombardo, Sarah↗
DOE OSTI2021

Online Detection of Low-Quality Synchrophasor Data Considering Frequency Similarity

Here, this letter proposes a new approach for online detection of low-quality synchrophasor data under both normal and event conditions. The proposed approach utilizes the features of synchrophasor data in time and frequency domains to distinguish multiple regional PMU signals and detect low-quality synchrophasor data. It is more effective to detect low-quality data with apparently indistinguishable profiles. Case studies from recorded synchrophasor measurements verify the effectiveness of the proposed approach for detecting low-quality synchrophasor data in frequency, voltage magnitude and voltage angle.

42 ENGINEERING↗
DOE OSTI2025

Toward engineering lattice structures with the material point method (MPM)

This study examines the potential of two variants of the material point method—the generalized interpolation material point (GIMP) and dual domain material point (DDMP) methods—in developing a robust computational framework for engineering lattice structures under different loading conditions. The study begins with assessing the ability of the two methods in predicting elastic buckling phenomena using column geometries with and without initial geometric imperfections. The results indicate that both methods effectively capture buckling phenomena when initial geometric imperfections are introduced. After this verification step, we create several models of tetrahedral lattice structures with varying strut diameter and orientation and subject them to quasi-static loading. We then validate the numerical results using laboratory test results. The results show that, while both methods accurately predict load–displacement curves in the pre-buckling regime, their predictive capabilities diminish in the post-buckling regime. Through visual comparison between the numerical and experimental deformed shapes, it appears that the discrepancies between model and experimental results are attributed to initial geometric imperfections in the lattices that occurred during 3D printing. We then establish a second set of lattice models where different types of initial geometric imperfections are considered. The results from these models show that imperfections have a negligible influence in the pre-buckling regime but affect the behavior considerably in the post-buckling regime. As a final step in this work, we subject the lattice models to impact loading and employ hypothetical soft and stiff materials. These results show that the lattice stiffness, which depends on material stiffness, strut diameter, and orientation, significantly influences the ability of a lattice structure to resist impact. In particular, we find that a stiffer lattice (i.e., one made with a stiff material and thicker struts) is capable of absorbing more energy than a softer one during impact. Although material nonlinearities, inelasticity, and detailed contact formulations are not considered in this study, the findings obtained herein lay the groundwork for engineering lattice structures under extreme loading conditions through a simulation-driven framework based on particle-based methods.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Controllable Reset Behavior in Domain Wall–Magnetic Tunnel Junction Artificial Neurons for Task-Adaptable Computation

Neuromorphic computing with spintronic devices has been of interest due to the limitations of CMOS-driven von Neumann computing. Domain wall–magnetic tunnel junction (DW-MTJ) devices have been shown to be able to intrinsically capture biological neuron behavior. Edgy-relaxed behavior, where a frequently firing neuron experiences a lower action potential threshold, may provide additional artificial neuronal functionality when executing repeated tasks. In this letter, we demonstrate that this behavior can be implemented in DW-MTJ artificial neurons via three alternative mechanisms: shape anisotropy, magnetic field, and current-driven soft reset. Using micromagnetics and analytical device modeling to classify the Optdigits handwritten digit dataset, we show that edgy-relaxed behavior improves both classification accuracy and classification rate for ordered datasets while sacrificing little to no accuracy for a randomized dataset. This letter establishes methods by which artificial spintronic neurons can be flexibly adapted to datasets.

42 ENGINEERING↗
DOE OSTI2020

GPU acceleration of all-electron electronic structure theory using localized numeric atom-centered basis functions

We present an implementation of all-electron density-functional theory for massively parallel GPU-based platforms, using localized atom-centered basis functions and real-space integration grids. Special attention is paid to domain decomposition of the problem on non-uniform grids, which enables compute- and memory-parallel execution across thousands of nodes for real-space operations, e.g. the update of the electron density, the integration of the real-space Hamiltonian matrix, and calculation of Pulay forces. To assess the performance of our GPU implementation, we performed benchmarks on three different architectures using a 103-material test set. We find that operations which rely on dense serial linear algebra show dramatic speedups from GPU acceleration: in particular, SCF iterations including force and stress calculations exhibit speedups ranging from 4.5 to 6.6. For the architectures and problem types investigated here, this translates to an expected overall speedup between 3–4 for the entire calculation (including non-GPU accelerated parts), for problems featuring several tens to hundreds of atoms. Additional calculations for a 375-atom Bi2Se3 bilayer show that the present GPU strategy scales for large-scale distributed-parallel simulations.

42 ENGINEERING↗
DOE OSTI2024

SEAS Communication Engine: An Extensible, Flexible Wrapper for Co-Simulation Agents

When modeling and analyzing the power grid and other large scale systems, researchers often express scenarios as optimization problems and feed them into advanced software solvers. In order to allow multiple solvers to communicate with each other and share data from different domains, the National Renewable Energy Laboratory (NREL) and associated Department of Energy (DOE) labs have developed a software framework called the Hierarchical Engine for Large-scale Infrastructure Co-Simulation (HELICS). HELICS allows cosimulation via a collection of client libraries for different languages that can be called from the appropriate optimization software. However, these client libraries do not provide a higher level of abstraction beyond reading and writing data off of the shared HELICS bus. In this paper, we describe a new software library called the SEAS Communication Engine that exposes a higher-level API for running cosimulation problems. The SEAS Engine provides a class-based abstraction on top of the Python HELICS client, in order to allow users to implement their domain-specific cosimulations without needing to interact with core HELICS primitives. This will make adoption of HELICS and cosimulation in general easier, by exposing a simpler API. In the second part of the paper, we validate our library on a collection of different simulation examples, including the canonical IEEE 13 Bus Feeder. Lastly, we demonstrate using the SEAS Engine to directly call domain-specific code written in the Julia programming language. Our hope is that this will serve as a template for easily calling software in different programming languages via the SEAS Engine, thereby avoiding code duplication and complexity.

co-simulation↗
DOE OSTI2019

Preferential interactions of primary amine-terminated quantum dots with membrane domain boundaries and lipid rafts revealed with nanometer resolution

The initial interactions of engineered nanoparticles (NPs) with living cells are governed by physicochemical properties of the NP and the molecular composition and structure of the cell membrane. Eukaryotic cell membranes contain lipid rafts – liquid-ordered nanodomains involved in membrane trafficking and molecular signaling. However, the impact of these membrane structures on cellular interactions of NPs remains unclear. Here we investigate the role of membrane domains in the interactions of primary amine-terminated quantum dots (Qdots) with liquid-ordered domains or lipid rafts in model membranes and intact cells, respectively. Using correlative atomic force and fluorescence microscopy, we found that the Qdots preferentially localized to boundaries between liquid-ordered and liquid-disordered phases in supported bilayers. The Qdots also induced holes at these phase boundaries. Using super resolution fluorescence microscopy (STORM), we found that the Qdots preferentially co-localized with lipid rafts in the membrane of intact trout gill epithelial cells – a model cell type for environmental exposures. Our observations uncovered preferential interactions of amine-terminated Qdots with liquid-ordered domains and their boundaries, possibly due to membrane curvature at phase boundaries creating energetically favorable sites for NP interactions. The preferential interaction of the Qdots with lipid rafts supports their potential internalization via lipid raft-mediated endocytosis and interactions with raft-resident signaling molecules.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2021

Manipulating ferroelectric behaviors via electron-beam induced crystalline defects

Ferroelectric nanoplates are attractive for applications in nanoelectronic devices. Defect engineering has been an effective way to control and manipulate ferroelectric properties in nanoscale devices. Defects can act as pinning centers for ferroelectric domain wall motion, altering the switching properties and domain dynamics of ferroelectrics. However, there is a lack of detailed investigation on the interactions between defects and domain walls in ferroelectric nanoplates due to the limitation of previous characterization techniques, which impedes the development of defect engineering in ferroelectric nanodevices. In this study, we applied in situ biasing transmission electron microscopy to explore how dislocation loops, which were judiciously introduced into barium titanate nanoplates via electron beam irradiation, affect the motion of ferroelectric domain walls. The results show that the motion was dramatically suppressed by these localized defects, because of the local strain fields induced by the defects. Additionally, the pinning effect can be further enhanced by multiple domain walls embedded with defect arrays. These results indicate the possibility of manipulating domain switching in ferroelectric nanoplates via the electron beam.

77 NANOSCIENCE AND NANOTECHNOLOGY↗