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At least 343 records · Page 19

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DOE OSTI2018

Electron Dose-Controlled Formation, Growth, and Assembly of Nanoclusters and Nanoparticles from Aurophilic Au(I)–Thiolate Ensemble on Surfaces

The ability to precisely control electron irradiationinduced formation, growth, and assembly of nanoclusters or nanoparticles on a solid surface is important for design and creation of catalytically or chemically active surface sites and interfaces free from chemical reducing agents. Here, we show the results of an investigation of the electron dose-controlled formation, growth, and assembly of nanoclusters and nanoparticles in a molecularly assembled thin film of Au(I)–thiolate motifs on a substrate, highlighting an in situ monitoring of the evolution of morphology under controlled electron dose. With aurophilic motifs of Au(I)–thiolate being confined by electrostatic interactions, the sizes of Au nanoclusters and nanoparticles were shown to increase with electron dose, revealing a propensity of a string alignment of the grown nanoclusters and nanoparticles. This growth preference to onedimensional assembly is supported by the analysis of the surface reaction kinetics in terms of the surface density of electron dose for the growth of the nanoclusters and nanoparticles. Here, the electron dose-controlled size-focusing and directional assembly of nanoclusters and nanoparticles may be exploited as new strategy for the precise control of nanoclusters or nanoparticles and their assemblies on solid surfaces not only free from chemical reducing agent but also with the ability of visual monitoring of the morphological evolution during growth.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Substrate-Directed Dimensional and Phase Control of Peptide Assemblies on Two-Dimensional van der Waals Materials

Understanding and controlling biomolecular self-assembly on van der Waals (vdW) materials has the potential to advance hybrid bioelectronic devices by enabling precise tuning of the interface and modulation of the resulting electronic properties of the biomolecule-vdW heterostructure. However, how surface properties of vdW materials direct biomolecule assembly remains poorly understood. To fill this knowledge gap, we investigated the assembly of a peptide known to assemble into two-dimensional (2D) crystalline films on MoS 2 on three representative vdW surfaces: WS 2 , MoS 2 , and highly oriented pyrolytic graphite (HOPG). Using in situ atomic force microscopy (AFM), we find that assembly is substrate-dependent, resulting in multilayers on WS 2 , monolayers on MoS 2 , and multiple coexisting phases on HOPG. WS 2 exhibits a higher negative charge, strong long-range electrostatic interactions, and extensive hydration layering that may promote multilayer stacking. In contrast, MoS 2 has stronger short-range interactions with the peptides but much weaker long-range interactions and hydration structure, which may favor monolayer formation. Molecular dynamics simulations predict a corresponding switch from monolayer to multilayer aggregates of the adsorbed monomers, reflected in their relative mobilities. On hydrophobic HOPG, the peptides bind most strongly and remain as monomers with high surface mobility. The peptide dimers comprising the basic unit of the crystals are more compact on HOPG, which has a smaller lattice constant than WS 2 or MoS 2 , suggesting strain contributes to stabilizing multiple phases. Our results provide mechanistic insights into how surface charge and hydration structure, and the lattice structure of the substrates governs peptide assembly on vdW materials, offering a framework to rationally control the 2D peptide-vdW heterostructures.

Molecular dynamics simulations↗

DOE OSTI2026

Polymorphism in Self-Assembly of Short Peptoid Sequences

Due to various applications enabled by diverse morphologies of self-assembled sequence-defined polymers, controlling the self-assembly of synthetic peptidomimetics into designed morphologies has emerged as a promising route for the development of bioinspired functional materials. Herein, we report morphological control over the assembly of a series of short peptoids, or poly-N-substituted glycines, that contain asymmetric hydrophobic domains. We demonstrate that the inherent flexibility of amphiphilic peptoid bilayers drives assembly polymorphism, resulting in the coexistence of nanosheets, twisted ribbons, and nanofibers three distinct morphologies. By tuning peptoid molecular interactions through variations in sequence design, solution pH, and temperature, we demonstrate precise control over the twisting and folding of peptoid bilayers, enabling the formation of well-defined nanosheets and nanohelices. Molecular dynamics simulations further unravel how the introduction of asymmetric hydrophobic domains enables the flexibility of peptoid bilayers and results in peptoid assembly polymorphism. By tuning peptoid molecular interactions through heating, we further demonstrate the transformation of nanosheets into nanohelices. We envision that our mechanistic investigation of peptoid assembly polymorphism provides a strong foundation for leveraging peptoid sequences and chemistries to achieve controlled molecular interactions, driving the creation of biomimetic materials with tailored morphologies and functionalities.

assembly polymorphism↗

DOE OSTI2018

Wind load analysis of a new linear Fresnel receiver assembly design

A linear Fresnel collector includes a low-profile reflector array and a receiver assembly with one or more absorber tubes and an optional secondary reflector. This combined optical system concentrates sunlight and converts it into thermal energy. The design of a receiver assembly is critical to the performance of a linear Fresnel collector. A position deviation of a few centimeters for the receiver assembly can result in notably reduced performance, thus leading to a direct loss in revenue associated with thermal power production. Wind load is one of the most significant environmental factors that can alter the optical - and therefore thermal - performance of a solar power system due to displacements after installation. At the same time, an over-designed receiver assembly may add unnecessary construction cost to a typically high-cost-constrained system. Thus, wind load analysis is particularly important when considering optimal engineering design of a receiver assembly and its supporting structure to cost-effectively mitigate the impacts of wind. In this study, a detailed computational fluid dynamics (CFD) model is adopted to derive the wind load of a commercial linear Fresnel receiver assembly. This wind load is then used as a reference to optimize the detailed engineering design. The CFD model is first carefully developed and benchmarked within a critical regime toward turbulence. The drag force, lift force, and vortex-shedding frequencies are derived at both the operating and survival wind-speed limits for target project deployment locations. The wind load analysis results provide a valuable reference for future engineering design and prototyping.

17 WIND ENERGY↗

DOE OSTI2019

Construction and comparison of three reference-quality genome assemblies for soybean

Here, we report reference-quality genome assemblies and annotations for two accessions of soybean (Glycine max) and for one accession of Glycine soja, the closest wild relative of G. max. The G. max assemblies provided are for widely used US cultivars: the northern line Williams 82 (Wm82) and the southern line Lee. The Wm82 assembly improves the prior published assembly, and the Lee and G. soja assemblies are new for these accessions. Comparisons among the three accessions show generally high structural conservation, but nucleotide difference of 1.7 single-nucleotide polymorphisms (snps) per kb between Wm82 and Lee, and 4.7 snps per kb between these lines and G. soja. snp distributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgression and haplotype structure. Comparisons against the US germplasm collection show placement of the sequenced accessions relative to global soybean diversity. Analysis of a pan-gene collection shows generally high conservation, with variation occurring primarily in genomically clustered gene families. We found approximately 40-42 inversions per chromosome between either Lee or Wm82v4 and G. soja, and approximately 32 inversions per chromosome between Wm82 and Lee. We also investigated five domestication loci. For each locus, we found two different alleles with functional differences between G. soja and the two domesticated accessions. The genome assemblies for multiple cultivated accessions and for the closest wild ancestor of soybean provides a valuable set of resources for identifying causal variants that underlie traits for the domestication and improvement of soybean, serving as a basis for future research and crop improvement efforts for this important crop species.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Assembly of the Populus Microbiome Is Temporally Dynamic and Determined by Selective and Stochastic Factors

Recent work shows that the plant microbiome, particularly the initial assembly of this microbiome, influences plant health, survival, and fitness. Here, we characterize the initial assembly of the Populus microbiome across ten genotypes belonging to two poplar species in a common garden using 16S rRNA gene and ITS2 region amplicon sequencing of the leaf endosphere, leaf surface, root endosphere, and rhizosphere. We sampled these microbiomes three times throughout the first growing season and found that the composition of the microbiome changed dramatically over time across all plant-associated habitats and host genotypes. For archaea and bacteria, these changes were dominated by strong homogenizing selection (accounting for 29 to 62% of pairwise comparisons). However, fungal assembly was generally characterized by multiple ecological assembly processes (i.e., a mix of weak selective and dispersal processes). Interestingly, genotype, while a significant moderator of microbiome composition, generally explained less variation than sample date across plant-associated habitats. We defined a set of core genera that accounted for, on average, 36% of the microbiome. The relative abundance of this core community was consistent over time. Additionally, using source tracking modeling, we determined that new microbial taxa colonize from both aboveground and belowground sources, and combined with our ecological assembly null models, we found that both selective and dispersal processes explained the differences between exo- (i.e., leaf surface and rhizosphere) and endospheric microbiomes. Taken together, our results suggest that the initial assembly of the Populus microbiome is time-, genotype-, and habitat-dependent and is moderated by both selective and stochastic factors.

16S rRNA↗

DOE OSTI2018

NovoGraph: Human genome graph construction from multiple long-read de novo assemblies

Genome graphs are emerging as an important novel approach to the analysis of high-throughput human sequencing data. By explicitly representing genetic variants and alternative haplotypes in a mappable data structure, they can enable the improved analysis of structurally variable and hyperpolymorphic regions of the genome. In most existing approaches, graphs are constructed from variant call sets derived from short-read sequencing. As long-read sequencing becomes more cost-effective and enables de novo assembly for increasing numbers of whole genomes, a method for the direct construction of a genome graph from sets of assembled human genomes would be desirable. Such assembly-based genome graphs would encompass the wide spectrum of genetic variation accessible to long-read-based de novo assembly, including large structural variants and divergent haplotypes. We present NovoGraph, a method for the construction of a human genome graph directly from a set of de novo assemblies. NovoGraph constructs a genome-wide multiple sequence alignment of all input contigs and creates a graph by merging the input sequences at positions that are both homologous and sequence-identical. NovoGraph outputs resulting graphs in VCF format that can be loaded into third-party genome graph toolkits. To demonstrate NovoGraph, we construct a genome graph with 23,478,835 variant sites and 30,582,795 variant alleles from de novo assemblies of seven ethnically diverse human genomes (AK1, CHM1, CHM13, HG003, HG004, HX1, NA19240). Initial evaluations show that mapping against the constructed graph reduces the average mismatch rate of reads from sample NA12878 by approximately 0.2%, albeit at a slightly increased rate of reads that remain unmapped.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Inferring the Contribution of Microbial Taxa and Organic Matter Molecular Formulas to Ecological Assembly

Understanding the mechanisms underlying the assembly of communities has long been the goal of many ecological studies. While several studies have evaluated community wide ecological assembly, fewer have focused on investigating the impacts of individual members within a community or assemblage on ecological assembly. Here, we adapted a previous null model β-nearest taxon index (βNTI) to measure the contribution of individual features within an ecological community to overall assembly. This new metric, called feature-level βNTI (βNTI feat ), enables researchers to determine whether ecological features (e.g., individual microbial taxa) contribute to divergence, convergence, or have insignificant impacts across spatiotemporally resolved metacommunities or meta-assemblages. Using βNTI feat , we revealed that unclassified microbial lineages often contributed to community divergence while diverse groups (e.g., Crenarchaeota, Alphaproteobacteria, and Gammaproteobacteria) contributed to convergence. We also demonstrate that βNTI feat can be extended to other ecological assemblages such as organic molecules comprising organic matter (OM) pools. OM had more inconsistent trends compared to the microbial community though CHO-containing molecular formulas often contributed to convergence, while nitrogen and phosphorus-containing formulas contributed to both convergence and divergence. A network analysis was used to relate βNTI feat values from the putatively active microbial community and the OM assemblage and examine potentially common contributions to ecological assembly across different communities/assemblages. This analysis revealed that P-containing formulas often contributed to convergence/divergence separately from other ecological features and N-containing formulas often contributed to assembly in coordination with microorganisms. Additionally, members of Family Geobacteraceae were often observed to contribute to convergence/divergence in conjunction with both N- and P-containing formulas, suggesting a coordinated ecological role for family members and the nitrogen/phosphorus cycle. Overall, we show that βNTI feat offers opportunities to investigate the community or assemblage members, which shape the phylogenetic or functional landscape, and demonstrate the potential to evaluate potential points of coordination across various community types.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2023

MMIC-I: A Robotic Platform for Assembly Integration and Internal Locomotion through Mechanical Meta-Material Structures

In-space assembly is crucial to creating large-scale space structures and enabling long term space missions. Natural limitations in the size of transportation vehicles and ISRU production facilities necessitate an additive strategy with the size of the typical structural unit being essentially fixed and inversely proportional to the final assembly size. In prior robotic and space assembly examples, reversible mechanical integration of structural modules is typically achieved with actuated alignment and fastening mechanisms onboard every structural module. Additive assembly or manufacturing planning approaches often feature a “build front” that receives new materials or parts and progresses gradually across the target geometry. The system we describe here places much of the alignment and fastener actuation systems onboard a mobile robot that can operate at a build front while companion robots (Scaling Omni-directional Lattice Locomoting Explorer, SOLLE) provide part or material transportation. The design and evaluation of this Mobile Meta-Material Interior Co-Integrator (MMIC-I), an inchworm-style locomoting robotic assembler, is described here with an emphasis on ease of assembly and a low number of unique parts for a simple design. It is designed to assist in alignment of cuboctahedron structural unit cells with captive fasteners, defining the build front in operation. Adjacent structural unit cells are locked together with specified axial and rotational actuation of the fasteners. Hardware prototypes show that the robot is able to successfully locomote to any indexed location within a lattice structure and bolt together each set of fasteners on any interface.

Robotics↗

DOE OSTI2019

A mini review on two-dimensional nanomaterial assembly

Two-dimensional (2D) nanomaterials have attracted a great deal of attention since the discovery of graphene in 2004, due to their intriguing physicochemical properties and wide-ranging applications in catalysis, energy-related devices, electronics and optoelectronics. To maximize the potential of 2D nanomaterials for their technological applications, controlled assembly of 2D nanobulding blocks into integrated systems is critically needed. This mini review summarizes the reported strategies of 2D materials-based assembly into integrated functional nanostructures, from in-situ assembly method to post-synthesis assembly. Here, the applications of 2D assembled integrated structures are also covered, especially in the areas of energy, electronics and sensing, and we conclude with discussion on the remaining challenges and potential directions in this emerging field.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2024

Nanocrystal Assemblies: Current Advances and Open Problems

Here we explore the potential of nanocrystals (a term used equivalently to nanoparticles) as building blocks for nanomaterials, and the current advances and open challenges for fundamental science developments and applications. Nanocrystal assemblies are inherently multiscale, and the generation of revolutionary material properties requires a precise understanding of the relationship between structure and function, the former being determined by classical effects and the latter often by quantum effects. With an emphasis on theory and computation, we discuss challenges that hamper current assembly strategies and to what extent nanocrystal assemblies represent thermodynamic equilibrium or kinetically trapped metastable states. We also examine dynamic effects and optimization of assembly protocols. Finally, we discuss promising material functions and examples of their realization with nanocrystal assemblies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2020

State of the Profession Considerations: NASA Langley Research Center Capabilities / Technologies for Autonomous In-Space Assembly and Modular Persistent Assets

Successfully implementing OSAM into next generation revolutionary observatories requires integrating expertise and technologies in modular space structures, assembly operations, autonomy, and modeling/simulation. LaRC OSAM technologies/capabilities have been presented to inform the Planetary Science and Astrobiology Decadal Survey community of the robust and mature existing capability to support an OSAM based architecture for their next observatory. LaRC Structures and Assembly capabilities enable; a modular telescope architecture, high-performance structural modules, and robotic assembly techniques. LaRC Autonomy capabilities ensure that the robotic assembly will be accomplished in a safe and robust manner and only require humans in a supervisory role. The LaRC toolbox of Modeling and Simulation capabilities that is calibrated using module-level ground testing, will ensure that the performance of the fully assembled observatory, a very large zero-g system that will never be assembled/tested in a gravity environment, meets all performance requirements when it enters into service. Integrating all three LaRC capabilities and including embedded metrology, will enable servicing, repair, instrument upgrades (and/or replacement) while ensuring a very long lifetime for the observatory and providing a return-on-investment that is substantially greater than the initial cost. Further confidence will be achieved as OSAM technologies are validated in a new LaRC OSAM laboratory that allows large-scale collaborative testing of modular hardware, simulation software and algorithms, and autonomous agents.

Large space structures↗

DOE OSTI2018

Design Rules for Self-Assembly of 2D Nanocrystal/Metal–Organic Framework Superstructures

Here, we demonstrate the guiding principles behind simple two dimensional self-assembly of MOF nanoparticles (NPs) and oleic acid capped iron oxide (Fe 3 O 4 ) NCs into a uniform two-dimensional bi-layered superstructure. This self-assembly process can be controlled by the energy of ligand–ligand interactions between surface ligands on Fe 3 O 4 NCs and Zr 6 O 4 (OH) 4 (fumarate) 6 MOF NPs. Scanning transmission electron microscopy (TEM)/energy-dispersive X-ray spectroscopy and TEM tomography confirm the hierarchical co-assembly of Fe 3 O 4 NCs with MOF NPs as ligand energies are manipulated to promote facile diffusion of the smaller NCs. First-principles calculations and event-driven molecular dynamics simulations indicate that the observed patterns are dictated by combination of ligand–surface and ligand–ligand interactions. This study opens a new avenue for design and self-assembly of MOFs and NCs into high surface area assemblies, mimicking the structure of supported catalyst architectures, and provides a thorough fundamental understanding of the self-assembly process, which could be a guide for designing functional materials with desired structure.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2019

Cooperative Self‐Assembly of Pyridine‐2,6‐Diimine‐Linked Macrocycles into Mechanically Robust Nanotubes

Abstract Nanotubes assembled from macrocyclic precursors offer a unique combination of low dimensionality, structural rigidity, and distinct interior and exterior microenvironments. Usually the weak stacking energies of macrocycles limit the length and mechanical strength of the resultant nanotubes. Imine‐linked macrocycles were recently found to assemble into high‐aspect ratio (>10 3 ), lyotropic nanotubes in the presence of excess acid. Yet these harsh conditions are incompatible with many functional groups and processing methods, and lower acid loadings instead catalyze macrocycle degradation. Here we report pyridine‐2,6‐diimine‐linked macrocycles that assemble into high‐aspect ratio nanotubes in the presence of less than 1 equiv of CF 3 CO 2 H per macrocycle. Analysis by gel permeation chromatography and fluorescence spectroscopy revealed a cooperative self‐assembly mechanism. The low acid concentrations needed to induce assembly enabled nanofibers to be obtained by touch‐spinning, which exhibit higher Young's moduli (1.33 GPa) than many synthetic polymers and biological filaments. These findings represent a breakthrough in the design of inverse chromonic liquid crystals, as assembly under such mild conditions will enable the design of structurally diverse and mechanically robust nanotubes from synthetically accessible macrocycles.

Strauss, Michael J.↗

DOE OSTI2023

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

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

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2018

Design Rules for Self-Assembly of 2D Nanocrystal/Metal-Organic Framework Superstructures

Here we demonstrate the guiding principles behind simple two dimensional self-assembly of MOF nanoparticles (NPs) and oleic acid capped iron oxide (Fe 3 O 4 ) NCs into a uniform two-dimensional bi-layered superstructure. This self-assembly process can be controlled by the energy of ligand–ligand interactions between surface ligands on Fe 3 O 4 NCs and Zr 6 O 4 (OH) 4 (fumarate) 6 MOF NPs. Scanning transmission electron microscopy (TEM)/energy-dispersive X-ray spectroscopy and TEM tomography confirm the hierarchical co-assembly of Fe 3 O 4 NCs with MOF NPs as ligand energies are manipulated to promote facile diffusion of the smaller NCs. First-principles calculations and event-driven molecular dynamics simulations indicate that the observed patterns are dictated by combination of ligand–surface and ligand–ligand interactions. This study opens a new avenue for design and self-assembly of MOFs and NCs into high surface area assemblies, mimicking the structure of supported catalyst architectures, and provides a thorough fundamental understanding of the self-assembly process, which could be a guide for designing functional materials with desired structure.

36 MATERIALS SCIENCE↗

DOE OSTI2023

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

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

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2018

Heat shock protein 70 and heat shock protein 90 synergistically increase hepatitis B viral capsid assembly

Highlights: • Heat shock protein 70 (Hsp70) interacts with Cp149 dimer. • Hsp70 synergistically increases formation of HBV capsid with Hsp90. • Inhibition of Hsp70 reduces HBV biogenesis through suppression of HBV capsid assembly. Hepatitis B virus (HBV) infection can cause chronic liver diseases, cirrhosis, and hepatocellular carcinoma (HCC). Heat shock proteins (Hsps) are important factors in the formation of the HBV capsid and in genome replication during the viral life cycle. Hsp90 is known to promote capsid assembly. However, the functional roles of Hsp70 in HBV capsid assembly with Hsp90 have not been studied so far. Using microscale thermophoresis analyses and in vitro nucleocapsid formation assays, we found that Hsp70 bound to a HBV core protein dimer and facilitated HBV capsid assembly. Inhibition of Hsp70 by methylene blue (MB) led to a decrease in capsid assembly. Moreover, Hsp70 inhibition reduced intracellular capsid formation and HBV virus particle number in HepG2.2.15 cells. Furthermore, we examined synergism between Hsp70 and Hsp90 on HBV capsid formation in vitro. Our results clarify the role of Hsp70 in HBV capsid formation via an interaction with core dimers and in synergistically promoting capsid assembly with Hsp90.

60 APPLIED LIFE SCIENCES↗