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DOE OSTI2023

Sneaking in SpyCatcher using cell penetrating peptides for in vivo imaging

Abstract In vivo imaging of protein complexes is a powerful method for understanding the underlying biological function of these key biomolecules. Though the engineering of small, high affinity nanobodies have become more prevalent, the off-rates of these tags may result in incomplete or partial labeling of proteins in live cells. The SpyCatcher003 and SpyTag split protein system allow for irreversible, covalent binding to a short target peptide unlike nanobody-affinity based probes. However, delivering these tags into a cell without disrupting its normal function is a key challenge. Cell penetrating peptides (CPPs) are short peptide sequences that facilitate the transduction of otherwise membrane-impermeable ‘cargo’ , such as proteins, into cells. Here we report on our efforts to engineer and characterize CPP-SpyCatcher003 fusions as modular imaging probes. We selected three CPPs, CUPID, Pentratin, and pVEC, to engineer fusion protein probes for superresolution microscopy, with the aim to eliminate prior permeabilization treatments that could introduce imaging artifacts. We find that fusing the CPP sequences to SpyCatcher003 resulted in dimer and multimer formation as determined by size exclusion chromatography, dynamic light scattering, and SDS resistant dimers on SDS-PAGE gels. By isolating and labeling the monomeric forms of the engineered protein, we show these constructs retained their ability to bind SpyTag and all three CPP sequences remain membrane active, as assessed by CD spectroscopy in the presence of SDS detergent. Using fluorescence and super resolution Lattice structured illumination microscopy (Lattice SIM) imaging we show that the CPPs did not enhance uptake of SpyCatcher by E. coli, however with Caulobacter crescentus cells, we show that Penetratin, and to a lesser degree CUPID, does enhance uptake. Our results demonstrate the ability of the CPP-SpyCatcher003 to label targets within living cells, providing the groundwork for using split protein systems for targeted in vivo imaging.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Spectroscopic Signature of Metal-hydroxo and Peroxo Species in K-edge X-ray Absorption Spectra

Metal-dioxygen species are important intermediates formed during dioxygen activations by metalloenzymes in various biological processes, by catalysts in fuel cells, and prior to O 2 evolution by photosystem II. In this work, we focus on manganese-porphyrin complexes using tetramesitylporphyrin ligand (TMP) to explore changes in Mn K-edge X-ray absorption spectroscopy (XAS) associated with the formation of Mn-hydroxide and Mn–O 2 peroxide species. With limited spectroscopic characterization of these compounds, Mn K β X-ray emission spectroscopy (XES), XAS, density functional theory (DFT), and time-dependent DFT (TD-DFT) analysis will enhance our understanding of their complex electronic structure. We show that the shape of the pre-edge in the K-edge Mn X-ray absorption near-edge structure (XANES) can serve as a spectroscopic signature of the Mn III -peroxo formation and thus can be used to track the presence of the side-on peroxide as an intermediate in time-resolved or in situ experiments. In conclusion, our results will help to further summarize the spectroscopic fingerprints for peroxo and hydroxo species, addressing the challenge of identifying the reactive metal species in catalytic reactions.

Extended X-ray absorption fine structure↗

DOE OSTI2021

Shear Stress Dependence of Force Networks in 3D Dense Suspensions

The geometric organization and force networks of 3D dense suspensions that exhibit both shear thinning and thickening have been examined as a function of varying strength of interparticle attractive interactions using lubrication flow discrete element simulations. Significant rearrangement of the geometric topology does not occur at either the local or global scale as these systems transition across the shear thinning and shear thickening regimes. In contrast massive rearrangements in the balance of attractive, lubrication, and contact forces are observed with interesting behavior of network growth and competition. In agreement with prior work, in shear thinning regions the attractive force is dominant, however as the shear thickening region is approached there is growth of lubrication forces. Lubrication forces oppose the attraction forces, but as viscosity continues to increase under increasing shear stress, the lubrication forces are dominated by contact forces that also resist attraction. Contact forces are the dominant interactions during shear thickening and are an order of magnitude higher than their values in the shear-thinning regime. At high attractive interaction strength, contact networks can form even under shear thinning conditions, however high shear stress is still required before contact networks become the driving mechanism of shear thickening. Analysis of the contact force network during shear thickening generally indicate a uniformly spreading network that rapidly forms across empty domains, however the growth patterns have structure that are significantly dependent upon the strength of interparticle interactions, indicating subtle variations in the mechanism of shear thickening.

Edens, Lance E.↗

DOE OSTI2020

Sensitivity Studies of Premixed Flame Response to Transverse, High Frequency Disturbances

This study analyzes the response of premixed flames to high frequency transverse acoustic disturbances. A significant body of experiment, modeling and simulation efforts has been performed to understand the response of the spatially integrated heat release of premixed flames to low-frequency disturbances. These studies quantified this sensitivity through the Flame Transfer Function (FTF), as the global heat release is the key quantity influencing thermoacoustic stability for acoustically compact flames. Recent efforts have expanded these models to consider high-frequency acoustic disturbances, and the sensitivity of premixed flames through the Rayleigh integral (RI). The full Rayleigh Integral, as opposed to simply the spatially integrated heat release, must be considered in these cases where the flame is not acoustically compact. Prior modeling studies considered several effects - stability of axisymmetric flames centered in a cylindrical combustion chamber and the effect of flame offset from the combustor axis and the effect of mean flame asymmetries in the flame centered in the combustor. These studies showed that the flame's stability was sensitive to all these parameters, as well as to the transverse mode in question. In this paper, we quantify these different parametric sensitivities of premixed flame stability in the presence of high-frequency transverse acoustic modes - specifically sensitivity to flame length and nozzle location within the acoustic mode shape for 2 different transverse modes. The sensitivity of the RI to these control parameters provides an improved understanding of which flame parameters are critical to improve the overall thermoacoustic stability of the system.

Acharya, Vishal S.↗

DOE OSTI2020

Deprotection of N ‐ tert ‐Butoxycarbonyl (Boc) Protected Functionalized Heteroarenes via Addition–Elimination with 3‐Methoxypropylamine

Continued pursuit of functionalized soft‐N‐donor complexant scaffolds with favorable solubility and kinetics profiles applicable for the separation of the trivalent minor actinides from the lanthanides has attracted significant interest over the last three decades. Recent work from this laboratory resulted in the production of various N ‐Boc protected [1,2,4]triazinyl‐pyridin‐2‐yl indole Lewis basic procomplexants which necessitated the removal of the indole N ‐Boc protecting group prior to evaluation of complexant efficacy in separations assays. Traditional deprotection strategies involving trifluoroacetic and other protic and Lewis acids proved unsuccessful in removal of the recalcitrant indole‐ N ‐Boc protecting group necessitating the development of a new strategy for deprotection of this complexant class. A serendipitous result facilitated utilization of 3‐methoxypropylamine as a mild deprotecting agent for various N ‐Boc protected heteroarenes via a proposed addition–elimination mechanism. Method development, application to various heteroarenes including indoles, 1,2‐indazoles, 1,2‐pyrazoles, and related derivatives, a ten‐fold scale‐up reaction, and experimental evaluation of a preliminary mechanistic hypothesis are reported herein.

Gulledge, Zachary Z.↗

DOE OSTI2025

Facet-Dependent Doping and Dopant-Dependent Faceting in Si-Doped GaAsSb Nanowires

Here, we correlate the spatial distributions of Si, Sb, and rotational twins in Si-doped GaAs 1-x Sb x nanowires. GaAs 1-x Sb x nanowires were grown epitaxially on Si(111) substrates by tuning process conditions to achieve repeated nucleation of rotational twins and growth along the [111]B direction; dilute Sb and Si fluxes were chosen to create a sufficient twin density to achieve high yield while avoiding growth of the wurtzite phase. While the impact of Si and Sb on twin density and nanowire growth rate has been previously reported, the facet-dependent incorporation of these species has not been established. Scanning transmission electron microscopy was used to confirm that Sb incorporates preferentially on the (111)B facets relative to {1 ̅1 ̅0} facets prior to nucleation of a rotational twin. With periodic twinning, this facet dependence leads to alternating regions of enriched and depleted Sb concentration attributed to a growth rate-dependent Sb-As-exchange mechanism. Atom probe tomography measurements establish that while Si doping is not perturbed by twinning on (111)B facets, Si and Sb concentrations are anti-correlated for growth on non-(111)B facets. Density functional theory calculations underpin a thermodynamic model that explains the observed anisotropies in dopant incorporation.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Linking structural and rheological memory in disordered soft materials

Linking the macroscopic flow properties and nanoscopic structure is a fundamental challenge to understanding, predicting, and designing disordered soft materials. Under small stresses, these materials are soft solids, while larger loads can lead to yielding and the acquisition of plastic strain, which adds complexity to the task. In this work, we connect the transient structure and rheological memory of a colloidal gel under cyclic shearing across a range of amplitudes via a generalized memory function using rheo-X-ray photon correlation spectroscopy (rheo-XPCS). Our rheo-XPCS data show that the nanometer scale aggregate-level structure recorrelates whenever the change in recoverable strain over some interval is zero. The macroscopic recoverable strain is therefore a measure of the nano-scale structural memory. We further show that yielding in disordered colloidal materials is strongly heterogeneous and that memories of prior deformation can exist even after the material has been subjected to flow.

Kamani, Krutarth M. [Univ. of Illinois at Urbana-C↗

DOE OSTI2023

SA508 low alloy steel to 316L stainless steel dissimilar metal joint made by powder metallurgy hot isostatic pressing

Joining ferritic SA508 low alloy steel (LAS) and austenitic 316 L stainless steel (SS) via powder metallurgy hot isostatic pressing (PM-HIP) was evaluated as an alternative method to welding. This study investigated the mechanical and microstructural evolutions of the bimetallic interface under different joint designs and heat treatments. Here, the direct joining of dissimilar metal alloys by PM-HIP method resulted in two designs: 1) powder SA508 to solid bar 316 L (P508–B316L) and 2) powder 316 L solid bar SA508 (P316L-B508). In both cases, P508–B316L and P316L-demonstrated satisfactory tensile strength, however, high hardness and severe depreciation in toughness were located on the bimetallic interface. The mechanisms responsible for the detrimental mechanical properties were verified. Large oxides were observed in P508–B316L due to the prior powder boundary (PPB) oxides present in SA508 powder. The intense sensitization occurred from the formation of M 23 C 6 carbides, consequently from the slow cooling after PM-HIP in P316L-B508. Post-HIP heat treatments were explored to reduce the distance of carbide formation; however, the heat treatment could not eliminate the carbides. The experimental results were compared to the diffusion couple simulation as a function of carbide formation with distance. The analysis also showed the high hardness at the bimetallic interface was primarily contributed by solid solution strengthening. In conclusion, the direct joining of P316L-B508 and P508–B316L via PM-HIP was deemed to be unfeasible, and a transitional material is necessary to impede the diffusion of carbon.

316L stainless Steel↗

DOE OSTI2023

BeyondPlanck: XV. Limits on large-scale polarized anomalous microwave emission from Planck LFI and WMAP

We constrained the level of polarized anomalous microwave emission (AME) on large angular scales using Planck Low-Frequency Instrument (LFI) and WMAP polarization data within a Bayesian cosmic microwave background (CMB) analysis framework. We modeled synchrotron emission with a power-law spectral energy distribution, as well as the sum of AME and thermal dust emission through linear regression with the Planck High-Frequency Instrument (HFI) 353 GHz data. This template-based dust emission model allowed us to constrain the level of polarized AME while making minimal assumptions on its frequency dependence. We neglected CMB fluctuations, but show through simulations that these fluctuations have a minor impact on the results. We find that the resulting AME polarization fraction confidence limit is sensitive to the polarized synchrotron spectral index prior. In addition, for prior means β s < -3.1 we find an upper limit of p AME max ≲ 0.6% (95% confidence). In contrast, for means β s = -3.0, we find a nominal detection of p AME = 2.5 ± 1.0% (95% confidence). These data are thus not strong enough to simultaneously and robustly constrain both polarized synchrotron emission and AME, and our main result is therefore a constraint on the AME polarization fraction explicitly as a function of β s . Combining the current Planck and WMAP observations with measurements from high-sensitivity low-frequency experiments such as C-BASS and QUIJOTE will be critical to improve these limits further.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

Thermal and mechanical influences on shear band formation and suppression in shocked 1,3,5-trinitroperhydro-1,3,5-triazine (RDX)

High-pressure shear band formation is a critical phenomenon in energetic materials because of its ability to form hotspots and influence mechanical strength. Shear banding is known to occur in a variety of these materials, but the governing dynamics of the mechanisms are not well defined for molecular crystals. Our previous work has found that at high pressures in 1,3,5-trinitroperhydro-1,3,5-triazine (RDX), the initial formation sites for shear bands, called “embryos”, form in excess and rapidly lower deviatoric stresses prior to shear band formation and growth, suppressing the shear banding nucleation and growth. Here, in this work, we assess the influence of a variety of changes to the material state on this phenomenon, including altered initial temperature, lateral strain that confines the system in tension or pressure, and initial molecular vacancies throughout the crystal. Shear band suppression and the nature of the shear band network are assessed as a function of each of these.

36 MATERIALS SCIENCE↗

DOE OSTI2020

SIGNAL Game Manual

SIGNAL is a first of its kind experimental wargame developed as part of the Project on Nuclear Gaming (PoNG). In this document we describe the rules and game mechanics associated with the online version of SIGNAL created by team members from the University of California, Berkeley, Sandia National Laboratories, and Lawrence Livermore National Laboratory and sponsored by the Carnegie Corporation of New York. The game was developed as part of a larger research project to develop the experimental wargaming methodology and explore its use on a model scenario: the impact of various military capabilities on conflict escalation dynamics. We discuss the results of this research in a forthcoming paper that will include this manual as an appendix. It is our hope that this manual will both contribute to our players' understanding of the game prior to play and that it will allow for replication of the SIGNAL game environment for future research purposes. The manual begins by introducing the terminology used throughout the document. It then outlines the technical requirements required to run SIGNAL. The following section provides a description of the map, resources, infrastructure, tokens, and action cards used in the game environment. The manual then describes the user interface including the chat functions, trade mechanism, currency and population counts necessary for players to plan their actions. It then turns to the sequence of player actions in the game describing the signaling, action, and upkeep phases that comprise each round of play. It then outlines the use of diplomacy including alliances with minor states and trade between players. The manual also describes the process for scoring the game and determining the winner. The manual concludes with tips for players to remember as they embark upon playing the game.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

New Insights Into Lignification via Network and Multi-Omics Analyses of Arogenate Dehydratase Knock-Out Mutants in Arabidopsis thaliana

Multiple Arabidopsis arogenate dehydratase (ADT) knock-out (KO) mutants, with phenotypes having variable lignin levels (up to circa 70% reduction), were studied to investigate how differential reductions in ADTs perturb its overall plant systems biology. Integrated "omics" analyses (metabolome, transcriptome, and proteome) of wild type (WT), single and multiple ADT KO lines were conducted. Transcriptome and proteome data were collapsed into gene ortholog (GO) data, with this allowing for enzymatic reaction and metabolome cross-comparisons to uncover dominant or likely metabolic biosynthesis reactions affected. Network analysis of enzymes-highly correlated to stem lignin levels-deduced the involvement of novel putative lignin related proteins or processes. These included those associated with ribosomes, the spliceosome, mRNA transport, aminoacyl tRNA biosynthesis, and phosphorylation. While prior work helped explain lignin biosynthesis regulation at the transcriptional level, our data here provide support for a new hypothesis that there are additional post-transcriptional and translational level processes that need to be considered. These findings are anticipated to lead to development of more accurate depictions of lignin/phenylpropanoid biosynthesis models in situ, with new protein targets identified for further biochemical analysis and/or plant bioengineering. Additionally, using KEGG defined functional categorization of proteomics and transcriptomics analyses, we detected significant changes to glucosinolate, a-linolenic acid, nitrogen, carotenoid, aromatic amino acid, phenylpropanoid, and photosynthesis-related metabolic pathways in ADT KO mutants. Metabolomics results also revealed that putative carotenoid and galactolipid levels were generally increased in amount, whereas many glucosinolates and phenylpropanoids (including flavonoids and lignans) were decreased in the KO mutants.

Arabidopsis, arogenate dehydratases, lignin, multi↗

DOE OSTI2020

A Statistical Standard Siren Measurement of the Hubble Constant from the LIGO/Virgo Gravitational Wave Compact Object Merger GW190814 and Dark Energy Survey Galaxies

We present a measurement of the Hubble constant H 0 using the gravitational wave (GW) event GW190814, which resulted from the coalescence of a 23 M ⊙ black hole with a 2.6 M ⊙ compact object, as a standard siren. No compelling electromagnetic counterpart has been identified for this event; thus our analysis accounts for thousands of potential host galaxies within a statistical framework. The redshift information is obtained from the photometric redshift (photo- z ) catalog from the Dark Energy Survey. The luminosity distance is provided by the LIGO/Virgo gravitational wave sky map. Since this GW event has the second-smallest localization volume after GW170817, GW190814 is likely to provide the best constraint on cosmology from a single standard siren without identifying an electromagnetic counterpart. Furthermore, our analysis uses photo- z probability distribution functions and corrects for photo- z biases. We also reanalyze the binary black hole GW170814 within this updated framework. We explore how our findings impact the H 0 constraints from GW170817, the only GW merger associated with a unique host galaxy. From a combination of GW190814, GW170814, and GW170817, our analysis yields H 0 =72.0$_{+12}^{–8.2}$ km s -1 Mpc -1 (68% highest-density interval, HDI) for a prior in H 0 uniform between [20 and 140] km s -1 Mpc -1 . The addition of GW190814 and GW170814 to GW170817 improves the 68% HDI from GW170817 alone by ~18%, showing how well-localized mergers without counterparts can provide a significant contribution to standard siren measurements, provided that a complete galaxy catalog is available at the location of the event.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Electrostatic Potential of Functional Cations as a Predictor of Hydroxide Diffusion Pathways in Nanoconfined Environments of Anion Exchange Membranes

Nanoconfined anion exchange membranes (AEMs) play a vital role in emerging electrochemical technologies. The ability to control dominant hydroxide diffusion pathways is an important goal in the design of nanoconfined AEMs. Such control can shorten hydroxide transport pathways between electrodes, reduce transport resistance, and enhance device performance. In this work, we propose an electrostatic potential (ESP) approach to explore the effect of the polymer electrolyte cation spacing on hydroxide diffusion pathways from a molecular perspective. By exploring cation ESP energy surfaces and validating outcomes through prior ab initio molecular dynamics simulations of nanoconfined AEMs, we find that we can achieve control over preferred hydroxide diffusion pathways by adjusting the cation spacing. The results presented in this work provide a unique and straightforward approach to predict preferential hydroxide diffusion pathways, enabling efficient design of highly conductive nanoconfined AEM materials for electrochemical technologies.

25 ENERGY STORAGE↗

DOE OSTI2025

Iron-sulfur clusters: the road to room temperature

Abstract Iron-sulfur proteins perform a wide variety of reactions central to the metabolisms of all living organisms. Foundational to their reaction chemistry are the rich electronic structures of their constituent Fe-S clusters, which differ in important ways from the active sites of mononuclear Fe enzymes. In this perspective, we summarize the essential electronic structure features that make Fe-S clusters unique, and point to the need for studies aimed at understanding the electronic basis for their reactivity under physiological conditions. Specifically, at ambient temperature, both the ground state and a large number of excited states are thermally populated, and thus a complete understanding of Fe-S cluster reactivity must take into account the properties, energies, and reactivity patterns of these excited states. We highlight prior research toward characterizing the low-energy excited states of Fe-S clusters that has established what is now a consensus model of these excited state manifolds and the bonding interactions that give rise to them. In particular, we discuss the low-energy alternate spin states and valence electron configurations that occur in Fe-S clusters of varying nuclearities, and finally suggest that there may be unrecognized functional roles for these states. Graphical abstract

Skeel, Brighton A. (ORCID:000000018458088X)↗

DOE OSTI2026

High-throughput computation of electric polarization in solids via Berry flux diagonalization

Electric polarization in the absence of an externally applied electric field is a key property of polar materials, but the standard interpolation-based ab initio approach to compute polarization differences within the modern theory of polarization presents challenges for automated high-throughput calculations. Berry flux diagonalization [J. Bonini et al., Phys. Rev. B 102, 045141 (2020)] has been proposed as an efficient and reliable alternative, though it has yet to be widely deployed. Here, we assess Berry flux diagonalization using ab initio calculations of a large set of materials, introducing and validating heuristics that ensure branch alignment with a minimal number of intermediate interpolated structures. Our automated implementation of Berry flux diagonalization succeeds in cases where prior interpolation-based workflows fail due to band-gap closures or branch ambiguities. Benchmarking with ab initio calculations of 176 candidate ferroelectrics, we demonstrate the efficacy of the approach on a broad range of insulating materials and obtain accurate effective polarization values with fewer interpolated structures than prior automated interpolation-based workflows. Our real-space heuristics that can predict gauge stability a priori from ionic displacements enable a general automated framework for reliable polarization calculations and efficient high-throughput screening of chemically and structurally diverse polar insulators. These results establish Berry flux diagonalization as a robust and efficient method to compute the effective polarization of solids and to accelerate the data-driven discovery of functional polar materials.

Poteshman, Abigail N. [University of Chicago, IL (↗

DOE OSTI2023

Radiation effects on materials for electrochemical energy storage systems

Batteries and electrochemical capacitors (ECs) are of critical importance for applications such as electric vehicles, electric grids, and mobile devices. However, the performance of existing battery and EC technologies falls short of meeting the requirements of high energy/high power and long durability for increasing markets such as the automotive industry, aerospace, and grid-storage utilizing renewable energies. Therefore, improving energy storage materials performance metrics is imperative. In the past two decades, radiation has emerged as a new means to modify functionalities in energy storage materials. There exists a common misconception that radiation with energetic ions and electrons will always cause radiation damage to target materials, which might potentially prevent its applications in electrochemical energy storage systems. But in this review, we summarize recent progress in radiation effects on materials for electrochemical energy storage systems to show that radiation can have both beneficial and detrimental effects on various types of energy materials. Prior work suggests that fundamental understanding toward the energy loss mechanisms that govern the resulting microstructure, defect generation, interfacial properties, mechanical properties, and eventual electrochemical properties is critical. Here, we discuss radiation effects in the following categories: (1) defect engineering, (2) interface engineering, (3) radiation-induced degradation, and (4) radiation-assisted synthesis. We analyze the significant trends and provide our perspectives and outlook on current research and future directions in research seeking to harness radiation as a method for enhancing the synthesis and performance of battery materials.

25 ENERGY STORAGE↗

DOE OSTI2022

Fuzzy dark matter and the Dark Energy Survey Year 1 data

ABSTRACT Gravitational weak lensing by dark matter haloes leads to a measurable imprint in the shear correlation function of galaxies. Fuzzy dark matter (FDM), composed of ultralight axion-like particles of mass m ∼ 10−22 eV, suppresses the matter power spectrum and shear correlation with respect to standard cold dark matter. We model the effect of FDM on cosmic shear using the optimized halo model HMCode, accounting for additional suppression of the mass function and halo concentration in FDM as observed in N-body simulations. We combine Dark Energy Survey Year 1 (DES-Y1) data with the Planck cosmic microwave background anisotropies to search for shear correlation suppression caused by FDM. We find no evidence of suppression compared to the preferred cold dark matter model, and thus set a new lower limit to the FDM particle mass. Using a log-flat prior and marginalizing over uncertainties related to the non-linear model of FDM, we find a new, independent 95 per cent C.L. lower limit log10m > −23 combining Planck and DES-Y1 shear, an improvement of almost two orders of magnitude on the mass bound relative to CMB-only constraints. Our analysis is largely independent of baryonic modelling, and of previous limits to FDM covering this mass range. Our analysis highlights the most important aspects of the FDM non-linear model for future investigation. The limit to FDM from weak lensing could be improved by up to three orders of magnitude with $\mathcal {O}(0.1)$ arcmin cosmic shear angular resolution, if FDM and baryonic feedback can be simultaneously modelled to high precision in the halo model.

79 ASTRONOMY AND ASTROPHYSICS↗