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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 523 records · Page 29
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Designing 1D multiheme peptide amphiphile assemblies reminiscent of natural systems

We discuss protein assemblies that bind and organize ordered arrays of cofactors yield function structures. Multiheme assemblies found in nature yield electronically conductivity 1D nanoscale fibers and are employed in anaerobic respiration. To understand the fundamental characteristics of these organized arrays, the design of peptide amphiphiles that assemble into 1D nanostructures and yield metalloporphyrin binding sites is presented. One challenge with this class of peptide amphiphiles is identifying the correct sequence composition for high affinity binding with high heme density. Here, the peptide c16-AH(Kx)n-CO 2 H is explored to identify the impact of sequence length (n) and amino acid identity (x = L, I, or F) on binding affinity and midpoint potential. When n = 2, the peptide assembly yields the greatest affinity. The resulting nanoscale assemblies yield ordered arrays of the redox active molecule heme and have potential utility in the development of supramolecular bioelectronic materials useful in sensing as well as the development of enzymatic materials.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2023

Sequence-dependent self-assembly of supramolecular nanofibers in periodic dynamic block copolymers

Block copolymers (BCPs) can spontaneously self-assemble into various nanostructured morphologies which enable their diverse applications in selective membranes, polymer electrolytes, and optoelectronics. To expand the range of nanostructures accessible to block copolymers, we designed dynamic block copolymers (DBCPs) that combine the phase separation of traditional block copolymers with the supramolecular self-assembly of periodic dynamic polymers. We demonstrate that DBCPs synthesized with a periodic block sequence self-assemble into high aspect ratio supramolecular nanofibers with well-ordered PEG and PDMS domains, in contrast to those synthesized with a random sequence which do not form nanofibers but have disordered morphologies. The periodicity of the block sequence ensures regular placement of dynamic bonds along the polymer chain, which enables stacking of the hydrogen bonding units into ordered 1D supramolecular nanofibers and delays the onset of terminal flow by up to 60 °C compared to the random block sequence. The hierarchically assembled supramolecular nanofibers display complex mechanical and thermal phase behavior arising from the interplay between phase separation of the dissimilar polymer backbones and supramolecular interactions between dynamic bonds. Despite identical bulk composition, the periodic DBCPs demonstrate ionic conductivity values over two orders of magnitude higher than their random counterparts due to the formation of well-ordered, interconnected, high aspect ratio ion-transporting PEG domains. In conclusion, these results highlight the potential for DBCPs as an emerging material platform to achieve advanced, self-assembled nanostructured morphologies.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Assembly of small silica nanoparticles using lipid-tethered DNA ‘bonds’

Single-stranded DNA molecules modified with cholesterol functional groups are physically tethered to silica nanoparticles (diameter 25 nm) that are encapsulated in a lipid bilayer. Such tethering increases the azimuthal mobility of the DNA molecules across the nanoparticle surface and enables nonspecific bonding, eliminating the need for specialized surface chemistries (such as silane or thiol ligands). To induce assembly, double-stranded DNA ‘bridge’ molecules are then added with complementary nucleotides to the DNA ‘anchor’ molecules that are physically tethered to the lipids on the surface of the particles. Assembly is observed to occur at room temperature and without the need for temperature annealing. Using automated liquid handling tools, assemblies are created in high throughput and rapidly characterized using SAXS. It is determined that the relative concentration of DNA-to-silica and the ionic strength of the solution are important parameters that affect the resulting assembly. Analysis of SAXS data is performed using coarse-grained particle dynamics simulations. The results support the spontaneous formation of semi-crystalline particle assemblies by particle condensation, where the interparticle distance is tuned by the sequence of the DNA ‘bridge’ used to link the particles. Crystallinity analysis performed on the resulting simulations, optimized to match SAXS observations, suggest that particle clusters display increased crystallinity in the center of the clusters, but their maximum size remains relatively small (sub-micron) before settling occurs, which limits the extent of crystallization.

Chiang, Huat Thart [Univ. of Washington, Seattle, ↗
DOE OSTI2025

Electrosome assembly: Structural insights from high voltage-activated calcium channel (CaV)–chaperone interactions

Ion channels are multicomponent complexes (termed here as“electrosomes”) that conduct the bioelectrical signals required for life. It has been appreciated for decades that assembly is critical for proper channel function, but knowledge of the factors that undergird this important process has been lacking. Although there are now exemplar structures of representatives of most major ion channel classes, there has been no direct structural information to inform how these complicated, multipart complexes are put together or whether they interact with chaperone proteins that aid in their assembly. Recent structural characterization of a complex of the endoplasmic membrane protein complex (EMC) chaperone and a voltage-gated calcium channel (CaV) assembly intermediate comprising the pore-forming CaVα1 and cytoplasmic CaVβ subunits offers the first structural view into the assembly of a member of the largest ion channel class, the voltagegated ion channel (VGIC) superfamily. The structure shows how the EMC remodels the CaVα1/CaVβ complex through a set of rigid body movements for handoff to the extracellular CaVα2δ subunit to complete channel assembly in a process that involves intersubunit coordination of a divalent cation and ordering of CaVα1 elements. These findings set a new framework for deciphering the structural underpinnings of ion channel biogenesis that has implications for understanding channel function, how drugs and disease mutations act, and for investigating how other membrane proteins may engage the ubiquitous EMC chaperone.

Biochemistry & Molecular Biology↗
DOE OSTI2019

Free energy of metal-organic framework self-assembly

Metal-organic frameworks (MOFs) represent an important class of materials. Careful selection of building blocks allows for tailoring of the properties of the resulting framework. The self-assembly process, however, is not understood, and without detailed knowledge of the underlying molecular mechanism, it is difficult to anticipate whether a particular design can be realized, or whether the material adopts a metastable, kinetically arrested state. We present a detailed examination of early-stage self-assembly pathways of the MOF-5. Enhanced sampling techniques are used to model a self-assembly in an explicit solvent (dimethylformamide, DMF). We identify several free energy barriers encountered during the assembly of the final MOF, which arise from structural rearrangements preceding MOF formation and from disrupted MOF-solvent interactions as formation proceeds. In all cases considered here, MOFs exhibit favorable entropic gains during the assembly. More generally, the strategy presented provides a step toward the experimental design characterizing the formation of ordered frameworks and possible sources of polymorphism.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Dissipative particle dynamics for directed self-assembly of block copolymers

The dissipative particle dynamics (DPD) simulation method has been shown to be a promising tool to study self-assembly of soft matter systems. In particular, it has been used to study block copolymer (BCP) self-assembly. However, previous parameterizations of this model are not able to capture most of the rich phase behaviors of BCPs in thin films nor in directed self-assembly (chemoepitaxy or graphoepitaxy). Here, we extend the applicability of the DPD method for BCPs to make it applicable to thin films and directed self-assembly. Our new reparameterization not only is able to reproduce the bulk phase behavior but also manages to predict thin film structures obtained experimentally from chemoepitaxy or graphoepitaxy. A number of different complex structures, such as bilayer nanomeshes, 90° bend structures, circular cylinders/lamellae and Frank-Kasper phases directed by trenches, and post arrays or chemically patterned substrates, have all been reproduced in this work. This reparameterized DPD model should serves as a powerful tool to predict BCP self-assembly, especially in some complex systems where it is difficult to implement self-consistent field theory.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Photophysics of graphene quantum dot assemblies with axially coordinated cobaloxime catalysts

We report a study of chromophore-catalyst assemblies composed of light harvesting hexabenzocoronene (HBC) chromophores axially coordinated to two cobaloxime complexes. The chromophore-catalyst assemblies were prepared using bottom-up synthetic methodology and characterized using solid-state NMR, IR, and x-ray absorption spectroscopy. Detailed steady-state and time-resolved laser spectroscopy was utilized to identify the photophysical properties of the assemblies, coupled with time-dependent DFT calculations to characterize the relevant excited states. The HBC chromophores tend to assemble into aggregates that exhibit high exciton diffusion length (D = 18.5 molecule 2 /ps), indicating that over 50 chromophores can be sampled within their excited state lifetime. We find that the axial coordination of cobaloximes leads to a significant reduction in the excited state lifetime of the HBC moiety, and this finding was discussed in terms of possible electron and energy transfer pathways. By comparing the experimental quenching rate constant (1.0 × 10 9 s -1 ) with the rate constant estimates for Marcus electron transfer (5.7 × 10 8 s -1 ) and Förster/Dexter energy transfers (8.1 × 10 6 s -1 and 1.0 × 10 10 s -1 ), we conclude that both Dexter energy and Marcus electron transfer process are possible deactivation pathways in CoQD-A. No charge transfer or energy transfer intermediate was detected in transient absorption spectroscopy, indicating fast, subpicosecond return to the ground state. Finally, these results provide important insights into the factors that control the photophysical properties of photocatalytic chromophore-catalyst assemblies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Upsampling Monte Carlo reactor simulation tallies in depleted LWR assemblies fueled with LEU and HALEU using a convolutional neural network

Simulating nuclear reactor cores at the highest achievable spatial and energy resolution is critical in modeling these systems accurately. Increasing the resolution, however, can dramatically increase the memory and central processing unit time required to run simulations. A convolutional neural network was shown previously to accurately upsample tally results of simulated light water reactor assemblies fueled with fresh, low enriched uranium. Here, we show that a convolutional neural network can be used to upsample tally results in assemblies containing fresh and depleted fuel enriched from 1.6 to 19.9 atom percent. The network was trained using neutron flux tallies from simulations of light water reactor assemblies with a range of fuel and coolant temperatures and a diverse selection of geometries. Accurate predictions of flux tallies are possible even on test assemblies with geometries and burnup levels well outside the range of those present in the training and validation data. The network improves the data density by a factor of 8 over a broad range of light water reactor assemblies while incurring insignificant additional computational cost to a Monte Carlo simulation.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2019

Retractile lysyl-tRNA synthetase-AIMP2 assembly in the human multi-aminoacyl-tRNA synthetase complex

Multi-aminoacyl-tRNA synthetase complex (MSC) is the second largest machinery for protein synthesis in human cells and also regulates multiple nontranslational functions through its components. Prior studies have shown that the MSC can respond to external signals by releasing its components to function outside it. The internal assembly is fundamental to MSC regulation. Here, using crystal structural analyses (at 1.88 Å resolution) along with molecular modeling, gel-filtration chromatography, and co-immunoprecipitation, we report that human lysyl-tRNA synthetase (LysRS) forms a tighter assembly with the scaffold protein aminoacyl-tRNA synthetase complex-interacting multifunctional protein 2 (AIMP2) than previously observed. Wefound that two AIMP2 N-terminal peptides form an antiparallel scaffold and hold two LysRS dimers through four binding motifs and additional interactions. Of note, the four catalytic subunits of LysRS in the tightly assembled complex were all accessible for tRNA recognition. We further noted that two recently reported human disease-associated mutations conflict with this tighter assembly, cause LysRS release from the MSC, and inactivate the enzyme. These findings reveal a previously unknown dimension of MSC subcomplex assembly and suggest that the retractility of this complex may be critical for its physiological functions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Structure and function of Spc42 coiled-coils in yeast centrosome assembly and duplication

Centrosomes and spindle pole bodies (SPBs) are membraneless organelles whose duplication and assembly is necessary for bipolar mitotic spindle formation. The structural organization and functional roles of major proteins in these organelles can provide critical insights into cell division control. Spc42, a phosphoregulated protein with an N-terminal dimeric coiled-coil (DCC), assembles into a hexameric array at the budding yeast SPB core, where it functions as a scaffold for SPB assembly. Here, we present in vitro and in vivo data to elucidate the structural arrangement and biological roles of Spc42 elements. Crystal structures reveal details of two additional coiled-coils in Spc42: a central trimeric coiled-coil and a C-terminal antiparallel DCC. Contributions of the three Spc42 coiled-coils and adjacent undetermined regions to the formation of an ~145 Å hexameric lattice in an in vitro lipid monolayer assay and to SPB duplication and assembly in vivo reveal structural and functional redundancy in Spc42 assembly. We propose an updated model that incorporates the inherent symmetry of these Spc42 elements into a lattice, and thereby establishes the observed sixfold symmetry. The implications of this model for the organization of the central SPB core layer are discussed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

On the influence of halo mass accretion history on galaxy properties and assembly bias

Halo assembly bias is the secondary dependence of the clustering of dark matter haloes on their assembly histories at fixed halo mass. This established dependence is expected to manifest itself on galaxy clustering, a potential effect commonly known as galaxy assembly bias. Using the IllustrisTNG300 magnetohydrodynamical simulation, in this work we analyse the dependence of the properties and clustering of galaxies on the specific mass accretion history of their hosting haloes (sMAH). We first show that several halo and galaxy properties strongly correlate with the slope of the sMAH (β) at fixed halo mass. Haloes with increasingly steeper β increment their masses faster early on, and their hosted galaxies present larger stellar-to-halo mass ratios, lose their gas faster, reach the peak of their star formation histories at higher redshift, and become quenched earlier. We also demonstrate that β provides a more stable link to these key galaxy formation properties than other broadly employed halo proxies, such as formation time. Finally, we measure the secondary dependence of galaxy clustering on β at fixed halo mass. By tracing back the evolution of individual haloes, we show that the amplitude of the galaxy assembly bias signal for the progenitors of z = 0 galaxies increases with redshift, reaching a factor of 2 at z = 1 for haloes of Mhalo = 10 11.5 –10 12 h –1 M ⊙ . The measurement of the evolution of assembly bias along the merger tree provides a new theoretical perspective to the study of secondary bias. Our findings have also important implications for the generation of mock catalogues for upcoming cosmological surveys.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2018

Programmable self-assembly of diamond polymorphs from chromatic patchy particles

In this paper, we present a method of controlling polymorphism in self-assembly and apply it to the long-standing problem of assembly of a colloidal diamond. The latter is often viewed as the “holy grail” of the self-assembly field, due to the challenge that it presents as well as thanks to its potential as a step towards manufacturing of photonic band-gap materials. In our approach, we use a “chromatic” version of traditional building blocks, the so-called patchy particle. Namely, the individual patches that belong to the same particle in our model are distinguishable (“colored”) and their pairwise interactions are color dependent, which could be implemented with the help of DNA fictionalization. We propose a design procedure and verify it with the help of Brownian dynamics simulations. Not only are we able to “program” the self-assembly of a high-quality cubic diamond lattice, but a small modification of the coloring scheme also allows us to “reprogram” the system to assemble into the alternative polymorph, a hexagonal diamond.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Parallel String Graph Construction and Transitive Reduction for De Novo Genome Assembly

One of the most computationally intensive tasks in computational biology is de novo genome assembly, the decoding of the sequence of an unknown genome from redundant and erroneous short sequences. A common assembly paradigm identifies overlapping sequences, simplifies their layout, and creates consensus. Despite many algorithms developed in the literature, the efficient assembly of large genomes is still an open problem. In this work, we introduce new distributed-memory parallel algorithms for overlap detection and layout simplification steps of de novo genome assembly, and implement them in the diBELLA 2D pipeline. Our distributed memory algorithms for both overlap detection and layout simplification are based on linear-algebra operations over semirings using 2D distributed sparse matrices. Our layout step consists of performing a transitive reduction from the overlap graph to a string graph. We provide a detailed communication analysis of the main stages of our new algorithms. diBELLA 2D achieves near linear scaling with over 80% parallel efficiency for the human genome, reducing the runtime for overlap detection by 1.2-1.3× for the human genome and 1.5-1.9× for C.elegans compared to the state-of-the-art. Our transitive reduction algorithm outperforms an existing distributed-memory implementation by 10.5-13.3× for the human genome and 18-29× for the C. elegans. Our work paves the way for efficient de novo assembly of large genomes using long reads in distributed memory.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Dynamic microbial assembly processes correspond to soil fertility in sustainable paddy agroecosystems

1. Microorganisms underpin the sustainability of agroecosystems, but we have a poor understanding of how the assembly processes that govern microbial community structure interact through time to maintain soil fertility. 2. Ancient rice paddies have a history of cultivation spanning hundreds or thousands of years and provide an ideal opportunity to explore relationships between community assembly processes and long-term agroecosystem sustainability. We used statistical null models to evaluate temporal patterns of bacterial community assembly processes across rice cultivation years and their associations with increases in soil fertility in paddy agroecosystems. 3. We found that stochasticity was a persistent force structuring paddy soil microbial communities, putatively due to frequent flooding that facilities dispersal. However, determinism gradually increased over centuries of agriculture and corresponded to increases in soil fertility. Accordingly, multifunctionality, calculated using enzymes catalyzing key soil functions in carbon, nitrogen, phosphorous and sulfur cycling significantly increased along rice cultivation years. We therefore propose that balanced assembly processes preserve a diverse array of traits that can dominate under various circumstances (stochasticity) while allowing for traits relevant to soil fertility to be selected for by soil fertility (determinism), thus supporting multifunctionality that underlies sustainable agroecosystems. 4. In total, our results highlight that knowledge on temporal microbial assembly processes, community composition, and ecological function in context of soil fertility is key to understanding ecological mechanisms maintaining agroecosystems sustainability.

Liu, Wenjing↗
DOE OSTI2022

The ecological assembly of bacterial communities in Antarctic wetlands varies across levels of phylogenetic resolution

Summary As functional traits are conserved at different phylogenetic depths, the ability to detect community assembly processes can be conditional on the phylogenetic resolution; yet most previous work quantifying their influence has focused on a single level of phylogenetic resolution. Here, we have studied the ecological assembly of bacterial communities from an Antarctic wetland complex, applying null models across different levels of phylogenetic resolution (i.e. clustering ASVs into OTUs with decreasing sequence identity thresholds). We found that the relative influence of the community assembly processes varies with phylogenetic resolution. More specifically, selection processes seem to impose stronger influence at finer (100% sequence similarity ASV) than at coarser (99%–97% sequence similarity OTUs) resolution. We identified environmental features related with the ecological processes and propose a conceptual model for the bacterial community assembly in this Antarctic ecosystem. Briefly, eco‐evolutionary processes appear to be leading to different but very closely related ASVs in lotic, lentic and terrestrial environments. In all, this study shows that assessing community assembly processes at different phylogenetic resolutions is key to improve our understanding of microbial ecology. More importantly, a failure to detect selection processes at coarser phylogenetic resolution does not imply the absence of such processes at finer resolutions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

HiFiAdapterFilt, a memory efficient read processing pipeline, prevents occurrence of adapter sequence in PacBio HiFi reads and their negative impacts on genome assembly

Abstract Background Pacific Biosciences HiFi read technology is currently the industry standard for high accuracy long-read sequencing that has been widely adopted by large sequencing and assembly initiatives for generation of de novo assemblies in non-model organisms. Though adapter contamination filtering is routine in traditional short-read analysis pipelines, it has not been widely adopted for HiFi workflows. Results Analysis of 55 publicly available HiFi datasets revealed that a read-sanitation step to remove sequence artifacts derived from PacBio library preparation from read pools is necessary as adapter sequences can be erroneously integrated into assemblies. Conclusions Here we describe the nature of adapter contaminated reads, their consequences in assembly, and present HiFiAdapterFilt, a simple and memory efficient solution for removing adapter contaminated reads prior to assembly.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

PRESERVATION OF THE HIGH QUALITY FACTOR AND ACCELERATING GRADIENT OF Nb3Sn-COATED CAVITY DURING PAIR ASSEMBLY

Two CEBAF 5-cell accelerator cavities have been coated with Nb3Sn film using the vapor diffusion technique. One cavity was coated in the Jefferson Lab Nb3Sn cavity coating system, and the other in the Fermilab Nb3Sn coating system. Both cavities were measured at 4 K and 2 K in the vertical dewar test in each lab and then assembled into a cavity pair at Jefferson Lab. Previous attempts to assemble Nb3Sn cavities into a cavity pair degraded the superconducting properties of Nb3Sn-coated cavities. This contribution discusses the efforts to identify and mitigate the pair assembly challenges and will present the results of the vertical tests before and after pair assembly. Notably, one of the cavities reached the highest gradient above 80 mT in the vertical test after the pair assembly.

Eremeev, G.V.↗
DOE OSTI2019

Gamma-ray Analysis of the Pressurized-Water-Reactor and Boiling-Water-Reactor Assemblies

Conclusions: Passive gamma analysis can be used to determine BU, CT, and IE of spent fuel assembly. Assemblies with small CT give best results.; Without any operator declaration, a 10 minutes measurement time of a PWR assembly can give the results for BU, CT, and IE with about 3% accuracy.; BWR analysis is more complicated and less effective than PWR and the results are somewhat less accurate.; A set of 4 measurements at 4 corners of an assembly can average out the variations of the assembly positions in the reactor during the burn cycles and can result in a better accuracy.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗