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DOE OSTI2024

Construction of Reconfigurable and Polymorphic DNA Origami Assemblies with Coiled‐Coil Patches and Patterns

Abstract DNA origami nanodevices achieve programmable structure and tunable mechanical and dynamic properties by leveraging the sequence‐specific interactions of nucleic acids. Previous advances have also established DNA origami as a useful building block to make well‐defined micron‐scale structures through hierarchical self‐assembly, but these efforts have largely leveraged the structural features of DNA origami. The tunable dynamic and mechanical properties also provide an opportunity to make assemblies with adaptive structures and properties. Here the integration of DNA origami hinge nanodevices and coiled‐coil peptides are reported into hybrid reconfigurable assemblies. With the same dynamic device and peptide interaction, it is made multiple higher‐order assemblies (i.e., polymorphic assembly) by organizing clusters of peptides into patches or arranging single peptides into patterns on the surfaces of DNA origami to control the relative orientation of devices. The coiled‐coil interactions are used to construct circular and linear assemblies whose structure and mechanical properties can be modulated with DNA‐based reconfiguration. Reconfiguration of linear assemblies leads to micron scale motions and ≈2.5‐10‐fold increase in bending stiffness. The results provide a foundation for stimulus‐responsive hybrid assemblies that can adapt their structure and properties in response to nucleic acid, peptide, protein, or other triggers.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

One-pot synthesis of mechanically robust hierarchical graphene-polyethylene aerogels

Fabricating mechanically robust graphene aerogels (GAs) without compromising their notable features including superelasticity, large surface area, high porosity, and low density is challenging. Here, this work presents a new one-pot strategy based on ambient drying to fabricate a three-dimensional (3D) graphene-polyethylene aerogel (G-PEA) with a unique hierarchical porous structure, in which the highly porous polyethylene is encapsulated by graphene frameworks. The hierarchical G-PEA exhibited substantially enhanced compressive strength while maintaining low density and superelasticity comparable to those of bare GAs. The G-PEAs with 5 wt% PE (G-PEA5) showed a significant improvement (up to 2083 %) in compressive stress compared to bare GAs, which can be attributed to the porous PE support within the GA framework. The G-PEA5 retained 94% of its compressive stress after 100 compression cycles, which is still higher than that (∼80%) of bare GAs, and maintained good elastic recovery. The designed hierarchical G-PEAs show great promise in the applications that require outstanding mechanical properties.

Composite↗

DOE OSTI2022

Additively manufactured metal energetic ligand precursors and combustion synthesis

Processes for tailoring the macroscopic shape, metallic composition, mechanical properties, and pore structure of nanoporous metal foams prepared through combustion synthesis via direct write 3D printing of metal energetic ligand precursor inks made with water and an organic thickening agent are disclosed. Such processes enable production of never before obtainable metal structures with hierarchical porosity, tailorable from the millimeter size regime to the nanometer size regime. Structures produced by these processes have numerous applications including, but not limited to, catalysts, heat exchangers, low density structural materials, biomedical implants, hydrogen storage medium, fuel cells, and batteries.

Tappan, Bryce↗

DOE OSTI2022

Traffic safety analysis and model updating for freeways using Bayesian method

Freeway crash prediction models are the basic of traffic safety research, yet crash occurrence and the influencing factors change over time. In order to make sure the implemented safety models fit the current traffic environment, this study conducts a comparative analysis of 2017 and 2020 datasets collected from freeways in Suzhou, China. Herein, considering the spatial correlation among analysis units and the hierarchical data structure, a Bayesian conditional autoregressive negative binomial (CAR-NB) model and a Bayesian hierarchical CAR-NB (HCAR-NB) model were used to explore the safety influencing factors, and a traditional NB model was developed for further comparison. To update the HCAR-NB model from 2017 to 2020, Bayesian inference with informative priors was used to improve its goodness of fit and efficiency. Preliminary results showed that 1) the HCAR-NB model outperformed the NB model and CAR-NB model in prediction accuracy, and 2) the number of crashes was significantly correlated with average speed, speed variance, road segment length, number of lanes, and presence of ramps. The potential for safety improvement (PSI) method was applied to the modeling results to identify hotspots for the two years. The results confirmed that the hotspots spatiotemporally shifted among the freeways. The proposed crash prediction model and updating method are expected to assist implementation of informed countermeasures for freeway safety improvement.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Green Electrode Processing Enabled by Fluoro-Free Multifunctional Binders for Lithium-Ion Batteries

The eco-friendly processing of conjugated polymer binder for lithium-ion batteries demands improved polymer solubility by introducing functional moieties, while this strategy will concurrently sacrifice polymer conductivity. Employing the polyfluorene-based binder poly(2,7-9,9 (di(oxy-2,5,8-trioxadecane))fluorene) (PFO), soluble in water-ethanol mixtures, a novel approach is presented to solve this trade-off, which features integration of aqueous solution processing with subsequent controlled thermal-induced cleavage of solubilizing side chains, to produce hierarchically ordered structures (HOS). The thermal processing can enhance the intermolecular π–π stacking of polyfluorene backbone for better electrochemical performance. Notably, HOS-PFO demonstrated a substantial 6–7 orders of magnitude enhancement in electronic conductivity, showcasing its potential as a functional binder for lithium-ion batteries. As an illustration, HOS-PFO protected SiOx anodes, utilizing in situ side chain decomposition of PFO surrounding SiOx particles after aqueous processing are fabricated. HOS-PFO contributed to the stable cycling and high-capacity retention of practical SiOx anodes (3.0 mAh cm -2 ), without the use of any conducting carbon additives or fluorinated electrolyte additives. It is proposed that this technique represents a universal approach for fabricating electrodes with conjugated polymer binders from aqueous solutions without compromising conductivity.

25 ENERGY STORAGE↗

DOE OSTI2026

Assessing the Application of a Genomic Network Analysis in Population Ecology: Inferring Patterns of Dispersal and Geographic Structure in the Emerging Pathogen, Coccidioides

A challenge in population ecology studies is identifying how to best group individuals into populations, especially when individual origin is unknown. Machine learning has improved upon traditional methods of identifying population structure and is more efficient at handling large, complex datasets. We demonstrate the applicability of a machine learning method to identify hierarchical population structure in an emerging pathogen, Coccidioides spp., the causative agent of Valley fever. We compared the network clusters to structure identified by traditional tools as a validation of the network performance. We used publicly available whole-genome data for 48 C. immitis and 102 C. posadasii, resulting in 168,211 genome-wide SNPs among the two species. The network analysis grouped samples into populations comparable to the literature for these species but also identified fine-scale geographic structure and travel-associated cases not reported thus far. Exploring different resolutions in the network made it easy to identify unique genotypes specific to California and possibly Nevada, as well as Phoenix- and Tucson-acquired infections in non-endemic areas, regardless of reported travel history. The present study provides a promising example of how a ML-based network analysis can improve our ability to understand pathogen ecology, group cases into populations and infer travel-associated infections.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Containers for Massive Ensemble of I/O Bound Hierarchical Coupled Simulations

We present our experience using containers to scale up a massive ensemble of coupled I/O bound workloads on the NERSC Cori supercomputer. We describe the design of a hierarchical simulation structure using the Integrated Plasma Simulator (IPS) that enables the flexible execution of coupled simulations at the system, node, and core level using the same coupling abstraction and API. The hierarchical design allows for the node-level execution to be efficiently executed using containers while not impacting the structure of the simulation at the system level. We demonstrate the viability of the approach by presenting experimental results from applications in coupled fusion plasma simulations that illustrate the performance impact of using containers to deploy the node-level workloads, in conjunction with the user mountable XFS file systems to ameliorate the load on the Lustre parallel file system. We also present results from production runs showing the ability of the ensemble simulations to scale to hundreds of Cori Haswell nodes, with little or no overhead.

Elwasif, Wael↗

DOE OSTI2022

Membrane synthesis via in-situ pore formation in silica gels through dynamic miscibility with soybean oil

The dynamic immiscibility between vegetable oil and organic silica precursors during sol-gel synthesis was used to tailor the microstructure of gels made with tetraethoxysilane (TEOS) or tetraethoxysilane+methyltrimethoxysilane (MTMS). Vegetable oil was investigated as an environmentally friendly and cheaper alternative to many other porogens. Oil concentrations of 9.09 v/v% and 33.33 v/v% were studied. For both TEOS and TEOS+MTMS gels, the miscibility of the oil and precursor decreases as the silica gel network forms, leading to oil-rich regions within the silica matrix. Gels containing MTMS maintained partial miscibility with the oil during gel formation due to the non-hydrolysable methyl groups on the MTMS. The pore structure of MTMS gels appeared more interconnected compared to the isolated pores observed in gels made with only TEOS. To create membranes with hierarchical pore structures, solvent exchanges were performed on gels or dried gels (i.e., xerogels) were calcined. The effect of the methyl group was also observed in the results of the time sweep rheology, as the addition of oil to the TEOS+MTMS gels caused an increase in the time to form the spanning gel. The trend was the opposite for oil additions to TEOS gels, which only contained polar groups. Xerogel membranes made with TEOS+MTMS had higher specific surface areas (SSAs) than those made with TEOS. For oil concentrations of 33.33 v/v%, xerogels made from TEOS+MTMS had an average SSA of 1068 + 113 m2 g-1, an order of magnitude higher than the average SSA of 103 + 6 m2 g-1 for xerogels made with TEOS.

sol-gel, dynamic immiscibility, oil-alkoxide inter↗

DOE OSTI2023

Higher-Order VLP-Based Protein Macromolecular Framework Structures Assembled via Coiled-Coil Interactions

Hierarchical organization is one of the fundamental features observed in biological systems that allows for efficient and effective functioning. Virus-like particles (VLPs) are elegant examples of a hierarchically organized supramolecular structure, where many subunits are self-assembled to generate the functional cage-like architecture. Utilizing VLPs as building blocks to construct two- and three-dimensional (3D) higher-order structures is an emerging research area in developing functional biomimetic materials. VLPs derived from P22 bacteriophages can be repurposed as nanoreactors by encapsulating enzymes and modular units to build higher-order catalytic materials via several techniques. In this study, we have used coiled-coil peptide interactions to mediate the P22 interparticle assembly into a highly stable, amorphous protein macromolecular framework (PMF) material, where the assembly does not depend on the VLP morphology, a limitation observed in previously reported P22 PMF assemblies. Many encapsulated enzymes lose their optimum functionalities under the harsh conditions that are required for the P22 VLP morphology transitions. Therefore, the coiled-coil-based PMF provides a fitting and versatile platform for constructing functional higher-order catalytic materials compatible with sensitive enzymes. Finally, we have characterized the material properties of the PMF and utilized the disordered PMF to construct a biocatalytic 3D material performing single- and multistep catalysis.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

In Situ 4D‐STEM Imaging of the Orientation of Lamellar Clusters in Polymer Crystallization

In semi‐crystalline polymeric materials, the initial stages of nucleation and the growth path of crystalline domains can determine the final performance. Here, in this work, we used four‐dimensional scanning transmission electron microscopy (4D‐STEM) imaging to analyze the changes in lamellar orientation in high‐density polyethylene (HDPE) during heating and cooling. This method allowed us to quantitatively detect the formation of lamellae clusters with different in‐plane orientations, which are not visible with traditional methods. Our analysis provided detailed insights into the orientation and size changes of crystalline domains. Additionally, this technique enabled direct observation of lattice structures in hierarchical lamellae and the growth of crystals, confirming the local variability in lamellar orientation. This innovative approach significantly improves our understanding of polymer crystallization, linking changes in morphology and lattice structures at different length scales.

4D-STEM↗

DOE OSTI2022

Multifunctional nanopore electrode array method for characterizing and manipulating single entities in attoliter-volume enclosures

Structurally regular nanopore arrays fabricated to contain independently controllable annular electrodes represent a new kind of architecture capable of electrochemically addressing small collections of matter—down to the single entity (molecule, particle, and biological cell) level. Furthermore, these nanopore electrode arrays (NEAs) can also be interrogated optically to achieve single entity spectroelectrochemistry. Larger entities such as nanoparticles and single bacterial cells are investigated by dark-field scattering and potential-controlled single-cell luminescence experiments, respectively, while NEA-confined molecules are probed by single molecule luminescence. By carrying out these experiments in arrays of identically constructed nanopores, massively parallel collections of single entities can be investigated simultaneously. The multilayer metal–insulator design of the NEAs enables highly efficient redox cycling experiments with large increases in analytical sensitivity for chemical sensing applications. NEAs may also be augmented with an additional orthogonally designed nanopore layer, such as a structured block copolymer, to achieve hierarchically organized multilayer structures with multiple stimulus-responsive transport control mechanisms. Finally, NEAs constructed with a transparent bottom layer permit optical access to the interior of the nanopore, which can result in the cutoff of far-field mode propagation, effectively trapping radiation in an ultrasmall volume inside the nanopore. Furthermore, the bottom metal layer may be used as both a working electrode and an optical cladding layer, thus, producing bifunctional electrochemical zero-mode waveguide architectures capable of carrying out spectroelectrochemical investigations down to the single molecule level.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Phase-field simulation of domain size effect on dielectric and piezoelectric responses in K 0.5 Na 0.5 NbO 3 epitaxial thin films with superdomain structures

Size effects of mesoscale ferroelectric domains on the macroscopic dielectric and piezoelectric responses in domain-engineered bulk piezocrystals have been extensively studied for more than two decades. However, less is known about the domain size effects in ferroelectric epitaxial thin films, especially for films consisting of low-symmetry ferroelectric phases and exhibits hierarchical superdomain structures. Herein, using phase-field simulations, we systemically evaluate the effective out-of-plane dielectric and piezoelectric coefficients, κ$^{*}_{33}$ and d$^{*}_{33}$, as a function of the domain periods for two types of superdomain structures in ferroelectric K 0.5 Na 0.5 NbO 3 epitaxial thin films. In one type of the superdomain structures, we find that more than 70% increase of κ$^{*}_{33}$ and nearly 20% increase of d$^{*}_{33}$ can be achieved by tuning the domain period by a few tens of nanometers. Dissimilar behaviors are found when the domain period varies along different lateral directions, suggesting anisotropic domain size effects in thin films. By analyzing the local dielectric and piezoelectric responses from each domain variants and domain walls, we reveal that the domain size effect is governed by the variation of out-of-plane polarization inside the domains. Moreover, we also demonstrate enhanced domain size effects by modulating the misfit strains and temperature to approach the polymorphic phase boundaries, suggesting tunability of the size effect by doping and strain engineering. Furthermore, our results reveal multimodal domain size dependence of dielectric and piezoelectric responses in low-symmetry ferroelectric epitaxial thin films, implying that domain size engineering can be used to tune macroscopic properties of thin-film ferroelectrics, similar to their bulk counterparts.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Perfect quantum state transfer on diamond fractal graphs

In the quest for designing novel protocols for quantum information and quantum computation, an important goal is to achieve perfect quantum state transfer for systems beyond the well-known one- dimensional cases, such as 1D spin chains. Here, we use methods from fractal analysis and probability to find a new class of quantum spin chains on fractal-like graphs (known as diamond fractals) which support perfect quantum state transfer and which have a wide range of different Hausdorff and spectral dimensions. The resulting systems are spin networks combining Dyson hierarchical model structure with transverse permutation symmetries of varying order.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

3D Printed Nickel–Molybdenum-Based Electrocatalysts for Hydrogen Evolution at Low Overpotentials in a Flow-Through Configuration

Three-dimensional (3D) printed, hierarchically porous nickel molybdenum (NiMo) electrocatalysts were synthesized and evaluated in a flow-through configuration for the hydrogen evolution reaction (HER) in 1.0 M KOH(aq) in a simple electrochemical H-cell. 3D NiMo electrodes possess hierarchically porous structures because of the resol-based aerogel precursor, which generates superporous carbon aerogel as a catalyst support. Relative to a traditional planar electrode configuration, the flow-through configuration allowed efficient removal of the hydrogen bubbles from the catalyst surface, especially at high operating current densities, and significantly decreased the overpotentials required for HER. An analytical model that accounted for the electrokinetics of HER as well as the mass transport with or without the flow-through configuration was developed to quantitatively evaluate voltage losses associated with kinetic overpotentials and ohmic resistance due to bubble formation in the porous electrodes. Furthermore, the chemical composition, electrochemical surface area (ECSA), and roughness factor (RF) were also systematically studied to assess the electrocatalytic performance of the 3D printed, hierarchically porous NiMo electrodes. An ECSA of 25163 cm2 was obtained with the highly porous structures, and an average overpotential of 45 mV at 10 mA cm–2 was achieved over 24 h by using the flow-through configuration. The flow-through configuration evaluated in the simple H-cell achieved high electrochemical accessible surface areas for electrochemical reactions and provided useful information for adaption of the porous electrodes in flow cells.

08 HYDROGEN↗

DOE OSTI2023

Dark matter halo mass functions and density profiles from mass and energy cascade

Abstract Halo abundance and structure play a central role for modeling structure formation and evolution. Without relying on a spherical or ellipsoidal collapse model, we analytically derive the halo mass function and cuspy halo density (inner slope of −4/3) based on the mass and energy cascade theory in dark matter flow. The hierarchical halo structure formation leads to halo or particle random walk with a position-dependent waiting time $$\tau _g$$ τ g . First, the inverse mass cascade from small to large scales leads to the halo random walk in mass space with $$\tau _g\propto m_h^{-\lambda }$$ τ g ∝ m h - λ , where $$m_h$$ m h is the halo mass and $$\lambda$$ λ is a halo geometry parameter with predicted value of 2/3. The corresponding Fokker-Planck solution for halo random walk in mass space gives rise to the halo mass function with a power-law behavior on small scale and exponential decay on large scale. This can be further improved by considering two different $$\lambda$$ λ for haloes below and above a critical mass scale $$m_h^*$$ m h ∗ , i.e. a double- $$\lambda$$ λ halo mass function. Second, a double- $$\gamma$$ γ density profile can be derived based on the particle random walk in 3D space with a position-dependent waiting time $$\tau _g \propto \Phi (r)^{-1} \propto r^{-\gamma }$$ τ g ∝ Φ ( r ) - 1 ∝ r - γ , where $$\Phi$$ Φ is the gravitational potential and r is the particle distance to halo center. Theory predicts $$\gamma =2/3$$ γ = 2 / 3 that leads to a cuspy density profile with an inner slope of −4/3, consistent with the predicted scaling laws from energy cascade. The Press-Schechter mass function and Einasto density profile are just special cases of proposed models. The small scale permanence can be identified due to the scale-independent rate of mass and energy cascade, where density profiles of different halo masses and redshifts converge to the $$-4/3$$ - 4 / 3 scaling law ( $$\rho _h \propto r^{-4/3}$$ ρ h ∝ r - 4 / 3 ) on small scales. Theory predicts the halo number density scales with halo mass as $$\propto m_h^{-1.9}$$ ∝ m h - 1.9 , while the halo mass density scales as $$\propto m_h^{4/9}$$ ∝ m h 4 / 9 . Results were compared against the Illustris simulations. This new perspective provides a theory for nearly universal halo mass functions and density profiles.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Controlling reversible phase transitions in rare-earth nickelates for novel memory devices

Resistive switching in correlated complex oxides is lucrative for emerging applications in neuromorphic computing, and densely scaled non-volatile memory. Electrical conductance of such complex oxides can be controllable switched across multiple orders of magnitude by either (a) electroforming a conduction channel (e.g., in tungsten oxide), or (b) inducing Mott-Hubbard transition (e.g., in rare-earth nickelates)– both via controlled migration of defects (such as oxygen vacancies) under applied bias. Nevertheless, the promise of such defect-driven electronic transitions are far from realized due to a lack of fundamental understanding of the atomic-scale processes that underlie migration and spatiotemporal evolution of oxygen vacancies over nano-to-mesoscopic length/timescales under applied electric field. In this project, we employ a synergistic integration of density functional theory (DFT) calculations, ab initio/classical molecular dynamics (AIMD/CMD) simulations, machine learning (ML), precision synthesis, and multi-modal X-ray imaging experiments to address this knowledge gap. Such an integrated approach offers to elucidate the correlations between subtle structural distortion and oxidation states; treat localized charge carriers; describe defect/ion transport in the presence of electric field; and, in turn, greatly advance the current understanding of microstructural evolution in complex oxides under applied bias. The fundamental knowledge gained from this work will enable precise control over hierarchical defect structures and unravel new routes to manipulate resistance states in complex oxides. This, in turn, will accelerate design of novel devices with desired set of neural functionalities, and high-speed densely-scaled resistive random access memory technologies.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Hierarchical morphologies in co-sputter deposited thin films

Co-depositions of immiscible alloy films at specific processing conditions have yielded hierarchical microstructures which consist of distinct features at multiple length scales, often agglomerates and concentration modulations on the sub-micrometer-scale and fine nanoprecipitates in a matrix on the nanoscale. The present work examined a series of immiscible alloy systems: Cu-Mo, Cu-Ag, Cu-Fe, Cu-Ta, Mo-Ag, Cu-Mo-Ag, to determine the kinetic conditions favorable for hierarchical organization and the formation mechanism of such structures. Thin films of six immiscible systems were sputter co-deposited over a range of deposition rates from 0.12 to 2 nm/s and various temperatures from 400 to 800°C. The resulting microstructures indicate that hierarchical structures form with sufficient disparity in kinetic energy between the constituent atoms, one species being highly mobile (A) and the other relatively immobile (B). This condition arises typically at elevated deposition temperatures and reduced deposition rates but is also alloy dependent. The hierarchical structures form during deposition via phase separation and self-organization processes across the multiple length scales. The adatoms diffuse on the film surface with the highly mobile species swiftly agglomerating into A-rich domains within which B-rich nanoprecipitates form, often self-organizing into periodic arrays. The smallest B-rich nanoprecipitates in the A-rich domains are found to be coherent and in a metastable crystal structure (B taking the structure of A), but coarser precipitates that exhibit the equilibrium structure of B element. The A-rich domains are surrounded by a B-rich matrix that phase-separates into a concentration modulated structure. In conclusion, the observations are interpreted via a model incorporating material properties and process parameters.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Hierarchical quark and lepton masses with sequential U(1) gauge symmetry

Instead of right-handed neutrino singlets, the standard model is extended to include lepton triplets (Σ + , Σ 0 , Σ - ). Each quark and lepton family may now transform under an anomaly-free U(1) X gauge symmetry, known already for many years. A new sequential application is presented, using just the one Higgs doublet of the standard model, together with two U(1) X Higgs singlets. The resulting structure has hierarchical quark and lepton masses, as well as a viable seesaw neutrino mass matrix.

79 ASTRONOMY AND ASTROPHYSICS↗