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DOE OSTI2020

Imaging Supramolecular Morphogenesis with Confocal Laser Scanning Microscopy at Elevated Temperatures

The morphogenesis of supramolecular assemblies is a highly dynamic process that has only recently been recognized, and our understanding of this phenomenon will require imaging techniques capable of crossing scales. Shape transformations depend both on the complex energy landscapes of supramolecular systems and the kinetically controlled pathways that define their structures and functions. We report here the use of confocal laser scanning microscopy coupled with a custom-designed variable-temperature sample stage that enables in situ observation of such shape changes. The submicrometer resolution of this technique allows for real-time observation of the nanostructures in the native liquid environments in which they transform with thermal energy. We use this technique to study the temperature-dependent morphogenic behavior of peptide amphiphile nanofibers and photocatalytic chromophore amphiphile nanoribbons. Furthermore, the variable-temperature confocal microscopy technique demonstrated in this work can sample a large volume and provides real-time information on thermally induced morphological changes in the solution.

36 MATERIALS SCIENCE↗

DOE OSTI2018

Anomalous Shape Evolution of Ag 2 O 2 Nanocrystals Modulated by Surface Adsorbates during Electron Beam Etching

An understanding of nanocrystal shape evolution is significant for the design, synthesis, and applications of nanocrystals with surface-enhanced properties such as catalysis or plasmonics. Surface adsorbates that are selectively attached to certain facets may strongly affect the atomic pathways of nanocrystal shape development. However, it is a great challenge to directly observe such dynamic processes in situ with a high spatial resolution. In this work, we report the anomalous shape evolution of Ag 2 O 2 nanocrystals modulated by the surface adsorbates of Ag clusters during electron beam etching, which is revealed through in situ transmission electron microscopy (TEM). In contrast to the Ag 2 O 2 nanocrystals without adsorbates, which display the near-equilibrium shape throughout the etching process, Ag 2 O 2 nanocrystals with Ag surface adsorbates show distinct facet development during etching by electron beam irradiation. Three stages of shape changes are observed: a sphere-to-a cube transformation, side etching of a cuboid, and bottom etching underneath the surface adsorbates. We find that the Ag adsorbates modify the Ag 2 O 2 nanocrystal surface configuration by selectively capping the junction between two neighboring facets. They prevent the edge atoms from being etched away and block the diffusion path of surface atoms. Finally, our findings provide critical insights into the modulatory function of surface adsorbates on the shape control of nanocrystals.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2026

Operando Depth-Resolved Measurement of Solvation Entropy, Interfacial Transport, and Charge-Transfer Kinetics in Lithium-Ion Batteries

Understanding and improving the performance and longevity of lithium-ion batteries critically depends on insight into the dynamic processes occurring at buried electrode-electrolyte interfaces. However, direct, depth-resolved, and operando diagnosis of these interfaces remains a longstanding challenge due to their inaccessibility beneath bulk materials, the limitations of conventional surface- and bulk-sensitive characterization tools, and the difficulty of maintaining realistic cell environments during measurement. These challenges have made it nearly impossible to uniquely resolve important interfacial properties such as charge transfer resistance, SEI (solid electrolyte interphase) resistance, and solvation entropy at the individual electrode interfaces within a working cell, information that is essential for mechanistic insight and accelerated battery design. Here, in this study, we report the development of multiharmonic electro-thermal spectroscopy (METS), an operando technique that enables depth-resolved measurement of solvation entropy, interfacial transport resistance, charge-transfer resistance, and SEI resistance at individual electrode-electrolyte interfaces within practical lithium-ion batteries. By leveraging frequency-dependent, thermal-wave sensing and interface-specific modeling, METS uniquely attributes interfacial properties to specific electrodes, as validated by comparison with traditional electrochemical impedance spectroscopy (EIS). The ability to spatially and temporally resolve interfacial processes in real time provides new diagnostic capabilities that are crucial for mechanistic studies of battery degradation and for the rapid development of next-generation energy storage systems.

Chalise, Divya [University of California, Berkeley↗

DOE OSTI2021

Visualizing Lithium Dendrite Formation within Solid-State Electrolytes

Solid-state electrolyte (SSE) is promising for application in allsolid-state lithium metal batteries because of its reliable safety and longevity. The failure of SSE to suppress dendrite formation of Li metal anodes has been conventionally explained by uneven Li deposition at Li/SSE interfaces and its subsequent dendritic growth. While Li deposition within SSE has been recently proposed as another key cause for SSE failure, little is known regarding the Li growth details inside the SSE itself. In this work, we performed in situ microscopic observation of Li deposition inside the SSE and obtained visualized evidence regarding the dynamic process of Li dendrite formation and growth. Here, Li is seen to directly nucleate and propagate within the SSE, leading to its structural cracking. Such behavior should be caused by the presence of P- and S-based crystalline defects in Li 3 PS 4 SSE, which is consistent with the cryo-transmission electron microscopy observations and theoretical calculations. This observation provides important insights into the growth mechanisms of Li dendrites within a working lithium battery.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Stimulated Nucleation of Skyrmions in a Centrosymmetric Magnet

Understanding the dynamics of skyrmion nucleation and manipulation is important for applications in spintronic devices. In this contribution, the spin textures at magnetic domain-boundaries stimulated by application of in-plane magnetic fields in a centrosymmetric kagome ferromagnet, Fe 3 Sn 2 , with thickness gradient are investigated using Lorentz transmission electron microscopy. Switching of the in-plane magnetic field is shown to induce a reversible transformation from magnetic stripes to skyrmions, or vice versa, at the interface between differently oriented domains. Micromagnetic simulations combined with experiments reveal that the rotatable anisotropy and thickness dependence of the response to the external in-plane field are the critical factors for the skyrmion formation. In addition, it is shown that the helicity of skyrmions can also be controlled using this dynamic process. Finally, the results suggest that magnetic materials with rotatable anisotropy are potential skyrmionic systems and provides a different approach for nucleation and manipulation of skyrmions in spintronic devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2016

Atomistic-scale simulations of defect formation in graphene under noble gas ion irradiation

Despite the frequent use of noble gas ion irradiation of graphene, the atomistic-scale details, including the effects of dose, energy, and ion bombardment species on defect formation, and the associated dynamic processes involved in the irradiations and subsequent relaxation have not yet been thoroughly studied. Here, we simulated the irradiation of graphene with noble gas ions and the subsequent effects of annealing. Lattice defects, including nanopores, were generated after the annealing of the irradiated graphene, which was the result of structural relaxation that allowed the vacancy-type defects to coalesce into a larger defect. Larger nanopores were generated by irradiation with a series of heavier noble gas ions, due to a larger collision cross section that led to more detrimental effects in the graphene, and by a higher ion dose that increased the chance of displacing the carbon atoms from graphene. Overall trends in the evolution of defects with respect to a dose, as well as the defect characteristics, were in good agreement with experimental results. In addition, the statistics in the defect types generated by different irradiating ions suggested that the most frequently observed defect types were Stone-Thrower-Wales (STW) defects for He + irradiation and monovacancy (MV) defects for all other ion irradiations.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Impact of Photon Recycling, Grain Boundaries, and Nonlinear Recombination on Energy Transport in Semiconductors

Energy carrier transport and recombination in semiconductors can be directly monitored with optical microscopy, revealing key insights into fundamental photophysics and informs efficient optoelectronic device design. Oftentimes, energy transport is measured by monitoring a time-resolved expanding carrier profile after optical excitation under a focused laser beam. Although this approach has gained widespread adoption, the presence of competing dynamic processes, such as diffusion and photon recycling, has made it difficult to accurately extract and understand important semiconductor properties. Here, we develop and apply a new framework for modeling energy transport in both excitonic and free carrier semiconductors. Here, we demonstrate that processes such as nonlinear recombination and photon recycling can have a significant impact on the apparent energy carrier profiles, especially for excitonic materials with short radiative lifetimes. Additionally, we find that film microstructure can lead to unique transport profiles that strongly depends on material boundary behavior and the difference between feature size and diffusion length. Here, these findings provide a deeper understanding of energy transport in semiconducting materials and provide new strategies for the design and optimization of electronic and optoelectronic devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

A High-Fidelity Molecular Model of the Cu(111) Repeating Unit

Dynamic processes at surfaces are central to heterogeneous catalysis, but their atomistic mechanism(s) can prove difficult to elucidate due to variations in material structure and the corresponding impact on reactivity. Moreover, disparities between reaction conditions and those employed for spectroscopic characterization at surfaces can inhibit detailed understanding of catalysis-relevant chemistries. Herein, we substantiate the so-called “cluster-surface” analogy by leveraging a low-valent tricopper architecture ( 1 ) as a model system for small molecule activation at Cu(111). Two reaction classes are explored: the adsorption of carbon monoxide (CO) and the dissociative adsorption of dihydrogen (H 2 ). These processes serve as an ideal testbed to compare the reactivity of a molecular cluster ( 1 ) to that of a heterogeneous surface, as both reactions have empirical data from measurements performed on crystalline Cu(111). Cluster 1 reversibly binds CO. Variable temperature NMR analysis with 13 CO reveals a favorable enthalpy but large negative entropy (−5.1 kcal × mol –1 and −22.9 cal × mol –1 × K –1 , respectively) for CO binding, affording a process that is marginally endergonic at room temperature (ΔG ads (298.15 K) = 1.7 ± 0.5 kcal × mol –1 ). Similarly, analogous to a Cu(111) surface, 1 is shown to oxidatively add (chemisorb) H 2 . Kinetic parameters were determined for this process and the activation enthalpy (8.4 ± 0.5 kcal × mol –1 ) closely mirrors that established for H 2 binding at the Cu(111) facet (6.0 to 12.4 kcal × mol –1 ). Together, these results showcase that a trinuclear cluster can reproduce the small molecule binding and activation energetics of a bulk crystalline surface, setting the stage for studying less-defined surface processes in an atomically precise molecular setting.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2019

Mechanisms of Methane Hydrate Formation in Geological Systems

Natural gas hydrate is ice-like mixture of gas (mostly methane) and water that is widely found in sediments along the world's continental margins and within and beneath permafrost and glaciers in a near-surface depth interval where the pressure is sufficiently high and temperature sufficiently low for gas hydrate to be stable. We categorize the myriad of geological gas hydrate deposits into five characteristic types. We then review the multiple quantitative models that have proposed to describe the genesis of these deposits and describe how each may have formed. We emphasize the importance of coupling multiphase flow (free gas and liquid water) and multicomponent reactive transport with geological history to describe the dynamical processes of gas hydrate formation and evolution in geological systems. A better insight into the kinetics of methane formation from microbial biogenesis and the processes of multiphase flow at the pore scale will advance our knowledge of how these systems form. By understanding the generation and evolution of gas hydrate through time, we will better decipher the role of gas hydrate in the carbon cycle, its potential to contribute to climate change and geohazards, and how to design optimal strategies for gas production from hydrate reservoirs.

58 GEOSCIENCES↗

DOE OSTI2021

Atmospheric River Lifecycle Responses to the Madden‐Julian Oscillation

Abstract We investigate how the Madden‐Julian Oscillation (MJO), the dominant mode of tropical subseasonal variability, modulates the lifecycle of cool‐season North Pacific atmospheric rivers (ARs). When the enhanced (suppressed) convection center is located over the Indian Ocean (western Pacific), more AR events originate over eastern Asia and with fewer over the subtropical northern Pacific. When the enhanced (suppressed) convection is over the western Pacific (Indian Ocean), the opposite changes occur, with more AR events originate over the subtropical northern Pacific and fewer over eastern Asia. Dynamical processes involving anomalous MJO wind and seasonal mean moisture are found to be the dominant factors impacting these variations in AR origins. The MJO‐related anomalous geopotential height patterns are also shown to modulate the propagation of the AR events. These MJO–AR lifecycle relationships are further supported by model simulations.

Zhou, Yang↗

DOE OSTI2022

Importance of the Antarctic Slope Current in the Southern Ocean Response to Ice Sheet Melt and Wind Stress Change

Abstract We use two coupled climate models, GFDL‐CM4 and GFDL‐ESM4, to investigate the physical response of the Southern Ocean to changes in surface wind stress, Antarctic meltwater, and the combined forcing of the two in a pre‐industrial control simulation. The meltwater cools the ocean surface in all regions except the Weddell Sea, where the wind stress warms the near‐surface layer. The limited sensitivity of the Weddell Sea surface layer to the meltwater is due to the spatial distribution of the meltwater fluxes, regional bathymetry, and large‐scale circulation patterns. The meltwater forcing dominates the Antarctic shelf response and the models yield strikingly different responses along West Antarctica. The disagreement is attributable to the mean‐state representation and meltwater‐driven acceleration of the Antarctic Slope Current (ASC). In CM4, the meltwater is efficiently trapped on the shelf by a well resolved, strong, and accelerating ASC which isolates the West Antarctic shelf from warm offshore waters, leading to strong subsurface cooling. In ESM4, a weaker and diffuse ASC allows more meltwater to escape to the open ocean, the West Antarctic shelf does not become isolated, and instead strong subsurface warming occurs. The CM4 results suggest a possible negative feedback mechanism that acts to limit future melting, while the ESM4 results suggest a possible positive feedback mechanism that acts to accelerate melt. Our results demonstrate the strong influence the ASC has on governing changes along the shelf, highlighting the importance of coupling interactive ice sheet models to ocean models that can resolve these dynamical processes.

Beadling, R. L.↗

DOE OSTI2021

Multiscale Simulation of Precipitation Over East Asia by Variable Resolution CAM-MPAS

This study evaluates the precipitation over East Asia simulated by the variable resolution CAM-MPAS featuring the Model for Prediction Across Scales (MPAS) atmospheric dynamical core coupled with the physics parameterizations of the Community Atmosphere Model (CAM) version 5.4. Two CAM-MPAS experiments, one with a global quasi-uniform resolution mesh of 120 km (MPAS-UR) and the other with a variable resolution mesh of 30 to 120 km refined over East Asia (MPAS-VR), are conducted from 1989 to 2005 following the Atmospheric Model Intercomparison Project protocol. Two regional climate model simulations at ~25 km resolution from the Coordinated Regional Downscaling Experiment East Asia second plan are also analyzed for comparison. Results show that CAM-MPAS performs better than the selected regional models in simulating the precipitation climatology over East Asia. Compared with MPAS-UR, MPAS-VR with refinement over East Asia better simulates the precipitation over and around the Tibetan Plateau (TP), the frequency distribution of light, moderate, and heavy precipitation in various regions of China, and the interannual precipitation pattern associated with the East Asian summer monsoon. The improvements in MPAS-VR relative to MPAS-UR largely come from the decreased grid spacing rather than the use of finer-scale terrain information. Particularly, decreased grid spacing is more essential for simulating the precipitation magnitude over TP and the location of peak precipitation south of TP, likely due to the better resolved physical and dynamical processes associated with orographic precipitation. The 30-120 km CAM-MPAS model is shown to be a promising tool for precipitation simulation over East Asia.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Coupling Warm Rain With an Eddy Diffusivity/Mass Flux Parameterization: 1. Model Description and Validation

A new version of the stochastic multiplume Jet Propulsion Laboratory Eddy-Diffusivity/Mass-Flux (JPL-EDMF) parameterization which consistently couples the simplified Khairoutdinov and Kogan (2000), https://doi.org/10.1175/1520-0493(2000)128<0229:ANCPPI>2.0.CO;2, warm phase cloud microphysical parameterization with the parameterization of cloud macrophysical and subgrid scale dynamical processes is described. The new parameterization combines the EDMF approach with an assumed shape of a joint probability density function of thermodynamic and kinematic variables which provide the basis for the computation of all parameterized processes. As far as we are aware this is the first attempt to consistently couple all of these parameterized processes in the EDMF framework. This paper is part one of a two paper series. Here, the JPL-EDMF parameterization is described and benchmark simulations of precipitating stratocumulus and cumulus convection are performed in a single-column-model framework. The parameterization results compare favorably to the reference large-eddy-simulation results. In the second part (Smalley et al., 2022, https://doi.org/10.1029/2021MS002729) the JPL-EDMF parameterization is validated for a wide range of observation-based scenarios covering the continuous transition from subtropical stratocumulus to cumulus convection derived from global reanalysis, and parameterization uncertainties are studied in detail.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Quantification of Physical and Numerical Mixing in a Coastal Ocean Model Using Salinity Variance Budgets

Numerical mixing, the spurious mixing primarily generated by the discretization of advection, is often significant in estuarine and coastal models due to sharp, energetic fronts. In this study, we compare on- and offline estimates of numerical mixing in a submesoscale-resolving realistic simulation of the ocean state over the Texas-Louisiana continental shelf. While offline estimates of numerical mixing differ from online estimates, offline methods may be the only analysis available. This study offers insight into the differences between the on- and offline methods. We use two methods to estimate numerical mixing offline, based on salinity squared $s^2$ and volume-mean salinity variance $s^{\prime^2}$. Numerical mixing estimated from the $s^{\prime^2}$ budget is generally within 60\% of the magnitude for the online method but captures the temporal variability well. However, the $s^2$ budget compares poorly due to larger truncation errors associated with the tendency and advection terms, which can be reduced by increasing the model output frequency. We also investigate the effects of horizontal resolution on numerical mixing using a two-way nested grid. The volume-integrated numerical mixing constitutes 57\% of the bulk physical mixing -- the mixing prescribed by the turbulence closure scheme -- in the coarse model and may exceed the physical mixing by half an order of magnitude. We find that numerical mixing is reduced by 35\% on average in the nested model, less than expected based on scaling of the numerical mixing for an upwind advection scheme, likely due to new dynamical processes that emerge in the nested simulation.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Coupled Transport, Reactivity, and Mechanics in Fractured Shale Caprocks

Abstract Shales are low‐permeability caprocks that confine fluid, such as CO 2 , nuclear waste, and hydrogen, in storage formations. Stress‐induced fractures in shale caprocks provide pathways for fluid to leak and potentially contaminate fresh water aquifers. Fractured shales are also increasingly considered as resources for CO 2 sequestration, enhanced geothermal, and unconventional energy recovery. Injecting reactive fluids into shales introduces chemical disequilibrium, causing an onset of a series of dissolution, precipitation, and fines mobilization mechanisms. The reactions have rapid kinetics and significant impact on porosity and permeability; consequently, flow and storage properties of caprocks. While previous research has explored the separate effects of these reactions, this study aims to uncover their simultaneous occurrence and collective influence. This study unveils these highly coupled transport and reactivity mechanisms by tracking and visualizing the reaction‐induced alterations in the matrix, microcracks, and fractures of shales over time. We conducted brine injection experiments sequentially at pH 4 and 2 in a naturally fractured Wolfcamp shale sample while simultaneously imaging the dynamic processes using X‐ray computed tomography (CT). CT images are validated by finer resolution images obtained using micro‐CT and scanning electron microscopy. We also tracked the sample permeability and fluid chemistry using brine permeability and inductively coupled plasma mass spectrometry, respectively. Findings show that fluid primarily flowed through fractures, dissolving reactive minerals and mobilizing fines on fracture surfaces. Dissolution of fracture asperities under confining stress resulted in the closing of fractures. Clogging in narrow fracture pathways, caused by fines accumulation, diverted fluid flow into matrix pores.

58 GEOSCIENCES↗

DOE OSTI2026

Capturing Secondary Kinetic Instabilities in Three‐Dimensional Dayside Reconnection Using an Improved Gradient‐Based Closure

Magnetic reconnection is a highly dynamic process that excites a wide variety of kinetic waves and instabilities. Transverse current sheet instabilities such as the lower-hybrid drift and secondary drift-kink instabilities in particular have been shown by kinetic simulations to modify the reconnection and introduce significant turbulence and mixing to the reconnection layer. Past studies using the ten-moment fluid model to capture important kinetic physics such as the electron inertia and full representation of the pressure tensor proved advantageous to a two-fluid representation of reconnection, but the model struggled when using a local relaxation closure for the heat flux to replicate the current sheet instabilities and subsequent mixing seen in kinetic simulations. This work uses the Gkeyll software framework to perform simulations of asymmetric reconnection based on the 16 October 2015 MMS crossing of a diffusion region, the Burch event. An improved gradient-based heat flux closure is implemented, showing significant improvement in secondary kinetic instabilities that grow in the current sheet. These instabilities generate turbulence which leads to growth of secondary magnetic islands and flux ropes.

Bradshaw, K. [Princeton University, NJ (United Sta↗

DOE OSTI2016

Phase retrieval by coherent modulation imaging

Phase retrieval is a long-standing problem in imaging when only the intensity of the wavefield can be recorded. Coherent diffraction imaging (CDI) is a lensless technique that uses iterative algorithms to recover amplitude and phase contrast images from diffraction intensity data. For general samples, phase retrieval from a single diffraction pattern has been an algorithmic and experimental challenge. Here we report a method of phase retrieval that uses a known modulation of the sample exit-wave. This coherent modulation imaging (CMI) method removes inherent ambiguities of CDI and uses a reliable, rapidly converging iterative algorithm involving three planes. It works for extended samples, does not require tight support for convergence, and relaxes dynamic range requirements on the detector. CMI provides a robust method for imaging in materials and biological science, while its single-shot capability will benefit the investigation of dynamical processes with pulsed sources, such as X-ray free electron laser.

36 MATERIALS SCIENCE↗

DOE OSTI2016

The ReaxFF reactive force-field: Development, applications, and future directions

The reactive force-field (ReaxFF) interatomic potential is a powerful computational tool for exploring, developing and optimizing material properties. Methods based on the principles of quantum mechanics (QM), while offering valuable theoretical guidance at the electronic level, are often too computationally intense for simulations that consider the full dynamic evolution of a system. Alternatively, empirical interatomic potentials that are based on classical principles require significantly fewer computational resources, which enables simulations to better describe dynamic processes over longer timeframes and on larger scales. Such methods, however, typically require a predefined connectivity between atoms, precluding simulations that involve reactive events. The ReaxFF method was developed to help bridge this gap. Approaching the gap from the classical side, ReaxFF casts the empirical interatomic potential within a bond-order formalism, thus implicitly describing chemical bonding without expensive QM calculations. As a result, this article provides an overview of the development, application, and future directions of the ReaxFF method.

97 MATHEMATICS AND COMPUTING↗