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DOE OSTI2023

Video-rate Raman-based metabolic imaging by Airy light-sheet illumination and photon-sparse detection

Despite its massive potential, Raman imaging represents just a modest fraction of all research and clinical microscopy to date. This is due to the ultralow Raman scattering cross-sections of most biomolecules that impose low-light or photon-sparse conditions. Bioimaging under such conditions is suboptimal, as it either results in ultralow frame rates or requires increased levels of irradiance. Here, we overcome this tradeoff by introducing Raman imaging that operates at both video rates and 1,000-fold lower irradiance than state-of-the-art methods. To accomplish this, we deployed a judicially designed Airy light-sheet microscope to efficiently image large specimen regions. Further, we implemented subphoton per pixel image acquisition and reconstruction to confront issues arising from photon sparsity at just millisecond integrations. We demonstrate the versatility of our approach by imaging a variety of samples, including the three-dimensional (3D) metabolic activity of single microbial cells and the underlying cell-to-cell variability. To image such small-scale targets, we again harnessed photon sparsity to increase magnification without a field-of-view penalty, thus, overcoming another key limitation in modern light-sheet microscopy.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Shear-based deformation processing of age-hardened aluminum alloy for single-step sheet production

Shear-based deformation processing by hybrid cutting-extrusion and free machining are used to make continuous strip, of thickness up to one millimeter, from low-workability AA6013-T6 in a single deformation step. The intense shear can impose effective strains as large as 2 in the strip without pre-heating of the workpiece. The creation of strip in a single step is facilitated by three factors inherent to the cutting deformation zone: highly confined shear deformation, in situ plastic deformation-induced heating and high hydrostatic pressure. The hybrid cutting-extrusion, which employs a second die located across from the primary cutting tool to constrain the chip geometry, is found to produce strip with smooth surfaces (S a < 0.4 μm) that is similar to cold-rolled strip. The strips show an elongated grain microstructure that is inclined to the strip surfaces – a shear texture – that is quite different from rolled sheet. Furthermore, this shear texture (inclination) angle is determined by the deformation path. Through control of the deformation parameters such as strain and temperature, a range of microstructures and strengths could be achieved in the strip. When the cutting-based deformation was done at room temperature, without workpiece pre-heating, the starting T6 material was further strengthened by as much as 30% in a single step. In elevated-temperature cutting-extrusion, dynamic recrystallization was observed, resulting in a refined grain size in the strip. Implications for deformation processing of age-hardenable Al alloys into sheet form, and microstructure control therein, are discussed.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Sensitivities of the West Greenland Current to Greenland Ice Sheet Meltwater in a Mesoscale Ocean/Sea Ice Model

Abstract Meltwater from the Greenland Ice Sheet can alter the continental shelf/slope circulation and cross-shelf freshwater fluxes and limit deep convection in adjacent basins through surface freshening. We explore the impacts on the West Greenland Current and eastern Labrador Sea with different vertical distributions of the meltwater forcing. In this study, we present the results from global coupled ocean/sea ice simulations, forced with atmospheric reanalysis, that are mesoscale eddy-active (∼2–3-km horizontal spacing) and eddy-permitting (∼6–7-km horizontal spacing) in the study region. We compare the West Greenland Current in mesoscale eddy-active and eddy-permitting without meltwater to highlight the role of small-scale features. The mesoscale eddy-active configuration is then used to assess the change in the eastern Labrador Sea when meltwater is added to the surface or vertically distributed to account for mixing within fjords. In both simulations with meltwater, the West Greenland and West Greenland Coastal Currents are faster than in the simulation with no meltwater; their mean surface speeds are the highest in the vertical distribution case. In the latter case, there is enhanced baroclinic conversion at the shelf break compared to the simulation with no meltwater. When meltwater is vertically distributed, there is an increase in baroclinic conversion at the shelf break associated with increased eddy kinetic energy. In addition, in the eastern Labrador Sea, the salinity is lower and the meltwater volume is greater when meltwater is vertically distributed. Therefore, the West Greenland Current is sensitive to how meltwater is added to the ocean with implications for the freshening of the Labrador Sea. Significance Statement Our goal is to understand how the flux of freshwater across the West Greenland continental slope into the Labrador Sea is modified by meltwater from the Greenland Ice Sheet. We compare the simulations of the ocean that capture key dynamics along the West Greenland continental slope that have no meltwater, meltwater added to the ocean surface, and meltwater distributed vertically to represent the mixing within fjords. When meltwater is added, the currents along the continental slope are faster, with the greatest increase when meltwater is vertically distributed. In that case, there is enhanced freshening of the Labrador Sea because modified density gradients generate more eddies. Proper representation of the vertical structure of meltwater is important for projecting the impact of freshwater on the subpolar North Atlantic.

58 GEOSCIENCES↗

DOE OSTI2023

Performance portable ice-sheet modeling with MALI

High-resolution simulations of polar ice sheets play a crucial role in the ongoing effort to develop more accurate and reliable Earth system models for probabilistic sea-level projections. These simulations often require a massive amount of memory and computation from large supercomputing clusters to provide sufficient accuracy and resolution; therefore, it has become essential to ensure performance on these platforms. Many of today’s supercomputers contain a diverse set of computing architectures and require specific programming interfaces in order to obtain optimal efficiency. In an effort to avoid architecture-specific programming and maintain productivity across platforms, the ice-sheet modeling code known as MPAS-Albany Land Ice (MALI) uses high-level abstractions to integrate Trilinos libraries and the Kokkos programming model for performance portable code across a variety of different architectures. In this article, we analyze the performance portable features of MALI via a performance analysis on current CPU-based and GPU-based supercomputers. The analysis highlights not only the performance portable improvements made in finite element assembly and multigrid preconditioning within MALI with speedups between 1.26 and 1.82x across CPU and GPU architectures but also identifies the need to further improve performance in software coupling and preconditioning on GPUs. We perform a weak scalability study and show that simulations on GPU-based machines perform 1.24–1.92x faster when utilizing the GPUs. The best performance is found in finite element assembly, which achieved a speedup of up to 8.65x and a weak scaling efficiency of 82.6% with GPUs. We additionally describe an automated performance testing framework developed for this code base using a changepoint detection method. The framework is used to make actionable decisions about performance within MALI. We provide several concrete examples of scenarios in which the framework has identified performance regressions, improvements, and algorithm differences over the course of 2 years of development.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Evolution of the Antarctic Ice Sheet from 2000–2300 and beyond: model sensitivity and uncertainty analysis using MPAS-Albany Land Ice

We present a description of the Antarctic Ice Sheet model configuration submitted to the ISMIP6-Antarctica-2300 experiment using the MPAS-Albany Land Ice model, along with three new sets of simulations: (1) a set of extended simulations to 2500 for three forced experiments and to 2775 for the control experiment; (2) a sensitivity analysis of our model configuration to parameters controlling basal sliding and sub-shelf melt, and to model structural choices including the choice of the energy and stress balances; and (3) a 72-member ensemble run on graphics processing units (GPUs) and analysis of variance to determine the primary sources of uncertainty in our ice-sheet model projections. Our extended simulations predict rapid retreat beginning after 2300 for SSP1-2.6 forcing and after 2500 for present-day (control) forcing, primarily in the Amundsen Sea Embayment. We find that varying the sub-shelf melt parameter between the 5th to 95th percentile values for a mean-Antarctic calibration target results in an up to ∼ ± 40 % change in sea-level contribution relative to our baseline simulations that used the median value. Using a linear basal sliding law reduces sea-level contribution by 51 %–73 % relative to our baseline nonlinear sliding law with an exponent of 1/5. When using basal sliding law exponents of 1/3 and 1/10, the overall difference from our baseline simulations at 2300 is on the order of 10 %. The Amundsen Sea Embayment region displays a strongly non-linear dependence of mass loss on the sliding law exponent, with no discernible relationship between the sliding law exponent and the mass loss by 2300, while the sectors feeding the Ross and Filchner-Ronne ice shelves exhibit more mass loss with a more-plastic sliding law. Our model fidelity sensitivity experiments reveal a 9 %–31 % increase in sea-level contribution when using a depth-integrated stress balance approximation relative to our three-dimensional solver, while using a fixed-in-time temperature field increases sea-level contribution by 14 %–88 % relative to two thermomechanically coupled configurations. Our 72-member ensemble and analysis of variance show that the uncertainty in long-term projections is dominated by the choice of Earth system model forcing and the presence or absence of hydrofracture forcing, rather than uncertainty in sliding and sub-shelf melt parameters.

58 GEOSCIENCES↗

DOE OSTI2021

Fusing Quantitative-Phase Imaging with Airy Light- Sheet Microscopy

We report the integration of quantitative-phase imaging (QPI) with light-sheet (LS) fluorescent microscopy on to a standard inverted microscope that retains compatibility with microfluidics. QPI enables label-free imaging and number-density quantification of single cells and their organelles. Conversely, LS yields considerable speed and phototoxicity gains in quantifying the 4D dynamics of gene-encoded fluorescent biomarkers. We will detail the system design that relied on spatial light interferometry for QPI and an accelerating Airy- beam light-sheet for fluorescence, its performance, as well as results of a representative multivariate imaging analysis of single-cell metabolism.

imaging, lattice light sheet, Yarrowia lipolytica,↗

DOE OSTI2021

Carbon fiber/epoxy vitrimer composite patch cured with bio‐based curing agents for one‐step repair metallic sheet and its recyclability

Abstract Vitrimers have gained a great deal of attention from researchers, yet research on its application is still lacking. This study, a novel bio‐based vitrimer was developed from epoxy (EP) and bio‐based curing agents, that is, cashew nut shell liquid (CNSL) and citric acid (CA), and then reinforced by carbon fiber. The vitrimers with different ratios of acid to epoxy (R ratio) at 0.30–0.40 contained ester and ether linkages. All EP/CA/CNSL vitrimers showed the stress relaxation over 70–100°C due to transesterification. The vitrimers were applied as polymer matrices for the carbon fiber composites and then used as repair patches. By using the carbon fiber‐reinforced vitrimer with the R ratio of 0.30, patch repair on a damaged alloy sheet revealed that approximately 98% of the tensile strength of the damaged alloy sheet was recovered. The vitrimer can be dissolved from carbon fiber composite to recover carbon fiber. The recovered carbon fiber retained good tensile strength compared to the pristine composite. Based on this study, the EP/CA/CNSL vitrimers showed the comparable thermomechanical properties with the epoxy vitrimer cured by the petroleum‐based curing agent. The vitrimer composite patch could therefore be an alternative new repair method to extend the service life of damaged structures.

Lorwanishpaisarn, Narubeth↗

DOE OSTI2020

Tumorigenic p53 mutants undergo common structural disruptions including conversion to α‐sheet structure

Abstract The p53 protein is a commonly studied cancer target because of its role in tumor suppression. Unfortunately, it is susceptible to mutation‐associated loss of function; approximately 50% of cancers are associated with mutations to p53, the majority of which are located in the central DNA‐binding domain. Here, we report molecular dynamics simulations of wild‐type (WT) p53 and 20 different mutants, including a stabilized pseudo‐WT mutant. Our findings indicate that p53 mutants tend to exacerbate latent structural‐disruption tendencies, or vulnerabilities, already present in the WT protein, suggesting that it may be possible to develop cancer therapies by targeting a relatively small set of structural‐disruption motifs rather than a multitude of effects specific to each mutant. In addition, α‐sheet secondary structure formed in almost all of the proteins. α‐Sheet has been hypothesized and recently demonstrated to play a role in amyloidogenesis, and its presence in the reported p53 simulations coincides with the recent re‐consideration of cancer as an amyloid disease.

Bromley, Dennis↗

DOE OSTI2020

Scale-Enhanced Magnetism in Exfoliated Atomically Thin Magnetite Sheets

The discovery of ferromagnetism in atomically thin layers at room temperature widens the prospects of 2D materials for device applications. Recently, two independent experiments demonstrated magnetic ordering in two dissimilar 2D systems, CrI 3 and Cr 2 Ge 2 Te 6 , at low temperatures and in VSe 2 at room temperature, but observation of intrinsic room-temperature magnetism in 2D materials is still a challenge. Here a transition at room temperature that increases the magnetization in magnetite while thinning down the bulk material to a few atom-thick sheets is reported. DC magnetization measurements prove ferrimagnetic ordering with increased magnetization and density functional theory calculations ascribe their origin to the low dimensionality of the magnetite layers. Additionally, surface energy calculations for different cleavage planes in passivated magnetite crystal agree with the experimental observations of obtaining 2D sheets from non-van der Waals crystals.

2D Magnetism↗

DOE OSTI2021

Review: Magnesium Sheet Alloy Development for Room Temperature Forming

Sheet metal forming operations in the automotive industry, including stamping, flanging, bending, hemming and trimming, are dominantly done at room temperature (RT). Unfortunately, the poor RT formability of magnesium due to its hexagonal close packed (HCP) structure and generally strong texture has limited the use of these processes in high-volume automotive production. However, the formability of magnesium can be improved via fine grain structure and random texture to enable some RT forming operations. Here, this paper presents the latest magnesium alloy development and evaluation by the United States Automotive Materials Partnership (USAMP) in collaboration with its university partners. A new sheet alloy developed in a recent USAMP project, ZAXME11100 (USAMP Alloy 2 Plus), offers excellent ductility (31% tensile elongation) and RT formability (7.8 mm Erichsen Index) in solution-treated condition (T4), and a high yield strength (270 MPa) upon post-forming aging treatment (T6), promising RT forming for automotive applications.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Multimodal 3D quantification of particle stimulated nucleation in industrially manufactured aluminium AA5182 sheet

Particle stimulated nucleation is a dominant recrystallisation mechanism observed in many industrially relevant aluminium alloys during thermomechanical processing. Here, in this work, we quantify particle stimulated nucleation in 3D in an aluminium AA5182 alloy sheet cold-rolled to 75% thickness reduction. Second phase particles and nuclei are mapped in the same sample volume by conventional laboratory absorption X-ray tomography and synchrotron X-ray Laue micro-diffraction. The large second phase particles are classified as Fe- and Mg-rich phases. It is found that 84% of the nuclei are particle stimulated and 40% of the particles stimulate nucleation. The critical particle diameter is found to be 4 μm. Deviatoric elastic strains are derived from micro-diffraction data and it is found that elastic strains are present in the recrystallised nuclei. The effects of the different particle types, particle clustering, particle size and aspect ratio as well as strain inheritance are discussed. This work provides a full 3D quantification of particle stimulated nucleation behaviour in AA5182 alloy sheet deformed to high strain.

Deviatoric strain↗

DOE OSTI2025

Promising performance of sulfide catholytes compared to halide alternatives in NMC811 cathodes for sheet-type sulfide solid-state batteries

Sulfide-based solid-state batteries (SSBs) show promise in achieving energy densities over 350 Wh/kg, yet challenges persist with their incorporation of high-voltage, nickel-rich layered oxide cathodes, such as LiNi₀.₈Mn₀.₁Co₀.₁O₂ (NMC811), due to the poor oxidation stability of sulfide solid-state electrolytes (SSEs) like Li₆PS₅Cl (LPSCl). Although halide SSEs such as Li₃InCl₆ (LIC) and Li₃YCl₆ (LYC) have previously shown promise in stabilizing high-voltage NMC cathodes, our research reveals that sulfide SSE catholytes, particularly when combined with surface-coated NMC cathodes, deliver superior performance. Here, this investigation assesses the cycling stability of various catholytes—LPSCl, LIC, Li₁₀GeP₂S₁₂ (LGPS), combined LIC-LPSCl, and LYC-LPSCl—in SSBs with LiNbO₃-coated NMC811 cathodes against sheet-type LPSCl separators. Findings indicate that while LGPS-based cathodes maintain higher capacity retention, they yield lower deliverable capacity, and LIC cathodes experience significant electrochemical degradation. Importantly, our results underscore that sulfide SSE catholytes, in conjunction with LiNbO₃-coated cathodes, optimize the cathode-electrolyte interphase (CEI), enhancing both kinetics and mass transport. These insights provide a strategic direction for optimizing catholyte composition in the development of sheet-type sulfide-based SSBs.

Catholyte↗

DOE OSTI2021

Interfacial thermal conductance between multi-layer graphene sheets and solid/liquid octadecane: A molecular dynamics study

Mixtures of paraffin and carbon nanofillers have promising potential for thermal storage, as paraffin (the matrix) possesses high latent heat and the nanofillers compensate for the low thermal conductivity (TC) of paraffin. Understanding thermal transport in these materials is essential for practical applications, as weak thermal transport hinders fast charge/discharge of thermal energy. Here, we use non-equilibrium molecular dynamics (NEMD) simulations to study the interfacial thermal conductance (ITC) between graphene sheets and octadecane (C18H38) matrix under the limiting conditions of the sheets being parallel or perpendicular to the direction of the imposed heat flux. The findings show that the systems containing thin graphene layers exhibit higher values of ITC. This study captures the asymptotic saturation of thermal conductance for the liquid phase of the perpendicular structure. Besides, given the greater number of structured layers of paraffin upon phase change, the ITC for the solid paraffin-graphene system is higher than the conductance of the liquid paraffin-graphene interface. We use the Pearson correlation coefficients of the vibrational power spectrum (VPS) of interfacing materials to explain the orders of magnitude variations of the observed ITC.

25 ENERGY STORAGE↗

DOE OSTI2021

Neutron diffraction discriminates between models for the nanoarchitecture of graphene sheets in glassy carbon

Glassy carbon is a chemically inert, biocompatible, disordered material with the graphene sheet as its basic building block. Structural characterisation techniques have so far been unable to provide definitive distinction between the many proposed models for its structure. Computer based simulation methods have made a step forward by predicting structure from interaction potentials, but the results are sensitive to the choice of the potential. Here we use the white neutron beam of the Spallation Neutron Source at Oak Ridge National Laboratory coupled with the SNAP time-of-flight diffractometer to sample the reciprocal space of glassy carbon and calculate accurate radial distribution functions. From the radial distribution information, we determine graphene sheet dimensions, registration, curvature, and assess defect content to rank the proposed structures in terms of their agreement with experimental data. In this work, we find that the recent models derived from empirical potentials give the best agreement.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Improved Protein Semi-Synthesis Enables Biophysical Studies of Thioamide Destabilization of β-Sheet Interactions

Abstract Thioamides are natural post-translational modifications of the peptide backbone and can be introduced synthetically to probe protein folding or functionalize peptides for translational applications. In this work, we demonstrate that thioamide-containing peptides with C-terminal thioesters can be efficiently generated using Knorr pyrazole activation and used in subsequent native chemical ligation reactions to generate thioamide-containing proteins. We compare this method to acyl azide activation and find that both routes provide similar yields. We also investigate ultrasound-mediated desulfurization of the ligation site cysteine for potential advantages over chemical radical initiators. Scaling up our syntheses allows us to study thioamide perturbations to the β-sheet region of the B1 domain of protein G (GB1) as well as β-strand interactions in amyloid fibrils of the Parkinson’s disease protein α-synuclein. In both contexts, we observe dramatic destabilization of the β-sheet networks, manifested in decreased GB1 thermal stability and altered folding and slowed aggregation of α-synuclein. These findings illustrate the impact that a single atom substitution can have on cooperative hydrogen-bonding networks and prompt future study of both systems.

Yanagawa, Evan S. K. [University of Pennsylvania ,↗

DOE OSTI2022

Hierarchical Self-Assembly Pathways of Peptoid Helices and Sheets

Peptoids (N-substituted glycines) are a class of tailorable synthetic peptidomic polymers. Amphiphilic diblock peptoids have been engineered to assemble 2D crystalline lattices with applications in catalysis and molecular separations. Assembly is induced in an organic solvent/water mixture by evaporating the organic phase, but the assembly pathways remain uncharacterized. We conduct all-atom molecular dynamics simulations of Nbrpe6Nc6 as a prototypical amphiphilic diblock peptoid comprising an NH 2 -capped block of six hydrophobic N-((4-bromophenyl)ethyl)glycine residues conjugated to a polar NH 3 (CH 2 ) 5 CO tail. We identify a thermodynamically controlled assembly mechanism by which monomers assemble into disordered aggregates that self-order into 1D chiral helical rods then 2D achiral crystalline sheets. We support our computational predictions with experimental observations of 1D rods using small-angle X-ray scattering, circular dichroism, and atomic force microscopy and 2D crystalline sheets using X-ray diffraction and atomic force microscopy. Furthermore, this work establishes a new understanding of hierarchical peptoid assembly and principles for the design of peptoid-based nanomaterials.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

THD-C Sheet: A Novel Nonbenzenoid Carbon Allotrope with Tetra-, Hexa-, and Dodeca-Membered Rings

Here, we propose a novel two-dimensional carbon-based structure with tetra-, hexa-, and dodeca-membered rings, which we refer to by the abbreviated name, THD-C. The structure presents a mixture of sp–sp 2 hybridization and can potentially be synthesized by the topological assembly of 4-ethynyldiphenylacetylene molecules. By employing first-principles calculations, the stability and ease of synthesis of the sheet are investigated and compared with various C-allotropes. We predict its metallic behavior and excellent kinetic and dynamic stability. Due to the crystal structure of the sheet, a strong mechanical anisotropy is observed. The effects of functionalization on the electronic properties of the material are also studied, and different semiconducting systems are obtained. The potential of THD-C for energy storage in metal-based batteries, hydrogen storage, and catalysis is also investigated, and we find a superior performance in comparison to graphite and other allotropes. The quantum confinement effect is investigated by constructing nanoribbons and nanotubes of various sizes. For ribbons, we find that tailor-made electronic and magnetic properties can be obtained and explored in potential spintronic devices. Additionally, we observe that nanotubes are conducting irrespective of their chirality and can potentially be used for capture, storage, and separation of industrially relevant small gas molecules.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Comparative Pore Structure and Dynamics for Bacterial Microcompartment Shell Protein Assemblies in Sheets or Shells

Bacterial microcompartments (BMCs) are protein-bound organelles found in some bacteria that encapsulate enzymes for enhanced catalytic activity. These compartments spatially sequester enzymes within semipermeable shell proteins, analogous to many membrane-bound organelles. The shell proteins assemble into multimeric tiles; hexamers, trimers, and pentamers, and these tiles self-assemble into larger assemblies with icosahedral symmetry. While icosahedral shells are the predominant form in vivo , the tiles can also form nanoscale cylinders or sheets. The individual multimeric tiles feature central pores that are key to regulating transport across the protein shell. Our primary interest is to quantify pore shape changes in response to alternative component morphologies at the nanoscale. We used molecular modeling tools to develop atomically detailed models for both planar sheets of tiles and curved structures representative of the complete shells found in vivo . Subsequently, these models were animated using classical molecular dynamics simulations. From the resulting trajectories, we analyzed the overall structural stability, water accessibility to individual residues, water residence time, and pore geometry for the hexameric and trimeric protein tiles from the Haliangium ochraceu m model BMC shell. These exhaustive analyses suggest no substantial variation in pore structure or solvent accessibility between the flat and curved shell geometries. We additionally compare our analysis to hydroxyl radical footprinting data to serve as a check against our simulation results, highlighting specific residues where water molecules are bound for a long time. Although with little variation in morphology or water interaction, we propose that the planar and capsular morphology can be used interchangeably when studying permeability through BMC pores.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗