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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 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Hydration Free Energies of Polypeptides from Popular Implicit Solvent Models versus All-Atom Simulation Results Based on Molecular Quasichemical Theory

Calculating the hydration free energy of a macromolecule in all-atom simulations has long remained a challenge, necessitating the use of models wherein the effect of the solvent is captured without explicit account of solvent degrees of freedom. This situation has changed with developments in the molecular quasi-chemical theory (QCT)-an approach that enables calculation of the hydration free energy of macromolecules within all-atom simulations at the same resolution as is possible for small molecular solutes. The theory also provides a rigorous and physically transparent framework to conceptualize and model interactions in molecular solutions and thus provides a convenient framework to investigate the assumptions in implicit solvent models. In this study, we compare the results using molecular QCT versus predictions from EEF1, ABSINTH, and GB/SA implicit solvent models for polyglycine and polyalanine solutes covering a range of chain lengths and conformations. The hydration free energies or the differences in hydration free energies between conformers obtained from the implicit solvent models do not agree with explicit solvent results, with the deviations being largest for the group additive EEF1 and ABSINTH models. GB/SA does better in capturing the qualitative trends seen in explicit solvent results. Finally, analysis founded on QCT reveals the critical importance of the cooperativity of hydration that is inherent in the hydrophilic and hydrophobic contributions to hydration-physics that is not well captured in additive models but somewhat better accounted for by means of a dielectric in the GB/SA approach.

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

Atomic-Scale Imaging of Condensed Counterions

Here, the functioning of a wide variety of charged macromolecules, from DNA to fuel cell membranes, is dependent on how the counterions surrounding them are arranged. In order to decrease Coulombic repulsion, some of the fixed charges on these molecules are neutralized by a fraction of the counterions-this phenomenon is called counterion condensation. The nature of counterion condensation can be only be inferred indirectly from traditional experiments such as X-ray scattering and modern experiments such as single molecule electrometry. The prevalent conclusion in the literature, based on both theory and experiment, is that the distribution of counterions is peaked right next to the macromolecule, i.e., condensation results in the formation of contact ion pairs. In this study, cryogenic electron microscopy (cryo-EM) was used to study the arrangement of condensed halide counterions near a positively charged polypeptoid nanofiber. The locations of both condensed and fixed charges were determined directly from atomic-scale images. Our experimentally determined counterion distributions were peaked at distances of about 5 Å away from the fixed positive charge, indicating the presence of a layer of water molecules between condensed ion pairs. We posit that this distribution is driven by the entropy of the condensed ions.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Radical Polymer-Based Organic Electrochemical Transistors

Organic electrochemical transistors (OECTs) are an emerging platform for bioelectronic applications. Significant effort has been placed in designing advanced polymers that simultaneously transport both charge and ions (i.e., macromolecules that are mixed conductors). Furthermore, the considerations for mixed organic conductors are often different from the established principles that are well-known in the solid-state organic electronics field; thus, the discovery of new OECT macromolecular systems is highly desired. Here, we demonstrate a new materials system by blending a radical polymer (i.e., a macromolecule with a nonconjugated backbone and with stable open-shell sites at its pendant group) with a frequently used conjugated polymer. Specifically, poly(4-glycidyloxy-2,2,6,6-tetramethylpiperidine-1-oxyl) (PTEO) was blended with poly(3-hexylthiophene) (P 3 HT) to create thin films with distinct closed-shell and open-shell domains. Importantly, the sharp and unique oxidation–reduction (redox) potential associated with the radical moieties of the PTEO chain provided a distinct actuation feature to the blended films that modulated the ionic transport of the OECT devices. In turn, this led to controlled regulation of the doping of the P 3 HT phase in the composite film. By decoupling the ionic and electronic transport into two distinct phases and by using an ion transport phase with well-controlled redox activity, never-before-seen performance for a P3HT-based OECT was observed. That is, at loadings as low as 5% PTEO (by weight) OECTs achieved figure-of-merit (i.e., μC*) values >150 F V –1 cm –1 s –1 , which place the performance on the same order as state-of-the-art conjugated polymers despite the relatively common conjugated macromolecular moiety implemented. As such, this effort presents a design platform by which to readily create a tailored OECT response through strategic macromolecular selection and polymer processing.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Structure–Function Relationships in Sequence-Controlled Copolymers for Rare Earth Element Chelation

The ability to tune material function through primary sequence is a defining feature of biological macromolecules, allowing precise control over structure and target interactions in complex aqueous environments. However, translating sequence–structure–function relationships to synthetic macromolecules is challenging due to their dispersity in sequence, conformation, and composition. Here, we report systematic studies of amphiphilic polymer chelators designed to probe how composition and patterning influence binding affinity and selectivity for rare earth elements (REEs), a series of technologically relevant metals with challenging separation profiles. A library of copolymers varying hydrophobic monomer composition and patterning was synthesized via reversible addition–fragmentation chain transfer (RAFT) polymerization, spanning statistical, gradient, and block architectures. REE binding was quantified using a high-throughput colorimetric assay, and reconstruction of polymer ensembles using kinetic stochastic simulations enabled quantitative comparisons of sequence heterogeneity, linking local monomer colocalization to emergent REE binding. Further, we investigated the role of different hydrophobic comonomers in tuning metal coordination, with binding trends linked to structural features that influence binding site desolvation. Complementary dynamic light scattering (DLS) and small-angle X-ray scattering (SAXS) measurements showed that both polymer and monomer architecture modulate metal-induced conformational changes, and that multichain assembly behavior emerges beyond critical hydrophobic thresholds. Sequence control also altered REE selectivity, with nonmonotonic differences observed across compositionally identical polymers with different sequence architectures. Together, these findings establish design principles that connect polymer sequence and structure to binding performance, guiding the design of macromolecular chelators with enhanced affinity and selectivity for applications in separations, sensing, and catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Releasing chemical energy in spatiallyprogrammed ferroelectrics

Chemical energy ferroelectrics are generally solid macromolecules showing spontaneous polarization and chemical bonding energy. These materials still suffer drawbacks, including the limited control of energy release rate, and thermal decomposition energy well below total chemical energy. To overcome these drawbacks, we report the integrated molecular ferroelectric and energetic material from machine learning-directed additive manufacturing coupled with the ice-templating assembly. The resultant aligned porous architecture shows a low density of 0.35 g cm -3 , polarization-controlled energy release, and an anisotropic thermal conductivity ratio of 15. Thermal analysis suggests that the chlorine radicals react with macromolecules enabling a large exothermic enthalpy of reaction (6180 kJ kg -1 ). In addition, the estimated detonation velocity of molecular ferroelectrics can be tuned from 6.69 ± 0.21 to 7.79 ± 0.25 km s -1 by switching the polarization state. These results provide a pathway toward spatially programmed energetic ferroelectrics for controlled energy release rates.

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

Single-cell isotope tracing reveals functional guilds of bacteria associated with the diatom Phaeodactylum tricornutum

Abstract Bacterial remineralization of algal organic matter fuels algal growth but is rarely quantified. Consequently, we cannot currently predict whether some bacterial taxa may provide more remineralized nutrients to algae than others. Here, we quantified bacterial incorporation of algal-derived complex dissolved organic carbon and nitrogen and algal incorporation of remineralized carbon and nitrogen in fifteen bacterial co-cultures growing with the diatom Phaeodactylum tricornutum at the single-cell level using isotope tracing and nanoSIMS. We found unexpected strain-to-strain and cell-to-cell variability in net carbon and nitrogen incorporation, including non-ubiquitous complex organic nitrogen utilization and remineralization. We used these data to identify three distinct functional guilds of metabolic interactions, which we termed macromolecule remineralizers, macromolecule users, and small-molecule users, the latter exhibiting efficient growth under low carbon availability. The functional guilds were not linked to phylogeny and could not be elucidated strictly from metabolic capacity as predicted by comparative genomics, highlighting the need for direct activity-based measurements in ecological studies of microbial metabolic interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Variations of organic functional chemistry in carbonaceous matter from the asteroid 162173 Ryugu

Abstract Primordial carbon delivered to the early earth by asteroids and meteorites provided a diverse source of extraterrestrial organics from pre-existing simple organic compounds, complex solar-irradiated macromolecules, and macromolecules from extended hydrothermal processing. Surface regolith collected by the Hayabusa2 spacecraft from the carbon-rich asteroid 162173 Ryugu present a unique opportunity to untangle the sources and processing history of carbonaceous matter. Here we show carbonaceous grains in Ryugu can be classified into three main populations defined by spectral shape: Highly aromatic (HA), Alkyl-Aromatic (AA), and IOM-like (IL). These carbon populations may be related to primordial chemistry, since C and N isotopic compositions vary between the three groups. Diffuse carbon is occasionally dominated by molecular carbonate preferentially associated with coarse-grained phyllosilicate minerals. Compared to related carbonaceous meteorites, the greater diversity of organic functional chemistry in Ryugu indicate the pristine condition of these asteroid samples.

Science & Technology - Other Topics↗
DOE OSTI2026

Integrated fluorescence light microscopy-guided cryo-focused ion beam-milling for in situ montage cryo-ET

Cryogenic-electron tomography (cryo-ET) permits the in situ visualization of biological macromolecules at the molecular level. Owing to the variable thickness of cells, tissues and organisms, frozen specimens may need to be thinned by cryo-focused ion beam (FIB) milling to produce thin (<500 nm) cryo-lamellae suitable for cryo-ET. Locating regions of interest remains a challenge because untargeted milling can lead to inadvertent ablation and removal of regions of interest. Correlative light and electron microscopy, combined with cryo-FIB milling, can guide the identification of labeled targets in the cellular milieu. Multiple transfers between cryo-imaging instruments, cumbersome correlation algorithms, limited accuracy and low throughput have hindered the routine adoption of cryo-FIB milling within a multimodal correlative workflow for in situ structural biology. Here, in this study, we present a workflow for 3D correlative cryo-fluorescence light microscopy-FIB-ET that streamlines fluorescence light microscopy-guided FIB milling, improving throughput while preserving both structural and contextual information. The complete integration of hardware and software described here minimizes sample contamination from cross-platform exchanges and greatly enhances the efficiency of 3D targeting in cryo-milling. We then describe procedures for implementing montage parallel array cryo-ET (MPACT), which can be easily adapted to any modern life-science transmission electron microscope. MPACT supports high-throughput cryo-ET acquisitions (10 tilt series in 1.5 h) for structure determination and comprehensive contextual understanding of macromolecules within their native surroundings. A complete session from sample preparation to MPACT data processing takes 5−7 d for an individual experienced in both cryo-EM and cryo-FIB milling.

Yang, Jie E. [Univ. of Wisconsin, Madison, WI (Uni↗
DOE OSTI2020

LoTToR: An Algorithm for Missing-Wedge Correction of the Low-Tilt Tomographic 3D Reconstruction of a Single-Molecule Structure

A single-molecule three-dimensional (3D) structure is essential for understanding the thermal vibrations and dynamics as well as the conformational changes during the chemical reaction of macromolecules. Individual-particle electron tomography (IPET) is an approach for obtaining a snap-shot 3D structure of an individual macromolecule particle by aligning the tilt series of electron tomographic (ET) images of a targeted particle through a focused iterative 3D reconstruction method. The method can reduce the influence on the 3D reconstruction from large-scale image distortion and deformation. Due to the mechanical tilt limitation, 3D reconstruction often contains missing-wedge artifacts, presented as elongation and an anisotropic resolution. Here, we report a post-processing method to correct the missing-wedge artifact. This low-tilt tomographic reconstruction (LoTToR) method contains a model-free iteration process under a set of constraints in real and reciprocal spaces. A proof of concept is conducted by using the LoTToR on a phantom, i.e., a simulated 3D reconstruction from a low-tilt series of images, including that within a tilt range of ±15°. The method is validated by using both negative-staining (NS) and cryo-electron tomography (cryo-ET) experimental data. A significantly reduced missing-wedge artifact verifies the capability of LoTToR, suggesting a new tool to support the future study of macromolecular dynamics, fluctuation and chemical activity from the viewpoint of single-molecule 3D structure determination.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Catalytic upcycling of high-density polyethylene via a processive mechanism

The overconsumption of single-use plastics is creating a global waste catastrophe, with widespread environmental, economic and health-related consequences. In this work we show that the benefits of processive enzyme-catalysed conversions of biomacromolecules can be leveraged to affect the selective hydrogenolysis of high-density polyethylene into a narrow distribution of diesel and lubricant-range alkanes using an ordered, mesoporous shell/active site/core catalyst architecture that incorporates catalytic platinum sites at the base of the mesopores. Solid-state nuclear magnetic resonance revealed that long hydrocarbon macromolecules readily move within the pores of this catalyst, with a subsequent escape being inhibited by polymer–surface interactions, a behaviour that resembles the binding and translocation of macromolecules in the catalytic cleft of processive enzymes. Accordingly, the hydrogenolysis of polyethylene with this catalyst proceeds processively to yield a reliable, narrow and tunable stream of alkane products.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

In situ transmission electron microscopy observations of CaCO 3 crystallization onto polysaccharide-coated nanoparticles

Polysaccharides and proteoglycans are widely associated with the organic matrix at sites of CaCO 3 biomineralization, and previous studies indicate that these macromolecules may confer greater roles in mineral nucleation than previously recognized. This investigation uses in situ liquid-phase transmission electron microscopy (LP-TEM) to observe CaCO 3 nucleation onto aminated silica (SiO 2 –NH 3 + ) nanoparticles treated with a layer of chitosan (near-neutral derivative of chitin) or heparin (a carboxylated and highly sulfated glycosaminoglycan). In the absence of polysaccharides, few CaCO 3 particles formed and exhibited mobility. However, the SiO 2 –NH 3 + nanoparticles were enveloped in a region of higher mass density relative to the bulk solution, suggesting the development of a local solute-rich environment that surrounds the charged NH 3 + groups. The heparin- or chitosan-coated silica particles also exhibited regions of higher mass density around the nanoparticles. In the presence of these polysaccharide coatings, we observed the nucleation of abundant CaCO 3 particles whereby the polyanionic heparin promoted more nucleation than the weakly cationic chitosan. Many crystallites appeared to form at the polysaccharide–TEM cell membrane–solution interface, further indicating interfacial and macromolecule-specific control on crystallization. The combined results demonstrate that chitosan and heparin have an appreciable effect on the timing, size, and location of CaCO 3 nucleation compared to the polysaccharide-free nanoparticles.

15 GEOTHERMAL ENERGY↗
DOE OSTI2020

Shape-preserving amorphous-to-crystalline transformation of CaCO3 revealed by in situ TEM

Organisms use inorganic ions and macromolecules to regulate crystallization from amorphous- precursors, endowing natural biominerals with complex morphologies and enhanced properties. The mechanisms by which modifiers enable these shape preserving transformations are poorly understood. We used in situ liquid-phase transmission electron microscopy to follow the evolution from amorphous calcium carbonate to calcite in the presence of additives. A combination of contrast analysis and infrared spectroscopy shows that Mg ions, which are widely present in seawater and biological fluids, alter the transformation pathway in a concentration-dependent manner. The ions bring excess (structural) water into the amorphous bulk so that a direct transformation is triggered by dehydration in the absence of morphological changes. Molecular dynamics simulations suggest Mg-incorporated water induces structural fluctuations, allowing transformation without the need to nucleate a separate crystal. Thus, the obtained calcite retains the original morphology of the amorphous state, biomimetically achieving the morphological control of crystals seen in biominerals

crystallization, biomineralization, calcium carbon↗
DOE OSTI2023

Engineered molecular sensors for quantifying cell surface crowding

Cells mediate interactions with the extracellular environment through a crowded assembly of transmembrane proteins, glycoproteins and glycolipids on their plasma membrane. The extent to which surface crowding modulates the biophysical interactions of ligands, receptors, and other macromolecules is poorly understood due to the lack of methods to quantify surface crowding on native cell membranes. In this work, we demonstrate that physical crowding on reconstituted membranes and live cell surfaces attenuates the effective binding affinity of macromolecules such as IgG antibodies in a surface crowding-dependent manner. We combine experiment and simulation to design a crowding sensor based on this principle that provides a quantitative readout of cell surface crowding. Our measurements reveal that surface crowding decreases IgG antibody binding by 2 to 20 fold in live cells compared to a bare membrane surface. Our sensors show that sialic acid, a negatively charged monosaccharide, contributes disproportionately to red blood cell surface crowding via electrostatic repulsion, despite occupying only ~1% of the total cell membrane by mass. We also observe significant differences in surface crowding for different cell types and find that expression of single oncogenes can both increase and decrease crowding, suggesting that surface crowding may be an indicator of both cell type and state. Our high-throughput, single-cell measurement of cell surface crowding may be combined with functional assays to enable further biophysical dissection of the cell surfaceome.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Polyubiquitin ligand-induced phase transitions are optimized by spacing between ubiquitin units

Biomolecular condensates form via multivalent interactions among key macromolecules and are regulated through ligand binding and/or posttranslational modifications. One such modification is ubiquitination, the covalent addition of ubiquitin (Ub) or polyubiquitin chains to target macromolecules. Specific interactions between polyubiquitin chains and partner proteins, including hHR23B, NEMO, and UBQLN2, regulate condensate assembly or disassembly. Here, we used a library of designed polyubiquitin hubs and UBQLN2 as model systems for determining the driving forces of ligand-mediated phase transitions. Perturbations to either the UBQLN2-binding surface of Ub or the spacing between Ub units reduce the ability of hubs to modulate UBQLN2 phase behavior. By developing an analytical model based on polyphasic linkage principles that accurately described the effects of different hubs on UBQLN2 phase separation, we determined that introduction of Ub to UBQLN2 condensates incurs a significant inclusion energetic penalty. This penalty antagonizes the ability of polyUb hubs to scaffold multiple UBQLN2 molecules and cooperatively amplify phase separation. The extent to which polyubiquitin hubs promote UBQLN2 phase separation is encoded in the spacings between Ub units. This spacing is modulated by chains of different linkages and designed chains of different architectures, thus illustrating how the ubiquitin code regulates functionality via the emergent properties of the condensate. The spacing in naturally occurring linear polyubiquitin chains is already optimized to promote phase separation with UBQLN2. We expect our findings to extend to other condensates, emphasizing the importance of ligand properties, including concentration, valency, affinity, and spacing between binding sites in studies and designs of condensates.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Redox poise in R. rubrum phototrophic growth drives large-scale changes in macromolecular pathways

During photoheterotrophic growth on organic substrates, purple nonsulfur photosynthetic bacteria like Rhodospirillum rubrum can acquire electrons by multiple means, including oxidation of organic substrates, oxidation of inorganic electron donors (e.g., H 2 ), and by reverse electron flow from the photosynthetic electron transport chain. These electrons are stored as reduced electron-carrying cofactors (e.g., NAD(P)H and ferredoxin). The overall ratio of oxidized to reduced cofactors (e.g., NAD(P)+:NAD(P)H), or ’redox poise’, is difficult to understand or predict, as are the cellular processes for dissipating these reducing equivalents. Using physics-based models that capture mass action kinetics consistent with the thermodynamics of reactions and pathways, a range of redox conditions for heterophototrophic growth are evaluated, from conditions in which the NADP+/NADPH levels approach thermodynamic equilibrium to conditions in which the NADP+/NADPH ratio is far above the typical physiological values. Modeling predictions together with experimental measurements indicate that the redox poise of the cell results in large-scale changes in the activity of biosynthetic pathways and, thus, changes in cell macromolecule levels (DNA, RNA, proteins, and fatty acids). Furthermore, modeling predictions indicate that during phototrophic growth, reverse electron flow from the quinone pool is a minor contributor to the production of reduced cofactors (e.g., NAD(P)H) compared to other oxidative processes (H 2 and carbon substrate oxidation). Instead, the quinone pool primarily operates to aid ATP production. The high level of ATP, in turn, drives reduction processes even when NADPH levels are relatively low compared to NADP+ by coupling ATP hydrolysis to the reductive processes. The model, in agreement with experimental measurements of macromolecule ratios of cells growing on different carbon substrates, indicates that the dynamics of nucleotide versus lipid and protein production is likely a significant mechanism of balancing oxidation and reduction in the cell.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Modulating ion-binding at macromolecular interfaces during (bio)mineralization: A snapshot review for calcium carbonate and calcium phosphate systems

Abstract Local environments have strict influence over (bio)mineralization in calcifying systems. This snapshot review discusses recent insights into the roles of Ca 2+ -macromolecule interactions on the nucleation of calcium carbonate and calcium phosphate minerals. Experimental findings combined with simulations/modeling are providing breakthrough information and raising important questions for future studies. The emerging picture is that both nucleation and growth are driven by local ordering of ions and water about the macromolecule interface, rather than broader properties or molecular class. Tuning macromolecular properties at the atomic scale thus provides opportunities for highly specific controls on mineralization; however, many limitations and challenges remain. We highlight studies employing in-situ atomic force microscopy (AFM) and transmission electron microscopy (TEM) to observe crystallization processes on or near macromolecular substrates. As the distribution and ability of these techniques increases, fundamental studies integrating experimental and computational methods will be crucial to inform a broad range of applications. Graphical abstract

Knight, Brenna M. (ORCID:0000000244000067)↗
DOE OSTI2025

Redox Poise during Rhodospirillum rubrum Phototrophic Growth Drives Large-scale Changes in Macromolecular Synthesis Pathways

During photoheterotrophic growth on organic substrates, purple nonsulfur photosynthetic bacteria like Rhodospirillum rubrum can acquire electrons by multiple means, including oxidation of organic substrates, oxidation of inorganic electron donors (e.g., H2), and by reverse electron flow from the photosynthetic electron transport chain. These electrons are stored as reduced electron-carrying cofactors (e.g., NAD(P)H and ferredoxin). The overall ratio of oxidized to reduced cofactors (e.g., NAD(P)+:NAD(P)H), or ’redox poise’, is difficult to understand or predict, as are the cellular processes for dissipating these reducing equivalents. Using physics-based models that capture mass action kinetics consistent with the thermodynamics of reactions and pathways, a range of redox conditions for heterophototrophic growth are evaluated, from conditions in which the NADP+/NADPH levels approach thermodynamic equilibrium to conditions in which the NADP+/NADPH ratio is far above the typical physiological values. Modeling predictions together with experimental measurements indicate that the redox poise of the cell results in large-scale changes in the activity of biosynthetic pathways and, thus, changes in cell macromolecule levels (DNA, RNA, proteins, and fatty acids). Furthermore, modeling predictions indicate that during phototrophic growth, reverse electron flow from the quinone pool is a minor contributor to the production of reduced cofactors (e.g., NAD(P)H) compared to other oxidative processes (H2 and carbon substrate oxidation). Instead, the quinone pool primarily operates to aid ATP production. The high level of ATP, in turn, drives reduction processes even when NADPH levels are relatively low compared to NADP+ by coupling ATP hydrolysis to the reductive processes. The model, in agreement with experimental measurements of macromolecule ratios of cells growing on different carbon substrates, indicates that the dynamics of nucleotide versus lipid and protein production is likely a significant mechanism of balancing oxidation and reduction in the cell.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

A new chapter for RCSB Protein Data Bank Molecule of the Month in 2025

The online Molecule of the Month series authored by David S. Goodsell and published by the Research Collaboratory for Structural Biology Protein Data Bank at PDB101.RCSB.org has highlighted stories about the biomolecular structures driving fundamental biology, biomedicine, bioenergy, and biotechnology since January 2000. A new chapter begins in 2025: Janet Iwasa has taken over as the series creator of stories about critically important biological macromolecules in a rapidly changing world.

Bioenergy↗