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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 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Coarse-Grained Simulations of Polyrotaxane Hydrogels under Quiescent and Shear Conditions

Cyclodextrin-based polyrotaxanes (PR) form hydrogels in water through cyclodextrin (CD) aggregation and crystallization. These networks can break under shear flows, making them versatile platforms for extrusion-based 3D printing. To optimize the material properties of 3D-printed PR gels, a microscopic understanding of the structural evolution during 3D printing is necessary. Here, we employ coarse-grained (CG) simulations to reveal the PR assembly process at the molecular level. Our simulations reproduce the experimental crystal morphologies of PR at varying concentrations and chain lengths under quiescent conditions. Using nonequilibrium simulations, we show shear flow ruptures crystalline domain connectivity in PR gels and stacks the lamellae in the gradient direction, allowing the materials to flow during 3D printing. After the cessation of flow, the anisotropic crystal alignment and absence of available dangling PR diminish the intercrystal connectivity. The printed materials are therefore mechanically weaker than the pristine hydrogels, in agreement with experimental results. Nonetheless, by relating the microscopic structural evolution with viscoelastic properties of PR gels and solutions, we elucidate how flow conditions and sample composition affect the 3D printing performance of PR hydrogels.

Smith, Cameron D. [Dartmouth College, Hanover, NH ↗
DOE OSTI2024

Symmetry-Breaking Charge Transfer in Metal–Organic Frameworks

High quantum-yield charge carrier generation from the initially prepared excitons defines a key step in the light-harvesting and conversion scheme. Photoinduced charge transfer in molecular electron donor—acceptor assemblies is driven by a sizable ΔG 0 , which compromises the potential of the generated carriers. Reminiscent of the special pair at the reaction center of the natural light-harvesting complex, symmetry-breaking charge transfer (SBCT) within a pair of identical struts of metal-organic framework (MOF) will facilitate the efficient generation of long-lived charge carriers with maximized potentials without incorporating any foreign redox species. We report SBCT in pyrene-based zirconium metal–organic framework (MOF) NU-1000 that leads to efficient generation of radical ions in a polar solvent and bound CT states in a low-polar solvent. Further, the probe unveils the role of the low-lying non-Franck–Condon excitonic states as intermediates in the formation of the SBCT state from the initially prepared Franck–Condon S 1 states. Ultrafast and transient spectroscopy—probed over 200 fs-30 μs time scale-evinces a k SBCT = (110 ps) -1 in polar media (ε s = 37.5) forming solvated radical ions with recombination rate k CR = (~45 ns) -1 . A slower rate with k SBCT = (203 ps) -1 was recorded in low-polar (ε s = 7.0) solvent manifesting a bound [TBAPy •+ TBAPy •– ] state with k CR ≈ (17 μs) -1 . This discovery, along with other unique photophysical features relevant to light harvesting, should define a MOF-based platform for developing heterogeneous artificial photon energy conversion systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Metaproteomics reveals insights into microbial structure, interactions, and dynamic regulation in defined communities as they respond to environmental disturbance

Abstract Background Microbe-microbe interactions between members of the plant rhizosphere are important but remain poorly understood. A more comprehensive understanding of the molecular mechanisms used by microbes to cooperate, compete, and persist has been challenging because of the complexity of natural ecosystems and the limited control over environmental factors. One strategy to address this challenge relies on studying complexity in a progressive manner, by first building a detailed understanding of relatively simple subsets of the community and then achieving high predictive power through combining different building blocks (e.g., hosts, community members) for different environments. Herein, we coupled this reductionist approach with high-resolution mass spectrometry-based metaproteomics to study molecular mechanisms driving community assembly, adaptation, and functionality for a defined community of ten taxonomically diverse bacterial members of Populus deltoides rhizosphere co-cultured either in a complex or defined medium. Results Metaproteomics showed this defined community assembled into distinct microbiomes based on growth media that eventually exhibit composition and functional stability over time. The community grown in two different media showed variation in composition, yet both were dominated by only a few microbial strains. Proteome-wide interrogation provided detailed insights into the functional behavior of each dominant member as they adjust to changing community compositions and environments. The emergence and persistence of select microbes in these communities were driven by specialization in strategies including motility, antibiotic production, altered metabolism, and dormancy. Protein-level interrogation identified post-translational modifications that provided additional insights into regulatory mechanisms influencing microbial adaptation in the changing environments. Conclusions This study provides high-resolution proteome-level insights into our understanding of microbe-microbe interactions and highlights specialized biological processes carried out by specific members of assembled microbiomes to compete and persist in changing environmental conditions. Emergent properties observed in these lower complexity communities can then be re-evaluated as more complex systems are studied and, when a particular property becomes less relevant, higher-order interactions can be identified.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Permeability of the HIV-1 capsid to metabolites modulates viral DNA synthesis

Reverse transcription, an essential event in the HIV-1 life cycle, requires deoxynucleotide triphosphates (dNTPs) to fuel DNA synthesis, thus requiring penetration of dNTPs into the viral capsid. The central cavity of the capsid protein (CA) hexamer reveals itself as a plausible channel that allows the passage of dNTPs into assembled capsids. Nevertheless, the molecular mechanism of nucleotide import into the capsid remains unknown. Employing all-atom molecular dynamics (MD) simulations, we established that cooperative binding between nucleotides inside a CA hexamer cavity results in energetically favorable conditions for passive translocation of dNTPs into the HIV-1 capsid. Furthermore, binding of the host cell metabolite inositol hexakisphosphate (IP 6 ) enhances dNTP import, while binding of synthesized molecules like benzenehexacarboxylic acid (BHC) inhibits it. The enhancing effect on reverse transcription by IP 6 and the consequences of interactions between CA and nucleotides were corroborated using atomic force microscopy, transmission electron microscopy, and virological assays. Collectively, our results provide an atomistic description of the permeability of the HIV-1 capsid to small molecules and reveal a novel mechanism for the involvement of metabolites in HIV-1 capsid stabilization, nucleotide import, and reverse transcription.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Biomolecular Films for Direct Air Capture of CO 2

Efficient utilization of CO 2 is amongst the most critical cost drivers in algal biomass production in open pond systems. CO 2 delivery costs represent approximately 20% of the final biomass selling price in algal mass cultivation systems. Technologies that enable direct air capture (DAC) of atmospheric CO 2 to decouple algae cultivation from CO 2 point sources thus present an opportunity to improve the economics and resource potential of algal biomass. Current DAC technologies typically employ amine- or caustic-based absorption, demanding significant water and/or energy inputs and incurring substantial capital expenditures. Conversely, bio-based approaches to DAC offer a means to bypass conventional technoeconomic and sustainability hurdles. We integrate recent advances in computational metabolic modeling, algal genetic engineering, algal cultivation, and algal biomass upgrading to enable directed localization and self-assembly of carbonic anhydrase molecular films to gas-liquid interfaces for enhanced CO 2 capture and conversion.

09 BIOMASS FUELS↗
NASA NTRS1996

Template-Directed Ligation of Peptides to Oligonucleotides

Synthetic oligonucleotides and peptides have enjoyed a wide range of applications in both biology and chemistry. As a consequence, oligonucleotide-peptide conjugates have received considerable attention, most notably in the development of antisense constructs with improved pharmacological properties. In addition, oligonucleotide-peptide conjugates have been used as molecular tags, in the assembly of supramolecular arrays and in the construction of encoded combinatorial libraries. To make these chimeric molecules more accessible for a broad range of investigations, we sought to develop a facile method for joining fully deprotected oligonucleotides and peptides through a stable amide bond linkage. Furthermore, we wished to make this ligation reaction addressable, enabling one to direct the ligation of specific oligonucleotide and peptide components.To confer specificity and accelerate the rate of the reaction, the ligation process was designed to be dependent on the presence of a complementary oligonucleotide template.

Bruick, Richard K.↗
NASA NTRS2005

The Future of Bio-technology

Hosts of technologies, most notably in electronics, have been on the path of miniaturization for decades and in 2005 they have crossed the threshold of the nano-scale. Crossing the nano-scale threshold is a milestone in miniaturization, setting impressive new standards for component-packing densities. It also brings technology to a scale at which quantum effects and fault tolerance play significant roles and approaches the feasible physical limit form many conventional "top-down" manufacturing methods. I will suggest that the most formidable manufacturing problems in nanotechnology will be overcome and major breakthroughs will occur in a host of technologies, when nanotechnology converges with bio-technology; i.e. I will argue that the future of bio-technology is in nanotechnology. In 2005, methods in molecular biology, microscopy, bioinformatics, biochemistry, and genetic engineering have focused considerable attention on the nano-scale. On this scale, biology is a kind of recursive chemistry in which molecular recognition, self-assembly, self-organization and self-referencing context-control lead to the emergence of the complexity of structures and processes that are fundamental to all life forms. While we are still far from understanding this complexity, we are on the threshold of being able to use at least some of these biological properties for .technology. I will discuss the use of biomolecules, such as DNA, RNA, and proteins as "tools" for the bio-technologist of the future. More specifically, I will present in some detail an example of how we are using a genetically engineered 60-kDa protein (HSP60) from an organism living in near boiling sulfuric acid to build nano-scale templates for arranging metallic nanoparticles. These "extremophile" HSP60s self-assemble into robust double-ring structures called "chaperonins," which further assemble into filaments and arrays with nanometer accuracy. I will discuss our efforts to use chaperonins to organize quantum dots, electronic and magnetic nano-particles for electronic and photonic applications.

Trent, Jonathan↗
NASA NTRS2015

Development of a Test for Evaluation of the Hydrothermal Stability of Sorbents Used in Closed-Loop CO2 Removal Systems

The International Space Station Carbon Dioxide Removal Assembly uses zeolite 5A molecular sieve material packed into beds for the capture of cabin CO2. The beds are cyclically heated to drive off the CO2 and restore the removal capacity. Over time, the sorbent material has been found to break down resulting in dust that restricts flow through the beds. Humidity adsorbed in the 5A zeolite when it is heated is a suspected cause of this sorbent degradation. To evaluate the impact of adsorbed water during thermal cycling, the Hydrothermal Stability Test was developed. The test configuration provides comparative side-by-side flow restriction data for two sorbent materials at specifically controlled humidity levels. While the initial focus of the testing is on 5A zeolite materials currently used on the ISS, the system will also be used to evaluate future candidate materials. This paper describes the approach, the test system, current results, and future testing.

Knox, James C.↗
NASA NTRS2022

Design of synthetic collagens that assemble into supramolecular banded fibers as a functional biomaterial testbed

Collagens are the most abundant proteins of the extracellular matrix, and the hierarchical folding and supramolecular assembly of collagens into banded fibers is essential for mediating cell-matrix interactions and tissue mechanics. Collagen extracted from animal tissues is a valuable commodity, but suffers from safety and purity issues, limiting its biomaterials applications. Synthetic collagen biomaterials could address these issues, but their construction requires molecular-level control of folding and supramolecular assembly into ordered banded fibers, comparable to those of natural collagens. Here, we show an innovative class of banded fiber-forming synthetic collagens that recapitulate the morphology and some biological properties of natural collagens. The synthetic collagens comprise a functional-driver module that is flanked by adhesive modules that effectively promote their supramolecular assembly. Multiscale simulations support a plausible molecular-level mechanism of supramolecular assembly, allowing precise design of banded fiber morphology. We also experimentally demonstrate that synthetic fibers stimulate osteoblast differentiation at levels comparable to natural collagen. This work thus deepens understanding of collagen biology and disease by providing a ready source of safe, functional biomaterials that bridge the current gap between the simplicity of peptide biophysical models and the complexity of in vivo animal systems.

Jinyuan Hu↗
DOE OSTI2021

Ce IV 70 oxosulfate rings, frameworks, supramolecular assembly and redox activity

M IV molecular oxo-clusters (M=Zr, Hf, Ce, Th, U, Np, Pu) are prolific in bottoms-up material design, catalysis, and elucidating reaction pathways in nature and in synthesis. Here we introduce Ce 70 , a wheel-shaped oxo-cluster, [Ce IV 70 -(OH) 36 (O) 64 (SO 4 ) 60 (H 2 O) 10 ] 4- . Ce 70 crystallizes into intricate high pore volume frameworks with divalent transition metals and Ce-monomer linkers. Eight crystal-structures feature four framework types in which the Ce 70 -rings are linked as propellers, in offset-stacks, in a tartan pattern, and as isolated rings. In this work, small-angle X-ray scattering of Ce 70 dissolved in butylamine, with and without added cations (Ce IV , alkaline earths, Mn II ), shows the metals‘ differentiating roles in ring linking, leading to supramolecular assemblies. The large acidic pores and abundant terminal sulfates provide ion-exchange behavior, demonstrated with U IV and Nd III . Frameworks featuring Ce III/IV -monomer linkers demonstrate both oxidation and reduction. Furthermore, this study opens the door to mixed-metal, highly porous framework catalysts, and new clusters for metal-organic framework design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Fragment-based drug nanoaggregation reveals drivers of self-assembly

Drug nanoaggregates are particles that can deleteriously cause false positive results during drug screening efforts, but alternatively, they may be used to improve pharmacokinetics when developed for drug delivery purposes. The structural features of molecules that drive nanoaggregate formation remain elusive, however, and the prediction of intracellular aggregation and rational design of nanoaggregate-based carriers are still challenging. We investigate nanoaggregate self-assembly mechanisms using small molecule fragments to identify the critical molecular forces that contribute to self-assembly. We find that aromatic groups and hydrogen bond acceptors/donors are essential for nanoaggregate formation, suggesting that both π-π stacking and hydrogen bonding are drivers of nanoaggregation. We apply structure-assembly-relationship analysis to the drug sorafenib and discover that nanoaggregate formation can be predicted entirely using drug fragment substructures. We also find that drug nanoaggregates are stabilized in an amorphous core-shell structure. These findings demonstrate that rational design can address intracellular aggregation and pharmacologic/delivery challenges in conventional and fragment-based drug development processes.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2025

Efficient analysis of small-angle scattering curves for large biomolecular assemblies using Monte Carlo methods

Structure elucidation from small-angle scattering curves of large biomolecular assemblies is notoriously challenging. This is because the simulation of high-resolution features in the structure of large macromolecular assemblies, such as de novo protein assemblies, is computationally demanding when it needs to cover a broad range of length scales. Conventional methods, such as the numerical approximation to the Debye equation or the use of spherical harmonics, do not scale well as the size of the assembly increases, which limits their application to small structures (e.g. individual proteins). This work explores the effectiveness of a Monte Carlo method to simulate and fit scattering curves for large biomolecular assemblies spanning over ranges covering atomic and molecular detail (e.g. spacing and orientation of proteins in an assembly) as well as large-scale (hundreds of nanometres) features. Owing to its speed and scalability, it can be combined with a fitting algorithm to extract structural features from experimental small-angle scattering curves in biomolecular assemblies that are otherwise intractable for interpretation. This work first demonstrates the effectiveness of the tool using experimental small-angle X-ray scattering (SAXS) data from tile-like proteins that assemble into 1D tube-like macromolecular structures. Here, the diameter distribution of tubes is extracted from SAXS fits, and this is quantitatively compared with distributions from electron microscopy. SAXS data are also obtained from 2D sheet-like protein assemblies, and the proposed method is used to quantify structural features such as the separation distance between protein building blocks and the flexing of the sheet. An open-source implementation of the methodology is provided for use in a broad range of biological systems involving multi-scale scattering analysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Cooperative Role of Mixed Solvent in the Evaporation-Induced Self-Assembly of Polypeptoid Nanocrystals

Peptoids, or polypeptoids, are biomimetic polymers that can self-assemble into nanocrystals for biomedical and biotechnological applications. Polypeptoid nanocrystals can be prepared by evaporation-induced self-assembly, but the roles of solvent components for this process have long been overlooked at the molecular level, leaving a tunable parameter for improving self-assembly protocols. This work utilized molecular dynamics simulations to study the effects of water and the commonly used tetrahydrofuran (THF) on the assembly of nanosheets from molecules of acetylated diblock polypeptoid, poly-(N-decylglycine)-b-poly-(N-2-(2-(2-methoxyethoxy)-ethoxy) ethylglycine), abbreviated as Ac-Ndc10-Nte10. To probe the stages of self-assembly, isolated molecules and preassembled nanofibers/nanosheets were simulated in pure THF, water, and their mixtures, respectively. The assembly energies show that the THF/water mixture has a greater tendency to form nanosheets than pure water. In a THF/water mixture, polypeptoids were found more uncoiled in isolated states, less compact in disordered agglomerates, and with reduced requirement for the Nte block to cover hydrophobic Ndc surfaces in the nanocrystals. Mixed solvent is vital to initiating self-assembly, as THF assists in the opening of coiled polypeptoid molecules, while water provides the thermodynamics to aggregate and ultimately form nanocrystals. To obtain wider nanosheets, it is recommended that some THF be maintained in the aqueous solvent before it becomes exhausted by evaporation. Near the nanosheet surface, the THF concentration is higher than that in bulk solution (3-4 times in 4 M THF/water). The strong adsorption of THF indicates the self-assembly in a de facto mixed solvent. These results are expected to guide the refinement of evaporation-induced self-assembly protocols for polypeptoid nanocrystals.

Luo, Xubo↗
DOE OSTI2024

Developmental assembly of multi-component polymer systems through interconnected synthetic gene networks in vitro

Abstract Living cells regulate the dynamics of developmental events through interconnected signaling systems that activate and deactivate inert precursors. This suggests that similarly, synthetic biomaterials could be designed to develop over time by using chemical reaction networks to regulate the availability of assembling components. Here we demonstrate how the sequential activation or deactivation of distinct DNA building blocks can be modularly coordinated to form distinct populations of self-assembling polymers using a transcriptional signaling cascade of synthetic genes. Our building blocks are DNA tiles that polymerize into nanotubes, and whose assembly can be controlled by RNA molecules produced by synthetic genes that target the tile interaction domains. To achieve different RNA production rates, we use a strategy based on promoter “nicking” and strand displacement. By changing the way the genes are cascaded and the RNA levels, we demonstrate that we can obtain spatially and temporally different outcomes in nanotube assembly, including random DNA polymers, block polymers, and as well as distinct autonomous formation and dissolution of distinct polymer populations. Our work demonstrates a way to construct autonomous supramolecular materials whose properties depend on the timing of molecular instructions for self-assembly, and can be immediately extended to a variety of other nucleic acid circuits and assemblies.

Science & Technology - Other Topics↗
DOE OSTI2023

A coarse-grained simulation model for colloidal self-assembly via explicit mobile binders

Colloidal particles with mobile binding molecules constitute a powerful platform for probing the physics of self-assembly. Binding molecules are free to diffuse and rearrange on the surface, giving rise to spontaneous control over the number of droplet–droplet bonds, i.e., valence, as a function of the concentration of binders. This type of valence control has been realized experimentally by tuning the interaction strength between DNA-coated emulsion droplets. Optimizing for valence two yields droplet polymer chains, termed ‘colloidomers’, which have recently been used to probe the physics of folding. To understand the underlying self-assembly mechanisms, here we present a coarse-grained molecular dynamics (CGMD) model to study the self-assembly of this class of systems using explicit representations of mobile binding sites. Further, we explore how valence of assembled structures can be tuned through kinetic control in the strong binding limit. More specifically, we optimize experimental control parameters to obtain the highest yield of long linear colloidomer chains. Subsequently tuning the dynamics of binding and unbinding via a temperature-dependent model allows us to observe a heptamer chain collapse into all possible rigid structures, in good agreement with recent folding experiments. Our CGMD platform and dynamic bonding model (implemented as an open-source custom plugin to HOOMD-Blue) reveal the molecular features governing the binding patch size and valence control, and opens the study of pathways in colloidomer folding. This model can therefore guide programmable design in experiments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Computational Prediction of Coiled–Coil Protein Gelation Dynamics and Structure

Protein hydrogels represent an important and growing biomaterial for a multitude of applications, including diagnostics and drug delivery. We have previously explored the ability to engineer the thermoresponsive supramolecular assembly of coiled–coil proteins into hydrogels with varying gelation properties, where we have defined important parameters in the coiled–coil hydrogel design. Using Rosetta energy scores and Poisson–Boltzmann electrostatic energies, we iterate a computational design strategy to predict the gelation of coiled–coil proteins while simultaneously exploring five new coiled–coil protein hydrogel sequences. Provided this library, we explore the impact of in silico energies on structure and gelation kinetics, where we also reveal a range of blue autofluorescence that enables hydrogel disassembly and recovery. As a result of this library, we identify the new coiled–coil hydrogel sequence, Q5, capable of gelation within 24 h at 4 °C, a more than 2-fold increase over that of our previous iteration Q2. The fast gelation time of Q5 enables the assessment of structural transition in real time using small-angle X-ray scattering (SAXS) that is correlated to coarse-grained and atomistic molecular dynamics simulations revealing the supramolecular assembling behavior of coiled–coils toward nanofiber assembly and gelation. This work represents the first system of hydrogels with predictable self-assembly, autofluorescent capability, and a molecular model of coiled–coil fiber formation.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Investigation of design principles for metal-binding and conductive protein assemblies

Throughout the lifetime of this initiative, including renewals, we focused on understanding the fundamental principles of protein-protein interface design that enable predictable and modular spatial and kinetic control of multi-component protein self-assembly in 1D, 2D, and 3D, including the interface with inorganic materials, small molecules, and metal ions. We designed individual protein components that bind specific metal ions, including REEs and transport ions across lipid membranes. We created helical 1D filaments of repeating units with programmed periodicity, pitch, and multi-component environmentally responsive self-assembling protein fibers. We showed that these filaments reversibly assemble and disassemble under specific pH conditions and created end-specific caps that independently tune the balance of attachment and detachment rates at each terminus of the filament. Using similar filaments, we succeeded in binding arrays of heme and chlorophyll molecules and assembling patterned helical coatings around carbon nanotubes in efforts to create de novo conductive nanowires. By arraying REE binding sites in a large circular tandem array with a repeat protein-based cyclic oligomer, we created a molecular scaffold for superradiance and paramagnetic quantum sensing. We created a range of one-component and two-component self-assembling 2D arrays and showed that when designed to engage cell receptors, these arrays can control cell behavior from outside the cell signal to inside the cell. We designed helical repeat proteins with variable lengths displaying charged residues in a pattern matched to the cation lattice of mica. achieved a range of ordered states with an epitaxial match to the underlying crystal lattice. We further applied the learned principles of protein-induced biomineralization to design proteins with an interface lattice matching CaCO 3 and guide the formation of specific crystal forms of CaCO 3 from solution, a significant advance toward the global need to manage carbon. In all cases of mineral lattice matching and biomineralization, we followed assembly using molecularly resolved in situ AFM imaging and extracted information about assembly pathways and energetics, applying deep learning to quantify the dynamics of protein self-organization. We developed techniques for using dynamic metal-dependent interfaces on protein nanopores for discriminatively sensing dilute REEs in solution and demonstrated the use of strong metal-binding interfaces to drive nanocage disassembly for conditional nanocompartmentalization applications. This grant supported 11 people, including Asim Bera, Evans Brackenbrough, Andrew Borst, Nikita Hanikel, Timothy Huddy, Emily Joyce, Alex Young-Seug Kang, Ryan Kibler, Joshua Morris Lubner, Harley Pyles, and Shuai Zhang. The research effort culminated in the production of published papers and theses. Electronic Thesis/Dissertation are distributed by ProQuest/UMI Dissertation Publishing and made available on an open access basis through UW Libraries ResearchWorks Service.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗