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At least 253 records · Page 14

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DOE OSTI2024

Dephasingless two-color terahertz generation

A laser pulse composed of a fundamental and an appropriately phased second harmonic can drive a time-dependent current of photoionized electrons that generates broadband THz radiation. Over the propagation distances relevant to many experiments, dispersion causes the relative phase between the harmonics to evolve. This “dephasing” slows the accumulation of THz energy and results in a multi-cycle THz pulse with significant angular dispersion. Here, we introduce a novel optical configuration that compensates the relative phase evolution, allowing for the formation of a half-cycle THz pulse with almost no angular dispersion. The configuration uses the spherical aberration of an axilens to map a prescribed radial phase variation in the near field to a desired longitudinal phase variation in the far field. Simulations that combine this configuration with an ultrashort flying focus demonstrate the formation of a half-cycle THz pulse with a controlled emission angle and 1/4 the angular divergence of the multi-cycle pulse created by a conventional optical configuration.

47 OTHER INSTRUMENTATION↗

DOE OSTI2025

Engineering a new tripartite split-ccGFP system from Corynactis californica for detecting protein–protein interactions

Protein-protein interactions (PPIs) are critical to a range of biological processes and, consequently, aberrant interactions are implicated in many disorders. The study of the complex networks of PPIs promises to elucidate undiscovered roles in cellular processes and the mechanisms of disease. To accomplish this, tools to effectively sense PPIs are necessary. Effective PPI sensors must rapidly detect interactions in real-time with high sensitivity without perturbing the proteins of interest (POIs) under study. Split fluorescent proteins have previously been used to successfully monitor PPIs, in part due to the small size of the tags. Here, we developed an optimized tripartite split GFP system based on Corynactis californica GFP (ccGFP) to detect PPIs in vitro. In this sensor system, ccGFP fragments ccGFP10 and ccGFP11 are tagged to two POIs. PPIs can then be detected via fluorescence by complementation to the third fragment, ccGFP1-9, which reconstitutes functional ccGFP. The optimized ccGFP system shows improved detection kinetics and pH and temperature stability compared to a previous system. We then validated the sensor by monitoring PPIs in two model systems: attractive/repulsive coiled-coils and rapamycin-inducible FRB/FKBP heterodimerization. Finally, we developed an anti-tripartite ccGFP single-chain variable fragment (scFv), which could enable versatile detection of identified protein-protein complexes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Defective internal allosteric network imparts dysfunctional ATP/substrate-binding cooperativity in oncogenic chimera of protein kinase A

An aberrant fusion of the DNAJB1 and PRKACA genes generates a chimeric protein kinase (PKA-C DNAJB1 ) in which the J-domain of the heat shock protein 40 is fused to the catalytic α subunit of cAMP-dependent protein kinase A (PKA-C). Deceivingly, this chimeric construct appears to be fully functional, as it phosphorylates canonical substrates, forms holoenzymes, responds to cAMP activation, and recognizes the endogenous inhibitor PKI. Nonetheless, PKA-C DNAJB1 has been recognized as the primary driver of fibrolamellar hepatocellular carcinoma and is implicated in other neoplasms for which the molecular mechanisms remain elusive. Here we determined the chimera’s allosteric response to nucleotide and pseudo-substrate binding. We found that the fusion of the dynamic J-domain to PKA-C disrupts the internal allosteric network, causing dramatic attenuation of the nucleotide/PKI binding cooperativity. Our findings suggest that the reduced allosteric cooperativity exhibited by PKA-C DNAJB1 alters specific recognitions and interactions between substrates and regulatory partners contributing to dysregulation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Pan-cancer proteogenomic investigations identify post-transcriptional kinase targets

Identifying genomic alterations of cancer proteins has guided the development of targeted therapies, but proteomic analyses are required to validate and reveal new treatment opportunities. Herein, we develop a new algorithm, OPPTI, to discover overexpressed kinase proteins across 10 cancer types using global mass spectrometry proteomics data of 1,071 cases. OPPTI outperforms existing methods by leveraging multiple co-expressed markers to identify targets overexpressed in a subset of tumors. OPPTI-identified overexpression of ERBB2 and EGFR proteins correlates with genomic amplifications, while CDK4/6, PDK1, and MET protein overexpression frequently occur without corresponding DNA- and RNA-level alterations. Analyzing CRISPR screen data, we confirm expression-driven dependencies of multiple currently-druggable and new target kinases whose expressions are validated by immunochemistry. Identified kinases are further associated with up-regulated phosphorylation levels of corresponding signaling pathways. Collectively, our results reveal protein-level aberrations—sometimes not observed by genomics—represent cancer vulnerabilities that may be targeted in precision oncology.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Huntingtin structure is orchestrated by HAP40 and shows a polyglutamine expansion-specific interaction with exon 1

Huntington’s disease results from expansion of a glutamine-coding CAG tract in the huntingtin (HTT) gene, producing an aberrantly functioning form of HTT. Both wildtype and disease-state HTT form a hetero-dimer with HAP40 of unknown functional relevance. Here, we demonstrate in vivo and in cell models that HTT and HAP40 cellular abundance are coupled. Integrating data from a 2.6 Å cryo-electron microscopy structure, cross-linking mass spectrometry, small-angle X-ray scattering, and modeling, we provide a near-atomic-level view of HTT, its molecular interaction surfaces and compacted domain architecture, orchestrated by HAP40. Native mass spectrometry reveals a remarkably stable hetero-dimer, potentially explaining the cellular inter-dependence of HTT and HAP40. The exon 1 region of HTT is dynamic but shows greater conformational variety in the polyglutamine expanded mutant than wildtype exon 1. Our data provide a foundation for future functional and drug discovery studies targeting Huntington’s disease and illuminate the structural consequences of HTT polyglutamine expansion.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

The sol–gel autocombustion as a route towards highly CO 2 -selective, active and long-term stable Cu/ZrO 2 methanol steam reforming catalysts

The adaption of the sol-gel autocombustion method to the Cu/ZrO 2 system opens new pathways for the specific optimisation of the activity, long-term stability and CO 2 selectivity of methanol steam reforming (MSR) catalysts. Calcination of the same post-combustion precursor at 400 °C, 600 °C or 800 °C allows accessing Cu/ZrO 2 interfaces of metallic Cu with either amorphous, tetragonal or monoclinic ZrO 2 , influencing the CO 2 selectivity and the MSR activity distinctly different. While the CO 2 selectivity is less affected, the impact of the post-combustion calcination temperature on the Cu and ZrO 2 catalyst morphology is more pronounced. A porous and largely amorphous ZrO 2 structure in the sample, characteristic for sol-gel autocombustion processes, is obtained at 400 °C. This directly translates into superior activity and long-term stability in MSR compared to Cu/tetragonal ZrO 2 and Cu/monoclinic ZrO 2 obtained by calcination at 600 °C and 800 °C. The morphology of the latter Cu/ZrO 2 catalysts consists of much larger, agglomerated and non-porous crystalline particles. Based on aberration-corrected electron microscopy, we attribute the beneficial catalytic properties of the Cu/amorphous ZrO 2 material partially to the enhanced sintering resistance of copper particles provided by the porous support morphology.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Single atoms and small clusters of atoms may accompany Au and Pd dendrimer-encapsulated nanoparticles

Here we report the presence of small clusters of atoms (<1 nm) (SCs) and single atoms (SAs) in solutions containing 1–2 nm dendrimer-encapsulated nanoparticles (DENs). Au and Pd DENs were imaged using aberration-corrected scanning transmission electron microscopy (ac-STEM), and energy dispersive spectroscopy (EDS) was used to identify and quantify the SAs/SCs. Two main findings have emerged from this work. First, the presence or absence of SAs/SCs depends on both the terminal functional group of the dendrimer (–NH 2 or –OH) and the elemental composition of the DENs (Au or Pd). Second, dialysis can be used to remove the majority of SAs/SCs in cases where a high density of SAs/SCs are present. The foregoing conclusions provide insights into the mechanisms for Au and Pd DEN synthesis and stability. Ultimately, these results demonstrate the need for careful characterization of systems containing nanoparticles to ensure that SAs/SCs, which may be below the detection limit of most analytical methods, are taken into consideration (especially for catalysis experiments).

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2025

Building workflows for an interactive human-in-the-loop automated experiment (hAE) in STEM-EELS

Exploring the structural, chemical, and physical properties of matter on the nano- and atomic scales has become possible with the recent advances in aberration-corrected electron energy-loss spectroscopy (EELS) in scanning transmission electron microscopy (STEM). However, the current paradigm of STEM-EELS relies on the classical rectangular grid sampling, in which all surface regions are assumed to be of equal a priori interest. However, this is typically not the case for real-world scenarios, where phenomena of interest are concentrated in a small number of spatial locations, such as interfaces, structural and topological defects, and multi-phase inclusions. One of the foundational problems is the discovery of nanometer- or atomic-scale structures having specific signatures in EELS spectra. Herein, we systematically explore the hyperparameters controlling deep kernel learning (DKL) discovery workflows for STEM-EELS and identify the role of the local structural descriptors and acquisition functions in experiment progression. In agreement with the actual experiment, we observe that for certain parameter combinations the experiment path can be trapped in the local minima. We demonstrate the approaches for monitoring the automated experiment in the real and feature space of the system and knowledge acquisition of the DKL model. Based on these, we construct intervention strategies defining the human-in-the-loop automated experiment (hAE). This approach can be further extended to other techniques including 4D STEM and other forms of spectroscopic imaging. The hAE library is available on Github at https://github.com/utkarshp1161/hAE/tree/main/hAE.

Pratiush, Utkarsh [Univ. of Tennessee, Knoxville, ↗

DOE OSTI2020

Design and performance of a superconducting neutron resonance spin flipper

Despite the challenges, neutron resonance spin echo still holds the promise to improve upon neutron spin echo for the measurement of slow dynamics in materials. We present a bootstrap, radio frequency neutron spin flipper using high temperature superconducting technology capable of flipping neutron spin with either nonadiabatic or adiabatic modes. A frequency of 2 MHz has been achieved, which would achieve an effective field integral of 0.35 T m for a meter of separation in a neutron resonance spin echo spectrometer at the current device specifications. In bootstrap mode, the self-cancellation of Larmor phase aberrations can be achieved with the appropriate selection of the polarity of the gradient coils.

47 OTHER INSTRUMENTATION↗

DOE OSTI2020

On the redistribution of charge in La 0.7 Sr 0.3 CrO 3 /La 0.7 Sr 0.3 MnO 3 multilayer thin films

The atomic and electronic structures of La 0.7 Sr 0.3 MnO 3 (LSMO)/La 0.7 Sr 0.3 CrO 3 (LSCO) multilayer thin films are investigated using aberration corrected scanning transmission electron microscopy (STEM) imaging and spectroscopy. Atomic resolution high angle annular dark-field reveals that LSMO layers have an expanded out-of-plane lattice parameter compared to compressed LSCO layers, contrasting with x-ray diffraction measurements. The expansion is found to result from preferential oxygen vacancy formation in LSMO during STEM sample preparation as determined by electron energy-loss spectroscopy. The La/Sr atom column intensity is also found to oscillate by about 4% between the LSMO and LSCO layers, indicative of La/Sr concentration variation. Using energy-dispersive x-ray spectroscopy in combination with image simulations, we confirm the La/Sr inhomogeneity and elucidate the origin of charge redistribution within the multilayer. These results illuminate the sensitivity of the technique to subtle structural, chemical, and electronic features that can arise to compensate charge imbalances in complex oxide heterostructures.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Dark field proton radiography

A pre- and post-collimation scheme has been applied to high energy proton radiography to establish a dark field condition, which defaults to a state of no transmission until a scatterer is placed at the object plane. This technique, dark field proton radiography, provides two additional capabilities to a standard proton radiography setup. First, protons with a high degree of angular dispersion are removed from the beam, reducing the effects of chromatic aberrations and decreasing noise. Second, protons below the same threshold are removed from the beam downstream of the objects, effectively making the transmission highly sensitive to small amounts of scatter at the object plane. Finally, initial results indicate that the system is highly sensitive to the presence of thinner materials and improves sensitivity to subtle areal density variations in thick objects.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Structure evolution of single-site Pt in a metal–organic framework

Heterogeneous single-metal-site catalyst or single-atom catalyst research has grown rapidly due to the accessibility of modern characterization techniques that can provide invaluable information at the atomic-scale. Herein, we study the structural evolution of isolated single Pt sites incorporated in a metal–organic framework containing bipyridine functional groups using in situ diffuse reflectance infrared Fourier transform spectroscopy with CO as the probe molecule. The structure and electronic properties of the isolated Pt sites are further corroborated by x-ray photoelectron spectroscopy and aberration-corrected scanning transmission electron microscopy. Here, we find the prerequisite of high temperature He treatment for Pt activation and CO insertion and inquire into the structural transformation of Pt site process by dynamic nuclear polarization-enhanced solid-state nuclear magnetic resonance spectroscopy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Correction and verification of x-ray imaging crystal spectrometer analysis on Wendelstein 7-X through x-ray ray tracing

X-ray ray tracing is used to develop ion-temperature corrections for the analysis of the X-ray Imaging Crystal Spectrometer (XICS) used at Wendelstein 7-X (W7-X) and perform verification on the analysis methods. The XICS is a powerful diagnostic able to measure ion-temperature, electron-temperature, plasma flow, and impurity charge state densities. While these systems are relatively simple in design, accurate characterization of the instrumental response and validation of analysis techniques are difficult to perform experimentally due to the requirement of extended x-ray sources. For this reason, a ray tracing model has been developed that allows characterization of the spectrometer and verification of the analysis methods while fully considering the real geometry of the XICS system and W7-X plasma. Through the use of ray tracing, several important corrections have been found that must be accounted for in order to accurately reconstruct the ion-temperature profiles. The sources of these corrections are described along with their effect on the analyzed profiles. The implemented corrections stem from three effects: (1) effect of sub-pixel intensity distribution during de-curving and spatial binning, (2) effect of sub-pixel intensity distribution during forward model evaluation and generation of residuals, and (3) effect of defocus and spherical aberrations on the instrumental response. Possible improvements to the forward model and analysis procedures are explored, along with a discussion of trade-offs in terms of computational complexity. Finally, the accuracy of the tomographic inversion technique in stellarator geometry is investigated, providing for the first time a verification exercise for inversion accuracy in stellarator geometry and a complete XICS analysis tool-chain.

47 OTHER INSTRUMENTATION↗

DOE OSTI2021

Beyond optimization—supervised learning applications in relativistic laser-plasma experiments

We explore the applications of machine learning techniques in relativistic laser-plasma experiments beyond optimization purposes. We predict the beam charge of electrons produced in a laser wakefield accelerator given the laser wavefront change caused by a deformable mirror. Machine learning enables feature analysis beyond merely searching for an optimal beam charge, showing that specific aberrations in the laser wavefront are favored in generating higher beam charges. Supervised learning models allow characterizing the measured data quality as well as recognizing irreproducible data and potential outliers. Furthermore, we also include virtual measurement errors in the experimental data to examine the model robustness under these conditions. This work demonstrates how machine learning methods can benefit data analysis and physics interpretation in a highly nonlinear problem of relativistic laser-plasma interaction.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

CO 2 laser heating system for in situ radial x-ray absorption at 16-BM-D at the Advanced Photon Source

Here we present a portable CO 2 laser heating system for in situ x-ray absorption spectroscopy (XAS) studies at 16-BM-D (High Pressure Collaborative Access Team, Advanced Photon Source, Argonne National Laboratory). Back scattering optical measurements are made possible by the implementation of a Ge beamsplitter. Optical pyrometry is conducted in the near-infrared, and our temperature measurements are free of chromatic aberration due to the implementation of the peak-scaling method and mode scrambling of the input signal. Laser power stabilization is established using electronic feedback, providing a steady power over second timescales - crucial for longer XAS collections. Examples of in situ high pressure–temperature extended x-ray absorption fine structure measurements of ZrO 2 are presented to demonstrate this new capability.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Modeling of high intensity orbital angular momentum beams for laser–plasma interactions

In this work, we explore the field of high intensity orbital angular momentum (OAM) beams, their generation with spiral phase mirrors, and the theory behind modeling both ideal and realistic beams. We explore OAM beam asymmetries introduced by aberrations in the beam, manufacturing defects, and bandwidth. A full three-dimensional description of the paraxial Laguerre–Gaussian (LG) modes suitable for modeling beams down to f/2 focal geometries is derived. A perturbative approach to modeling asymmetric OAM beams is introduced showing that only three LG modes are sufficient to model a wide variety of OAM asymmetries. The models are compared with experimental results followed by a discussion on the future of high intensity OAM beams in plasma physics.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

Meter-scale plasma waveguides for multi-GeV laser wakefield acceleration

Here, we present results from two new techniques for the generation of meter-scale, low density (~10 17 cm -3 on axis) plasma waveguides, the “two-Bessel” technique, and the “self-waveguiding” technique. Plasma waveguides of this density and length range are needed for demonstration of a ~10 GeV laser wakefield accelerator module, key for future staging for a ~TeV lepton collider. Both techniques require the use of high quality ultrashort pulse Bessel beams to efficiently and uniformly ionize hydrogen gas in meter-scale supersonic gas jets via optical field ionization. We review these two techniques, describe our meter-scale gas jets, and present a new method for correction of optical aberrations in Bessel beams. Finally, we briefly present results from recent experiments employing one of our techniques, demonstrating quasi-monoenergetic acceleration of ~5 GeV electron bunches in 20 cm long, low density plasma waveguides.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2023

Interface atomic structures in a cadmium arsenide/III–V semiconductor heterostructure

The interface atomic structure between an epitaxial thin film of the prototype topological semimetal cadmium arsenide (Cd 3 As 2 ) and a III–V semiconductor layer is investigated using high-angle annular dark-field imaging in an aberration-corrected scanning transmission electron microscope. We find that the interface unit cell adopts a defined stoichiometry that is CdSb-like, which is achieved through the insertion of periodically arranged Cd vacancies in the terminating Cd-plane of Cd 3 As 2 . This interface stoichiometry is consistent with the Sb-termination of the III–V layer and the fact that CdSb is the thermodynamically stable phase in the Cd–Sb binary system. We find at least two distinct alignments of the film with respect to the buffer layer, which are characterized by a $\frac{1}{4}$ <100> Cd 3 As 2 shift parallel to the interface. We show that steps of half unit cell height in the III–V layer can produce these distinct interface structures.

74 ATOMIC AND MOLECULAR PHYSICS↗