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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 739 records · Page 41
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Highly Active Hydrogen Evolution Reaction (HER) Catalysts Formed by Energetic Pt n Cluster Deposition: Deposition Dynamics and the HER Mechanism

Mass-selected Pt n + (n ≤ 7) were deposited at variable energies on highly oriented pyrolytic graphite (HOPG), creating highly active hydrogen evolution reaction (HER) electrocatalysts. HER mass activities were ~2 to >10 times higher than those for the surface atoms in bulk Pt and for Pt n deposited on several other supports. Thus, high activity reflects the Pt-C structures formed by energetic Pt n -HOPG impacts, in addition to high Pt surface availability. The Pt n /HOPG electrodes were probed by X-ray photoelectron spectroscopy, low energy ion scattering, and electron microscopy. Born-Oppenheimer molecular dynamics (BOMD) was used to simulate Pt n - HOPG impacts, revealing the types of structures formed at different energies, then DFT was used to probe their most important HER pathways. For low deposition energies, the Pt n deposit onto the HOPG surface with sub-unit sticking probability, aggregating at defects. With increasing deposition energy, the sticking probability initially decreases, then rises to unity as subplantation and defect creation allow formation of strongly bonded platinum-carbon structures. Barriers for HER on these structures were found to be low and weakly dependent on Pt n size, consistent with experiment. The activities were highest for small covalently-bonded Pt-C structures created at high deposition energies. The larger aggregated structures formed at low energies were less active, but still substantially better than the bulk Pt surface monolayer. The catalysts were stable in repeated potential cycling at reducing potentials, but electrodes containing subplanted Pt became more active when scanned to oxidizing potentials, due to emergence of subplanted Pt onto the surface.

08 HYDROGEN↗
DOE OSTI2021

Active Phase on SrCo 1–x Fe x O -δ (0 ≤ x ≤ 0.5) Perovskite for Water Oxidation: Reconstructed Surface versus Remaining Bulk

Perovskite oxides based on earth-abundant transition metals have been extensively explored as promising oxygen evolution reaction (OER) catalysts in alkaline media. The (electro)chemically induced transformation of their initially crystalline surface into an amorphous state has been reported for a few highly active perovskite catalysts. However, little knowledge is available to distinguish the contribution of the amorphized surface from that of the remaining bulk toward the OER. In this work, we utilize the promoting effects of two types of Fe modification, i.e., bulk Fe dopant and Fe ions absorbed from the electrolyte, on the OER activity of SrCoO 3-δ model perovskite to identify the active phase. Transmission electron microscopy and X-ray photoelectron spectroscopy confirmed the surface amorphization of SrCoO 3-δ as well as SrCo 0.8 Fe 0.2 O 3-δ after potential cycling in Fe-free KOH solution. By further cycling in Fe-spiked electrolyte, Fe was incorporated into the amorphized surface of SrCoO 3-δ (SrCoO 3-δ + Fe 3+ ), yielding approximately sixfold increase in activity. Despite the difference in remaining perovskites, SrCoO 3-δ + Fe 3+ and SrCo 0.8 Fe 0.2 O 3-δ exhibited remarkably similar activity. These results reflect that the in situ developed surface species are directly responsible for the measured OER activity, whereas the remaining bulk phases have little impact.

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

A molecular switch regulating transcriptional repression and activation of PPARγ

Nuclear receptor (NR) transcription factors use a conserved activation function-2 (AF-2) helix 12 mechanism for agonist-induced coactivator interaction and NR transcriptional activation. In contrast, ligand-induced corepressor-dependent NR repression appears to occur through structurally diverse mechanisms. We report two crystal structures of peroxisome proliferator-activated receptor gamma (PPARγ) in an inverse agonist/corepressor-bound transcriptionally repressive conformation. Helix 12 is displaced from the solvent-exposed active conformation and occupies the orthosteric ligand-binding pocket enabled by a conformational change that doubles the pocket volume. Paramagnetic relaxation enhancement (PRE) NMR and chemical crosslinking mass spectrometry confirm the repressive helix 12 conformation. PRE NMR also defines the mechanism of action of the corepressor-selective inverse agonist T0070907, and reveals that apo-helix 12 exchanges between transcriptionally active and repressive conformations—supporting a fundamental hypothesis in the NR field that helix 12 exchanges between transcriptionally active and repressive conformations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Genome dependent Cas9/gRNA search time underlies sequence dependent gRNA activity

Abstract CRISPR-Cas9 is a powerful DNA editing tool. A gRNA directs Cas9 to cleave any DNA sequence with a PAM. However, some gRNA sequences mediate cleavage at higher efficiencies than others. To understand this, numerous studies have screened large gRNA libraries and developed algorithms to predict gRNA sequence dependent activity. These algorithms do not predict other datasets as well as their training dataset and do not predict well between species. Here, to better understand these discrepancies, we retrospectively examine sequence features that impact gRNA activity in 44 published data sets. We find strong evidence that gRNA sequence dependent activity is largely influenced by the ability of the Cas9/gRNA complex to find the target site rather than activity at the target site and that this drives sequence dependent differences in gRNA activity between different species. This understanding will help guide future work to understand Cas9 activity as well as efforts to identify optimal gRNAs and improve Cas9 variants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Genome-wide functional screens enable the prediction of high activity CRISPR-Cas9 and -Cas12a guides in Yarrowia lipolytica

Abstract Genome-wide functional genetic screens have been successful in discovering genotype-phenotype relationships and in engineering new phenotypes. While broadly applied in mammalian cell lines and in E. coli , use in non-conventional microorganisms has been limited, in part, due to the inability to accurately design high activity CRISPR guides in such species. Here, we develop an experimental-computational approach to sgRNA design that is specific to an organism of choice, in this case the oleaginous yeast Yarrowia lipolytica . A negative selection screen in the absence of non-homologous end-joining, the dominant DNA repair mechanism, was used to generate single guide RNA (sgRNA) activity profiles for both SpCas9 and LbCas12a. This genome-wide data served as input to a deep learning algorithm, DeepGuide, that is able to accurately predict guide activity. DeepGuide uses unsupervised learning to obtain a compressed representation of the genome, followed by supervised learning to map sgRNA sequence, genomic context, and epigenetic features with guide activity. Experimental validation, both genome-wide and with a subset of selected genes, confirms DeepGuide’s ability to accurately predict high activity sgRNAs. DeepGuide provides an organism specific predictor of CRISPR guide activity that with retraining could be applied to other fungal species, prokaryotes, and other non-conventional organisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural and mechanistic insights into activation of the human RNA ligase RTCB by Archease

Abstract RNA ligases of the RTCB-type play an essential role in tRNA splicing, the unfolded protein response and RNA repair. RTCB is the catalytic subunit of the pentameric human tRNA ligase complex. RNA ligation by the tRNA ligase complex requires GTP-dependent activation of RTCB. This active site guanylylation reaction relies on the activation factor Archease. The mechanistic interplay between both proteins has remained unknown. Here, we report a biochemical and structural analysis of the human RTCB-Archease complex in the pre- and post-activation state. Archease reaches into the active site of RTCB and promotes the formation of a covalent RTCB-GMP intermediate through coordination of GTP and metal ions. During the activation reaction, Archease prevents futile RNA substrate binding to RTCB. Moreover, monomer structures of Archease and RTCB reveal additional states within the RNA ligation mechanism. Taken together, we present structural snapshots along the reaction cycle of the human tRNA ligase.

Science & Technology - Other Topics↗
DOE OSTI2024

Learning protocols for the fast and efficient control of active matter

Exact analytic calculation shows that optimal control protocols for passive molecular systems often involve rapid variations and discontinuities. However, similar analytic baselines are not generally available for active-matter systems, because it is more difficult to treat active systems exactly. Here we use machine learning to derive efficient control protocols for active-matter systems, and find that they are characterized by sharp features similar to those seen in passive systems. We show that it is possible to learn protocols that effect fast and efficient state-to-state transformations in simulation models of active particles by encoding the protocol in the form of a neural network. We use evolutionary methods to identify protocols that take active particles from one steady state to another, as quickly as possible or with as little energy expended as possible. Our results show that protocols identified by a flexible neural-network ansatz, which allows the optimization of multiple control parameters and the emergence of sharp features, are more efficient than protocols derived recently by constrained analytical methods. Our learning scheme is straightforward to use in experiment, suggesting a way of designing protocols for the efficient manipulation of active matter in the laboratory.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Predicting the propensity for thermally activated β events in metallic glasses via interpretable machine learning

Abstract The elementary excitations in metallic glasses (MGs), i.e., β processes that involve hopping between nearby sub-basins, underlie many unusual properties of the amorphous alloys. A high-efficacy prediction of the propensity for those activated processes from solely the atomic positions, however, has remained a daunting challenge. Recently, employing well-designed site environment descriptors and machine learning (ML), notable progress has been made in predicting the propensity for stress-activated β processes (i.e., shear transformations) from the static structure. However, the complex tensorial stress field and direction-dependent activation could induce non-trivial noises in the data, limiting the accuracy of the structure-property mapping learned. Here, we focus on the thermally activated elementary excitations and generate high-quality data in several Cu-Zr MGs, allowing quantitative mapping of the potential energy landscape. After fingerprinting the atomic environment with short- and medium-range interstice distribution, ML can identify the atoms with strong resistance or high compliance to thermal activation, at a high accuracy over ML models for stress-driven activation events. Interestingly, a quantitative “between-task” transferring test reveals that our learnt model can also generalize to predict the propensity of shear transformation. Our dataset is potentially useful for benchmarking future ML models on structure-property relationships in MGs.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Computational design of highly signalling-active membrane receptors through solvent-mediated allosteric networks

Abstract Protein catalysis and allostery require the atomic-level orchestration and motion of residues and ligand, solvent and protein effector molecules. However, the ability to design protein activity through precise protein–solvent cooperative interactions has not yet been demonstrated. Here we report the design of 14 membrane receptors that catalyse G protein nucleotide exchange through diverse engineered allosteric pathways mediated by cooperative networks of intraprotein, protein–ligand and –solvent molecule interactions. Consistent with predictions, the designed protein activities correlated well with the level of plasticity of the networks at flexible transmembrane helical interfaces. Several designs displayed considerably enhanced thermostability and activity compared with related natural receptors. The most stable and active variant crystallized in an unforeseen signalling-active conformation, in excellent agreement with the design models. The allosteric network topologies of the best designs bear limited similarity to those of natural receptors and reveal an allosteric interaction space larger than previously inferred from natural proteins. The approach should prove useful for engineering proteins with novel complex protein binding, catalytic and signalling activities.

Chemistry↗
DOE OSTI2020

Dynamic stability of active sites in hydr(oxy)oxides for the oxygen evolution reaction

The poor activity and stability of electrode materials for the oxygen evolution reaction are the main bottlenecks in the water-splitting reaction for H 2 production. In this work, by studying the activity–stability trends for the oxygen evolution reaction on conductive M 1 O x H y , Fe–M 1 O x H y and Fe–M 1 M 2 O x H y hydr(oxy)oxide clusters (M 1 = Ni, Co, Fe; M 2 = Mn, Co, Cu), we show that balancing the rates of Fe dissolution and redeposition over a MO x H y host establishes dynamically stable Fe active sites. Together with tuning the Fe content of the electrolyte, the strong interaction of Fe with the MO x H y host is the key to controlling the average number of Fe active sites present at the solid/liquid interface. We suggest that the Fe–M adsorption energy can therefore serve as a reaction descriptor that unifies oxygen evolution reaction catalysis on 3 d transition-metal hydr(oxy)oxides in alkaline media. Thus, the introduction of dynamically stable active sites extends the design rules for creating active and stable interfaces.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Fluctuating hydrodynamics of chiral active fluids

Active materials are characterized by continuous injection of energy at the microscopic level and typically cannot be adequately described by equilibrium thermodynamics. Here we study a class of active fluids in which equilibrium-like properties emerge when fluctuating and activated degrees of freedom are statistically decoupled, such that their mutual information is negligible. We analyse three paradigmatic systems: chiral active fluids composed of spinning frictional particles that are free to translate, oscillating granular gases and active Brownian rollers. In all of these systems, a single effective temperature generated by activity parameterizes both the equation of state and the emergent Boltzmann statistics. The same effective temperature, renormalized by velocity correlations, relates viscosities to steady-state stress fluctuations via a Green–Kubo relation. To rationalize these observations, we develop a theory for the fluctuating hydrodynamics of these non-equilibrium fluids and validate it through large-scale molecular dynamics simulations. Our work sheds light on the microscopic origin of odd viscosities and stress fluctuations characteristic of parity-violating fluids, in which mirror symmetry and detailed balance are broken.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Operando studies reveal active Cu nanograins for CO 2 electroreduction

Carbon dioxide electroreduction facilitates the sustainable synthesis of fuels and chemicals. Although Cu enables CO 2 -to-multicarbon product (C 2+ ) conversion, the nature of the active sites under operating conditions remains elusive. Importantly, identifying active sites of high-performance Cu nanocatalysts necessitates nanoscale, time-resolved operando techniques. Here, we present a comprehensive investigation of the structural dynamics during the life cycle of Cu nanocatalysts. A 7 nm Cu nanoparticle ensemble evolves into metallic Cu nanograins during electrolysis before complete oxidation to single-crystal Cu 2 O nanocubes following post-electrolysis air exposure. Operando analytical and four-dimensional electrochemical liquid-cell scanning transmission electron microscopy shows the presence of metallic Cu nanograins under CO 2 reduction conditions. Correlated high-energy-resolution time-resolved X-ray spectroscopy suggests that metallic Cu, rich in nanograin boundaries, supports undercoordinated active sites for C–C coupling. Quantitative structure–activity correlation shows that a higher fraction of metallic Cu nanograins leads to higher C 2+ selectivity. A 7 nm Cu nanoparticle ensemble, with a unity fraction of active Cu nanograins, exhibits sixfold higher C 2+ selectivity than the 18 nm counterpart with one-third of active Cu nanograins. Importantly, the correlation of multimodal operando techniques serves as a powerful platform to advance our fundamental understanding of the complex structural evolution of nanocatalysts under electrochemical conditions.

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

Complex motion of steerable vesicular robots filled with active colloidal rods

Abstract While the collective motion of active particles has been studied extensively, effective strategies to navigate particle swarms without external guidance remain elusive. We introduce a method to control the trajectories of two-dimensional swarms of active rod-like particles by confining the particles to rigid bounding membranes (vesicles) with non-uniform curvature. We show that the propelling agents spontaneously form clusters at the membrane wall and collectively propel the vesicle, turning it into an active superstructure. To further guide the motion of the superstructure, we add discontinuous features to the rigid membrane boundary in the form of a kinked tip, which acts as a steering component to direct the motion of the vesicle. We report that the system’s geometrical and material properties, such as the aspect ratio and Péclet number of the active rods as well as the kink angle and flexibility of the membrane, determine the stacking of active particles close to the kinked confinement and induce a diverse set of dynamical behaviors of the superstructure, including linear and circular motion both in the direction of, and opposite to, the kink. From a systematic study of these various behaviors, we design vesicles with switchable and reversible locomotions by tuning the confinement parameters. The observed phenomena suggest a promising mechanism for particle transportation and could be used as a basic element to navigate active matter through complex and tortuous environments.

42 ENGINEERING↗
DOE OSTI2020

Operando identification of site-dependent water oxidation activity on ruthenium dioxide single-crystal surfaces

Understanding the nature of active sites is central to controlling (electro)catalytic activity. Here we employed surface X-ray scattering coupled with density functional theory and surface-enhanced infrared absorption spectroscopy to examine the oxygen evolution reaction on RuO 2 surfaces as a function of voltage. At 1.5 V RHE , our results suggest that there is an –OO group on the coordinatively unsaturated ruthenium (Ru CUS ) site of the (100) surface (and similarly for (110)), but adsorbed oxygen on the Ru CUS site of (101). Density functional theory results indicate that the removal of –OO from the Ru CUS site, which is stabilized by a hydrogen bond to a neighbouring –OH (–OO–H), could be the rate-determining step for (100) (similarly for (110)), where its reduced binding on (100) increased activity. A further reduction in binding energy on the Ru CUS site of (101) resulted in a different rate-determining step (–O + H 2 O – (H + + e - ) → –OO–H) and decreased activity. Our study provides molecular details on the active sites, and the influence of their local coordination environment on activity.

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

Coordination and activation of nitrous oxide by iron zeolites

Iron-containing zeolites are heterogeneous catalysts that exhibit remarkable activity in the selective oxidation of inert hydrocarbons and catalytic decomposition of nitrous oxide (N 2 O). The reduction of N 2 O is critical to both these functions, but experimental data tracking the iron active sites during N 2 O binding and activation are limited. Here, the N 2 O-ligated Fe(ii) active site in iron-exchanged zeolite beta is isolated and characterized by variable-temperature Mössbauer, diffuse reflectance UV-vis-NIR and Fourier transform infrared spectroscopy. N 2 O binds through the terminal nitrogen atom with substantial backbonding from the Fe(ii) centre at low temperature. At higher temperatures, the Fe–N 2 O interaction is weakened, facilitating isomerization to the O-bound form, which is competent in O-atom transfer. Density functional theory calculations show the geometric and electronic structure requirements for N 2 O binding and activation. A geometric distortion imposed by the zeolite lattice plays an important role in activating N 2 O. As a result, this highlights a mechanism for structural control over function in Fe-zeolite catalysts.

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

Spontaneous self-propulsion and nonequilibrium shape fluctuations of a droplet enclosing active particles

Active particles, such as swimming bacteria or self-propelled colloids, spontaneously assemble into large-scale dynamic structures. Geometric boundaries often enforce different spatio-temporal patterns compared to unconfined environment and thus provide a platform to control the behavior of active matter. Here, we report collective dynamics of active particles enclosed by soft, deformable boundary, that is responsive to the particles’ activity. We reveal that a quasi two-dimensional fluid droplet enclosing motile colloids powered by the Quincke effect (Quincke rollers) exhibits strong shape fluctuations with a power spectrum consistent with active fluctuations driven by particle-interface collisions. A broken detailed balance confirms the nonequilibrium nature of the shape dynamics. We further find that rollers self-organize into a single drop-spanning vortex, which can undergo a spontaneous symmetry breaking and vortex splitting. The droplet acquires motility while the vortex doublet exists. Our findings provide insights into the complex collective behavior of active colloidal suspensions in soft confinement.

42 ENGINEERING↗
DOE OSTI2024

Photosynthetically-powered phototactic active nematic liquid crystal fluids and gels

Abstract One of the most ancient forms of life dating to ~3.5 billion years ago, cyanobacteria are highly abundant organisms that convert light into energy and motion, often within conjoined filaments and larger colonies that attract a great deal of interest but their active nematic behavior remained unexplored. Here we demonstrate how light causes a spontaneous self-assembly of two- and three-dimensional active nematic states of cyanobacterial filaments, with a plethora of topological defects. We quantify light-controlled evolutions of orientational and velocity order parameters during the transition between disordered and orientationally ordered states of photosynthetic active matter, as well as the subsequent active nematic’s fluid-gel transformation. Patterned illumination and foreign inclusions with different shapes interact with cyanobacterial active nematics in nontrivial ways while inducing interfacial boundary conditions and fractional boojum defects. Our phototactic model system promises opportunities to systematically explore fundamental properties and technological utility of the liquid crystalline active matter.

Repula, Andrii↗
DOE OSTI2025

NADH-bound AIF activates the mitochondrial CHCHD4/MIA40 chaperone by a substrate-mimicry mechanism

Mitochondrial metabolism requires the chaperoned import of disulfide-stabilized proteins via CHCHD4/MIA40 and its enigmatic interaction with oxidoreductase Apoptosis-inducing factor (AIF). By crystallizing human CHCHD4’s AIF-interaction domain with an activated AIF dimer, we uncover how NADH allosterically configures AIF to anchor CHCHD4’s β-hairpin and histidine-helix motifs to the inner mitochondrial membrane. The structure further reveals a similarity between the AIF-interaction domain and recognition sequences of CHCHD4 substrates. NMR and X-ray scattering (SAXS) solution measurements, mutational analyses, and biochemistry show that the substrate-mimicking AIF-interaction domain shields CHCHD4’s redox-sensitive active site. Disrupting this shield critically activates CHCHD4 substrate affinity and chaperone activity. Regulatory-domain sequestration by NADH-activated AIF directly stimulates chaperone binding and folding, revealing how AIF mediates CHCHD4 mitochondrial import. These results establish AIF as an integral component of the metazoan disulfide relay and point to NADH-activated dimeric AIF as an organizational import center for CHCHD4 and its substrates. Importantly, AIF regulation of CHCHD4 directly links AIF’s cellular NAD(H) sensing to CHCHD4 chaperone function, suggesting a mechanism to balance tissue-specific oxidative phosphorylation (OXPHOS) capacity with NADH availability.

Brosey, Chris A↗