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DOE OSTI2022

AlphaFold and Structural Mass Spectrometry Enable Interrogations on the Intrinsically Disordered Regions in Cyanobacterial Light-harvesting Complex Phycobilisome

Intrinsically disordered proteins/regions (IDPRs) are a very large and functionally important class of proteins that participate in weak multivalent interactions in protein complexes. They are recalcitrant for interrogations using X-ray crystallography and cryo-EM. The IDPRs observed at the interface of the photosynthetic pigment protein complexes (PPCs) remain much less clear, e.g., the major cyanobacterial light-harvesting complex (PBS) contains an unstructured PB-loop insertion in the phycocyanobilin domain (PB domain) of ApcE (the largest polypeptide in PBS). Here, a joint platform is built to probe such structural domains. This platform is characterized by two-round progressive justifications of in silico models by using the structural mass spectrometry data. First, the AlphaFold-generated 3D structure of the PB domain (containing PB-loop) was justified in the context of PBS. Second, docking the AlphaFold-generated ApcG (a ligand) into the first-step justified structure (a receptor). The final ligand-receptor complex was then subjected to a second-round justification, again, by using unequivocal isotopically-encoded cross-links identified in LC-MS/MS. This work reveals a full-length PB-loop structure modelled in the PBS basal cylinder, free from any spatial conflicts against the other subunits in PBS. The structure of PB domain highlights the close associations of the intrinsically disordered PB-loop with its binding partners in PBS, including ApcG, another IDPR. The PB-loop region involved in the binding of photosystem II (PSII) is also discussed in the context of excitation energy transfer regulation. Finally, this work calls attention to the highly disordered, yet interrogatable interface between the light-harvesting antenna complexes and the reaction centers.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Multidifferential study of identified charged hadron distributions in Z -tagged jets in proton-proton collisions at $\sqrt{s} =13$ TeV

Jet fragmentation functions are measured for the first time in proton-proton collisions for charged pions, kaons, and protons within jets recoiling against a Z boson. The charged-hadron distributions are studied longitudinally and transversely to the jet direction for jets with transverse momentum 20 < p T < 100 GeV and in the pseudorapidity range 2.5 < η <4. The data sample was collected with the LHCb experiment at a center-of-mass energy of 13 TeV, corresponding to an integrated luminosity of 1.64 fb –1 . Triple differential distributions as a function of the hadron longitudinal momentum fraction, hadron transverse momentum, and jet transverse momentum are also measured for the first time. This helps constrain transverse-momentum-dependent fragmentation functions. Differences in the shapes and magnitudes of the measured distributions for the different hadron species provide insights into the hadronization process for jets predominantly initiated by light quarks.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Investigation into the event-activity dependence of $\Upsilon$(nS) relative production in proton-proton collisions at $ \sqrt{s} $ = 7 TeV

The ratios of the production cross sections between the excited ϒ(2S) and ϒ(3S) mesons and the ϒ(1S) ground state, detected via their decay into two muons, are studied as a function of the number of charged particles in the event. The data are from proton-proton collisions at $ \sqrt{s} $ = 7 TeV, corresponding to an integrated luminosity of 4.8 fb$^{−1}$, collected with the CMS detector at the LHC. Evidence of a decrease in these ratios as a function of the particle multiplicity is observed, more pronounced at low transverse momentum $ {p}_{\mathrm{T}}^{\upmu \upmu} $. For ϒ(nS) mesons with $ {p}_{\mathrm{T}}^{\upmu \upmu} $> 7 GeV, where most of the data were collected, the correlation with multiplicity is studied as a function of the underlying event transverse sphericity and the number of particles in a cone around the ϒ(nS) direction. The ratios are found to be multiplicity independent for jet-like events. The mean $ {p}_{\mathrm{T}}^{\upmu \upmu} $ values for the ϒ(nS) states as a function of particle multiplicity are also measured and found to grow more steeply as their mass increases.[graphic not available: see fulltext]

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Quenching of the quantum p -strength in light exotic nuclei

One-nucleon spectroscopic overlaps, their strength or spectroscopic factors (SFs), and nucleon removal cross sections for light nuclei in the mass range A≤12 were evaluated using the fully correlated Quantum Monte Carlo (QMC) wave functions (WFs). Harder (AV18+UX) and softer (NV2+3) bare interactions were used providing consistent results. The SFs were also taken from simple Shell Model (SM) calculations. This structure information was incorporated in the standard three-body Faddeev/Alt-Grassberger-Sandhas reaction formalism to evaluate the (p,pN) cross sections. The results further our understanding of the quenching of the quantum p-shell strength obtained from structure and reactions. We have found the ratios of the total QMC sums of SFs to the SM ones to be uniform and ∼ 3/4. The corresponding ratios of the sums Below Particle Threshold (BPT) of SFs, as well as of total cross sections, deviate strikingly from the uniform trend in some special cases. We find these ratios to be close to unit for 9 Li → 8 Li + n and 9 C → 8 B + p. In contrast, they are strongly reduced for 11 C → 10 C + n and 11 B → 10 Be + p mirror transitions, resulting from the quenching of the strength for low-lying 2 + final state transitions. The QMC theoretical cross section BPT for 11 C(p,pn) is about two times smaller than the experimental data.

(p,pN) reactions↗

DOE OSTI2023

Shaping Nanobodies and Intrabodies against Proteoforms

Proteoforms expand genomic diversity and direct developmental processes. While high-resolution mass spectrometry has accelerated characterization of proteoforms, molecular techniques working to bind, and disrupt the function of specific proteoforms have lagged behind. In this study, we worked to develop intrabodies capable of binding specific proteoforms. Herein we employed a synthetic camelid nanobody library expressed in yeast to identify nanobody binders of different SARS-CoV-2 receptor binding domain (RBD) proteoforms. Importantly, employment of the positive and negative selection mechanism inherent to the synthetic system allowed for amplification of nanobody-expressing yeast that bind to the original (Wuhan strain RBD) but not the E484K (Beta variant) mutation. Nanobodies raised against specific RBD proteoforms were validated by yeast-2-hybrid analysis and sequence comparisons. These results provide a clear framework for development of proteoform-specific nanobodies and intrabodies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Oxidation of Silicon Carbide with Atomic Oxygen through the Passive-to-Active Transition

The inelastic and reactive scattering dynamics of O( 3 P) atoms on a 6H-silicon carbide (SiC) surface were investigated as a function of temperature with a molecular beam-surface scattering technique that employed a rotatable mass spectrometer detector. One set of experiments used a pulsed hyperthermal beam that produced ~8 km s –1 O atoms, and another set of experiments used a continuous beam that contained O atoms with a nominal velocity of ~2 km s –1 . When exposed to the relatively low-flux, pulsed hyperthermal O-atom beam, a passive oxide layer on the SiC that formed at lower temperatures decomposed as the temperature increased above 1673 K. Instead of entering an active oxidation regime, a graphitic layer formed on the surface and largely protected the underlying SiC from incoming O atoms. Investigation of the oxide decomposition without O-atom bombardment revealed volatile Si and SiO products at the moment that the oxide decomposed, implying that Si sublimation occurs concurrently with oxide decomposition. In the experiment with the continuous (higher flux) O-atom beam, volatile SiO and CO products were observed after the passive oxide decomposed, indicating that active oxidation was reached. Finally, the results of this study provide evidence for the importance of Si sublimation within the active oxidation regime. Above the passive-to-active transition temperature, Si sublimation is an ongoing process, and continuous active oxidation will only occur if sufficient oxygen reacts with the surface to produce SiO more quickly than a graphitic layer can form. Thus, accurate models of SiC ablation by atomic oxygen must account for multiple competing mechanisms that depend on the surface temperature and incident O-atom flux.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Moments of the Boltzmann collision operator for Coulomb interactions

Exact moments of the Boltzmann collision operator are calculated in the irreducible Hermitian moment expansion written in terms of the random-velocity variable of each species. The formulas are presented in closed, algebraic form and can be straightforwardly implemented in computer algebra systems. They are valid for two arbitrary masses, temperatures, and flow velocities, and hence include all other existing results derived for distribution functions expanded with respect to reference states of one temperature and flow velocity. In comparison, the Landau collisional moments are good approximations for large Coulomb logarithm and small relative flow velocity, but they fail to predict the correct behavior of most collisional moments for large relative flow even for weakly coupled plasmas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2023

The simulated catalogue of optical transients and correlated hosts (SCOTCH)

ABSTRACT As we observe a rapidly growing number of astrophysical transients, we learn more about the diverse host galaxy environments in which they occur. Host galaxy information can be used to purify samples of cosmological Type Ia supernovae, uncover the progenitor systems of individual classes, and facilitate low-latency follow-up of rare and peculiar explosions. In this work, we develop a novel data-driven methodology to simulate the time-domain sky that includes detailed modelling of the probability density function for multiple transient classes conditioned on host galaxy magnitudes, colours, star formation rates, and masses. We have designed these simulations to optimize photometric classification and analysis in upcoming large synoptic surveys. We integrate host galaxy information into the snana simulation framework to construct the simulated catalogue of optical transients and correlated hosts (SCOTCH, a publicly available catalogue of 5-million idealized transient light curves in LSST passbands and their host galaxy properties over the redshift range 0 < z < 3. This catalogue includes supernovae, tidal disruption events, kilonovae, and active galactic nuclei. Each light curve consists of true top-of-the-galaxy magnitudes sampled with high (≲2 d) cadence. In conjunction with SCOTCH, we also release an associated set of tutorials and transient-specific libraries to enable simulations of arbitrary space- and ground-based surveys. Our methodology is being used to test critical science infrastructure in advance of surveys by the Vera C. Rubin Observatory and the Nancy G. Roman Space Telescope.

Astronomy & Astrophysics↗

DOE OSTI2025

Measurements of hadron production in 90 GeV/𝑐 proton-carbon interactions

This paper presents the multiplicity of neutral and charged hadrons produced in 90 GeV/𝑐 proton-carbon interactions from a dataset taken by the NA61/SHINE experiment in 2017. Particle identification via d⁢𝐸/d⁢𝑥 was performed for the charged hadrons 𝜋 ± , 𝐾 ± , and $p/\bar{p}$; the neutral hadrons $K^0_S$, $Λ$, and $\bar{Λ}$ were identified via an invariant mass analysis of their decays to charged hadrons. Double-differential multiplicity results as a function of laboratory momentum and polar angle are presented for each particle species; these results provide vital constraints on the predicted neutrino beam flux for current and future long-baseline neutrino oscillation experiments.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Centrality and transverse-momentum dependence of higher-order flow harmonics of identified hadrons in Au+Au collisions at s N N = 200 GeV

Here we present high-precision measurements of elliptic, triangular, and quadrangular flow v 2 , v 3 , and v 4 , respectively, at midrapidity for identified hadrons π, p, K, φ, K s , Λ as a function of centrality and transverse momentum in Au+Au collisions at the center-of-mass energy √ s NN = 200 GeV. We observe similar v n trends between light and strange mesons which indicates that the heavier strange quarks flow as strongly as the lighter up and down quarks. The number-of-constituent-quark scaling for v 2 , v 3 , and v 4 is found to hold within statistical uncertainty for 0–10%, 10–40%, and 40–80% collision centrality intervals. The results are compared to several viscous hydrodynamic calculations with varying initial conditions, and could serve as an additional constraint to the development of hydrodynamic models.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2021

Detecting the stochastic gravitational wave background from massive gravity with pulsar timing arrays

We explore the potential of pulsar timing arrays (PTAs) such as NANOGrav, EPTA, and PPTA to detect the stochastic gravitational wave background in theories of massive gravity. In general relativity, the function describing the dependence of the correlation between the arrival times of signals from two pulsars on the angle between them is known as the Hellings-Downs curve. We compute the analogous overlap reduction function for massive gravity, including the additional polarization states and the correction due to the mass of the graviton, and compare the result with the Hellings-Downs curve. The primary result is a complete analytical form for the analog Hellings-Downs curve, providing a starting point for future numerical studies aimed at a detailed comparison between PTA data and the predictions of massive gravity. We study both the massless limit and the stationary limit as checks on our calculation, and discuss how our formalism also allows us to study the impact of massive spin-2 dark matter candidates on data from PTAs.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2021

Visualizing electron localization of WS 2 /WSe 2 moiré superlattices in momentum space

The search for materials with flat electronic bands continues due to their potential to drive strong correlation and symmetry breaking orders. Electronic moirés formed in van der Waals heterostructures have proved to be an ideal platform. However, there is no holistic experimental picture for how superlattices modify electronic structure. By combining spatially resolved angle-resolved photoemission spectroscopy with optical spectroscopy, we report the first direct evidence of how strongly correlated phases evolve from a weakly interacting regime in a transition metal dichalcogenide superlattice. By comparing short and long wave vector moirés, we find that the electronic structure evolves into a highly localized regime with increasingly flat bands and renormalized effective mass. The flattening is accompanied by the opening of a large gap in the spectral function and splitting of the exciton peaks. These results advance our understanding of emerging phases in moiré superlattices and point to the importance of interlayer physics.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Heterologous synthesis of a simplified nitrogenase analog in Escherichia coli

The heterologous synthesis of a nitrogen-fixing system in a non-diazotrophic organism is a long-sought-after goal because of the crucial importance of nitrogenase for agronomy, energy, and the environment. Here, we report the heterologous synthesis of a two-component nitrogenase analog fromAzotobacter vinelandii, which consists of the reductase component (NifH) and the cofactor maturase (NifEN), inEscherichia coli. Metal, electron paramagnetic resonance, and activity analyses verify the cluster composition and functional competence of the heterologously expressed NifH and NifEN. Nuclear magnetic resonance, nanoscale secondary ion mass spectrometry, and growth experiments further illustrate the ability of the NifH/NifEN system to reduce N 2 and incorporate the reduced N into the cellular mass. These results establish NifEN/NifH as a simplified nitrogenase analog that could be optimized and engineered to facilitate transgenic expression and biotechnological adaptations of this important metalloenzyme.

Science & Technology - Other Topics↗

DOE OSTI2020

In situ electrochemical scanning/transmission electron microscopy of electrode–electrolyte interfaces

Insights into the dynamics of electrochemical processes are critically needed to improve our fundamental understanding of electron, charge, and mass transfer mechanisms and reaction kinetics that influence a broad range of applications, from the functionality of electrical energy-storage and conversion devices (e.g., batteries, fuel cells, and supercapacitors), to materials degradation issues (e.g., corrosion and oxidation), and materials synthesis (e.g., electrodeposition). To unravel these processes, in situ electrochemical scanning/transmission electron microscopy (ec-S/TEM) was developed to permit detailed site-specific characterization of evolving electrochemical processes that occur at electrode–electrolyte interfaces in their native electrolyte environment, in real time and at high-spatial resolution. This approach utilizes “closed-form” microfabricated electrochemical cells that couple the capability for quantitative electrochemical measurements with high spatial and temporal resolution imaging, spectroscopy, and diffraction. Here, we review the state-of-the-art instrumentation for in situ ec-S/TEM and how this approach has resulted in new observations of electrochemical processes.

25 ENERGY STORAGE↗

DOE OSTI2022

Di-$\pi^0$ correlations in p+p, p+Al and p+Au collisions at $\sqrt{s_{NN}}$ = 200 GeV at STAR

The STAR Collaboration reports measurements of back-to-back azimuthal correlations of di- \pi^0 π 0 produced at forward pseudorapidity ( 2.6<\eta<4.0 2.6 < η < 4.0 ) in p+ p + p p , p+ p + \mathrm{Al} A l and p+ p + \mathrm{Au} A u collisions at a center-of-mass energy per nucleon-nucleon pair of 200 GeV. A clear suppression of the correlated away-side yields is observed in p+ p + \mathrm{Au} A u and for the first time in p+ p + \mathrm{Al} A l collisions, compared with the p p + + p p data. The enhanced suppression found in p+ p + \mathrm{Au} A u with respect to p+ p + \mathrm{Al} A l collisions exhibits the saturation scale ( Q_s^2 Q s 2 ) dependence on the mass number A A . The observed suppression of back-to-back pairs as a function of event activity and transverse momentum points to non-linear gluon dynamics arising at high parton densities.

Chu, Xiaoxuan↗

DOE OSTI2023

Oak Ridge Subcritical Assembly Final Design and Current Progress [Slides]

This presentation shows how ORSA design has moved from conceptual to implementable. Additionally, that the ORSA hands-on experiments will remain subcritical under normal and credible abnormal conditions it is fully assembled k eff = 0.95024 ± 0.0003 and USL = 0.9763. This presentation finds locations will have minimal security and safety basis impact. Available options can meet security criteria for ORSA material and Options will have less mass than the ANS-8.1 single parameter limit for 235 U either by segregation or functioning as its own facility. Further, Locations are feasible for a diversity of students and the implementation of ORSA will improve upon NCSP T&E’s vision to remain adaptable and responsive.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2022

Current Progress of the Final Design of a Subcritical Assembly at Oak Ridge National Laboratory [Slides]

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2024

Air Carbon for Algae Production (AirCAP) – Expanding algae resource potential via direct (in-pond) air-CO2 capture.

Microalgae biofuel production potential in the United States is constrained by a lack of suitable cultivation locations within a close proximity to CO2 point-sources. Initial estimates suggest that removing the requirement of a concentrated CO2 source expands resource potential ten-fold, allowing the projection of production levels that approach levels of current U.S. diesel consumption. Decoupling cultivation locations from concentrated CO2 point-sources requires direct capture of air-CO2 into the pond bulk at a rate sufficient to meet maximum expected carbon assimilation rates (10 g C/m2-day and higher). Enhancement of the ingassing rate via chemical reaction, the direct reaction of dissolved CO2 with hydroxide ions, has been proposed as a mechanism to increase the ingassing rate of air-CO2. The central objectives of this project are to validate whether chemically enhanced air-CO2 ingassing rates in large raceway ponds can meet or exceed the level required to support high levels of algae productivity, then subsequently identify alkaliphilic strains able to withstand such conditions while maintaining a biomass productivity that enables process economics. Full scale ponds (~1 acre, unlined) will be used to validate ingassing rates as a function of pH expected at scale in a series of abiotic experiments. To date, mass-transfer dynamics have been characterized in ponds ranging from 1 to 1,000 m2. Initial results will be presented describing the mass transfer coefficient in 1-acre (~4,000 m2), unlined ponds. The maximum expected carbon ingassing rate will be measured during ingassing trials, in which pond pH is displaced from equilibrium via the addition of a strong base, with the subsequent decrease in pH (and increase in dissolved inorganic carbon) corresponding to the air-CO2 absorption rate. A mass-transfer model, validated with experimental results, will be used to project ingassing rates expected at pond scales (10 acres) required for production of commodity chemicals.

09 BIOMASS FUELS↗