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DOE OSTI2023

Mechanisms of Biomolecular Self–Assembly Investigated Through In Situ Observations of Structures and Dynamics

Biomolecular self-assembly of hierarchical materials is a precise and adaptable bottom-up approach to synthesizing across scales with considerable energy, health, environment, sustainability, and information technology applications. To achieve desired functions in biomaterials, it is essential to directly observe assembly dynamics and structural evolutions that reflect the underlying energy landscape and the assembly mechanism. This review will summarize the current understanding of biomolecular assembly mechanisms based on in situ characterization and discuss the broader significance and achievements of newly gained insights. In addition, we will also introduce how emerging deep learning/machine learning-based approaches, multiparametric characterization, and high-throughput methods can boost the development of biomolecular self-assembly. Furthermore, the objective of this review is to accelerate the development of in situ characterization approaches for biomolecular self-assembly and to inspire the next generation of biomimetic materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

The Two Arctic Wintertime Boundary Layer States: Disentangling the Role of Cloud and Wind Regimes in Reanalysis and Observations During MOSAiC

The wintertime central Arctic atmosphere comprises a radiatively clear and a radiatively opaque state, which are linked to synoptic forcing and mixed-phase clouds. Weather and climate models often lack process representations surrounding these states, but prior work mostly treated the problem as an aggregate of synoptic conditions, resulting in partially overlapping biases. Here, we disaggregate the Arctic states and confront ERA5 reanalysis with observations from the MOSAiC campaign over the central Arctic sea ice during winter 2019/2020. Low-level winds and liquid water path (LWP) are combined to derive different synoptic classes. Results show that the clear state is primarily formed by weak/moderate winds and the absence of liquid-bearing clouds, while strong winds and enhanced LWP primarily form the radiatively opaque state. ERA5 struggles to reproduce these basic statistics, shows too weak sensitivity of thermal radiation to synoptic forcing, and overestimates thermal radiation for similar LWP amounts. The latter is caused by a warm bias, which has a pronounced inversion structure and is largest in clear and calm conditions. Under strong synoptic forcing, the warm bias is constant with height and discrepancies in mixed-phase cloud altitude appear. Separating synoptic conditions is regarded as useful for process-oriented evaluation of the Arctic troposphere in models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

XAS and EPR in Situ Observation of Ru(V) Oxo Intermediate in a Ru Water Oxidation Complex**

In this study, we combine in situ spectroelectrochemistry coupled with electron paramagnetic resonance (EPR) and X-ray absorption spectroscopies (XAS) to investigate a molecular Rubased water oxidation catalyst bearing a polypyridinic backbone [Ru II (OH 2 )(Py 2 Metacn)] 2+ . Although high valent key intermediate species arising in catalytic cycles of this family of compounds have remain elusive due to the lack of additional anionic ligands that could potentially stabilize them, mechanistic studies performed on this system proposed a water nucleophilic attack (WNA) mechanism for the O O bond formation. Employing in situ experimental conditions and complementary spectroscopic techniques allowed to observe intermediates that provide support for a WNA mechanism, including for the first time a Ru(V) oxo intermediate based on the Py 2 Metacn ligand, in agreement with the previously proposed mechanism

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Indirectly Detected DNP-Enhanced 17 O NMR Spectroscopy: Observation of Non-Protonated Near-Surface Oxygen at Naturally Abundant Silica and Silica-Alumina

Recent studies have shown that dynamic nuclear polarization (DNP) can be used to detect 17 O solid-state NMR spectra of naturally abundant samples within a reasonable experimental time. Observations using indirect DNP, which relies on 1 H mediation in transferring electron hyperpolarization to 17 O, are currently limited mostly to hydroxyls. Direct DNP schemes can hyperpolarize non-protonated oxygen near the radicals; however, they generally offer much lower signal enhancements. In this study, we demonstrate the detection of signals from non-protonated 17 O in materials containing silicon. The sensitivity boost that made the experiment possible originates from three sources: indirect DNP excitation of 29 Si via protons, indirect detection of 17 O through 29 Si nuclei using two-dimensional 29 Si{ 17 O} D-HMQC, and Carr-Purcell-Meiboom-Gill refocusing of 29 Si magnetization during acquisition. This 29 Si-detected scheme enabled, for the first time, 2D 17 O– 29 Si heteronuclear correlation spectroscopy in mesoporous silica and silica-alumina surfaces at natural abundance. In contrast to the silanols showing motion-averaged 17 O signals, the framework oxygens exhibit unperturbed powder patterns as unambiguous fingerprints of surface sites. Furthermore, along with hydroxyl oxygens, detection of these moieties will help in gaining more atomistic-scale insights into surface chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Direct Experimental Observations of Ion Distributions during Overcharging at the Muscovite–Water Interface by Adsorption of Rb + and Halides (Cl – , Br – , I – ) at High Salinity

Classical electric double layer (EDL) models have been widely used to describe ion distributions at charged solid-water interfaces in dilute electrolytes. However, the chemistry of EDLs remains poorly constrained at high ionic strength where ion-ion correlations control non-classical behavior such as overcharging, i. e., the accumulation of counter-ions in amounts exceeding the substrate's surface charge. Here, we provide direct experimental observations of correlated cation and anion distributions adsorbed at the muscovite (001)-aqueous electrolyte interface as a function of dissolved RbBr concentration ([RbBr]=0.01–5.8 M) using resonant anomalous X-ray reflectivity. Our results show alternating cation-anion layers in the EDL when [RbBr]≳100 mM, whose spatial extension (i. e., ~20 Å from the surface) far exceeds the dimension of the classical Stern layer. Comparison to RbCl and RbI electrolytes indicates that these behaviors are sensitive to the choice of co-ion. This new in-depth molecular-scale understanding of the EDL structure during transition from classical to non-classical regimes supports the development of realistic EDL models for technologies operating at high salinity such as water purification applications or modern electrochemical storage.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Nitrification, denitrification, and competition for soil N : Evaluation of two Earth System Models against observations

Abstract Earth System Models (ESMs) have implemented nitrogen (N) cycles to account for N limitation on terrestrial carbon uptake. However, representing inputs, losses, and recycling of N in ESMs is challenging. Here, we use global rates and ratios of key soil N fluxes, including nitrification, denitrification, mineralization, leaching, immobilization, and plant uptake (both NH 4 + and NO 3 − ), from the literature to evaluate the N cycles in the land model components of two ESMs. The two land models evaluated here, E3SM Land Model version 1 (ELMv1)‐ECA and CLM5.0, originated from a common model but have diverged in their representation of plant–microbe competition for soil N. The models predict similar global rates of gross primary productivity (GPP) but have approximately two‐fold to three‐fold differences in their underlying global mineralization, immobilization, plant N uptake, nitrification, and denitrification fluxes. Both models dramatically underestimate the immobilization of NO 3 − by soil bacteria compared with literature values and predict dominance of plant uptake by a single form of mineral nitrogen (NO 3 − for ELM, with regional exceptions, and NH 4 + for CLM5.0). CLM5.0 strongly underestimates the global ratio of gross nitrification:gross mineralization and both models are likely to substantially underestimate the ratio of nitrification:denitrification. Few experimental data exist to evaluate this last ratio, in part because nitrification and denitrification are quantified using different techniques and because denitrification fluxes are difficult to measure at all. More observational constraints on soil nitrogen fluxes such as nitrification and denitrification, as well as greater scrutiny of the functional impact of introducing separate NH 4 + and NO 3 − pools into ESMs, could help to improve confidence in present and future simulations of N limitation on the carbon cycle.

Nevison, Cynthia↗
DOE OSTI2022

Variability in observed stable water isotopes in snowpack across a mountainous watershed in Colorado

In this study, isotopic information from 81 snowpits was collected over a 5-year period in a large, Colorado watershed. Data spans gradients in elevation, aspect, vegetation, and seasonal climate. They are combined with overlapping campaigns for water isotopes in precipitation and snowmelt, and a land-surface model for detailed estimates of snowfall and climate at sample locations. Snowfall isotopic inputs, describe the majority of δ18O snowpack variability. Aspect is a secondary control, with slightly more enriched conditions on east and north facing slopes. This is attributed to preservation of seasonally enriched snowfall and vapour loss in the early winter. Sublimation, expressed by decreases in snowpack d-excess in comparison to snowfall contributions, increases at low elevation and when seasonal temperature and solar radiation are high. At peak snow accumulation, post-depositional fractionation appears to occur in the top 25 ± 14% of the snowpack due to melt-freeze redistribution of lighter isotopes deeper into the snowpack and vapour loss to the atmosphere during intermittent periods of low relative humidity and high windspeed. Relative depth of fractionation increases when winter daytime temperatures are high and winter precipitation is low. Once isothermal, snowpack isotopic homogenization and enrichment was observed with initial snowmelt isotopically depleted in comparison to snowpack and enriching over time. The rate of δ18O increase (d-excess decrease) in snowmelt was 0.02‰ per day per 100-m elevation loss. Isotopic data suggests elevation dictates snowpack and snowmelt evolution by controlling early snow persistence (or absence), isotopic lapse rates in precipitation and the ratio of energy to snow availability. Hydrologic tracer studies using stable water isotopes in basins of large topographic relief will require adjustment for these elevational controls to properly constrain stream water sourcing from snowmelt.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Integrating phytoplankton pigment and DNA meta-barcoding observations to determine phytoplankton composition in the coastal ocean

Quantifying phytoplankton composition is critical to predicting marine ecosystem structure and function. DNA meta-barcoding and high-performance liquid chromatography (HPLC) pigment analysis are two widely used methods for assessing phytoplankton composition; however, comparing their performance has been done only rarely. Here, we integrate DNA meta-barcoding and HPLC pigment observations to determine eukaryotic phytoplankton composition in the Santa Barbara Channel, California. We find that both methods identify the same four dominant eukaryotic phytoplankton taxa (diatoms, dinoflagellates, chlorophytes, and prymnesiophytes), but inter- and intra-lineage variability in biomarker pigmentation (associated with both a lack of taxonomic specificity of biomarker pigments and intrinsic differences in accessory pigmentation) drives substantial disagreement between the methods. Covariation network analysis circumvents this disagreement and reveals that diverse assemblages of phytoplankton and other protists covary with distinct suites of biomarker pigments. Our results highlight the strengths and weaknesses of each method in characterizing phytoplankton composition and reveal novel insights into phytoplankton physiology that could only be gained by integrating the two methods. Finally, we suggest a path to monitor eukaryotic plankton communities on unprecedented spatiotemporal scales based on the covariation of unique phytoplankton and protistan assemblages with remotely sensible phytoplankton pigment concentrations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

1D to 2D Transition in Tellurium Observed by 4D Electron Microscopy

A new microwave-enhanced synthesis method for the production of tellurium nanostructures is reported here—with control over products from the 1D regime (sub-5 nm diameter nanowires), to nanoribbons, to the 2D tellurene regime—along with a new methodology for local statistical quantification of the crystallographic parameters of these materials at the nanometer scale. Using a direct electron detector and image-corrected microscope, large and robust 4D scanning transmission electron microscopy datasets for accurate structural analysis are obtained. These datasets allow the adaptation of quantitative techniques originally developed for X-ray diffraction (XRD) refinement analyses to transmission electron microscopy, enabling the first demonstration of sub-picometer accuracy lattice parameter extraction while also obtaining both the size of the coherent crystallite domains and the nanostrain, which is observed to decrease as nanowires transition to tellurene. This new local analysis is commensurate with global powder XRD results, indicating the robustness of both the new synthesis approach and new structural analysis methodology for future scalable production of 2D tellurene and characterization of nanomaterials.

2D materials↗
DOE OSTI2022

Decoding the Mechanisms of Phase Transitions from In Situ Microscopy Observations

Abstract Analysis of the temperature‐ and stimulus‐dependent imaging data toward elucidation of the physical transformations is an ubiquitous problem in multiple fields. Here, temperature‐induced phase transition in BaTiO 3 is explored using the machine learning analysis of domain morphologies visualized via variable‐temperature scanning transmission electron microscopy (STEM) imaging data. This approach is based on the multivariate statistical analysis of the time or temperature dependence of the statistical descriptors of the system, derived in turn from the categorical classification of observed domain structures or projection on the continuous parameter space of the feature extraction‐dimensionality reduction transform. The proposed workflow offers a powerful tool for the exploration of the dynamic data based on the statistics of image representation as a function of the external control variable to visualize the transformation pathways during phase transitions and chemical reactions. This can include the mesoscopic STEM data as demonstrated here, but also optical, chemical imaging, etc., data. It can further be extended to the higher dimensional spaces, for example, analysis of the combinatorial libraries of materials compositions.

Valleti, Sai Mani Prudhvi↗
DOE OSTI2022

A Survey on Sustainable Software Ecosystems to Support Experimental and Observational Science at Oak Ridge National Laboratory

In the search for a sustainable approach for software ecosystems that supports experimental and observational science (EOS) across Oak Ridge National Laboratory (ORNL), we conducted a survey to understand the current and future landscape of EOS software and data. This paper describes the survey design we used to identify significant areas of interest, gaps, and potential opportunities, followed by a discussion on the obtained responses. The survey formulates questions about project demographics, technical approach, and skills required for the present and the next five years. The study was conducted among 38 ORNL participants between June and July of 2021 and followed the required guidelines for human subjects training. We plan to use the collected information to help guide a vision for sustainable, community-based, and reusable scientific software ecosystems that need to adapt effectively to: i) the evolving landscape of heterogeneous hardware in the next generation of instruments and computing (e.g. edge, distributed, accelerators), and ii) data management requirements for data-driven science using artificial intelligence.

Bernholdt, David↗
DOE OSTI2023

In-Situ Observation of the Formation of Laser-Induced Periodic Surface Structures with Extreme Spatial and Temporal Resolution

Irradiation of solid surfaces with intense ultrashort laser pulses represents a unique way of depositing energy into materials. It allows to realize states of extreme electronic excitation and/or very high temperature and pressure and to drive materials close to and beyond fundamental stability limits. As a consequence, structural changes and phase transitions often occur along unusual pathways and under strongly nonequilibrium conditions. Furthermore, due to the inherent multiscale nature—both temporally and spatially—of these irreversible processes, their direct experimental observation requires techniques that combine high temporal resolution with the appropriate spatial resolution and the capability to obtain good quality data on a single pulse/event basis. In this respect, fourth-generation light sources, namely, short wavelength and short pulse free electron lasers (FELs), are offering new and fascinating possibilities. As an example, this chapter will discuss the results of scattering experiments carried out at the FLASH free electron laser at DESY (Hamburg, Germany), which allowed us to resolve laser-induced structure formation at surfaces on the nanometer to submicron length scale and in temporal regimes ranging from picoseconds to several nanoseconds with sub-picosecond resolution.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Yang-Mills observables: from $\mathrm{KMOC}$ to eikonal through $\mathrm{EFT}$

We obtain a conservative Hamiltonian describing the interactions of two charged bodies in Yang-Mills through $\mathcal{O}$ (α 2 ) and to all orders in velocity. Our calculation extends a recently-introduced framework based on scattering amplitudes and effective field theory (EFT) to consider color-charged objects. These results are checked against the direct integration of the observables in the Kosower-Maybee-O’Connell (KMOC) formalism. At the order we consider we find that the linear and color impulses in a scattering event can be concisely described in terms of the eikonal phase, thus extending the domain of applicability of a formula originally proposed in the context of spinning particles.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Observation of the ${K}^{+}\to {\pi}^{+}\nu \overline{\nu}$ decay and measurement of its branching ratio

A measurement of the ${K}^{+}\to {\pi}^{+}\nu \overline{\nu}$ decay by the NA62 experiment at the CERN SPS is presented, using data collected in 2021 and 2022. This dataset was recorded, after modifications to the beamline and detectors, at a higher instantaneous beam intensity with respect to the 2016–2018 data taking. Combining NA62 data collected in 2016–2022, a measurement $\mathcal{B} ({K}^{+}\to {\pi}^{+}\nu \overline{\nu}) = \large{(}13.0^{+3.3}_{-3.0}\large{)}$ x $10^{-11}$ of is reported. With 51 signal candidates observed and an expected background of $18^{+3}_{-2}$ events, $\mathcal{B} ({K}^{+}\to {\pi}^{+}\nu \overline{\nu})$ becomes the smallest branching ratio measured with a signal significance above 5σ.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2026

Quantum mechanics and observers for gravity in a closed universe

Recent arguments based on the quantum extremal surface formula or the gravitational path integral have given fairly compelling evidence that the Hilbert space of quantum gravity in a closed universe is one-dimensional and real. How can this be consistent with the complexity of our own experiences? In this paper we propose that the experiences of any observer Ob in a closed universe can be approximately described by a quantum mechanical theory with a Hilbert space whose dimension is roughly e S Ob , where S Ob is the number of degrees of freedom of Ob. Moreover we argue that the errors in this description are exponentially small in S Ob . We give evidence for this proposal by incorporating it into the gravitational path integral and the coding interpretation of holography in simple models and seeing that it works, and we explain how similar effects arise in black hole physics in appropriate circumstances.

AdS-CFT Correspondence↗
DOE OSTI2021

Observation of the ${B}_s^0 $ → D*±D∓ decay

A search for the B 0 → D *± D ∓ decay is performed using proton-proton collision data at centre-of-mass energies of 7, 8 and 13 TeV collected by the LHCb experiment, corresponding to an integrated luminosity of 9 fb -1 . The decay is observed with a high significance and its branching fraction relative to the B 0 → D *± D ∓ decay is measured to be $\frac{\mathrm{\mathcal{B}}\left({B}_s^0\to {D}^{\ast \pm }{D}^{\mp}\right)}{\mathrm{\mathcal{B}}\left({B}^0\to {D}^{\ast \pm }{D}^{\mp}\right)}=0.137\pm 0.017\pm 0.002\pm 0.006$, where the first uncertainty is statistical, the second systematic and the third is due to the uncertainty on the ratio of the $B_{s}^{0}$ and $B^{0}$ hadronisation fractions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Observation of $Λ^0_b$ → $D^+ρπ^-π^-$ and $Λ^0_b$ → $D^{*+}ρπ^-π^-$ decays

The multihadron decays $Λ^0_b$ → $D+ρπ-π-$ and $Λ^0_b$ → $D^*+ρπ-π-$ are observed in data corresponding to an integrated luminosity of 3 fb -1 , collected in proton-proton collisions at centre-of-mass energies of 7 and 8 TeV by the LHCb detector. Using the decay $Λ^0_b$ → $Λ^+_cπ^+π^-π^-$ as a normalisation channel, the ratio of branching fractions is measured to be $\frac {\mathcal{B} ( Λ^0_b → D^+ρπ^-π^-)} {\mathcal{B} (Λ^0_b → Λ^0_cπ^+π^-π^-)}$ x $\frac{\mathcal{B} (D^+ → K^-π^+π^+)} {\mathcal{B}(Λ^o_c → ρK^-π^-)}$ = (%.35 ± 0.21 ± 0.16)%, where the first uncertainty is statistical and the second systematic. The ratio of branching fractions for the $Λ^0_b$ → $D^{*+}ρπ^-π^-$ and $Λ^0_b$ → $D^+ρπ^-π^-$ decays is found to be $\frac {\mathcal{B} ( Λ^0_b → D^{*+}ρπ^-π^-)} {\mathcal{B} (Λ^0_b → D^+ρπ^-π^-)}$ X ($\mathcal{B} (D^{*+}→ D^+π^0)$ + $\mathcal{B} (D^{*+}→ D^+γ)$) = (61.3 ± 4.3 ± 4.0)%.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

First observation and study of the $K^± → π^0π^0μ^±ν$ decay

The NA48/2 experiment at CERN reports the first observation of the $K^± → π^0π^0μ^±$ν decay based on a sample of 2437 candidates with 15% background contamination collected in 2003–2004. The decay branching ratio in the kinematic region of the squared dilepton mass above 0.03 GeV 2 /c 4 is measured to be (0.65 ± 0.03) × 10 –6 . The extrapolation to the full kinematic space, using a specific model, is found to be (3.45 ± 0.16) × 10 –6 , in agreement with chiral perturbation theory predictions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗