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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 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Mass spectrometry-based technologies for probing the 3D world of plant proteins

Abstract Over the past two decades, mass spectrometric (MS)-based proteomics technologies have facilitated the study of signaling pathways throughout biology. Nowhere is this needed more than in plants, where an evolutionary history of genome duplications has resulted in large gene families involved in posttranslational modifications and regulatory pathways. For example, at least 5% of the Arabidopsis thaliana genome (ca. 1,200 genes) encodes protein kinases and protein phosphatases that regulate nearly all aspects of plant growth and development. MS-based technologies that quantify covalent changes in the side-chain of amino acids are critically important, but they only address one piece of the puzzle. A more crucially important mechanistic question is how noncovalent interactions—which are more difficult to study—dynamically regulate the proteome’s 3D structure. The advent of improvements in protein 3D technologies such as cryo-electron microscopy, nuclear magnetic resonance, and X-ray crystallography has allowed considerable progress to be made at this level, but these methods are typically limited to analyzing proteins, which can be expressed and purified in milligram quantities. Newly emerging MS-based technologies have recently been developed for studying the 3D structure of proteins. Importantly, these methods do not require protein samples to be purified and require smaller amounts of sample, opening the wider proteome for structural analysis in complex mixtures, crude lysates, and even in intact cells. These MS-based methods include covalent labeling, crosslinking, thermal proteome profiling, and limited proteolysis, all of which can be leveraged by established MS workflows, as well as newly emerging methods capable of analyzing intact macromolecules and the complexes they form. In this review, we discuss these recent innovations in MS-based “structural” proteomics to provide readers with an understanding of the opportunities they offer and the remaining challenges for understanding the molecular underpinnings of plant structure and function.

Plant Sciences↗
DOE OSTI2024

Evolution of Efimov states

The Efimov phenomenon manifests itself as an emergent discrete scaling symmetry in the quantum three-body problem. In the unitarity limit, it leads to an infinite tower of three-body bound states with energies forming a geometric sequence. Here in this work, we study the evolution of these so-called Efimov states using relativistic scattering theory. We identify them as poles of the three-particle S matrix and trace their trajectories in the complex energy plane as they evolve from virtual states through bound states to resonances. We dial the scattering parameters toward the unitarity limit and observe the emergence of the universal scaling of energies and couplings - a behavior known from the non-relativistic case. Interestingly, we find that Efimov resonances follow unusual, cyclic trajectories accumulating at the three-body threshold and then disappear at some values of the two-body scattering length. We propose a partial resolution to this ?missing states? problem.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Insights into negative differential resistance in MoS 2 Esaki diodes: A first-principles perspective

MoS 2 is a two-dimensional material with a band gap depending on the number of layers and tunable by an external electric field. The experimentally observed intralayer band-to-band tunneling and interlayer band-to-band tunneling in this material present an opportunity for new electronic applications in tunnel field-effect transistors. However, such a widely accepted concept has yet to be been supported by theoretical investigations based on first principles. In this paper, using density functional theory, in conjunction with nonequilibrium Green's function techniques and our electric field gating method, enabled by a large-scale computational approach, we study the relation between band alignment and transmission in planar and side-stack MoS 2 p–i–n junction configurations. Here, we demonstrate the presence of negative differential resistance for both in-plane and interlayer current, a staple characteristic of tunnel diode junctions, and analyze the physical origin of such an effect. Electrostatic potentials, the van der Waals barrier, and a complex band analysis are also examined for a thorough understanding of Esaki diodes.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Multiresonant metasurfaces for arbitrarily broad bandwidth pulse chirping and dispersion compensation

Here, we show that ultrathin metasurfaces with a specific multiresonant response can enable simultaneously arbitrarily strong and arbitrarily broadband dispersion compensation, pulse (de)chirping, and compression or broadening. This breakthrough overcomes the fundamental limitations of both conventional nonresonant approaches (bulky) and modern singly resonant metasurfaces (narrowband) for quadratic phase manipulations of electromagnetic signals. The required nonuniform trains of resonances in the electric and magnetic sheet conductivities that completely control phase delay, group delay, and chirp are rigorously derived and the limitations imposed by fundamental physical constraints are thoroughly discussed. Subsequently, a practical, truncated approximation by finite sequences of physically realizable linear resonances is constructed and the associated error is quantified. By appropriate spectral ordering of the resonances, operation can be achieved either in transmission or reflection mode, enabling full space coverage. The proposed concept is not limited to dispersion compensation, but introduces a generic and powerful ultrathin platform for the spatiotemporal control of broadband real-world signals with a myriad of applications in modern optics, microwave photonics, radar, and communication systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Systematic study of the validity of the eikonal model including uncertainties

Nuclear reactions at intermediate beam energies are often interpreted using the eikonal model. In the analysis of complex reaction probes, where few-body reaction methods are needed, the eikonal method may be used as an efficient way for describing the fragment-target reaction process. In this work, we perform a systematic study to test the validity of the eikonal approximation for nucleon-nucleus reactions. We also quantify uncertainties due to the nucleon optical potential on reaction observables. We inspect the validity of the eikonal model and its semiclassical correction by comparing it to exact solutions (obtained from solving the optical-model equation with a finite-differences method) for a wide range of reactions. We also study the effect of relativistic corrections, both kinematic and dynamic, by effectively incorporating the relativistic effects at intermediate energies. The uncertainties from a Bayesian global optical potential (KDUQ) are propagated to the observables of interest. Our study includes neutron and proton reactions on 27 Al , 40 Ca , 90 Zr , and 208 Pb , for a wide range of energies 𝐸 lab = 0–400 MeV. We calculate neutron-total cross sections (elastic and reactions) as well as proton-absorption cross sections as a function of beam energy, using the eikonal model, the eikonal model with a semiclassical correction, and the exact solution. Here, we also compute angular distributions for the methods above. Our results show that for the proton-absorption cross section, the eikonal model can be used down to around 60 MeV and the semiclassical correction extends its use to 30 MeV. However, the validity of the eikonal model for the neutron-total cross section only goes down to ≈120 MeV, a range extended to ≈ 50 MeV when using the semiclassical correction. We find the semiclassical correction to the eikonal model to be less effective in describing the angular distributions. The 1⁢𝜎 uncertainty intervals on the observables we studied is less than 5% for most of the energies considered, but increases rapidly for higher energies, namely energies outside the range of KDUQ (𝐸 lab > 200MeV).

Cluster models↗
DOE OSTI2023

A Review of Axial Flux Permanent Magnet Machine Technology

Axial flux permanent magnet machines (AFPM) are popular for applications that benefit from high torque density and an axially compact form factor, such as in-wheel traction drives. Although the radial flux permanent magnet machine (RFPM) and the AFPM work based on the same underlying principle, the differences in their geometry introduce complexities in analysis of the AFPM. In this paper, the different AFPM design variants, their sizing approaches, computationally efficient design optimization techniques, and manufacturing techniques reported in literature are reviewed. In addition to classical AFPM machines, emerging variants and research opportunities with potential to push the boundaries of electric machine technology are reviewed. Furthermore, these include bearingless AFPMs, magnetically geared AFPMs, and combined radial-axial flux machines.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2025

Database of low‐temperature absorption and fluorescence spectra of native photosynthetic tetrapyrrole macrocycles

Low-temperature (77 K) absorption and fluorescence spectra of 12 naturally occurring photosynthetic tetrapyrrole macrocycles have been recorded in a frozen glass (2-methyltetrahydrofuran). The compounds encompass distinct chromophore classes: porphyrin, chlorophyll c 2 ; chlorin, chlorophylls a, b, d, f and bacteriochlorophylls c, d, e, f; and bacteriochlorin, bacteriochlorophylls a, b, g. The spectra are compared with those of the same pigment in liquid solution (predominantly 2-methyltetrahydrofuran) at room temperature (293 K). The measured Stokes shifts at 77 K across the 12 macrocycles range from ~30 to 300 cm −1 . The spectral data in digital form are made available as part of the PhotochemCAD databases. Literature searches have revealed extensive published data for Chl a (often in biological matrices) but at best rather limited data for less common macrocycles. The availability of a systematic collection of curated spectral data collected at low temperature should be useful for a variety of assessments, including reconstruction of absorption spectra of (bacterio)chlorophyll-containing protein complexes, vibrational analysis of absorption and fluorescence spectra, and calculations where knowledge of energy levels is important.

Niedzwiedzki, Dariusz M. [Washington University in↗
DOE OSTI2025

Using AI tools to analyze periodic phenomena

Here, in this report, we describe how students can use natural language to prompt ChatGPT to conduct the analysis of complex periodic acceleration data collected using their smartphones. Students may use this approach to characterize human physiological tremor frequency. Students can choose to use their own data, or, for privacy purposes, use an anonymized set of data provided to them.

Klay, Jennifer L. [California Polytechnic State Un↗
DOE OSTI2024

Structure and in vivo psoralen DNA crosslink repair activity of mycobacterial Nei2

Mycobacterium smegmatis Nei2 is a monomeric enzyme with AP β-lyase activity on single-stranded DNA. Expression of Nei2, and its operonic neighbor Lhr (a tetrameric 3'-to-5' helicase), is induced in mycobacteria exposed to DNA damaging agents. Here, we find that nei2 deletion sensitizes M. smegmatis to killing by DNA inter-strand crosslinker trimethylpsoralen but not to crosslinkers mitomycin C and cisplatin. By contrast, deletion of lhr sensitizes to killing by all three crosslinking agents. We report a 1.45 Å crystal structure of recombinant Nei2, which is composed of N and C terminal lobes flanking a central groove suitable for DNA binding. The C lobe includes a tetracysteine zinc complex. Mutational analysis identifies the N-terminal proline residue (Pro2 of the ORF) and Lys51, but not Glu3, as essential for AP lyase activity. We find that Nei2 has 5-hydroxyuracil glycosylase activity on single-stranded DNA that is effaced by alanine mutations of Glu3 and Lys51 but not Pro2. Testing complementation of psoralen sensitivity by expression of wild-type and mutant nei2 alleles in Δnei2 cells established that AP lyase activity is neither sufficient nor essential for crosslink repair. By contrast, complementation of psoralen sensitivity of Δlhr cells by mutant lhr alleles depended on Lhr’s ATPase/helicase activities and its tetrameric quaternary structure. The lhr–nei2 operon comprises a unique bacterial system to rectify inter-strand crosslinks.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Improved Guarantees for Optimal Nash Equilibrium Seeking and Bilevel Variational Inequalities

We consider a class of hierarchical variational inequality (VI) problems that subsumes VI-constrained optimization and several other problem classes, including the optimal solution selection problem and the optimal Nash equilibrium (NE) seeking problem. Our main contribution is threefold. (i) We consider bilevel VIs with monotone and Lipschitz continuous mappings and devise a single-timescale iteratively regularized extragradient method, named IR-EG 𝚖,𝚖 . We improve the existing iteration complexity results for addressing both bilevel VI and VI-constrained convex optimization problems. (ii) Under the strong monotonicity of the outer-level mapping, we develop a method named IR-EG 𝚜,𝚖 and derive faster guarantees than those in (i). We also study the iteration complexity of this method under a constant regularization parameter. These results appear to be new for both bilevel VIs and VI-constrained optimization. (iii) To our knowledge, complexity guarantees for computing the optimal NE in nonconvex settings do not exist. Motivated by this lacuna, we consider VI-constrained nonconvex optimization problems and devise an inexactly projected gradient method, named IPR-EG, where the projection onto the unknown set of equilibria is performed using IR-EG 𝚜,𝚖 with a prescribed termination criterion and an adaptive regularization parameter. We obtain new complexity guarantees in terms of a residual map and an infeasibility metric for computing a stationary point. Here, we validate the theoretical findings using preliminary numerical experiments for computing the best and the worst NEs.

bilevel optimization↗
DOE OSTI2025

Complex deuteron NMR signals

To determine the spin polarization of deuterons, nuclear magnetic resonance (NMR) is used. This is necessary for polarized targets, such as for the upcoming A zz and b 1 experiment at Jefferson Lab. NMR measures the impedance of a solenoid around a deuterated sample. Although the impedance is a complex value, conventionally only the real part of the impedance has been used for this purpose. However, often the tune is not precisely real, meaning the signal has at least some small imaginary portion. This conventionally has been dealt with by an offset parameter, such as Dulya’s false asymmetry method. For vector polarization, this suffices, as the tuning is factored into the overall error of the results, and for a small phase angle doesn’t make much of a difference. However, for tensor polarization, the exact lineshape of the signal is quite significant, and treating the impedance as complex during analysis removes the need for an offset parameter. As a result, it also provides more accurate results, as the conventional false asymmetry method over- or underestimates polarization, depending on the sign of the phase angle.

McClellan, Michael [University of New Hampshire, D↗
DOE OSTI2025

TalkPipe

SAND2025-11168O TalkPipe is a software tool to help users create and manage complex data analysis tasks involving Large Language Models. Its easy-to-use interface allows users to combine different analytical processes. TalkPipe includes a Python library, a scripting language, and can be run in a Docker container, making it simple to customize and extend. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Bauer, Travis [Sandia National Lab. (SNL-CA), Live↗
DOE OSTI2024

WEC as a multiport

SAND2025-00555O WEC as a multiport is a software tool that simplifies the modeling and design of ocean wave energy converters (WECs) using a multi-port network framework in the frequency domain. Users can simulate the dynamic interactions between WECs and ocean waves, optimizing energy extraction and system performance. This tool supports the analysis of complex wave energy systems, aiding in the development of efficient and effective WEC designs. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Coe, Ryan↗
DOE OSTI2023

Data-Driven Transition Path Analysis Yields a Statistical Understanding of Sudden Stratospheric Warming Events in an Idealized Model

Abstract Atmospheric regime transitions are highly impactful as drivers of extreme weather events, but pose two formidable modeling challenges: predicting the next event (weather forecasting) and characterizing the statistics of events of a given severity (the risk climatology). Each event has a different duration and spatial structure, making it hard to define an objective “average event.” We argue here that transition path theory (TPT), a stochastic process framework, is an appropriate tool for the task. We demonstrate TPT’s capacities on a wave–mean flow model of sudden stratospheric warmings (SSWs) developed by Holton and Mass, which is idealized enough for transparent TPT analysis but complex enough to demonstrate computational scalability. Whereas a recent article (Finkel et al. 2021) studied near-term SSW predictability, the present article uses TPT to link predictability to long-term SSW frequency. This requires not only forecasting forward in time from an initial condition, but also backward in time to assess the probability of the initial conditions themselves. TPT enables one to condition the dynamics on the regime transition occurring, and thus visualize its physical drivers with a vector field called the reactive current . The reactive current shows that before an SSW, dissipation and stochastic forcing drive a slow decay of vortex strength at lower altitudes. The response of upper-level winds is late and sudden, occurring only after the transition is almost complete from a probabilistic point of view. This case study demonstrates that TPT quantities, visualized in a space of physically meaningful variables, can help one understand the dynamics of regime transitions.

Meteorology & Atmospheric Sciences↗
DOE OSTI2022

SAXS analysis of the intrinsic tenase complex bound to a lipid nanodisc highlights intermolecular contacts between factors VIIIa/IXa

Abstract The intrinsic tenase (Xase) complex, formed by factors (f) VIIIa and fIXa, forms on activated platelet surfaces and catalyzes the activation of factor X to Xa, stimulating thrombin production in the blood coagulation cascade. The structural organization of the membrane-bound Xase complex remains largely unknown, hindering our understanding of the structural underpinnings that guide Xase complex assembly. Here, we aimed to characterize the Xase complex bound to a lipid nanodisc with biolayer interferometry (BLI), Michaelis–Menten kinetics, and small-angle X-ray scattering (SAXS). Using immobilized lipid nanodiscs, we measured binding rates and nanomolar affinities for fVIIIa, fIXa, and the Xase complex. Enzyme kinetic measurements demonstrated the assembly of an active enzyme complex in the presence of lipid nanodiscs. An ab initio molecular envelope of the nanodisc-bound Xase complex allowed us to computationally model fVIIIa and fIXa docked onto a flexible lipid membrane and identify protein–protein interactions. Our results highlight multiple points of contact between fVIIIa and fIXa, including a novel interaction with fIXa at the fVIIIa A1–A3 domain interface. Lastly, we identified hemophilia A/B-related mutations with varying severities at the fVIIIa/fIXa interface that may regulate Xase complex assembly. Together, our results support the use of SAXS as an emergent tool to investigate the membrane-bound Xase complex and illustrate how mutations at the fVIIIa/fIXa dimer interface may disrupt or stabilize the activated enzyme complex.

Hematology↗
DOE OSTI2022

Theoretical analysis of the role of complex transition dipole phase in XUV transient-absorption probing of charge migration

We theoretically investigate the role of complex dipole phase in the attosecond probing of charge migration. The iodobromoacetylene ion (ICCBr + ) is considered as an example, in which one can probe charge migration by accessing both the iodine and bromine ends of the molecule with different spectral windows of an extreme-ultraviolet (XUV) pulse. The analytical expression for transient absorption shows that the site-specific information of charge migration is encoded in the complex phase of cross dipole products for XUV transitions between the I-4 d and Br-3 d spectral windows. Ab-initio quantum chemistry calculations on ICCBr + reveal that there is a constant π phase difference between the I-4 d and Br-3 d transient-absorption spectral windows, irrespective of the fine-structure energy splittings. Transient absorption spectra are simulated with a multistate model including the complex dipole phase, and the results correctly reconstruct the charge-migration dynamics via the quantum beats in the two element spectral windows, exhibiting out-of-phase oscillations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗